ARTICLE | doi:10.20944/preprints201808.0483.v1
Subject: Physical Sciences, Nuclear And High Energy Physics Keywords: spectroscopy; plasma diagnostics
Online: 29 August 2018 (06:16:51 CEST)
We describe electron temperature measurements in the SSX MHD wind tunnel using two different methods. First, we estimate Te along a chord by measuring the ratio of the C_III 97.7 nm to CIV 155 nm line intensities using a vacuum ultraviolet monochrometer. Second, we record a biasing scan to a double Langmuir probe to obtain a local measurement of Te. The aim of these studies is to increase the Taylor state lifetime, primarily by increasing the electron temperature. Also, a model is proposed to predict magnetic lifetime of relaxed states and is found of predict the lifetime satisfactorily. Furthermore, we find that proton cooling can be explained by equilibration with the electrons.
REVIEW | doi:10.20944/preprints202307.0247.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: antimicrobial resistance, antimicrobial peptides, aptamers, companion diagnostics, bacteriophages, companion diagnostics
Online: 4 July 2023 (14:08:46 CEST)
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with emergence of resistance resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies, that are clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers and phages. Clinical diagnostics optimizes the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious disease include detection, monitoring of response and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives into the use of alternate therapeutics with a particular focus on companion diagnostic applications in infectious diseases.
REVIEW | doi:10.20944/preprints202308.0784.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Tumor; microbiota; microbiome; diagnostics
Online: 10 August 2023 (10:17:59 CEST)
Tumor-associated microbiota refers to the community of microorganisms found in tumors and is part of the larger tumor microenvironment (TME). The discovery of the complex relationship between these microbial populations and the growth of cancer has prompted the creation of cutting-edge tailored methods to cancer treatment. In recent years, microbiota profiling's potential as a diagnostic, prognostic, and therapeutic optimization tool has been increasingly apparent. The diagnostic and prognostic use of microbiota profiling is explored in this abstract. Microbiota profiling shows potential for early cancer detection, improved risk stratification, and greater prediction of treatment outcomes by identifying different microbial signatures associated with early-stage tumors, aggressive characteristics, and responses to treatment. In addition, this method provides the way for individualized medicinal approaches based on an individual's specific microbiome.Microbiota profiling is investigated as a means of customizing treatment plans, illuminating how knowledge of an individual's microbiome might direct the development of individualized treatments and multimodal approaches. These kind of interventions have the potential to herald in a new era of patient-centered oncology care by increasing treatment efficacy while decreasing side effects. Despite significant promise, microbiota profiling has obstacles that must be overcome before it can be successfully translated into therapeutic practice. This abstract highlights the revolutionary potential of microbiota-based approaches in cancer care and the need for ongoing research and technology improvements to harness the power of the tumor-associated microbiome for improved patient outcomes.
ARTICLE | doi:10.20944/preprints202212.0240.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: diagnostics, manufacturing, pandemic preparedness,
Online: 14 December 2022 (01:17:31 CET)
Rapidly providing a definitive diagnostic test that can be used broadly by healthcare providers and members of the public in the setting of a disease emergency is critical to limit pathogen spread, develop and deploy medical countermeasures, and mitigate the social and economic harms of a serious epidemic or pandemic. There is extraordinary expertise within and outside of government working on these issues, and major accomplishments have been made to accelerate test development, expand laboratory testing capacity, and establish widespread point-of-care testing. Still, the United States does not have a plan to rapidly respond, to develop, manufacture, or deploy at national scale diagnostic testing in the earliest days of a new infectious disease crisis. Nor does the nation have a plan to sustain testing capacity at high volume over the course ofan enduring epidemic or pandemic. To address this gap, we are proposing a National Diagnostics Action Plan that describes the steps that are urgently needed to prepare for future infectious disease emergencies, as well as the actions we must take at the first signs of such events. These recommendations require substantial collaboration between the US government (USG) and the private sector to solve a series of challenges now, as well as to prepare for the massive and rapid scale-up of laboratory and point-of-care test development and testing capacity in future emergencies. The recommendations include establishing pre-event contracts; ensuring rapid access to clinical samples; creating a permanent public-private testing coordinating body to allow for rapid information sharing and improved cooperation among the USG, test developers, and clinical laboratories; and accelerating testing rollout at the beginning of an event—andthus, the effective public health management of a disease crisis. These recommendations were informed by extensive discussion with people who managed the COVID-19 and monkeypox responses, review of past reports written on diagnostic challenges, and the experiences of the authors.
ARTICLE | doi:10.20944/preprints202007.0740.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; Virus Detection; Viral Diagnostics; Diagnostics; SARS-CoV-2; Coronavirus; PCR
Online: 31 July 2020 (09:31:18 CEST)
Accurate and timely testing has become an essential measure in combatting the COVID-19 global pandemic. Currently, polymerase chain reaction (PCR) based assays are the most relied on methods for SARS-CoV-2 detection. This traditional workflow involves a viral RNA extraction from the viral transport media storing nasopharyngeal swabs collected from patients, followed by PCR based detection. While accurate, this methodology is time consuming and resource heavy, causing for delays in receiving results or limited access to testing. Herein, we demonstrate a validated method for SARS-CoV-2 detection from viral transport media using a two-step, direct-to-PCR workflow revolving around shaker-mill homogenization. This method completely bypasses the extraction steps of the traditional workflow, replacing it with 30 seconds of mechanical disruption sufficient to allow for COVID-19 detection with a 96.43% sensitivity and 100% specificity when compared to traditional extraction to PCR based methods.
ARTICLE | doi:10.20944/preprints202310.0863.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: canine; respiratory; virus; disease; diagnostics
Online: 13 October 2023 (08:12:33 CEST)
Canine infectious respiratory disease complex (CIRDC) is caused by different viruses and bacteria. Viruses associated with CIRDC include canine adenovirus-2 (CAV-2), canine distemper virus (CDV), canine influenza virus (CIV), canine herpesvirus (CHV), canine coronavirus (CCoV) and canine parainfluenza virus (CPIV). Bacteria associated with CIRDC include Bordetella bronchiseptica, Streptococcus equi subspecies zooepidemicus, and Mycoplasma spp. The present study examined the prevalence of pathogens associated with CIRDC in specimens received by a Veterinary Diagnostic Laboratory in Georgia from 2018 to 2022. Out of 459 cases, viral agents were detected in 34% cases and bacterial agents were detected in 58% cases. A single pathogen was detected in 31% cases, while two or more pathogens were identified in 24% cases. The percentages of viral agents identified were CAV-2 (4%), CDV (3%), CPIV (16%), CCoV (7%), and CIV (2%). The percentages of bacterial agents were Bordetella bronchiseptica (10%), Mycoplasma canis (24%), Mycoplasma cynos (21%), and S treptococcus zooepidemicus (2%). Positive viral cases ranged from 2-4% for CAV-2, 1-7% for CDV, 1-4% for CHV, 9-22% for CPIV, 4-13% for CCoV, and 1-4% for CIV. Overall, the study showed that the most prevalent pathogens associated with CIRDC during the study period were CPIV, M. canis, and M. cynos.
REVIEW | doi:10.20944/preprints202312.0632.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Breast cancer; Nanocarriers; Tumor location; Diagnostics
Online: 9 December 2023 (08:19:16 CET)
Breast cancer (BC) is one of the most common types of cancer in women. Triple-negative breast cancer (TNBC), characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), exhibits a highly aggressive phenotype with increased metastasis and resistance to conventional treatments. Nanocarrier technology is consistently employed to overcome limitations associated with traditional breast cancer therapy. The targeted drug delivery approach using nanocarriers enhances bioavailability, prolongs circulation, and facilitates effective drug accumulation at the tumor site through active or passive targeting. Currently, the FDA has approved a few nanocarrier systems, and numerous nano formulations are undergoing preclinical and clinical development for breast cancer targeting. Common nanocarrier types include polymeric micelles, microemulsions, magnetic microemulsions, liposomes, dendrimers, carbon nanotubes, and magnetic nanoparticles (NPs). This review extensively explores the targeting potential of nanocarriers in breast cancer. This study will provide a concise summary of current advances in treatment of breast cancer and diagnostics.
REVIEW | doi:10.20944/preprints202312.0052.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: skin disease; skin cancer; diagnostics; treatments
Online: 1 December 2023 (08:12:16 CET)
When the skin is afflicted by disease such as cancer, these essential functions are disrupted, putting the entire person at risk. While the American Cancer Society lists 6 major cancer types, the National Institute of Arthritis and Musculoskeletal and Skin Diseases identifies 13 significant benign skin disorders, reflecting the diversity of skin conditions in dermatology. This topical review aims to provide an overview of the pathophysiology of these major skin cancers and disorders and summarize conventional diagnostic methods and current treatment approaches.
ARTICLE | doi:10.20944/preprints202310.1237.v1
Subject: Medicine And Pharmacology, Otolaryngology Keywords: objective measurement; cochlear implant; differential diagnostics
Online: 19 October 2023 (13:20:43 CEST)
Background: By using outcome prediction scores, it is possible to distinguish between good and poor performers with cochlear implants (CI) after CI implantation. The reasons for poor performance, despite good basic conditions, can be manifold. On the one hand, the postoperative fitting may be inadequate; on the other, neurophysiological disease processes may impair speech understanding with a CI. These disease processes are not yet fully understood. In acoustics, it is known that the auditory brainstem responses (ABR) and their latencies and amplitudes allow differential diagnosis based on reference values for normal-hearing individuals. The aim of this study was to provide reference values for electrically evoked brainstem responses (EABRs) in terms of rate-dependent latencies and amplitudes. Methods: 20 experienced adult CI recipients with a predicted and measured good postoperative word recognition score were recruited from the clinic’s patient pool. In the same stimulation mode and intensity we measured latencies and interpeak-latencies of EABRs and electrically evoked compound action potentials (ECAPs). With a defined supra-threshold stimulation intensity above the individual ECAP threshold, we applied stimulation at several rates between 11 and 91 stimuli per second. Results: We found rate dependences for EABR latency t3 and t5 in the order of 0.19 ms and 0.37 ms respectively, while ECAP was not affected by rate. Correspondingly, the interpeak intervalls’ rate dependences for t5-t1, t5-t3 and t3-t1 were of the order of 0.37 ms, 0.18 ms and 0.19 ms. Comparing the EABR amplitudes between the stimulation rates 11/s and 81/s, we found that at 81/s the amplitudes were significantly reduced down: to 73% for A3 and 81% for A5. These rate dependences of latency and amplitude in EABR have characteristics comparable to those of acoustic ABR. Conclusions: These data may serve to provide reference values for EABR and ECAP latencies, interpeak intervals and amplitudes with respect to stimulation rate. Altered response patterns of ECAPs and EABRs to normalised stimulation modes could be used in the future to describe and classify neuropathological processes in a better-differentiated way.
ARTICLE | doi:10.20944/preprints202310.0841.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: HCVcoreAg; antibody; aptamer; nanoribbon biosensor; diagnostics
Online: 13 October 2023 (04:34:39 CEST)
The performance of the nanoribbon biosensor upon the use of two different types of molecular probes — the antibodies and the aptamers against HCVcoreAg — has been tested. The sensor chips employed are based on “silicon-on-insulator structures”. Two different HCVcoreAg preparations have been tested: recombinant b-galactosidase-conjugated HCVcoreAg (“Virogen”, USA) and recombinant HCVcoreAg (“Vector-Best”, Russia). Upon the detection of either type of the antigen preparation, the lowest concentration of the antigen detectable in buffer with pH 5.1 has been found to be approximately equal, amounting to ~10–14 M. This value has been found to be similar upon the use of either type of molecular probes.
REVIEW | doi:10.20944/preprints202309.1940.v1
Subject: Biology And Life Sciences, Parasitology Keywords: horse; helminth; cyathostomins; Anoplocephala perfoliata; diagnostics
Online: 28 September 2023 (09:56:56 CEST)
Helminths are commonly found in grazing equids, with the cyathostomin nematodes and the cestode, Anoplocephala perfoliata, being the most prevalent. Most horses harbour low burdens of these parasites and do not develop signs of infection; however, in a small number of animals, high burdens can accumulate and cause disease. Cyathostomins are associated with a syndrome known as larval cyathostominosis. This occurs when large numbers of larvae emerge from the large intestinal wall. This disease has a case fatality rate of up to 50%. A. perfoliata infection has been associated with various types of colic, with burdens of >20 worms associated with pathogenicity. Anthelmintic resistance is a serious problem in cyathostomins and is emerging in A. perfoliata. Control methods that reduce reliance on anthelmintics now need to be applied, especially as no new dewormer compounds are on the horizon. Sustainable control methods must employ diagnostics to identify horses that require treatment. Coprological tests (faecal egg counts, FEC), have been used for several decades to inform treatment decisions to reduce helminth egg shedding. These tests cannot be used to assess host burdens as FEC do not correlate with cyathostomin or A. perfoliata burdens. In the last decade, new tests have become available that measure parasite-specific antibodies, levels of which have been shown to correlate with parasite burden. These tests measure antigen-specific IgG(T) and are available in serum (cyathostomin, A. perfoliata) or saliva (A. perfoliata) formats. Tests for other helminths have been developed as research tools and need to be translated to support equine clinicians in practice. A key element of sustainable control strategies is that diagnostics must be used in combination with management approaches to reduce environmental transmission of helminths; this will help limit the proportion of horses harbouring parasite burdens that need to be targeted by treatment.
ARTICLE | doi:10.20944/preprints202212.0417.v1
Subject: Biology And Life Sciences, Virology Keywords: RNA sequencing; metagenomics; infectious diseases; diagnostics
Online: 22 December 2022 (04:25:19 CET)
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol – the RAPIDprep assay – with the aim to provide cause agnostic laboratory diagnosis of infection within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities and extraction kits using a single protocol without input nucleic acid quantification or quality assessment. Furthermore, we demonstrate the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift towards integration of modern genomic techniques to infectious disease investigations.
ARTICLE | doi:10.20944/preprints202202.0010.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: elastic map; clustering; classification; degeneration; diagnostics
Online: 1 February 2022 (12:26:27 CET)
Positron-emission tomography is powerful but costly tool for various medical investigations. In particular, it is used in Parkinson’s disease and essential tremor diagnostics. However, yet there is no standardized figures of the references, for it. We examined the PET efficiency for the analysis of development and degradation of dophaminergic neurons in Parkinson’s disease. The informative indices are determined from the observed PET data. Also, high efficiency of PET for Parkinson’s disease as approved.
ARTICLE | doi:10.20944/preprints202309.0559.v1
Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: RT-QuIC; Chronic Wasting Disease; Diagnostics; Optimization
Online: 7 September 2023 (15:45:02 CEST)
Real-time quaking-induced conversion (RT-QuIC) assays have become common in the detection of chronic wasting disease (CWD) and are very sensitive provided the assay duration is sufficient. However, a prolonged assay duration may lead to non-specific signal amplification. The wide range of pre-defined assay durations in current RT-QuIC applications presents a need for optimization of the RT-QuIC assay duration. In this study, receiver operating characteristic (ROC) analysis was applied to optimize assay duration for detection of CWD in obex and retropharyngeal lymph node (RLN) tissue specimens. Two different fluorescence thresholds were used: a fixed threshold based on background fluorescence (Tstdev) and a max-point ratio (maximum/background fluorescence) threshold (TMPR) to determine CWD positivity. The optimal assay duration was 27 h for both obex and RLN based on Tstdev, and 27 and 28 h for obex and RLN, respectively, based on TMPR. The optimized assay durations were then evaluated for screening CWD in white-tailed deer from an affected farm. Results by RT-QuIC using optimized duration based on Tstdev and TMPR were in 100% and 92.3 % or higher agreement with those by the widely used screening assay, ELISA. In comparison, when using a 40 h assay duration, the agreement between RT-QuIC and ELISA reduced to 89.2% or higher, and the RT-QuIC results were significantly (p < 0.05) different from those using optimum durations. These findings demonstrated that the application of ROC analysis for the optimization of assay duration could improve the RT-QuIC assay for screening CWD in white-tailed deer.
ARTICLE | doi:10.20944/preprints202308.1788.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: macrophage-based biochip; CD206; bronchoalveolar lavage; diagnostics
Online: 25 August 2023 (07:51:34 CEST)
Progress in macrophage research is crucial for numerous applications in medicine, including cancer and infectious diseases. However, the existing methods to manipulate living macrophages are labor intense and inconvenient. Here we show that macrophage membranes can be reconstituted after storage for months at 4C, with their CD206 receptor selectivity and specificity being similar to that in the living cells. Then, we have developed a mannose ligand, specific to CD206, linked with PEG as IR spectroscopy marker to detect binding with the macrophage receptor. PEG was selected due to its unique adsorption band of C-O-C group at IR spectra, which does not overlap with other biomolecule’s spectroscopic feature. Next, competitive binding assay versus the PEG-bound ligand, has enabled selection of other higher-affinity ligands specific to CD206. Further, those higher-affinity ligands were used to differentiate activated macrophages in patient’s bronchoalveolar (BAL) or nasopharyngeal (NPL) lavage. CD206- control cells (HEK293T) showed only non-specific binding. Therefore, biochips based on reconstituted macrophage membranes as well as PEG-trimannoside as an IR spectroscopic marker, can be used to develop new methods facilitating macrophage research and macrophage-focused drug discovery.
ARTICLE | doi:10.20944/preprints202101.0115.v1
Subject: Physical Sciences, Acoustics Keywords: machine learning; virtual diagnostics; reinforcement learning control
Online: 6 January 2021 (11:58:41 CET)
We discuss the implementation of a suite of virtual diagnostics at the FACET-II facility currently under commissioning at SLAC National Accelerator Laboratory. The diagnostics will be used for prediction of the longitudinal phase space along the linac, spectral reconstruction of the bunch profile and non-destructive inference of transverse beam quality (emittance) using edge radiation at the injector dogleg and bunch compressor locations. These measurements will be folded in to adaptive feedbacks and ML-based reinforcement learning controls to improve the stability and optimize the performance of the machine for different experimental configurations. In this paper we describe each of these diagnostics with expected measurement results based on simulation data and discuss progress towards implementation in regular operations.
ARTICLE | doi:10.20944/preprints202009.0005.v1
Subject: Biology And Life Sciences, Virology Keywords: mink astrovirus; molecular diagnostics; molecular polymorphism; phylogenetics
Online: 1 September 2020 (11:18:15 CEST)
Mink astrovirus infection remains a poorly understood disease entity, and the aetiological agent itself causes disease with a heterogeneous course, including gastrointestinal and neurological symptoms. This paper presents cases of astrovirus infection in mink from continental Europe. RNA was isolated from the brains and intestines of animals showing symptoms typical of shaking mink syndrome (n = 6). RT-PCR was used to detect astrovirus genetic material, and the reaction products were separated on a 1% agarose gel. The specificity of the reaction was confirmed by sequencing all samples. The presence of astrovirus RNA was detected in each of the samples tested. Sequencing and bioinformatic analysis indicated the presence of the same variant of the virus in all samples. Comparison of the variant with the sequences available in bioinformatics databases confirmed that the Polish isolates form a separate clade, closely related to Danish isolates. The similarity of the Polish variant to those isolated in other countries ranged from 2.4% (in relation to Danish isolates) to 7.1% (in relation to Canadian isolates). Phylogenetic relationships between variants appear to be associated with the geographic distances between them. To our knowledge, this work describes the first results on the molecular epidemiology of MAstV in continental Europe. The detection of MAstV in Central Europe indicates the need for further research to broaden our understanding of the molecular epidemiology of MAstV in Europe.
REVIEW | doi:10.20944/preprints201806.0292.v1
Subject: Engineering, Bioengineering Keywords: 3D printing; diagnostics; optics; bioprinting, electronics, microfluidics
Online: 19 June 2018 (10:41:57 CEST)
AbstractWhile the technology is relatively new, low cost 3D printing has impacted many aspects of human life. 3D printers are being used as manufacturing tools for a wide variety of devices in a spectrum of applications ranging from diagnosis to implants to external prostheses. The ease of use and availability of 3D design software and low cost has made 3D printing an accessible manufacturing and fabrication tool in many research laboratories. 3D printers can print materials with varying density, optical character, strength and chemical properties providing platforms for a huge number of strategies that can be chosen for user’s needs. In this review, we focus on applications in biomedical diagnostics and how this revolutionary technique is facilitating development of low cost, sensitive and often geometrically complex tools. 3D printing in fabrication of microfluidics, supporting equipment, optical and electronic components of diagnostic devices is presented. Emerging diagnostic 3D bioprinting as a tool to incorporate living cells or biomaterials into 3D printing is also discussed.
ARTICLE | doi:10.20944/preprints202312.0208.v1
Subject: Biology And Life Sciences, Parasitology Keywords: Canine leishmaniosis; CanL; POC diagnostics for leishmaniosis; lateral flow test; line blot; Leishmania improved sero-diagnostics; Leishmania ELISA
Online: 4 December 2023 (15:15:26 CET)
Control of canine infections with Leishmania infantum (L. infantum), a major zoonotic disease in Brazil and southern Europe is becoming increasingly important due to their close proximity to humans, the increasing import of dogs from endemic regions and impact of climate change on vector spreading. Simple, rapid and reliable diagnostic tests are therefore needed to detect infected dogs. Here, we re-evaluated different serological methods for the diagnosis of canine leishmaniosis (CanL) in Croatia and Brazil. The diagnostic performance of the indirect fluorescent antibody test (IFAT) and the VetLine® Leishmania ELISA was compared with three rKLi8.3 based diagnostic test systems, the rKLi8.3 ELISA, the INgezim® Leishma CROM lateral flow test (LFT) and the VetBlot® Leishmania LineBlot. CanL symptomatic dogs were efficiently diagnosed by all tests, except the VetLine® Leishmania ELISA, which is based on whole Leishmania antigens. The advantage of rKLi8.3 was also observed in oligo-and asymptomatic dogs from Brazil and Croatia, although with reduced diagnostic efficiency compared to symptomatic dogs. Similar to IFAT and rKLi8.3 ELISA, the LFT did not cross-react with other common canine pathogens, showed a very high specificity for healthy dogs from endemic regions of both countries and did not react with healthy, vaccinated dogs in Brazil. In conclusion, sero-diagnostic tests based on the rKLi8.3 antigens are superior to whole parasite antigens and the LFT has the advantage of providing a laboratory independent, rapid and specific diagnosis of CanL.
ARTICLE | doi:10.20944/preprints201801.0217.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: data assimilation; statistical diagnostics of analysis residuals; estimation of analysis error, air quality model diagnostics; Desroziers method; cross-validation
Online: 23 January 2018 (16:23:25 CET)
We examine how observations can be used to evaluate an air quality analysis by verifying against passive observations (i.e. cross-validation) that are not used to create the analysis and we compare these verifications to those made against the same set of (active) observations that were used to generate the analysis. The results show that both active and passive observations can be used to evaluate of first moment metrics (e.g. bias) but only passive observations are useful to evaluate second moment metrics such as variance of observed-minus-analysis and correlation between observations and analysis. We derive a set of diagnostics based on passive observation–minus-analysis residuals and we show that the true analysis error variance can be estimated, without relying on any statistical optimality assumption. This diagnostic is used to obtain near optimal analyses that are then used to evaluate the analysis error using several different methods. We compare the estimates according to the method of Hollingsworth Lonnberg, Desroziers, a diagnostic we introduce, and the perceived analysis error computed from the analysis scheme, to conclude that as long as the analysis is optimal, all estimates agrees within a certain error margin. The analysis error variance at passive observation sites is also obtained.
ARTICLE | doi:10.20944/preprints202311.0837.v1
Subject: Chemistry And Materials Science, Applied Chemistry Keywords: wall painting; restoration; enzymatic cleaning; non-invasive diagnostics
Online: 13 November 2023 (15:58:04 CET)
A 17th century wall painting representing a Virgin between two Saints in a noble Italian renaissance palace, Palazzo Gallo in Bagnaia (Viterbo, Italy), was restored in 2021 in the context of a wider restoration campaign interesting the main room of the palace built by cardinal Sansoni Riario. Diagnostic analyses done with traditional characterization techniques (optical microscopy on micro-stratigraphic sections, X-ray fluorescence spectroscopy and Fourier transform infrared spectroscopy) provided the identification of both original painting and restoration materials, while imaging investigations as ultraviolet fluorescence photography, false color images and multispectral mapping provided by hypercolorimetric multispectral imaging (HMI) technique enabled the evaluation of the state of conservation, locating restoration interventions and supporting the monitoring of the cleaning procedure. An altered protective Paraloid-based coating dating from early 2000s had to be removed due to the unpleasant glossy finishing given to the painted surface, making the scene barely readable. To pursue a restoration protocol based on environmental sustainability and green chemistry, enzyme-based gels marketed by Nasier-Brenta© and CTS© companies were tested in different protocols for the cleaning of the mash covering the painting. Although some interesting results were observed, the enzymatic cleaning had a scarce effectiveness with timing beyond a reasonable interval. Traditional chemical solvents as Dowanol PM (methoxy-propanol) and benzyl alcohol were necessary to complete the cleaning of the painting surface.
ARTICLE | doi:10.20944/preprints202307.1748.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: mycobacteria; Mycobacterium Tuberculosis; diagnostics; antimicrobial peptide; hormetic response
Online: 26 July 2023 (10:16:04 CEST)
Antimicrobial peptides (AMPs) can directly kill Gram-positive bacteria, Gram-negative bacteria, mycobacteria, fungi, enveloped viruses and parasites. At sublethal concentrations some AMPs and also conventional antibiotics can stimulate bacteria response to increase their resilience, also called the hormetic response. That can include stimulation of growth, mobility, and biofilm production. Here, we have discovered AMPs that stimulate the growth of certain mycobacteria. Peptide 14 for example showed growth stimulating effect on M. tuberculosis, M. bovis, M. avium subsp. paratuberculosis (MAP), M. marinum, M. avium-intracellulare, M. celatum and M. abscessus. The effect was more pronounced at low bacterial inocula. The peptides induce a faster transition from the lag phase to the log phase and keep the bacteria longer in the log phase before entering the stationary phase compared to non treated control. In some cases, an increase in the division rate was observed. An initial screen using MAP and a collection of 75 peptides revealed 13 peptides with a hormetic effect. For M. tuberculosis a collection of 25 artificial peptides were screened and 9 were found to reduce the time to positivity (TTP), improving growth. A screen of 43 naturally occurring peptides, 11 fragments of naturally occurring peptides and 5 designed peptides, all taken from the APD3, identified a further 44 peptides that also lowered TTP by at least 5%. Lasioglossin LL-III (Bee) and Ranacyclin E (Frog) were the most active natural peptides, the human cathelicidin LL37 fragment GF-17 and a porcine cathelicidin protegrin-1 fragment was the most active fragment of naturally occurring peptides. Peptide 14 showed growth-stimulating activity between 50 ng/ml and 10 µg/ml whereas the stability-optimised peptide 14D had a narrow activity range of 0.1 - 1 µg/ml. Peptides identified in this study are now part of novel products improving the diagnosis of mycobacteria in humans and animals.
BRIEF REPORT | doi:10.20944/preprints202003.0221.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: COVID-19; 2019-nCoV; diagnostics; antibodies; structural vaccinology
Online: 12 March 2020 (15:02:49 CET)
The appearance of the novel betacoronavirus 2019-nCoV represents a major threat to human health, and its diffusion around the world is predicted to have dramatic economic consequences. The knowledge of the 3D structures of 2019-nCoV proteins can facilitate the development of diagnostic and therapeutic molecules. Herein, we apply our energy-based method for the prediction of potential epitopes on viral proteins to design peptide-based molecules that can subsequently be used in diagnostic and therapeutic applications. We discuss these aspects in the paper.The designs have not been tested. Our aim is to share information that can be useful in the development of novel biomolecules with potential interesting activities against 2019-nCoV.
REVIEW | doi:10.20944/preprints201912.0002.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: tuberculosis (TB); diagnostics; lipoarabinomannan (LAM); urinary test; diagnosis
Online: 2 December 2019 (04:18:41 CET)
Most diagnostic tests for tuberculosis (TB) rely on sputum samples, which are difficult to obtain and have low sensitivity in immunocompromised patients, patients with disseminated TB, and children, delaying treatment initiation. The World Health Organization (WHO) calls for the development of a rapid, biomarker-based, non-sputum test capable of detecting all forms of TB at the point-of-care to enable immediate treatment initiation. Lipoarabinomannan (LAM) is the only WHO-endorsed TB biomarker which can be detected in urine, an easily collected sample. This review discusses the characteristics of LAM as a biomarker, describes the performance of first-generation urine LAM tests and reasons for slow uptake, and presents considerations for developing the next-generation of more sensitive and impactful tests. Next-generation urine LAM tests have the potential to reach adult and pediatric patients regardless of HIV status or site of infection and facilitate global TB control. Implementation and scale-up of existing LAM tests and development of next-generation assays should be prioritized.
ARTICLE | doi:10.20944/preprints201907.0296.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: point-of-care; cholesterol; clinical diagnostics; laboratory test
Online: 26 July 2019 (01:13:11 CEST)
Managing blood cholesterol levels is important for the treatment and prevention of diabetes, cardiovascular disease, and obesity. An easy-to-use, portable cholesterol blood test will accelerate more frequent testing by patients and at-risk populations. We aim to evaluate the performance of smartphone-based point-of-care cholesterol blood tests as compared to that of hospital-grade laboratory tests. We used smartphone systems that are already familiar to many people. Because smartphone systems can be carried around everywhere, blood can be measured easily and frequently. We compared the results of cholesterol tests with those of existing clinical diagnostic laboratory methods. We found that smartphone-based point-of-care lipid blood tests are as accurate as hospital-grade laboratory tests (N=116, R>0.97, P<0.001 for all 3 cholesterol blood tests: total cholesterol, high density lipoprotein, and triglyceride). Our system will be useful for those who need to manage blood cholesterol levels to motivate them to track and control their behavior.
ARTICLE | doi:10.20944/preprints201711.0047.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: data assimilation; statistical diagnostics of analysis residuals; estimation of analysis error, air quality model diagnostics; Desroziers et al. method; cross-validation
Online: 7 November 2017 (10:09:42 CET)
We present a general theory of estimation of analysis error covariances based on cross-validation as well as a geometric interpretation of the method. In particular we use the variance of passive observation–minus-analysis residuals and show that the true analysis error variance can be estimated, without relying on the optimality assumption. This approach is used to obtain near optimal analyses that are then used to evaluate the air quality analysis error using several different methods at active and passive observation sites. We compare the estimates according to the method of Hollingsworth-Lönnberg, Desroziers et al., a new diagnostic we developed, and the perceived analysis error computed from the analysis scheme, to conclude that, as long as the analysis is near optimal, all estimates agree within a certain error margin.
ARTICLE | doi:10.20944/preprints202210.0401.v1
Subject: Biology And Life Sciences, Virology Keywords: diagnostics; rose virus; Capillovirus; Ilarvirus; Luteovirus; Partitiviridae; RNA-seq
Online: 26 October 2022 (07:22:18 CEST)
Rose (Rosa spp.), especially R. hybrida, is one of the most popular ornamental plants in the world and the third largest cut flower crop in Taiwan. Rose mosaic disease (RMD), showing mosaic, line patterns and ringspots on leaves, is a common rose disease caused by complex infection of various viruses. Due to pests and diseases, the rose planting area in Taiwan has been decreasing since 2008; however, no rose virus disease has been reported in the past five decades. In the spring of 2020, rose samples showing RMD-like symptoms were observed at an organic farm in Chiayi, central Taiwan. The virome in the farm was analyzed by RNA-seq. Rose genomic sequences were filtered from the obtained reads. The remaining reads were de novo assembled to generate 294 contigs, 50 of which were annotated as viral sequences corresponding to 10 viruses. Through reverse transcription-polymerase chain reaction validation, a total of seven viruses were detected, including six known rose viruses, namely apple mosaic virus, prunus necrotic ringspot virus, rose partitivirus, apple stem grooving virus, rose spring dwarf-associated virus and rose cryptic virus 1, and a novel ilarvirus. After completing the whole genome sequencing and sequence analysis, the unknown ilarvirus was demonstrated as a new species, tentatively named rose ilarvirus 2. This is the first report of the rose viruses in Taiwan.
ARTICLE | doi:10.20944/preprints202207.0454.v1
Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: orthodontics; airway; clear aligners; 3D diagnostics; sleep apnea; CBCT
Online: 29 July 2022 (09:37:56 CEST)
This retrospective study evaluated changes in the pharyngeal portion of the upper airway in pa-tients with constricted and normal airway treated with clear aligners (Invisalign, Align). Additionally, the paper has assessed the change of tongue position in the oral cavity from lateral view. Evaluation was performed with specialized software (Invivo 6.0, Anatomage) on pre-treatment and posttreatment pairs of cone beam computed tomography imaging (CBCT) data. The level of airway constriction, volume, cross-section minimal area, and tongue profile were evaluated. Patients with malocclusion, with pair or initial and finishing CBCT and without sig-nificant weight change between the scans, treated with Invisalign clear aligners were distributed in two groups. Group A consisted of fifty-five patients with orthodontic malocclusion and con-stricted upper airway. Control group B consisted of thirty-one patients with orthodontic malocclusions without any airway constriction. In the group with airway constriction, there was a statistically significant increase in volume during therapy (p<0.001). The surface of the most con-stricted cross-section of airway did not change significantly after treatment in any of the groups. The airway constriction was most frequently localized at the level of 2nd cervical vertebra. The final tongue position was different from initial in 62.2% of all clear aligner treatments.
ARTICLE | doi:10.20944/preprints202110.0098.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: FPGA; Wishbone; Control interface; VHDL; System management; System diagnostics
Online: 6 October 2021 (09:48:08 CEST)
FPGA-based data acquisition and processing systems play an important role in modern high-speed, multichannel measurement systems, especially in High-Energy and Plasma Physics. Such FPGA-based systems require an extended control and diagnostics part corresponding to the complexity of the controlled system. Managing the complex structure of registers while keeping the tight coupling between hardware and software is a tedious and potentially error-prone process. Various existing solutions aimed at helping that task do not perfectly match all specific requirements of that application area. The paper presents a new solution based on the XML system description, facilitating the automated generation of the control system’s HDL code and software components and enabling easy integration with the control software. The emphasis is put on reusability, ease of maintenance in case of system modification, easy detection of mistakes, and the possibility of use in modern FPGAs. The presented system has been successfully used in data acquisition and preprocessing projects in High-Energy Physics experiments. It enables easy creation and modification of the control system definition and convenient access to the control and diagnostic blocks. The presented system is an open-source solution and may be adopted by the user for particular needs.
CONCEPT PAPER | doi:10.20944/preprints202106.0505.v1
Subject: Physical Sciences, Acoustics Keywords: ATR, THz, synchrotron radiation, diagnostics, polariscopy, four polarisation method
Online: 21 June 2021 (11:28:36 CEST)
Capabilities of the Attenuated Total Reflection (ATR) at THz wavelengths for increased sub-surface depth characterisation of (bio-)materials is presented. The penetration depth of a THz evanescent wave in biological samples is dependent on the wavelength and temperature and can reach 0.1-0.5 mm depth due to strong refractive index change ∼0.4 of the ice-water transition; this is quite significant and important when studying biological samples. Technical challenges are discussed when using ATR for uneven, heterogeneous, high refractive index samples with possibility of frustrated total internal reflection (a breakdown of the ATR reflection-mode into transmission-mode). Local field enhancements at the interface are discussed with numerical/analytical examples. Maxwell’s scaling was used to model behaviour of absorber-scatterer inside materials at the interface with ATR prism for realistic complex refractive indices of bio-materials. Modality of ATR with polarisation analysis is proposed and its principle illustrated, opening an invitation for its experimental validation. The sensitivity of the polarised ATR mode to the refractive index between the sample and ATR prism is revealed. Design principles of polarisation active optical elements and spectral filters are outlined. The results and concepts are based on experiments carried out at the THz beamline of the Australian Synchrotron.
REVIEW | doi:10.20944/preprints202005.0481.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: COVID-19; SARS-CoV-2; diagnostics; point of care
Online: 31 May 2020 (16:35:25 CEST)
COVID-19, the disease caused by the new coronavirus, SARS-CoV-2, has caused significant human and economic burden. Of the three major methods to mitigate the effect of the virus, diagnostics have become the focal point because vaccines and therapeutics, despite the intense effort of scientists worldwide, will take months to develop, test for safety and efficacy, scaleup and distribute to millions. This perspective aims to clarify some of the issues related to COVID-19 diagnostics and highlights some of the challenges key stakeholders including policymakers, businesses, managers, scientists and individuals face during this evolving pandemic.
ARTICLE | doi:10.20944/preprints201908.0227.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: dermatophyte; porcupine; Erethizon, fungus; metagenomics; fungal genetics; molecular diagnostics
Online: 21 August 2019 (12:58:19 CEST)
Twelve wild North American Porcupines (Erethizon dorsatum) were diagnosed with dermatopathies while being cared for at two wildlife rehabilitation clinics. Biopsy and necropsy were performed on 7 and 5 animals respectively. Atypical dermatophytosis was diagnosed in all cases. Lesions consisted of diffuse severe epidermal hyperkeratosis and mild hyperplasia, with mild lymphoplasmacytic dermatitis, and no folliculitis. Dermatophytes were noted histologically as hyphae and spores in hair shafts, and follicular and epidermal keratin. Trichophyton sp. was grown in 5/6 animals where culture was performed, with molecular diagnosis of Arthroderma benhamiae / Trichophyton mentagrophytes in these 5 cases. Metagenomic analysis of formalin-fixed paraffin-embedded tissue samples from 3 cases identified fungi from 17 orders in phyla Basidiomycota and Ascomycota. Alteration of therapy from ketaconazole, which was unsuccessful in 4 of 5 early cases, to terbinafine or nitraconazole lead to resolution of disease and recovery to release in four subsequent animals. In all, 6 animals were euthanized or died due to dermatopathy, no cases resolved spontaneously, and 6 cases resolved with therapy. The work we present demonstrates an atypical lesion and anatomical distribution due to dermatophytosis in a series of free-ranging wild porcupines and successful development of novel techniques for extraction and sequencing nucleic acids from fungus in archival formalin-fixed paraffin-embedded animal tissue.
ARTICLE | doi:10.20944/preprints202310.1852.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: bioinformatics; cannabis; hemp; hop latent viroid; molecular diagnostics; plant pathogens
Online: 30 October 2023 (09:54:14 CET)
The increased cultivation of Cannabis sativa L. in North America, represented by high Δ9-tetrahydrocannabinol-containing (high-THC) cannabis genotypes and low THC-containing hemp genotypes, has been impacted by an increasing number of plant pathogens. These include fungi which destroy roots, stems and leaves, in some cases causing a build-up of populations and mycotoxins in the inflorescences that can negatively impact quality. Viroids and viruses have also increased in prevalence and severity and can reduce plant growth and product quality. Rapid diagnosis of the occurrence and spread of these pathogens is critical. Techniques in the area of molecular diagnostics have been applied to study these pathogens in both cannabis and hemp. These include polymerase chain reaction (PCR)-based technologies, including RT-PCR, multiplex RT-PCR, RT-qPCR, and ddPCR, as well as whole genome sequencing (NGS) and bioinformatics. In this study, examples of how these technologies have enhanced the rapidity and sensitivity of pathogen diagnosis on cannabis and hemp will be illustrated. These molecular tools have also enabled studies on the diversity and origins of specific pathogens, specifically viruses and viroids, and these will be illustrated. Comparative studies on the genomics and metabolomics of healthy and diseased plants are urgently needed to provide insight into their impact on quality and composition of cannabis and hemp-derived products. Management of these pathogens will require monitoring of their spread and survival using the appropriate technologies to allow accurate detection, followed by appropriate implementation of disease control measures.
ARTICLE | doi:10.20944/preprints202307.1571.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: Laser-Plasma Ion Sources; High Power Laser Applications; Ion Diagnostics
Online: 24 July 2023 (08:53:29 CEST)
An experimental platform for laser-driven ion (sub-MeV) acceleration and potential applications was recently commissioned at the HiLASE laser facility. The auxiliary beam of the Bivoj laser system operating at GW peak power (~10 J in 5-10 ns) and 1-10 Hz repetition rate enabled a sta-ble production of high-current ion beams of multiple species (Al, Ti, Fe, Si, Cu, Sn). The pro-duced laser-plasma ion sources were fully characterized against the laser intensity on target (1013-1015 W/cm2) by varying the laser energy, focal spot size, and pulse duration. This al-lowed to provide accurate scaling laws of the maximum ion energy for the different target ma-terials investigated. Such experimental scaling laws are presented for the first time in the inves-tigated laser intensity range and for ns-class laser pulses, and allow to provide a qualitative in-terpretation of the laser-plasma interaction underpinning physics, thus to tune the main features of the accelerated ion beams (energy, temperature, and current). Such a detailed study was facil-itated by the large amount of data acquired at high repetition rate (1-10 Hz) provided by the Bivoj laser system. The versatility and tuneability of such high-repetition-rate laser-plasma ion sources are of po-tential interest for multidisciplinary user applications.
ARTICLE | doi:10.20944/preprints202211.0187.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: magnetic levitation; multiple sclerosis; diagnostics; robust machine learning; pattern recognition
Online: 10 November 2022 (03:16:37 CET)
The emerging advancements in separation and classification of various biological matters (e.g., living cells and proteins) using magnetic levitation (MagLev) technology have proven to be effective for improving disease diagnostics. MagLev technique has the capacity to detect and separate useful diagnostic biomarkers from biocomplex environments (e.g., blood and plasma), minimizing the unpleasant daunting task of sample preparations and labeling procedures. Here, we demonstrate the capability of this technique combined with image analysis and machine learning approaches for discriminating the various types of multiple sclerosis (MS) as an important model disease. To arrive at a systematic expert system, we combined robust statistical analysis with machine learning to (1) detect and remove outliers from the raw MagLev image datasets; then (2) process the images and output a low dimensional representation of massive data without losing the main statistical features; and finally (3) predict the MS clinical disease type (Relapsing-Remitting, Primary–Progressive, or Secondary–Progressive) using a classifier. This is expected to improve MS diagnostics since the current practices rely solely on clinical observation and central nervous system imaging, making management approaches are often reactional and inefficient. Thus, there is a need to identify the disease type early on. MagLev is expected to improve MS diagnostics, thereby aiding in prognosis and guiding adequate treatment choices before the patient exhibits signs of permanent neurological deficits.
ARTICLE | doi:10.20944/preprints202210.0266.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Breast cancer; early diagnostics; passive microwave radiometry (MWR); MicroRNA (miRNA)
Online: 19 October 2022 (04:11:29 CEST)
Breast cancer prevention is very important for a woman's health worldwide. We have demonstrated a correlation between mammography and ultrasound with diagnoses using passive microwave radiometry (MWR) and a miRNA oncopanel. While mammography screening dynamics could be completed in 3-6 months, MWR will provide us with a prediction in a matter of weeks or even days with the potential for complementary miRNA diagnostics. An early breast cancer diagnosis may be accomplished using either one of these novel techniques alone or in conjunction with more established techniques
ARTICLE | doi:10.20944/preprints202205.0130.v1
Subject: Public Health And Healthcare, Health Policy And Services Keywords: Kenya; COVID-19; community representatives; self-testing; diagnostics; qualitative research
Online: 10 May 2022 (09:38:58 CEST)
Rapid SARS-CoV-2 self-tests have the potential to expand access to COVID-19 testing and improve community-level case detection, particularly in resource-constrained countries such as Kenya. However, prior to their introduction, their acceptability must be assessed. This qualitative study explored key decision-takers’ values towards SARS-CoV-2 self-testing in Kenya. Healthcare workers, representatives of civil society, and potential implementors from Mombasa and Taita-Taveta were selected as decision-takers. Semi-structured interviews and focus group discussions were used to collect data on their values towards self-testing. A thematic analysis approach was applied. Most informants considered that the Kenyan public is equipped to accept and use self-testing safely as an approach to help to reduce workload at public healthcare facilities, and know one’s COVID-19 status in a private manner. The informants emphasized the need to provide counselling to end-users, to support those needing to self-isolate, and to engage different civil society stakeholders in information provision on self-testing. Fear of stigma and of forced isolation were noted as potential deterrents to self-testing uptake for some individuals. In conclusion, there is high acceptability of self-testing in Kenya among decision-takers. However, enhanced education, counselling, and addressing deterrents to testing would be helpful to ensure effective use of SARS-CoV-2 self-testing in Kenya.
ARTICLE | doi:10.20944/preprints202011.0058.v1
Subject: Engineering, Automotive Engineering Keywords: technical diagnostics; identification; modeling; modal analysis; control and measurement system
Online: 2 November 2020 (15:31:12 CET)
In this article authors shows chosen problems of technical state diagnosis with the use of identification and technical diagnostics methods such as experimental modal analysis. Relations between methods of dynamic state evaluation and methods of technical state evaluation were indicated. Example modal analysis results illustrate the complexity of projecting dynamic state researches into diagnostic researches of state evaluation.
REVIEW | doi:10.20944/preprints202004.0359.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; genetic diversity; genome evolution; diagnostics; therapeutics; vaccines
Online: 20 April 2020 (02:33:15 CEST)
A novel coronavirus COVID-19 was first emerged in Wuhan city of Hubei Province in China in December 2019. The COVID-19, since then spreads to 213 countries and territories, and has become a pandemic. Genomic analyses have indicated that the virus, popularly named as corona, originated through a natural process and is probably not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Genome-wide annotation of thousands of genomes revealed that more than 1,407 nucleotide mutations and 722 amino acids replacements occurred at different positions of the SARS-CoV-2. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, rapid, and specific diagnostic tools targeting IgM/IgG or newly developed plug and play methods should be available for resource-poor developing countries. Some drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools and the preventive or therapeutic remedies of the COVID-19, and discusses on scopes for further research and effective management and surveillance of COVID-19.
ARTICLE | doi:10.20944/preprints202312.0003.v1
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Respiratory Distress Syndrome; Chest X-ray; Diagnostics; Image Segmentation; Performance Evaluation
Online: 1 December 2023 (04:59:28 CET)
This research addresses the respiratory distress syndrome (RDS) in preterm newborns, caused by insufficient surfactant synthesis, which can lead to serious complications, including pneumothorax, pulmonary hypertension, and pulmonary hemorrhage, increasing the risk of a fatal outcome. By analyzing chest radiographs and blood gases, we specifically focus on the significant contributions of these parameters to the diagnosis and analysis of the recovery of patients with RDS. The study involved 32 preterm newborns, and the analysis of gas parameters before and after the administration of surfactants and inhalation corticosteroid therapy revealed statistically significant changes in values of parameters such as FiO2, pH, pCO2, HCO3 and BE (Sig.<0.05), ehile the pO2 parameter showed a potential change (Sig.=0.061). Parallel to this, the research emphasizes the development of a lung segmentation algorithm implemented in the MATLAB programming environment. The key steps of the algorithm include preprocessing, segmentation, and visualization for a more detailed understanding of the recovery dynamics after RDS. These algorithms have achieved promising results, with a global accuracy of 0.93±0.06, precision 0.81±0.16 and an F-score of 0.82±0.14. These results highlight the potential application of algorithms in the analysis and monitoring of recovery in newborns with RDS, also underscoring the need for further development of software solutions in medicine, particularly in neonatology, to enhance the diagnosis and treatment of preterm newborns with respiratory distress syndrome.
REVIEW | doi:10.20944/preprints202305.1549.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: multiple sclerosis; oligodendrocyte; myelination; inflammation; microglia; macrophage; bi-omarkers; imaging diagnostics
Online: 23 May 2023 (03:39:19 CEST)
Multiple sclerosis (MS) is a heterogeneous disease of the central nervous system that is governed by neural tissue loss and dystrophy during its progressive phase, with complex reactive pathological cellular changes. The immune-mediated mechanisms that promulgate the demyelinating lesions during the relapses of acute episodes are not characteristic of chronic lesions during progressive MS. This has limited our capacity to target the disease effectively as it evolves within the central nervous system white and gray matter, thereby leaving neurologists without effective options to manage individuals as they transition to a secondary progressive phase. The current review highlights the molecular and cellular sequelae that have been identified to cooperate and/or contribute to neurodegeneration that identifies individuals with progressive forms of MS. We emphasize the need for appropriate monitoring via known and novel molecular and imaging biomarkers that can accurately detect and predict progression for the purposes of newly designed clinical trials that may demonstrate efficacy of neuroprotection and potentially neurorepair. To achieve neurorepair, we focus on the modifications required in the reactive cellular and extracellular milieu, in order to enable endogenous cell growth as well as transplanted cells that can integrate and/or renew the degenerative MS plaque.
REVIEW | doi:10.20944/preprints202305.0369.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: SARS-CoV-2; clinical diagnostics; molecular assays; direct test; indirect test
Online: 5 May 2023 (14:07:20 CEST)
Due to species barriers and poor adaptability to new host environments, few pathogens cause global pandemics. But, SARS-CoV-2 is one exception with its high transmissivity and delayed onset of symptoms. Fortunately, the world was able to tap on the technologies especially the maturing RT-qPCR designed to combat SARS to launch an initial offensive on SARS-CoV-2. These initial efforts may have bought time for scientists to develop more refined diagnostic tests that specifically target SARS-CoV-2. This article describes the effort put forth by the biotech industry and academia in Singapore to develop diagnostic tests that aid the early detection of positive cases, and thereby help contain the virus. Direct tests such as RT-qPCR and antigen rapid test profile the virus nucleic acid and surface proteins, respectively. But, of equal importance in case detection and treatment is serological tests that measure the relative abundance of IgM and IgG which is indicative of infection phase and quality of immune response in positive cases. Other tests such as isothermal amplification, CRISPR-based diagnostics and breath tests are also in development or at initial field deployment, and would undoubtedly provide valuable use experience useful for the development of molecular assays to detect and combat the next pathogen of global concern.
ARTICLE | doi:10.20944/preprints202104.0385.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: antibiotic resistance; antimicrobial susceptibility testing; novel diagnostics; polymicrobial; sputum; drug resistant
Online: 14 April 2021 (14:21:15 CEST)
For polymicrobial infections, AtbFinder utilizes a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting the antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media and enabled, already within 4h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, AtbFinder system may be a valuable tool in improving antibiotic selection, enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.
ARTICLE | doi:10.20944/preprints202010.0241.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: tribotechnical diagnostics; engine oil; wear out; oil change interval; risk analysis
Online: 12 October 2020 (12:44:36 CEST)
This article focuses on the issue of motor oils used in the engines of off-road mobile machinery (NRMM), more specifically tractors. The primary goal of the paper is to determine the appropriate replacement interval for these oils. The physical properties of the examined samples were first determined by conventional instruments. Furthermore, the concentration of abrasive metals, contaminants, and additive elements were measured using an optical emission spectrometer. Lastly, the content of water, fuel, glycol, and the products of oxidation, nitration, and sulphation were determined by using infrared spectrometry. The measured values were compared to the limit values. Based on the processing and evaluation of these analyses, the overall condition of the oils was assessed and subsequently the optimal exchange interval of the examined oils was determined. In addition, a risk analysis of the outage was performed. Due to the high yields of crops, farmers can lose a significant amount of product when a tractor is not functioning during the harvest period. This loss for calculated in the paper.
REVIEW | doi:10.20944/preprints202006.0145.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Exosome; Extracellular Vesicle; Diagnostics; Vaccine; Treatment
Online: 12 June 2020 (09:01:02 CEST)
Our first modern global pandemic is caused by a nanosized lipid vesicle, called SARS-CoV-2. Its molecular structure and biogenesis have remarkable similarities with Extracellular Vesicles (EVs, most notably exosomes) that are constantly shed by all cells during their life. Their resemblance may not be a coincidence. Growing body of evidence has shown that EVs have significant roles in various biological processes, including viral infection, transmission and anti-viral response. Drawing comparison with the virus might shed light on how we could fight the COVID-19 disease. This may include novel EV research and diagnostics technologies as well as novel EV-based treatments.
ARTICLE | doi:10.20944/preprints201907.0155.v1
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: immune system; immunedeficiency; respiratory tract infections; children; impedance; serum; laboratory diagnostics
Online: 11 July 2019 (09:12:55 CEST)
Despite considerable progress in the diagnosis of various diseases, an ideal, simple tool for diagnosing patients with respiratory tract infections has not yet been invented. Many simple diagnostic tests are widely available to most doctors, provided they are aware of the prevalence of primary immunodeficiency. Other, more accurate studies are available only to immunologists. The aim of the study was to investigate the occurrence of dependence between selected physical parameters of serum such as: electrical conductivity, electrical permeability, dielectric loss factor, and selected parameters of the immune system. In addition, we have also included the ionogram (Na, K, Cl, Ca, Mg) and glucose concentration. As a result of research, the statistically significant, but very weak correlations between impedance magnitude |Z| and platelet counts (PLT), mean platelet volume (MPV) and chloride ions (Cl-) were found. The statistically significant differences according |Z| between children with and without deficiency in parameters of the immune system were noticed. Values of |Z| are higher in the case of children without deficiency in parameters of the immune system. The method of impedance measurements presented in our work is significantly easier then biosensors presented by other scientists. Taking into account our results, it can be stated that this method is promising for fast and easy detection of immunological disorders.
ARTICLE | doi:10.20944/preprints202312.0281.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: metabolomics; amino acids; diagnostics; neonatal asphyxia; liquid chromatography–mass spectrometry; newborn screening
Online: 5 December 2023 (15:31:23 CET)
Hypoxic-ischemic encephalopathy (HIE) is one of the most common causes of childhood disability. Hypothermic therapy is currently the only approved neuroprotective approach. However, early diagnosis of HIE can be challenging, especially in the first hours after birth when the decision to treat with hypothermic therapy is critical. Differentiating HIE from other neonatal conditions, such as sepsis, further complicates the diagnosis. This study investigated the utility of a metabolomic-based approach using the NeoBase 2 MSMS kit to diagnose HIE using dry blood stains in a Rice-Vannucci model of HIE in rats. We evaluated the diagnostic accuracy of this method between 3 and 6 hours after the onset of HIE, including in the context of systemic inflammation and concomitant hypothermic therapy. Discriminant analysis revealed several metabolite patterns associated with HIE. A logistic regression model using glycine levels achieved high diagnostic accuracy with areas under the curve (AUC) of 0.94 at 3 hours and 0.96 at 6 hours after the onset of HIE. In addition, orthogonal partial least squares discriminant analysis, which included five metabolites, achieved 100% sensitivity and 80% specificity within 3 hours of HIE. These results highlight the significant potential of the NeoBase 2 MSMS kit for the early diagnosis of HIE and could improve patient management and outcomes in this serious illness.
ARTICLE | doi:10.20944/preprints202308.1802.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Liquid biopsy; DNA methylation; biomarker; cancer; multi-cancer; bisulfite sequencing; diagnostics; screening
Online: 28 August 2023 (10:22:29 CEST)
Abstract: The ability to detect several types of cancer using a non-invasive, blood-based test holds the potential to revolutionize oncology screening. We mined tumor methylation array data from the Cancer Genome Atlas (TCGA) covering 14 cancer types and identified two novel, broadly oc-curring methylation markers at TLX1 and GALR1. To evaluate their performance as a general-ized blood-based screening approach, along with our previously reported methylation bi-omarker, ZNF154, we rigorously assessed each marker individually or combined. Utilizing the TCGA methylation data and applying logistic regression models within each individual cancer type, we found that the three-marker combination significantly increased the average area under the ROC curve (AUC) across the 14 tumor types compared to single markers (p= 1.158e-10; Friedman test). Furthermore, we simulated dilutions of tumor DNA into healthy blood cell DNA and demonstrated increased AUC of combined markers across all dilution levels. Finally, we evaluated assay performance in bisulfite sequenced DNA from patient tumors and plasma, in-cluding early-stage samples. When combining all three markers the assay achieved 100% sensi-tivity and specificity, as demonstrated in lung cancer plasma samples. In patient plasma from hepatocellular carcinoma, ZNF154 alone yielded the highest combined sensitivity and specificity values averaging 68% and 72%, whereas multiple markers could achieve higher sensitivity or specificity, but not both. Altogether this study presents a comprehensive pipeline for the identifi-cation, testing and validation of multi-cancer methylation biomarkers with a considerable poten-tial for detecting a broad range of cancer types in patient blood samples.
REVIEW | doi:10.20944/preprints202308.0229.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Anthracnose fruit rot; Colletotrichum acutatum; Diagnostics; crop protection; sustainable management techniques; strawberry
Online: 3 August 2023 (10:08:31 CEST)
Anthracnose and root rot are major foliar and root diseases of strawberry, respectively that cause most yield and quality losses. Anthracnose is caused by multiple species belonging to Colletotrichum spp complex. This disease alone can causeup to 70% yield loss in North America. Colletotrichum spp. cause several disease symptoms on strawberries, including root, fruit, and crown rot, lesions on petioles and runners, and irregular black spots on the leaf. In many cases, a lower level of infection on foliage remains non-symptomatic (quiescent), posing a challenge to growers as these plants can be a significant source of inoculum for the fruiting field. Reliable detection methods for quiescent infection should play an important role in preventing infected plants' entry into the production system or guiding growers to take appropriate preventative measures to control the disease. The selection of highly effective fungicides and including them in a schedule to prevent the development of fungicide resistance in fungal populations will remain an area of continued research. Disease management methods should entail sensitive molecular testing of suspected fungal isolates for resistance, rotation of products, and monitoring of quiescent infections in transplant materials. Testing and the inclusion of non-chemical methods such as biologicals and biorational treatments especially for soilborne pathogens will also be necessary to make disease management economically feasible and sustainable.
ARTICLE | doi:10.20944/preprints202011.0064.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: manual muscle testing; neuromuscular diagnostics; force profiles; reproducibility; Adaptive Force; handheld device
Online: 2 November 2020 (16:36:04 CET)
The manual muscle test (MMT) is a flexible diagnostic tool, which is used in many disciplines, applied in several ways. The main problem is the subjectivity of the test. The MMT in the version of a “break test” depends on the tester’s force rise and the patient’s ability to resist the applied force. As a first step, the investigation of the reproducibility of the testers’ force profiles is required for valid application. The study examined the force profiles of n=29 testers (n=9 experiences (Exp), n=8 little experienced (LitExp), n =12 beginners (Beg)). The testers performed 10 MMTs according to the test of hip flexors, but against a fixed leg to exclude the patient’s reaction. A handheld device recorded the temporal course of the applied force. The results show significant differences between Exp and Beg concerning the starting force (padj=0.029), the ratio of starting to maximum force (padj=0.005) and the normalized mean Euclidean distances between the 10 trials (padj=0.015). The slope is significantly higher in Exp vs. LitExp (p=0.006) and Beg (p=0.005). The results also indicate that experienced testers show inter-tester differences and partly even a low intra-tester reproducibility. That highlights the necessity of an objective MMT-assessment. Furthermore, an agreement on a standardized force profile is required – a suggestion is given.
REVIEW | doi:10.20944/preprints202008.0672.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: breakthrough invasive fungal infections; invasive candidiasis; invasive mold infections; endemic mycoses; diagnostics
Online: 30 August 2020 (15:13:51 CEST)
Breakthrough invasive fungal infections (bIFI) cause significant morbidity and mortality. Their diagnosis can be challenging due to reduced sensitivity of conventional culture techniques, serologic tests, and PCR-based assays in patients on antifungal therapy, and their diagnosis can be delayed contributing to poor patient outcomes. In this review, we provide consensus recommendations on behalf of the European Confederation for Medical Mycology (ECMM) for the diagnosis of bIFI caused by invasive yeasts, molds, and endemic mycoses, to guide diagnostic efforts in patients receiving antifungals and support the design of future clinical trials in the field of clinical mycology. The cornerstone of lab-based diagnosis of breakthrough infections for yeast and endemic mycoses remain conventional culture, to accurately identify the causative pathogen and allow for antifungal susceptibility testing. The impact of non-culture-based methods are not well-studied for the definite diagnosis of breakthrough invasive yeast infections. Non-culture-based methods have an important role for the diagnosis of breakthrough invasive mold infections, in particular invasive aspergillosis, and a combination of testing involving conventional culture, antigen-based assays, and PCR-based assays should be considered. Multiple diagnostic modalities, including histopathology, culture, antibody and/or antigen tests and occasionally PCR-based assays may be required to diagnose breakthrough endemic mycoses. A need exists for diagnostic tests that are effective, simple, cheap, and rapid to enable the diagnosis of bIFI in patients taking antifungals.
ARTICLE | doi:10.20944/preprints201911.0309.v1
Subject: Engineering, Bioengineering Keywords: in vitro diagnostics; microfluidics; full integration; lab-on-a-chip; pathogen detection
Online: 26 November 2019 (09:56:47 CET)
Microfluidics is facing critical challenges in the quest of miniaturizing, integrating, and automating in vitro diagnostics, including the increasing complexity of assays, the gap between the macroscale world and the microscale devices, and the diverse throughput demands in various clinical settings. Here a “3D extensible” microfluidic design paradigm that consists of a set of basic structures and unit operations was developed for constructing any application-specific assay. Four basic structures- check valve (in), check valve (out), double-check valve (in and out), and on-off valve, were designed to mimic basic acts in biochemical assays. By combining these structures linearly, a series of unit operations can be readily formed. We then proposed a “3D extensible” architecture to fulfill the needs of the function integration, the adaptive “world-to-chip” interface, and the adjustable throughput in the X, Y, and Z directions, respectively. To verify this design paradigm, we developed a fully integrated loop-mediated isothermal amplification microsystem that can directly accept swab samples and detect Chlamydia trachomatis automatically with a sensitivity one order higher than that of the conventional kit. This demonstration validated the feasibility of using this paradigm to develop integrated and automated microsystems in a less risky and more consistent manner.
ARTICLE | doi:10.20944/preprints201808.0214.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: immunomagnetic separation (IMS); bacterial pathogen; 3D printing; preconcentration; DNA purification; molecular diagnostics
Online: 12 August 2018 (19:26:04 CEST)
Molecular detection of pathogens in clinical samples often requires pretreatment techniques, including immunomagnetic separation and magnetic silica bead (MSB)-based DNA purification to obtain the purified DNA of pathogens. These two techniques usually rely on handling small tubes containing a few millilitres of the sample and manual operation, implying that an automated system encompassing both techniques is needed for larger quantities of the samples. Here, we report a 3D-printed microfluidic platform that enables bacterial preconcentration and genomic DNA (gDNA) purification for improving the molecular detection of target pathogens in blood samples. The device consists of two microchannels and one chamber, which can be used to preconcentrate pathogens bound to antibody-conjugated magnetic nanoparticles (Ab-MNPs) and subsequently extract gDNA using magnetic silica beads (MSBs) in a sequential manner. The device was able to preconcentrate very low concentrations of pathogens and extract their genomic DNA in 10 mL of 10% blood within 30 min, and thus allowed polymerase chain reaction (PCR) and quantitative PCR to detect 1 colony forming unit of Escherichia coli O157:H7 in 10% blood. The results suggest that the 3D-printed microfluidic platform is highly useful for lowering the limitations on molecular detection in blood by preconcentrating the target pathogen and isolating its DNA in a large volume of the sample.
REVIEW | doi:10.20944/preprints202311.0189.v1
Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: vital pulp therapy; irreversible pulpitis; pulpotomy; deep caries; carious pulp exposure; pulpal diagnostics
Online: 3 November 2023 (03:30:36 CET)
A partial or complete pulpotomy is a type of vital pulp therapy (VPT) that aims to remove the in-flamed, infected pulp, leaving behind healthy, vital pulp that is capable of healing. VPT has gained renewed popularity as a treatment option in permanent mature posterior teeth with irre-versible/moderate-severe pulpitis, its high success rates matching that of root canal treatment (RCT). There is currently no consensus regarding diagnostic and prognostic predictors of success of pulpotomies for managing such cases. Therefore, we conducted a scoping review to identify and analyze how these factors affect the outcome of treatment. A literature search using the PRISMA guidelines was undertaken using PubMed and Scopus on July 7, 2023. A total of 22 studies met the inclusion criteria and were qualitatively analyzed by two reviewers. The follow-ing diagnostic and prognostic factors were recognized and discussed; presenting signs and symptoms, periapical diagnosis, bleeding time, indicators of inflammation (bleeding time, con-centration of inflammatory biomarkers), patient age and medical status, the depth, activity and location of caries, and restorative factors. Based on the studies assessed, there is limited evidence to support their prognostic value. Further research is necessary to identify solid predictors of outcome.
ARTICLE | doi:10.20944/preprints202306.2200.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Internet of things; digital platform; vibration diagnostics; calibration; accelerometer; industrial equipment; Allan variance
Online: 30 June 2023 (11:23:28 CEST)
The subject of study in the article is the method of industrial equipment vibration diagnostics using Allan variance. The goal is to increase the precision and accuracy of industrial equipment's vibration diagnostics processes by developing and implementing IoT-oriented solutions based on intelligent sensors and actuators per the IEEE 1451.0-2007 standard. Tasks: justify the feasibility of using platform-oriented technologies for vibration diagnostics of industrial equipment and choose a cloud service for the implementation of the platform; develop software and hardware solutions of the IoT platform for vibration diagnostics of industrial equipment; calibrate the vibration diagnostics system and check the measurement precision and accuracy. The methods used are the microservice approach, multilevel architecture, and assessing equipment state-based Allan variance. We obtained the following results. The architecture of the IoT system for vibration diagnostics of industrial equipment developed and presented in the article is three-level. The level of autonomous sensors provides readings of vibration acceleration indicators and transmits data to the Hub level, which is implemented based on a BeagleBone single-board microcomputer through the BLE digital wireless data transmission channel. BeagleBone computing power provides work with artificial intelligence algorithms. At the third level of the server platform, the tasks of diagnosing and predicting the condition of the equipment are solved, for which the Dictionary Learning algorithm implemented in the Python programming language is applied. Verifying the accelerometer calibration method for vibration diagnostics of industrial equipment was performed using a unique stand. Correct operation of the entire system is confirmed by the coincidence of expected and measured results. In the next step, we plan the development of additional microservices that will provide the possibility of using time series analysis methods and modern artificial intelligence technologies for complex diagnostics and forecasting of the equipment state.
ARTICLE | doi:10.20944/preprints202305.0858.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Gram-negative bacilli bacteremia; multidrug resistance; 28-day mortality; procalcitonin; rapid molecular diagnostics
Online: 11 May 2023 (13:34:03 CEST)
The incidence of multidrug-resistant (MDR) bloodstream infections (BSI) is associated with high morbidity and mortality. Little evidence exists regarding the epidemiology of BSIs and the use of appropriate empirical antimicrobial therapy in endemic regions. Novel diagnostic tests (RDTs) may facilitate and improve patient management. Data from patients with MDR GNB bacteremia at a university tertiary hospital were assessed over a 12-month period. 157 episodes of MDR GNB BSI were included in the study. Overall mortality rate was 50,3 percent. Rapid molecular diagnostic tests were used in 94% of BSI episodes. In univariate analysis, age (OR 1.05 (95% CI 1.03, 1.08) p<0.001), Charlson Comorbidity Index (OR 1.51 (95% CI 1.25, 1.83) p<0.001), Procalcitonin≥1(OR 3.67 (CI 95% 1.73, 7.79) p<0.001) and monotherapy with tigecycline (OR 3.64 (95% CI 1.13, 11.73) p=0.030) were the only factors associated with increased overall mortality. Surprisingly, time to appropriate antimicrobial treatment had no impact on mortality. MDR pathogen isolation, other than Klebsiella pneumoniae and Acinetobacter baumanii was associated with decreased mortality (OR 0.35 (95% CI 0.16, 0.79) p=0.011). In multivariate analysis though the only significant factor for mortality was Procalcitonin≥1(OR 2.84 (95% CI 1.13, 7.11) p=0.025). In conclusion, in an endemic area, mortality rates in MDR BSI remain high. High procalcitonin was the only variable that predicted death. The use of rapid diagnostics did not improve mortality rate.
REVIEW | doi:10.20944/preprints202304.1185.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: renal cell carcinoma; liquid biopsy; blood; extracellular vesicles; microRNA; biomarker; diagnostics; prognosis; prediction
Online: 28 April 2023 (13:00:31 CEST)
Renal cell carcinoma (RCC) is the second most common cancer of the urinary system. The current therapeutic strategies are based on partial or total nephrectomy and/or targeted therapies based on immune checkpoint inhibitors to which patients are often refractory. Preventive and screening strategies are not existing and the few available biomarkers for RCC are characterized by the lack of sensitivity, outlining the need of novel noninvasive and sensitive biomarkers for an early diag-nosis and a better disease monitoring. Blood liquid biopsy (LB) is a non- or minimally invasive procedure for a more representative view of tumor heterogeneity than the tissue biopsy, poten-tially allowing real-time monitoring of cancer evolution. Growing interest is focused on the extra-cellular vesicles (EVs) secreted by either healthy or tumoral cells and recovered in a variety of bio-logical matrices, blood included. EVs are involved in cell-to-cell crosstalk transferring their mRNAs, miRNAs, and proteins content. In particular, transferred miRNAs may regulate the tu-morigenesis and proliferation also impacting on resistance to apoptosis, thus representing poten-tial useful biomarkers. Here we present the latest efforts in the identification of circulating miR-NAs in blood samples, focusing on the potential use of EV derived miRNAs as RCC diagnostic, prognostic markers.
REVIEW | doi:10.20944/preprints202212.0300.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: medulloblastoma; TP53 mutation; molecular classification; diagnostics; liquid biopsy; animal models; transcriptome; precision oncology
Online: 16 December 2022 (08:47:35 CET)
A recent paradigm shift in diagnostics of medulloblastoma allows the distinction of four major groups defined by genetic data rather than histology. This new molecular classification correlates better with prognosis and will allow better clinical management for therapies targeting druggable mutations, but also offers a new combination of monitoring tumor development in real-time and treatment response by sequential liquid biopsy. This review highlights recent developments after a century of milestones in neurosurgery, radio- and chemotherapy, but also controversial theories on the cell of origin, animal models and the use of liquid biopsy.
Subject: Physical Sciences, Acoustics Keywords: exponential atmosphere; acoustic wave; diagnostics; projection operators; artificial periodic irregularities; neutral temperature; density
Online: 26 July 2021 (18:04:42 CEST)
The main result of this work is the estimation of the entropy mode accompanying a wave disturbance, observed at the atmosphere heights range of 90-120km. The study is the direct continuation and development of recent results on diagnosis of the acoustic wave with the separation on direction of propagation. The estimation of the entropy mode contribution relies upon the measurements of the three dynamic variables (the temperature, density and vertical velocity perturbations) of the neutral atmosphere measured by the method of the resonant scattering of radio waves on the artificial periodic irregularities of the ionospheric plasma. The measurement of the atmosphere dynamic parameters has been carried out on the SURA heating facility. The mathematical foundation of the mode separation algorithm is based on the dynamic projecting operator technique. The operators are constructed via the eigenvectors of the coordinate evolution operator of the transformed system of balance equations of the hydro-thermodynamics.
ARTICLE | doi:10.20944/preprints202105.0123.v1
Subject: Engineering, Automotive Engineering Keywords: conveyor belts; magnetic method; diagnostics; NDT method; belt damage; statistical analysis; neural networks
Online: 7 May 2021 (09:03:23 CEST)
The paper presents the identification and classification of steel cord failures in the conveyor belt core based on an analysis of a two-dimensional image of magnetic field changes recorded using the Diagbelt system around scanned failures in the test belt. The obtained set of identified changes in images obtained for numerous devices parameters settings were the base for statistical analysis. It makes it possible to determine the Pearson’s linear correlation coefficient between the parameters being changed and the image of the failures. In the second stage of the research, artificial intelligence methods were applied to construct a multilayer neural network (MLP) and to teach its appropriate identification of damage. In both methods were used the same data sets, which made it possible to compare methods.
ARTICLE | doi:10.20944/preprints202008.0569.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Recombinase polymerase amplification; Treponema pallidum; Haemophilus ducreyi; Molecular diagnostics; Point-of-care test
Online: 26 August 2020 (09:01:07 CEST)
Yaws is a skin debilitating disease caused by Treponema pallidum subspecies pertenue with most cases reported in children. World Health Organization (WHO) aims at total eradication of this disease through mass treatment of suspected cases followed by an intensive follow-up program. However, effective diagnosis is pivotal in the successful implementation of this control program. Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification technique offers a wider range of differentiation of pathogens including those isolated from chronic skin ulcers with similar characteristics such as Haemophilus ducreyi (H. ducreyi). We have developed a duplex RPA assay for the simultaneous detection of Treponema pallidum (T. pallidum) and H. ducreyi (TPHD-RPA). TPHD-RPA assay demonstrated no cross-reaction with other pathogens and enable detection of T. pallidum and H. ducreyi within 15 minutes at 42 oC. The duplex RPA assay was validated with 49 clinical samples from individuals confirmed to have yaws by serological tests. Compared with commercial multiplex real-time PCR, the TPHD-RPA assay demonstrated 94-95% sensitivity for T. pallidum and H. ducreyi confirmed samples, respectively and 100% specificity. This simple novel TPHD-RPA assay enables the rapid detection of both T. pallidum and H. ducreyi in yaws-like lesions. This test could support the yaws eradication programs by ensuring effective diagnosis as well as enable monitoring of eradication efforts success or failure and planning of follow-up interventions at the community level.
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: veterinary diagnostics; lateral flow tests; rapid tests; functionalized nanoparticles; signal enhancement; cow diseases
Online: 28 November 2019 (11:07:05 CET)
In this article, we describe an immunochromatographic test system developed for rapid serodiagnostics of cattle brucellosis using two markers: gold nanoparticles (GNPs) and quantum dots (QDs). The test system was compared with immunochromatographic serodiagnostics systems that use only one marker. The approbation of the test system was conducted on samples of cattle sera with low, but diagnostically significant titers of specific antibodies. We show that when two conjugates are used, the intensity of the detectable signal increases by 2–3 times compared with the test system using the QD conjugate and by more than 9 times compared with the system using the GNP conjugate.
ARTICLE | doi:10.20944/preprints202309.1796.v2
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: telecytology; ROSE, telepathology; EBUS; lung cytology; endoscopic diagnostics; whole-slide imaging; diagnostic accuracy; cytopathology
Online: 18 October 2023 (04:23:27 CEST)
Background: This prospective study assesses the use of Rapid Remote Online Cytological Evaluation analysis for diagnosing endoscopical achieved biopsies. It focuses on its effectiveness in identifying benign and malignant conditions using digital image processing. Methods: The study was conducted between April 2021 and September 2022 and involved a total of 314 Rapid Remote Online Cytological Evaluations (17 brush, 143 fine needle aspirations and 154 imprint cytologies) analyses performed on 239 patients at the LungenClinic Grosshansdorf. During on-site evaluation via telecytology, the time requirement was determined and the findings were compared with the cyto-/histological and final diagnoses. Results: By means of Rapid Remote Online Evaluation, 86 cytological benign and 190 malignant and 38 findings of unclear diagnosis were recorded (Ø assessment time 100 sec., range 11 - 370sec.). In 27 of the 38 cases with unclear diagnosis, the final findings were malignant tumours and only 6 were benign changes. The diagnosis of another five of these 38 cases remained unclear. Excluding these 38 findings, the Rapid Remote online cytology achieved a sensitivity of 78.6% with a specificity of 99.5% and a correct classification rate of 93.1% with regard to the final diagnosis of all cases. As expected, an increase in the sensitivity rate for the cytological detection of malignant tumours (76.1% vs. 92.5%) was found especially in fine-needle aspirations. Conclusions: Rapid remote online analysis allows fast quantitative and qualitative evaluation of clinically obtained cytological specimens. With a correct classification rate of more than 93%, sampling deficiencies can be corrected promptly and diagnostic and therapeutic approaches can be derived.
REVIEW | doi:10.20944/preprints202308.1539.v2
Subject: Biology And Life Sciences, Life Sciences Keywords: machine learning; reinforcement learning; deep learning; Gaussian process; artificial neural networks; real-time diagnostics
Online: 25 September 2023 (05:19:01 CEST)
Plasma technology shows tremendous potential for revolutionizing oncology research and treatment. Reactive oxygen and nitrogen species, electromagnetic emissions generated through gas plasma jets, have attracted significant attention due to their selective cytotoxicity towards cancer cells. To leverage the full potential of plasma medicine, researchers have explored the use of mathematical models and various subsets of machine learning, such as reinforcement learning, and deep learning. This review emphasizes the significant application of AI algorithms in the adaptive plasma system, paving the way for precision and dynamic cancer treatment. Realizing the full potential of AI in plasma medicine, requires research efforts, data sharing and interdisciplinary collaborations. Unravelling the complex mechanisms, developing real-time diagnostics, and optimizing AI models will be crucial to harness the true power of plasma technology in oncology. The integration of personalized and dynamic plasma therapies, alongside AI and diagnostic sensors, presents a transformative approach to cancer treatment with the potential to improve outcomes globally.
ARTICLE | doi:10.20944/preprints202306.1261.v1
Subject: Physical Sciences, Optics And Photonics Keywords: ultrashort laser pulse; water droplet; fluorescence; multiphoton absorption; plasma emission; angular diagram; remote diagnostics
Online: 16 June 2023 (16:24:57 CEST)
Femtosecond laser-induced fluorescence (FLIF) and femtosecond laser-induced optical breakdown spectroscopy (FIBS) are important tools for remote diagnostics of atmospheric aerosols using LiDAR techniques. They are based on light emission excitation in disperse medium via the multiphoton nonlinear processes in aerosol particles induced by high-power optical pulses. To date, the main challenge restraining the large-scale application of the FLIF and FIBS in atmospheric studies is the lack of valued theory of the stimulated light emission in liquid microparticles with sufficiently broad range of sizes. In this paper, we fill this gap and present the theoretical model of dye water droplets emission under high-intense laser exposure that adequately simulates the processes of multiphoton excited fluorescence and optical breakdown plasma emission in microparticles and gives quantitative estimates of the angular and power characteristics of the nonlinear emission. The model is based on the numerical solution to the inhomogeneous Helmholtz equations for the stimulating (primary) and nonlinear (secondary) waves provided by the random nature of molecule emission in particles. We show that droplet fluorescence stimulated by the multiphoton absorption generally becomes more intensive with increasing particle size. Moreover, far-field plasma emission from liquid particles demonstrates larger angular diversity when changing droplet radius in comparison with the multiphoton excited fluorescence, which is mainly due to the excitation of the internal optical field resonances in spherical particles.
REVIEW | doi:10.20944/preprints202301.0323.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: next-generation sequencing; nanopore sequencing; biosensors; single-molecule analysis; molecular diagnostics; genetics; transcriptomics; epigenetics
Online: 18 January 2023 (07:36:43 CET)
There have been several developments in the field of nanopore biosensor development and sequencing applications that address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making these platforms a mainstay in contemporary research labs. Equipped with the ability to provide long and short-read sequencing information with quick turn-around times and simple sample preparation, nanopore sequencers are quickly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We conclude with examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
ARTICLE | doi:10.20944/preprints202209.0220.v1
Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: TrueDepth; CBCT; Orthodontics; Face scan; Smartphone; Facial diagnostics; Smartphone-based sensors; Facially driven orthodontics
Online: 15 September 2022 (05:45:29 CEST)
The current paradigm shift in orthodontic treatment planning is based on facially driven diagnostics. This requires an affordable, convenient, and non-invasive solution for face scanning. Therefore, utilization of smartphones` TrueDepth sensors is very tempting. TrueDepth refers to front-facing cameras with a dot projector in Apple devices that provide real-time depth data in addition to visual information. There are several applications that tout themselves as accurate solutions for 3D scanning of the face in dentistry. Their clinical accuracy has been uncertain. This study focuses on evaluating the accuracy of the Bellus3D Dental Pro app, which uses Apple's TrueDepth sensor. The app reconstructs a virtual, high-resolution version of the face, which is available for download as a 3D object. In this paper, sixty TrueDepth scans of the face were compared to sixty corresponding facial surfaces segmented from CBCT. Difference maps were created for each pair and evaluated in specific facial regions. The results confirmed statistically significant differences in some facial regions in amplitudes greater than 3 mm, suggesting that current technology has limited applicability for clinical use. The clinical utilization of facial scanning for orthodontic evaluation, which does not require accuracy in the lip region below 3 mm, can be considered.
ARTICLE | doi:10.20944/preprints202205.0302.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: skin cancer; melanoma; computer-aided diagnostics; image classification; CoAtNet; convolutional neural networks; deep learning
Online: 23 May 2022 (10:55:45 CEST)
Melanoma is considered to be the most aggressive form of skin cancer. Due to the similar shape of malignant and benign cancerous lesions, doctors spend considerably more time when diagnosing these findings. At present, the evaluation of malignancy is performed primarily by invasive histological examination of the suspicious lesion. Developing an accurate classifier for early and efficient detection can minimize and monitor the harmful effects of skin cancer and increase patient survival rates. This paper proposes a multi-class classification task using the CoAtNet architecture, a hybrid model that combines the depthwise convolution matrix operation of traditional convolutional neural networks with the strengths of Transformer models and self-attention mechanics to achieve better generalization and capacity. The proposed multi-class classifier achieves an overall precision of 0.901, recall 0.895, and AP 0.923, indicating high performance compared to other state-of-the-art networks.
REVIEW | doi:10.20944/preprints202203.0089.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: CRISPR-Cas; SARS-CoV-2; molecular diagnostics; isothermal amplification; comparative analysis; nucleic acid detection
Online: 7 March 2022 (04:53:25 CET)
The emergence of the COVID-19 pandemics prompted a fast development of novel diagnostic methods of the etiologic virus SARS-CoV-2. Methods based on CRISPR-Cas systems have been particularly promising because they can achieve a similar sensitivity and specificity to the golden standard RT-qPCR, especially when coupled to an isothermal pre-amplification step. Furthermore, they have also solved inherent limitations of RT-qPCR that impede its decentralized use and deployment in the field, such as the need for expensive equipment, high cost per reaction, and delivery of results in hours, among others. In this review, we evaluate publicly available methods to detect SARS-CoV-2 that are based on CRISPR-Cas and isothermal amplification. We critically analyze the steps required to obtain a successful result from clinical samples and pinpoint key experimental conditions and parameters that could be optimized or modified to improve clinical and analytical outputs. The COVID outbreak has propelled intensive research in a short time, which is paving the way to develop effective and very promising CRISPR-Cas systems for the precise detection of SARS-CoV-2. This review could also serve as an introductory guide to new labs delving into this technology.
ARTICLE | doi:10.20944/preprints202112.0522.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: lithium battery; electrochemical power sources; diagnostics; battery management system; load variation; in situ method
Online: 31 December 2021 (12:59:15 CET)
The relaxation process of lithium batteries caused by load variation is considered. It is shown that such processes have strong dependence on internal physical and chemical processes and battery technical conditions. Theoretical expressions of the relaxation process caused by a step-like load variation have been obtained for 1st and 2nd order equivalent electrical circuits. The experimental investigations show that the obtained models fit the real relaxation processes and the behavior of the identified parameters could be explained by specific features of physical and chemical processes within the lithium battery. It should be noted that the obtained results can be generalized for a different type of electrochemical power source. The proposed approach makes it possible to provide means for electrochemical power source characterization and diagnostic, the main advantages of which are good time localization of measurement procedures and inexpensive apparatus implementation.
ARTICLE | doi:10.20944/preprints202103.0274.v2
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: acoustics of non-uniform media; wave mode diagnostics; entropy mode; initialization of hydrodynamic field
Online: 13 May 2021 (13:57:12 CEST)
Diagnostics and decomposition of atmospheric disturbances in a planar flow are considered and applied to numerical modeling results with the direct possibility to use in atmosphere monitoring especially in such strong events which follow magnetic storms. The study examines a situation in which the stationary equilibrium temperature of a gas may depend on a vertical coordinate, that seriously complicates the problem solution. The relations connecting perturbations for acoustic and entropy modes are analytically established and led to the solvable diagnostic equations. These perturbation structures, found as the equation solutions specify acoustic and entropy modes in an arbitrary stratified gas under the condition of stability. These time-independent diagnostic relations link gas perturbation variables of the acoustic and the entropy modes. Hence, they provide the ability to decompose the total vector of perturbations into acoustic and non-acoustic (entropy) parts uniquely at any instant within the all accessible heights range. As a prospective model, we consider the diagnostics at the height interval [120;180] km, where the equilibrium temperature of a gas depends linearly on the vertical coordinate. For such a heights range it is possible to proceed with analytical expressions for pressure and entropy perturbations of gas variables. Individual profiles of acoustic and entropy parts for some data, obtained by numerical experiment, are illustrated by the plots for the pure numerical data against ones obtained by the model. The total energy of a flow is determined for both approaches and its height profiles are compared.
ARTICLE | doi:10.20944/preprints201911.0323.v1
Subject: Medicine And Pharmacology, Tropical Medicine Keywords: Zika virus; flavivirus; cross-reactivity; neutralization; diagnostics; serology; plaque reduction neutralization test; flavivirus exposure
Online: 27 November 2019 (03:45:37 CET)
Zika virus (ZIKV) co-circulates with several closely related flaviviruses which exhibit similar clinical manifestations thus, clinicians rely on molecular and serological techniques for diagnosis. Cross-reactivity of patient specimens to flaviviruses is a significant impediment to serological diagnosis in areas where multiple flaviviruses co-circulate. Furthermore, patient exposure history to any of these viruses could complicate serological response patterns which could result in over and/or underdiagnosis of ZIKV infection. Three strains of ZIKV, dengue serotypes 1-4, West Nile virus, Japanese Encephalitis virus, and Yellow Fever virus were evaluated for neutralizing properties against 3 monoclonal antibodies, 4 ZIKV-naïve patients with flavivirus exposure history, 5 patients with verified ZIKV exposure and unknown flavivirus exposure history, and 5 flavivirus-naive patients with ZIKV-only exposure. Patients naïve for ZIKV exposure effectively neutralized multiple strains of ZIKV. Overall, the prototype ZIKV isolate MR-766 did not behave like the other ZIKV isolated used in this study. MR-766 was neutralized more completely by polyclonal patient serum than recent ZIKV isolates. MR-766 was neutralized better than dengue virus in ZIKV-naïve patients with prior dengue exposure. MR-766 was neutralized significantly less than recent ZIKV isolates when treated with monoclonal antibodies. The data herein show that without RT-PCR, serological diagnosis may not be possible in areas where multiple flaviviruses are endemic.
COMMUNICATION | doi:10.20944/preprints202306.1389.v1
Subject: Public Health And Healthcare, Other Keywords: Diagnostics; Lower and Middle-Income Countries; Extreme Poverty; Limited-resource settings; infectious diseases; Africa; Sub-Saharan Africa; Nigeria; Antimicrobial; poverty; paper devices; mobile phone; smartphones; microfluidics; multiplexing; inexpensive diagnostics; medical devices; repairability
Online: 20 June 2023 (05:17:19 CEST)
Diagnostics is believed to drive about 70% of medical interventions, but this may not be true for all demographics. With more than 30% of the African population living in extreme poverty ($1.9 per day - 2022); and healthcare costs competing unfavorably against unbridled access to antibiotics and herbal concoctions, especially in Sub-Saharan Africa, how do you convince such a people to choose diagnostics first? More importantly, how do you design a medical device targeted at meeting the diagnostic needs of this demographic? In developing diagnostic devices for such a market, what is worth sacrificing? How dire is the need for advanced technologies in devices developed for such a demographic? These are questions that remain unaddressed by the technological breakthroughs and current research in medical device development, especially for infectious disease diagnostics. The objective of this paper is to underscore critical concerns which must be considered in the bid to successfully design medical diagnostic devices for Africa and perhaps, other limited-resource settings. It is also written as a suggestive guidance document for researchers whose interest is in the development of infectious disease diagnostic platforms for rural Africa and similar limited-resource environments.
REVIEW | doi:10.20944/preprints202109.0491.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Tuberculosis; Mycobacterium; Diagnostics; Drug Discovery; Antibiotics; Antimicrobial Re-sistance; Microfluidics; Single-Cell Analysis; Bioengineered Models
Online: 29 September 2021 (11:34:04 CEST)
Tuberculosis (TB) remains a global healthcare crisis with an estimated 10 million new cases and 1.4 million deaths per year TB is caused by infection with the major human pathogen Mycobacte-rium tuberculosis, which is difficult to rapidly diagnose and treat. There is an urgent need for new methods of diagnosis, sufficient in vitro models which capably mimic all physiological condi-tions of the infection, and high-throughput drug screening platforms. Microfluidic-based tech-niques provide single-cell analysis which reduces experimental time, the cost of reagents, and have been extremely useful for gaining insight into monitoring microorganisms. This review out-lines the field of microfluidics and discusses the use of this novel technique so far in M. tuberculo-sis diagnostics, research methods, and drug discovery platforms. The practices of microfluidics have promising future applications for diagnosing and treating TB.
ARTICLE | doi:10.20944/preprints202104.0086.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: DNA sensor; point of care diagnostics; methicillin-resistant Staphylococcus aureus; label free biosensor; AC electrokicetics
Online: 5 April 2021 (10:11:51 CEST)
Biosensors have shown great potential in realizing rapid, low cost and portable on-site detection for diseases. This work reports the development of a new bioelectronic sensor called AC electrokinetics-based capacitive (ABC) biosensor, for the detection of genomic DNA (gDNA) of methicillin-resistant Staphylococcus aureus (MRSA). The ABC sensor is based on interdigitated microelectrodes biofunctionalized with oligonucleotide probes. It uses a special AC signal for direct capacitive monitoring of topological change on nanostructured sensor surface, which simultaneously induce dieletrophoretic enrichment of target gDNAs. As a result, rapid and specific detection of gDNA/probe hybridization can be realized with high sensitivity. It requires no signal amplification such as labelling, hybridization chain reaction, or nucleic acid sequence-based amplification. This method involves only simple sample preparation. After optimization of nano-structured sensor surface and signal processing, the ABC sensor demonstrated fast turnaround of results (~10 s detection), excellent sensitivity (a detection limit of 4.7 DNA copies /µL MRSA gDNA) and high specificity, suitable for point of care diagnosis. As a bioelectronic sensor, the developed ABC sensors can be easily adapted for detection of other infectious agents.
REVIEW | doi:10.20944/preprints202309.1312.v1
Subject: Engineering, Bioengineering Keywords: deep learning; deep neural networks; robustness; stability; generalization; physics-driven learning; medical imaging; computer aided diagnostics
Online: 20 September 2023 (08:42:06 CEST)
Deep Neutral Networks (DNNs) were initially proposed towards the midst of the 20th century, motivated by the neural structure and mechanism of the human brain. Thanks to major ad-vancements in computational resources, during the past decade DNN-based systems have demonstrated unprecedented performance in terms of accuracy and speed. However, recent work has shown that such models may not be sufficiently robust during the inference process. Furthermore, due to the data-driven learning nature of DNNs, designing interpretable and gen-eralizable networks is a major challenge, especially in critical applications, such as medical Computer Aided Diagnostics (CAD) and other medical imaging tasks, including classification, regression and reconstruction. Within this context, a line of physics-driven approaches for deep learning has recently emerged, aimed at improving the stability and generalization capacity of DNNs for medical imaging applications. In this paper, we review recent work focused on phys-ics-driven or prior-information learning for a variety of imaging modalities and medical applica-tions. We discuss how the inclusion of domain-related knowledge into the learning process and networks’ design supports their stability and generalization capability. In addition, we highlight current and future challenges within this scope.
REVIEW | doi:10.20944/preprints202302.0312.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Nucleic acid detection; microfluidics; portable devices; molecular diagnostics; isothermal amplification; lab on chip; Nucleic Acid Testing
Online: 17 February 2023 (13:42:33 CET)
Conventional diagnostic techniques are based on utilization of analyte sampling, sensing and signalling on separate platforms for detection purposes, that must be evaded and integrated to a single step procedure in point of care (POC) testing devices. Therefore, the trend has been shifted towards utilization of microfluidic platforms for detection of analytes in biochemical, clinical and food technology due to its being expeditious. Microfluidic systems moulded with polymer substances or glass offer specific and sensitive detection of infectious and non-infectious diseases by providing innumerable benefits including less cost, good biological affinity, strong capillary action and simple process of fabrication. In the case of nucleic acid-based nanosensors, there are some challenges that need to be addressed such as cellular lysis, isolation and amplification of nucleic acid required to be accomplished prior to its detection. To avoid utilization of laborious steps for executing these steps, advances have been deployed in this perspective for on-chip sample preparation, amplification and detection which not only improves sensitivity and selectivity but also saves time and resources. This review emphasizes the significance of microfluidic technology for nucleic acid detection of infectious and non-infectious diseases. The implementation of isothermal amplification in concomitance with lateral flow assay greatly increases the binding efficiency of nanoparticles and biomolecules, improves limit of detection and sensitivity. Most importantly deployment of paper-based material made of cellulose reduces the overall cost. Microfluidic technology in nucleic acid testing has been discussed by explicating its applications in different fields. This review concludes with the prospects and proposes future directions in microfluidic based methods in disease diagnosis.
CASE REPORT | doi:10.20944/preprints202012.0548.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: next-generation sequencing; hereditary breast cancer; Homologous Recombination Repair; hereditary cancer syndrome; Clinical genomics; Molecular diagnostics
Online: 22 December 2020 (10:17:48 CET)
Next Generation Sequencing based cancer risk screening with multigene panels has become the most successful method for programming cancer prevention strategies. ATM germ-line heterozygosity has been described as able to increase tumor susceptibility. In particular, families that carry heterozygous germ-line variants of ATM gene show a 5- to 9-fold risk of developing breast cancer. Recent studies identified ATM as the second most mutated gene after CHEK2 in BRCA-negative patients. Nowadays, more than 170 potential missense variants and several truncating mutations have been identified in ATM gene. Here we present the molecular characterization a new ATM deletion, identified thanks to the CNV algorithm implemented in the NGS analysis pipeline. An automated workflow implementing the SOPHiA Genetics’ Hereditary Cancer Solution (HCS) protocol was used to generate NGS libraries that were sequenced on Illumina MiSeq Platform. NGS data analysis allowed to identify a new inactivating deletion of exons 19-27 of ATM gene. DNA breakpoint was characterized both at DNA and RNA level
REVIEW | doi:10.20944/preprints201911.0085.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mendelian disease; diagnostics; variant interpretation; variant prioritization; rna splicing; bioinformatics; machine learning; genomic medicine; effect prediction
Online: 8 November 2019 (04:07:16 CET)
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient’s variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this Review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
ARTICLE | doi:10.20944/preprints202310.1129.v1
Subject: Physical Sciences, Particle And Field Physics Keywords: Plasma wakefields; electron beam; betatron radiation; FACET-II; beam diagnostics; multi-shot radiation; Compton spectrometer; pair spectrometer
Online: 18 October 2023 (08:24:49 CEST)
A new method for multi-shot reconstruction of high-energy photon distributions in the context of studying the interaction between a beam and a plasma in plasma wakefield acceleration (PWFA) experiments is presented. The study investigates the effects of beam perturbations on betatron radiation and analyzes how these perturbations can lead to hosing, a transverse instability that can degrade the quality of the beam. The potential of betatron radiation spectroscopy as a non-invasive diagnostic technique for PWFA experiments is also emphasized.
REVIEW | doi:10.20944/preprints202009.0526.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19 testing; molecular diagnostics; immunological testing; RT-qPCR; ELISA; pool PCR; lateral flow assay; rapid assay
Online: 23 September 2020 (03:33:12 CEST)
Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The COVID-19, caused by the SARS-CoV-2 virus is a pandemic that has affected 214 countries affecting more than 30.8 million people causing 0.957 million deaths as of third week of September, 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a check-list of factors to be taken care to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories
REVIEW | doi:10.20944/preprints202002.0007.v1
Subject: Biology And Life Sciences, Virology Keywords: molecular diagnostics; molecular epidemiology; HIV; HBV; HCV; HPV; Zika virus; Dengue virus; tuberculosis; SARS; MERS; nCov-2019
Online: 3 February 2020 (03:47:27 CET)
Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas9, Cas12, Cas13, Cas14) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, or lateral flow assay detection. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing coronoviral nCov-2019 infection) urgently need the developing of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.
REVIEW | doi:10.20944/preprints201805.0459.v1
Subject: Physical Sciences, Astronomy And Astrophysics Keywords: white dwarfs; burning in stars; plasma diagnostics; atomic spectra; plasma spectroscopy; laser spectroscopy; laser-induced breakdown spectroscopy
Online: 31 May 2018 (05:13:00 CEST)
This work communicates a review on Balmer series hydrogen beta line measurements and applications for analysis of white dwarf stars. Laser-induced plasma investigations explore electron density and temperature ranges comparable to white dwarf star signatures such as Sirius B, the companion to the brightest star observable from the earth. Spectral line shape characteristics of the hydrogen beta line include width, peak separation, and central dip-shift, thereby providing three indicators for electron density measurements. The hydrogen alpha line shows two primary line-profile parameters for electron density determination, namely, width and shift. Both Boltzmann plot and line-to-continuum ratios yield temperature. The line-shifts recorded with temporally- and spatially- resolved optical emission spectroscopy of hydrogen plasma in laboratory settings can be larger than gravitational redshifts that occur in absorption spectra from radiating white dwarfs. Published astrophysical spectra display significantly diminished Stark or pressure broadening contributions to red-shifted atomic lines. Gravitational redshifts allow one to assess the ratio of mass and radius of these stars, and subsequently, the mass from cooling models.
ARTICLE | doi:10.20944/preprints202306.0384.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; COVID19; Laboratory diagnostics; Cycle threshold; PCR platforms; median Ct; moving average; variants; continuous quality monitoring
Online: 6 June 2023 (05:35:27 CEST)
The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID19 pandemic, resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms. Novel approaches were required to monitor test quality especially during the introduction of newly circulating variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from six commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays’ gene targets. This continuous quality monitoring rapidly identified delayed hybridization of RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® Xpress SARS-CoV-2 due to XBB.1.5. This near “real-time” monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.
ARTICLE | doi:10.20944/preprints202102.0384.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: acute mesenteric ischemia (AMI); optical coherence tomography (OCT); optical coherence angiography (OCA); intraoperative diagnostics; gut vitality; image assessment
Online: 17 February 2021 (12:02:23 CET)
Introduction: Despite the introduction of increasingly multifaceted diagnostic techniques and the general progress of emergency abdominal and vascular surgery, the outcome of treatment of patients with acute impaired intestinal circulation remains unsatisfactory. The non-invasive and high-resolution technique of optical coherence tomography (OCT) can be used intraoperatively to assess intestine viability and associated conditions that frequently emerge under conditions of impaired blood circulation. This study aims to demonstrate the effectiveness of multimodal (MM) OCT for intraoperative diagnostics of both the microstructure (cross-polarization OCT mode) and microcirculation (OCT angiography mode) of the small intestine wall in patients with acute mesenteric ischemia (AMI). Methods and Participants: A total of 18 patients were enrolled in the study. Nine of them suffered from AMI in segments II-III of the superior mesenteric artery (AMI group), where the ischemic segments of the intestine were examined. Nine others were operated for adenocarcinoma of the colon (control group), thus allowing areas of their normal small intestine to be examined for comparison. Data on the microstructure and microcirculation in the walls of the small intestine were obtained intraoperatively from the side of the serous membrane using the MM OCT system (IAP RAS, Russia) before bowel resection. The MM OCT data were compared with the results of histological examination. Results: The study finds that MM OCT visualized the damage to serosa, muscularis externa, and blood vessels localized in these layers in 100% of AMI cases. It also visualized the submucosa in 33.3% of AMI cases. The MM OCT image of non-ischemic (control group), viable ischemic and necrotic small intestines (AMI group) differed significantly across stratification of the distinguishable layers, the severity of intermuscular fluid accumulations and the type and density of the vasculature. Conclusion: The MM OCT diagnostic procedure optimally meets the requirements of emergency surgery. Data on the microstructure and microcirculation of the intestinal wall can be obtained simultaneously in real time without requiring contrast agent injections. The depth of visualization of the intestinal wall from the side of the serous membrane is sufficient to assess the volume of the affected tissues. However, the methodology for obtaining MM OCT data needs to be improved to minimize the motion artefacts generated in actual clinical conditions.
REVIEW | doi:10.20944/preprints202304.1013.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Solid-phase optical biosensors; virus diagnostics; fluorescence-based sensors; surface plasmon resonance; optical resonators; interferometric biosensors; single virus detection
Online: 27 April 2023 (03:25:54 CEST)
Viral infections can endanger public health by causing serious illness, leading to pandemics and burdening healthcare systems. Moreover, in the situation of a global spread, disruptions occur in every aspect of life including business, education, and social life. Fast and accurate diagnosis of viral infections has huge implications for saving people’s lives, preventing spread of the diseases, and minimizing social and economic damages. In the last decades, polymerase chain reaction (PCR) based techniques have been frequently used to detect viruses in the clinic. However, in a situation where rapid virus detection is the primary measure in preventing the spread, as in the case of ongoing COVID-19 pandemic, disadvantages of PCR, such as long processing times and requirement of sophisticated laboratory instruments, have been faced. Due to the urgent need for accurate techniques for virus detection, biosensor systems involved in many applications in biological detection are being developed for rapid, real-time, and high-throughput detection of viruses. Among various sensing platforms, optical devices are of great interest due to their advantages such as high sensitivity and direct readout. In the current review, usability of sensing techniques depending on optical phenomena, such as fluorescence-based sensors, surface plasmon resonance (SPR), surface enhanced Raman scattering (SERS), optical resonators and interferometry-based platforms, is discussed for virus diagnostics applications. Then, we focus on an interferometric biosensor developed by our group, single-particle interferometric reflectance imaging sensor (SP-IRIS), which has the capability to visualize single nanoparticles, to demonstrate its application for digital virus detection.
ARTICLE | doi:10.20944/preprints202208.0392.v1
Subject: Biology And Life Sciences, Virology Keywords: Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV2), COVID-19, molecular diagnostics, real-time polymerase chain reaction (RT-qPCR)
Online: 23 August 2022 (03:55:44 CEST)
Background: Coronavirus disease (COVID-19) is an infectious disease caused by the SARS-CoV-2. In Colombia, many commercial methods are now available to perform the RT-qPCR assays, and the laboratories must evaluate its diagnostic accuracy to ensure reliable results to suspected COVID-19 patients. The purpose of the study was to compare four commercial RT-qPCR assays for detection of SARS-CoV2 virus, from nasopharyngeal swab samples referred to Laboratorio Carvajal IPS, SAS of Tunja, Boyacá - Colombia. Methods: This prospective study was conducted on 152 samples of respiratory tract samples (Nasopharyngeal Swab) from patients with suspected SARS-CoV-2 infection. Diagnostic accuracy of GeneFinderTM COVID-19 Plus RealAmp (In Vitro diagnostic), One-Step Real-Time RT-PCR (Vitro Master diagnostica), Berlin modified protocol and gold standard Berlin protocol (Berlin Charite Probe One-Step RT-qPCR Kit, New England Biolabs) as reference was assessed. Operational characteristics were estimated in terms of sensitivity, specificity, agreement, and predictive values. Results: Using Berlin Charite Probe One-Step RT-qPCR Kit as reference, the sensitivity/specificity for the diagnostic tests were found to be GeneFinderTM COVID-19 Plus RealAmp Kit 100%/92.7%, One-Step Real-Time RT-PCR, One-Step Real-Time RT-PCR 92.75%/67.47%, and Berlin modified protocol 100%/96.39%. The results of four commercially available methods were found to be consistent with those obtained from Berlin Modified protocol analysis for % of the samples and showed good agreement (κ= 0.96). Concordant SARS-CoV2 negative and positive RT-qPCR results were reported for xxx and xxx samples, respectively. Summarize something about the Ct. Conclusion: Our data demonstrate that all commercially available methods are rapid and reliable for the identification of SARS-CoV-2 virus associated with COVID-19. One-Step RT-qPCR Kit and GeneFinderTM COVID-19 Plus RealAmp assay show optimal sensitivity compared with Belin modified protocol. In addition, there is no significant correlation between xxxxx
REVIEW | doi:10.20944/preprints202103.0636.v2
Subject: Chemistry And Materials Science, Biomaterials Keywords: Silicon nitride; structure; properties; processing; coatings; spinal implants; arthroplastic implants; bone scaffolds; dental implants; neural circuits; biosensors; medical diagnostics.
Online: 15 April 2021 (12:55:38 CEST)
This topical review describes the results of recent research into and development of silicon nitride, a ceramic material with unique properties. The outcome of this ongoing research strongly encourages the use of monolithic silicon nitride and coatings as contemporary and future biomaterial for a variety of medical applications. Crystallographic structure, synthesis and processing of monolithic structures and coatings, and examples of their medical applications are covered that relate to spinal, orthopedic and dental implants, bone grafts and scaffolds, platforms for intelligent synthetic neural circuits, antibacterial and antiviral particles and coatings, optical biosensors, and nano-photonic waveguides for sophisticated medical diagnostic devices. The examples provided show convincingly that silicon nitride is destined to become a leader to replace titanium and other entrenched biomaterials in many fields of medicine.
ARTICLE | doi:10.20944/preprints202103.0708.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Adolescents; high sensitivity C-reactive protein; Insulin-like growth factor binding proteins; Obesity; Oxidized Low-Density Lipoprotein; Predictive diagnostics
Online: 29 March 2021 (16:33:20 CEST)
Insulin-like growth factor binding proteins (IGFBPs) are critical modulators of the metabolism. In adults, IGFBPs are associated with obesity and insulin resistance but the association of IGFBPs with metabolic homeostasis in children and adolescents is not fully characterized. In this study we investigated the association of plasma IGFBPs (IGFBP-1, 3 and 7) with weight status, central adiposity and cardiovascular disease markers Hs-CRP and Ox-LDL. A total of 420 adolescents (age 11-14 years) were randomly recruited from public middle schools in Kuwait. IGFBPs were measured using bead-based multiplexing while Hs-CRP and Ox-LDL were measured using ELISA. IGFBP-1 levels were significantly lower in obese and overweight participants compared to normal weight children. Only IGFBP-1 was negatively associated with waist circumference to height (WC/Ht) ratio. IGFBP-1 was negatively correlated with Hs-CRP while IGFBP-3 and IGFBP-7 were negatively correlated with Ox-LDL. These data demonstrate a robust negative association of IGFBP-1, but not IGFBP-3 or -7, with overweight and obesity, and the inflammation marker Hs-CRP. Central adiposity (WC/Ht ratio) was a stronger predictor of IGFBP-1 than BMI-for-age z-score. IGFBP-1 could thus be used as a sensitive predictive diagnostic tool for obesity and its subsequent effects in screening and monitoring of obesity-related metabolic complications in adolescents.
Subject: Physical Sciences, Atomic And Molecular Physics Keywords: plasma diagnostics; molecular spectra; diatomic molecules; plasma spectroscopy; laser spectroscopy; laser-induced breakdown spectroscopy; optical emission spectroscopy; hypersonic expansion
Online: 15 January 2020 (07:12:25 CET)
This article reports new measurements of laser-induced plasma hypersonic expansion measurements of diatomic molecular cyanide (CN). Focused, high-peak power 1064-nm Q-switched radiation of the order of 1 TW/cm2 generates optical breakdown plasma in a cell containing a 1:1 molar gas mixture of N2 and CO2 at a fixed pressure of 1.1 × 105 Pascal and in a 100 ml/min flow of the mixture. Line-of-sight (LOS) analysis of recorded molecular spectra indicate the outgoing shockwave at expansion speeds well in excess of Mach number 5. Spectra of atomic carbon confirm an increased electron density near the shock wave, and equally, molecular CN spectra reveal higher excitation temperature near the shockwave. The results are consistent with corresponding high-speed shadow graphs obtained by visualization with an effective shutter speed of five n anosecond. In addition, LOS analysis and application of integral inversion techniques allow inferences about the spatio-temporal distribution of the plasma.
ARTICLE | doi:10.20944/preprints202310.0364.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Oct4; Sox2; AURKA; Vimentin; breast cancer; Alisertib; epithelial to mesenchymal transition; asymmetric cell division; NUMB; stem cell; diagnostics; intervention; chemotherapy
Online: 9 October 2023 (15:14:51 CEST)
Aurora Kinase A being overexpressed in majority of cancers, appear to be an attractive therapeutic target. However, a Phase III clinical trial of Alisertib, a selective AURKA inhibitor, resulted in no better response compared to the comparator arm of chemotherapeutic regimen raising question regarding ability of the same to target the undetectable stem cell functions. In silico analysis indicated regulation of AURKA by the stemness factors Oct4 and Sox2. TCGA data indicated positive correlation of each of the factors with AURKA which were eventually validated in cell lines, patient tissues and blood by flow cytometry along with Oct4 binding on AURKA promoter being detected by ChIP assay. However, indirect immunofluorescence and cell cycle analyses indicated proliferation-independent AURKA functions during asymmetric cell division, a characteristic feature of stem cells. Thorough screening of the AURKA positive cells in patient samples denoted epithelial to mesenchymal transition and significant upregulation of Vimentin, a mesenchymal marker and ABCG2, a drug resistance marker under Oct4 or Sox2 influence. Overall, our study demonstrated combinatorial selection Oct4, Sox2, AURKA, Vimentin and ABCG2 for diagnostics and intervention of circulating breast cancer stem cells as a blood-based, cost-effective and simple approach which will be beneficial in reducing relapse.
ARTICLE | doi:10.20944/preprints202106.0553.v1
Subject: Engineering, Bioengineering Keywords: Iron-oxide nanoparticles, primary-secondary method, diagnostics of cancer, A549 cell line, transferrin protein receptors, adenocarcinoma, biotin-streptavidin, biotinylated antibodies
Online: 23 June 2021 (09:17:59 CEST)
The streptavidin and biotin interaction is one of the strongest non-covalent interactions in nature. As a result, this non-covalent interaction has been of great interest when it comes to biochemical assays, diagnosis of diseases, and cell-targeted drug delivery. Past research has proven that biotin-streptavidin is useful in biosensor development to improve the detection of a system when conjugated to nanoparticles. This study aims to prove that streptavidin-coated nanoparticles can be conjugated with biotinylated antibodies using the primary-secondary method to non-invasively detect adenocarcinoma in-vitro. While the use of nanoparticles is not uncommon to the diagnostics area of scientific research, the technique this research aims to investigate is a non-invasive one, utilizing the primary-secondary method. Specifically, the increased stability of fluorophores when bound to antibodies as opposed to nanoparticles directly can be indicative of the particles conjugated through the primary-secondary method’s ability to specifically bind to overexpressed transferrin receptors in the A549 cell line. In this paper, streptavidin-coated nanoparticles were conjugated with biotinylated anti-transferrin receptor antibodies and AlexaFluor-488 secondary antibodies were used to enable fluorescence-based detection. The efficiency of these particles were observed quantitatively through a plate reader and qualitatively through a fluorescence microscope. I demonstrated that these nanoparticles are able to specifically bind to the target proteins in this study. These findings contribute to the field of nanoparticle diagnostics and can be extended to different diseases caused by overexpression of proteins in the future. While this was conducted in-vitro, conjugates can be prepared to detect cancer in-vivo and can be tested with magnetic relaxometry in the future.
REVIEW | doi:10.20944/preprints202101.0426.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: deep learning; machine learning; ischemic stroke; demyelinating disease; image processing; computer aided diagnostics; brain MRI; CNN; White Matter Hyperintensities; VOSViewer
Online: 21 January 2021 (14:55:05 CET)
Medical brain image analysis is a necessary step in the Computers Assisted /Aided Diagnosis (CAD) systems. Advancements in both hardware and software in the past few years have led to improved segmentation and classification of various diseases. In the present work, we review the published literature on systems and algorithms that allow for classification, identification, and detection of White Matter Hyperintensities (WMHs) of brain MRI images specifically in cases of ischemic stroke and demyelinating diseases. For the selection criteria, we used the bibliometric networks. Out of a total of 140 documents we selected 38 articles that deal with the main objectives of this study. Based on the analysis and discussion of the revised documents, there is constant growth in the research and proposal of new models of deep learning to achieve the highest accuracy and reliability of the segmentation of ischemic and demyelinating lesions. Models with indicators (Dice Score, DSC: 0.99) were found, however with little practical application due to the uses of small datasets and lack of reproducibility. Therefore, the main conclusion is to establish multidisciplinary research groups to overcome the gap between CAD developments and their complete utilization in the clinical environment.
ARTICLE | doi:10.20944/preprints202005.0416.v1
Subject: Physical Sciences, Quantum Science And Technology Keywords: X-rays; free electron laser (FEL); ultra-short phenomena; pump-probe; warm-dense matter; astrophotonics; co-axial volumetric interaction diagnostics
Online: 26 May 2020 (03:53:19 CEST)
We put forward a co-axial pump(optical)-probe(X-rays) experimental concept and show performance of the optical component. A Bessel beam generator with a central 100 micrometers-diameter hole (on the optical axis) was fabricated using femtosecond (fs) laser structuring inside a silica plate. This flat-axicon optical element produces a needle-like axial intensity distribution which can be used for the optical pump pulse. The fs-X-ray free electron laser (X-FEL) beam of sub-1 micrometer diameter can be introduced through the central hole along the optical axis onto a target as a probe. Different realisations of optical pump are discussed. Such optical elements facilitate alignment of ultra-short fs-pulses in space and time and can be used in light-matter interaction experiments at extreme energy densities on the surface and in the volume of targets. Full advantage of ultra-short 10 fs X-FEL probe pulses with fs-pump(optical) opens an unexplored temporal dimension of phase transitions and the fastest laser-induced rates of material heating and quenching. A wider field of applications of fs-laser-enabled structuring of materials and design of specific optical elements for astrophotonics is presented.
ARTICLE | doi:10.20944/preprints201803.0037.v1
Subject: Physical Sciences, Atomic And Molecular Physics Keywords: Stark broadening; van der Waals broadening; line shapes; helium plasma; corona discharge; plasma diagnostics; code comparison; neutral broadening; pressure broadening
Online: 7 March 2018 (13:36:47 CET)
Passive plasma spectroscopy is a well-established non-intrusive diagnostic technique. Depending on the emitter and its environment which determine the dominant interactions and effects governing emission line shapes, passive spectroscopy allows the determination of electron densities, emitter and perturber temperatures as well as other quantities like abundances. However, using spectroscopy needs appropriate line shape codes retaining all the physical effects governing the emission line profiles. This requires for line shape code developers to continuously correct or improve them to increase their accuracy when applied for diagnostics. This is exactly the aim expected from code-code and code-data comparisons. In this context, the He I 492 nm emitted in a helium corona discharge at room temperature represents an ideal case since its profile results from several broadening mechanisms: Stark, Doppler, resonance and van der Waals. The importance of each broadening mechanism depends on the plasma parameters. Here the profiles of the He I 492 nm in a helium plasma computed by various codes are compared for a selected set of plasma parameters. In addition, preliminary results related to plasma parameter determination using experimental spectra from a helium corona discharge at low pressure 1- 2 bars, are presented.
ARTICLE | doi:10.20944/preprints201803.0040.v1
Subject: Physical Sciences, Atomic And Molecular Physics Keywords: stark broadening; van der waals broadening; line shapes; helium plasma; corona discharge; plasma diagnostics; code comparison; neutral broadening; pressure broadening
Online: 6 March 2018 (03:51:17 CET)
Many spectroscopic diagnostics are routinely used as a technique to infer the plasma parameters from line emission spectra but their accuracy depends on the numerical model or code used for the fitting process. However, the validation of a line shape code requires some steps : comparison of the line shape code with other similar codes for some academic (simple) cases and then more complex ones, comparison of the fitting parameters obtained from the best fit of the experimental spectra with those obtained with other diagnostic techniques and/or comparison of the fitting parameters obtained by different codes to fit the same experimental data. Here we compare the profiles of the hydrogen Balmer β line in a helium plasma computed by six codes for a selected set of plasma parameters and we report on the plasma parameters inferred by each of them from the fitting to a number of experimental spectra measured in a helium corona discharge where the pressure was in the range 1- 5 bar.
REVIEW | doi:10.20944/preprints202306.0228.v2
Subject: Engineering, Electrical And Electronic Engineering Keywords: Prognostics; Ageing; Lithium-Ion Batteries; EV Batteries; Degradation; Electric vehicles; Failure; Solid Electrolyte Interphase; Lifespan Estimation; Battery Performance; Diagnostics; Lifetime Prediction
Online: 21 November 2023 (13:16:44 CET)
Lithium-ion batteries with improved energy densities have made understanding the Solid Electrolyte Interphase (SEI) generation mechanisms that cause mechanical, thermal, and chemical failures more complicated. SEI processes reduce battery capacity and power. Thus, a review of this area's understanding is important. It is essential to know how batteries degrade in EVs to estimate battery lifespan as it goes, predict, and minimize losses, and determine the ideal time for a replacement. Lithium-ion batteries used in EVs mainly suffer two types of degradation: calendar degradation and cycling degradation. Despite the existence of several existing works in the literature, several aspects of battery degradation remain unclear or have not been analyzed in detail. This work presents a systematic review of existing works in the literature. The results of the present investigation provide insight into the complex relationships among various factors affecting battery degradation mechanisms. Specifically, this systematic review examined the effects of time, side reactions, temperature fluctuations, high charge/discharge rates, depth of discharge, mechanical stress, thermal stress, and the voltage relationship on battery performance and longevity. The results revealed that these factors interact in complex ways to influence the degradation mechanisms of batteries. For example, high charge currents and deep discharges were found to accelerate degradation, while low temperatures and moderate discharge depths were shown to be beneficial for battery longevity. Additionally, the results showed that the relationship between cell voltage and State-of-Charge (SOC) plays a critical role in determining the rate of degradation. Overall, these findings have important implications for the design and operation of battery systems, as they highlight the need to carefully manage a range of factors to maximize battery performance and longevity. The result is an analysis of the main articles published in this field in recent years. This work aims to present new knowledge about fault detection, diagnosis, and management of lithium-ion batteries based on battery degradation concepts. The new knowledge is presented and discussed in a structured and comprehensive way.
ARTICLE | doi:10.20944/preprints202110.0433.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: X-ray Imaging; Plasma Diagnostics; Electron Cyclotron Resonance Ion Sources; High Dynamical Range Analysis; Single-Photon-Counted Images; X-ray Spatially-resolved Spectroscopy
Online: 28 October 2021 (11:39:28 CEST)
At INFN-LNS, and in collaboration with the ATOMKI laboratories, an innovative multi-diagnostic system with advanced analytical methods has been designed and implemented. This is based on several detectors and techniques (Optical Emission Spectroscopy, RF systems, Interfero-polarimetry, X-ray detectors) and here we focus on high resolution spatially-resolved X-ray spectroscopy, performed by means of a X-ray pin-hole camera setup operating in the 0.5−20 keV energy domain. The diagnostic system was installed at a 14 GHz Electron Cyclotron Resonance (ECR) ion source (ATOMKI, Debrecen), enabling high precision X-ray spectrally-resolved imaging of ECR plasmas heated by hundreds of Watts. The achieved spatial and energy resolution were 0.5 mm and 300 eV at 8 keV, respectively. We here present the innovative analysis algorithm that we properly developed for obtaining Single Photon-Counted (SPhC) images providing the local plasma emitted spectrum in a High-Dynamic-Range (HDR) mode, by distinguishing fluorescence lines of the materials of the plasma chamber (Ti, Ta) from plasma (Ar). This method allows a quantitative characterization of warm electrons population in the plasma (and its 2D distribution) which are the most important for ionization, and also to estimate local plasma density and spectral temperatures. The developed post-processing analysis is also able to remove the readout noise, that is often observable at very low exposure times (msec). The setup is now under update including fast shutters and trigger systems in order to allow simultaneously space and time-resolved plasma spectroscopy during transients, stable and turbulent regimes.
ARTICLE | doi:10.20944/preprints202002.0207.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Antibody ID; antibody registry; Research Resource Identifier; RRID; reproducibility; quality control; documentation; traceability; clones; biochemical reagents; diagnostics; immunoassays; ELISA; western blot; immunohistochemistry; microarray; biosensor
Online: 15 February 2020 (15:46:27 CET)
Thousands of antibodies for diagnostic and other analytical purposes are on the market. However, it is often difficult to identify duplicates, reagent changes, and to assign the correct original publications to an antibody. This slows down scientific progress and might even be a cause of irreproducible research and a waste of resources. Recently, activities were started to suggest the sole use of recombinant antibodies in combination with the open communication of their sequence. In this case, such uncertainties should be eliminated. Unfortunately, this approach seems to be rather a long-term vision since the development and manufacturing of recombinant antibodies remain quite expensive in the foreseeable future. Also, nearly all commercial antibody suppliers may be reluctant to publish the sequence of their antibodies, since they fear counterfeiting. De-novo sequencing of antibodies is also not feasible today for a reagent user without access to the hybridoma clone. Nevertheless, it seems to be crucial for any scientist to have the opportunity to identify an antibody undoubtedly to guarantee the traceability of any research activity using antibodies from a third party as a tool. For this purpose, we developed a method for the identification of antibodies based on a MALDI-TOF-MS fingerprint. To circumvent lengthy denaturation, reduction, alkylation, and enzymatic digestion steps, the fragmentation was performed with a simple formic acid hydrolysis step. Eighty-nine unknown monoclonal antibodies were used for this study to examine the feasibility of this approach. Although the molecular assignment of peaks was rarely possible, antibodies could be easily recognized in a blinded test, simply from their mass-spectral fingerprint. A general protocol is given, which could be used without any optimization to generate fingerprints for a database. We want to propose that in most scientific projects relying critically on antibody reagents, such a fingerprint should be established to prove and document the identity of the used antibodies and to assign a specific reagent to a datasheet of a commercial supplier, a public database record or an antibody ID.
ARTICLE | doi:10.20944/preprints202002.0053.v1
Subject: Physical Sciences, Chemical Physics Keywords: plasma diagnostics; molecular spectra; diatomic molecules; plasma spectroscopy; laser spectroscopy; laser-induced breakdown spectroscopy; optical emission spectroscopy; molecular excitation temperature; combustion analysis; astrophysical spectroscopy
Online: 5 February 2020 (03:27:47 CET)
This article discusses laser-induced laboratory-air plasma measurements and analysis of hydroxyl (OH) ultraviolet spectra. New experiments with Q-switched laser pulses illustrate occurrence of molecular recombination spectra for time delays of the order of several dozen of microseconds after plasma initiation. The computation of the emission spectra utilizes line strength data that are communicated as a supplementary file. Applications of detailed OH computations include laser-induced plasma and combustion analyses, to name but two applications.