ARTICLE | doi:10.20944/preprints202101.0047.v1
Subject: Biology, Anatomy & Morphology Keywords: Stool; Fecal; Microbiome; Microbiota; Heterogeneous; Homogeneous; Sample
Online: 4 January 2021 (13:29:00 CET)
Background. Inferior quality of biological material compromises data, slows discovery, and wastes research funds. The gut microbiome plays a critical role in human health and disease, yet little attention has been given to optimizing collection and processing methods of human stool. Methods. We collected the entire bowel movement from 2 healthy volunteers: one to examine stool sample heterogeneity and one to test stool sample handling parameters. Sequencing and bi-oinformatic analyses were used to examine the microbiome composition. Results. The microbiome profile varied depending on where the subsample was obtained from the stool. The exterior cortex of the stool was rich in specific phyla and deficient in others while the interior core of the stool revealed opposite microbiome profiles. Sample processing also re-sulted in varying microbiome profiles. Homogenization and stabilization at 4°C gave superior microbial diversity profiles compared to the fresh or frozen subsamples of the same stool sample. Bacterial proliferation continued in the fresh subsample when processed at ambient temperature. Bacteroidetes proliferated and Firmicutes diminished during the 30-minute processing of fresh sample. The frozen sample had good overall diversity but Proteobacteria diminished likely be-cause of the freeze/thaw. Conclusions. The microbiome profile is specific to the section of the stool being sampled. Stool sample collection, homogenization, and stabilization at 4°C for 24 hours provides a “neat”, high-quality sample of sufficient quantity that can be banked into aliquots with nearly identical microbial diversity profiles. This collection pipeline is essential to accelerate our understanding of the gut microbiome in health and disease.
REVIEW | doi:10.20944/preprints201905.0140.v2
Subject: Life Sciences, Molecular Biology Keywords: protein crystallization; protein sample qualification; JAXA PCG; microgravity
Online: 15 December 2019 (13:43:29 CET)
We summarize how to obtain protein crystals from which better diffraction images can be obtained. In particular, we describe in detail the quality evaluation of the protein sample, the crystallization methods and crystallization conditions, the flash-cooling protection of the crystal, and the crystallization under a microgravity environment.
ARTICLE | doi:10.20944/preprints202106.0530.v1
Subject: Earth Sciences, Atmospheric Science Keywords: airborne LiDAR; forest attributes; multivariate power model; sample size
Online: 22 June 2021 (13:03:33 CEST)
Exploring the effect of the sample size on the estimation accuracy of airborne LiDAR forest attributes in a large-scale area can help in optimizing the technical application scheme of operational ALS-based large-scale forest stand inventories. In our study, sample datasets composed of different sample plots were constructed by repeated sampling from 1003 sample plots in a subtropical study area covering 2376 × 103 km2. Sixteen multiplicative power models were built in each forest type consisting of four forest attributes. Through these models, the variations of standard deviation (SD) and coefficient of variation (CV) of R2 and rRMSE of forest attribute estimation models for different quantity levels of sample plots were also analyzed. The results showed that, first, when the sample size increased from 30 to the top limit, the SD of the forest attributes and LiDAR variables showed a decreasing trend. Second, as the sample size increased, the rRMSE of the 16 forest attribute estimation models gradually decreased, while the R2 gradually increased. Third, when the sample size was small, both the SD of R2 and rRMSE of the models were large, and the SD of R2 and rRMSE gradually decreased as the sample size increased. In 50 models conducted for each attribute at the same sample size, for the mean standard deviations of forest attributes, the ten best performing models were lower than those of the total 50 models, and the worst ten models were the opposite. When the sample size increased, the accuracy of each forest attribute estimation model for each forest type gradually improved. The variation of forest attributes and the LiDAR variable of the construction model are critical factors that affect the model’s accuracy. To efficiently apply airborne LiDAR in order to survey large-scale subtropical forest resources, the sample size of the Chinese fir forest, pine forest, eucalyptus forest, and broad-leaved forest should be 110, 80, 85, and 70, respectively.
ARTICLE | doi:10.20944/preprints201910.0210.v1
Subject: Physical Sciences, Applied Physics Keywords: scanning magnetic microscopy; Hall sensor; magnetic measurements; geological sample
Online: 18 October 2019 (08:53:15 CEST)
Scanning magnetic microscopy is a new tool that has recently been used to map magnetic fields with good spatial resolution and field sensitivity. This technology has great advantages over other instruments; for example, its operation does not require cryogenic technology, which reduces its operational cost and complexity. Here, we describe the construction of a customizing scanning magnetic microscope based on commercial Hall-effect sensors at room temperature that achieves a spatial resolution of 200 µm. Two scanning stages on the x- and y-axes of precision, consisting of two coupled actuators, control the position of the sample, and this microscope can operate inside or outside a magnetic shield. We obtained magnetic field sensitivities better than 521 nTrms/√Hz between 1 and 10 Hz, which correspond to a magnetic momentum sensitivity of 9.20 × 10–10 Am2. In order to demonstrate the capability of the microscopy, polished thin sections of geological samples, samples containing microparticles and magnetic nanoparticles were measured. For the geological samples, a theoretical model was adapted from the magnetic maps obtained by the equipment. Vector field maps are valuable tools for the magnetic interpretation of samples with a high spatial variability of magnetization. These maps can provide comprehensive information regarding the spatial distribution of magnetic carriers. In addition, this model may be useful for characterizing isolated areas over samples or investigating the spatial magnetization distribution of bulk samples at the micro and millimeter scales. As an auxiliary technique, a magnetic sweep map was created using Raman spectroscopy; this map allowed the verification of different minerals in the samples. This equipment can be useful for many applications that require samples that need to be mapped without a magnetic field at room temperature, including rock magnetism, the nondestructive testing of steel materials and the testing of biological samples. The equipment can not only be used in cutting-edge research but also serve as a teaching tool to introduce undergraduate, master's and Ph.D. students to the measurement methods and processing techniques used in scanning magnetic microscopy.
ARTICLE | doi:10.20944/preprints201903.0158.v1
Subject: Physical Sciences, Applied Physics Keywords: magnetic scanning microscope; hall sensor; magnetic materials; geological sample
Online: 15 March 2019 (02:12:54 CET)
We improved a magnetic scanning microscope for measuring the magnetic properties of minerals in thin sections of geological samples at submillimeter scales. The microscope is comprised of a 200 µm diameter Hall sensor that is 142 µm from the sample; an electromagnet capable of applying to the sample up to 500 mT dc magnetic fields over a 40 mm diameter region; a second Hall sensor arranged in a gradiometric configuration to cancel the background signal applied by the electromagnet and reduce overall noise in the system; a custom-designed electronics to bias the sensors and provide adjustment for background signal cancelation; and a scanning XY stage with micrometer resolution. Our system achieves a spatial resolution of 220 µm with noise at 6.0 Hz of »300 nTrms/(Hz)1/2 in an unshielded environment. The magnetic moment sensitivity is 1.3 × 10−11 Am2.1/2 We successfully measured the representative magnetization of a geological sample using an alternative model that takes into account the sample geometry and identified different micrometric characteristics in the sample slice.
ARTICLE | doi:10.20944/preprints202110.0369.v1
Subject: Chemistry, Analytical Chemistry Keywords: Macrocyclic lactones; agricultural crops; food; sample preparation; UHPLC-MS/MS
Online: 25 October 2021 (15:50:47 CEST)
Soybean, maize and bean are crops of great economic importance, but in the last years suffered with infestations of the caterpillar Helicoverpa armigera, being the main problem the resistance of this pest to most pesticides. Avermectin emamectin benzoate was recently released to control this pest. Other avermectins, like abamectin, doramectin, eprinomectin and ivermectin are used in large scale because they potent acaricidal, anthelmintic, and insecticidal activities. Thus, a simple and fast method for the determination of avermectins in these crops based on a quick, easy, cheap, effective, rugged and safe (QuEChERS) extraction procedure and ultra-high performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) analysis was developed and validated. For extraction, water followed by acetonitrile:isopropanol and a partition step with salts was stablished. With the clean-up step using activated EMR-Lipid, limits of detection of 1.2 μg kg-1 for abamectin, doramectin, emamectin benzoate and ivermectin, and of 2.4 μg kg-1 for eprinomectin were achieved. Accuracy and precision evaluated at low levels presented satisfactory results. The method was successfully applied in commercial samples and is a good alternative for routine analysis.
ARTICLE | doi:10.20944/preprints202107.0069.v1
Subject: Engineering, Automotive Engineering Keywords: fresh agricultural products; harvest schedule; stochastic programming; sample-average approximation
Online: 2 July 2021 (15:44:52 CEST)
This study focuses on the decisions of picking, inventory, ripening, delivering, and selling mangoes in a harvesting season. Demand, supply, and prices are uncertain, and their probability density functions are fitted based on actual trading data collected from the largest spot market in Taiwan. A stochastic programming model is formulated to minimize the expected cost under the considerations of labor, storage space, shelf life, and transportation restrictions. We implement the sample-average approximation to obtain a high-quality solution of the stochastic program. The analysis compares deterministic and stochastic solutions to assess the uncertain effect on the harvest decisions. Finally, the optimal harvest schedule of each mango type is suggested based on the stochastic program solution.
ARTICLE | doi:10.20944/preprints202009.0090.v1
Subject: Life Sciences, Other Keywords: age; coring sample; forest productivity; Nepal; P. roxburghii; stand structure
Online: 4 September 2020 (08:08:30 CEST)
Distinguishable annual growth rings produce in Pinus roxburghii are an asset to find out the age of individual tree. This paper aimed to determine the age of P. roxburghii through coring samples and test the relationship with forest production. The biomass estimated, girths measured at two different sections and heights measured which allowed to determine the rate of tapering of the stand. The regression analysis was performed to test the relationship between various variables. The mean age of the P. roxburghii stand was found to be 23.97 (~24 years). The result showed the significant (p<0.05) positive correlation coefficient has been seen between age with girth at breast height, biomass, volume and carbon stock. However, no significant (p>0.05) correlation (r = 0.08) was found between age and height of the stand. In contrast, a correlation between diameter at breast height (DBH) was significant (p<0.05) and positive with volume, biomass, but no significant (p>0.05) correlation (r = 0.14) found between DBH and height of the stand. However, height has a significant (p<0.05) positive correlation with biomass. The mean biomass was 375 kg and mean annual increment (MAI) was 15 kg per tree. Rate of tapering of the studied stand predicted to be 3 cm diameter decreased with trunk height running at 100 cm from base to upward of P. roxburghii stand and vice versa. Result suggests that height-age relation is very weak whereas age, DBH, biomass and carbon has a significant correlation signifies that time-based forests' production and potential production estimation can be obtained in a relatively accurate way by utilizing the age of stand. The time-based forest production analysis is pioneer work in Nepal. The study affirms the tree ring count in P. roxburghii would be a credible and accurate method to determine the age of standing trees.
ARTICLE | doi:10.20944/preprints202007.0612.v1
Subject: Materials Science, General Materials Science Keywords: Mössbauer spectroscopy; X-ray diffraction; Vibrating sample magnetometry; NdFeB magnets
Online: 25 July 2020 (15:54:31 CEST)
In this work, the structural, magnetic, and mechanical properties of Nd16Fe76-xCoxB8 alloys varying the Co content at x = 0, 10, 20 and 25, were experimentally investigated by X-Ray Diffraction (XRD), Mössbauer Spectrometry (MS), Vibrating Sample Magnetometry (VSM) at room temperature (RT), and microhardness test were performed too. The system presents the hard Nd2Fe14B and the Nd1.1Fe4B4 phases for samples with x = 0 and 10. When concentration increases to x= 20 and 25, the CoO phase appears. All MS show the ferromagnetic behavior (eight sextets: sites 16k1, 16k2, 8j1, 8j2, 4c, 4e, sb) associated to the hard and soft magnetic phases, and one paramagnetic component (doublet: site d) associated to the minority Nd1.1Fe4B4 phase, which was not identified by XRD. All samples are magnetically hard present a hard magnetic behavior. The increase of Co content in these samples did not improve the hard magnetic behavior, but increased the critical temperature of the system and decrease the crystallite size of the hard phase. The hysteresis loop showed that predominates the Nd2Fe14B hard magnetic phase. There is a general tendency to increase microhardness with cobalt content, attributable to cobalt doping reduces the lattice parameters and porosities in the sample improving it hardness.
ARTICLE | doi:10.20944/preprints201909.0102.v1
Subject: Social Sciences, Econometrics & Statistics Keywords: ARIMA Methodology; Out-of-Sample Forecast; Tourist Arrivals; Sierra Leone
Online: 9 September 2019 (12:11:03 CEST)
This study have uniquely mad use of Box-Jenkins ARIMA models to address the core of the threes objectives set out in view of the focus to add meaningful value to knowledge exploration. The outcome of the research have testify the achievements of this through successful nine months out-of-sample forecasts produced from the program codes, with indicating best model choices from the empirical estimation. In addition, the results also provide description of risks produced from the uncertainty Fan Chart, which clearly outlined possible downside and upside risks to tourist visitations in the country. In the conclusion, it was suggested that downside risks to the low level tourist arrival can be managed through collaboration between authorities concerned with the management of tourist arrivals in the country.
ARTICLE | doi:10.20944/preprints201812.0184.v1
Subject: Keywords: Metagenomics; Metatranscriptomics; Environmental sample; Homology searches; Taxonomic profile; Functional profile
Online: 17 December 2018 (09:51:22 CET)
Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy . When using taxonomy-dependent alignment-based methods to classify and label reads, such as MEGAN , the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (i.e., nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX . Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show differences, which can be notorious when working with RNA-seq (Personal observation; Graphical abstract). These inconsistencies led us to develop the HoSeIn workflow to determine the unequivocal taxonomic and functional profile of environmental samples, based on the assumption that the sequences that correspond to a certain taxon are composed of (Graphical abstract): 1) sequences that were assigned to the same taxon by both homology searches, plus 2) sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one, and vice versa.
ARTICLE | doi:10.20944/preprints201810.0459.v1
Subject: Earth Sciences, Environmental Sciences Keywords: Sample size, Measurement error, Generalized Additive Model, GAM, Réseau Hydrique.
Online: 19 October 2018 (16:53:50 CEST)
Live fuel moisture content (LFMC) influences fire activity at landscape scale and fire behavior in laboratory experiments. However, field evidences linking LFMC to fire behavior are very limited despite numerous field experiments. In the present study, we reanalyze a shrubland fire dataset with a special focus on LFMC to explain this counterintuitive outcome. We found that this controversy might result from three reasons. First, the range of experimental LFMC data was too moist to reveal significant effect with the widespread exponential or power functions. Indeed, LFMC exhibited a strong effect below 100%, but marginal above this threshold, contrary to these functions. Second, we found that the LFMC significance was unlikely when the size of the dataset was smaller than 40. Finally, a complementary analysis suggested that 10 to 15% of random measurement error in variables could lead to an underestimation by 30 % of the LFMC effect. The effect of LFMC in field experiments is thus stronger than previously reported in the range prevailing during the actual French fire season and in accordance with observations at different scales. This highlights the need to improve our understanding of the relationship between LFMC and fire behavior to refine fire danger predictions.
ARTICLE | doi:10.20944/preprints202207.0055.v1
Subject: Chemistry, Analytical Chemistry Keywords: NMR; chemometrics; chloroform; phosgene; hydrochloric acid; sample degradation; pH-shift; protonation
Online: 5 July 2022 (03:53:09 CEST)
Highly reactive decomposition products of (deuterated) chloroform can deteriorate samples dissolved in this commonly used NMR solvent. For sensitive samples (such as peptides, unsaturated fatty acids, vitamins), this can lead to abnormal NMR spectra (e.g. signal shifts depending on pH, attenuation of signals over time due to chemical changes of analytes, new signals from reaction products). Such irreproducibly influenced spectra are especially problematic for non-targeted analysis methods. To prevent these artefacts, chlorine, phosgene and hydrochloric acid need to be eliminated from deuterated chloroform prior to its use. Since the common stabilization methods have proven insufficient for sensitive NMR samples, another purging method has been tested: Mitigation is easily and reliably achieved by washing the deuterated chloroform with concentrated Na2CO3-solution and subsequent desiccation with oven-dried Na2CO3.
ARTICLE | doi:10.20944/preprints202102.0199.v1
Subject: Physical Sciences, Acoustics Keywords: Microfluidics; Micro-Jet; Sub-millisecond mixing; Simulation; Sample delivery for XFEL
Online: 8 February 2021 (12:12:47 CET)
Microfluidic devices which integrate both rapid mixing and liquid jetting for sample delivery are an emerging solution for studying molecular dynamics via X-ray diffraction. Here we use finite element modelling to investigate the efficiency and time-resolution achievable using microfluidic mixers within the parameter range required for producing stable liquid jets. Three-dimensional simulations, validated by experimental data, are used to determine the velocity and concentration distribution within these devices. The results show that by adopting a serpentine geometry, it is possible to induce chaotic mixing, which effectively reduces the time required to achieve a homogeneous mixture for sample delivery. Further, we investigate the effect of flow rate and the mixer microchannel size on the mixing efficiency and minimum time required for complete mixing of the two solutions whilst maintaining a stable jet. In general, we find that the smaller the cross-sectional area of the mixer microchannel, the shorter the time needed to achieve homogeneous mixing for a given flow rate. The results of these simulations will form the basis for optimised designs enabling the study of molecular dynamics occurring on millisecond timescales using integrated mix-and-inject microfluidic devices.
ARTICLE | doi:10.20944/preprints202011.0551.v1
Subject: Medicine & Pharmacology, Allergology Keywords: steroids; steroid panel; clinical mass spectrometry; plasma; sample automation; endocrine; Synacthen
Online: 21 November 2020 (08:36:10 CET)
Steroid analysis is important in the clinical assessment of endocrine function in health and disease. Although tandem mass spectrometry methods coupled with chromatographic separation are considered the gold standard analytical technique in this setting, enabling profiling of multiple steroids in a single sample, sample processing can be labour-intensive. Here we present a simple, efficient automated 96-well Supported Liquid Extraction method with dichloromethane/isopropanol as organic solvent, carried out on a Extrahera automated sample handler (Biotage), which completes sample preparation of 80 plasma samples (200µL) in 90 minutes. Compounds were separated on a Kinetex C18 column (150x3mm;2.6um) using a mobile phase of methanol and water (0.1% formic acid). The run time was 16 minutes on a Nexera uHPLC system (Shimadzu) with a QTrap 6500+ linear ion trap mass spectrometer (AB Sciex). Precisions ranged 8.1 to 18.1% RSD, bias -10.1-5.8%, and extraction recoveries 73.5-111.9%. LOQs ranged between 0.025–0.500 ng/mL.
ARTICLE | doi:10.20944/preprints201803.0052.v1
Subject: Social Sciences, Economics Keywords: Burkina Faso, Economic Well-Being, Gender inequality, Literacy status, Sample Selection
Online: 7 March 2018 (09:27:26 CET)
This paper models the factors explaining households members economic well-being in Burkina Faso, with a focus on the relative influence of gender inequality in literacy status. It does so, using data from the 2014 survey on household living conditions and a semi-parametric bi-variate sample selection modeling approach. This approach compared to the classic Heckman two-step estimator is methodologically innovative because it deals simultaneously with non-random sample selection using conventional systems of two equations, non-linear covariates' effects using spline approach, and the non-normal bivariate distribution using copula functions. The graphical results from the Lorenz curves combined with the numerical Atkinson and Gini coefficients suggest that inequality in overall per-capita consumption spending among households headed by literates is higher than that of their illiterate counterparts in 2009 and 2014. However, independently of the head of household’s literacy status, the level of inequality in total economic well-being decreased from 2009 to 2014. Using the poverty indices of Watts, Sen, Foster ( alpha= 1)) we found that poverty among households headed by literates is lower than that of their illiterates counterparts for both years, although overall poverty decreased nationally between 2009 and 2014. The results also show that although the gender inequality in literacy status does not translate into inequalities in non-food wellness, it does however for food-wellness as female headed households have 38.9% less per-capita food consumption spending than their men counterparts. Combining both food and non-food consumption spending, total economic well-being also seems to exhibit gender inequality as female headed households now have relatively 26.7% less combined per-capita consumption spending.
ARTICLE | doi:10.20944/preprints202209.0223.v1
Subject: Life Sciences, Other Keywords: Covid; Covid testing; sample pooling; resources; time; binary system; probability; positivity rate
Online: 15 September 2022 (08:14:36 CEST)
In Los Angeles, at one point, the Covid-19 testing positivity rate was 6.25%, or one in sixteen. This translates to, on average, one in sixteen specimens testing positive and the vast majority testing negative. Usually, we run sixteen tests on sixteen specimens to identify the positive one(s). This process can be time consuming and expensive. Since a group of negative specimens pooled together for testing will produce a negative result, one single test could potentially eliminate many specimens. Only when the pooled specimen tests positive do we need further testing to identify the positive one(s). Based on this concept, we designed a strategy that will identify the positive specimen(s) efficiently. Assuming one in sixteen specimens is positive, we find that only four tests are needed. Furthermore, we can run them simultaneously, saving both resources and time. Although, in the real world, we cannot make the assumption of only one positive specimen, the same strategy works with slight modification and proves to be much more efficient than the conventional testing. Our strategy returns an answer 48% of the time in four tests and one time cycle. Overall, the average number of tests is seven or eight depending on the follow-up testing, and the average time cycle is about one and a half.
ARTICLE | doi:10.20944/preprints202205.0162.v1
Subject: Earth Sciences, Other Keywords: anastomosing; erodibility; planform; Fourier transform; power spectral density; sample entropy; approximate entropy
Online: 12 May 2022 (08:03:34 CEST)
The Brahmaputra is one of the largest rivers in the world, ranking fifth in average discharge. As a result, it is heavily braided with various intricate paths in order to dissipate its huge energy. Although this river is normally classed as a braided river, it has recently been classified as an anastomosing river due to its multi-channel features over alluvial plains. Additionally, the Brahmaputra river’s morphology is random in nature as a result of its high flow variability and bank erodibility. Its anastomosing planform changes in response to seasonal water and sediment waves, resulting in a morphology that is extremely complex. The purpose of this study is to examine the Brahmaputra river’s anastomosing planform entropy as a measure of complexity, power spectral density as a measure of fluctuation and their relationship to the energy expenditure as an imprint of flflow rate of river systems on alluvial landscapes.
ARTICLE | doi:10.20944/preprints201901.0258.v1
Subject: Chemistry, Analytical Chemistry Keywords: Fabric phase sorptive extraction; Gas chromatography-Mass Spectrometry; Organochlorine pesticides; Sample preparation
Online: 25 January 2019 (14:56:26 CET)
Fabric phase sorptive extraction, an innovative integration of solid phase extraction and solid phase microextraction principles, has been combined with gas chromatography-mass spectrometry for the rapid extraction and determination of nineteen organochlorine pesticides in various fruit juices and water samples. FPSE consolidates the advanced features of sol-gel derived extraction sorbents with the rich surface chemistry of cellulose fabric substrate, which could directly extract target analytes from complex sample matrices and substantially simplifies the sample preparation operation. Important FPSE parameters including sorbent chemistry, extraction time, stirring speed, type and volume of back-extraction solvent and back-extraction time have been optimized. Calibration curves were obtained in the concentration range 0.1-500 ng/mL. Under the optimum conditions, the limits of detection were obtained in the range 0.007-0.032 ng/mL with satisfactory precision (RSD<6%). The relative recoveries obtained by spiking organochlorine pesticides in water and selected juice samples were in the range of 91.56–99.83%. The sorbent sol-gel poly(ethylene glycol)-poly(propylene glycol)-poly(ethylene glycol) was applied for the extraction and preconcentration of organochlorine pesticides in aqueous and fruit juice samples prior to analysis with gas chromatography-mass spectrometry. The results demonstrated that the present method is simple, rapid, and precise for the determination of organochlorine pesticides in aqueous samples.
ARTICLE | doi:10.20944/preprints201709.0117.v1
Subject: Mathematics & Computer Science, Applied Mathematics Keywords: significance level; sample size; bayes ratio; likelihood function; optimal decision; significance test
Online: 25 September 2017 (08:33:18 CEST)
The main objective of this paper is to find a close link between the adaptive level of significance, presented here, and the sample size. We, statisticians, know of the inconsistency, or paradox, in the current classical tests of significance that are based on p-value statistics that is compared to the canonical significance levels (10%, 5% and 1%): "Raise the sample to reject the null hypothesis" is the recommendation of some ill-advised scientists! This paper will show that it is possible to eliminate this problem of significance tests. The Bayesian Lindley's paradox – "increase the sample to accept the hypothesis" – also disappears. Obviously, we present here only the beginning of a possible prominent research. The intention is to extend its use to more complex applications such as survival analysis, reliability tests and other areas. The main tools used here are the Bayes Factor and the extended Neyman-Pearson Lemma.
ARTICLE | doi:10.20944/preprints202206.0101.v1
Subject: Medicine & Pharmacology, Other Keywords: Ayurveda research; good research; hypothesis generation; hypothesis testing; managing bias and sample size
Online: 7 June 2022 (09:45:11 CEST)
Ayurveda as a healthcare system has survived for thousands of years but continues to be dogged by reported lack of efficacy of the treatments in clinical trials. The reported lack of efficacy could be due to a real lack of efficacy (which then contradicts the survival of Ayurveda as a functional medical system enjoying considerable public patronage) or could be attributed to inadequacies in the efforts towards evidence generation or in a larger context the overall scientific conduct of research in Ayurveda. In an effort towards better evidence generation, there is an immediate need for standardizing the design, conduct and reporting of clinical trials of Ayurveda but it is a daunting task. For this effort to benefit the scientific endeavors of Ayurveda researchers, it should allow the researchers to be able to apply Ayurveda’s multi-component, individualized and inherently holistic approach. Statistical principles can benefit this effort. Statistical hypothesis testing (SHT) is central to these statistical principles and also aligns well with conventional scientific principles of evidence generation. Although there are challenges with SHT, good practitioners engaged in it do much more than just apply the mathematical theory behind it. As a particular example, lot of time in clinical trial designing is spent in addressing biases and designing trials prudently by minimizing the effect of such biases. SHT can benefit such an effort objectively. There is a need for Ayurveda researchers to engage deeply and mindfully about biases in study design in order to gain scientific validity and acceptability. The article highlights issues that arise in Ayurveda research, and discusses few ways of dealing with these issues using statistical principles.
ARTICLE | doi:10.20944/preprints202105.0250.v1
Subject: Chemistry, Analytical Chemistry Keywords: acid dissolution; neodymium magnet; open system; microwave sample preparation system; ICP-MS analysis
Online: 11 May 2021 (15:06:50 CEST)
The separation of rare earth metals (REM) from a neodymium magnet has been widely studied in the last year. We have shown that the waste of computer hard disk contains 25.41 % neodymium, 64.09 % iron, and <<1 % boron. To further isolate rare-earth metals, the magnet was acidically dissolved in open and closed systems. In both methods of dissolution was used concentrated nitric acid. The difference between these methods are the conditions of dissolution of magnet. The magnet was dissolved in a microwave sample preparation system at different temperatures and pressures in a closed system. In the open system, the acid dissolution of the magnet conducted at room temperature. 0.2 g of the neodymium magnet sample was taken under two conditions, and the dissolution process in the closed system lasted 1 hour, and in the open system-30-40 minutes. The open system is a non-laborious, simple and cheap method of dissolving the magnet by comparing both systems. Therefore, an open sample preparation system is used for further work. To remove the iron in the magnet, oxalic acid was used and precipitated as oxalates under both conditions. According to the result of the ICP-MS method, it is shown that the neodymium and iron contents in the precipitate are 24.66 % and 0.06 %, respectively. This shows that the iron has almost completely passed to the filtrate. Thus, it is possible to remove the iron from the sample.
ARTICLE | doi:10.20944/preprints202011.0278.v1
Subject: Engineering, Automotive Engineering Keywords: Eddy current sensor; lift-off measurement; thickness measurement; non-destructive testing; sample-independence.
Online: 9 November 2020 (11:11:44 CET)
For the electromagnetic eddy current testing, various methods have been proposed for reducing the lift-off error on the measurement of samples. In this paper, instead of eliminating the measurement error caused by the lift-off effect, an algorithm has been proposed to directly measure the lift-off distance between the sensor and non-magnetic conductive plates. The algorithm is based on a sample-independent inductance (SII) feature. That is, under high working frequencies, the inductance is found sensitive to the lift-off distance and independent of the test piece under an optimal single high working frequency (43.87 kHz). Furthermore, the predicted lift-off distance is used for the thickness prediction of the non-magnetic conductive samples using an iterative method. Considering the eddy current skin depth, the thickness prediction is operated under a single lower frequency (0.20 kHz). As the inductance has different sensitivities to the lift-off and thickness, the prediction error of the sample thickness is different from that of the lift-off distance. From the experiments on three different nonmagnetic samples – aluminium, copper, and brass, the maximum prediction error of the lift-off distance and sample thickness is 1.1 mm and 5.42 % respectively at the lift-off of 12.0 mm.
ARTICLE | doi:10.20944/preprints201701.0085.v2
Subject: Chemistry, Analytical Chemistry Keywords: fabric phase sorptive extraction (FPSE); sol-gel; phenols; environmental pollution; sample preparation; microextraction; green analytical chemistry (GAC)
Online: 10 May 2017 (04:37:58 CEST)
The theory and working principle of fabric phase sorptive extraction (FPSE) is presented that eloquently explains the mystery behind this new and powerful sample preparation technique. FPSE innovatively integrates the benefits of sol-gel coating technology and the rich surface chemistry of cellulose/polyester/fiberglass fabric, resulting in a microextraction device with very high sorbent loading in the form of an ultra-thin coating. This porous sorbent coating and the permeable substrate synergistically facilitate very fast extraction equilibrium. The flexibility of the FPSE device allows for direct insertion into original, unmodified samples of different origin. Strong chemical bonding between the sol-gel sorbent and the fabric substrate permits the exposure of FPSE devices to any organic solvent for analyte back-extraction/elution and to highly acidic or basic environments (pH 1-12) if required. A sol-gel derived sorbent, highly polar sol-gel poly(ethylene glycol) coating, was generated on cellulose substrates. Five cm2 segments of these coated fabrics were used as the FPSE devices for sample preparation using direct immersion. An important class of environmental pollutants, substituted phenols, was used as model compounds to evaluate the extraction performance of FPSE. The high primary contact surface area (PCSA) of the FPSE device and porous structure of the sol-gel coatings resulted in very high sample capacities and incredible extraction sensitivities for both the compound classes in a relatively short period of time. Different extraction parameters were evaluated and optimized. The new extraction devices demonstrated part per trillion level detection limits for substituted phenols, a wide range of detection linearity, and good performance reproducibility.
ARTICLE | doi:10.20944/preprints202012.0237.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: Biometrics; Face Recognition; Single Sample Face Recognition; Binarized Statistical Image Features; K-Nearest Neighbors
Online: 9 December 2020 (18:25:02 CET)
Single sample face recognition (SSFR) is a computer vision challenge. In this scenario, there is only one example from each individual on which to train the system, making it difficult to identify persons in unconstrained environments, particularly when dealing with changes in facial expression, posture, lighting, and occlusion. This paper suggests a different method based on a variant of the Binarized Statistical Image Features (BSIF) descriptor called Multi-Block Color-Binarized Statistical Image Features (MB-C-BSIF) to resolve the SSFR Problem. First, the MB-C-BSIF method decomposes a facial image into three channels (e.g., red, green, and blue), then it divides each channel into equal non-overlapping blocks to select the local facial characteristics that are consequently employed in the classification phase. Finally, the identity is determined by calculating the similarities among the characteristic vectors adopting a distance measurement of the k-nearest neighbors (K-NN) classifier. Extensive experiments on several subsets of the unconstrained Alex & Robert (AR) and Labeled Faces in the Wild (LFW) databases show that the MB-C-BSIF achieves superior results in unconstrained situations when compared to current state-of-the-art methods, especially when dealing with changes in facial expression, lighting, and occlusion. Furthermore, the suggested method employs algorithms with lower computational cost, making it ideal for real-time applications.
Subject: Keywords: brain injuries; traumatic brain injury; children; diversity; student-led; participant-focused; recruitment; sample; methods
Online: 7 July 2020 (04:42:39 CEST)
The advancement of the pediatric traumatic brain injury (TBI) knowledge base requires biospecimens and data from large samples. This study seeks to describe a novel clinical research modality to establish best practices for enrolling a diverse pediatric TBI population and quantifying key information on enrollment into biobanks. Screening form responses were standardized and cleaned through Google Sheets. Data was used to analyze total individuals at each enrollment stage. R was utilized for final analysis, including chi-square goodness of fit and proportion statistical tests, to determine further significance and relationships. Issues throughout data cleaning shed light on limitations of the consent modality. Results suggest that through a diverse research team, the recruited sample exceeds traditional measures of representation (e.g. sex, race, ethnicity). Sex demographics of the study are representative of the local population. Screening for candidates is critical to the success of the consent modality. The consent modality may be modified to increase diversity of study population and accept bilingual candidates. Researchers must implement best practices, including increasing inclusivity of bilingual populations, utilizing technology, and improving participant follow-up, to improve health disparities for understudied clinical populations.
ARTICLE | doi:10.20944/preprints202002.0187.v1
Subject: Biology, Plant Sciences Keywords: dioecious; DNA quality; flower type; sample preservation method; sex genotype; sex phenotype; visual assay
Online: 14 February 2020 (04:22:20 CET)
Methods for high-quality DNA extraction and knowledge of sex expression and flowering time are essential for applying genomic-assisted breeding and improve the success with hybridization in Guinea yam. A dioecious or monoecious pattern of flowering and sometimes non-flowering is a common phenomenon within and between the Dioscorea species. The flowering in yam plants raised from botanical seeds often takes an extended period, mostly till the first clonal generation after propagation from the tubers. The prolonged process of testing required to identify plant sex and flowering intensity in yam breeding often poses a challenge to realize reduced breeding cycle and apply genomic selection. This study assessed sample preservation methods for DNA quality during extraction and potential of DNA marker to diagnose plant sex at the early seedling stage in white Guinea yam. The predicted sex at the seedling stage was further validated with the visual score for the sex phenotype at the flowering stage. DNA extracted from leaf samples preserved in liquid nitrogen, silica gel, dry ice, and oven drying methods was similar in quality with a high molecular weight than samples stored in ethanol solution. Yam plant sex diagnosis with the DNA marker (sp16) identified a higher proportion of ZW genotypes (female or monoecious phenotypes) than the ZZ genotypes (male phenotype) in the studied materials with 74% prediction accuracy. The results from this study provided valuable insights on suitable sample preservation methods for quality DNA extraction and the potential of DNA marker sp16 to predict sex in white Guinea yam.
ARTICLE | doi:10.20944/preprints201810.0376.v1
Subject: Earth Sciences, Other Keywords: thermal infrared; reflectance spectroscopy; emissivity; surface roughness; geological sample preparation; hyperspectral; drill core scanning
Online: 17 October 2018 (07:51:17 CEST)
High-resolution laboratory-based thermal infrared spectroscopy is an up-and-coming tool in the field of geological remote sensing. Its spatial resolution allows for detailed analyses at centimeter to sub-millimeter scale. However, this increase in resolution creates challenges with sample characteristics such as grain size, surface roughness and porosity that can influence the spectral signature. This research explores the effect of rock sample surface preparation on the TIR spectral signatures. We applied three surface preparation methods (split, saw and polish) to determine how the resulting differences in surface roughness affects both the spectral shape as well as the spectral contrast. The selected samples are a pure quartz sandstone, a quartz sandstone containing a small percentage of kaolinite, and an intermediate-grained gabbro. To avoid instrument or measurement type biases we conducted measurements on three TIR instruments, resulting in directional hemispherical reflectance spectra, emissivity spectra and bi-directional reflectance images. Surface imaging and analyses were performed with scanning electron microscopy and profilometer measurements. We demonstrate that surface preparation affects the TIR spectral signatures influencing both the spectral contrast as well as the spectral shape. The results show that polished surfaces predominantly display a high spectral contrast while the sawed and split surfaces display up to 25% lower reflectance values. Furthermore, the sawed and split surfaces display spectral signature shape differences at specific wavelengths, which we link to mineral transmission features, surface orientation effects and multiple reflections in fine-grained minerals. Hence, the influence of rock surface preparation should be taken in consideration to avoid an inaccurate geological interpretation.
ARTICLE | doi:10.20944/preprints201808.0521.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: Target difference, clinically important difference, sample size, guidance, randomised trial, effect size, realistic difference
Online: 30 August 2018 (10:33:40 CEST)
The aim of this document is to provide practical guidance on the choice of target difference used in the sample size calculation of a randomised controlled trial (RCT). Guidance is provided with a definitive trial, one that seeks to provide a useful answer, in mind and not those of a more exploratory nature. The term “target difference” is taken throughout to refer to the difference that is used in the sample size calculation (the one that the study formally “targets”). Please see the glossary for definitions and clarification with regards other relevant concepts. In order to address the specification of the target difference, it is appropriate, and to some degree necessary, to touch on related statistical aspects of conducting a sample size calculation. Generally the discussion of other aspects and more technical details is kept to a minimum, with more technical aspects covered in the appendices and referencing of relevant sources provided for further reading.The main body of this guidance assumes a standard RCT design is used; formally, this can be described as a two-arm parallel-group superiority trial. Most RCTs test for superiority of the interventions, that is, whether or not one of the interventions is superior to the other (See Box 1 for a formal definition of superiority, and of the two most common alternative approaches). Some common alternative trial designs are considered in Appendix 3. Additionally, it is assumed in the main body of the text that the conventional (Neyman-Pearson) approach to the sample size calculation of an RCT is being used. Other approaches (Bayesian, precision and value of information) are briefly considered in Appendix 2 with reference to the specification of the target difference.
ARTICLE | doi:10.20944/preprints202206.0312.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: refined multiscale entropy; sample entropy; bubble entropy; adaptive complex system; pressure ulcer; machine learning; body temperature
Online: 22 June 2022 (09:52:15 CEST)
This study examined the association between pressure injuries and complexity of abdominal temperature measured in residents of a nursing facility. The temperature served as a proxy measure for skin thermoregulation. Refined multiscale sample entropy and bubble entropy were used to measure the complexity of the temperature time series measured over two days at 1-minute intervals. Robust summary measures were derived for the multiscale entropies and used in predictive models for pressure injuries that were built with adaptive lasso regression and neural networks. Both types of entropies were lower in the group of participants with pressure injuries (n=11) relative to the group of non-injured participants (n=15). This was generally true at the longer temporal scales, with the effect peaking at scale τ=23 minutes. Predictive models for pressure injury on the basis of refined multiscale sample entropy and bubble entropy yielded 92% accuracy, outperforming predictions based on any single measure of entropy. Combining entropy measures with a widely used risk assessment score led to the best prediction accuracy. Complexity of abdominal temperature series could therefore serve as an indicator of risk of pressure injury.
ARTICLE | doi:10.20944/preprints202101.0440.v1
Subject: Chemistry, Analytical Chemistry Keywords: glycosphingolipids; lipidomics; mass spectrometry; hydrophilic interaction liquid chromatography; human plasma; lipid profile; sample preparation; fragmentation behavior
Online: 22 January 2021 (11:31:39 CET)
Glycosphingolipids (GSL) represent a highly heterogeneous class of lipids with many cellular functions, implicated in a wide spectrum of human diseases. Their isolation, detection, and comprehensive structural analysis is a challenging task due to the structural diversity of GSL molecules. In this work, GSL subclasses are isolated from human plasma using an optimized monophasic ethanol–water solvent system capable to recover a broad range of GSL species. Obtained deproteinized plasma is subsequently purified and concentrated by C18-based solid-phase extraction (SPE). The hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization linear ion trap tandem mass spectrometry (ESI-LIT-MS/MS) is used for GSL analysis in the human plasma extract. Our results provide an in-depth profiling and structural characterization of glycosphingolipid and some phospholipid subclasses identified in the human plasma based on their retention times and the interpretation of tandem mass spectra. The structural composition of particular lipid species is readily characterized based on the detailed interpretation of MS and MS/MS spectra and further confirmed by specific fragmentation behavior following predictable patterns, which yields to the unambiguous identification of 154 GSL species within 7 lipid subclasses and 77 phospholipids representing the highest number of GSL species ever reported in the human plasma. The developed HILIC-ESI-MS/MS method can be used for further clinical and biological research of GSL in the human blood or other biological samples.
ARTICLE | doi:10.20944/preprints202005.0326.v3
Subject: Social Sciences, Econometrics & Statistics Keywords: COVID-19; SARS-Cov-2; coronavirus; sample selection bias; bivariate probit; social distancing; public goods; macroeconomic
Online: 9 June 2020 (07:46:26 CEST)
This paper surveys estimates of the transmission features of the novel coronavirus, and then proposes a model to address sample-selection bias in estimated determinants of infection. Containment assumptions of the infection forecasting models depend on assumed effects of policies and self-regulating behavior. In the commons dilemma of the pandemic, the perceived ‘low risks’ of unregulated marginal choices do not reflect the full social cost, implying non-pharmaceutical interventions (NPI) to reduce mortality can enhance social welfare. As more economic activity renews with liftings of restrictive NPI (RNPI), a critical question concerns the ability of milder NPI (MNPI) and voluntary precautions to mitigate the risk of greater infections and deaths while also limiting the pandemic’s economic damage and its social costs. Ineffective NPI could lead to continued COVID-19 waves and new types of crises, worsened expectations and delayed economic recoveries. From the central range of surveyed estimates of transmission and alternative herd-immunity-threshold estimates, a ‘worst-case’ virus guidepost suggests eventual deaths of around 25 to 41 million worldwide and 1.1 to 1.7 million in the U.S. needed to reach herd immunity with no vaccine or treatment. The most optimistic study surveyed (theoretical model from a non-reviewed preprint study) combined with the low end of the range of the estimated mortality rate suggests 6 to 9 million deaths worldwide and 250 to 370 thousand in the U.S. to reach herd immunity. Successes in the mix of NPI, treatments, and vaccine can limit the eventual global death toll of the virus. Improved estimation models for forecasting and decision making may assist in better targeting the local timings and mix of NPI. Diagnostic tests for the virus have been largely limited to symptomatic cases, causing possible sample selection bias. A recursive bivariate probit model of infection and testing is proposed along with several possible applications from cross-section or panel-data estimation. Multiple potential explanatory variables, data sources, and estimation needs are specified and discussed.
CONCEPT PAPER | doi:10.20944/preprints201911.0178.v1
Subject: Biology, Ecology Keywords: ecological monitoring methods; vegetation composition; vegetation cover; vegetation structure; soil sampling methods; sample management; electronic data collection
Online: 15 November 2019 (08:56:27 CET)
Ecosystem surveillance monitoring is critical to managing natural resources and especially so under changing environments. Despite this importance, the design and implementation of monitoring programs across large temporal and spatial scales has been hampered by the lack of appropriately standardised methods and data streams. To address this gap, we outline a surveillance monitoring method based on permanent plots and voucher samples suited to rangeland environments around the world that is repeatable, cost-effective, appropriate for large-scale comparisons and adaptable to other global biomes. The method provides comprehensive data on vegetation composition and structure along with soil attributes relevant to plant growth, delivered as a combination of modules that can be targeted for different purposes or available resources. Plots are located in a stratified design across vegetation units, landforms and climates to enhance continental and global comparisons. Changes are investigated through revisits. Vegetation is measured to inform on composition, cover and structure. Samples of vegetation and soils are collected and tracked by barcode labels and stored long-term for subsequent analysis. Technology is used to enhance the accuracy of field methods, including differential GPS r plot locations, instrument based Leaf Area Index (LAI) measures, and three dimensional photo-panoramas for advanced analysis. A key feature of the method is the use of electronic field data collection to enhance data delivery into a publicly-accessible database.Our method is pragmatic, whilst still providing consistent data, information and samples on key vegetation and soil attributes. The method is operational and has been applied at more than 704 field locations across the Australian rangelands as part of the Ecosystem Surveillance program of the Terrestrial Ecosystem Research Network (TERN). The methodology enables continental analyses, and has been tested in communities broadly representative of rangelands globally, with components being applicable to other biomes. Here we also recommend the consultative process and guiding principles that drove the development of this method as an approach for development of the method into other biomes. The consistent, standardised and objective method enables continental, and potentially global analyses than were not previously possible with disparate programs and datasets.
ARTICLE | doi:10.20944/preprints201702.0071.v1
Subject: Mathematics & Computer Science, Computational Mathematics Keywords: ordinal patterns; Permutation entropy; Approximate entropy; Sample entropy; Conditional entropy of ordinal patterns; Kolmogorov-Sinai entropy; classification
Online: 17 February 2017 (16:41:32 CET)
During the last years some new variants of Permutation entropy have been introduced and applied to EEG analysis, among them a conditional variant and variants using some additional metric information or being based on entropies different from the Shannon entropy. In some situations it is not completely clear what kind of information the new measures and their algorithmic implementations provide. We discuss the new developments and illustrate them for EEG data.
SHORT NOTE | doi:10.20944/preprints202206.0032.v1
Subject: Life Sciences, Other Keywords: Conformity assessment; lot inspection; acceptance sampling; Quality level; sample size; Bayesian statistics; prior distribution; posterior distribution; consumer risk; producer risk
Online: 2 June 2022 (10:59:47 CEST)
The ISO 2859 and ISO 3951 series provide acceptance sampling procedures for lot inspection, allowing both sample size and acceptance rule to be determined, starting from a specific value either for the consumer or producer risk. However, insufficient resources often make it difficult to implement “ISO sampling plans.” In cases where the sample size is determined by external constraints, the focus shifts from determining sample size to determining consumer and producer risks. Moreover, if the sample size is very low (e.g. one single item), prior information should be included in the statistical analysis. For this reason, it makes sense to work within a Bayesian theoretical framework, such as that described in JCGM 106. Accordingly, the approach from JCGM 106 is adopted and broadened so as to allow application to lot inspection. The discussion is based on a “real-life” example of lot inspection on the basis of a single item. Starting from simple assumptions, expressions for both the prior and posterior distributions are worked out, and it is shown how the concepts from JCGM 106 can be reinterpreted in the context of lot inspection. Conceptual differences regarding the definition of consumer and producer risks in JCGM 106 and in the ISO acceptance sampling standards are elucidated and a numerical example is provided.
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: physical activity; depression; elderly people living alone; Patient Health Questionnaire-10; flexibility exercise; muscular strength exercise; complex sample logistic regression
Online: 25 March 2019 (11:10:17 CET)
Background and objectives: Only a few studies analyzed the physical activity level of elderly people living alone in local communities and evaluated the relationship between it and mental health. The purpose of this study was to investigate the relationship between physical activity and depression in the elderly living alone and to provide basic data for the prevention of depression in the elderly. Materials and Methods: We analyzed 256 elderly people living alone aged 65 years or older who completed the 2014 Korea National Health and Nutrition Examination Survey. Depression was defined as a score of 10 or higher using Patient Health Questionnaire-10(PHQ-9). This study investigated walking per week, days of muscular strength exercise performance in the past one week, days of flexibility exercise in the past one week, mean hours in a sitting position per day, the numbers of days and hours conducting a high intensity physical activity in the past one week, and numbers of days and hours conducting a medium intensity physical activity in the past one week to define physical activity. Our study presented prevalence odds ratios (pOR) and 95% confidence interval (CI) by using complex sample logistic regression analysis in order to identify the relationship between physical activity and depression. Results: The results of complex sample logistic regression analysis showed that flexibility exercise was significantly related to depression (p <0.05). On the other hand, the mean hours in a sitting position per day, aerobic physical activity, walking, and muscular strength exercise were not significantly related to geriatric depression. Conclusions: The results of our study implied that persistent flexibility exercise might be more effective to maintain a healthy mental status than muscular strength exercise. A longitudinal study is required to prove the causal relationship between physical activity and depression in the old age.
DATA DESCRIPTOR | doi:10.20944/preprints202208.0112.v1
Subject: Earth Sciences, Geoinformatics Keywords: ground truth data; drone; mobile application; windshield survey; sample design; crop mapping; agriculture statistics; data dissemination; earth observation data; spatial database.
Online: 4 August 2022 (16:18:26 CEST)
Over the last few years, Earth Observation (EO) data has shifted towards increased use to produce official statistics, particularly in the agriculture sector. National statistics offices worldwide, including in Asia and the Pacific, are expanding their use of EO data to produce agricultural statistics such as crop classification, yield estimation, irrigation mapping, and crop loss estimation. The advances in image classification, such as pixel-based and phenology-based classifications, and machine learning create new opportunities for researchers to analyze EO data applied to agriculture statistics. However, it requires the ground truth (GT) data because classification result mainly depends on the quality of GT. Therefore, in this study, we introduced a random sampling approach to design and collect GT data using EO imagery and ancillary data. As a result of data collection, GT data improve the algorithms and validates classification results. Nevertheless, despite the importance of GT data, they are rarely disseminated as a data product in themselves. Thus, this results in an untapped opportunity to share GT data as a global public good, and improved use of survey and census data as a source of GT data.
ARTICLE | doi:10.20944/preprints202106.0100.v3
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: entropy; average information; degree of dependence; probability space; probability distribution; experiment in a sample space; linear system; affine isomorphism; classification space.
Online: 5 July 2021 (16:22:30 CEST)
We define degree of dependence of two events A and B in a probability space by using Boltzmann-Shannon entropy function of an appropriate probability distribution produced by these events and depending on one parameter (the probability of intersection of A and B) varying within a closed interval I. The entropy function attains its global maximum when the events A and B are independent. The important particular case of discrete uniform probability space motivates this definition in the following way. The entropy function has a minimum at the left endpoint of I exactly when one of the events and the complement of the other are connected with the relation of inclusion (maximal negative dependence). It has a minimum at the right endpoint of I exactly when one of these events is included in the other (maximal positive dependence). Moreover, the deviation of the entropy from its maximum is equal to average information that carries one of the binary trials defined by A and B with respect to the other. As a consequence, the degree of dependence of A and B can be expressed in terms of information theory and is invariant with respect to the choice of unit of information. Using this formalism, we describe completely the screening tests and their reliability, measure efficacy of a vaccination, the impact of some events from the financial markets to other events, etc. A link is available for downloading an Excel program which calculates the degree of dependence of two events in a sample space with equally likely outcomes.
ARTICLE | doi:10.20944/preprints202105.0396.v1
Subject: Earth Sciences, Atmospheric Science Keywords: ensemble modelling; seafloor mapping; sediment change analysis; seafloor sediment distribution; North Sea; seafloor classification; acoustic mapping; small sample size; ensemble map
Online: 17 May 2021 (16:58:50 CEST)
Recent studies on seafloor mapping have presented different modelling methods for the automatic classification of seafloor sediments. However, most of these studies have applied these models to seafloor data with appropriate number of ground-truth samples, which raises the question whether these methods are applicable to studies with smaller numbers of ground-truth data. In this study, we aim to address this issue by conducting sediment class-specific predictions using ensemble modelling to map areas with limited or without ground-truth data and combined with hydro-acoustic datasets. The resulting class-specific maps were then assembled into one map, where the most probable class was assigned to the appropriate location. Our approach was able to predict sediment classes without bias to the class with more ground-truth data and produced reliable seafloor sediment distributions maps that can be used for seafloor monitoring. Sediment shifts of a heterogenous seafloor in the Sylt Outer Reef, German North Sea were also assessed to understand the sediment dynamics in the area. The analyses of sediment shifts showed that the western area of the Sylt Outer Reef is highly active, and the results of the analyses assisted in providing recommendations on future seafloor monitoring activities.
ARTICLE | doi:10.20944/preprints202207.0358.v1
Subject: Life Sciences, Virology Keywords: Foot-and-mouth disease virus; safe sample transport; single-stranded positive-sense RNA; TRIzol extraction; naked RNA; infectivity; RNA transfection; lipofectamine; self-transfection; BHK cells
Online: 25 July 2022 (08:14:51 CEST)
Safe sample transport is of great importance for infectious diseases diagnostics. Various treatments and buffers are used to inactivate pathogens in diagnostic samples. At the same time, adequate sample preservation, particularly of nucleic acids, is essential to allow an accurate laboratory diagnosis. For viruses with single-stranded RNA genomes of positive polarity, such as foot-and-mouth disease virus (FMDV), however, naked full-length viral RNA can itself be infectious. In order to assess the risk of infection from inactivated FMDV samples, two animal experiments were performed. In the first trial, six cattle were injected with FMDV RNA (isolate A22/IRQ/24/64) into the tongue epithelium. All animals developed clinical disease within two days and FMDV was reisolated from serum and saliva samples. In the second trial, another group of six cattle was exposed to FMDV RNA by instilling it on the tongue and spraying it into the nose. The animals were observed for 10 days after exposure. All animals remained clinically unremarkable and virus isolation as well as FMDV genome detection in serum and saliva were negative. No transfection reagent was used for any of the animal inoculations. In conclusion, cattle can be infected by injection with naked FMDV RNA, but not by non-invasive exposure to the RNA. Inactivated FMDV samples that contain full-length viral RNA carry only a negligible risk of infecting animals.
ARTICLE | doi:10.20944/preprints202104.0612.v2
Subject: Engineering, Biomedical & Chemical Engineering Keywords: centrifugal microfluidics; Lab-on-a-Disc; centrifugo-pneumatic flow control; integration; multiplexing; parallelization; sample-to-answer; reliability; tolerances; design-for-manufacture; digital twin; event-triggering
Online: 8 June 2021 (11:23:58 CEST)
Fluidic larger-scale integration (LSI) resides at the heart of comprehensive sample-to-answer automation and parallelization of assay panels for frequent and ubiquitous bioanalytical testing in decentralized the point-of-use / point-of-care settings. This paper develops a novel “digital twin” strategy with an emphasis on rotational, centrifugo-pneumatic flow control. The underlying model systematically connects retention rates of rotationally actuated valves as a key element of LSI to experimental input parameters; for the first time, the concept of band widths in frequency space as the decisive quantity characterizing operationally robustness is introduced, a set of quantitative performance metrics guiding algorithmic optimization of disc layouts is defined, and the engineering principles of advanced, logical flow control and timing are elucidated. Overall, the digital twin enables efficient design for automating multiplexed bioassay protocols on such “Lab-on-a-Disc” (LoaD) systems featuring high packing density, reliability, configurability, modularity and manufacturability to eventually minimize cost, time and risk of development and production.
REVIEW | doi:10.20944/preprints202206.0040.v1
Subject: Chemistry, Other Keywords: Microsampling; sample miniaturisation; dried blood spot (DBS); dried plasma spot (DPS); dried serum spot (DSS); metabolic phenotyping; gas chromatography-mass spectrometry (GC-MS); liquid chromatog-raphy-mass spectrometry (LC-MS)
Online: 3 June 2022 (09:53:13 CEST)
Microsamples (collections usually less than 50 µL) have been introduced in pre-clinical, clinical, and research settings to overcome obstacles in sampling via traditional venipuncture. However, venipuncture remains the sampling gold standard for metabolic phenotyping of blood. This pre-sents several challenges in metabolic phenotyping workflows: accessibility for individuals in ru-ral and remote underserved areas (due to the need for trained personnel), the unamenable nature to frequent sampling protocols in longitudinal research (for its invasive nature), and sample col-lection difficulty in the young and elderly. Furthermore, venous sample stability may be compro-mised when temperate conditions necessary for cold-chain transport are beyond control. Alter-natively, research utilising microsamples extends phenotyping possibilities to inborn errors of metabolism, therapeutic drug monitoring, nutrition, as well as sport and anti-doping. Although the application of microsamples in metabolic phenotyping exists, it is still in its infancy, with whole blood being overwhelmingly the primary biofluid collected through the collection method of dried blood spots. Research into metabolic phenotyping of microsamples is limited; however, with advances in commercially available microsampling devices, common barriers such as volumetric inaccuracies and the ‘haematocrit effect’ in dried blood spot microsampling can be overcome. In this review, we provide an overview of the common uses and workflows for mi-crosampling in metabolic phenotyping research. We discuss the advancements in technologies, highlighting key considerations and remaining knowledge gaps for employment of microsamples in metabolic phenotyping research. Supporting the translation of research from the ‘bench to the community’.