Episcopic imaging using techniques such as High Resolution Episcopic Microscopy (HREM) and its variants, allows biological samples to be visualized in three dimensions over a large field of view. Quantitative analysis of episcopic image data is undertaken using a range of methods. In this systematic review, we look at trends in quantitative analysis of episcopic images and discuss avenues for further research. Papers published between 2011 and 2022 were analyzed for details about quantitative analysis approaches, methods of image annotation and choice of image processing software. It is shown that quantitative processing is becoming more common in episcopic microscopy and that manual annotation is the predominant method of image analysis. Our meta-analysis highlights where tools and methods require further development in this field, and we discuss what this means for the future of quantitative episcopic imaging, as well as how annotation and quantification may be automated and standardized across the field.

Assessment of the percentage of disease infected lung volume using computed tomography (CT) images can play an important role to detect lung diseases and predict disease severity. However, manual segmentation of disease infected regions from many CT image slices is tedious and not feasible in clinical practice. To help solve this clinical challenge, this study aims to investigate a new strategy to automatically segment disease infected regions and predict disease severity. We employed a public dataset acquired from 20 COVID-19 patients, which includes manually annotated lung and infections masks, to train a new ensembled deep learning (DL) model that combines the five customized residual attention UNet models to segment disease infected regions followed by a Feature Pyramid Network (FPN) model to classify severity stage of COVID-19 infection. To test potentially clinical utility of new model, we first gathered and processed another set of CT images acquired from 80 Covid-19 patients. Next, we asked two chest radiologists to read CT images of each patient and report the estimated percentage of infected lung volume and disease severity level. Additionally, we asked radiologists to rate acceptance of DL model-generated segmentation results using a 5-scale rating method. Data analysis results show that agreement between disease severity classification is >90% in 45 testing cases. Furthermore, >73% of cases received the high rating score from two radiologists (scored more than 4). This study demonstrates feasibility of developing a new DL-model to efficiently provide quantitative assessment of disease severity based on the automated segmentation of the disease infected regions to support improving efficacy of radiologists in disease diagnosis.

Polyacrylamide gel electrophoresis (PAGE) is widely used for studying proteins and protein-containing objects. However, it is employed most frequently as a qualitative method rather than a quantitative one. In this paper, we show the feasibility of routine digital image acquisition and mathematical processing of electrophoregrams for protein quantification. Both the well-studied model protein molecules (bovine serum albumin) and more complex real-world protein-based products (casein-containing isolate for sports nutrition), which were subjected to mechanical activation in a planetary ball mill to obtain samples characterized by different protein denaturation degrees, were used as study objects. Protein quantification in the mechanically activated samples was carried out. The degree of destruction of individual protein was shown to be higher compared to that of protein-containing mixture after mechanical treatment for an identical amount of time. The methodological approach used in this study can serve as guidance for other researchers who would like to use electrophoresis for protein quantification both in individual form and in protein mixtures. The findings prove that photographic imaging of gels followed by mathematical data processing can be applied for analyzing the electrophoretic data.

Spontaneous plants metabolites are more widespread for their properties and biological functions. Also, natural products have reminded diverse scientists to take a delight in their medical and insecticidal applications linked to the environmental. A variety of metabolites have a defensive function for the plants. Thus, three spontaneous plants: Caroxylon imbricatum, Tetraena alba and Cotula cinerea collected from two ecotypes and analyzed by two known conventional methods:Gas Chromatography‐Mass Spectrometry GC QTOF(quadrupole time of flight )_MS and Liquid Chromatography-Mass spectrometry LCQTOF(quadrupole time of flight )_MS. The investigation conducted out on the identification and quantification of metabolites revealed the main metabolites which have biological activities as a part of an alternative to synthetic insecticides. The chemical study showed the presence of N-Butylbenzensulfonamide and Sulfoxycaprylicacid in the three plants. N-Carboxy-methionineresidue, Butanoicacid and Valine were found in those of Cotula cinerea and Caroxylon imbricatum (Forssk.). Artomunoxanthentrione, Glycoaldehyde, Indoline, ,Benzensulfonamide and Oxoproline were detected in extracts of Caroxylon imbricatum (Forssk.) and Tetraena alba (L.f.) In addition, Pyrroline is the only compound common in Cotula cinerea and Tetraena alba (L.f.).

The extracts of Garcinia mangostana L. (mangosteen) are traditionally used for medicinal purposes in Asia. Phenols and xanthones are the two main phenolic compounds with anti-inflammatory activities in the pericarps of mangosteen. A simple and economic reverse-phase high-performance liquid chromatography (RP-HPLC) method has been developed for the simultaneous quantification of phenols (catechin, epicatechin, and procyanidin B2) in mangosteen. The mobile phase was acetonitrile: water (12:88) at 30°C, the flow rate was 1 mL/min, and the detection wavelength was 230 nm. The results showed good linear relationships for catechin from 50-250 ng and for epicatechin and procyanidin B2 from 250-1250 ng. The RP-HPLC fingerprint determination method of total xanthones in mangosteen was also established to provide a new method for quality control of mangosteen extract. The mobile phase was a methanol-water gradient elution at 30°C, the flow rate was 1 mL/min, and the detection wavelength was 320 nm. The similarity of fingerprints of 10 batches of total xanthones was more than 0.90. These methods had good precision, reproducibility, and stability and can be applied in the quality control of mangosteen extracts for medicinal purposes.

1) Background: Ultrasound-based strain imaging is now available in several ultrasound (US) scanners. Strain ratio (SR) can be used to quantify strain recorded simultaneously in two different user-selected areas, ideally exposed to the same amount of stress. The aim of this study was to evaluate SR variability when assessed in an in-vitro setup with a tissue-mimicking phantom, on resected tissue samples and in live tissue scanning with endoscopic applications. 2) Material and methods: Retrospective analysis of SR for quantification of elastic contrasts in a tissue-mimicking phantom containing four homogenous inclusions, in 38 resected bowel wall lesions and in 48 focal pancreatic lesions examined in vivo. Median SR and the inter-quartile range (IQR) was calculated on all external and endoscopic US-applications. The IQR/median provides a measure of the SR variability focusing on the two percentiles of the data closest to the median value. 3) Results: The overall variability of SR was lowest in a tissue-mimicking phantom (mean QR/median SR: 0.07). In resected bowel wall lesions representing adenomas, adenocarcinomas or Crohn lesions, the variability increased (mean IQR/Median: 0.62). During an endoscopic examination of focal pancreatic lesions in vivo, the variability increased further (mean IQR/Median: 2.04). 4) Conclusion: SR variability increased when assessed on different targets with growing heterogeneity and biological variability as one moved from homogeneous media to live tissues and endoscopic application. This may indicate a limitation for the accuracy SR evaluation in clinical applications.

Groundwater models serve as support tools to among others: assess water resources, evaluate management strategies, design remediation systems and optimize monitoring networks. Thus, the assimilation of information from observations into models is crucial to improve forecasts and reduce uncertainty of their results. As more information is collected routinely due to the use of automatic sensors, data loggers and real time transmission systems; groundwater modelers are becoming increasingly aware of the importance of using sophisticated tools to perform model calibration in combination with sensitivity and uncertainty analysis. Despite their usefulness, available approaches to perform this kind of analyses still present some challenges such as non-unique solution for the parameter estimation problem, high computational burden and a need of a deep understanding of the theoretical basis for the correct interpretation and use of their results, in particular the ones related to uncertainty analysis. We present a brief derivation of the main equations that serve as basis for this kind of analysis. We demonstrate how to use them to estimate parameters, assess the sensitivity and quantify the uncertainty of the model results using an example inspired by a real world setting. We analyze some of the main pitfalls that can occur when performing such kind of analyses and comment on practical approaches to overcome them. We also demonstrate that including groundwater flow estimations, although helpful in constraining the solution of the inverse problem as shown previously, may be difficult to apply in practice and, in some cases, may not provide enough information to significantly constrain the set of potential solutions.

In the last decade, the tremendous improvement in the sensitivity and also affordability of Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS) have revolutionized its application in pharmaceutical analysis, resulting in wide-spread of employing LC-MS/MS for determining pharmaceutical compounds including anticancer drugs in pharmaceutical research and also industries. Currently, LC-MS/MS has been widely used to quantify small molecule oncology drugs in various biological matrices to support preclinical and clinical Pharmacokinetic studies in R & D of oncology drugs. This mini-review article will describe the state-of-the art LC-MS/MS and its application in rapid quantification of small molecule anticancer drugs. In addition, efforts have also been made in this review to address several key aspects in the development of rapid LC-MS/MS methods, including sample preparation, chromatographic separation and matrix effect evaluation.

Identifying groups that share common features among datasets through clustering analysis is a typical problem in many fields of science, particularly in post-omics and systems biology research. In respect of this, quantifying how a measure can cluster or organize intrinsic groups is important since currently there is no statistical evaluation of how ordered is, or how much noise is embedded in the resulting clustered vector. Many of the literature focuses on how well the clustering algorithm orders the data, with several measures regarding external and internal statistical measures; but none measure has been developed to statistically quantify the noise in an arranged vector posterior a clustering algorithm, i.e., how much of the clustering is due to randomness. Here, we present a quantitative methodology, based on autocorrelation, to assess this problem.

The application of quantitative PCR (qPCR) as a routine method to detect and enumerate Paenibacillus larvae in honey and hive debris could greatly speed up the estimation of prevalence and outbreak risk of the American foulbrood (AFB) disease of Apis mellifera. However, none of the qPCR tests described so far has been officially proposed as a standard procedure for P. larvae detection and enumeration for surveillance purposes. Therefore, in this study inclusivity, exclusivity and sensitivity in detection of P. larvae spores directly in samples of honey and hive debris were re-evaluated for the previously published qPCR methods. To this aim recently acquired P. larvae sequence data were considered to assess inclusivity in silico and more appropriate non-target species were used to verify exclusivity experimentally. This led to the modification of one of the previously described methods resulting in a new test capable to allow the detection of P. larvae spores in honey and hive debris down to 1 CFU/g. The application of the qPCR test optimized in this study can allow to reliably detect and quantify P. larvae in honey and hive debris, thus circumventing the disadvantages of late AFB diagnosis based on clinical symptoms and possible underestimation of spore numbers that is the main drawback of culture-dependent procedures.

In most Eukaryotes, ubiquitin either exists as free monoubiquitin or as a molecule that is covalently linked to other proteins. These two forms cycle between each other and due to the concerted antagonistic activity of ubiquitylating and deubiquitylating enzymes, an intracellular ubiquitin equilibrium is maintained that is essential for normal biological function. However, measuring the level and ratio of these forms of ubiquitin has been difficult and time consuming. In this paper, we have adapted a simple immunoblotting technique to monitor ubiquitin content and equilibrium dynamics in different developmental stages and tissues of Drosophila. Our data show that the level of total ubiquitin is distinct in different developmental stages, lowest at the larval-pupal transition and in three days old adult males, and highest in first instar larvae. Interestingly, the ratio of free mono-ubiquitin remains within 30-50% range of the total throughout larval development, but peaks to 70-80% at the larval-pupal and the pupal-adult transitions. It stays within the 70-80% range in adults. In developmentally and physiologically active tissues, the ratio of free ubiquitin is similarly high, most likely reflecting a high demand for ubiquitin availability. We also used this method to demonstrate the disruption of the finely tuned ubiquitin equilibrium by the abolition of proteasome function or the housekeeping deubiquitylase, Usp5. Our data support the notion that the ubiquitin equilibrium is regulated by tissue- and developmental stage-specific mechanisms.

One of the most common forms of dementia is Alzheimer’s disease (AD), which leads to progressive mental deterioration. Unfortunately, there is no definitive diagnosis and cure that can stop the condition progressing. The diagnosis is often performed based on the clinical history and neuropsychological data, including magnetic resonance imaging (MRI). Deep neural networks (DNN) algorithms are gaining popularity for medical diagnosis, and have been used widely for the analysis of MRI data. DNNs can extract hidden features from thousands of training images automatically. However, they cannot judge how confident they are about their predictions. To use DNNs in safety-critical applications such as medical diagnosis, uncertainty quantification of DNNs predictions is crucial. For this purpose, Monte Carlo dropout (MCD) has been widely used, however, it may lead to overconfident and miss calibrated results. This paper proposes a framework in which the MCD algorithm’s hyper-parameters are optimized during training using Bayesian optimization for the first time. The conducted optimization leads to assigning high predictive entropy to erroneous predictions and making it possible to recognize risky predictions. The proposed framework is used for AD diagnosis, which has not been done before. We compare our method with some existing methods in the literature based on different uncertainty quantification criteria. The results of comprehensive experiments on the Kaggle dataset using a deep model pre-trained on the ImageNet dataset show that the proposed algorithm can quantify uncertainty much better than the existing methods.

Apoptosis is associated with numerous phenotypical characteristics, and is thus studied with many tools. In this study, we compared two broadly used apoptotic assays: TUNEL and staining with an antibody targeting the activated form of an effector caspase. To compare them, we developed a protocol based on commonly used tools such as filters, zprojection and thresholding. Even though it is commonly used in imageprocessing protocols, thresholding remains a recurring problem. Here we analyzed the impact of processing parameters and readout choice on the accuracy of apoptotic signal quantification. Our results show that TUNEL is quite robust, even if image processing parameters can allow or not to detect subtle differences of the apoptotic rate. On the contrary, images from anticleaved caspase staining are more sensitive to handle and proved to necessitate to be processed more carefully. We then developed an open source Fiji macro automatizing most steps of the image processing and quantification protocol. It is noteworthy that the field of application of this macro is wider than apoptosis as it can perfectly be used to treat and quantify other kind of images.

Purpose: Carotid intraplaque hemorrhage (IPH) increases risk of territorial cerebral ischemic events, but different sequences or criteria have been used to diagnose or quantify carotid IPH. The purpose of this study was to compare manual segmentation and semi-automatic segmentation for quantification of carotid IPH on magnetization-prepared rapid acquisition with gradient-echo (MPRAGE) sequences. Methods: Forty patients with 16–79% carotid stenosis and IPH on MPRAGE sequences were reviewed by two trained radiologists with more than five years of specialized experience in carotid plaque characterization with carotid plaque MRI. Initially, the radiologists manually viewed the IPH based on the MPRAGE sequence. IPH volume was then measured by three different semi-automatic methods, with high signal intensity 150%, 175%, and 200%, respectively, above that of adjacent muscle on the MPRAGE sequence. Agreement on measurements between manual segmentation and semi-automatic segmentation was assessed using the intraclass correlation coefficient (ICC). Results: There was near-perfect agreement between manual segmentation and the 150% and 175% criteria for semi-automatic segmentation in quantification of IPH volume. The ICC of each semi-automatic segmentation were as follows: 150% criteria: 0.861, 175% criteria: 0.809, 200% criteria: 0.491. The ICC value of manual vs. 150% criteria and manual vs. 175% criteria were significantly better than the manual vs. 200% criteria (p < 0.001). Conclusions: The ICC of 150% and 175% criteria for semi-automatic segmentation are more reliable for quantification of IPH volume. Semi-automatic classification tools may be beneficial in large-scale multicenter studies by reducing image analysis time and avoiding bias between human reviewers.

This paper focuses on quantifying the uncertainty in the specific absorption rate values of brain induced by the uncertain positions of the electroencephalography electrodes placed on patient's scalp. To avoid running a large number of simulations, an artificial neural network architecture for uncertainty quantification involving high-dimensional data is proposed in this paper. The proposed method is demonstrated to be an attractive alternative to conventional uncertainty quantification methods because of its considerable advantage in the computational expense and speed.

Bladder cancer is one of the most common malignant diseases in the urinary system and a highly aggressive neoplasm. The prognosis is not favourable usually and its evolution for particular patients is very difficult to find out. In this paper we propose a dynamic mathematical model that describes the bladder tumor growth and the immune response evolution. This model is customized for a single patient, determining appropriate model parameter values via model calibration. Due to the uncertainty of the tumor evolution, using the calibrated model parameters, we predict the tumor size and the immune response evolution over the next few months assuming three different scenarios: favourable, neutral and unfavourable. In the former, the cancer disappears; in the second a 5mm tumor is expected around the middle of August 2018; in the worst scenario, a 5mm tumor is expected around the end of May 2018. The patient has been cited around June 15th, 2018, to check the tumor size, if it exists.

Over a billion people live in slums, with poor sanitation, education, property rights and working conditions having direct impact on current residents and future generations. A key problem in relation to slums is slum mapping. Without delineations of where all slum settlements are, informed decisions cannot be made by policymakers in order to benefit the most in need. Satellite images have been used in combination with machine learning models to try and fill the gap in data availability of slum locations. Deep learning has been used on RGB images with some success but since labeled satellite images of slums are relatively low quality and the physical/visual manifestation of slums significantly varies within and across countries, it is important to quantify the uncertainty of predictions for reliable application in downstream tasks. Our solution is to train Monte Carlo dropout U-Net models on multispectral 13-band Sentinel-2 images from which we can calculate pixelwise epistemic (model) and aleatoric (data) uncertainty in our predictions. We trained our model on labelled images of Mumbai and verified our epistemic and aleatoric uncertainty quantification approach using altered models trained on modified datasets. We also used SHAP values to investigate how the different features contribute towards the model’s predictions and this showed that certain short-wave infrared and red-edge image bands are powerful features for determining the locations of slums within images. Having created our model with uncertainty quantification, in the future it can be applied to downstream tasks and decision-makers will know where predictions have been made with low uncertainty, giving them greater confidence in its deployment.

The quantity of soil loss as a result of soil erosion is dramatically increasing in catchment where land resources management is very weak. In this paper, a RUSLE model-based soil loss quanti-fication technique is presented to estimate the annual soil loss and identify the severity of the erosion in the catchment. This study uses Fincha catchment in Abay river basin as the study area to quantify the annual soil loss by implementing Revised Universal Soil Loss Equation (RUSLE) model developed in ArcGIS version 10.4. Digital Elevation Model (12.5 x 12.5), LANDSAT 8 of Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS), Annual Rainfall of 10 stations and soil maps of the catchment were used as input parameters to generate the significant factors. Rainfall erosivity factor (R), soil erodibility factor (K), cover and management factor (C), slope length and steepness factor (LS) and support practice factor (P) were used as soil loss quantification significant factors. A model builder for the RUSLE model was developed and raster map calcula-tion algebra was applied in ArcGIS version 10.4 to quantify the total annual soil loss. It was found that the quantified average annual soil loss ranges from 0.0 to 76.5 t ha-1 yr-1 was obtained in the catchment. The area coverage of soil erosion severity with 55%, 35% and 10% as low to moderate, high and very high respectively were identified. The information about the spatial variation of soil loss severity map generated in RUSLE model has a paramount role to alert land resources man-agers and all stakeholders in controlling the effects via implementation of both structural and non-structural mitigations. The results of the RUSLE model can also be further considered along with the catchment for practical soil loss quantification that can help for protection practices.

Atrophy quantification is fundamental for understanding brain development and diagnosing and monitoring brain diseases. FSL-SIENA is a well-known fully-automated method that has been widely used in brain magnetic resonance imaging studies. However, intensity variations arising during image acquisition that may compromise evaluation, analysis and even diagnosis. In this work, we study whether intensity standardisation can improve longitudinal atrophy quantification. We considered seven methods comprising z-score, fuzzy c-means, Gaussian mixture model, kernel density, histogram matching, white stripe, and removal of artificial voxel effects by linear regression (RAVEL). We used a total of 330 scans from two publicly-available datasets, ADNI and OASIS. In scan-rescan assessments, that measures robustness to subtle imaging variations, intensity standardisation did not compromise the robustness of FSL-SIENA significantly (p>0.1). In power analysis assessments, that measures the ability to discern between two groups of subjects, three methods led to consistent improvements in both datasets with respect to the original: fuzzy c-means, Gaussian mixture model, and kernel density estimation. Reduction in sample size using these three methods ranged from 17% to 95%. The performance of the other four methods was affected by spatial normalisation, skull stripping errors, presence of periventricular white matter hyperintensities, or tissue proportion variations over time. Our work evinces the relevance of appropriate intensity standardisation in longitudinal cerebral atrophy assessments using FSL-SIENA.

In proteomics, it is essential to quantify proteins in absolute terms if we wish compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allows protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.

Surrogate model based optimization method is widely-used to accelerate the design and optimization process~\cite{marler2004survey}. The input of regression model used in the surrogate model are numbers, which requires users to parametrize the geometries. In this paper, a new parameterization-free surrogate model is introduced and its corresponding uncertainty quantification and sensitivity analysis method are discussed. The input of new surrogate model methods is surface mesh of simulation domain. \Gls{gnns} is used to extract geometric information, and \Gls{cnns} is used to predict contours. This framework bypasses parameterization,as a consequence, uncertainties introduced by manual parameterization is reduced. However, such changes compared with conventional surrogate model methods impose great challenge on uncertainties quantification and sensitivity analysis. Uncertainties quantification in this paper means the error bar of prediction results, which is calculated by Gaussian Process Regression method in current surrogate method. In this paper, a new quantification method achieved by Kullback-Leibler divergence (KLD) is introduced. And the sensitivity analysis is conducted by Automatic Differentiation, which gives a Jacobian matrix of inputs. The method and analysis mentioned above are demonstrated by a low-pressure steam turbine rotator and its exhaust system.

Isometric exercises for physiotherapeutic rehabilitation are often prescribed, with little quantification of the load being prescribed. This article aimed to provide a framework and practical examples of how the physiotherapist may take a more quantitative evidence-based approach to isometric assessment, monitoring, and exercise prescription of knee osteoarthritis, by integrating a strain gauge into their practice. Strength measures to monitor were discussed. A series of fourteen studies were reviewed, with the intent of identifying isometric exercises that had been utilized in the rehabilitation of knee osteoarthritis. Of the fourteen studies, the three most identified isometric exercises were seated knee extension, knee flexion, and the supine straight leg raise. The integration of strain gauge technology with these exercises provided the focus of the remainder of the article.

Hepatitis-C is one of the most common viral diseases caused by hepatitis C virus (HCV). It is responsible for millions of deaths each year in the developing world. The common dissemination paths of HCV include the use of contaminated water and transfusion of infected blood. Control of this virus has become a challenge for scientists and health professionals due to its versatility and adaptability in different host environments. Along with other problems, lack of efficient diagnosis, quantification and genotyping of viral strains are the major hindrances in a management of this notorious epidemic. The knowledge of HCV genotype and an amount of virus in patient’s blood are pre-requisites to determine the duration and method of treatment. In this review, we discuss the implications of HCV molecular diagnostic methods and their clinical applications. We conclude that while, several commercial and home-brewed methods are available for this purpose, and there is a visible vacuum for cost effective, robust, sensitive assays that can detect multiple viral genotypes in a single reaction. We are of the view that the level of sensitivity offered by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) technique is unequivocal as compared to other techniques. Therefore, researchers may explore further possibilities using this technique in the management of HCV.

Central nervous system (CNS) uses vision, vestibular, and somatosensory information to maintain body stability. Research has shown that there is more lumbar proprioception error among low back pain (LBP) individuals as compared to healthy people. In this study, two groups of 20 healthy people and 20 non-specific low back pain participants (LBP) took part in this investigation. This investigation focused on somatosensory sensors and in order to alter proprioception, a vibrator (frequency of 70Hz, amplitude of 0.5 mm) was placed on the soleus muscle area of each leg and two vibrators were placed bilaterally across the lower back muscles. Individuals, whose vision was occluded, were placed on two surfaces (foam and rigid) on force plate, and trunk angles were recorded simultaneously. Tests were performed in 8 separate trials; the independent variables were vibration (4 levels) and surface (2 levels) for within subjects and 2 groups (healthy and LBP) for between subjects (4×2×2). MANOVA and multi-factor ANOVA tests were done. Linear parameters for center of pressure (COP) (deviation of amplitude, deviation of velocity, phase plane portrait (PPP), and overall mean velocity) and nonlinear parameters for COP and trunk angle ((recurrence quantification analysis) RQA and Lyapunov exponents) were chosen as dependent variables. Results indicated that NSLBP individuals relied more on ankle proprioception for postural stability. Similarly, RQA parameters for the COP on both sides and for the trunk sagittal angle indicated more repeated patterns of movement among the LBP cohort. Analysis of short and long Lyapunov exponents showed that people with LBP caused no use of all joints in their bodies (non-flexible), are less stable than healthy subjects.

Industrial dynamical systems often exhibit multi-scale response due to material heterogeneities, operation conditions and complex environmental loadings. In such problems, it is the case that the smallest length-scale of the systems dynamics controls the numerical resolution required to effectively resolve the embedded physics. In practice however, high numerical resolutions is only required in a confined region of the system where fast dynamics or localized material variability are exhibited, whereas a coarser discretization can be sufficient in the rest majority of the system. To this end, a unified computational scheme with uniform spatio-temporal resolutions for uncertainty quantification can be very computationally demanding. Partitioning the complex dynamical system into smaller easier-to-solve problems based of the localized dynamics and material variability can reduce the overall computational cost. However, identifying the region of interest for high-resolution and intensive uncertainty quantification can be a problem dependent. The region of interest can be specified based on the localization features of the solution, user interest, and correlation length of the random material properties. For problems where a region of interest is not evident, Bayesian inference can provide a feasible solution. In this work, we employ a Bayesian framework to update our prior knowledge on the localized region of interest using measurements and system response. To address the computational cost of the Bayesian inference, we construct a Gaussian process surrogate for the forward model. Once, the localized region of interest is identified, we use polynomial chaos expansion to propagate the localization uncertainty. We demonstrate our framework through numerical experiments on a three-dimensional elastodynamic problem

In this paper, we present a method for detecting and quantifying pathogens in water samples. The method proposes a portable dark field imaging and analysis system for quantifying E. coli concentrations in water after being labeled with magnetic particles. The system utilizes the tracking of moving micro/nano objects close to or below the optical resolution limit confined in small sample volumes (~ 10 µl). In particular, the system analyzes the effect of volumetric changes due to bacteria conjugation to magnetic microparticles (MP) on their Brownian motion while being suspended in liquid buffer solution. The method allows for a simple inexpensive implementation and the possibility to be used as point-of-need testing system. Indeed, a work-ing prototype is demonstrated with the capacity of quantifying E. coli colony forming units (CFU) at a range of 1x10³ - 6x10³ CFU/mL.

We consider a class of density-driven flow problems. We are particularly interested in the problem of the salinization of coastal aquifers. We consider the Henry saltwater intrusion problem with uncertain porosity, permeability, and recharge parameters as a test case. The reason for the presence of uncertainties is the lack of knowledge, inaccurate measurements, and inability to measure parameters at each spatial or time location. This problem is nonlinear and time-dependent. The solution is the salt mass fraction, which is uncertain and changes in time. Uncertainties in porosity, permeability, recharge, and mass fraction are modeled using random fields. This work investigates the applicability of the well-known multilevel Monte Carlo (MLMC) method for such problems. The MLMC method can reduce the total computational and storage costs. Moreover, the MLMC method runs multiple scenarios on different spatial and time meshes and then estimates the mean value of the mass fraction. The parallelization is performed in both the physical space and stochastic space. To solve every deterministic scenario, we run the parallel multigrid solver ug4 in a black-box fashion. We use the solution obtained from the quasi-Monte Carlo method as a reference solution.

RNA editing involves the insertion, deletion or substitution of single nucleotides within a RNA molecule, without altering the DNA sequence. Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. Initially, the A-to-I RNA editing phenomenon was discovered and studied in messenger RNAs (mRNAs), where it can influence RNA splicing and cause the recoding of codon sequences. The employment of more powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.

In this paper we perform numerous numerical studies for the problem of low-rank matrix completion. We compare the Bayesian approaches and a recently introduced de-biased estimator which provides a useful way to build confidence intervals of interest. From a theoretical viewpoint, the de-biased estimator comes with a sharp minimax-optimal rate of estimation error whereas the Bayesian approach reaches this rate with an additional logarithmic factor. Our simulation studies show originally interesting results that the de-biased estimator is just as good as the Bayesian estimators. Moreover, Bayesian approaches are much more stable and can outperform the de-biased estimator in the case of small samples. However, we also find that the length of the confidence intervals revealed by the de-biased estimator for an entry is absolutely shorter than the length of the considered credible interval. These suggest further theoretical studies on the estimation error and the concentration for Bayesian methods as they are being quite limited up to present.

Nanotechnology has enabled the development of novel therapeutic strategies such as targeted nanodrug delivery systems, control and stimulus-responsive release mechanisms, and the production of theranostic agents. As a prerequisite for the use of nanoparticles as drug delivery systems, the amount of loaded drug must be precisely quantified, a task for which two approaches are currently used. However, both approaches suffer from the inefficiencies of drug extraction and of the solid-liquid separation process, as well as from dilution errors. This work describes a new, reliable, and simple method for direct drug quantification in polymeric nanoparticles using attenuated total reflection Fourier transform infrared spectroscopy, which can be adapted for a wide variety of drug delivery systems. Silk fibroin nanoparticles and naringenin were used as model polymeric nanoparticle carrier and drug, respectively. The specificity, linearity, detection limit, precision and accuracy of the spectroscopic approach were determined in order to validate the method. A good linear relation was observed within 0.00 to 7.89 % of naringenin relative mass with an R2 of 0.973. The accuracy was determined by the spike and recovery method. Results showed an average 104% recovery. The limit of detection and limit of quantification of the drug loading content were determined to be 0.3 and 1.0 %, respectively. The method's robustness is demonstrated by the notable similarities between the calibrations carried out in two different equipment and institutions.

Bayesian model calibration techniques are commonly employed in the characterization of nonlinear dynamic systems, as they provide a conceptual and effective framework to deal with model uncertainties, experimental errors and procedure assumptions. This understanding has resulted in the need to introduce a model discrepancy term to account for the differences between model-based predictions and real observations. Indeed, the goal of this work is to enhance model-driven Structural Health Monitoring procedures by incorporating the posterior uncertainty linked to updated model discrepancy, and thus make relevant considerations for its use in the Structural Health Monitoring. Specifically, the Bayesian inference has been applied to the calibration of nonlinear hysteretic systems to both provide: (i) most probable values (MPV) of the parameters following the calibration, and; (ii) estimates of the model discrepancy posterior distribution. The effect of the model discrepancy in the calibration is first illustrated recurring to a single degree of freedom Bouc-Wen type oscillator, and then applied for calibrating a reference nonlinear Bouc-Wen model, deriving from real data acquired on a monitored masonry building.