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Translating the vast data generated by genomic platforms into reliable predictions of clinical outcomes remains a critical challenge in realizing the promise of genomic medicine largely due to small number of independent samples. In this paper, we show that neural networks can be trained to predict clinical outcomes u... |
The novel coronavirus (2019-nCoV) has been declared to be a new international health emergence and no specific drug has been yet identified. Several methods are currently being evaluated such as protease and glycosylated spike (S) protein inhibitors, that outlines the main fusion site among coronavirus and host cells.... |
This technical note introduces parametric dynamic causal modelling, a method for inferring slow changes in biophysical parameters that control fluctuations of fast neuronal states. The application domain we have in mind is inferring slow changes in variables (e.g., extracellular ion concentrations or synaptic efficacy... |
Electrophoretic separation of a mixture of chemical species is a fundamental technique of great usefulness in biology, health care and forensics. In capillary electrophoresis the sample migrates in a microcapillary in the presence of a background electrolyte. |
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. |
Identifying predictive features from high-dimensional datasets is a major task in biomedical research. However, it is difficult to determine the robustness of selected features. |
Metastatic prostate cancer is one of the leading causes of cancer-related morbidity and mortality worldwide. It is characterized by a high mortality rate and a poor prognosis. |
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5 ecosystem, is phconvert, an extensible python library that allows converting p... |
Oscillatory behavior is a key property of many biological systems. The Small-Gain Theorem (SGT) for input/output monotone systems provides a sufficient condition for global asymptotic stability of an equilibrium and hence its violation is a necessary condition for the existence of periodic solutions. |
Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OM... |
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicti... |
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially reflecting disease subtypes that can be captured using MRI and machine learning... |
Aim: Approximately six million people suffer cardiac arrests worldwide per year with very low survival rates (<1%). Thus, the aim of this study is to estimate the probability of a poor outcome after cardiac arrest. |
The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter lea... |
To investigate possible errors, length-weight parameters from <a href="http://FishBase.org" rel="external noopener nofollow" class="link-external link-http">this http URL</a> were used to graph length-weight curves for six different species: channel catfish, black crappie, largemouth bass, rainbow trout, flathead catfi... |
Sleep has been shown to be an indispensable and important component of patients recovery process. Nonetheless, sleep quality of patients in the Intensive Care Unit (ICU) is often low, due to factors such as noise, pain, and frequent nursing care activities. |
We present a novel approach to tackle explainability of deep graph networks in the context of molecule property prediction tasks, named MEG (Molecular Explanation Generator). We generate informative counterfactual explanations for a specific prediction under the form of (valid) compounds with high structural similarit... |
Two non-integer parameters are defined for MAX statistics, which are maxima of $d$ simpler test statistics. The first parameter, $d_{MAX}$, is the fractional number of tests, representing the equivalent numbers of independent tests in MAX. |
The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remain... |
Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for... |
The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks ... |
Persistent homology has been applied to brain network analysis for finding the shape of brain networks across multiple thresholds. In the persistent homology, the shape of networks is often quantified by the sequence of $k$-dimensional holes and Betti <a href="http://numbers.The" rel="external noopener nofollow" class... |
Motivation: We investigate whether a template-based classification pipeline could be used to identify immunophenotypes in (and thereby classify) a heterogeneous disease with many subtypes. The disease we consider here is Acute Myeloid Leukemia, which is heterogeneous at the morphologic, cytogenetic and molecular level... |
Many stochastic systems in physics and biology are investigated by recording the two-dimensional (2D) positions of a moving test particle in regular time intervals. The resulting sample trajectories are then used to induce the properties of the underlying stochastic process. |
Neuronal activity in the brain generates synchronous oscillations of the Local Field Potential (LFP). The traditional analyses of the LFPs are based on decomposing the signal into simpler components, such as sinusoidal harmonics. |
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various tissues. However, scRNA-seq based identification of discrete cell-types is still labor... |
Advances in machine learning have enabled the prediction of immune system responses to prophylactic and therapeutic vaccines. However, the engineering task of designing vaccines remains a challenge. |
In silico methods evaluating the mutation effects of missense mutations are providing an important approach for understanding mutations in personal genomes and identifying disease-relevant biomarkers. However, existing methods, including deep learning methods, heavily rely on sequence-aware information, and do not ful... |
The statistical analysis of the structure of bipartite ecological networks has increased in importance in recent years. Yet, both algorithms and software packages for the analysis of network structure focus on properties of unipartite networks. |
Evapotranspiration (ET) represents the largest water loss flux in drylands, but ET and its partition into plant transpiration (T) and soil evaporation (E) are poorly quantified, especially at fine temporal scales. Physically-based remote sensing models relying on sensible heat flux estimates, like the two-source energ... |
A fibration of graphs is an homomorphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. Recently, it has been shown that graph fibrations are useful tools to uncover symmetries and synchronization patterns in biological networks ra... |
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. |
The aim of this study was to assess the potential environmental impacts associated with high rate algal ponds (HRAP) systems for wastewater treatment and resource recovery in small communities. To this aim, a Life Cycle Assessment (LCA) and an economic assessment were carried out evaluating two alternatives: |
Spike patterns have been reported to encode sensory information in several brain areas. Here we assess the role of specific patterns in the neural code, by comparing the amount of information transmitted with different choices of the readout neural alphabet. |
We present a method for hierarchical clustering of data called {\it mutual information clustering} (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects $X, Y,$ and $Z$ is equal to the sum of the MI between $X$ and $Y$, plus the MI bet... |
Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from c... |
Cerebral autoregulation plays a key physiological role by limiting blood flow changes in the face of pressure fluctuations. Although the involved cellular processes are mechanically driven, the quantification of haemodynamic forces in in-vivo settings remains extremely difficult and uncertain. |
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent progresses in machine learning techniques. RNAglib is a library that eases the use o... |
The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations ... |
Flavor is expressed through interaction of molecules via gustatory and olfactory mechanisms. Knowing the utility of flavor molecules in food and fragrances, it is valuable to add a comprehensive repository of flavor compounds characterizing their flavor profile, chemical properties, regulatory status, consumption stat... |
Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for parameter estimation that return point estimates of the best-fit parameters are insufficient when models are high dimensional and under-const... |
This study proposes a novel stochastic model for the study of hyposmotic hemolysis. This model is capable of reproducing both the kinetics in the transient phase and the lysis equilibrium in the stationary phase, as well as the variability of the experimental measurements. |
An accurate map of intracellular organelle pH is crucial for comprehending cellular metabolism and organellar functions. However, a unified intracellular pH spectrum using a single probe is still lack. |
The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants... |
Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific, isolated biomedical properties. |
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. |
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. |
In situ measurement of cellular metabolites is still a challenge in biology. Conventional methods, such as mass spectrometry or fluorescence microscopy, would either destruct the sample or introduce strong perturbations to the functions of target molecules. |
We exploit Surface-Enhanced Raman Scattering (SERS) to investigate aqueous droplets of genomic DNA deposited onto silver-coated silicon nanowires and we show that it is possible to efficiently discriminate between spectra of tumoral and healthy cells. To assess the robustness of the proposed technique, we develop two ... |
An enduring challenge in computational biology is to balance data quality and quantity with model complexity. Tools such as identifiability analysis and information criterion have been developed to harmonise this juxtaposition, yet cannot always resolve the mismatch between available data and the granularity required ... |
System identification techniques -- projection pursuit regression models (PPRs) and convolutional neural networks (CNNs) -- provide state-of-the-art performance in predicting visual cortical neurons' responses to arbitrary input stimuli. However, the constituent kernels recovered by these methods are often noisy a... |
Motivation: Automatic Anatomical Therapeutic Chemical (ATC) classification is a critical and highly competitive area of research in bioinformatics because of its potential for expediting drug develop-ment and research. Predicting an unknown compound's therapeutic and chemical characteristics ac-cording to how thes... |
This paper presents a novel application of compositional data analysis methods in the context of color image processing. A vector decomposition method is proposed to reveal compositional components of any vector with positive components followed by compositional data analysis to demonstrate the relation between color ... |
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics datasets, guiding feature selection and dimensionality reduction for dynamic mode... |
Brain stroke remains one of the principal causes of death and disability worldwide, yet most tabular-data prediction models still hover below the 95% accuracy threshold, limiting real-world utility. Addressing this gap, the present work develops and validates a completely data-driven and interpretable machine-learning... |
Being motivated by recent progress in nanopore sensing, we develop a theory of the effect of large analytes, or blockers, trapped within the nanopore confines, on diffusion flow of small solutes. The focus is on the nanopore diffusion resistance which is the ratio of the solute concentration difference in the reservoi... |
High-throughput data analyses are becoming common in biology, communications, economics and sociology. The vast amounts of data are usually represented in the form of matrices and can be considered as knowledge networks. |
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, together with other important features, such as small size, short generation time, small genome size, and wide geographic distribution, make it an ideal model organism for unde... |
Quantification of system-wide perturbations from time series -omic data (i.e. a large number of variables with multiple measures in time) provides the basis for many downstream hypothesis generating tools. Here we propose a method, Massively Parallel Analysis of Time Series (MPATS) that can be applied to quantify tran... |
Understanding primate behavior is a mission-critical goal of both biology and biomedicine. Despite the importance of behavior, our ability to rigorously quantify it has heretofore been limited to low-information measures like preference, looking time, and reaction time, or to non-scaleable measures like ethograms. |
Frailty is a geriatric syndrome associated with the lack of physiological reserve and consequent adverse outcomes (therapy complications and death) in older adults. Recent research has shown associations between heart rate (HR) dynamics (HR changes during physical activity) with frailty. |
The random motion of molecules in living cells has consistently been reported to deviate from standard Brownian motion, a behavior coined as ``anomalous diffusion''. Fluorescence Correlation Spectroscopy (FCS) is a powerful method to quantify molecular motions in living cells but its application is limited to ... |
Damage to the inferior frontal gyrus (Broca's area) can cause agrammatic aphasia wherein patients, although able to comprehend, lack the ability to form complete sentences. This inability leads to communication gaps which cause difficulties in their daily lives. |
The noisy dynamics of chemical systems is commonly studied using either the chemical master equation (CME) or the chemical Fokker-Planck equation (CFPE). The latter is a continuum approximation of the discrete CME approach. |
Support vector machines and kernel methods have recently gained considerable attention in chemoinformatics. They offer generally good performance for problems of supervised classification or regression, and provide a flexible and computationally efficient framework to include relevant information and prior knowledge a... |
Recurrent respiratory symptoms are common in infants but the paucity of lung function tests suitable for routine use in infants is a widely acknowledged clinical problem. In this study we evaluated tidal breathing variability (expiratory variability index, EVI) measured at home during sleep using impedance pneumograph... |
Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shib... |
Diversity measurement underpins the study of biological systems, but measures used vary across disciplines. Despite their common use and broad utility, no unified framework has emerged for measuring, comparing and partitioning diversity. |
To better understand and manage complex systems like ecosystems it is critical to know the relative contribution of system components to system functioning. Ecologists and social scientists have described many ways that individuals can be important; This paper makes two key contributions to this research area. |
Biological systems often exhibit a heterogeneous arrangement of objects, such as assorted nuclear chromatin patterns in a tumor, assorted species of bacteria in biofilms, or assorted aggregates of subcellular particles. Principle Component Analysis (PCA) and Multiple Component Analysis (MCA) provide information about ... |
1. Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis, where animal space use is derived from available ha... |
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly sought after as they could yield significant advances in drug discovery and des... |
Optical diffraction tomography (ODT) is a tomographic technique that can be used to measure the three-dimensional (3D) refractive index distribution within living cells without the requirement of any marker. In principle, ODT can be regarded as a generalization of optical projection tomography which is equivalent to c... |
The relation between ecological conditions and geomorphological factors is considered the basis for species distribution in Romania. In this context, the location of each species within parts of the mountain slopes is difficult on a medium to brad scale level. |
Three major biomarkers: beta-amyloid (A), pathologic tau (T), and neurodegeneration (N), are recognized as valid proxies for neuropathologic changes of Alzheimer's disease. While there are extensive studies on cerebrospinal fluids biomarkers (amyloid, tau), the spatial propagation pattern across brain is missing a... |
Protein solubility plays a critical role in improving production yield of recombinant proteins in biocatalyst and pharmaceutical field. To some extent, protein solubility can represent the function and activity of biocatalysts which are mainly composed of recombinant proteins. |
Ecosystem approach to fisheries requires a thorough understanding of fishing impacts on ecosystem status and processes as well as predictive tools such as ecosystem models to provide useful information for management. The credibility of such models is essential when used as decision making tools, and model fitting to ... |
Effective characterisation of the brain grey matter cytoarchitecture with quantitative sensitivity to soma density and volume remains an unsolved challenge in diffusion MRI (dMRI). Solving the problem of relating the dMRI signal with cytoarchitectural characteristics calls for the definition of a mathematical model th... |
Logan's graphical analysis (LGA) is a widely-used approach for quantification of biochemical and physiological processes from Positron emission tomography (PET) image data. A well-noted problem associated with the LGA method is the bias in the estimated parameters. |
We show that the natural scaling of measurement for a particular problem defines the most likely probability distribution of observations taken from that measurement scale. Our approach extends the method of maximum entropy to use measurement scale as a type of information constraint. |
Carotid artery stenosis is the narrowing of carotid arteries, which supplies blood to the neck and head. In this work, we train a model to predict the severity of the stenosis blockage based on SRUC criteria variables and other patient information. |
We have compared a recently developed module-based algorithm LeMoNe for reverse-engineering transcriptional regulatory networks to a mutual information based direct algorithm CLR, using benchmark expression data and databases of known transcriptional regulatory interactions for Escherichia coli and Saccharomyces cerevi... |
Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by... |
One of the key challenges to predict odor from molecular structure is unarguably our limited understanding of the odor space and the complexity of the underlying structure-odor relationships. Here, we show that the predictive performance of machine learning models for structure-based odor predictions can be improved u... |
Acute kidney injury (AKI) commonly occurs in hospitalized patients and can lead to serious medical complications. In order to optimally predict AKI before it develops at any time during a hospital stay, we present a novel framework in which AKI is continually predicted automatically from EHR data over the entire hospi... |
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon, termed dynamic disorder, has become possible due to advances in single-molecule... |
The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational spac... |
Understanding the impact of tumor biology on the composition of nearby cells often requires characterizing the impact of biologically distinct tumor regions. Biomarkers have been developed to label biologically distinct tumor regions, but challenges arise because of differences in the spatial extent and distribution o... |
The aim of the systematic review was to assess recently published studies on diagnostic test accuracy of glioblastoma treatment response monitoring biomarkers in adults, developed through machine learning (ML). Articles were searched for using MEDLINE, EMBASE, and the Cochrane Register. |
In vivo measurements of the passive movements of biomolecules or vesicles in cells consistently report ''anomalous diffusion'', where mean-squared displacements scale as a power law of time with exponent $\alpha< 1$ (subdiffusion). While the detailed mechanisms causing such behaviors are not always ... |
The generation of conformers has been a long-standing interest to structural chemists and biologists alike. A subset of proteins known as intrinsically disordered proteins (IDPs) fail to exhibit a fixed structure and, therefore, must also be studied in this light of conformer generation. |
Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences l... |
With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods suitable for parameter inference with this type of data. However, most of the currently available methods treat s... |
Insect flight is a strongly nonlinear and actuated dynamical system. As such, strategies for understanding its control have typically relied on either model-based methods or linearizations thereof. |
The Implicit Association Test (IAT) is a common behavioral paradigm to assess implicit attitudes in various research contexts. In recent years, researchers have sought to collect IAT data remotely using online applications. |
Objective: This study illustrates the ambiguity of ROC in evaluating two classifiers of 90-day LVAD mortality. This paper also introduces the precision recall curve (PRC) as a supplemental metric that is more representative of LVAD classifiers performance in predicting the minority class. |
DNA-Encoded Library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially-generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads of molecules tagged with unique DNA-barcodes that survive a series of selectio... |
Biological sequence design (DNA, RNA, or peptides) with desired functional properties has applications in discovering novel nanomaterials, biosensors, antimicrobial drugs, and beyond. One common challenge is the ability to optimize complex high-dimensional properties such as target emission spectra of DNA-mediated flu... |
Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Background: The proliferation of archetypes as a means to represent information of Electronic Health Records has raised the need of binding terminological... |
Tongue cancer is a common oral cavity malignancy that originates in the mouth and throat. Much effort has been invested in improving its diagnosis, treatment, and management. |
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