Steps to Facilitate the Use of Clinical Gait Analysis in Stroke Patients: The Validation of a Single 2D RGB Smartphone Video-Based System for Gait Analysis.

Clinical gait analysis plays a central role in the rehabilitation of stroke patients. However, practical and technical challenges limit their use in clinical settings. This study aimed to validate SMARTGAIT, a deep learning-based gait analysis system that addresses these limitations.

AI-smartphone markerless motion capturing of hip, knee, and ankle joint kinematics during countermovement jumps.

Recently, AI-driven skeleton reconstruction tools that use multistage computer vision pipelines were designed to estimate 3D kinematics from 2D video sequences. In the present study, we validated a novel markerless, smartphone video-based artificial intelligence (AI) motion capture system for hip, knee, and ankle angles during countermovement jumps (CMJs). Eleven participants performed six CMJs.

Feasibility Study of a Low-Carbohydrate/Time-Restricted Eating Protocol for Insulin-Using Type 2 Diabetic Patients.

Introduction: Low-carbohydrate diets and time-restricted eating are methods to improve hemoglobin A1C in patients with type 2 diabetes. However, insulin-using patients are often counseled against these practices due to hypoglycemia concerns. This observational study evaluated a protocol utilizing both methods coupled with proactive insulin titration.

Singularity and Commonality in Response to SARS-CoV-2 in Lung and Colon Cell Models.

The systemic nature of COVID-19 with multiple extrapulmonary manifestations of disease, largely due to the wide tissue expression of SARS-CoV-2 major entry factors, as well as the patient-specific features of COVID-19 pathobiology, determine important directions for basic and translational research. In the current study, we addressed the questions of singularities and commonalities in cellular responses to SARS-CoV-2 and related SARS-CoV on the basis of compendium-wide analysis of publicly available transcriptomic datasets as part of the herein implemented multi-modular UNCOVIDING approach. We focused on cellular models attributed to the epithelial cells of the respiratory system, the Calu-3 cell line, and epithelial cells of the gastrointestinal tract, the Caco-2 cell line, infected with either SARS-CoV-2 or SARS-CoV.

AID and APOBECs as Multifaceted Intrinsic Virus-Restricting Factors: Emerging Concepts in the Light of COVID-19.

The AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme catalytic subunit) family with its multifaceted mode of action emerges as potent intrinsic host antiviral system that acts against a variety of DNA and RNA viruses including coronaviruses. All family members are cytosine-to-uracil deaminases that either have a profound role in driving a strong and specific humoral immune response (AID) or restricting the virus itself by a plethora of mechanisms (APOBECs). In this article, we highlight some of the key aspects apparently linking the AID/APOBECs and SARS-CoV-2.

The Immune Phenotype of Isolated Lymphoid Structures in Non-Tumorous Colon Mucosa Encrypts the Information on Pathobiology of Metastatic Colorectal Cancer.

The gut-associated lymphoid tissue represents an integral part of the immune system. Among the powerful players of the mucosa-associated lymphoid tissue are isolated lymphoid structures (ILSs), which as information centers, drive the local (and systemic) adaptive immune responses. Germinal center reactions, taking place within ILSs, involve the coordinated action of various immune cell types with a central role given to B cells.

Interrelations of Sphingolipid and Lysophosphatidate Signaling with Immune System in Ovarian Cancer.

The sphingolipid and lysophosphatidate regulatory networks impact diverse mechanisms attributed to cancer cells and the tumor immune microenvironment. Deciphering the complexity demands implementation of a holistic approach combined with higher-resolution techniques. We implemented a multi-modular integrative approach consolidating the latest accomplishments in gene expression profiling, prognostic/predictive modeling, next generation digital pathology, and systems biology for epithelial ovarian cancer.

AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer.

Background: Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority.

Exploring the role of sphingolipid machinery during the epithelial to mesenchymal transition program using an integrative approach.

The epithelial to mesenchymal transition (EMT) program is activated in epithelial cancer cells and facilitates their ability to metastasize based on enhanced migratory, proliferative, anti-apoptotic, and pluripotent capacities. Given the fundamental impact of sphingolipid machinery to each individual process, the sphingolipid-related mechanisms might be considered among the most prominent drivers/players of EMT; yet, there is still limited knowledge. Given the complexity of the interconnected sphingolipid system, which includes distinct sphingolipid mediators, their synthesizing enzymes, receptors and transporters, we herein apply an integrative approach for assessment of the sphingolipid-associated mechanisms underlying EMT program.

ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions.

Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions.

Large-scale gene expression profiling data for the model moss Physcomitrella patens aid understanding of developmental progression, culture and stress conditions.

The moss Physcomitrella patens is an important model organism for studying plant evolution, development, physiology and biotechnology. Here we have generated microarray gene expression data covering the principal developmental stages, culture forms and some environmental/stress conditions. Example analyses of developmental stages and growth conditions as well as abiotic stress treatments demonstrate that (i) growth stage is dominant over culture conditions, (ii) liquid culture is not stressful for the plant, (iii) low pH might aid protoplastation by reduced expression of cell wall structure genes, (iv) largely the same gene pool mediates response to dehydration and rehydration, and (v) AP2/EREBP transcription factors play important roles in stress response reactions.

Global regulatory architecture of human, mouse and rat tissue transcriptomes.

Background: Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species.

Results: Here, we present a large-scale comparative analysis of organ and tissue transcriptomes involving the three mammalian species human, mouse and rat. To this end, we created a unique, highly standardized compendium of tissue expression.

Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies.

Background: It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a particular purpose. In most cases, the practical application of these ontologies has been limited to systematically storing experimental data.

A multilevel gamma-clustering layout algorithm for visualization of biological networks.

Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings.

The Arabidopsis Rho of plants GTPase AtROP6 functions in developmental and pathogen response pathways.

How plants coordinate developmental processes and environmental stress responses is a pressing question. Here, we show that Arabidopsis (Arabidopsis thaliana) Rho of Plants6 (AtROP6) integrates developmental and pathogen response signaling. AtROP6 expression is induced by auxin and detected in the root meristem, lateral root initials, and leaf hydathodes.

Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome.

Background: Renal cell carcinoma (RCC) is characterized by a number of diverse molecular aberrations that differ among individuals. Recent approaches to molecularly classify RCC were based on clinical, pathological as well as on single molecular parameters. As a consequence, gene expression patterns reflecting the sum of genetic aberrations in individual tumors may not have been recognized.

The importance of size: successful recanalization by intravenous thrombolysis in acute anterior stroke depends on thrombus length.

Background And Purpose: We hypothesize that in acute middle cerebral artery stroke, thrombus lengths measured in thin-slice nonenhanced CT images define a limit beyond which systemic thrombolysis will fail to recanalize occluded arteries.

Methods: In 138 patients who presented with acute middle cerebral artery stroke and who were treated with intravenous thrombolysis (IVT), we measured lengths of thrombotic clots depicted as arterial hyperdensities in admission nonenhanced CT images with 2.5-mm slice width.

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization.

Background: RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts.

The hyperdense anterior cerebral artery sign (HACAS) as a computed tomography marker for acute ischemia in the anterior cerebral artery territory.

Background: Hyperdense arteries in cranial CT of acute stroke patients have been described as a sign for acute ischemia in various brain-feeding arteries. However, only 1 case of a hyperdense anterior cerebral artery sign (HACAS) has been published to date. In this study, the frequency and association of HACAS with clinical symptoms and outcome are described.

Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases.

The wide-spread use of microarray technologies to study plant transcriptomes has led to important discoveries and to an accumulation of profiling data covering a wide range of different tissues, developmental stages, perturbations, and genotypes. Querying a large number of microarray experiments can provide insights that cannot be gained by analyzing single experiments. However, such a meta-analysis poses significant challenges with respect to data comparability and normalization, systematic sample annotation, and analysis tools.

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys.

Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.

The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis.

Network analysis of systems elements.

A central goal of postgenomic research is to assign a function to every predicted gene. Because genes often cooperate in order to establish and regulate cellular events the examination of a gene has also included the search for at least a few interacting genes. This requires a strong hypothesis about possible interaction partners, which has often been derived from what was known about the gene or protein beforehand.