4,769 results match your criteria Acm Transactions On Algorithms[Journal]


Activation of astrocytic sigma-1 receptor exerts antidepressant-like effect via facilitating CD38-driven mitochondria transfer.

Glia 2020 May 27. Epub 2020 May 27.

Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.

Despite sigma-1 receptor (Sig-1R) is a promising therapeutic target in depression, little is known regarding the cellular mechanisms underlying its antidepressant responses. Here, we demonstrated that astrocyte can be a direct cellular target of Sig-1R exerting antidepressant-like effect. In multiple behavioral models including forced swimming test (FST), tail suspension test (TST), open field test (OFT), and chronic unpredictable mild stress (CUMS), inhibition of astrocyte function blocked pharmacological Sig-1R activation-induced antidepressant-like effect, while specific activation of astrocytc Sig-1R by adeno-associated virus (AAV) was sufficient to produce antidepressant-like effect. Read More

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http://dx.doi.org/10.1002/glia.23850DOI Listing

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.

ACM BCB 2019 Sep;2019:144-153

Computational Biology Department, Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA.

Protein complexes play a significant role in the core functionality of cells. These complexes are typically identified by detecting densely connected subgraphs in protein-protein interaction (PPI) networks. Recently, multiple large-scale mass spectrometry-based experiments have significantly increased the availability of PPI data in order to further expand the set of known complexes. Read More

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http://dx.doi.org/10.1145/3307339.3342150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7249224PMC
September 2019

Identification of the Destruction Model of Ventilated Facade under the Influence of Fire.

Materials (Basel) 2020 May 22;13(10). Epub 2020 May 22.

Faculty of Civil Engineering, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.

Ventilated facades are becoming an increasingly popular solution for external part of walls in the buildings. They may differ in many elements, among others things: claddings (fiber cement boards, HPL plates, large-slab ceramic tiles, ACM panels, stone cladding), types of substructures, console supports, etc. The main part that characterizes ventilated facades is the use of an air cavity between the cladding and thermal insulation. Read More

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http://dx.doi.org/10.3390/ma13102387DOI Listing

Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated Mutation.

Genes (Basel) 2020 May 20;11(5). Epub 2020 May 20.

Cardiac Arrhythmia Research Centre, Centro Cardiologico Monzino IRCCS, 20141 Milan, Italy.

Plakophilin-2 () is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the p. Read More

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http://dx.doi.org/10.3390/genes11050571DOI Listing

micro-Stress EMA: A Passive Sensing Framework for Detecting in-the-wild Stress in Pregnant Mothers.

Proc ACM Interact Mob Wearable Ubiquitous Technol 2019 Sep;3(3)

Northwestern University, United States.

High levels of stress during pregnancy increase the chances of having a premature or low-birthweight baby. Perceived self-reported stress does not often capture or align with the physiological and behavioral response. But what if there was a self-report measure that could better capture the physiological response? Current perceived stress self-report assessments require users to answer multi-item scales at different time points of the day. Read More

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http://dx.doi.org/10.1145/3351249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236910PMC
September 2019

Probabilistic Human Intent Recognition for Shared Autonomy in Assistive Robotics.

ACM Trans Hum Robot Interact 2019 Dec;9(1)

Northwestern University, USA and Shirley Ryan AbilityLab, USA.

Effective human-robot collaboration in shared autonomy requires reasoning about the intentions of the human partner. To provide meaningful assistance, the autonomy has to first correctly predict, or infer, the intended goal of the human collaborator. In this work, we present a mathematical formulation for intent inference during assistive teleoperation under shared autonomy. Read More

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http://dx.doi.org/10.1145/3359614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233691PMC
December 2019

Explainable artificial intelligence models using real-world electronic health record data: a systematic scoping review.

J Am Med Inform Assoc 2020 May 17. Epub 2020 May 17.

School of Information, Florida State University, Tallahassee, Florida, USA.

Objective: To conduct a systematic scoping review of explainable artificial intelligence (XAI) models that use real-world electronic health record data, categorize these techniques according to different biomedical applications, identify gaps of current studies, and suggest future research directions.

Materials And Methods: We searched MEDLINE, IEEE Xplore, and the Association for Computing Machinery (ACM) Digital Library to identify relevant papers published between January 1, 2009 and May 1, 2019. We summarized these studies based on the year of publication, prediction tasks, machine learning algorithm, dataset(s) used to build the models, the scope, category, and evaluation of the XAI methods. Read More

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http://dx.doi.org/10.1093/jamia/ocaa053DOI Listing

P-wave axis is associated with all-cause mortality in diabetes: The ACCORD trial.

J Electrocardiol 2020 May 1;60:184-187. Epub 2020 May 1.

Section of Cardiology, Department of Internal Medicine, Wake Forest School of Medicine, NC, United States of America. Electronic address:

Abnormal P-wave axis (PWA) has emerged as a novel marker of risk for both cardiovascular disease (CVD) and all-cause mortality (ACM) in the general population, though this relationship has not been adequately explored among those with type 2 diabetes (DM2). We aimed to explore the association between abnormal PWA and ACM among a large, well-phenotyped group of participants with DM2 from the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. This analysis included 8899 ACCORD participants with available PWA data on baseline electrocardiogram. Read More

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http://dx.doi.org/10.1016/j.jelectrocard.2020.04.023DOI Listing

Resolution of Tonsillar Herniation and Syringomyelia Following Resection of a Large Anterior Frontal Parasagittal Meningioma.

Cureus 2020 Apr 11;12(4):e7636. Epub 2020 Apr 11.

Neurosurgery, New York University (NYU) School of Medicine, New York, USA.

Chiari I malformation is the herniation of cerebellar tonsils below the level of the foramen magnum due to congenital or acquired pathologies. Acquired Chiari I malformation (ACM) may occur secondary to space-occupying lesions (SOLs), such as intracranial tumors due to elevated intracranial pressure (ICP), and can be accompanied by syringomyelia. ACM and syringomyelia have been shown to resolve after resection of the SOL, without the need for adjuvant posterior fossa decompression. Read More

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http://dx.doi.org/10.7759/cureus.7636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7213766PMC

Integrative Biological Network Analysis to Identify Shared Genes in Metabolic Disorders.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 8. Epub 2020 May 8.

Identification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). Read More

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http://dx.doi.org/10.1109/TCBB.2020.2993301DOI Listing

Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings from a Multiple Sequence Alignment.

Authors:
Sanzo Miyazawa

IEEE/ACM Trans Comput Biol Bioinform 2020 May 8. Epub 2020 May 8.

The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protein structure and evolution. We study regularization and learning methods and how to tune regularization parameters to correctly infer interactions in Boltzmann machine learning. Using L regularization for fields, group L for couplings is shown to be very effective for sparse couplings in comparison with L and L . Read More

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http://dx.doi.org/10.1109/TCBB.2020.2993232DOI Listing

EBST: An Evolutionary Multi-Objective Optimization Based Tool for Discovering Potential Biomarkers in Ovarian Cancer.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 7. Epub 2020 May 7.

Ovarian cancer is the deadliest gynecologic malignancy, mainly due to limitations in early diagnosis. With advances in high-throughput technologies, research interest in identifying novel and customized tumor biomarkers for early detection and diagnosis is rapidly growing. Here we introduce a new tool called EBST to select microRNAs with biomarker potency in ovarian cancer. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2993150DOI Listing

Sorting Signed Permutations by Intergenic Reversals.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 7. Epub 2020 May 7.

Genome rearrangements are mutations affecting large portions of a genome, and a reversal is one of the most studied genome rearrangements in the literature through the Sorting by Reversals (SbR) problem. SbR is solvable in polynomial time on signed permutations (i.e. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2993002DOI Listing

Functional culture and in vitro genetic and small-molecule manipulation of adult mouse cardiomyocytes.

Commun Biol 2020 May 11;3(1):229. Epub 2020 May 11.

Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, Canada.

Primary adult cardiomyocyte (aCM) represent the mature form of myocytes found in the adult heart. However, culture of aCMs in particular is challenged by poor survival and loss of phenotype, rendering extended in vitro experiments unfeasible. Here, we establish murine aCM culture methods that enhance survival and maintain sarcomeric structure and Ca cycling to enable physiologically relevant contractile force measurements. Read More

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http://dx.doi.org/10.1038/s42003-020-0946-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214405PMC

Comparing phylogenetic approaches to reconstructing cell lineage from microsatellites with missing data.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 6. Epub 2020 May 6.

Due to the imperfect fidelity of DNA replication, somatic cells acquire DNA mutations at each division which record their lineage history. Microsatellites, tandem repeats of DNA nucleotide motifs, mutate more frequently than other genomic regions and by observing microsatellite lengths in single cells and implementing suitable inference procedures, the cell lineage tree of an organism can be reconstructed. Due to recent advances in single cell Next Generation Sequencing (NGS) and the phylogenetic methods used to infer lineage trees, this work investigates which computational approaches best exploit the lineage information found in single cell NGS data. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2992813DOI Listing

Unsupervised learning framework with multidimensional scaling in predicting epithelial-mesenchymal transitions.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 6. Epub 2020 May 6.

Clustering tumor metastasis samples from gene expression data at the whole genome level remains an arduous challenge, in particular, when the number of experimental samples is small and the number of genes is huge. We focus on the prediction of the epithelial-mesenchymal transition (EMT), which is an underlying mechanism of tumor metastasis, here, rather than tumor metastasis itself, to avoid confounding effects of uncertainties derived from various factors. In this paper, we propose a novel model in predicting EMT based on multidimensional scaling (MDS) strategies and integrating entropy and random matrix detection strategies to determine the optimal reduced number of dimension in low dimensional space. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2992605DOI Listing
May 2020
1.438 Impact Factor

Multi-objective Simulated Annealing Variants to Infer Gene Regulatory Network: A Comparative Study.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 4. Epub 2020 May 4.

Gene Regulatory Network (GRN) is formed due to mutual transcriptional regulation within a set of protein coding genes in cellular context of an organism. Computational inference of GRN is important to understand the behavior of each gene in terms of change in its protein production rate (expression level). As Recurrent Neural Network (RNN) is efficient in GRN modeling, a bi-objective RNN formulation has been applied here. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2992304DOI Listing

Serum iron concentration in cattle with endotoxaemia.

Acta Vet Hung 2020 May 4. Epub 2020 May 4.

School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunnkyoudai, Ebetsu, Hokkaido, 069-8501, Japan.

The objective of this study was to examine whether serum iron (Fe) concentration is useful as a prognostic biomarker for cows with acute coliform mastitis (ACM). Our study was composed of determining the reproducibility of serum Fe concentration as a prognostic criterion in cows with ACM (Study 1) and clarifying the sequential changes in serum Fe concentration in cattle that received endotoxin (Study 2). Seventy-seven cows with (n = 47) or without (n = 30) ACM were enrolled in Study 1. Read More

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http://dx.doi.org/10.1556/004.2020.00016DOI Listing

High-frequency repetitive transcranial magnetic stimulation improves functional recovery by inhibiting neurotoxic polarization of astrocytes in ischemic rats.

J Neuroinflammation 2020 May 6;17(1):150. Epub 2020 May 6.

Department of Neurology, Jingling Hospital, Nanjing University School of Medicine, 305# East Zhongshan Road, Nanjing, 210002, Jiangsu, China.

Background: Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive treatment for ischemic stroke. Astrocytes regulation has been suggested as one mechanism for rTMS effectiveness. But how rTMS regulates astrocytes remains largely undetermined. Read More

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http://dx.doi.org/10.1186/s12974-020-01747-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203826PMC

On accident causation models, safety training and virtual reality.

Int J Occup Saf Ergon 2020 May 6:1-32. Epub 2020 May 6.

Department of Industrial and Systems Engineering, Indian Institute of Technology Kharagpur, West Bengal, 721302.

Inefficiency in real-time visualization and user interaction in traditional accident causation models (ACMs) necessitates the development of a dynamic accident causation model, which can foster real-time hazard identification, accident prevention, and interactive safety training. A virtual reality (VR) based accident causation model (VR-ACM) may serve such purpose. In this study, we have done a comprehensive literature review on different ACMs and safety training practices. Read More

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http://dx.doi.org/10.1080/10803548.2020.1766290DOI Listing

ALT-to-Lymphocyte Ratio as a Predictor of Long-Term Mortality in Patients with Normal Liver Function Presenting Coronary Artery Disease after Undergoing PCI: A Retrospective Cohort Study.

J Interv Cardiol 2020 21;2020:4713591. Epub 2020 Apr 21.

Department of Cardiology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.

Background: Alanine aminotransferase (ALT) is referred as liver transaminase and predominantly expressed by hepatocytes. Previous evidences showed that high levels of ALT were reversely associated with short- and long-term outcomes in patients with myocardial infarction. Besides, low lymphocyte has been demonstrated to be significantly correlated with adverse clinical outcomes in coronary artery disease (CAD). Read More

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http://dx.doi.org/10.1155/2020/4713591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193295PMC

Netboost: Boosting-supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 1. Epub 2020 May 1.

State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. We present Netboost, a three-step dimension reduction technique. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2983010DOI Listing

Prolonged astrocyte-derived erythropoietin expression attenuates neuronal damage under hypothermic conditions.

J Neuroinflammation 2020 May 2;17(1):141. Epub 2020 May 2.

Department of Pathobiology, Nagoya City University Graduate School of Pharmaceutical Sciences, 3-1 Tanabedori, Mizoho-ku, Nagoya, Aichi, 467-8603, Japan.

Background: Hypoxic-ischemic encephalopathy (HIE) has a high morbidity rate and involves severe neurologic deficits, including cerebral palsy. Therapeutic hypothermia (TH) has been shown to decrease the mortality rate and provide neuroprotection in infants with HIE. However, death and disability rates in HIE infants treated with TH remain high. Read More

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http://dx.doi.org/10.1186/s12974-020-01831-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195727PMC

Cluster Detection Mechanisms for Syndromic Surveillance Systems: Systematic Review and Framework Development.

JMIR Public Health Surveill 2020 May 26;6(2):e11512. Epub 2020 May 26.

Department of Computer Science, University of Tromsø, The Arctic University of Norway, Gjøvik, Norway.

Background: The time lag in detecting disease outbreaks remains a threat to global health security. The advancement of technology has made health-related data and other indicator activities easily accessible for syndromic surveillance of various datasets. At the heart of disease surveillance lies the clustering algorithm, which groups data with similar characteristics (spatial, temporal, or both) to uncover significant disease outbreak. Read More

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http://dx.doi.org/10.2196/11512DOI Listing

Protein Fold Recognition Based on Auto-Weighted Multi-view Graph Embedding Learning Model.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 29. Epub 2020 Apr 29.

Protein fold recognition is critical for studies of the protein structure prediction and drug design. Several methods have been proposed to obtain discriminative features from the protein sequences for fold recognition. However, the ensemble methods that combine the various features to improve predictive performance remain the challenge problems. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2991268DOI Listing

Understanding the Limit of Open Search in the Identification of Peptides with Post-translational Modifications - A Simulation-based Study.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 29. Epub 2020 Apr 29.

Peptide identification from tandem mass spectrometry data is a fundamental task in computational proteomics. Traditional algorithms perform well when facing unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2991207DOI Listing

A Transfer Learning Based Super-Resolution Microscopy for Biopsy Slice Images: The Joint Methods Perspective.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 29. Epub 2020 Apr 29.

Biopsy slices are widely used in medical practice. Higher-resolution biopsy slice images reveal many details, which are helpful to doctors and scientists. However, it is time-consuming to take the high-resolution slice images. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2991173DOI Listing

The additive value of restaging-CT during neoadjuvant chemotherapy for gastric cancer.

Eur J Surg Oncol 2020 Apr 14. Epub 2020 Apr 14.

Department of Surgery, University Medical Center Utrecht, Utrecht, the Netherlands. Electronic address:

Introduction: Computed tomography (CT) is used for restaging of gastric cancer patients during neoadjuvant chemotherapy (NAC). The treatment strategy could be altered after detection of distant interval metastases, possibly leading to a reduction in unnecessary chemotherapy cycles, its related toxicity, and surgical procedures. The aim of this study was to evaluate the additive value of restaging-CT during NAC in guiding clinical decision making in gastric cancer. Read More

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http://dx.doi.org/10.1016/j.ejso.2020.04.002DOI Listing

A Systematic Review of Health Dialog Systems.

Methods Inf Med 2019 Dec 29;58(6):179-193. Epub 2020 Apr 29.

Department of Biobehavioral Health Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States.

Background:  Health dialog systems have seen increased adoption by patients, hospitals, and universities due to the confluence of advancements in machine learning and the ubiquity of high-performance hardware that supports real-time speech recognition, high-fidelity text-to-speech, and semantic understanding of natural language.

Objectives:  This review seeks to enumerate opportunities to apply dialog systems toward the improvement of health outcomes while identifying both gaps in the current literature that may impede their implementation and recommendations that may improve their success in medical practice.

Methods:  A search over PubMed and the ACM Digital Library was conducted on September 12, 2017 to collect all articles related to dialog systems within the domain of health care. Read More

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http://dx.doi.org/10.1055/s-0040-1708807DOI Listing
December 2019

Influences on the Uptake of and Engagement With Health and Well-Being Smartphone Apps: Systematic Review.

J Med Internet Res 2020 Mar 23. Epub 2020 Mar 23.

School of Health Sciences, University of East Anglia, Norwich Research Park, Norwich, GB.

Background: The public health impact of health and well-being digital interventions is dependent upon sufficient real-world uptake and engagement. Uptake is currently largely dependent on popularity indicators (eg, ranking and user ratings on app stores), which may not correspond with effectiveness, and rapid disengagement is common. Therefore, there is an urgent need to identify factors that influence uptake and engagement with health and well-being apps to inform new approaches that promote the effective use of such tools. Read More

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http://dx.doi.org/10.2196/17572DOI Listing

Human iPSCs derived astrocytes rescue rotenone-induced mitochondrial dysfunction and dopaminergic neurodegeneration in vitro by donating functional mitochondria.

Transl Neurodegener 2020 Apr 24;9(1):13. Epub 2020 Apr 24.

Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA, 95817, USA.

Background: Parkinson's disease (PD) is one of the neurodegeneration diseases characterized by the gradual loss of dopaminergic (DA) neurons in the substantia nigra region of the brain. Substantial evidence indicates that at the cellular level mitochondrial dysfunction is a key factor leading to pathological features such as neuronal death and accumulation of misfolded α-synuclein aggregations. Autologous transplantation of healthy purified mitochondria has shown to attenuate phenotypes in vitro and in vivo models of PD. Read More

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http://dx.doi.org/10.1186/s40035-020-00190-6DOI Listing

Prediction of drug-target interactions based on network representation learning and ensemble learning.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 23. Epub 2020 Apr 23.

Identifying interactions between drugs and target proteins is a critical step in the drug development process, as it helps identify new targets for drugs and accelerate drug development. The number of known drug-protein interactions (positive samples) is much lower than that of the unknown ones (negative samples), which forms a class imbalance. Most previous methods only utilised part of the negative samples to train the prediction model, so most of the information on negative samples was neglected. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2989765DOI Listing

Facile Mixing of Phospholipids Promotes Self-Assembly of Low-Molecular-Weight Biodegradable Block Co-Polymers into Functional Vesicular Architectures.

Polymers (Basel) 2020 Apr 22;12(4). Epub 2020 Apr 22.

Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore.

In this work, we have used low-molecular-weight (PEG--PCL, PEG--PCL or PEG--PLA; M, 1.25-3.45 kDa) biodegradable block co-polymers to construct nano- and micron-scaled hybrid (polymer/lipid) vesicles, by solvent dispersion and electroformation methods, respectively. Read More

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http://dx.doi.org/10.3390/polym12040979DOI Listing

Convolutional Neural Network with Graphical Lasso to Extract Sparse Topological Features for Brain Disease Classification.

Authors:
Junzhong Ji Yao Yao

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 21. Epub 2020 Apr 21.

The functional connectivity provides new insights into the mechanisms of the human brain at network-level, which has been proved to be an effective biomarker for brain disease classification. Recently, machine learning methods have played an important role in functional connectivity classification, among which convolutional neural network (CNN) based methods become a new hot topic since they can extract topological features in the brain network. However, the conventional CNN-based methods haven't taken sparse connectivity patterns (SCPs) of the human brain into consideration, which may lead to redundancy of the topological features, and limit their performance and generalization. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2989315DOI Listing

Manipulating extracellular matrix organizations and parameters to control local cancer invasion.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 21. Epub 2020 Apr 21.

Metastasis contributes to over 90% of cancer mortalities and may be influenced by the extracellular matrix (ECM). ECM microenvironments differ in matrix organization, cell-matrix adhesions, and fiber rigidity, which may affect cancer migration and, thus, should be investigated. To understand the interactions between cancer cells and the ECM, we simulate local invasion through ECM organizations of varying determinants. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2989223DOI Listing

A Convolutional Deep Clustering Framework for Gene Expression Time Series.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 21. Epub 2020 Apr 21.

The functional or regulatory processes within the cell are explicitly governed by the expression levels of a subset of its genes. Gene expression time series captures activities of individual genes over time and aids revealing underlying cellular dynamics. An important step in high-throughput gene expression time series experiment is clustering genes based on their temporal expression patterns and is conventionally achieved by unsupervised machine learning techniques. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2988985DOI Listing

Computing the Inversion-Indel Distance.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 21. Epub 2020 Apr 21.

The inversion distance, that is the distance between two genomes with the same content allowing only inversions of DNA segments, can be exactly computed thanks to an approach of Hannenhalli and Pevzner from 1995. In 2000, El-Mabrouk extended the inversion model to perform the comparison of genomes with unequal contents, combining inversions with insertions and deletions (indels) of DNA segments, giving rise to the inversion-indel distance. However, only a heuristic was provided for its computation. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2988950DOI Listing

A Novel Feature Selection Method for Uncertain Features: An Application to the Prediction of Pro-/Anti- Longevity Genes.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 20. Epub 2020 Apr 20.

Understanding the ageing process is a very challenging problem for biologists. To help in this task, there has been a growing use of classification methods (from machine learning) to learn models that predict whether a gene influences the process of ageing or promotes longevity. One type of predictive feature often used for learning such classification models is Protein-Protein Interaction (PPI) features. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2988450DOI Listing

SNP data science for classification of bipolar disorder I and bipolar disorder II.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 20. Epub 2020 Apr 20.

Bipolar disorder I (BD-I) and bipolar disorder II (BD-II) have specific characteristics and clear diagnostic criteria, but quite different treatment guidelines. In clinical practice, BD-II is commonly mistaken as a mild form of BD-I. This study uses data science technique to identify the important Single Nucleotide Polymorphisms (SNPs) significantly affecting the classifications of BD-I and BD-II, and develops a set of complementary diagnostic classifiers to enhance the diagnostic process. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2988024DOI Listing

Analysis of a catastrophic commercial coach crash based on an improved accident causation model (ACM): Causes classification and lessons learned.

Int J Occup Saf Ergon 2020 Apr 23:1-21. Epub 2020 Apr 23.

School of Transportation and Logistics Engineering, Shandong Jiaotong University, China.

IntroductionThis study aimed to perform an in-depth analysis on a catastrophic coach crash that occurred on the Chinese expressway, and thus, useful lessons can be drawn to avoid similar mistakes. Various causes were identified from the investigation report based on a proposed accident causation model (ACM) which provides a universal pathway for accident analysis from the individual level to the organizational level. The driver's error in an emergency affected by the fatigue and speeding led to the crash directly. Read More

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http://dx.doi.org/10.1080/10803548.2020.1759314DOI Listing

To Mask or Not to Mask? Balancing Privacy with Visual Confirmation Utility in Activity-Oriented Wearable Cameras.

Proc ACM Interact Mob Wearable Ubiquitous Technol 2019 Sep;3(3)

Northwestern University.

Activity-oriented cameras are increasingly being used to provide visual confirmation of specific hand-related activities in real-world settings. However, recent studies have shown that bystander privacy concerns limit participant willingness to wear a camera. Researchers have investigated different image obfuscation methods as an approach to enhance bystander privacy; however, these methods may have varying effects on the visual confirmation utility of the image, which we define as the ability of a human viewer to interpret the activity of the wearer in the image. Read More

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http://dx.doi.org/10.1145/3351230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173332PMC
September 2019

Fibrosis in Arrhythmogenic Cardiomyopathy: The Phantom Thread in the Fibro-Adipose Tissue.

Front Physiol 2020 3;11:279. Epub 2020 Apr 3.

Vascular Biology and Regenerative Medicine Unit, Centro Cardiologico Monzino IRCCS, Milan, Italy.

Arrhythmogenic cardiomyopathy (ACM) is an inherited heart disorder, predisposing to malignant ventricular arrhythmias leading to sudden cardiac death, particularly in young and athletic patients. Pathological features include a progressive loss of myocardium with fibrous or fibro-fatty substitution. During the last few decades, different clinical aspects of ACM have been well investigated but still little is known about the molecular mechanisms that underlie ACM pathogenesis, leading to these phenotypes. Read More

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http://dx.doi.org/10.3389/fphys.2020.00279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147329PMC

A Titanium Metal-Organic Framework with Visible-Light-Responsive Photocatalytic Activity.

Angew Chem Int Ed Engl 2020 Apr 21. Epub 2020 Apr 21.

Advanced Catalytic Materials, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.

The one-step synthesis and characterization of a new and robust titanium-based metal-organic framework, ACM-1, is reported. In this structure, which is based on infinite Ti-O chains and 4,4',4'',4'''-(pyrene-1,3,6,8-tetrayl) tetrabenzoic acid as a photosensitizer ligand, the combination of highly mobile photogenerated electrons and a strong hole localization at the organic linker results in large charge-separation lifetimes. The suitable energies for band gap and conduction band minimum (CBM) offer great potential for a wide range of photocatalytic reactions, from hydrogen evolution to the selective oxidation of organic substrates. Read More

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http://dx.doi.org/10.1002/anie.202000158DOI Listing
April 2020
11.261 Impact Factor

Might definitive local therapy of the primary tumor improve the survival benefits of metastatic prostate cancer? -evidence from a meta-analysis.

Ann Palliat Med 2020 Apr 20. Epub 2020 Apr 20.

Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.

Background: With the successful application of local therapy (LT) of the primary tumor in other metastatic disease and the demonstration of their better survival benefits, the traditionally seldom involved role of LT for metastatic prostate cancer (mPCa) had gained a lot of interest. Hence, this meta-analysis was conducted to clarify its efficacy in mPCa.

Methods: A comprehensive search of major databases (PubMed, EMBASE and Web of Science) was conducted for eligible studies, up to May 2019. Read More

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http://dx.doi.org/10.21037/apm.2020.04.21DOI Listing

Predicting drug-drug interactions based on integrated similarity and semi-supervised learning.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 16. Epub 2020 Apr 16.

A drug-drug interaction (DDI) is defined as an association between two drugs where the pharmacological effects of a drug are influenced by another drug. Positive DDIs can usually improve the therapeutic effects of patients, but negative DDIs cause the major cause of adverse drug reactions and even result in drugs withdrawal from market and the patient death. Therefore, identifying DDIs has become a key process to the drug development and disease treatment. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2988018DOI Listing

Continuous Hydrogenation of Aqueous Furfural Using a Metal-Supported Activated Carbon Monolith.

ACS Omega 2020 Apr 3;5(14):7836-7849. Epub 2020 Apr 3.

Biochemical Engineering, College of Engineering Driftmier Engineering Center, The University of Georgia, 597 D.W. Brooks Drive, Athens, Georgia 30602, United States.

Continuous hydrogenation of aqueous furfural (4.5%) was studied using a monolith form (ACM) of an activated carbon Pd catalyst (∼1.2% Pd). Read More

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http://dx.doi.org/10.1021/acsomega.9b04010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160850PMC

Identifying Microbe-Disease Association Based on a Novel Back-Propagation Neural Network Model.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 13. Epub 2020 Apr 13.

Over the years, numerous evidences have demonstrated that microbes living in the human body are closely related to human life activities and human diseases. However, traditional biological experiments are time-consuming and expensive, so it has become a research topic in bioinformatics to predict potential microbe-disease associations by adopting computational methods. In this study, a novel calculative method called BPNNHMDA is proposed to identify potential microbe-disease associations. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2986459DOI Listing

Identifying molecular biomarkers for diseases with machine learning based on integrative omics.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 14. Epub 2020 Apr 14.

Molecular biomarkers are certain molecules or set of molecules that can be of help for diagnosis or prognosis of diseases or disorders. In the past decades, thanks to the advances in high-throughput technologies, a huge amount of molecular 'omics' data, e.g. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2986387DOI Listing

Multi-neighborhood Learning for Global Alignment in Biological Networks.

IEEE/ACM Trans Comput Biol Bioinform 2020 Apr 14. Epub 2020 Apr 14.

The global alignment of biological networks (GABN) aims to find an optimal alignment between proteins across species, such that both the biological structures and the topological structures of the proteins are maximally conserved. The research on GABN has attracted great attention due to its applications on species evolution, orthology detection and genetic analyses. Most of the existing methods for GABN are difficult to obtain a good tradeoff between the conservation of the biological structures and topological structures. Read More

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http://dx.doi.org/10.1109/TCBB.2020.2985838DOI Listing

A comparison of stage-specific all-cause mortality between testicular sex cord stromal tumors and germ cell tumors: results from the National Cancer Database.

BMC Urol 2020 Apr 17;20(1):40. Epub 2020 Apr 17.

Department of Urology, University of California, San Francisco, 550 16th Street, 6th Floor, San Francisco, CA, 94158, USA.

Background: Testicular sex cord stromal tumors (SCSTs) are managed similarly to germ cell tumors (GCTs); however, few studies have directly compared outcomes between these tumor types. Using the National Cancer Database (NCDB), we sought to compare overall and stage-specific all-cause mortality (ACM) between SCSTs versus GCTs.

Methods: NCDB was queried for patients diagnosed with SCSTs and GCTs between 2004 and 2013. Read More

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http://dx.doi.org/10.1186/s12894-020-00609-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164279PMC