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ACM BCB 2019 Sep;2019:485-493

Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332.

Breast cancer is a deadly disease that affects millions of women worldwide. The International Conference on Image Analysis and Recognition in 2018 presents the BreAst Cancer Histology (ICIAR2018 BACH) image data challenge that calls for computer tools to assist pathologists and doctors in the clinical diagnosis of breast cancer subtypes. Using the BACH dataset, we have developed an image classification pipeline that combines both a shallow learner (support vector machine) and a deep learner (convolutional neural network). Read More

Spinal Cord Ser Cases 2019 Jul 9;5(1):65. Epub 2019 Jul 9.

Stoke Mandeville Hospital, Buckinghamshire Healthcare NHS Trust, Aylesbury, UK.

Introduction: Chiari malformation is characterized by caudal descent of the cerebellar tonsils through the foramen magnum. Acquired Chiari malformations (ACM) have previously been described after a variety of pathologies including lumbar puncture, cerebrospinal fluid (CSF) drainage, lumboperitoneal shunts, and conditions causing craniocephalic disproportion.

Case Presentation: We present four cases of ACM following spinal cord injury (SCI), which has not previously been described in the literature. Read More

Acta Neurol Belg 2020 Jul 6. Epub 2020 Jul 6.

Laboratory for Epilepsy Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.

Epilepsy affects 50 million patients and their caregivers worldwide. Devices that facilitate the detection of seizures can have a large influence on a patient's quality of life, therapeutic decisions and the conduct of clinical trials with anti-epileptic drugs. This article provides an up-to-date overview and comparison between wearable seizure detection devices (WSDDs), taking into account the newly proposed standards for testing and clinical validation of devices. Read More

PLoS One 2020 6;15(7):e0235852. Epub 2020 Jul 6.

Department of Pediatrics, Division of Neonatology, Developmental Vascular Biology Program, Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America.

The medulloblastoma (MB) microenvironment is diverse, and cell-cell interactions within this milieu is of prime importance. Astrocytes, a major component of the microenvironment, have been shown to impact primary tumor cell phenotypes and metastasis. Based on proximity of MB cells and astrocytes in the brain microenvironment, we investigated whether astrocytes may influence MB cell phenotypes directly. Read More

Physiother Theory Pract 2020 Jul 6:1-13. Epub 2020 Jul 6.

Physical Therapy Department, Aspirus Langlade Health and Rehabilitation , Antigo, WI, USA.

Introduction: Upright infant active cervical motion (ACM) is difficult to measure accurately by a single examiner. Clinically, physical therapists use visual estimation, which has limited reliability and concurrent validity with gold standards. Consistent, reliable, and valid active motion measurements are needed to document infant status and response to intervention. Read More

J Biomed Inform 2020 Jul 2;108:103500. Epub 2020 Jul 2.

Department of Computer Science & Engineering, Delhi Technological University, Delhi 110042, India.

Background: Real-time surveillance in the field of health informatics has emerged as a growing domain of interest among worldwide researchers. Evolution in this field has helped in the introduction of various initiatives related to public health informatics. Surveillance systems in the area of health informatics utilizing social media information have been developed for early prediction of disease outbreaks and to monitor diseases. Read More

Diabetes Care 2020 Jul 2. Epub 2020 Jul 2.

Melbourne EpiCentre, University of Melbourne and Melbourne Health, Melbourne, Victoria, Australia

Objective: To evaluate temporal prevalence trend, cardiometabolic risk factors, and the risk of atherosclerotic cardiovascular disease (ASCVD) and all-cause mortality (ACM) in incident young- and usual-onset type 2 diabetes.

Research Design And Methods: From the U.K. Read More

J Immunother Cancer 2020 Jul;8(2)

Medical Oncology, University Hospital Basel, Basel, Switzerland

Background: The costimulatory receptor 4-1BB (CD137, TNFRSF9) plays an important role in sustaining effective T cell immune responses and is investigated as target for cancer therapy. Systemic 4-1BB directed therapies elicit toxicity or low efficacy, which significantly hampered advancement of 4-1BB-based immunotherapy. Therefore, targeted delivery of 4-1BB agonist to the tumor side is needed for eliciting antitumor efficacy while avoiding systemic toxicity. Read More

J Antimicrob Chemother 2020 Jul 1. Epub 2020 Jul 1.

UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.

Objectives: poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts.

Methods: poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Read More

Sensors (Basel) 2020 Jun 28;20(13). Epub 2020 Jun 28.

School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China.

Segmentation of the hippocampus (HC) in magnetic resonance imaging (MRI) is an essential step for diagnosis and monitoring of several clinical situations such as Alzheimer's disease (AD), schizophrenia and epilepsy. Automatic segmentation of HC structures is challenging due to their small volume, complex shape, low contrast and discontinuous boundaries. The active contour model (ACM) with a statistical shape prior is robust. Read More

Prog Urol 2020 Jun 24. Epub 2020 Jun 24.

Service d'urologie et transplantation rénale, CHU de Pointe-à-Pitre/Abymes, 97110 Pointe-À-Pitre, France.

Background: Prostate cancer is supposedly more aggressive among Afro-Caribbean men. There is a lack of data in this population for active surveillance. Published series are retrospective or have small samples and results are discordant. Read More

J Dent 2020 Jun 24:103415. Epub 2020 Jun 24.

Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil. Electronic address:

Objective: This study evaluated the antibiofilm and anti-caries effects of an experimental mouth rinse containing aqueous extract of Matricaria chamomilla L.

Methods: Microcosm biofilm was produced on bovine enamel, from pooled human saliva mixed with McBain saliva, under 0.2 % sucrose exposure, for 5 days. Read More

Games Health J 2020 Jun 24. Epub 2020 Jun 24.

Department of Computer Science and Software Engineering, Xi'an Jiaotong-Liverpool University, Suzhou, China.

This article presents the results of a systematic review of the latest, state-of-the-art research on videogames designed for older adults (i.e., those aged 65 or older) and the health benefits derived from playing these games. Read More

ACM BCB 2017 Aug;2017:233-240

Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332.

The increasing accumulation of healthcare data provides researchers with ample opportunities to build machine learning approaches for clinical decision support and to improve the quality of health care. Several studies have developed conventional machine learning approaches that rely heavily on manual feature engineering and result in task-specific models for health care. In contrast, healthcare researchers have begun to use deep learning, which has emerged as a revolutionary machine learning technique that obviates manual feature engineering but still achieves impressive results in research fields such as image classification. Read More

ACM BCB 2016 Oct;2016:337-344

Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332.

Patient similarity measurement is an important tool for cohort identification in clinical decision support applications. A reliable similarity metric can be used for deriving diagnostic or prognostic information about a target patient using other patients with similar trajectories of health-care events. However, the measure of similar care trajectories is challenged by the irregularity of measurements, inherent in health care. Read More

Int J Colorectal Dis 2020 Jun 20. Epub 2020 Jun 20.

Grossman School of Medicine, New York University, New York, NY, 10016, USA.

Objectives: The impact of diabetes mellitus (DM) on colorectal cancer (CRC) outcomes remains unknown. We studied this by conducting a meta-analysis to evaluate (1) CRC outcomes with and without DM and (2) treatment patterns.

Methods: We searched PubMed, EMBASE, Google Scholar, and CINAHL for full-text English studies from 1970 to 12/31/2017. Read More

J Biomed Inform 2020 Jun 18;107:103463. Epub 2020 Jun 18.

INESC-ID Lisboa, Instituto Superior Técnico, Universidade de Lisboa, Portugal. Electronic address:

One of the most promising applications of Optical See-Through Augmented Reality is minimally laparoscopic surgery, which currently suffers from problems such as surgeon discomfort and fatigue caused by looking at a display positioned outside the surgeon's visual field, made worse by the length of the procedure. This fatigue is especially felt on the surgeon's neck, as it is strained from adopting unnatural postures in order to visualise the laparoscopic video feed. Throughout this paper, we will present work in Augmented Reality, as well as developments in surgery and Augmented Reality applied to both surgery in general and laparoscopy in particular to address these issues. Read More

Int J Cardiol 2020 Jun 16. Epub 2020 Jun 16.

Department of Cardiac, Thoracic and Vascular Sciences and Public Health, University of Padova, Italy.

The original designation of "Arrhythmogenic right ventricular (dysplasia/) cardiomyopathy"(ARVC) was used by the scientists who first discovered the disease, in the pre-genetic and pre-cardiac magnetic resonance era, to describe a new heart muscle disease predominantly affecting the right ventricle, whose cardinal clinical manifestation was the occurrence of malignant ventricular arrhythmias. Subsequently, autopsy investigations, genotype-phenotype correlations studies and the increasing use of contrast-enhancement cardiac magnetic resonance showed that the fibro-fatty replacement of the myocardium represents the distinctive phenotypic feature of the disease that affects the myocardium of both ventricles, with left ventricular involvement which may parallel or exceed the severity of right ventricular involvement. This has led to the new designation of "Arrhythmogenic Cardiomyopathy" (ACM), that represents the evolution of the original term of ARVC. Read More

ACM BCB 2019 Sep;2019:466-474

Georgia Institute of Technology and Emory University Atlanta, GA.

Stain normalization is a crucial pre-processing step for histopathological image processing, and can help improve the accuracy of downstream tasks such as segmentation and classification. To evaluate the effectiveness of stain normalization methods, various metrics based on color-perceptual similarity and stain color evaluation have been proposed. However, there still exists a huge gap between metric evaluation and human perception, given the limited explainability power of existing metrics and inability to combine color and semantic information efficiently. Read More

J Nucl Cardiol 2020 Jun 18. Epub 2020 Jun 18.

Turku PET Centre, University of Turku and Turku University Hospital, Turku, Finland.

Introduction: The purpose of this study was to evaluate subjects with high-risk alcohol cardiotoxicity and patients with alcoholic cardiomyopathy (ACM) via dynamic C-Acetate positron emission tomography (PET) imaging as a myocardial oxidative metabolic probe.

Methods And Results: We recruited 37 subjects with chronic alcohol consumption [18 with moderate consumption (MC), 19 with heavy consumption (HC)], 5 ACM patients, and 12 healthy controls to receive dynamic C-Acetate PET scans. PET imaging data were analyzed to calculate kinetic parameters (e. Read More

Eur J Ophthalmol 2020 Jun 19:1120672120936182. Epub 2020 Jun 19.

Department of Ophthalmology, Scientific Institute San Raffaele, Vita-Salute University, Milan, Italy.

Amelanotic choroidal melanoma (ACM) is an extremely rare malignant tumor affecting the uvea. Because of the complex structure characterizing this kind of lesions, its morphologic features are partially understood, especially if looking to its vascular network. In this paper, we described in details the multimodal imaging features of ACM. Read More

Front Oncol 2020 25;10:634. Epub 2020 May 25.

Department of Neurosurgery, Changzheng Hospital, Naval Medical University, Shanghai, China.

Surgical removal of anterior clinoidal meningiomas (ACMs) remains a challenge because of its complicated relationship with surrounding meninges, major arteries and cranial nerves. This study aims to define the meningeal structures around the anterior clinoid process (ACP) and its surgical implications. Five dry skulls and 19 cadavers were used in the anatomical study. Read More

Genes (Basel) 2020 Jun 13;11(6). Epub 2020 Jun 13.

National Germplasm Center of Domestic Animal Resources, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), No. 2 Yuanmingyuan West Rd., Haidian, Beijing 100193, China.

Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. Read More

Mayo Clin Proc Innov Qual Outcomes 2020 Jun 5;4(3):229-237. Epub 2020 Jun 5.

Department of Imaging, Department of Medicine, and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA.

Objective: To assess whether self-reported physical activity during daily life reduces the mortality risk associated with atherosclerotic burden, as measured by coronary artery calcium (CAC) scanning.

Methods: We assessed 2318 patients aged 65 to 84 years who underwent CAC scanning from August 31, 1998, through November 16, 2016, and had daily life physical activity assessed by a single-item question that was used to divide patients by low, moderate, and high physical activity levels. Patients were followed for a mean ± SD of 10. Read More

BMC Med 2020 Jun 16;18(1):139. Epub 2020 Jun 16.

Vincent Gnanapragasam, Academic Urology Group, University of Cambridge, Cambridge, UK.

Background: PREDICT Prostate is an endorsed prognostic model that provides individualised long-term prostate cancer-specific and overall survival estimates. The model, derived from UK data, estimates potential treatment benefit on overall survival. In this study, we externally validated the model in a large independent dataset and compared performance to existing models and within treatment groups. Read More

ACM BCB 2019 Sep;2019:423-428

University of Connecticut Storrs, Connecticut 06269.

Next-generation sequencing (NGS) technologies offer new opportunities for precise and accurate identification of genomic aberrations, including copy number variations (CNVs). For high-throughput NGS data, using depth of coverage has become a major approach to identify CNVs, especially for whole exome sequencing (WES) data. Due to the high level of noise and biases of read-count data and complexity of the WES data, existing CNV detection tools identify many false CNV segments. Read More

ACM Trans Comput Hum Interact 2019 Sep;26(5)

Department of Psychology, University of Florida, Gainesville, Florida, U. S. A.

Phishing is fundamental to cyber attacks. This research determined the effect of Internet user age and email content such as weapons of influence (persuasive techniques that attackers can use to lure individuals to fall for an attack) and life domains (a specific topic or aspect of an individual's life that attackers can focus an emails on) on spear-phishing (targeted phishing) susceptibility. One-hundred young and 58 older users received, without their knowledge, daily simulated phishing emails over 21 days. Read More

Autophagy 2020 Jun 7:1-6. Epub 2020 Jun 7.

Canada's Michael Smith Genome Sciences Centre, BC Cancer , Vancouver, BC, Canada.

Proteome profiling and global protein-interaction approaches have significantly improved our knowledge of the protein interactomes of autophagy and other cellular stress-response pathways. New discoveries regarding protein complexes, interaction partners, interaction domains, and biological roles of players that are part of these pathways are emerging. The fourth Vancouver Autophagy Symposium showcased research that expands our understanding of the protein interaction networks and molecular mechanisms underlying autophagy and other cellular stress responses in the context of distinct stressors. Read More

IEEE/ACM Trans Comput Biol Bioinform 2020 May-Jun;17(3):1092

Proc ACM Interact Mob Wearable Ubiquitous Technol 2019 Dec;3(4)

University of Pennsylvania, USA.

Estimating the category and quality of interpersonal relationships from ubiquitous phone sensor data matters for studying mental well-being and social support. Prior work focused on using communication volume to estimate broad relationship categories, often with small samples. Here we contextualize communications by combining phone logs with demographic and location data to predict interpersonal relationship roles on a varied sample population using automated machine learning methods, producing better performance (1 = 0. Read More

Stem Cell Res 2020 07 5;46:101835. Epub 2020 May 5.

Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands. Electronic address:

Arrhythmogenic Cardiomyopathy (ACM) is a rare inherited heart muscle disease characterised by progressive fibro-fatty replacement of the ventricular myocardium leading to life-threatening arrhythmias. We generated human induced pluripotent stem cells (hiPSCs) from a patient affected by ACM and carrying the heterozygous c.2013delC (p. Read More

J Innov Card Rhythm Manag 2019 Oct 15;10(10):3848-3852. Epub 2019 Oct 15.

Division of Pediatric Cardiology, Department of Pediatrics, University of Louisville, Louisville, KY, USA.

Capture management algorithms in current cardiac implantable electronic devices (CIEDs) can enhance device performance and battery longevity. Although generally safe, these algorithms have on rare occasions been implicated in the onset of significant complications, especially in pacemaker-dependent patients. CIEDs implanted in patients with postoperative congenital heart disease (CHD) often require epicardial pacing leads rather than transvenous leads; unfortunately, epicardial leads can experience higher rates of malfunction. Read More

J Cardiovasc Dev Dis 2020 May 26;7(2). Epub 2020 May 26.

Departments of Physiology and Cell Biology and Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH 43210, USA.

Arrhythmogenic cardiomyopathy (ACM) is an inherited disorder characterized by structural and electrical cardiac abnormalities, including myocardial fibro-fatty replacement. Its pathological ventricular substrate predisposes subjects to an increased risk of sudden cardiac death (SCD). ACM is a notorious cause of SCD in young athletes, and exercise has been documented to accelerate its progression. Read More

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

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

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

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

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

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

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

J Electrocardiol 2020 May - Jun;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

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

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

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

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

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

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

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

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

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