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Acm Journal On Computing And Cultural H... Publications | PubFacts

4,195 results match your criteria Acm Journal On Computing And Cultural Heritage[Journal]


Metabopolis: scalable network layout for biological pathway diagrams in urban map style.

BMC Bioinformatics 2019 Apr 15;20(1):187. Epub 2019 Apr 15.

Research Division of Computer Graphics, Institute of Visual Computing and Human- Centered Technology, TU Wien, Vienna, Austria.

Background: Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire image to large biochemical systems such as human metabolic pathways.

Results: Our work is inspired by concepts from urban planning since we create a visual hierarchy of biological pathways, which is analogous to city blocks and grid-like road networks in an urban area. Read More

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http://dx.doi.org/10.1186/s12859-019-2779-4DOI Listing

Screening pipeline for Flavivirus based Inhibitors for Zika Virus NS1.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 15. Epub 2019 Apr 15.

In-silico pipeline is applied for identifying and designing novel inhibitors against ZIKV NS1 protein. Comparative molecular docking studies are performed to explore the binding of structurally diverse compounds to ZIKV NS1 by AutoDock/Vina and GOLD. The Zika virus (ZIKV) is a flavivirus, responsible for life-threatening infections and transmitted by Aedes mosquitoes in other organisms. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2911081DOI Listing
April 2019
1 Read

A Network-based Comparison between Molecular Apocrine Breast Cancer Tumor and Basal and Luminal Tumors by Joint Graphical Lasso.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 15. Epub 2019 Apr 15.

Joint graphical lasso(JGL) approach is a Gaussian graphical model to estimate multiple graphical models corresponding to distinct but related groups. Molecular apocrine (MA) breast cancer tumor has similar characteristics to luminal and basal subtypes. Due to the relationship between MA tumor and two other subtypes, this paper investigates the similarities and differences between the MA genes association network and the ones corresponding to other tumors by taking advantageous of JGL properties. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2911074DOI Listing

An efficient algorithm for identifying mutated subnetworks associated with survival in cancer.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 15. Epub 2019 Apr 15.

Protein-protein interaction (PPI) network models interconnections between protein-encoding genes. Group of proteins that perform similar functions are often connected to each other in PPI network. The corresponding genes form pathways or functional modules. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2911069DOI Listing

RFCM3: Computational Method for Identification of miRNA-mRNA Regulatory Modules in Cervical Cancer.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 15. Epub 2019 Apr 15.

Cervical cancer is a leading severe malignancy throughout the world. Molecular processes and biomarkers leading to tumor progression in cervical cancer are either unknown or only partially understood. An increasing number of studies have shown that microRNAs play an important role in tumorigenesis so understanding the regulatory mechanism of miRNAs in gene-regulatory network will help elucidate the complex biological processes that occur during malignancy. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2910851DOI Listing

[A standardized health report tool for 12 year old children in the Academy of Grenoble].

Sante Publique 2019 November December;30(6):845-857

Introduction: Grenoble's regional education authority must provide pupils with medical and screening visits so as to detect health issues or care deficiencies early. The 12th year health check-up for pupils is therefore compulsory. We wanted to offer a standardized tool, the Obi-12, in order to guide that assessment. Read More

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http://dx.doi.org/10.3917/spub.187.0845DOI Listing

MCNF: A novel method for cancer subtyping by integrating multi-omics and clinical data.

Authors:
Lan Zhao Hong Yan

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 11. Epub 2019 Apr 11.

In the age of personalized medicine, there is a great need to classify cancer (from the same organ site) into homogeneous subtypes. Recent technology advancements in genome-wide molecular profiling have made it possible to profiling multiple molecular datasets to characterize the genomic changes in various cancer types. How to take full advantage of the availability of these omics data? And how to integrate these molecular data with patient clinical data to do a more systematic subtyping of cancer are the focuses of the paper. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2910515DOI Listing

RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 11. Epub 2019 Apr 11.

RNA-Protein binding plays important roles in the field of gene expression. With the development of high throughput sequencing, several conventional methods and deep learning-based methods have been proposed to predict the binding preference of RNA-protein binding. These methods can hardly meet the need of consideration of the dependencies between subsequence and the various motif lengths of different translation factors (TFs). Read More

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http://dx.doi.org/10.1109/TCBB.2019.2910513DOI Listing

Deep Learning Benchmarks on L1000 Gene Expression Data.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 11. Epub 2019 Apr 11.

Gene expression data can offer deep, physiological insights beyond the static coding of the genome alone. We believe that realizing this potential requires specialized, high-capacity machine learning methods capable of using underlying biological structure, but the development of such models is hampered by the lack of published benchmark tasks and well characterized baselines. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2910061DOI Listing

Can TiF varnish or TiF/NaF solution stain eroded and sound enamel?

J Dent 2019 Apr 12. Epub 2019 Apr 12.

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

Objectives: This study evaluated the staining potential of TiF varnish and TiF/NaF solution on both sound and previously eroded enamel in vitro.

Methods: One hundred and eighty bovine enamel samples were polished; half of them remained sound and the other half was eroded (4 × 90 s each, using a 0.1% citric acid). Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03005712193006
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http://dx.doi.org/10.1016/j.jdent.2019.04.006DOI Listing
April 2019
1 Read

Bootstrapping variables in algebraic circuits.

Proc Natl Acad Sci U S A 2019 Apr 11. Epub 2019 Apr 11.

Department of Computer Science & Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India

We show that for the blackbox polynomial identity testing (PIT) problem it suffices to study circuits that depend only on the first extremely few variables. One needs only to consider size-s degree-s circuits that depend on the first [Formula: see text] variables (where c is a constant and composes a logarithm with itself c times). Thus, the hitting-set generator (hsg) manifests a bootstrapping behavior-a partial hsg against very few variables can be efficiently grown to a complete hsg. Read More

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http://dx.doi.org/10.1073/pnas.1901272116DOI Listing

Bovine fetal mesenchymal stem cells exert antiproliferative effect against mastitis causing pathogen Staphylococcus aureus.

Vet Res 2019 Apr 11;50(1):25. Epub 2019 Apr 11.

Department of Animal Production Science, Faculty of Veterinary Medicine, University of Chile, 8820808, Santiago, Chile.

Staphylococcus aureus is the most commonly isolated pathogen from clinical bovine mastitis samples and a difficult pathogen to combat. Mesenchymal stem cells (MSC) are multipotent progenitor cells equipped with a variety of factors that inhibit bacterial growth. The aim of the present study was to evaluate the in vitro antibacterial potential against S. Read More

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http://dx.doi.org/10.1186/s13567-019-0643-1DOI Listing

SL 2 MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 9. Epub 2019 Apr 9.

Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell lines. Therefore, computational prediction methods are needed to address these issues. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2909908DOI Listing

Capsule Network based Modeling of Multi-omics Data for Discovery of Breast Cancer-related Genes.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 9. Epub 2019 Apr 9.

Breast cancer is one of the most common cancers all over the world, which bring about more than 450,000 deaths each year. Although this malignancy has been extensively studied by a large number of researchers, its prognosis is still poor. Since therapeutic advance can be obtained based on gene signatures, there is an urgent need to discover genes related to breast cancer that may help uncover the mechanisms in cancer progression. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2909905DOI Listing
April 2019
3 Reads

[Telemedicine projects in rural areas of Germany A systematic evaluation with the "Model for Assessment of Telemedicine"].

Z Evid Fortbild Qual Gesundhwes 2019 Apr 5. Epub 2019 Apr 5.

Institut für Allgemeinmedizin, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.

Background: The term telemedicine describes the delivery of healthcare services through the use of information and communication technologies in a situation where the actors are at different locations. While telemedical applications are piloted in research projects in Germany, they have rarely become part of everyday care. In order to find indications as to why the transfer of knowledge into practice has so far been slow, it is necessary to examine telemedical projects for aspects of implementation science. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S18659217193003
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http://dx.doi.org/10.1016/j.zefq.2019.03.005DOI Listing
April 2019
3 Reads

Socio-spatial Self-organizing Maps: Using Social Media to Assess Relevant Geographies for Exposure to Social Processes.

Proc ACM Hum Comput Interact 2018 Nov;2

New York University, USA.

Social media offers a unique window into attitudes like racism and homophobia, exposure to which are important, hard to measure and understudied social determinants of health. However, individual geo-located observations from social media are noisy and geographically inconsistent. Existing areas by which exposures are measured, like Zip codes, average over irrelevant administratively-defined boundaries. Read More

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http://dx.doi.org/10.1145/3274414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448781PMC
November 2018

A Parkinson's disease gene, DJ-1, regulates anti-inflammatory roles of astrocytes through prostaglandin D synthase expression.

Neurobiol Dis 2019 Apr 4;127:482-491. Epub 2019 Apr 4.

Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Worldcup-ro 164, Suwon 16499, Republic of Korea; Department of Pharmacology, Ajou University School of Medicine, Worldcup-ro 164, Suwon 16499, Republic of Korea; Chronic Inflammatory Disease Research Center, Ajou University School of Medicine, Worldcup-ro 164, Suwon 16499, Republic of Korea; Department of Brain Science, Ajou University School of Medicine, Worldcup-ro 164, Suwon 16499, Republic of Korea. Electronic address:

Dysfunctional regulation of inflammation may contribute to the progression of neurodegenerative diseases. The results of this study revealed that DJ-1, a Parkinson's disease (PD) gene, regulated expression of prostaglandin D synthase (PTGDS) and production of prostaglandin D (PGD), by which DJ-1 enhanced anti-inflammatory function of astrocytes. In injured DJ-1 knockout (KO) brain, expression of tumor necrosis factor-alpha (TNF-α) was more increased, but that of anti-inflammatory heme oxygenase-1 (HO-1) was less increased compared with that in injured wild-type (WT) brain. Read More

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http://dx.doi.org/10.1016/j.nbd.2019.04.003DOI Listing

Persistent Central Apnea and Long-Term Outcome After Posterior Fossa Decompressive Surgery for Arnold Chiari Type 1 Malformation in a Pediatric Patient.

J Clin Sleep Med 2019 Apr 2. Epub 2019 Apr 2.

Abstract: Arnold Chiari malformation (ACM) is the most common cause of central sleep apnea (CSA) in otherwise healthy children. Although there are several case reports and series reported on this topic, there are limited descriptions of the long-term course of these children after the surgical interventions. Posterior fossa decompression surgery to relieve pressure of the herniating cerebellum on the brainstem is generally thought to significantly improve CSA in most cases, however, there are very limited data on the natural course of CSA in children following decompression surgery. Read More

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April 2019
1 Read

Predicting DNA methylation states with hybrid information based deep-learning model.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 3. Epub 2019 Apr 3.

DNA methylation plays an important role in the regulation of some biological processes. Up to now, with the development of machine learning models, there are several sequence-based deep learning models designed to predict DNA methylation states, which gain better performance than traditional methods like random forest and SVM. However, convolutional network based deep learning models that use one-hot encoding DNA sequence as input may discover limited information and cause unsatisfactory prediction performance, so more data and model structures of diverse angles should be considered. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2909237DOI Listing

Which treatment is best for patients with AJCC stage IV bladder cancer?

Int Urol Nephrol 2019 Apr 4. Epub 2019 Apr 4.

Department of Urology, Shanghai Tenth People's Hospital, Tongji University, No. 301, Yanchang Road, Jing'an District, Shanghai, 200072, China.

Purpose: We sought to identify the method that could obtain the best survival rate for AJCC stage IV bladder cancer (BCa) patients.

Methods: Patients with AJCC stage IV BCa diagnosed between 2004 and 2015 were identified using the Surveillance, epidemiology and end results (SEER) database. Kaplan-Meier curves and log-rank test were used for overall survival (OS) and cancer-specific survival (CSS). Read More

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http://dx.doi.org/10.1007/s11255-019-02105-5DOI Listing
April 2019
1 Read

Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation.

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 1. Epub 2019 Apr 1.

Engineering stable proteins is crucial to various industrial purposes. Several machine learning methods have been developed to predict changes in the stability of proteins upon single point mutations. To improve accuracy of the prediction, we propose a new unsupervised descriptor for protein sequences that is based on a sequence-to-sequence (seq2seq) neural network model combined with a sequence-compression method called byte-pair encoding (BPE). Read More

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http://dx.doi.org/10.1109/TCBB.2019.2908641DOI Listing

A systematic review of just-in-time adaptive interventions (JITAIs) to promote physical activity.

Int J Behav Nutr Phys Act 2019 Apr 3;16(1):31. Epub 2019 Apr 3.

School of Health Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.

Background: Progress in mobile health (mHealth) technology has enabled the design of just-in-time adaptive interventions (JITAIs). We define JITAIs as having three features: behavioural support that directly corresponds to a need in real-time; content or timing of support is adapted or tailored according to input collected by the system since support was initiated; support is system-triggered. We conducted a systematic review of JITAIs for physical activity to identify their features, feasibility, acceptability and effectiveness. Read More

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https://ijbnpa.biomedcentral.com/articles/10.1186/s12966-019
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http://dx.doi.org/10.1186/s12966-019-0792-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448257PMC
April 2019
12 Reads

Application of An Electrical Resistance Sensor-Based Automated Corrosion Monitor in the Study of Atmospheric Corrosion.

Materials (Basel) 2019 Apr 1;12(7). Epub 2019 Apr 1.

Research Institute, Nanjing Iron & Steel Co., Ltd., Nanjing 210035, China.

An automated corrosion monitor, named the Internet of Things atmospheric corrosion monitor (IoT ACM) has been developed. IoT ACM is based on electrical resistance sensor and enables accurate and continuous measurement of corrosion data of metallic materials. The objective of this research is to study the characteristics of atmospheric corrosion by analyzing the acquired corrosion data from IoT ACM. Read More

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http://dx.doi.org/10.3390/ma12071065DOI Listing
April 2019
2 Reads

BRWMDA:Predicting microbe-disease associations based on similarities and bi-random walk on disease and microbe networks.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 26. Epub 2019 Mar 26.

Many current studies have evidenced that microbes play important roles in human diseases. Therefore, discovering the associations between microbes and diseases is beneficial to systematically understanding the mechanisms of diseases, diagnosing and treating complex diseases. It is well known that finding new potential microbe-disease associations via biological experiments is a time-consuming and expensive process. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2907626DOI Listing

Deep collaborative filtering for prediction of disease genes.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 26. Epub 2019 Mar 26.

Accurate prioritization of potential disease genes is a fundamental challenge in biomedical research. Various algorithms have been developed to solve such problems. Inductive Matrix Completion (IMC) is one of the most reliable models for its well established framework and its superior performance in predicting gene-disease associations. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2907536DOI Listing
March 2019
1 Read

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 26. Epub 2019 Mar 26.

Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2907492DOI Listing

Relation between therapy-induced changes in natriuretic peptide levels and long-term therapeutic effects on mortality in patients with heart failure and reduced ejection fraction.

Eur J Heart Fail 2019 Mar 27. Epub 2019 Mar 27.

Division of Cardiology and the CardioVascular Center, Tufts Medical Center, Boston, MA, USA.

Aims: To assess whether natriuretic peptides (NPs) can be used to reliably predict long-term therapeutic effect on clinical outcomes for patients with heart failure and reduced ejection fraction (HFrEF).

Methods And Results: HFrEF intervention trials with mortality data were identified. Subsequently, we identified trials assessing therapy-induced changes in NPs. Read More

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http://dx.doi.org/10.1002/ejhf.1411DOI Listing

Direct Resazurin Microplate Assay in Drug Susceptibility Testing of Smear-Positive Sputum Samples against .

Malays J Med Sci 2018 Nov 28;25(6):59-66. Epub 2018 Dec 28.

School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.

Background: A new direct microplate-based colorimetric drug susceptibility test that omits the initial isolation of from sputum specimens was evaluated.

Methods: A total of 51 acid fast bacilli (AFB) smear-positive sputum specimens were inoculated directly into drug-free and serial dilutions of drug-containing Middlebrook 7H9 broth media. With this direct resazurin micro plate assay (REMA) method, resazurin dye was used as a growth indicator in microplate wells. Read More

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http://dx.doi.org/10.21315/mjms2018.25.6.6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422566PMC
November 2018
1 Read

Wearable Activity Trackers, Accuracy, Adoption, Acceptance and Health Impact: A Systematic Literature Review.

J Biomed Inform 2019 Mar 22:103153. Epub 2019 Mar 22.

School of Information and Library Science, University of North Carolina at Chapel Hill, USA. Electronic address:

Wearable activity trackers (WAT) are electronic monitoring devices that enable users to track and monitor their health-related physical fitness metrics including steps taken, level of activity, walking distance, heart rate, and sleep patterns. Despite the proliferation of these devices in various contexts of use and rising research interests, there is limited understanding of the broad research landscape. The purpose of this systematic review is therefore to synthesize the existing wealth of research on WAT, and to provide a comprehensive summary based on common themes and approaches. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S15320464193007
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http://dx.doi.org/10.1016/j.jbi.2019.103153DOI Listing
March 2019
2 Reads

Contributions of Mass Spectrometry to the Identification of Low Molecular Weight Molecules Able to Reduce the Toxicity of Amyloid-β Peptide to Cell Cultures and Transgenic Mouse Models of Alzheimer's Disease.

Molecules 2019 Mar 24;24(6). Epub 2019 Mar 24.

Center for Advanced Research and Development in Experimental Medicine (CEMEX), "Grigore T. Popa" University of Medicine and Pharmacy, 16 Universității Street, 700115 Iaşi, Romania.

Alzheimer's Disease affects approximately 33 million people worldwide and is characterized by progressive loss of memory at the cognitive level. The formation of toxic amyloid oligomers, extracellular amyloid plaques and amyloid angiopathy in brain by amyloid beta peptides are considered a part of the identified mechanism involved in disease pathogenesis. The optimal treatment approach leads toward finding a chemical compound able to form a noncovalent complex with the amyloid peptide thus blocking the process of amyloid aggregation. Read More

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http://dx.doi.org/10.3390/molecules24061167DOI Listing
March 2019
2 Reads

A Method for Estimating Time-Dependent Corrosion Depth of Carbon and Weathering Steel Using an Atmospheric Corrosion Monitor Sensor.

Sensors (Basel) 2019 Mar 22;19(6). Epub 2019 Mar 22.

Steel Structure Research Group, 100 Songdogwahak-ro, Yeonsu-gu, Incheon 21985, Korea.

In this study, a time-dependent corrosion depth estimation method using atmospheric corrosion monitor (ACM) sensor data to evaluate time-dependent corrosion behaviors is proposed. For the time-dependent corrosion depth estimation of uncoated carbon steel and weathering steel, acceleration corrosion tests were conducted in salt-spray corrosion environments and evaluated with a corrosion damage estimation method using ACM sensing data and corrosion loss data of the tested steel specimens. To estimate the time-dependent corrosion depth using corrosion current by an ACM sensor, the relationship between the mean corrosion depth calculated from the weight loss method and the corrosion current was evaluated. Read More

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http://dx.doi.org/10.3390/s19061416DOI Listing

A systematic literature review of machine learning in online personal health data.

J Am Med Inform Assoc 2019 Mar 25. Epub 2019 Mar 25.

Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.

Objective: User-generated content (UGC) in online environments provides opportunities to learn an individual's health status outside of clinical settings. However, the nature of UGC brings challenges in both data collecting and processing. The purpose of this study is to systematically review the effectiveness of applying machine learning (ML) methodologies to UGC for personal health investigations. Read More

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https://academic.oup.com/jamia/advance-article/doi/10.1093/j
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http://dx.doi.org/10.1093/jamia/ocz009DOI Listing
March 2019
8 Reads

SNeCT: Scalable Network Constrained Tucker Decomposition for Multi-Platform Data Profiling.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 19. Epub 2019 Mar 19.

How do we integratively profile large-scale multi-platform genomic data that are high dimensional and sparse? Furthermore, how can we incorporate prior knowledge, such as the association between genes, in the analysis systematically to find better latent relationships? To solve this problem, we propose a Scalable Network Constrained Tucker decomposition method (SNeCT). SNeCT adopts parallel stochastic gradient descent approach on the proposed parallelizable network constrained optimization function. SNeCT decomposition is applied to a tensor constructed from a large scale multi-platform multi-cohort cancer data, PanCan12, constrained on a network built from PathwayCommons database. Read More

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https://ieeexplore.ieee.org/document/8669882/
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http://dx.doi.org/10.1109/TCBB.2019.2906205DOI Listing
March 2019
1 Read

Bio-curation for cellular signalling: the KAMI project.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 19. Epub 2019 Mar 19.

The general question of what constitutes bio-curation for rule-based modelling of cellular signalling is posed. A general approach to the problem is presented, based on rewriting in hierarchies of graphs, together with a specific instantiation of the methodology that addresses our particular bio-curation problem. The current state of the ongoing development of the KAMI bio-curation tool, based on this approach, is outlined along with our plans for future development. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2906164DOI Listing

Causal Disturbance Analysis: A Novel Graph Centrality Based Method for Pathway Enrichment Analysis.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 25. Epub 2019 Mar 25.

Pathway enrichment analysis models (PEM) are the premier methods for interpreting genetic perturbations from high-throughput experiments. PEM often use a priori background knowledge to infer the underlying biological functions and mechanisms. A shortcoming of standard PEM is their disregarding of genetic interactions for mathematical simplicity, which potentially results in partial and inaccurate inference. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2907246DOI Listing

Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 25. Epub 2019 Mar 25.

In recent years, single-cell RNA sequencing reveals diverse cell genetics at unprecedented resolutions. Such technological advances enable researchers to uncover the functionally distinct cell subtypes such as hematopoietic stem cell subpopulation identification. However, most of the related algorithms have been hindered by the high-dimensionality and sparse nature of single-cell RNA sequencing (RNA-seq) data. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2906601DOI Listing

Gene expression classification of lung adenocarcinoma into molecular subtypes.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 18. Epub 2019 Mar 18.

As one of the most common malignancies in the world, lung adenocarcinoma (LUAD) is currently difficult to cure. However, the advent of precision medicine provides an opportunity to improve the treatment of lung cancer. Subtyping lung cancer plays an important role in performing a specific treatment. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2905553DOI Listing
March 2019
1 Read

Sparse Reconstruction of Glucose Fluxes using Continuous Glucose Monitors.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 15. Epub 2019 Mar 15.

A new technique for estimating postprandial glucose flux profiles without the use of glucose tracers is proposed. The technique assumes knowledge of patient parameters relevant to the glucose, insulin and endogoneous glucose production subsystems. A convex Lasso formulation is used to estimate the glucose fluxes that combines (1) the known patient parameters; (2) a sparse vector space encoding the space of plausible glucose flux profiles; (3) continuous glucose monitor measurements taken during the meal; (4) amount of insulin injected; (5) amount of meal carbohydrates and (6) an estimate of the initial conditions. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2905198DOI Listing

Hydroimplantation versus viscoimplantation: comparison of intraocular lens implantation with and without ophthalmic viscoelastic device in phacoemulsification.

Rom J Ophthalmol 2018 Oct-Dec;62(4):282-287

Department of Ophthalmology, Kutahya Health Sciences University School of Medicine, Kutahya, Turkey.

To compare the efficacy and safety of intraocular lens implantation with and without ophthalmic viscoelastic device in phacoemulsification. A randomized prospective study was conducted on 84 eyes of 84 patients who underwent uneventful phacoemulsification by the same surgeon. Patients were divided into two groups after the completion of lens cortex removal. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421496PMC

Intravenous Sedation in Arnold-Chiari Malformation With Respiratory Failure.

Anesth Prog 2019 ;66(1):37-41

Department of Dental Anesthesiology, Nippon Dental University School of Life Dentistry, Tokyo, Japan.

Type II Arnold-Chiari malformation (ACM) is an abnormality in which the cerebellum, pons, and medulla oblongata are displaced downward into the spinal cord. Type II ACM is often complicated by respiratory depression, sleep-disordered breathing, and deglutition disorder as a result of medullary dysfunction and impairment of the lower cranial nerves. Bending and stretching of the neck is restricted, and anesthetic management is problematic in patients with the disorder. Read More

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http://dx.doi.org/10.2344/anpr-66-01-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424169PMC
January 2019
1 Read

Effect of Dapagliflozin on Heart Failure and Mortality in Type 2 Diabetes Mellitus.

Circulation 2019 Mar 18. Epub 2019 Mar 18.

Medicine, BWH/TIMI Study Group, Boston, MA.

Background: In DECLARE-TIMI 58, the sodium glucose co-transporter 2 inhibitor (SGLT2i) dapagliflozin reduced the composite endpoint of cardiovascular (CV) death/ hospitalization for heart failure (HHF) in a broad population of patients with T2DM. However, the impact of baseline left ventricular ejection fraction (EF) on the clinical benefit of SGLT2i is unknown.

Methods: In the DECLARE-TIMI 58 trial, baseline HF status was collected from all patients and EF where available. Read More

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http://dx.doi.org/10.1161/CIRCULATIONAHA.119.040130DOI Listing

Prognostic Differences in ISUP Grade Group 4: a Systematic Review and Meta-Analysis.

Pathol Oncol Res 2019 Mar 14. Epub 2019 Mar 14.

Urology Unit, Flinders Medical Centre, Bedford Park, Australia.

The ISUP (Internal Society of Urologic Pathology) recently adopted a five-tiered prognostication system. There is evidence to suggest that the ISUP grade group 4 is a heterogeneous entity regarding prognosis. Our aim was to systematically examine the existing evidence to determine if outcome differences exist within the ISUP grade group 4. Read More

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http://dx.doi.org/10.1007/s12253-019-00632-1DOI Listing

Mining Relationships among Multiple Entities in Biological Networks.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 13. Epub 2019 Mar 13.

Identifying topological relationships among multiple entities in biological networks is critical towards the understanding of the organizational principles of network functionality. Theoretically, this problem can be solved using minimum Steiner tree (MSTT) algorithms. However, due to large network size, it remains to be computationally challenging, and the predictive value of multi-entity topological relationships is still unclear. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2904965DOI Listing

Modeling Variability in Populations of Cells using Approximated Multivariate Distributions.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 11. Epub 2019 Mar 11.

We are interested in studying the evolution of large homogeneous populations of cells, where each cell is assumed to be composed of a group of biological players (species) whose dynamics is governed by a complex biological pathway, identical for all cells. Modeling the inherent variability of the species concentrations in different cells is crucial to understand the dynamics of the population. In this work, we focus on handling this variability by modeling each species by a random variable that evolves over time. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2904276DOI Listing

Extracting Inter-sentence Relations for Associating Biological Context with Events in Biomedical Text.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 11. Epub 2019 Mar 11.

We present an analysis of the problem of identifying biolog- ical context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descr iptions of the species, tissue type and cell type that are associated with biochemical events. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2904231DOI Listing
March 2019
1.438 Impact Factor

Immature surfactant protein-B impairs the antioxidant capacity of HDL.

Int J Cardiol 2019 Jun 27;285:53-58. Epub 2019 Feb 27.

Centro Cardiologico Monzino, IRCCS, Milano, Italy; Dipartimento di Scienze Cliniche e di Comunità, Sezione Cardiovascolare, Università di Milano, Italy.

Circulating immature surfactant protein B (proSP-B) forms emerged as the most reliable lung-specific circulating marker for alveolar-capillary membrane (ACM) dysfunction and for the overall clinical status of heart failure (HF). Notably, in terms of HF hospitalization, immature SP-B overwhelms the prognostic role of other most frequently used clinical parameters such as those related to lung dysfunction. The strong prognostic value of circulating proSP-B in HF suggests more widespread and possible systemic effects. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01675273183592
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http://dx.doi.org/10.1016/j.ijcard.2019.02.057DOI Listing
June 2019
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Submodularity of Distributed Join Computation.

Proc ACM SIGMOD Int Conf Manag Data 2018 Jun;2018:1237-1252

Northeastern University, Boston, USA.

We study distributed equi-join computation in the presence of join-attribute skew, which causes load imbalance. Skew can be addressed by more fine-grained partitioning, at the cost of input duplication. For random load assignment, e. Read More

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http://dx.doi.org/10.1145/3183713.3183728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404978PMC

Multimodal wrist-worn devices for seizure detection and advancing research: Focus on the Empatica wristbands.

Epilepsy Res 2019 Feb 27. Epub 2019 Feb 27.

Empatica, Milan, Italy; Empatica, Cambridge, MA, USA; MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

Wearable automated seizure detection devices offer a high potential to improve seizure management, through continuous ambulatory monitoring, accurate seizure counts, and real-time alerts for prompt intervention. More importantly, these devices can be a life-saving help for people with a higher risk of sudden unexpected death in epilepsy (SUDEP), especially in case of generalized tonic-clonic seizures (GTCS). The Embrace and E4 wristbands (Empatica) are the first commercially available multimodal wristbands that were designed to sense the physiological hallmarks of ongoing GTCS: while Embrace only embeds a machine learning-based detection algorithm, both E4 and Embrace devices are equipped with motion (accelerometers, ACC) and electrodermal activity (EDA) sensors and both the devices received medical clearance (E4 from EU CE, Embrace from EU CE and US FDA). Read More

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http://dx.doi.org/10.1016/j.eplepsyres.2019.02.007DOI Listing
February 2019
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CCFS: A Confidence-based Cost-effective feature selection scheme for healthcare data classification.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 7. Epub 2019 Mar 7.

Feature selection (FS) is one of fundamental data processing techniques in machine learning algorithms, especially for classification of healthcare data. It is a challenging issue due to the large search space. Binary Particle Swarm Optimization (BPSO) is an efficient evolutionary computation technique, and has been widely used in FS. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2903804DOI Listing
March 2019
1.438 Impact Factor

Classification of Antibacterial Peptides using Long Short-Term Memory Recurrent Neural Networks.

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 7. Epub 2019 Mar 7.

Antimicrobial peptides are short amino acid sequences that may be antibacterial, antifungal, and antiviral. Most machine learning methodologies applied to identifying antibacterial peptides have developed feature vectors of identical lengths for each peptide in a given dataset although the peptides themselves may differ in number of amino acids. Features are often chosen which represent certain periodic patterns in the peptide sequence without any initial guidance as to whether such patterns are relevant for the classification task at hand. Read More

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http://dx.doi.org/10.1109/TCBB.2019.2903800DOI Listing
March 2019
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