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https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#1
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27911938/motion-plan-changes-predictably-in-dyadic-reaching
#2
Atsushi Takagi, Niek Beckers, Etienne Burdet
Parents can effortlessly assist their child to walk, but the mechanism behind such physical coordination is still unknown. Studies have suggested that physical coordination is achieved by interacting humans who update their movement or motion plan in response to the partner's behaviour. Here, we tested rigidly coupled pairs in a joint reaching task to observe such changes in the partners' motion plans. However, the joint reaching movements were surprisingly consistent across different trials. A computational model that we developed demonstrated that the two partners had a distinct motion plan, which did not change with time...
2016: PloS One
https://www.readbyqxmd.com/read/27911734/the-spatiotemporal-regulation-of-ras-signalling
#3
REVIEW
Ana Herrero, David Matallanas, Walter Kolch
Nearly 30% of human tumours harbour mutations in RAS family members. Post-translational modifications and the localisation of RAS within subcellular compartments affect RAS interactions with regulator, effector and scaffolding proteins. New insights into the control of spatiotemporal RAS signalling reveal that activation kinetics and subcellular compartmentalisation are tightly coupled to the generation of specific biological outcomes. Computational modelling can help utilising these insights for the identification of new targets and design of new therapeutic approaches...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911345/computing-the-influences-of-different-intraocular-pressures-on-the-human-eye-components-using-computational-fluid-structure-interaction-model
#4
Alireza Karimi, Reza Razaghi, Mahdi Navidbakhsh, Toshihiro Sera, Susumu Kudo
BACKGROUND: Intraocular Pressure (IOP) is defined as the pressure of aqueous in the eye. It has been reported that the normal range of IOP should be within the 10-20 mmHg with an average of 15.50 mmHg among the ophthalmologists. Keratoconus is an anti-inflammatory eye disorder that debilitated cornea unable to reserve the normal structure contrary to the IOP in the eye. Consequently, the cornea would bulge outward and invoke a conical shape following by distorted vision. In addition, it is known that any alterations in the structure and composition of the lens and cornea would exceed a change of the eye ball as well as the mechanical and optical properties of the eye...
November 25, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/27908833/pilot-evaluation-of-a-method-to-assess-prescribers-information-processing-of-medication-alerts
#5
Alissa L Russ, Brittany L Melton, Joanne K Daggy, Jason J Saleem
BACKGROUND: Prescribers commonly receive alerts during medication ordering. Prescribers work in a complex, time-pressured environment; to enhance the effectiveness of safety alerts, the effort needed to cognitively process these alerts should be minimized. Methods to evaluate the extent to which computerized alerts support prescribers' information processing are lacking. OBJECTIVE: To develop a methodological protocol to assess the extent to which alerts support prescribers' information processing at-a-glance; specifically, the incorporation of information into working memory...
November 28, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27908025/geometry-of-behavioral-spaces-a-computational-approach-to-analysis-and-understanding-of-agent-based-models-and-agent-behaviors
#6
Martin Cenek, Spencer K Dahl
Systems with non-linear dynamics frequently exhibit emergent system behavior, which is important to find and specify rigorously to understand the nature of the modeled phenomena. Through this analysis, it is possible to characterize phenomena such as how systems assemble or dissipate and what behaviors lead to specific final system configurations. Agent Based Modeling (ABM) is one of the modeling techniques used to study the interaction dynamics between a system's agents and its environment. Although the methodology of ABM construction is well understood and practiced, there are no computational, statistically rigorous, comprehensive tools to evaluate an ABM's execution...
November 2016: Chaos
https://www.readbyqxmd.com/read/27903728/context-dependent-accumulation-of-sensory-evidence-in-the-parietal-cortex-underlies-flexible-task-switching
#7
Hironori Kumano, Yuki Suda, Takanori Uka
: Switching behavior based on multiple rules is a fundamental ability of flexible behavior. Although interactions among the frontal, parietal, and sensory cortices are necessary for such flexibility, little is known about the neural computations concerning context-dependent information readouts. Here, we provide evidence that neurons in the lateral intraparietal area (LIP) accumulate relevant information preferentially depending on context. We trained monkeys to switch between direction and depth discrimination tasks and analyzed the buildup activity in the LIP depending on task context...
November 30, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27903304/association-between-taenia-solium-infection-and-hiv-aids-in-northern-tanzania-a-matched-cross-sectional-study
#8
Veronika Schmidt, Christian Kositz, Karl-Heinz Herbinger, Hélène Carabin, Bernard Ngowi, Ezra Naman, Patricia P Wilkins, John Noh, William Matuja, Andrea Sylvia Winkler
BACKGROUND: The frequency of Taenia solium, a zoonotic helminth, is increasing in many countries of sub-Saharan Africa, where the prevalence of the human immunodeficiency virus (HIV) is also high. However, little is known about how these two infections interact. The aim of this study was to compare the proportion of HIV positive (+) and negative (-) individuals who are infected with Taenia solium (TSOL) and who present with clinical and neurological manifestations of cysticercosis (CC)...
December 1, 2016: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/27899673/diseasemeth-version-2-0-a-major-expansion-and-update-of-the-human-disease-methylation-database
#9
Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu, Yan Zhang
The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease-gene associations from 216 201 to 679 602...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899659/discovery-and-validation-of-information-theory-based-transcription-factor-and-cofactor-binding-site-motifs
#10
Ruipeng Lu, Eliseos J Mucaki, Peter K Rogan
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899641/3d-genome-structure-modeling-by-lorentzian-objective-function
#11
Tuan Trieu, Jianlin Cheng
The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899558/pathdip-an-annotated-resource-for-known-and-predicted-human-gene-pathway-associations-and-pathway-enrichment-analysis
#12
Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895772/hotair-a-long-non-coding-rna-driver-of-malignancy-whose-expression-is-activated-by-foxc1-negatively-regulates-mirna-1-in-hepatocellular-carcinoma
#13
Dong-Na Su, Shi-Pin Wu, Hong-Tao Chen, Jin-Hua He
Evidence is rapidly accumulating that long non-coding RNAs (lncRNAs) are involved in human tumorigenesis and are dysregulated in multiple cancers, including hepatocellular carcinoma (HCC). lncRNAs can regulate essential pathways that contribute to tumor initiation and progression with tissue specificity, which suggests that lncRNAs may be valuable biomarkers and therapeutic targets. HOX transcript antisense intergenic RNA (HOTAIR) has previously been demonstrated to be an oncogene and a negative prognostic factor in a variety of cancers; however, the factors that contribute to the upregulation of HOTAIR and the interaction between HOTAIR and microRNAs (miRNAs or miRs) are largely unknown...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27893894/face-exploration-dynamics-differentiate-men-and-women
#14
Antoine Coutrot, Nicola Binetti, Charlotte Harrison, Isabelle Mareschal, Alan Johnston
The human face is central to our everyday social interactions. Recent studies have shown that while gazing at faces, each one of us has a particular eye-scanning pattern, highly stable across time. Although variables such as culture or personality have been shown to modulate gaze behavior, we still don't know what shapes these idiosyncrasies. Moreover, most previous observations rely on static analyses of small-sized eye-position data sets averaged across time. Here, we probe the temporal dynamics of gaze to explore what information can be extracted about the observers and what is being observed...
November 1, 2016: Journal of Vision
https://www.readbyqxmd.com/read/27893365/design-and-choice-of-visual-display-solutions-in-the-training-domain
#15
Amela Sadagic
Visual display solutions are a key element of computer-based system architectures intended for human-system interaction. Particularly in the training domain, an ill-matched visual display can render a system unusable or ineffectual, which may cause underutilization or a negative transfer of training. This article outlines a set of approaches and best practices used in research efforts focused on the design of novel military training systems.
November 2016: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/27892818/interaction-of-stattic-a-stat3-inhibitor-with-human-serum-albumin-spectroscopic-and-computational-study
#16
Ida Syazwani M Affandi, Wei Qi Lee, Shevin R Feroz, Saharuddin B Mohamad, Saad Tayyab
No abstract text is available yet for this article.
November 28, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27891109/pulling-rank-military-rank-affects-hormone-levels-and-fairness-in-an-allocation-experiment
#17
Benjamin Siart, Lena S Pflüger, Bernard Wallner
Status within social hierarchies has great effects on the lives of socially organized mammals. Its effects on human behavior and related physiology, however, is relatively little studied. The present study investigated the impact of military rank on fairness and behavior in relation to salivary cortisol (C) and testosterone (T) levels in male soldiers. For this purpose 180 members of the Austrian Armed Forces belonging to two distinct rank groups participated in two variations of a computer-based guard duty allocation experiment...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27890158/improving-our-understanding-of-multi-tasking-in-healthcare-drawing-together-the-cognitive-psychology-and-healthcare-literature
#18
REVIEW
Heather E Douglas, Magdalena Z Raban, Scott R Walter, Johanna I Westbrook
Multi-tasking is an important skill for clinical work which has received limited research attention. Its impacts on clinical work are poorly understood. In contrast, there is substantial multi-tasking research in cognitive psychology, driver distraction, and human-computer interaction. This review synthesises evidence of the extent and impacts of multi-tasking on efficiency and task performance from health and non-healthcare literature, to compare and contrast approaches, identify implications for clinical work, and to develop an evidence-informed framework for guiding the measurement of multi-tasking in future healthcare studies...
March 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/27888933/review-on-modeling-heat-transfer-and-thermoregulatory-responses-in-human-body
#19
REVIEW
Ming Fu, Wenguo Weng, Weiwang Chen, Na Luo
Several mathematical models of human thermoregulation have been developed, contributing to a deep understanding of thermal responses in different thermal conditions and applications. In these models, the human body is represented by two interacting systems of thermoregulation: the controlling active system and the controlled passive system. This paper reviews the recent research of human thermoregulation models. The accuracy and scope of the thermal models are improved, for the consideration of individual differences, integration to clothing models, exposure to cold and hot conditions, and the changes of physiological responses for the elders...
December 2016: Journal of Thermal Biology
https://www.readbyqxmd.com/read/27885528/a-network-biology-approach-to-understanding-the-importance-of-chameleon-proteins-in-human-physiology-and-pathology
#20
Golnaz Bahramali, Bahram Goliaei, Zarrin Minuchehr, Sayed-Amir Marashi
Chameleon proteins are proteins which include sequences that can adopt α-helix-β-strand (HE-chameleon) or α-helix-coil (HC-chameleon) or β-strand-coil (CE-chameleon) structures to operate their crucial biological functions. In this study, using a network-based approach, we examined the chameleon proteins to give a better knowledge on these proteins. We focused on proteins with identical chameleon sequences with more than or equal to seven residues long in different PDB entries, which adopt HE-chameleon, HC-chameleon, and CE-chameleon structures in the same protein...
November 24, 2016: Amino Acids
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