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https://www.readbyqxmd.com/read/28432959/molecular-dynamics-simulation-studies-of-novel-%C3%AE-lactamase-inhibitor
#1
Farhan Ul Haq, Asma Abro, Saad Raza, Klaus R Liedl, Syed Sikander Azam
New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods...
April 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#2
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28431844/health-care-associated-infections-studies-project-an-american-journal-of-infection-control-and-national-healthcare-safety-network-data-quality-collaboration
#3
Henrietta Smith, Janet E Brooks, Denise Leaptrot, Katherine Allen-Bridson, Angela Anttila, Cindy Gross, Joan N Hebden, Georganne Ryan, Eileen Scalise, Marc-Oliver Wright
This case study is part of a series centered on the Centers for Disease Control and Prevention's National Healthcare Safety Network's (NHSN) health care-associated infection (HAI) surveillance definitions. The intent of the case study series is to foster standardized application of the NHSN's HAI surveillance definitions among infection preventionists and accurate determination of HAI events. This specific case study focuses on the definitions found within the surgical site infection (SSI) protocol. It aims to reflect the real life and complex patient scenario surrounding a bloodstream infection that is secondary to an SSI and the application of the Present at the Time of Surgery event detail...
April 18, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/28431620/role-of-inflammatory-molecules-in-the-alzheimer-s-disease-progression-and-diagnosis
#4
REVIEW
Eva Bagyinszky, Vo Van Giau, Kyuhwan Shim, Kyoungho Suk, Seong Soo A An, SangYun Kim
Alzheimer's disease (AD) is a complex disorder and the most common form of neurodegenerative dementia. Several genetic, environmental, and physiological factors, including inflammations and metabolic influences, are involved in the progression of AD. Inflammations are composed of complicated networks of many chemokines and cytokines with diverse cells. Inflammatory molecules are needed for the protection against pathogens, and maintaining their balances is important for normal physiological function. Recent studies demonstrated that inflammation may be involved in neurodegenerative dementia...
May 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28431241/akt-pkb-signaling-navigating-the-network
#5
REVIEW
Brendan D Manning, Alex Toker
The Ser and Thr kinase AKT, also known as protein kinase B (PKB), was discovered 25 years ago and has been the focus of tens of thousands of studies in diverse fields of biology and medicine. There have been many advances in our knowledge of the upstream regulatory inputs into AKT, key multifunctional downstream signaling nodes (GSK3, FoxO, mTORC1), which greatly expand the functional repertoire of AKT, and the complex circuitry of this dynamically branching and looping signaling network that is ubiquitous to nearly every cell in our body...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431138/cardiovascular-outcome-trials-in-patients-with-chronic-kidney-disease-challenges-associated-with-selection-of-patients-and-endpoints
#6
Patrick Rossignol, Rajiv Agarwal, Bernard Canaud, Alan Charney, Gilles Chatellier, Jonathan C Craig, William C Cushman, Ronald T Gansevoort, Bengt Fellström, Dahlia Garza, Nicolas Guzman, Frank A Holtkamp, Gerard M London, Ziad A Massy, Alexandre Mebazaa, Peter G M Mol, Marc A Pfeffer, Yves Rosenberg, Luis M Ruilope, Jonathan Seltzer, Amil M Shah, Salim Shah, Bhupinder Singh, Bergur V Stefánsson, Norman Stockbridge, Wendy Gattis Stough, Kristian Thygesen, Michael Walsh, Christoph Wanner, David G Warnock, Christopher S Wilcox, Janet Wittes, Bertram Pitt, Aliza Thompson, Faiez Zannad
Although cardiovascular disease is a major health burden for patients with chronic kidney disease, most cardiovascular outcome trials have excluded patients with advanced chronic kidney disease. Moreover, the major cardiovascular outcome trials that have been conducted in patients with end-stage renal disease have not demonstrated a treatment benefit. Thus, clinicians have limited evidence to guide the management of cardiovascular disease in patients with chronic kidney disease, particularly those on dialysis...
April 18, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#7
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430827/dual-role-of-the-toxoplasma-gondii-clathrin-adaptor-ap1-in-the-sorting-of-rhoptry-and-microneme-proteins-and-in-parasite-division
#8
Kannan Venugopal, Elisabeth Werkmeister, Nicolas Barois, Jean-Michel Saliou, Anais Poncet, Ludovic Huot, Fabien Sindikubwabo, Mohamed Ali Hakimi, Gordon Langsley, Frank Lafont, Sabrina Marion
Toxoplasma gondii possesses a highly polarized secretory system, which efficiently assembles de novo micronemes and rhoptries during parasite replication. These apical secretory organelles release their contents into host cells promoting parasite invasion and survival. Using a CreLox-based inducible knock-out strategy and the ddFKBP over-expression system, we unraveled novel functions of the clathrin adaptor complex TgAP1. First, our data indicate that AP1 in T. gondii likely functions as a conserved heterotetrameric complex composed of the four subunits γ, β, μ1, σ1 and interacts with known regulators of clathrin-mediated vesicular budding such as the unique ENTH-domain containing protein, which we named Epsin-like protein (TgEpsL)...
April 21, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28430663/co-expression-network-analysis-identified-six-hub-genes-in-association-with-metastasis-risk-and-prognosis-in-hepatocellular-carcinoma
#9
Pengfei Chen, Fan Wang, Juerong Feng, Rui Zhou, Ying Chang, Jing Liu, Qiu Zhao
Hepatocellular carcinoma (HCC) has a high incidence and mortality worldwide, and its carcinogenesis and progression are influenced by a complex network of gene interactions. A weighted gene co-expression network was constructed to identify gene modules associated with the clinical traits in HCC (n = 214). Among the 13 modules, high correlation was only found between the red module and metastasis risk (classified by the HCC metastasis gene signature) (R2 = -0.74). Moreover, in the red module, 34 network hub genes for metastasis risk were identified, six of which (ABAT, AGXT, ALDH6A1, CYP4A11, DAO and EHHADH) were also hub nodes in the protein-protein interaction network of the module genes...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430595/minus-end-directed-kinesin-14-kifc1-regulates-the-positioning-and-architecture-of-the-golgi-apparatus
#10
Zhen-Yu She, Meng-Ying Pan, Fu-Qing Tan, Wan-Xi Yang
The Golgi apparatus is the central organelle along the eukaryotic secretory and endocytic pathway. In non-polarized mammalian cells, the Golgi complex is usually located proximal to the nucleus at the cell center and is closely associated with the microtubule organizing center. Microtubule networks are essential in the organization and central localization of the Golgi apparatus, but the molecular basis underlying these processes are poorly understood. Here we reveal that minus end-directed kinesin-14 KIFC1 proteins are required for the structural integrity and positioning of the Golgi complex in non-polarized mammalian cells...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430248/accurate-determination-of-dielectric-permittivity-of-polymers-from-75%C3%A2-%C3%A2-ghz-to-1-6%C3%A2-%C3%A2-thz-using-both-s-parameters-and-transmission-spectroscopy
#11
Tianying Chang, Xiansheng Zhang, Xiaoxuan Zhang, Hong-Liang Cui
Interactions of terahertz (THz) electromagnetic radiation with polymer materials have been studied recently with increasing depth and breadth, for purposes of both using polymers in fabricating THz optical components such as lenses, waveplates, waveguides, and sample holders/containers, and employing THz spectral imaging as a new tool for nondestructive testing of polymer composite structures. Either endeavor cannot even begin without a quantitative knowledge of the complex dielectric permittivity, i.e., the propagation and attenuation properties of such polymers in the requisite wave band...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28430156/zero-sum-matrix-game-with-payoffs-of-dempster-shafer-belief-structures-and-its-applications-on-sensors
#12
Xinyang Deng, Wen Jiang, Jiandong Zhang
The zero-sum matrix game is one of the most classic game models, and it is widely used in many scientific and engineering fields. In the real world, due to the complexity of the decision-making environment, sometimes the payoffs received by players may be inexact or uncertain, which requires that the model of matrix games has the ability to represent and deal with imprecise payoffs. To meet such a requirement, this paper develops a zero-sum matrix game model with Dempster-Shafer belief structure payoffs, which effectively represents the ambiguity involved in payoffs of a game...
April 21, 2017: Sensors
https://www.readbyqxmd.com/read/28430044/syntactic-complexity-and-frequency-in-the-neurocognitive-language-system
#13
Yun-Hsuan Yang, William D Marslen-Wilson, Mirjana Bozic
Prominent neurobiological models of language follow the widely accepted assumption that language comprehension requires two principal mechanisms: a lexicon storing the sound-to-meaning mapping of words, primarily involving bilateral temporal regions, and a combinatorial processor for syntactically structured items, such as phrases and sentences, localized in a left-lateralized network linking left inferior frontal gyrus (LIFG) and posterior temporal areas. However, recent research showing that the processing of simple phrasal sequences may engage only bilateral temporal areas, together with the claims of distributional approaches to grammar, raises the question of whether frequent phrases are stored alongside individual words in temporal areas...
April 21, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/28429940/density-functional-theory-and-car-parrinello-molecular-dynamics-study-of-the-hydrogen-producing-mechanism-of-the-co-dmgbf2-2-and-co-dmgh-2-cobaloxime-complexes-in-the-acetonitrile-water-solvent
#14
Jinfan Chen, Patrick H-L Sit
The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts Co(dmgBF2)2 (dmgBF2=difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH=dimethylglyoxime), were studied by Density Functional Theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water...
April 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28429833/the-microbially-mediated-soil-organic-carbon-loss-under-degenerative-succession-in-an-alpine-meadow
#15
Yuguang Zhang, Xiao Liu, Jing Cong, Hui Lu, Yuyu Sheng, Xiulei Wang, Diqiang Li, Xueduan Liu, Huaqun Yin, Jizhong Zhou, Ye Deng
Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially-mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analyzed using high-throughput technologies, including Illumina sequencing and GeoChip functional gene arrays. The soil microbial community structure and diversity were significantly (P < 0...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28429729/weak-connections-form-an-infinite-number-of-patterns-in-the-brain
#16
Hai-Peng Ren, Chao Bai, Murilo S Baptista, Celso Grebogi
Recently, much attention has been paid to interpreting the mechanisms for memory formation in terms of brain connectivity and dynamics. Within the plethora of collective states a complex network can exhibit, we show that the phenomenon of Collective Almost Synchronisation (CAS), which describes a state with an infinite number of patterns emerging in complex networks for weak coupling strengths, deserves special attention. We show that a simulated neuron network with neurons weakly connected does produce CAS patterns, and additionally produces an output that optimally model experimental electroencephalograph (EEG) signals...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429415/rod-shaped-neural-units-for-aligned-3d-neural-network-connection
#17
Midori Kato-Negishi, Hiroaki Onoe, Akane Ito, Shoji Takeuchi
This paper proposes neural tissue units with aligned nerve fibers (called rod-shaped neural units) that connect neural networks with aligned neurons. To make the proposed units, 3D fiber-shaped neural tissues covered with a calcium alginate hydrogel layer are prepared with a microfluidic system and are cut in an accurate and reproducible manner. These units have aligned nerve fibers inside the hydrogel layer and connectable points on both ends. By connecting the units with a poly(dimethylsiloxane) guide, 3D neural tissues can be constructed and maintained for more than two weeks of culture...
April 21, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28429195/computer-assisted-diagnosis-system-for-breast-cancer-in-computed-tomography-laser-mammography-ctlm
#18
Afsaneh Jalalian, Syamsiah Mashohor, Rozi Mahmud, Babak Karasfi, M Iqbal Saripan, Abdul Rahman Ramli
Computed tomography laser mammography (Eid et al. Egyp J Radiol Nucl Med, 37(1): p. 633-643, 1) is a non-invasive imaging modality for breast cancer diagnosis, which is time-consuming and challenging for the radiologist to interpret the images. Some issues have increased the missed diagnosis of radiologists in visual manner assessment in CTLM images, such as technical reasons which are related to imaging quality and human error due to the structural complexity in appearance. The purpose of this study is to develop a computer-aided diagnosis framework to enhance the performance of radiologist in the interpretation of CTLM images...
April 20, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28429067/neuronal-oscillations-and-synchronicity-associated-with-gamma-hydroxybutyrate-during-resting-state-in-healthy-male-volunteers
#19
Robin von Rotz, Michael Kometer, Dario Dornbierer, Jürg Gertsch, M Salomé Gachet, Franz X Vollenweider, Erich Seifritz, Oliver G Bosch, Boris B Quednow
RATIONALE: Gamma-hydroxybutyrate (GHB) is a putative neurotransmitter, a drug of abuse, an anesthetic agent, and a treatment for neuropsychiatric disorders. In previous electroencephalography (EEG) studies, GHB was shown to induce an electrophysiological pattern of "paradoxical EEG-behavioral dissociation" characterized by increased delta and theta oscillations usually associated with sleep during awake states. However, no detailed source localization of these alterations and no connectivity analyses have been performed yet...
April 20, 2017: Psychopharmacology
https://www.readbyqxmd.com/read/28428822/in-muro-deacetylation-of-xylan-affects-lignin-properties-and-improves-saccharification-of-aspen-wood
#20
Prashant Mohan-Anupama Pawar, Marta Derba-Maceluch, Sun-Li Chong, Madhavi Latha Gandla, Shamrat Shafiul Bashar, Tobias Sparrman, Patrik Ahvenainen, Mattias Hedenström, Merve Özparpucu, Markus Rüggeberg, Ritva Serimaa, Martin Lawoko, Maija Tenkanen, Leif J Jönsson, Ewa J Mellerowicz
BACKGROUND: Lignocellulose from fast growing hardwood species is a preferred source of polysaccharides for advanced biofuels and "green" chemicals. However, the extensive acetylation of hardwood xylan hinders lignocellulose saccharification by obstructing enzymatic xylan hydrolysis and causing inhibitory acetic acid concentrations during microbial sugar fermentation. To optimize lignocellulose for cost-effective saccharification and biofuel production, an acetyl xylan esterase AnAXE1 from Aspergillus niger was introduced into aspen and targeted to cell walls...
2017: Biotechnology for Biofuels
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