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https://www.readbyqxmd.com/read/27914088/murine-mycobacterium-marinum-infection-as-a-model-for-tuberculosis
#1
Julia Lienard, Fredric Carlsson
Mycobacteria are a major human health problem globally. Regarding tuberculosis the situation is worsened by the poor efficacy of current vaccine regimens and by emergence of drug-resistant strains (Manjelievskaia J et al, Trans R Soc Trop Med Hyg 110: 110, 2016; Pereira et al., Lancet Infect Dis 12:300-306, 2012; http://www.who.int/tb/publications/global_report/en/) undermining both disease-prevention and available treatments. Thus, increased basic understanding of mycobacterial-and particularly Mycobacterium tuberculosis-virulence strategies and pathogenesis is of great importance...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#2
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#3
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#4
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914029/mid-term-results-and-responsiveness-predictors-after-two-step-single-anastomosis-duodeno-ileal-bypass-with-sleeve-gastrectomy
#5
José M Balibrea, Ramón Vilallonga, Marta Hidalgo, Andreea Ciudin, Óscar González, Enric Caubet, Andrés Sánchez-Pernaute, José M Fort, Manel Armengol-Carrasco
BACKGROUND: In patients with insufficient weight loss after sleeve gastrectomy (SG) or in super obese individuals, among many surgical options available, a single-anastomosis duodeno-ileal bypass (SADI) after SG (SADI-S) could be considered. Due to the limited information available about the use of SADI as a second-step procedure, the objective of this study was to evaluate the mid-term results and responsiveness of SADI after sleeve gastrectomy. METHODS: We present prospective data from 30 consecutive patients with a mean BMI of 40...
December 2, 2016: Obesity Surgery
https://www.readbyqxmd.com/read/27913989/cost-effectiveness-analysis-of-isavuconazole-vs-voriconazole-as-first-line-treatment-for-invasive-aspergillosis
#6
Rachel Harrington, Edward Lee, Hongbo Yang, Jin Wei, Andrew Messali, Nkechi Azie, Eric Q Wu, James Spalding
INTRODUCTION: Invasive aspergillosis (IA) is associated with a significant clinical and economic burden. The phase III SECURE trial demonstrated non-inferiority in clinical efficacy between isavuconazole and voriconazole. No studies have evaluated the cost-effectiveness of isavuconazole compared to voriconazole. The objective of this study was to evaluate the costs and cost-effectiveness of isavuconazole vs. voriconazole for the first-line treatment of IA from the US hospital perspective...
December 2, 2016: Advances in Therapy
https://www.readbyqxmd.com/read/27913916/development-of-international-terminology-and-definitions-for-texture-modified-foods-and-thickened-fluids-used-in-dysphagia-management-the-iddsi-framework
#7
Julie A Y Cichero, Peter Lam, Catriona M Steele, Ben Hanson, Jianshe Chen, Roberto O Dantas, Janice Duivestein, Jun Kayashita, Caroline Lecko, Joseph Murray, Mershen Pillay, Luis Riquelme, Soenke Stanschus
Dysphagia is estimated to affect ~8% of the world's population (~590 million people). Texture-modified foods and thickened drinks are commonly used to reduce the risks of choking and aspiration. The International Dysphagia Diet Standardisation Initiative (IDDSI) was founded with the goal of developing globally standardized terminology and definitions for texture-modified foods and liquids applicable to individuals with dysphagia of all ages, in all care settings, and all cultures. A multi-professional volunteer committee developed a dysphagia diet framework through systematic review and stakeholder consultation...
December 2, 2016: Dysphagia
https://www.readbyqxmd.com/read/27913884/plasmid-pvax1-nh36-purification-by-membrane-and-bead-perfusion-chromatography
#8
Diana Ivonne Franco-Medrano, Patricia Guerrero-Germán, Rosa María Montesinos-Cisneros, Jaime Ortega-López, Armando Tejeda-Mansir
The demand for plasmid DNA (pDNA) has increased in response to the rapid advances in vaccines applications to prevent and treat infectious diseases caused by virus, bacteria or parasites, such as Leishmania species. The immunization protocols require large amounts of supercoiled plasmid DNA (sc-pDNA) challenging the development of efficient and profitable processes for capturing and purified pDNA molecules from large volumes of lysates. A typical bioprocess involves four steps: fermentation, primary recovery, intermediate recovery and final purification...
December 2, 2016: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/27913859/complex-genetics-architecture-contributes-to-salmonella-resistance-in-acb60-mice
#9
Sean Beatty, Leïla Rached-D'Astous, Danielle Malo
Human infection with Salmonella is of global public health concern. In low- and middle-income countries, Salmonella infection is a major source of disease in terms of both mortality and morbidity, while in high-income nations, the pathogen is an ongoing threat to food security. The outcome of infection with Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) in mouse models is dependent upon a coordinated and complex immune response. A panel of recombinant congenic strains (RCS) derived from the reciprocal double backcross of A/J and C57BL/6J mice has been screened for their susceptibility to Salmonella infection, and the RCS AcB60 was identified to be the most resistant strain to Salmonella infection, more resistant than the parental strain A/J...
December 2, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/27913844/global-dna-methylation-profiling-of-manganese-exposed-human-neuroblastoma-sh-sy5y-cells-reveals-epigenetic-alterations-in-parkinson-s-disease-associated-genes
#10
Prashant Tarale, Saravanadevi Sivanesan, Atul P Daiwile, Reinhard Stöger, Amit Bafana, Pravin K Naoghare, Devendra Parmar, Tapan Chakrabarti, Krishnamurthi Kannan
Manganese (Mn) is an essential trace element required for optimal functioning of cellular biochemical pathways in the central nervous system. Elevated exposure to Mn through environmental and occupational exposure can cause neurotoxic effects resulting in manganism, a condition with clinical symptoms identical to idiopathic Parkinson's disease. Epigenetics is now recognized as a biological mechanism involved in the etiology of various diseases. Here, we investigated the role of DNA methylation alterations induced by chronic Mn (100 µM) exposure in human neuroblastoma (SH-SY5Y) cells in relevance to Parkinson's disease...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27913828/engineering-and-evolution-of-saccharomyces-cerevisiae-to-produce-biofuels-and-chemicals
#11
Timothy L Turner, Heejin Kim, In Iok Kong, Jing-Jing Liu, Guo-Chang Zhang, Yong-Su Jin
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology...
December 3, 2016: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/27913801/the-pressure-reduction-coefficient-a-new-parameter-to-assess-aneurysmal-blood-stasis-induced-by-flow-diverters-disruptors
#12
Gregory Gascou, Riccardo Ferrara, Dominique Ambard, Mathieu Sanchez, Kyriakos Lobotesis, Franck Jourdan, Vincent Costalat
BACKGROUND AND PURPOSE: Pore density (PD), surface metal coverage (SMC) and the number of wires are all different parameters which can influence the efficacy of a flow disruptor/diverter. Nevertheless, the relative importance of a parameter to induce intra-aneurysmal blood stasis is still poorly evaluated. Therefore, comparison between devices based on a unique value is not reliable. The aim of this study was to propose a new bench top parameter (the pressure reduction coefficient (PRC; ξ)) in order to assess the global haemodynamic effect of each flow diverter/disruptor to slow flow...
December 2, 2016: Interventional Neuroradiology
https://www.readbyqxmd.com/read/27913725/in-vivo-expression-technology-and-5-end-mapping-of-the-borrelia-burgdorferi-transcriptome-identify-novel-rnas-expressed-during-mammalian-infection
#13
Philip P Adams, Carlos Flores Avile, Niko Popitsch, Ivana Bilusic, Renée Schroeder, Meghan Lybecker, Mollie W Jewett
Borrelia burgdorferi, the bacterial pathogen responsible for Lyme disease, modulates its gene expression profile in response to the environments encountered throughout its tick-mammal infectious cycle. To begin to characterize the B. burgdorferi transcriptome during murine infection, we previously employed an in vivo expression technology-based approach (BbIVET). This identified 233 putative promoters, many of which mapped to un-annotated regions of the complex, segmented genome. Herein, we globally identify the 5' end transcriptome of B...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913648/cd36-mediated-uptake-of-surfactant-lipids-by-human-macrophages-promotes-intracellular-growth-of-mycobacterium-tuberculosis
#14
Claire E Dodd, Charlie J Pyle, Rebecca Glowinski, Murugesan V S Rajaram, Larry S Schlesinger
Mycobacterium tuberculosis imposes a large global health burden as the airborne agent of tuberculosis. Mycobacterium tuberculosis has been flourishing in human populations for millennia and is therefore highly adapted to the lung environment. Alveolar macrophages, a major host cell niche for M. tuberculosis, are not only phagocytose inhaled microbes and particulate matter but are also crucial in catabolizing lung surfactant, a lipid-protein complex that lines the alveolar spaces. Because macrophage host defense properties can be regulated by surfactant and M...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27913602/clonal-conversion-of-b-lymphoid-leukemia-reveals-cross-lineage-transfer-of-malignant-states
#15
Rajesh Somasundaram, Josefine Åhsberg, Kazuki Okuyama, Jonas Ungerbäck, Henrik Lilljebjörn, Thoas Fioretos, Tobias Strid, Mikael Sigvardsson
Even though leukemia is considered to be confined to one specific hematopoietic cell type, cases of acute leukemia of ambiguous lineage and patients relapsing in phenotypically altered disease suggest that a malignant state may be transferred between lineages. Because B-cell leukemia is associated with mutations in transcription factors of importance for stable preservation of lineage identity, we here investigated the potential lineage plasticity of leukemic cells. We report that primary pro-B leukemia cells from mice carrying heterozygous mutations in either or both the Pax5 and Ebf1 genes, commonly mutated in human leukemia, can be converted into T lineage leukemia cells...
December 2, 2016: Genes & Development
https://www.readbyqxmd.com/read/27913557/translation-and-validation-of-the-cancer-related-fatigue-scale-in-greek-in-a-sample-of-patients-with-advanced-prostate-cancer
#16
Andreas Charalambous, Charis Kaite, Marianna Constantinou, Christiana Kouta
OBJECTIVE: To translate and validate the Cancer-Related Fatigue (CRF) Scale in the Greek language. DESIGN: A cross-sectional descriptive design was used in order to translate and validate the CRF Scale in Greek. Factor analyses were performed to understand the psychometric properties of the scale and to establish construct, criterion and convergent validity. SETTING: Outpatients' oncology clinics of two public hospitals in Cyprus. PARTICIPANTS: 148 patients with advanced prostate cancer undergoing chemotherapy...
December 2, 2016: BMJ Open
https://www.readbyqxmd.com/read/27913362/learning-to-predict-eye-fixations-via-multiresolution-convolutional-neural-networks
#17
Nian Liu, Junwei Han, Tianming Liu, Xuelong Li
Eye movements in the case of freely viewing natural scenes are believed to be guided by local contrast, global contrast, and top-down visual factors. Although a lot of previous works have explored these three saliency cues for several years, there still exists much room for improvement on how to model them and integrate them effectively. This paper proposes a novel computation model to predict eye fixations, which adopts a multiresolution convolutional neural network (Mr-CNN) to infer these three types of saliency cues from raw image data simultaneously...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27913295/dissection-of-functional-lncrnas-in-alzheimer-s-disease-by-construction-and-analysis-of-lncrna-mrna-networks-based-on-competitive-endogenous-rnas
#18
Lian-Kun Wang, Xiao-Feng Chen, Dan-Dan He, You Li, Jin Fu
Alzheimer's disease (AD) is a neurodegenerative disorder that is the most common cause of dementia in the elderly, and intracellular neurofibrillary tangles (NFTs) are one of the pathological features of AD. Recent studies have suggested long noncoding RNAs (lncRNAs) play important roles in AD. Competing endogenous RNAs (ceRNAs) is a mechanism that has recently been proposed, in which lncRNAs compete for common miRNA-binding sites with mRNAs. However, the roles of lncRNAs and ceRNA in AD NFTs is limited. In this study, we constructed a global triple network based on ceRNA theory, then an AD NFT lncRNA-mRNA network (NFTLMN) was generated...
November 29, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27913280/neuropsychological-functioning-and-chronic-methadone-use-a-systematic-review-and-meta-analysis
#19
REVIEW
A Baldacchino, M Armanyous, D J K Balfour, G Humphris, K Matthews
INTRODUCTION: There is a presumption that neurocognition is commonly impaired in chronic methadone exposed individuals (CM) when compared with healthy controls (HP). Additionally, it remains unclear if short term (<1year) abstinence (AP) is associated with an altered cognitive profile when compared with CM. METHOD: A random effect model approach was used on data assembled into the Comprehensive Meta-Analysis programme. Cohen's d effect sizes and a significance levels of p<0...
November 29, 2016: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/27913272/the-northeast-regional-sps-meeting-update-safety-pharmacology-innovations-and-applications
#20
REVIEW
Malar Pannirselvam, Tiffini Brabham, Alfred W Botchway, Donald B Hodges, Martin Traebert, Michael K Pugsley
The Safety Pharmacology Society (SPS) held a Northeast (NE) regional meeting in Boston, MA on May 13, 2016 at the Vertex Pharmaceuticals Incorporated site. There were 103 attendees from the pharmaceutical industry, contract research organizations (CROs), academia, and global regulatory agencies. An assortment of scientific topics were presented by 7 speakers that included broad topics in the cardiovascular (organ on chip, statistical power and translation of rat cardiovascular telemetry data and dual inhibition of IKr and IKs on QT interval prolongation) and central nervous system (in vitro platform for neurotoxicity, an integrated risk assessment of suicidal ideation and behavior, and EEG advances in safety pharmacology) and a novel topic discussing preclinical challenges faced in the development of a novel gene therapy...
November 29, 2016: Journal of Pharmacological and Toxicological Methods
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