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https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#1
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/27913961/prediction-of-postoperative-clinical-recovery-of-drop-foot-attributable-to-lumbar-degenerative-diseases-via-a-bayesian-network
#2
Shota Takenaka, Hiroyuki Aono
BACKGROUND: Drop foot resulting from degenerative lumbar diseases can impair activities of daily living. Therefore, predictors of recovery of this symptom have been investigated using univariate or/and multivariate analyses. However, the conclusions have been somewhat controversial. Bayesian network models, which are graphic and intuitive to the clinician, may facilitate understanding of the prognosis of drop foot resulting from degenerative lumbar diseases. QUESTIONS/PURPOSES: (1) To show a layered correlation among predictors of recovery from drop foot resulting from degenerative lumbar diseases; and (2) to develop support tools for clinical decisions to treat drop foot resulting from lumbar degenerative diseases...
December 2, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27913431/pro-brain-derived-neurotrophic-factor-probdnf-mediated-p75ntr-activation-promotes-depolarizing-actions-of-gaba-and-increases-susceptibility-to-epileptic-seizures
#3
Baptiste Riffault, Nazim Kourdougli, Camille Dumon, Nadine Ferrand, Emmanuelle Buhler, Fabienne Schaller, Caroline Chambon, Claudio Rivera, Jean-Luc Gaiarsa, Christophe Porcher
The brain-derived neurotrophic factor (BDNF) is synthesized as a precursor, namely proBDNF, which can be processed into mature BDNF (mBDNF). Evidences suggest that proBDNF signaling through p75(NTR) may account for the emergence of neurological disorders. These findings support the view that the relative availability of mBDNF and proBDNF forms is an important mechanism underlying brain circuit formation and cognitive functions. Here we describe novel insights into the proBDNF/p75(NTR) mechanisms and function in vivo in modulating neuronal circuit and synaptic plasticity during the first postnatal weeks in rats...
December 1, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27913430/cortical-circuit-for-binding-object-identity-and-location-during-multiple-object-tracking
#4
Lauri Nummenmaa, Lauri Oksama, Erico Glerean, Jukka Hyönä
Sustained multifocal attention for moving targets requires binding object identities with their locations. The brain mechanisms of identity-location binding during attentive tracking have remained unresolved. In 2 functional magnetic resonance imaging experiments, we measured participants' hemodynamic activity during attentive tracking of multiple objects with equivalent (multiple-object tracking) versus distinct (multiple identity tracking, MIT) identities. Task load was manipulated parametrically. Both tasks activated large frontoparietal circuits...
December 1, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27913424/digital-3d-reconstructions-using-histological-serial-sections-of-lung-tissue-including-the-alveolar-capillary-network
#5
Roman Grothausmann, Lars Knudsen, Matthias Ochs, Christian Mühlfeld
The alveolar capillary network (ACN) provides an enormously large surface area that is necessary for pulmonary gas exchange. Changes of the ACN during normal or pathological development or in pulmonary diseases are of great functional impact and warrant further analysis. Due to the complexity of the three-dimensional (3D) architecture of the ACN, 2D approaches are limited in providing a comprehensive impression of the characteristics of the normal ACN or the nature of its alterations. Stereological methods offer a quantitative way to assess the ACN in 3D in terms of capillary volume, surface area or number but lack a 3D visualization to interpret the data...
December 2, 2016: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/27913387/using-multivariate-base-rates-to-interpret-low-scores-on-an-abbreviated-battery-of-the-delis-kaplan-executive-function-system
#6
Justin E Karr, Mauricio A Garcia-Barrera, James A Holdnack, Grant L Iverson
OBJECTIVE: Executive function consists of multiple cognitive processes that operate as an interactive system to produce volitional goal-oriented behavior, governed in large part by frontal microstructural and physiological networks. Identification of deficits in executive function in those with neurological or psychiatric conditions can be difficult because the normal variation in executive function test scores, in healthy adults when multiple tests are used, is largely unknown. This study addresses that gap in the literature by examining the prevalence of low scores on a brief battery of executive function tests...
December 1, 2016: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
https://www.readbyqxmd.com/read/27913370/asymptotic-fuzzy-neural-network-control-for-pure-feedback-stochastic-systems-based-on-a-semi-nussbaum-function-technique
#7
Ci Chen, Zhi Liu, Kan Xie, Yun Zhang, C L Philip Chen
Most existing control results for pure-feedback stochastic systems are limited to a condition that tracking errors are bounded in probability. Departing from such bounded results, this paper proposes an asymptotic fuzzy neural network control for pure-feedback stochastic systems. The control goal is realized by proposing a novel semi-Nussbaum function-based technique and employing it in adaptive backstepping controller design. The proposed Nussbaum function is integrated with adaptive control technique to guarantee that the tracking error is asymptotically stable in probability...
November 28, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/27913368/content-driven-associative-memories-for-color-image-patterns
#8
Mingming Li, Shuzhi Sam Ge, Tong Heng Lee
This paper presents a novel content-driven associative memory (CDAM) to associate large-scale color images based on the subjects that represent the images' content. Compared to traditional associative memories, CDAM inherits their tolerance to random noise in images and possesses greater robustness against correlated noise that distorts an image's spatial contextual structure. A three-layer recurrent neural tensor network (RNTN) is designed as the network model of CDAM. Multiple salient objects detection algorithm and partial radial basis function (PRBF) kernel are proposed for subject determination and content-driven association, respectively...
November 29, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/27913356/a-framework-for-integrating-multiple-biological-networks-to-predict-microrna-disease-associations
#9
Wei Peng, Wei Lan, Zeng Yu, Jianxin Wang, Yi Pan
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict the associations between MicroRNA and disease is still a big challenge. Previous researchers have pointed out that there are complex relationships among microRNAs, diseases and environment factors. There are inter-relationships between microRNAs, diseases or environment factors based on their functional similarity or phenotype similarity or chemical structure similarity and so on...
November 29, 2016: IEEE Transactions on Nanobioscience
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
#10
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/27913294/sleep-mediated-memory-consolidation-depends-on-the-level-of-integration-at-encoding
#11
Lea Himmer, Elias Müller, Steffen Gais, Monika Schönauer
There is robust evidence that sleep facilitates declarative memory consolidation. Integration of newly acquired memories into existing neocortical knowledge networks has been proposed to underlie this effect. Here, we test whether sleep affects memory retention for word-picture associations differently when it was learned explicitly or using a fast mapping strategy. Fast mapping is an incidental form of learning that references new information to existing knowledge and possibly allows neocortical integration already during encoding...
November 29, 2016: Neurobiology of Learning and Memory
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#12
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913189/construction-and-analysis-of-a-human-testis-sperm-enriched-interaction-network-unraveling-the-ppp1cc2-interactome
#13
Joana Vieira Silva, Sooyeon Yoon, Pieter-Jan De Bock, Alexander V Goltsev, Kris Gevaert, José Fernando F Mendes, Margarida Fardilha
BACKGROUND: Phosphoprotein phosphatase 1 catalytic subunit gamma 2 (PPP1CC2), a PPP1CC tissue-specific alternative splice restricted to testicular germ cells and spermatozoa, is essential for spermatogenesis and spermatozoa motility. The key to understand PPP1CC2 regulation lies on the characterization of its interacting partners. METHODS: We construct a testis/sperm-enriched protein interaction network and analyzed the topological properties and biological context of the network...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913157/further-evidence-of-alerted-default-network-connectivity-and-association-with-theory-of-mind-ability-in-schizophrenia
#14
Omar Mothersill, Noreen Tangney, Derek W Morris, Hazel McCarthy, Thomas Frodl, Michael Gill, Aiden Corvin, Gary Donohoe
BACKGROUND: Resting-state functional magnetic resonance imaging (rs-fMRI) has repeatedly shown evidence of altered functional connectivity of large-scale networks in schizophrenia. The relationship between these connectivity changes and behaviour (e.g. symptoms, neuropsychological performance) remains unclear. METHODS: Functional connectivity in 27 patients with schizophrenia or schizoaffective disorder, and 25 age and gender matched healthy controls was examined using rs-fMRI...
November 29, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27913149/mutations-at-protein-protein-interfaces-small-changes-over-big-surfaces-have-large-impacts-on-human-health
#15
REVIEW
Harry C Jubb, Arun P Pandurangan, Meghan A Turner, Bernardo Ochoa-Montaño, Tom L Blundell, David B Ascher
Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance...
November 29, 2016: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/27913140/comparative-analysis-of-tcdd-induced-ahr-mediated-gene-expression-in-human-mouse-and-rat-primary-b-cells
#16
Natalia Kovalova, Rance Nault, Robert Crawford, Timothy R Zacharewski, Norbert E Kaminski
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental pollutant that activates the aryl hydrocarbon receptor (AhR) resulting in altered gene expression. In vivo, in vitro, and ex vivo studies have demonstrated that B cells are directly impaired by TCDD, and are a sensitive target as evidenced by suppression of antibody responses. The window of sensitivity to TCDD-induced suppression of IgM secretion among mouse, rat and human B cells is similar. Specifically, TCDD must be present within the initial 12h post B cell stimulation, indicating that TCDD disrupts early signaling network(s) necessary for B lymphocyte activation and differentiation...
November 29, 2016: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/27912160/successful-group-psychotherapy-of-depression-in-adolescents-alters-fronto-limbic-resting-state-connectivity
#17
J Straub, C D Metzger, P L Plener, M G Koelch, G Groen, B Abler
BACKGROUND: Current resting state imaging findings support suggestions that the neural signature of depression and therefore also its therapy should be conceptualized as a network disorder rather than a dysfunction of specific brain regions. In this study, we compared neural connectivity of adolescent patients with depression (PAT) and matched healthy controls (HC) and analysed pre-to-post changes of seed-based network connectivities in PAT after participation in a cognitive behavioral group psychotherapy (CBT)...
November 20, 2016: Journal of Affective Disorders
https://www.readbyqxmd.com/read/27912097/lncpress1-is-a-p53-regulated-lncrna-that-safeguards-pluripotency-by-disrupting-sirt6-mediated-de-acetylation-of-histone-h3k56
#18
Abhinav K Jain, Yuanxin Xi, Ryan McCarthy, Kendra Allton, Kadir C Akdemir, Lalit R Patel, Bruce Aronow, Chunru Lin, Wei Li, Liuqing Yang, Michelle C Barton
Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome-wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs highly expressed in pluripotent hESCs and repressed by p53 during differentiation to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27912071/classical-and-alternative-macrophages-have-impaired-function-during-acute-and-chronic-hiv-1-infection
#19
Leonardo J Galvão-Lima, Milena S Espíndola, Luana S Soares, Fabiana A Zambuzi, Maira Cacemiro, Caroline Fontanari, Valdes R Bollela, Fabiani G Frantz
OBJECTIVES: Three decades after HIV recognition and its association with AIDS development, many advances have emerged - especially related to prevention and treatment. Undoubtedly, the development of Highly Active Antiretroviral Therapy (HAART) dramatically changed the future of the syndrome that we know today. In the present study, we evaluate the impact of HAART on macrophage function and its relevance to HIV pathogenesis. METHODS: PBMCs were isolated from blood samples and monocytes (CD14+ cells) were purified...
November 29, 2016: Brazilian Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27911959/barriers-to-timely-and-safe-blood-transfusion-for-pph-patients-evidence-from-a-qualitative-study-in-dhaka-bangladesh
#20
Sadika Akhter, Iqbal Anwar, Rashida Akter, Feroza Akhter Kumkum, Monjura Khatun Nisha, Fatema Ashraf, Ferdousi Islam, Nazneen Begum, Mahbub Elahi Chowdhury, Anne Austin, Syed Shariful Islam, Aminur Rahman
BACKGROUND AND OBJECTIVES: In Bangladesh, postpartum hemorrhage (PPH) is the leading cause of maternal mortality accounting for 31% of all blood transfusions in the country. Although safe blood transfusion is one of the 8 signal functions of Comprehensive Emergency Obstetric Care (CEmOC) strategy, most of the designated public sector CEmOC facilities do not have on-site blood storage system. Emergent blood is mainly available from external blood banks. As a result, emergent patients are to rely on an unregulated network of brokers for blood which may raise question about blood safety...
2016: PloS One
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