428 Works

A data-driven acute inflammation therapy

Acute inflammation is a severe medical condition defined as an inflammatory response of the body to an infection. Its rapid progression requires quick and accurate decisions from clinicians. Inadequate and delayed decisions makes acute inflammation the 10th leading cause of death overall in United States with the estimated cost of treatment about $17 billion annually. However, despite the need, there are limited number of methods that could assist clinicians to determine optimal therapies for acute...

A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution

© Zhou et al. Understanding chromatin function requires knowing the precise location of nucleosomes. MNase-seq methods have been widely applied to characterize nucleosome organization in vivo, but generally lack the accuracy to determine the precise nucleosome positions. Here we develop a computational approach leveraging digestion variability to determine nucleosome positions at a base-pair resolution from MNase-seq data. We generate a variability template as a simple error model for how MNase digestion affects the mapping of...

A large-scale evaluation of computational protein function prediction

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction...

A comparative study of limiting strategies in discontinuous Galerkin schemes for the M1 model of radiation transport

© 2018 Elsevier B.V. The M1 minimum entropy moment system is a system of hyperbolic balance laws that approximates the radiation transport equation, and has many desirable properties. Among them are symmetric hyperbolicity, entropy decay, moment realizability, and correct behavior in the diffusion and free-streaming limits. However, numerical difficulties arise when approximating the solution of the M1 model by high order numerical schemes; namely maintaining the realizability of the numerical solution and controlling spurious oscillations....

A dense hierarchy of sublinear time approximation schemes for bin packing

The bin packing problem is to find the minimum number of bins of size one to pack a list of items with sizes a 1,..., a n in (0,1]. Using uniform sampling, which selects a random element from the input list each time, we develop a randomized (Formula Presented) time (1 + ε)- approximation scheme for the bin packing problem. We show that every randomized algorithm with uniform random sampling needs (Formula Presented) time to...

A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations

© 2016 American Chemical Society. We present a maximum-caliber method for inferring transition rates of a Markov state model (MSM) with perturbed equilibrium populations given estimates of state populations and rates for an unperturbed MSM. It is similar in spirit to previous approaches, but given the inclusion of prior information, it is more robust and simple to implement. We examine its performance in simple biased diffusion models of kinetics and then apply the method to...

Correction: P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma (Cell Death & Disease, (2020), 11, 9, (748), 10.1038/s41419-020-02940-w)

© 2020, The Author(s). Owing to an error in production, the original version of this Article contained an error in the author affiliations. Author Francesca Pentimalli was incorrectly associated with Histopathological Unit, IRCCS-Istituto Tumori “Giovanni Paolo II”, Viale Orazio Flacco 65, 70124 Bari, Italy. The author’s actual affiliation is Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCSFondazione G. Pascale, I-80131 Napoli, Italy. We apologise for this error, and confirm that it this has now been...

Are sedentary behavior and physical activity independently associated with cardiometabolic benefits? The Hispanic Community Health Study/Study of Latinos

© 2020 The Author(s). Background: Whether physical activity can reduce cardiometabolic risk particularly in understudied populations such as US Hispanics/Latinos is of public health interest. We prospectively examined the association of physical activity and cardiometabolic biomarkers in n = 8049 participants of the Hispanic Community Health Study/Study of Latinos, a community-based cohort study of 16,415 adults aged 18-74 yr who self-identified as Hispanic/Latino from four US urban centers. Methods: We assessed physical activity using accelerometry...

The crosstalk between prostate cancer and microbiota inflammation: Nutraceutical products are useful to balance this interplay?

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. The human microbiota shows pivotal roles in urologic health and disease. Emerging studies indicate that gut and urinary microbiomes can impact several urological diseases, both benignant and malignant, acting particularly on prostate inflammation and prostate cancer. Indeed, the microbiota exerts its influence on prostate cancer initiation and/or progression mechanisms through the regulation of chronic inflammation, apoptotic processes, cytokines, and hormonal production in response to different pathogenic...

Simple hydrogenic estimates for the exchange and correlation energies of atoms and atomic ions, with implications for density functional theory

© 2020 Author(s). Exact density functionals for the exchange and correlation energies are approximated in practical calculations for the ground-state electronic structure of a many-electron system. An important exact constraint for the construction of approximations is to recover the correct non-relativistic large-Z expansions for the corresponding energies of neutral atoms with atomic number Z and electron number N = Z, which are correct to the leading order (-0.221Z5/3 and -0.021Z ln Z, respectively) even in...

Where Did SARS-CoV-2 Come From?

© The Author(s) 2020. Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. Although Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their genetic dissimilarity to SARS-CoV-2 is so high that they are highly unlikely to be its direct ancestors. Thus, an intermediary host...

Condyle modeling stability, craniofacial asymmetry and ACTN3 genotypes: Contribution to TMD prevalence in a cohort of dentofacial deformities

© This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Craniofacial asymmetry, mandibular condylar modeling and temporomandibular joint disorders are common comorbidities of skeletally disproportionate malocclusions, but etiology of occurrence together is poorly understood. We compared asymmetry, condyle modeling stability and temporomandibular...

Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction

© 2020 Shapovalov et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Protein secondary structure prediction remains a vital topic with broad applications. Due to lack of a widely accepted standard in secondary structure predictor evaluation, a fair comparison of predictors is challenging. A detailed examination of factors...

PRMT5 silencing selectively affects MTAP-deleted mesothelioma: In vitro evidence of a novel promising approach

© 2020 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd Malignant mesothelioma (MM) is an aggressive asbestos-related cancer of the serous membranes. Despite intensive treatment regimens, MM is still a fatal disease, mainly due to the intrinsic resistance to current therapies and the lack of predictive markers and new valuable molecular targets. Protein arginine methyltransferase 5 (PRMT5) inhibition has recently emerged...

Progesterone Prolongs Viability and Anti-inflammatory Functions of Explanted Preterm Ovine Amniotic Membrane

© Copyright © 2020 Canciello, Teti, Mazzotti, Falconi, Russo, Giordano and Barboni. Amniotic membrane (AM) is considered an important medical device with many applications in regenerative medicine. The therapeutic properties of AM are due to its resistant extracellular matrix and to the large number of bioactive molecules released by its cells. An important goal that still remains to be achieved is the identification of cultural and preservation protocols able to maintain in time the membrane...

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

© The Author(s) 2020. The conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups...

Effects of air cavity in dynamic pressure sensors: Experimental validation

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. T. An air-backed diaphragm is the key structure of most dynamic pressure sensors and plays a critical role in determining the sensor performance. Our previous analytical model investigated the influence of air cavity length on the sensitivity and bandwidth. The model found that as the cavity length decreases, the static sensitivity monotonically decreases, and the fundamental natural frequency shows a three-stage trend: increasing in the long-cavity-length...

Virtual Reality for the Assessment of Everyday Cognitive Functions in Older Adults: An Evaluation of the Virtual Reality Action Test and Two Interaction Devices in a 91-Year-Old Woman

© Copyright © 2020 Chirico, Giovannetti, Neroni, Simone, Gallo, Galli, Giancamilli, Predazzi, Lucidi, De Pietro and Giordano. Performance-based functional tests for the evaluation of daily living activities demonstrate strong psychometric properties and solve many of the limitations associated with self- and informant-report questionnaires. Virtual reality (VR) technology, which has gained interest as an effective medium for administering interventions in the context of healthcare, has the potential to minimize the time-demands associated with the administration and...

Warming the postpartum body as a form of postnatal care: An ethnographic study of medical injections and traditional health practices in Cambodia

© 2020 Bazzano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Postpartum care is a critical element for ensuring survival and health of mothers and newborns but is often inadequate in low- and middle-income countries due to barriers to access and resource constraints. Newly delivered mothers and...

Comparative in vitro resistance of human periodontal bacterial pathogens to tinidazole and four other antibiotics

© 2020, MDPI AG. All rights reserved. The in vitro resistance of selected red/orange complex periodontal pathogens to tinidazole was compared with four other antibiotics. Subgingival biofilm samples from 88 adults with severe periodontitis were anaerobically incubated on enriched Brucella blood agar with and without supplementation with tinidazole (16 mg/L), metronidazole (16 mg/L), amoxicillin (8 mg/L), doxycycline (4 mg/L), or clindamycin (4 mg/L). Growth of Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia/nigrescens, Parvimonas micra, Fusobacterium nucleatum,...

Identification and Estimation of Treatment and Interference Effects in Observational Studies on Networks

© 2020, © 2020 American Statistical Association. Abstract–Causal inference on a population of units connected through a network often presents technical challenges, including how to account for interference. In the presence of interference, for instance, potential outcomes of a unit depend on their treatment as well as on the treatments of other units, such as their neighbors in the network. In observational studies, a further complication is that the typical unconfoundedness assumption must be extended—say,...

Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage

© Copyright 2020 Auscavitch et al. In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus...

A population genetic assessment of taxonomic species: The case of Lake Malawi cichlid fishes

© 2019 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd. Organisms sampled for population-level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of...

Prescribed fire maintains host plants of a rare grassland butterfly

© 2019, The Author(s). As grassland ecosystems transform globally due to anthropogenic pressures, improvements in our understanding of the effect of management on rare and threatened species in such landscapes has become urgent. Although prescribed fire is a very efficient tool for habitat restoration and endangered species management on fire-adapted ecosystems, the specific mechanisms underlying potential effects of burning on population dynamics of butterfly host plants are poorly understood. We analyzed a 12-year dataset (2004–2015),...

The PROSPECT reactor antineutrino experiment

© 2019 Elsevier B.V. The Precision Reactor Oscillation and Spectrum Experiment, PROSPECT, is designed to make both a precise measurement of the antineutrino spectrum from a highly-enriched uranium reactor and to probe eV-scale sterile neutrinos by searching for neutrino oscillations over meter-long baselines. PROSPECT utilizes a segmented 6 Li-doped liquid scintillator detector for both efficient detection of reactor antineutrinos through the inverse beta decay reaction and excellent background discrimination. PROSPECT is a movable 4-ton antineutrino...

Registration Year

  • 2020
    428

Resource Types

  • Text
    428