bluuebunny/crossref_metadata_2025_split huggingface dataset:
Butane dihedral angle dynamics in water is dominated by internal friction
Authors: Daldrop Jan O. , Kappler Julian , Brünig Florian N. , Netz Roland R. 
Published: April 2018

SignificanceThe interpretation of rates of reactions that take place in a solvent is complicated because of the entanglement of free-energy and history-dependent friction effects. In this context, the dihedral dynamics of butane has played a paradigmatic role since it is simple yet relevant for conformational transitions in polymers and proteins. We directly extract the friction that governs the dihedral dynamics in butane from simulations. We show that ∼89% of the total friction cannot be described as solvent friction and is caused by degrees of freedom that are orthogonal to the dihedral reaction coordinate. This shows that the hydrodynamic estimate of friction severely fails, even in the simplest molecular reaction.
An endogenous dAMP ligand inBacillus subtilisclass Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP
Authors: Parker Mackenzie J. , Maggiolo Ailiena O. , Thomas William C. , Kim Albert , Meisburger Steve P. , Ando Nozomi , Boal Amie K. , Stubbe JoAnne 
Published: April 2018

SignificanceNegative feedback regulation of ribonucleotide reductase (RNR) activity by dATP is important for maintaining balanced intracellular 2ʹ-deoxynucleoside triphosphate (dNTP) pools essential for the high fidelity of DNA replication and repair. To date, this type of allostery has been nearly universally associated with dATP binding to the N-terminal ATP-cone domain of the class Ia RNR large subunit (canonical α2), resulting in an altered quaternary structure that is unable to productively bind the second subunit (β2). Here, we report our studies on activity inhibition by dATP of theBacillus subtilisclass Ib RNR, which lacks a traditional ATP-cone domain. This unprecedented allostery involves deoxyadenosine 5′-monophosphate (dAMP) binding to a newly identified site in a partial N-terminal cone domain, forming an unprecedented noncanonical α2.
Comparative terrestrial feed and land use of an aquaculture-dominant world
Authors: Froehlich Halley E. , Runge Claire A. , Gentry Rebecca R. , Gaines Steven D. , Halpern Benjamin S. 
Published: April 2018

Significance
Studies are revealing the potential benefits of shifting human diets away from meat and toward other protein sources, including seafood. The majority of seafood is now, and for the foreseeable future, farmed (i.e., aquaculture). As the fastest-growing food sector, fed aquaculture species increasingly rely on terrestrial-sourced feed crops, but the comparative impact of aquaculture versus livestock on associated feed and land use is unclear––especially if human diets shift. Based on global production data, feed use trends, and human consumption patterns, we simulate how feed-crop and land use may increase by midcentury, but demonstrate that millions of tonnes of crops and hectares could be spared for most, but not all, countries worldwide in an aquaculture-dominant future.
Optimizing the impact of low-efficacy influenza vaccines
Authors: Sah Pratha , Medlock Jan , Fitzpatrick Meagan C. , Singer Burton H. , Galvani Alison P. 
Published: April 2018

Significance
The efficacy of the influenza vaccine against the predominant influenza strain appears to be relatively low during this 2017–2018 season. Our analyses demonstrate the substantial effect of even low-efficacy vaccines in averting infections, hospitalizations, and particularly deaths. Our results also demonstrate that the health burden resulting from influenza is more sensitive to changes to vaccination coverage than to changes to vaccine efficacy. We further determined the uptake distribution of the 140 million doses available that would maximize the effectiveness of vaccination. Our results inform current public health policies and underscore the importance of influenza vaccination.
Brain Mapping of drug addiction in witdrawal condition based P300 Signals
Authors: Turnip Arjon , Kusumandari Dwi Esti , Hidayat Teddy 
Published: April 2018

Abstract
Drug abuse for a long time will slowly cause changes in brain structure and performance. These changes tend to occur in the front of the brain which is directly interfere the concentration and the decision-making process. In this study an experiment involving 10 drug users was performed. The process of recording data with EEG system is conducted during craving condition and 1 hour after taking methadone. From brain mapping results obtained that brain activity tend to occur in the upper layer of the brain during craving conditions and tend to be in the midle layer of the brain after one hour of taking methadone.
What Could Total Worker Health® Look Like in Small Enterprises?
Authors: Rohlman Diane S , Campo Shelly , Hall Jennifer , Robinson Erin L , Kelly Kevin M 
Published: April 2018

Abstract
Small enterprises have fewer resources, are more financially precarious, and have higher rates of occupational injury and illness compared with larger enterprises. Interventions that address the promotion of health and well-being in addition to traditional occupational safety and health hazards, a Total Worker Health® (TWH) approach, may be effective in reducing injuries and preventing illness. However, little research has examined the impact of TWH interventions in small enterprises. The aim of this research was to explore and characterize health and safety practices, policies, and programs in small Midwestern enterprises from a TWH perspective. Utilizing a case studies approach, site visits were conducted with small business, between 10 and 250 employees, from 2014 through 2016 and included workplace audits and interviews with multiple employees in varying roles within each organization. Both open and closed coding were used to identify specific themes. Eight themes emerged from the site visits: value and return on investment, organizational factors, program design, engaging employees, low-cost strategies, evaluation, and integration. These themes overlapped with both the National Institute for Occupational Safety and Health’s (NIOSH) Essential Elements of TWH and the NIOSH Fundamentals. Industry sector and enterprise size also affect resources and integration of these resources. As TWH expands to organizations of all sizes, it is necessary to address the unique needs of smaller enterprises.
A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya
Authors: Miller J Michael , Binnicker Matthew J , Campbell Sheldon , Carroll Karen C , Chapin Kimberle C , Gilligan Peter H , Gonzalez Mark D , Jerris Robert C , Kehl Sue C , Patel Robin , Pritt Bobbi S , Richter Sandra S , Robinson-Dunn Barbara , Schwartzman Joseph D , Snyder James W , Telford Sam , Theel Elitza S , Thomson Richard B , Weinstein Melvin P , Yao Joseph D 
Published: April 2018

AbstractThe critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.
Does Stereotactic Radiosurgery Have a Role in the Management of Patients Presenting With 4 or More Brain Metastases?
Authors: Soike Michael H , Hughes Ryan T , Farris Michael , McTyre Emory R , Cramer Christina K , Bourland J D , Chan Michael D 
Published: April 2018

Abstract
Stereotactic radiosurgery (SRS) and whole brain radiation therapy (WBRT) are effective treatments for management of brain metastases. Prospective trials comparing the 2 modalities in patients with fewer than 4 brain metastases demonstrate that overall survival (OS) is similar. Intracranial failure is more common after SRS, while WBRT is associated with neurocognitive decline. As technology has advanced, fewer technical obstacles remain for treating patients with 4 or more brain metastases with SRS, but level I data supporting its use are lacking.
Observational prospective studies and retrospective series indicate that in patients with 4 or more brain metastases, performance status, total volume of intracranial disease, histology, and rate of development of new brain metastases predict outcomes more accurately than the number of brain metastases. It may be reasonable to initially offer SRS to some patients with 4 or more brain metastases. Initiating therapy with SRS avoids the acute and late sequelae of WBRT. Multiple phase III trials of SRS vs WBRT, both currently open or under development, are directly comparing quality of life and OS for patients with 4 or more brain metastases to help answer the question of SRS appropriateness for these patients.
A systems framework for national assessment of climate risks to infrastructure
Authors: Dawson Richard J. , Thompson David , Johns Daniel , Wood Ruth , Darch Geoff , Chapman Lee , Hughes Paul N. , Watson Geoff V. R. , Paulson Kevin , Bell Sarah , Gosling Simon N. , Powrie William , Hall Jim W. 
Published: April 2018

Extreme weather causes substantial adverse socio-economic impacts by damaging and disrupting the infrastructure services that underpin modern society. Globally, $2.5tn a year is spent on infrastructure which is typically designed to last decades, over which period projected changes in the climate will modify infrastructure performance. A systems approach has been developed to assess risks across all infrastructure sectors to guide national policy making and adaptation investment. The method analyses diverse evidence of climate risks and adaptation actions, to assess the urgency and extent of adaptation required. Application to the UK shows that despite recent adaptation efforts, risks to infrastructure outweigh opportunities. Flooding is the greatest risk to all infrastructure sectors: even if the Paris Agreement to limit global warming to 2°C is achieved, the number of users reliant on electricity infrastructure at risk of flooding would double, while a 4°C rise could triple UK flood damage. Other risks are significant, for example 5% and 20% of river catchments would be unable to meet water demand with 2°C and 4°C global warming respectively. Increased interdependence between infrastructure systems, especially from energy and information and communication technology (ICT), are amplifying risks, but adaptation action is limited by lack of clear responsibilities. A programme to build national capability is urgently required to improve infrastructure risk assessment.
This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
Climate risk index for Italy
Authors: Mysiak Jaroslav , Torresan Silvia , Bosello Francesco , Mistry Malcolm , Amadio Mattia , Marzi Sepehr , Furlan Elisa , Sperotto Anna 
Published: April 2018

We describe a climate risk index that has been developed to inform national climate adaptation planning in Italy and that is further elaborated in this paper. The index supports national authorities in designing adaptation policies and plans, guides the initial problem formulation phase, and identifies administrative areas with higher propensity to being adversely affected by climate change. The index combines (i) climate change-amplified hazards; (ii) high-resolution indicators of exposure of chosen economic, social, natural and built- or manufactured capital (MC) assets and (iii) vulnerability, which comprises both present sensitivity to climate-induced hazards and adaptive capacity. We use standardized anomalies of selected extreme climate indices derived from high-resolution regional climate model simulations of the EURO-CORDEX initiative as proxies of climate change-altered weather and climate-related hazards. The exposure and sensitivity assessment is based on indicators of manufactured, natural, social and economic capital assets exposed to and adversely affected by climate-related hazards. The MC refers to material goods or fixed assets which support the production process (e.g. industrial machines and buildings); Natural Capital comprises natural resources and processes (renewable and non-renewable) producing goods and services for well-being; Social Capital (SC) addressed factors at the individual (people's health, knowledge, skills) and collective (institutional) level (e.g. families, communities, organizations and schools); and Economic Capital (EC) includes owned and traded goods and services. The results of the climate risk analysis are used to rank the subnational administrative and statistical units according to the climate risk challenges, and possibly for financial resource allocation for climate adaptation.This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
Efficient Merging of Genome Profile Alignments
Authors: Hennig André , Nieselt Kay 
Published: April 2018

AbstractMotivationWhole-genome alignment methods show insufficient scalability towards the generation of large-scale whole-genome alignments (WGAs). Profile alignment-based approaches revolutionized the fields of multiple sequence alignment construction methods by significantly reducing computational complexity and runtime. However, WGAs need to consider genomic rearrangements between genomes, which makes the profile-based extension of several whole-genomes challenging. Currently, none of the available methods offer the possibility to align or extend WGA profiles.ResultsHere, we present GPA, an approach that aligns the profiles of WGAs and is capable of producing large-scale WGAs many times faster than conventional methods. Our concept relies on already available whole-genome aligners, which are used to compute several smaller sets of aligned genomes that are combined to a full WGA with a divide and conquer approach. To align or extend WGA profiles, we make use of the SuperGenome data structure, which features a bidirectional mapping between individual sequence and alignment coordinates. This data structure is used to efficiently transfer different coordinate systems into a common one based on the principles of profiles alignments. The approach allows the computation of a WGA where alignments are subsequently merged along a guide tree. The current implementation uses progressiveMauve (Darling et al., 2010) and offers the possibility for parallel computation of independent genome alignments. Our results based on various bacterial data sets up to several hundred genomes show that we can reduce the runtime from months to hours with a quality that is negligibly worse than the WGA computed with the conventional progressiveMauve tool.AvailabilityGPA is freely available at https://lambda.informatik.uni-tuebingen.de/gitlab/ahennig/GPA. GPA is implemented in Java, uses progressiveMauve and offers a parallel computation of WGAs.Contactandre.hennig@uni-tuebingen.de
High impact journals in ecology cover proportionally more statistically significant findings
Authors: Ceausu Silvia , Borda-de-Água Luís , Merckx Thomas , Sossai Esther , Sapage Manuel , Miranda Murilo , Pereira Henrique M. 
Published: April 2018

AbstractUnbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.
Silencing of the CSNK2β gene by siRNA inhibits invasiveness and growth of MDA-MB-231 cells
Authors: Karna Shibendra Kumar Lal , Lone Bilal Ahmad , Ahmad Faiz , Shahi Nerina , Pokharel Yuba Raj 
Published: April 2018

AbstractBackgroundBreast cancer is most common cancer and accounts for one-fourth of all cancer diagnoses worldwide. Treatment of triple-negative breast cancer is major challenge and identification of specific drivers is required for targeted therapies. The aim of our present study is to elucidate the therapeutic potential of CSNK2ß silencing in triple negative breast cancer MDA-MB-231 cell.MethodsCSNK2ß gene has been knockdown using siRNA and silencing was estimated by both real time and western blot. Cell Titer-Glo (CTG) and colony formation assay and wound healing assay, cell cycle analysis by flow cytometry was performed to assess the role of CSNK2ß in cell proliferation, migration, cell cycle, and oncogenesis. Morphological assessment of nuclear condensation, apoptosis by Hoechst staining and measurement of intracellular ROS production was examined using fluorescence microscopy. Real time PCR and western blot was done to study the expression of genes related to cell proliferation, survival, metastasis, apoptosis, and autophagy.ResultsSilencing of CSNK2ß in MDA-MB-231 cells resulted in decreased cell viability, colony formation, and migratory potential. Cell cycle analysis showed that growth inhibitory effect was mediated by arresting the cells in G2/M phase. Furthermore, we demonstrated that silencing of CSNK2ß increased the nuclear condensation and intracellular ROS production. CSNK2ß regulates the expression of BAX, Bcl-xL, caspase 3, Beclin-1, LC3-I, p-ERK, p38-α, c-Myc, MAPK, c-Jun, NF-ĸB, β-catenin, E2F1, PCNA. We have also shown the functional relationship between CSNK2ß, PIN1, and PTOV1 by western blotting. We have first time reported that silencing CSNK2ß using siRNA can inhibit invasiveness and proliferation of MDA-MB-213 cells.ConclusionOur results suggested that CSNK2ß silencing may offer future therapeutic target in triple negative breast cancer.
Quantifying protein oligomerization in living cells: A systematic comparison of fluorescent proteins
Authors: Dunsing Valentin , Luckner Madlen , Zühlke Boris , Petazzi Roberto , Herrmann Andreas , Chiantia Salvatore 
Published: April 2018

AbstractFluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive studies of molecular interactions and dynamics in living cells. The quantification of e.g. protein oligomerization and absolute concentrations in the native cellular environment is highly relevant for a detailed understanding of complex signaling pathways and biochemical reaction networks. A parameter of particular relevance in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, potentially inducing non-fluorescent states, which strongly affect molecular brightness measurements. Although these processes have been occasionally reported, a comprehensive study addressing this issue is missing.Here, we investigate the suitability of commonly used FPs (i.e. mEGFP, mEYFP and mCherry), as well as novel red FPs (i.e. mCherry2, mRuby3, mCardinal, mScarlet and mScarlet-I) for the quantification of oligomerization based on the molecular brightness, as obtained by Fluorescence Correlation Spectroscopy (FCS) and Number&Brightness (N&B) measurements in living cells. For all FPs, we measured a lower than expected brightness of FP homo-dimers, allowing us to estimate, for each fluorescent label, the probability of fluorescence emission in a simple two-state model. By analyzing higher FP homo-oligomers and the Influenza A virus Hemagglutinin (HA) protein, we show that the oligomeric state of protein complexes can only be accurately quantified if this probability is taken into account. Further, we provide strong evidence that mCherry2, an mCherry variant, possesses a superior apparent fluorescence probability, presumably due to its fast maturation. We finally conclude that this property leads to an improved quantification in fluorescence cross-correlation spectroscopy measurements and propose to use mEGFP and mCherry2 as the novel standard pair for studying biomolecular hetero-interactions.
Annual changes in the Biodiversity Intactness Index in tropical and subtropical forest biomes, 2001-2012
Authors: Palma Adriana De , Hoskins Andrew , Gonzalez Ricardo E. , Börger Luca , Newbold Tim , Sanchez-Ortiz Katia , Ferrier Simon , Purvis Andy 
Published: April 2018

ABSTRACTFew biodiversity indicators are available that reflect the state of broad-sense biodiversity—rather than of particular taxa—at fine spatial and temporal resolution. The Biodiversity Intactness Index (BII) estimates how the average abundance of native terrestrial species in a region compares with their abundances before pronounced human impacts. BII is designed for use with data from a wide range of taxa and functional groups and for estimation at any resolution for which data on land use and related pressures are available. For each year from 2001 to 2012, we combined models of how land use and related pressures in tropical and subtropical forested biomes affect overall abundance and compositional similarity of plants, fungi, invertebrates and vertebrates, with data on anthropogenic pressures to produce annual maps of modelled BII at a spatial resolution of 30 arc seconds (roughly 1 km at the equator) across tropical and subtropical forested biomes. This is the first time temporal change in BII has been estimated across such a large region. The approach we have used to model compositional similarity uses data more efficiently than that used previously when estimating BII. Across tropical and subtropical biomes, BII fell by an average of 1.9 percentage points between 2001 and 2012, with 81 countries seeing an average reduction and 43 an average increase; the extent of primary forest fell by 3.9% over the same period. Changes are not strongly related to countries’ rates of economic growth over the same period.