bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limiting the climate impact of the Trump administration
Authors: Kemp Luke 
Published: October 2017

AbstractThe climate actions of the current US administration under President Trump will undoubtedly impact US domestic emissions. They could even potentially influence global action. But some will last longer than others. A simple heuristic for analysing actions is by looking at a combination of their likely attributable future emissions and ‘lock-in potential’. Lock-in potential refers to the probable lifespan and reversibility of emissions producing actions. Using the lens of lock-in potential reveals that the actions of Trump that have received the most backlash are often the least damaging. Low lock-in potential actions are measures that are easily reversed and will only shape US emissions in the short-term. This includes withdrawal from the Paris Agreement, which could realistically last less than three months. Withdrawal may have no lock-in potential if it does not impact the emissions of the US or others. High lock-in potential actions are policies that will change the emissions trajectory of the US in the long-term past 2030 and can only be reversed with high costs. For instance, the approval of the Keystone XL and Dakota Access pipelines will last for half a century or more and could result in additional annual emissions of more than 200 Mt CO2e. The perspective of lock-in potential is also applied to previous executives. Even progressive presidents such as Obama have been constrained and possess poor climate credentials due to the underlying culture and structure of US climate politics. This long-term view suggests that the fundamental problem is not the Trump administration. Instead, it is the domestic fossil fuel lobby and Republican party, which have shaped the policy course of Trump and other executives. Trump is not an aberration for US climate policy, but a predictable symptom of a locked-in pattern of behaviour.
How can we demonstrate the public value of evidence-based policy making when government ministers declare that the people ‘have had enough of experts’?
Authors: Andrews Leighton 
Published: October 2017

AbstractRecent political campaigns on both sides of the Atlantic have led some to argue that we live in the age of ‘post-factual’ or ‘post-truth’ politics, suggesting evidence has a limited role in debate and public policy. How can we demonstrate the public value of evidence-informed debate under those circumstances? Survey evidence on public attitudes to expertise offers some hope that the tone of much of this debate is unduly pessimistic. While policy-making always develops in an environment where evidence is contested, this paper will argue that understanding of the routines through which Ministers work and assimilate evidence is actually under-researched. Not only are Ministers open to evidence, but there is an institutional grounding for evidence-based policy in government. Meanwhile, the creation of devolved institutions has created new sites in the UK for evidence-based policy-making, despite the political tensions between UK and devolved governments. Drawing on academic and think tank insights, and experience as a Welsh Government Minister between 2007 and 2016, this paper argues for three key approaches for the academic community to adopt: understanding the temporal focus of ministers, building trust amongst ministers and those who advise them in the evidence-promoting capacity of the academic policy community, and shaping the wider authorising environment, including the media that contributes to the framing of key policy debates.
Solar geoengineering and the chemtrails conspiracy on social media
Authors: Tingley Dustin , Wagner Gernot 
Published: October 2017

AbstractDiscourse on social media of solar geoengineering has been rapidly increasing over the past decade, in line with increased attention by the scientific community and low but increasing awareness among the general public. The topic has also found increased attention online. But unlike scientific discourse, a majority of online discussion focuses on the so-called chemtrails conspiracy theory, the widely debunked idea that airplanes are spraying a toxic mix of chemicals through contrails, with supposed goals ranging from weather to mind control. This paper presents the results of a nationally representative 1000-subject poll part of the 36,000-subject 2016 Cooperative Congressional Election Study (CCES), and an analysis of the universe of social media mentions of geoengineering. The former shows ~ 10% of Americans declaring the chemtrails conspiracy as “completely” and a further ~ 20–30% as “somewhat” true, with no apparent difference by party affiliation or strength of partisanship. Conspiratorial views have accounted for ~ 60% of geoengineering discourse on social media over the past decade. Of that, Twitter has accounted for >90%, compared to ~ 75% of total geoengineering mentions. Further affinity analysis reveals a broad online community of conspiracy. Anonymity of social media appears to help its spread, so does the general ease of spreading unverified or outright false information. Online behavior has important real-world reverberations, with implications for climate science communication and policy.
Critical discourse analysis of war reporting in the international press: the case of the Gaza war of 2008–2009
Authors: Amer Mohammedwesam 
Published: October 2017

AbstractThis paper employs critical discourse analysis (CDA) to analyse the representation of political social actors in media coverage of the Gaza war of 2008–2009. The paper examines texts of systematically chosen news stories from four international newspapers: ‘The Guardian, The Times London, The New York Times and The Washington Post’. The findings show substantial similarities in representation patterns among the four newspapers. More specifically, the selected newspapers foreground Israeli agency in achieving a ceasefire, whereby Israeli actors are predominantly assigned activated roles. By contrast, the four newspapers foreground Palestinian agency in refusing ceasefire through assigning activated roles. The findings of this study suggest that news reports on the Gaza war of 2008–2009 are influenced by the political orientations of the newspapers and also their liberal and conservative ideological stances. Overall, the most represented actors are Israeli governmental officials, whereas Palestinian actors are Hamas members. This representation draws an overall image that the war is being directed against Hamas.
Intercellular competition and the inevitability of multicellular aging
Authors: Nelson Paul , Masel Joanna 
Published: October 2017

Significance
We lay out the first general model of the interplay between intercellular competition, aging, and cancer. Our model shows that aging is a fundamental feature of multicellular life. Current understanding of the evolution of aging holds that aging is due to the weakness of selection to remove alleles that increase mortality only late in life. Our model, while fully compatible with current theory, makes a stronger statement: Multicellular organisms would age even if selection were perfect. These results inform how we think about the evolution of aging and the role of intercellular competition in senescence and cancer.
Patterns of conserved gp120 epitope presentation on attached HIV-1 virions
Authors: Mengistu Meron , Tang Ai-hui , Foulke James S. , Blanpied Thomas A. , Gonzalez Mileidy W. , Spouge John L. , Gallo Robert C. , Lewis George K. , DeVico Anthony L. 
Published: October 2017

Significance
A complete picture of HIV antigenicity during early replication is needed to elucidate the full range of options for controlling infection through humoral immunity. The HIV envelope protein, gp120, experiences key structural rearrangements during host cell attachment, leading to exposure of highly conserved epitopes on the virion surface. These epitopes enable Fc-mediated antiviral effector functions that may be relevant to HIV prevention. Here, we used 3D superresolution microscopy to show how gp120 epitopes are rapidly exposed distal to cell–virus interfaces, introducing the opportunity for unconstrained antibody binding. These previously unrecognized facets of HIV antigenicity further define relationships between retroviral infection and immunity and should facilitate the development of antibody-based approaches for HIV prevention.
Mechanism of RNA polymerase II stalling by DNA alkylation
Authors: Malvezzi Stefano , Farnung Lucas , Aloisi Claudia M. N. , Angelov Todor , Cramer Patrick , Sturla Shana J. 
Published: October 2017

Significance
RNA polymerase II (Pol II) catalyzes the transcription of DNA to RNA in the nucleus. DNA alkylating cancer drugs can stall transcription; however, the basis for Pol II stalling when encountering a DNA template with minor-groove alkylation adducts has remained elusive due to its inherent chemical instability. We characterized the behavior of Pol II in transcription over minor-groove alkylation adducts and uncovered a previously unobserved mode of Pol II stalling wherein clashes between DNA adducts and the mobile trigger loop of RNA Pol II prevent translocation of the enzyme after nucleotide insertion. These results provide a molecular basis for how DNA damage in transcribed portions of the genome initiates DNA repair contributing to drug resistance.
Pathogen-mediated selection in free-ranging elk populations infected by chronic wasting disease
Authors: Monello Ryan J. , Galloway Nathan L. , Powers Jenny G. , Madsen-Bouterse Sally A. , Edwards William H. , Wood Mary E. , O’Rourke Katherine I. , Wild Margaret A. 
Published: October 2017

Significance
Chronic wasting disease (CWD) is a fatal neurodegenerative disease that can cause declines in deer and elk populations. Theoretical work suggests elk will adapt to the disease by favoring a naturally occurring but underrepresented prion protein variant (leucine allele) that enables individuals to live and reproduce for several years after infection with CWD. Using genetic and disease samples from different populations, we found that elk herds infected with CWD for 30–50 y exhibited leucine allele frequencies that were twice as great as those in unexposed populations. Our results are consistent with the hypothesis that genetic selection has occurred due to CWD, but it remains unknown if this will allow elk to mitigate the negative population impacts of CWD.
Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
Authors: Bazin Jérémie , Baerenfaller Katja , Gosai Sager J. , Gregory Brian D. , Crespi Martin , Bailey-Serres Julia 
Published: October 2017

Significance
Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits.
MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in
Arabidopsis thaliana
Authors: Kim Jong Hum , Cho Seok Keun , Oh Tae Rin , Ryu Moon Young , Yang Seong Wook , Kim Woo Taek 
Published: October 2017

Significance
The essential roles of cytoplasmic E3 ligases in the protein quality control (PQC) pathways have been increasingly highlighted in yeast and animal studies. However, in plants, only CHIP E3 ligase has been characterized, while the knowledge of cytoplasmic PQC E3 ligases remains rudimentary. Misfolded Protein Sensing RING E3 ligase 1 (MPSR1), a self-regulatory sensor system that functions only in the occurrence of misfolded proteins, is an identified cytoplasmic PQC E3 ligase in plants that directly recognizes emergent misfolded proteins independently of chaperones. In addition, MPSR1 sustains the integrity and activity of the 26S proteasome under proteotoxic stress. Given that MPSR1 RING E3 ligase is well conserved in eukaryotes, this study sheds light on a PQC pathway that is present particularly in plants and beyond.
Genome diversity of tuber-bearing
Solanum
uncovers complex evolutionary history and targets of domestication in the cultivated potato
Authors: Hardigan Michael A. , Laimbeer F. Parker E. , Newton Linsey , Crisovan Emily , Hamilton John P. , Vaillancourt Brieanne , Wiegert-Rininger Krystle , Wood Joshua C. , Douches David S. , Farré Eva M. , Veilleux Richard E. , Buell C. Robin 
Published: October 2017

Significance
Worldwide, potato is the third most important crop grown for direct human consumption, but breeders have struggled to produce new varieties that outperform those released over a century ago, as evidenced by the most widely grown North American cultivar (Russet Burbank) released in 1876. Despite its importance, potato genetic diversity at the whole-genome level remains largely unexplored. Analysis of cultivated potato and its wild relatives using modern genomics approaches can provide insight into the genomic diversity of extant germplasm, reveal historic introgressions and hybridization events, and identify genes targeted during domestication that control variance for agricultural traits, all critical information to address food security in 21st century agriculture.
Characterization of extracellular vesicles derived from cardiac cells in an in vitro model of preconditioning
Authors: Borosch Sebastian , Dahmen Eva , Beckers Christian , Stoppe Christian , Buhl Eva Miriam , Denecke Bernd , Goetzenich Andreas , Kraemer Sandra 
Published: October 2017

ABSTRACTPreconditioning is a promising technique to protect the heart from ischaemia‐reperfusion injury. In this context, the crosstalk between different cardiac cell types and especially the exchange of cardioprotective mediators has come into the focus of current research. Recently, extracellular vesicles (EVs), nano‐sized structures, emerged as possible communication mediators. They are taken up by recipient cells and can alter gene expression or activate intracellular signal cascades. It has been shown that all cardiac cell types are able to secrete EVs, but so far the influence of an in vitro preconditioning stimulus on EV concentration and composition has not been investigated. Therefore, we stimulated primary cardiac myocytes and fibroblasts from neonatal rats, as well as H9c2 cells, with two known in vitro preconditioning stimuli: hypoxia or isoflurane. EVs were isolated from cell culture supernatants 48 h after stimulation by differential centrifugation and size exclusion chromatography. They were characterized by transmission electron microscopy, tunable resistive pulse sensing, miRNA array and Western blot analysis. The detected EVs had the typical cup‐shaped morphology and a size of about 150 nm. No significant differences in EV concentration were observed between the different groups. The protein and miRNA load was affected by in vitro preconditioning with isoflurane or hypoxia. EV markers like Alix, CD63, flotillin‐1 and especially heat shock protein 70 were significantly up‐regulated by the treatments. Several miRNAs like miR‐92b‐3p, miR‐761 and miR‐101a‐5p were also significantly affected. A migration assay confirmed the physiological benefit of these EVs. Taken together, our findings show that a model of in vitro preconditioning of cardiac cells does not influence EV concentration but strongly regulates the EV cargo and affects migration. This might indicate a role for EV‐mediated communication in isoflurane‐ and hypoxia‐induced in vitro preconditioning.
On-site comparison of Quantum Hall Effect resistance standards of the CMI and the BIPM: ongoing key comparison BIPM.EM-K12
Authors: Gournay Pierre , Rolland Benjamin , Kučera Jan , Vojáčková Lucie 
Published: October 2017

An on-site comparison of the quantum Hall effect (QHE) resistance standards of the Czech Metrology Institute (CMI) and of the Bureau International des Poids et Mesures (BIPM) was made in April 2017. Measurements of a 100 Ω standard in terms of the conventional value of the von Klitzing constant, R
K-90, agreed to 6 parts in 1010 with a relative combined standard uncertainty u
c = 25 × 10−10. Measurements of 10000 Ω/100 Ω and 100 Ω/1 Ω ratios agreed to 11 parts in 1010 with u
c = 22 × 10−10 and to 33 parts in 1010 with u
c = 32 × 10−10, respectively. The influence of the current reversal time has been systematically investigated in order to take into account possible errors due to the Peltier effect, which may be particularly large in 1 Ω standards.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Supplementary comparison of 500 microgram, 200 microgram, 100 microgram and 50 microgram weights—EURAMET.M.M-S9
Authors: Davidson Stuart , Valcu Adriana , Medina Nieves , Zuda Jaroslav , Snopko Laurenc , Kolozinska Irena 
Published: October 2017

A comparison of sub-milligram mass standards was undertaken within EURAMET between NPL (as the pilot laboratory), INM (Romania), CEM (Spain), CMI (Czech Republic), SMU (Slovakia) and NSC IM (Ukraine). The weights circulated had nominal values of 500 micrograms, 200 micrograms (2 weights), 100 micrograms and 50 micrograms.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Stress Intensity Factors of Slanted Cracks in Bi-Material Plates
Authors: Ismail Al Emran , Kamarudin Kamarul Azhar , Nor Nik Hisyamudin Muhd 
Published: October 2017

Abstract
In this study, the stress intensity factors (SIF) of slanted cracks in bi-material plates subjected to mode I loading is numerically solved. Based on the literature survey, tremendous amount of research works are available studying the normal cracks in both similar and dissimilar plates. However, lack of SIF behavior for slanted cracks especially when it is embedded in bi-material plates. The slanted cracks are then modelled numerically using ANSYS finite element program. Two plates of different in mechanical properties are firmly bonded obliquely and then slanted edge cracks are introduced at the lower inclined edge. Isoparametric singular element is used to model the crack tip and the SIF is determined which is based on the domain integral method. Three mechanical mismatched and four slanted angles are used to model the cracks. According to the present results, the effects of mechanical mismatch on the SIF for normal cracks are not significant. However, it is played an important role when slanted angles are introduced. It is suggested that higher SIF can be obtained when the cracks are inclined comparing with the normal cracks. Consequently, accelerating the crack growth at the interface between two distinct materials.
Mosdepth: quick coverage calculation for genomes and exomes
Authors: Pedersen Brent S , Quinlan Aaron R 
Published: October 2017

Abstract

Summary
Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced.

Availability and implementation
mosdepth is available from https://github.com/brentp/mosdepth under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
BEAM web server: a tool for structural RNA motif discovery
Authors: Pietrosanto Marco , Adinolfi Marta , Casula Riccardo , Ausiello Gabriele , Ferrè Fabrizio , Helmer-Citterich Manuela 
Published: October 2017

Abstract

Motivation
RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies.

Results
The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it.

Availability and implementation
The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported.

Supplementary information
Supplementary data are available at Bioinformatics online.
2017 HIV Medicine Association of Infectious Diseases Society of America Clinical Practice Guideline for the Management of Chronic Pain in Patients Living With Human Immunodeficiency Virus
Authors: Bruce R Douglas , Merlin Jessica , Lum Paula J , Ahmed Ebtesam , Alexander Carla , Corbett Amanda H , Foley Kathleen , Leonard Kate , Treisman Glenn Jordan , Selwyn Peter 
Published: October 2017

Abstract
Pain has always been an important part of human immunodeficiency virus (HIV) disease and its experience for patients. In this guideline, we review the types of chronic pain commonly seen among persons living with HIV (PLWH) and review the limited evidence base for treatment of chronic noncancer pain in this population. We also review the management of chronic pain in special populations of PLWH, including persons with substance use and mental health disorders. Finally, a general review of possible pharmacokinetic interactions is included to assist the HIV clinician in the treatment of chronic pain in this population.
It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. The Infectious Diseases Society of American considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient’s individual circumstances.