bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Delivery of Species Distribution Models to Inform Decision-Making
Authors: Sofaer Helen R , Jarnevich Catherine S , Pearse Ian S , Smyth Regan L , Auer Stephanie , Cook Gericke L , Edwards Thomas C , Guala Gerald F , Howard Timothy G , Morisette Jeffrey T , Hamilton Healy 
Published: April 2019

Abstract
Information on where species occur is an important component of conservation and management decisions, but knowledge of distributions is often coarse or incomplete. Species distribution models provide a tool for mapping habitat and can produce credible, defensible, and repeatable information with which to inform decisions. However, these models are sensitive to data inputs and methodological choices, making it important to assess the reliability and utility of model predictions. We provide a rubric that model developers can use to communicate a model's attributes and its appropriate uses. We emphasize the importance of tailoring model development and delivery to the species of interest and the intended use and the advantages of iterative modeling and validation. We highlight how species distribution models have been used to design surveys for new populations, inform spatial prioritization decisions for management actions, and support regulatory decision-making and compliance, tying these examples back to our model assessment rubric.
The functional false discovery rate with applications to genomics
Authors: Chen Xiongzhi , Robinson David G , Storey John D 
Published: April 2019

SummaryThe false discovery rate (FDR) measures the proportion of false discoveries among a set of hypothesis tests called significant. This quantity is typically estimated based on p-values or test statistics. In some scenarios, there is additional information available that may be used to more accurately estimate the FDR. We develop a new framework for formulating and estimating FDRs and q-values when an additional piece of information, which we call an “informative variable”, is available. For a given test, the informative variable provides information about the prior probability a null hypothesis is true or the power of that particular test. The FDR is then treated as a function of this informative variable. We consider two applications in genomics. Our first application is a genetics of gene expression (eQTL) experiment in yeast where every genetic marker and gene expression trait pair are tested for associations. The informative variable in this case is the distance between each genetic marker and gene. Our second application is to detect differentially expressed genes in an RNA-seq study carried out in mice. The informative variable in this study is the per-gene read depth. The framework we develop is quite general, and it should be useful in a broad range of scientific applications.
Prescriber Behavior in Clostridioides difficile Testing: A 3-Hospital Diagnostic Stewardship Intervention
Authors: Mizusawa Masako , Small Bryce A , Hsu Yea-Jen , Sharara Sima L , Advic Edina , Kauffman Christopher , Milstone Aaron M , Feldman Leonard , Pahwa Amit K , Trivedi Julie B , Landrum Mark B , Maragakis Lisa L , Carroll Karen C , Cosgrove Sara E , Rock Clare 
Published: April 2019

Abstract
Computerized clinical decision support (CCDS) significantly reduced Clostridioides difficile testing at 3 hospitals; from 12.6 to 9.5, from 10.1 to 6.4, and from 14.0 to 9.6 average weekly tests per 1000 inpatient days. There were no related adverse events. Senior providers were more likely than interns or residents to follow CCDS.
Efficient Certificateless Signcryption in the Standard Model: Revisiting Luo and Wan’s Scheme from Wireless Personal Communications (2018)
Authors: Rastegari Parvin , Susilo Willy , Dakhlalian Mohammad 
Published: April 2019

Abstract
Certificateless public key cryptography (CL-PKC) promises a practical resolution in establishing practical schemes, since it addresses two fundamental issues, namely the necessity of requiring certificate managements in traditional public key infrastructure (PKI) and the key escrow problem in identity-based (ID-based) setting concurrently. Signcryption is an important primitive that provides the goals of both encryption and signature schemes as it is more efficient than encrypting and signing messages consecutively. Since the concept of certificateless signcryption (CL-SC) scheme was put forth by Barbosa and Farshim in 2008, many schemes have been proposed where most of them are provable in the random oracle model (ROM) and only a few number of them are provable in the standard model. Very recently, Luo and Wan (Wireless Personal Communication, 2018) proposed a very efficient CL-SC scheme in the standard model. Furthermore, they claimed that their scheme is not only more efficient than the previously proposed schemes in the standard model, but also it is the only scheme which benefits from known session-specific temporary information security (KSSTIS). Therefore, this scheme would indeed be very practical. The contributions of this paper are 2-fold. First, in contrast to the claim made by Luo and Wan, we show that unfortunately Luo and Wan made a significant error in the construction of their proposed scheme. While their main intention is indeed interesting and useful, the failure of their construction has indeed left a gap in the research literature. Hence, the second contribution of this paper is to fill this gap by proposing a CL-SC scheme with KSSTIS, which is provably secure in the standard model.
Cardiovascular biomarkers in patients with acute decompensated heart failure randomized to sacubitril-valsartan or enalapril in the PIONEER-HF trial
Authors: Morrow David A , Velazquez Eric J , DeVore Adam D , Prescott Margaret F , Duffy Carol I , Gurmu Yared , McCague Kevin , Rocha Ricardo , Braunwald Eugene 
Published: April 2019

Abstract

Aims
Circulating high-sensitivity cardiac troponin (hsTn) and soluble ST2 (sST2) reflect myocardial stress in patients with heart failure (HF). Production of cyclic guanosine 3′5′ monophosphate (cGMP) in response to activation of natriuretic peptide receptors reduces cardiac afterload and preload. We assessed the effects of sacubitril/valsartan on these biomarkers in patients with reduced ejection fraction and acute decompensated HF (ADHF).

Methods and results
PIONEER-HF was a randomized, double-blind trial of sacubitril/valsartan vs. enalapril in hospitalized patients with ADHF following haemodynamic stabilization. We measured circulating hsTnT, sST2, and urinary cGMP at baseline, 1, 2 (sST2, cGMP), 4, and 8 weeks (n = 694 with all baseline biomarkers). Ratios of geometric means (timepoint/baseline) were determined and compared as a ratio for sacubitril/valsartan vs. enalapril. Compared with enalapril, sacubitril/valsartan led to a significantly greater decline in hsTnT and sST2. This effect emerged as early as 1 week for sST2 and was significant for both at 4 weeks with a 16% greater reduction in hsTnT (P &lt; 0.001) and 9% greater reduction in sST2 (P = 0.0033). Serial urinary cGMP increased with sacubitril/valsartan compared with enalapril (P &lt; 0.001, 1 week). The significant differences between treatment groups for each biomarker were sustained at 8 weeks. In an exploratory multivariable-adjusted analysis of cardiovascular death or HF-rehospitalization, the concentrations of hsTnT, sST2 at week 1 were significantly associated with subsequent outcome.

Conclusion
Biomarkers of myocardial stress are elevated in patients with ADHF and associated with outcome. Compared with enalapril, sacubitril/valsartan reduces myocardial injury and haemodynamic stress as reflected by biomarkers, with an onset that is apparent within 1–4 weeks.

Clinical trials registration
NCT 02554890 clinical.trials.gov
A validation study of the European Society of Cardiology guidelines for risk stratification of sudden cardiac death in childhood hypertrophic cardiomyopathy
Authors: Norrish Gabrielle , Ding Tao , Field Ella , McLeod Karen , Ilina Maria , Stuart Graham , Bhole Vinay , Uzun Orhan , Brown Elspeth , Daubeney Piers E F , Lota Amrit , Linter Katie , Mathur Sujeev , Bharucha Tara , Kok Khoon Li , Adwani Satish , Jones Caroline B , Reinhardt Zdenka , Omar Rumana Z , Kaski Juan Pablo 
Published: April 2019

Abstract

Aims
Sudden cardiac death (SCD) is the most common cause of death in children with hypertrophic cardiomyopathy (HCM). The European Society of Cardiology (ESC) recommends consideration of an implantable cardioverter-defibrillator (ICD) if two or more clinical risk factors (RFs) are present, but this approach to risk stratification has not been formally validated.

Methods and results
Four hundred and eleven paediatric HCM patients were assessed for four clinical RFs in accordance with current ESC recommendations: severe left ventricular hypertrophy, unexplained syncope, non-sustained ventricular tachycardia, and family history of SCD. The primary endpoint was a composite outcome of SCD or an equivalent event (aborted cardiac arrest, appropriate ICD therapy, or sustained ventricular tachycardia), defined as a major arrhythmic cardiac event (MACE). Over a follow-up period of 2890 patient years (median 5.5 years), MACE occurred in 21 patients (7.5%) with 0 RFs, 19 (16.8%) with 1 RFs, and 3 (18.8%) with 2 or more RFs. Corresponding incidence rates were 1.13 [95% confidence interval (CI) 0.7–1.73], 2.07 (95% CI 1.25–3.23), and 2.52 (95% CI 0.53–7.35) per 100 patient years at risk. Patients with two or more RFs did not have a higher incidence of MACE (log-rank test P = 0.34), with a positive and negative predictive value of 19% and 90%, respectively. The C-statistic was 0.62 (95% CI 0.52–0.72) at 5 years.

Conclusions
The incidence of MACE is higher for patients with increasing numbers of clinical RFs. However, the current ESC guidelines have a low ability to discriminate between high- and low-risk individuals.
Complementary energy acquisition via aerobic anoxygenic photosynthesis and carbon monoxide oxidation by Planktomarina temperata of the Roseobacter group
Authors: Giebel Helge-Ansgar , Wolterink Mathias , Brinkhoff Thorsten , Simon Meinhard 
Published: April 2019

ABSTRACT
In marine pelagic ecosystems energy is often the limiting factor for growth of heterotrophic bacteria. Aerobic anoxygenic photosynthesis (AAP) and oxidation of carbon monoxide (CO) are modes to acquire complementary energy, but their significance in abundant and characteristic pelagic marine bacteria has not been well studied. In long-term batch culture experiments we found that Planktomarina temperata RCA23, representing the largest and most prominent subcluster of the Roseobacter group, maintains 2–3-fold higher cell numbers in the stationary and declining phase when grown in a light-dark cycle relative to dark conditions. Light enables P. temperata to continue to replicate its DNA during the stationary phase relative to a dark control such that when reinoculated into fresh medium growth resumed two days earlier than in control cultures. In cultures grown in the dark and supplemented with CO, cell numbers in the stationary phase remained significantly higher than in an unsupplemented control. Furthermore, repeated spiking with CO until day 372 resulted in significant CO consumption relative to an unsupplemented control. P. temperata represents a prominent marine pelagic bacterium for which AAP and CO consumption, to acquire complementary energy, have been documented.
Tropicalized Quartics and Canonical Embeddings for Tropical Curves of Genus 3
Authors: Hahn Marvin Anas , Markwig Hannah , Ren Yue , Tyomkin Ilya 
Published: April 2019

Abstract
In [8], it was shown that not all abstract non-hyperelliptic tropical curves of genus $3$ can be realized as a tropicalization of a quartic in $\mathbb R^2$. In this paper, we focus on the interior of the maximal cones in the moduli space and classify all curves, which can be realized as a faithful tropicalization in a tropical plane. Reflecting the algebro-geometric world, we show that these are all curves but the tropicalizations of realizably hyperelliptic algebraic curves. Our approach is constructive: for a curve that is not the tropicalization of a hyperelliptic algebraic curve, we explicitly construct a realizable model of the tropical plane in $\mathbb{R}^n$ and a faithfully tropicalized quartic in it. These constructions rely on modifications resp. tropical refinements. Conversely, we prove that the tropicalizations of hyperelliptic algebraic curves cannot be embedded in such a fashion. For that, we rely on the theory of tropical divisors and embeddings from linear systems [3, 21] and recent advances in the realizability of sections of the tropical canonical divisor [30].
Mental health, subjectivity and the city: an ethnography of migrant stress in Shanghai
Authors: Richaud Lisa , Amin Ash 
Published: April 2019

AbstractEthnography, with its focus on everyday experience, can yield significant insights into understanding migrant mental health in contexts where signs of severe mental distress remain largely imperceptible, and more generally, into how stresses and strains are lived through the spaces, times and affective atmospheres of the city. Migrant ethnography can help us reconsider the oft-made connection between everyday stress and mental ill health. In this contribution, drawing on field evidence in central and peripheral Shanghai, we highlight the importance of attending to the forms of spatial and temporal agency through which migrants actively manage the ways in which the city affects their subjectivity. These everyday subjective practices serve to problematize the very concept of ‘mental health’. The paper engages in a critical dialogue with sociological and epidemiological research that assesses migrant mental health states through the lens of the vulnerability or resilience of this social group, often reducing citiness to a series of environmental ‘stressors’. Distinct from methods ascertaining or arguing against the prevalence of mental disorders among urban migrants, the insight of urban ethnography is to open up a space to explore the mediations that operate dialogically between the city as lived by migrants through particular places and situations and forms of distress.
Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory
Authors: Blane Beth , Raven Kathy E , Leek Danielle , Brown Nicholas , Parkhill Julian , Peacock Sharon J 
Published: April 2019

Abstract

Background
Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with this step could reduce the time to infection control interventions.

Objectives
To develop and evaluate rapid sequencing of MRSA using primary clinical cultures.

Methods
Patients with samples submitted to the clinical laboratory at the Cambridge University Hospitals NHS Foundation Trust from which MRSA was isolated were identified, the routine laboratory culture plates obtained and DNA extraction and sequencing performed.

Results
An evaluation of routine MRSA cultures from 30 patients demonstrated that direct sequencing from bacterial colonies picked from four different culture media was feasible. The 30 clinical MRSA isolates were sequenced on the day of plate retrieval over five runs and passed quality control metrics for sequencing depth and coverage. The maximum contamination detected using Kraken was 1.09% fragments, which were identified as Prevotella dentalis. The most common contaminants were other staphylococcal species (25 isolate sequences) and Burkholderia dolosa (11 isolate sequences). Core genome pairwise SNP analysis to identify clusters based on isolates that were ≤50 SNPs different was used to triage cases for further investigation. This identified three clusters, but more detailed genomic and epidemiological evaluation excluded an acute outbreak.

Conclusions
Rapid sequencing of MRSA from clinical culture plates is feasible and reduces the delay associated with purity culture prior to DNA extraction.
The effect of dietary vitamin D supplementation on sodium-dependent phosphate uptake and expression of NaPi-IIb in the small intestine of weanling pigs
Authors: Saddoris Kari L , Fleet James C , Radcliffe John S 
Published: April 2019

Abstract
Two experiments were conducted to investigate the effects of 1,25(OH)2D3 to stimulate Na+-dependent phosphate uptake in Caco-2 cells, and the effects of dietary vitamin D supplementation to vitamin D-deficient nursery pigs on Na+-dependent nutrient uptake and mRNA expression of NaPi-IIb cotransporter and calbindin D9k in the jejunum. In Exp. 1, 250,000 Caco-2 cells were seeded on Costar 12 mm Snapwell inserts with a 0.40 µm polycarbonate filter and a seeding density of 0.25 × 106 and studied at 15 d postconfluence. Cells were treated with 10 nM of either 1,25(OH)2D3 or vehicle for 48 h and then mounted in modified Ussing chambers for transepithelial measurements. In Exp. 2, pigs (n = 32) were removed from sows at 3 d of age, placed on a vitamin D-deficient milk replacer diet and housed in a room devoid of sunlight and UV light in the range of 280 to 300 nm. On day 28, serum 25(OH)D3 concentrations were measured to verify low vitamin D status. Pigs (BW 10.10 ± 0.38 kg) were then individually housed day 28 postweaning and allotted to 1 of 2 dietary treatments. Dietary treatments consisted of corn-soybean-based diets with vitamin D supplementations of 0 or 1,500 IU/kg diet for 12 d. Blood samples were taken from the brachiocephalic vein on the initial (day 0) and final day (day 10, 11, or 12) of the study for analysis of serum 25(OH)D3, P, and Ca. Pigs were euthanized and jejunal segments were harvested and used in modified Ussing chambers and for RNA isolation and subsequent quantitative RT-PCR analysis. In Exp. 1, treating Caco-2 cells with 10 nM 1,25(OH)2D3 resulted in a 52% increase (P &lt; 0.005) in Na+-dependent phosphate uptake compared with cells treated with a vehicle. In Exp. 2, Na+-dependent phosphate and glucose transport did not differ (P &gt; 0.10) among treatment groups. Additionally, NaPi-IIb and calbindin D9k mRNA expression were not different (P &gt; 0.10) between treatment groups. No differences (P &gt; 0.10) were detected in final serum P or 25(OH)D3 concentrations between treatments. However, serum Ca linearly increased (P &lt; 0.05) as the concentration of supplemental vitamin D increased in the diet. Overall, while 1,25(OH)2D3 stimulated Na+-dependent phosphate uptake in Caco-2 cells, supplementing diets with 1,500 IU/kg vitamin D3 from cholecalciferol did not increase jejunal Na+-dependent phosphate uptake or NaPi-IIb mRNA expression over that of pigs fed diets with no supplemental cholecalciferol.
HighResNPS.com: An Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances
Authors: Mardal Marie , Andreasen Mette Findal , Mollerup Christian Brinch , Stockham Peter , Telving Rasmus , Thomaidis Nikolaos S , Diamanti Konstantina S , Linnet Kristian , Dalsgaard Petur Weihe 
Published: April 2019

Abstract
The number of new psychoactive substances (NPS) is constantly increasing. However, although the number might be large, most NPS have a low prevalence of use, so keeping screening libraries updated with the relevant analytical targets becomes a challenge. One way to ensure sufficient screening coverage is to use shared high resolution-mass spectrometry (HR-MS) databases, such as HighResNPS.com: a free, online, spreadsheet-format, crowd-sourced HR-MS database for NPS screening. The aims of this study were (i) to present the database to the scientific community and (ii) to verify that the HighResNPS database can be utilized in suspect screening workflows for LC–HR-MS instruments and software from four different instrument vendors. A sample was spiked with 10 NPS, and participating laboratories then analyzed the sample with their respective HR-MS vendor platforms and the HighResNPS database. The HighResNPS data were obtained via a spreadsheet converted to fit the import specifications of the different vendor platforms. Suspect screening was performed using LC–HR-MS vendor platforms from Thermo Fisher, Waters, Bruker and Agilent. All 10 NPS were identified in at least three workflows used for the four different vendor platforms. Multiple users have submitted data to HighResNPS for the same NPS, which resulted in multiple true-positive identifications for these NPS. Suspect screening with LC–HR-MS can be based on diagnostic fragment ions reported by users of different vendor platforms and can support NPS identification in biological samples and/or seizure analyses when no reference standard is available in-house. The present work clearly demonstrates that HighResNPS data is compatible with instruments and screening software from at least four different vendor platforms. The database can thus serve as a useful add-on in LC–HR-MS screening workflows.
Phosphorylation of TMEM55B by Erk/MAPK regulates lysosomal positioning
Authors: Takemasu Shinya , Nigorikawa Kiyomi , Yamada Miho , Tsurumi Go , Kofuji Satoshi , Takasuga Shunsuke , Hazeki Kaoru 
Published: April 2019

Abstract
TMEM55B is first identified as phosphatidylinositol-4,5-P24-phosphatases (PtdIns-4,5-P24-phosphatases) that catalyse dephosphorylation of PtdIns-4,5-P2 to PtdIns-5-P. We demonstrate for the first time that TMEM55B is phosphorylated by Erk/MAPK and that this mechanism participates in regulation of lysosomal clustering. Exposure of RAW264.7 macrophages to various stimuli induces phosphorylation of TMEM55B on Ser76 and Ser169, sites corresponding to consensus sequences (PX(S/T)P) for phosphorylation by MAPK. Of these stimuli, Toll-like receptor ligands most strongly induce TMEM55B phosphorylation, and this is blocked by the MEK1/2 inhibitor U0126. However, phosphorylation does not impact intrinsic phosphatase activity of TMEM55B. TMEM55B has recently been implicated in starvation induced lysosomal translocation. Amino acid starvation induces perinuclear lamp1 clustering in RAW264.7 macrophages, which was attenuated by shRNA-mediated knock-down or CRISPR/Cas9-mediated knock-out of TMEM55B. Cells exposed to U0126 also exhibit attenuated lamp1 clustering. Overexpression of TMEM55B but not TMEM55A notably enhances lamp1 clustering, with TMEM55B mutants (lacking phosphorylation sites or mimicking the phosphorylated state) exhibiting lower and higher efficacies (respectively) than wild-type TMEM55B. Collectively, results suggest that phosphorylation of TMEM55B by Erk/MAPK impacts lysosomal dynamics.