bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate change impacts on Canadian yields of spring wheat, canola and maize for global warming levels of 1.5 °C, 2.0 °C, 2.5 °C and 3.0 °C
Authors: Qian Budong , Zhang Xuebin , Smith Ward , Grant Brian , Jing Qi , Cannon Alex J , Neilsen Denise , McConkey Brian , Li Guilong , Bonsal Barrie , Wan Hui , Xue Li , Zhao Jun 
Published: April 2019

Abstract
Science-based assessments of climate change impacts on cropping systems under different levels of global warming are essential for informing stakeholders which global climate targets and potential adaptation strategies may be effective. A comprehensive evaluation of climate change impacts on Canada’s crop production under different levels of global warming is currently lacking. The DayCent, DNDC and DSSAT models were employed to estimate changes in crop yield and production for three prominent crops including spring wheat, canola and maize in current agricultural regions of Canada. Four warming scenarios with global mean temperature changes of 1.5 °C, 2.0 °C, 2.5 °C and 3.0 °C above the pre-industrial level were investigated. Climate scenarios from 20 Global Climate Models, included in the Coupled Model Intercomparison Project Phase 5 and downscaled with a multivariate quantile mapping bias correction method, were used to drive the crop simulation models. Simulated yield changes demonstrate a potentially positive impact on spring wheat and canola yields at all four temperature levels, particularly when shifting planting date is considered in the simulations. There was less consensus for the currently utilized short-season maize cultivars, as yields were only projected to increase by DNDC compared to a slight decrease by DayCent and a slight increase up to 2.5 °C followed by a decrease at 3.0 °C by DSSAT. These findings indicate that climate at the global warming levels up to 3.0 °C above the pre-industrial level could be beneficial for crop production of small grains in Canada. However, these benefits declined after warming reached 2.5 °C.
Effects of manipulated levels of predation threat on parental provisioning and nestling begging
Authors: Mutzel Ariane , Olsen Anne-Lise , Mathot Kimberley J , Araya-Ajoy Yimen G , Nicolaus Marion , Wijmenga Jan J , Wright Jonathan , Kempenaers Bart , Dingemanse Niels J 
Published: April 2019

AbstractParental provisioning behavior is a major determinant of offspring growth and survival, but high provisioning rates might come at the cost of increased predation threat. Parents should thus adjust provisioning activity according to current predation threat levels. Moreover, life-history theory predicts that response to predation threat should be correlated with investment in current reproduction. We experimentally manipulated perceived predation threat in free-living great tits (Parus major) by presenting parents with a nest predator model while monitoring different aspects of provisioning behavior and nestling begging. Experiments were conducted in 2 years differing greatly in ecological conditions, including food availability. We further quantified male territorial aggressiveness and male and female exploratory tendency. Parents adjusted provisioning according to current levels of threat in an apparently adaptive way. They delayed nest visits during periods of elevated perceived predation threat and subsequently compensated for lost feeding opportunities by increasing provisioning once the immediate threat had diminished. Nestling begging increased after elevated levels of predation threat, but returned to baseline levels by the end of the experiment, suggesting that parents had fully compensated for lost feeding opportunities. There was no evidence for a link between male exploration behavior or aggressiveness and provisioning behavior. In contrast, fast-exploring females provisioned at higher rates, but only in the year with poor environmental conditions, which might indicate a greater willingness to invest in current reproduction in general. Future work should assess whether these personality-related differences in delivery rates under harsher conditions came at a cost of reduced residual reproductive value.
Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants
Authors: Monger Steven , Troup Michael , Ip Eddie , Dunwoodie Sally L , Giannoulatou Eleni 
Published: April 2019

Abstract

Motivation
In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants.

Results
We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer.

Availability and implementation
Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts.

Supplementary information
Supplementary data are available at Bioinformatics online.
PyPore: a python toolbox for nanopore sequencing data handling
Authors: Semeraro Roberto , Magi Alberto 
Published: April 2019

Abstract

Motivation
The recent technological improvement of Oxford Nanopore sequencing pushed the throughput of these devices to 10–20 Gb allowing the generation of millions of reads. For these reasons, the availability of fast software packages for evaluating experimental quality by generating highly informative and interactive summary plots is of fundamental importance.

Results
We developed PyPore, a three module python toolbox designed to handle raw FAST5 files from quality checking to alignment to a reference genome and to explore their features through the generation of browsable HTML files. The first module provides an interface to explore and evaluate the information contained in FAST5 and summarize them into informative quality measures. The second module converts raw data in FASTQ format, while the third module allows to easily use three state-of-the-art aligners and collects mapping statistics.

Availability and implementation
PyPore is an open-source software and is written in Python2.7, source code is freely available, for all OS platforms, in Github at https://github.com/rsemeraro/PyPore

Supplementary information
Supplementary data are available at Bioinformatics online.
The Dynamics of Speech Motor Control Revealed with Time-Resolved fMRI
Authors: Janssen Niels , Mendieta Cristian Camilo Rincón 
Published: April 2019

Abstract
Holding a conversation means that speech must be started, maintained, and stopped continuously. The brain networks that underlie these aspects of speech motor control remain poorly understood. Here we collected functional magnetic resonance imaging (fMRI) data while participants produced normal and fast rate speech in response to sequences of visually presented objects. We took a non-conventional approach to fMRI data analysis that allowed us to study speech motor behavior as it unfolded over time. To this end, whole-brain fMRI signals were extracted in stimulus-locked epochs using slice-based fMRI. These data were then subjected to group independent component analysis to discover spatially independent networks that were associated with different temporal activation profiles. The results revealed two basic brain networks with different temporal dynamics: a cortical network that was activated continuously during speech production, and a second cortico-subcortical network that increased in activity during the initiation and suppression of speech production. Additional analyses explored whether key areas involved in motor suppression such as the right inferior frontal gyrus, sub-thalamic nucleus and pre-supplementary motor area provide first-order signals to stop speech. The results reveal for the first time the brain networks associated with the initiation, maintenance, and suppression of speech motor behavior.
How Introducing a Registry With Automated Alerts for Carbapenem-resistant Enterobacteriaceae (CRE) May Help Control CRE Spread in a Region
Authors: Lee Bruce Y , Bartsch Sarah M , Hayden Mary K , Welling Joel , DePasse Jay V , Kemble Sarah K , Leonard Jim , Weinstein Robert A , Mueller Leslie E , Doshi Kruti , Brown Shawn T , Trick William E , Lin Michael Y 
Published: April 2019

Abstract

Background
Regions are considering the use of electronic registries to track patients who carry antibiotic-resistant bacteria, including carbapenem-resistant Enterobacteriaceae (CRE). Implementing such a registry can be challenging and requires time, effort, and resources; therefore, there is a need to better understand the potential impact.

Methods
We developed an agent-based model of all inpatient healthcare facilities (90 acute care hospitals, 9 long-term acute care hospitals, 351 skilled nursing facilities, and 12 ventilator-capable skilled nursing facilities) in the Chicago metropolitan area, surrounding communities, and patient flow using our Regional Healthcare Ecosystem Analyst software platform. Scenarios explored the impact of a registry that tracked patients carrying CRE to help guide infection prevention and control.

Results
When all Illinois facilities participated (n = 402), the registry reduced the number of new carriers by 11.7% and CRE prevalence by 7.6% over a 3-year period. When 75% of the largest Illinois facilities participated (n = 304), registry use resulted in a 11.6% relative reduction in new carriers (16.9% and 1.2% in participating and nonparticipating facilities, respectively) and 5.0% relative reduction in prevalence. When 50% participated (n = 201), there were 10.7% and 5.6% relative reductions in incident carriers and prevalence, respectively. When 25% participated (n = 101), there was a 9.1% relative reduction in incident carriers (20.4% and 1.6% in participating and nonparticipating facilities, respectively) and 2.8% relative reduction in prevalence.

Conclusions
Implementing an extensively drug-resistant organism registry reduced CRE spread, even when only 25% of the largest Illinois facilities participated due to patient sharing. Nonparticipating facilities garnered benefits, with reductions in new carriers.
Pharmacokinetics and Pharmacodynamics of Oral and Intravenous Omadacycline
Authors: Rodvold Keith A , Pai Manjunath P 
Published: April 2019

AbstractOral and intravenous (IV) omadacycline formulations are approved in the United States for treating acute bacterial skin and skin structure infections and community-acquired bacterial pneumonia in adults. Oral omadacycline bioavailability is 34.5%; similar exposures are obtained following 300 mg oral and 100 mg IV doses. Oral administration should be in a fasted state, with dairy products, antacids, or multivitamins avoided for ≥4 hours after dosing. Low protein binding (21%), large volume of distribution (190 L), low systemic clearance (10 L/hour), and long elimination half-life (16–17 hours) support once-daily dosing. Omadacycline is excreted unchanged in feces (81.1%) and urine (14.4%), with low potential for drug–drug interactions. Dose adjustments are unnecessary for age, sex, and renal or hepatic impairment. Pharmacokinetic–pharmacodynamic studies identify fAUC0–24/MIC ratio as the parameter that correlates with in vivo efficacy. Systemic exposure of omadacycline in epithelial lining fluid is greater than/equal to plasma concentrations in healthy adults.
Near-optimal recovery of linear and N-convex functions on unions of convex sets
Authors: Juditsky Anatoli , Nemirovski Arkadi 
Published: April 2019

Abstract
In this paper we build provably near-optimal, in the minimax sense, estimates of linear forms and, more generally, ‘$N$-convex functionals’ (an example being the maximum of several fractional-linear functions) of unknown ‘signal’ from indirect noisy observations, the signal assumed to belong to the union of finitely many given convex compact sets. Our main assumption is that the observation scheme in question is good in the sense of Goldenshluger et al. (2015, Electron. J. Stat., 9, 1645–1712), the simplest example being the Gaussian scheme, where the observation is the sum of linear image of the signal and the standard Gaussian noise. The proposed estimates, same as upper bounds on their worst-case risks, stem from solutions to explicit convex optimization problems, making the estimates ‘computation-friendly’.
Early Clearance of Mycobacterium tuberculosis: The INFECT Case Contact Cohort Study in Indonesia
Authors: Verrall Ayesha J , Alisjahbana Bachti , Apriani Lika , Novianty Novianty , Nurani Andini C , van Laarhoven Arjan , Ussher James E , Indrati Agnes , Ruslami Rovina , Netea Mihai G , Sharples Katrina , van Crevel Reinout , Hill Philip C 
Published: April 2019

AbstractBackgroundEarly clearance of Mycobacterium tuberculosis is the eradication of infection before an adaptive immune response develops. We aimed to identify host factors associated with early clearance.MethodsIndonesian household contacts patients with smear-positive tuberculosis (TB) had an interferon-γ release assay (IGRA) at baseline and 14 weeks later. Early clearance was defined as a persistently negative IGRA. Contact characteristics, exposure, and disease phenotype were assessed for association with a positive IGRA at each time point.ResultsOf 1347 contacts of 462 TB cases, 780 (57.9%) were IGRA positive and 490 (36.3%) were IGRA negative. After 14 weeks, 116 of 445 (26.1%) initially negative contacts were IGRA converters; 317 (71.2%) remained persistently negative. BCG vaccination reduced the risk of a positive baseline IGRA (relative risk [RR], 0.89 [95% confidence interval {CI} .83–.97]; P = .01), and strongly reduced the risk of IGRA conversion (RR, 0.56 [95% CI, .40–.77]; P < .001). BCG protection decreased with increasing exposure (P = .05) and increasing age (P = .004). Risk of IGRA conversion was positively associated with hemoglobin concentration (P = .04).ConclusionsA quarter of household TB case contacts were early clearers. Protection against M. tuberculosis infection was strongly associated with BCG vaccination. Lower protection from BCG with increasing M. tuberculosis exposure and age can inform vaccine development.
Sphingosine 1-phosphate and inflammation
Authors: Obinata Hideru , Hla Timothy 
Published: April 2019

AbstractAbstractSphingosine 1-phosphate (S1P), a sphingolipid mediator, regulates various cellular functions via high-affinity G protein-coupled receptors, S1P1-5. The S1P-S1P receptor signaling system plays important roles in lymphocyte trafficking and maintenance of vascular integrity, thus contributing to the regulation of complex inflammatory processes. S1P is enriched in blood and lymph while maintained low in intracellular or interstitial fluids, creating a steep S1P gradient that is utilized to facilitate efficient egress of lymphocytes from lymphoid organs. Blockage of the S1P-S1P receptor signaling system results in a marked decrease in circulating lymphocytes because of a failure of lymphocyte egress from lymphoid organs. This provides a basis of immunomodulatory drugs targeting S1P1 receptor such as FTY720, an immunosuppressive drug approved in 2010 as the first oral treatment for relapsing–remitting multiple sclerosis. The S1P-S1P receptor signaling system also plays important roles in maintenance of vascular integrity since it suppresses sprouting angiogenesis and regulates vascular permeability. Dysfunction of the S1P-S1P receptor signaling system results in various vascular defects, such as exaggerated angiogenesis in developing retina and augmented inflammation due to increased permeability. Endothelial-specific deletion of S1P1 receptor in mice fed high-fat diet leads to increased formation of atherosclerotic lesions. This review highlights the importance of the S1P-S1P receptor signaling system in inflammatory processes. We also describe our recent findings regarding a specific S1P chaperone, apolipoprotein M, that anchors to high-density lipoprotein and contributes to shaping the endothelial-protective and anti-inflammatory properties of high-density lipoprotein.
BOARD INVITED REVIEW: Post-transfer consequences of in vitro-produced embryos in cattle
Authors: Ealy Alan D , Wooldridge Lydia K , McCoski Sarah R 
Published: April 2019

Abstract
In vitro embryo production (IVP) in cattle has gained worldwide interest in recent years, but the efficiency of using IVP embryos for calf production is far from optimal. This review will examine the pregnancy retention rates of IVP embryos and explore causes for pregnancy failures. Based on work completed over the past 25 yr, only 27% of cattle receiving IVP embryos will produce a live calf. Approximately 60% of these pregnancies fail during the first 6 wk of gestation. When compared with embryos generated by superovulation, pregnancy rates are 10% to 40% lower for cattle carrying IVP embryos, exemplifying that IVP embryos are consistently less competent than in vivo-generated embryos. Several abnormalities have been observed in the morphology of IVP conceptuses. After transfer, IVP embryos are less likely to undergo conceptus elongation, have reduced embryonic disk diameter, and have compromised yolk sac development. Marginal binucleate cell development, cotyledon development, and placental vascularization have also been documented, and these abnormalities are associated with altered fetal growth trajectories. Additionally, in vitro culture conditions increase the risk of large offspring syndrome. Further work is needed to decipher how the embryo culture environment alters post-transfer embryo development and survival. The risk of these neonatal disorders has been reduced by the use of serum-free synthetic oviductal fluid media formations and culture in low oxygen tension. However, alterations are still evident in IVP oocyte and embryo transcript abundances, timing of embryonic cleavage events and blastulation, incidence of aneuploidy, and embryonic methylation status. The inclusion of oviductal and uterine-derived embryokines in culture media is being examined as one way to improve the competency of IVP embryos. To conclude, the evidence presented herein clearly shows that bovine IVP systems still must be refined to make it an economical technology in cattle production systems. However, the current shortcomings do not negate its current value for certain embryo production needs and for investigating early embryonic development in cattle.
Phylogeography of Simulium Subgenus Wilhelmia (Diptera: Simuliidae)—Insights From Balkan Populations
Authors: Đuknić Jelena , Jovanović Vladimir M , Popović Nataša , Živić Ivana , Raković Maja , Čerba Dubravka , Paunović Momir 
Published: April 2019

AbstractMany morphologically similar species of the simuliid (Diptera: Simuliidae) subgenus Wilhelmia, Enderlein are difficult to distinguish. Thus, the revision of the subgenus using various morphological, cytogenetic, and genetic analyses has been attempted. Neglected until now, the Balkan Peninsula, a crossroad between Europe and Anatolia, provides insight which could resolve problematic interrelationships of the taxa within this subgenus. To uncover the status and relations within the subgenus Wilhelmia, mtDNA was extracted from 47 individuals of six morphospecies: Simulium balcanicum (Enderlein, 1924), Simulium turgaicum Rubtsov, 1940, Simulium lineatum (Meigen, 1804), Simulium pseudequinum Séguy, 1921, Simulium equinum (Linnaeus, 1758), and Simulium paraequinum Puri, 1933 from 21 sites throughout the Balkan Peninsula. Phylogenetic analysis of the Wilhelmia species using mitochondrial DNA barcoding (COI) gene showed two major branches, the lineatum branch, which includes the lineages sergenti, paraequinum, and lineatum, and the equinum branch. In the equinum branch, the mtDNA sequences formed six clades, with high genetic distances, suggesting the existence of different species. Historically, the clades of the equinum branch appeared at numerous islands, perhaps as a result of allopatric speciation. The paraequinum lineage (lineatum branch) is composed of two species. However, six clades of the lineatum lineage overlapped with intra- and interspecific genetic distances. Our results revealed that the species S. balcanicum, S. pseudequinum B, and S. equinum were omnipresent in the Balkans. The results point to not only the fair diversity of Wilhelmia species in the Balkans, but also indicate that most Wilhelmia species live in sympatry.
Proliferating Bias? American Political Science, Nuclear Weapons, and Global Security
Authors: Braut-Hegghammer Målfrid 
Published: April 2019

Abstract
This article examines whether there is a US bias affecting how American political scientist study nuclear weapons and their effects. US dominance in the production and dissemination of political science literature on nuclear weapons is reflected in concepts and theories of their spread and use, as well as prominent datasets on nuclear proliferation. More broadly, is there a US bias in scholarship on nuclear weapons produced by American political scientist? In this article I examine whether there is a US bias that affects what is studied, what kinds of questions are asked and what cases are examined, and how the evidence is interpreted.
Climate change impact on migration, travel, travel destinations and the tourism industry
Authors: Semenza Jan C , Ebi Kristie L 
Published: April 2019

Abstract

Background: Climate change is not only increasing ambient temperature but also accelerating the frequency, duration and intensity of extreme weather and climate events, such as heavy precipitation and droughts, and causing sea level rise, which can lead to population displacement. Climate change-related reductions in land productivity and habitability and in food and water security can also interact with demographic, economic and social factors to increase migration. In addition to migration, climate change has also implications for travel and the risk of disease. This article discusses the impact of climate change on migration and travel with implications for public health practice.

Methods: Literature review.

Results: Migrants may be at increased risk of communicable and non-communicable diseases, due to factors in their country of origin and their country of destination or conditions that they experience during migration. Although migration has not been a significant driver of communicable disease outbreaks to date, public health authorities need to ensure that effective screening and vaccination programmes for priority communicable diseases are in place.
Population growth coupled with socio-economic development is increasing travel and tourism, and advances in technology have increased global connectivity and reduced the time required to cover long distances. At the same time, as a result of climate change, many temperate regions, including high-income countries, are now suitable for vector-borne disease transmission. This is providing opportunities for importation of vectors and pathogens from endemic areas that can lead to cases or outbreaks of communicable diseases with which health professionals may be unfamiliar.

Conclusion: Health systems need to be prepared for the potential population health consequences of migration, travel and tourism and the impact of climate change on these. Integrated surveillance, early detection of cases and other public health interventions are critical to protect population health and prevent and control communicabledisease outbreaks.