bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCQM-K140: carbon stable isotope ratio delta values in honey
Authors: Dunn P J H , Goenaga-Infante H , Goren A C , Şimşek A , Bilsel M , Ogrinc N , Armishaw P , Hai L 
Published: February 2017

As there can be small but measureable differences in isotope ratios between different sources of the same element/compound/material, isotope ratio measurements are applied in a number of different fields including archaeology, environmental science, geochemistry, forensic science and ecology. Isotope ratios for the light elements (H, C, N, O and S) are typically reported as δ-values which are isotope ratios expressed relative to an internationally agreed standard (this standard is the zero-point on the scale), although absolute isotope ratios which are traceable to the SI have also been reported. The IAWG has been granted a traceability exception for the use of arbitrary delta scales until SI traceability can be established at the required level of uncertainty but this goal is some years away.
While the CCQM IAWG has previously organised several pilot studies on isotope ratio determination (CCQM-P75: Stable isotope delta values in methionine, 2006; CCQM-P105: Sr isotope ratios in wine, 2008; CCQM-K98: Pb isotope ratios in bronze with additional delta values in CCQM-P134, 2011), it has been a number of years since delta values of light elements have been considered and there has been no key comparison (KC). Therefore, the IAWG has included the need for a KC (CCQM-K140) based on an arbitrary delta scale in its program to support ongoing requirements to demonstrate core capabilities as well as specific claims of measurement capability (CMCs) in this area.
The performance of all five of the CCQM-K140 participants was very good, illustrating their ability to obtain accurate results for carbon isotope ratios, within the calibration range afforded by internationally agreed reference materials (δ13CVPDB-LSVEC between −47.32 % and +535.3 %) with measurement uncertainties of between 0.08 and 0.28 %. This was despite the fact that no two participants used exactly the same approach in terms of instrumentation or data treatment.

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 CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Integrative Blood Pressure Response to Upright Tilt Post Renal Denervation
Authors: Howden Erin J. , East Cara , Lawley Justin S. , Stickford Abigail S.L. , Verhees Myrthe , Fu Qi , Levine Benjamin D. 
Published: February 2017

Abstract

BACKGROUND
Whether renal denervation (RDN) in patients with resistant hypertension normalizes blood pressure (BP) regulation in response to routine cardiovascular stimuli such as upright posture is unknown. We conducted an integrative study of BP regulation in patients with resistant hypertension who had received RDN to characterize autonomic circulatory control.

METHODS
Twelve patients (60 ± 9 [SD] years, n = 10 males) who participated in the Symplicity HTN-3 trial were studied and compared to 2 age-matched normotensive (Norm) and hypertensive (unmedicated, HTN) control groups. BP, heart rate (HR), cardiac output (Qc), muscle sympathetic nerve activity (MSNA), and neurohormonal variables were measured supine, and 30° (5 minutes) and 60° (20 minutes) head-up-tilt (HUT). Total peripheral resistance (TPR) was calculated from mean arterial pressure and Qc.

RESULTS
Despite treatment with RDN and 4.8 (range, 3–7) antihypertensive medications, the RDN had significantly higher supine systolic BP compared to Norm and HTN (149 ± 15 vs. 118 ± 6, 108 ± 8 mm Hg, P &lt; 0.001). When supine, RDN had higher HR, TPR, MSNA, plasma norepinephrine, and effective arterial elastance compared to Norm. Plasma norepinephrine, Qc, and HR were also higher in the RDN vs. HTN. During HUT, BP remained higher in the RDN, due to increases in Qc, plasma norepinephrine, and aldosterone.

CONCLUSION
We provide evidence of a possible mechanism by which BP remains elevated post RDN, with the observation of increased Qc and arterial stiffness, as well as plasma norepinephrine and aldosterone levels at approximately 2 years post treatment. These findings may be the consequence of incomplete ablation of sympathetic renal nerves or be related to other factors.
Cognitive Associates of Current and More Intensive Control of Hypertension: Findings From the Hispanic Community Health Study/Study of Latinos
Authors: Lamar Melissa , Wu Donghong , Durazo-Arvizu Ramon A. , Brickman Adam M. , Gonzalez Hector M. , Tarraf Wassim , Daviglus Martha L. 
Published: February 2017

Abstract

BACKGROUND
Hypertension control in Hispanics/Latinos lag behind general US trends by 10–15%. Intensive systolic blood pressure (SBP) management &lt;120 mm Hg may significantly reduce morbidity/mortality risk in adults with hypertension; less is known about cognition. We investigated cross-sectional associations of cognition with observed hypertension control at currently recommended (SBP &lt; 140 mm Hg) and more intensive (SBP &lt; 120 mm Hg) levels using baseline data from the Hispanic Community Health Study/Study of Latinos.

METHODS
From this multicenter cohort study, we focused on 1,735 Hispanic/Latino men and women ages 45–74 years with hypertension and verified antihypertensive use. Verbal fluency, information processing speed, learning, and memory were tested in Spanish or English.

RESULTS
Separate linear regressions revealed that being on 1 vs. &gt;1 antihypertensive medication was not associated with cognition; however, individuals with SBP controlled to currently recommended levels outperformed individuals with uncontrolled SBP on verbal fluency [Beta = 1.44 (0.52), P &lt; 0.01] and information processing speed [Beta = 3.01 (0.89), P &lt; 0.001] in age-adjusted regression analyses; only information processing speed remained significant (P &lt; 0.05) after additional adjustments including acculturation, health insurance, and other cardiovascular disease risk factors. When regrouping individuals based on more intensive SBP control, individuals with levels &lt;120 mm Hg outperformed individuals with higher SBP on verbal fluency regardless of adjustments (P &lt; 0.01). More intensive rather than currently recommended levels of control associated with higher verbal fluency performance regardless of adjustments (P &lt; 0.05).

CONCLUSIONS
Individual cognitive test scores related to distinct SBP management with more intensive management appearing more robust against confounders. While cognitive associations with hypertension in Hispanics/Latinos may be multifactorial, different levels of SBP control should be considered in future prospective intervention studies.
LASER server: ancestry tracing with genotypes or sequence reads
Authors: Taliun Daniel , Chothani Sonia P , Schönherr Sebastian , Forer Lukas , Boehnke Michael , Abecasis Gonçalo R , Wang Chaolong 
Published: February 2017

Abstract

Summary
To enable direct comparison of ancestry background in different studies, we developed LASER to estimate individual ancestry by placing either sezquenced or genotyped samples in a common ancestry space, regardless of the sequencing strategy or genotyping array used to characterize each sample. Here we describe the LASER server to facilitate application of the method to a wide range of genetic studies. The server provides genetic ancestry estimation for different geographic regions and user-friendly interactive visualization of the results.

Availability and Implementation
The LASER server is freely accessible at http://laser.sph.umich.edu/

Supplementary information
Supplementary data are available at Bioinformatics online.
Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Authors: Hernandez-Armenta Claudia , Ochoa David , Gonçalves Emanuel , Saez-Rodriguez Julio , Beltrao Pedro 
Published: February 2017

Abstract

Motivation
Phosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.

Results
We used curated phosphoproteomic experiments and a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur to benchmark and compare different kinase activity inference strategies: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model. We also tested weighted variants of the Z-test and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence (in vivo, in vitro or in silico) supporting these influence the predictions.

Conclusions
Most models performed well with the Z-test and the GSEA performing best as determined by the area under the ROC curve (Mean AUC = 0.722). Weighting kinase targets by the kinase target sequence preference improves the results marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions.

Availability and Implementation
The KSEA implementation is available in https://github.com/ evocellnet/ksea. Additional data is available in http://phosfate.com

Supplementary information
Supplementary data are available at Bioinformatics online.
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
Authors: Baele Guy , Lemey Philippe , Rambaut Andrew , Suchard Marc A 
Published: February 2017

Abstract

Motivation
Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses.

Results
We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by &gt; 14-fold.

Availability and Implementation
Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference.

Supplementary information
Supplementary data are available at Bioinformatics online.
Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway
Authors: Palaniappan Sucheendra K , Bertaux François , Pichené Matthieu , Fabre Eric , Batt Gregory , Genest Blaise 
Published: February 2017

Abstract

Motivation
Quantitative models are increasingly used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting.

Results
In this paper, we propose to construct abstractions using information theory notions. Entropy is used to discretize the state space and mutual information is used to select a subset of all original variables and their mutual dependencies. We apply our method to an hybrid model of TRAIL-induced apoptosis in HeLa cell. Our abstraction, represented as a Dynamic Bayesian Network (DBN), reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet preserving essential features of cell death time distributions.

Availability and Implementation
This approach is implemented in the tool DBNizer, freely available at http://perso.crans.org/genest/DBNizer.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pln24NT: a web resource for plant 24-nt siRNA producing loci
Authors: Liu Qi , Ding Changjun , Chu Yanguang , Zhang Weixi , Guo Ganggang , Chen Jiafei , Su Xiaohua 
Published: February 2017

Abstract
In plants, 24 nucleotide small interfering RNAs (24-nt siRNAs) account for a large percentage of the total siRNA pool, and they play an important role in guiding plant-specific RNA-directed DNA methylation (RdDM), which transcriptionally silences transposon elements, transgenes, repetitive sequences and some endogenous genes. Several loci in plant genomes produce clusters of 24-nt RNAs, and these loci are receiving increasing attention from the research community. However, at present there is no bioinformatics resource dedicated to 24-nt siRNA loci and their derived 24-nt siRNAs. Thus, in this study, Pln24NT, a freely available web resource, was created to centralize 24-nt siRNA loci and 24-nt siRNA information, including fundamental locus information, expression profiles and annotation of transposon elements, from next-generation sequencing (NGS) data for 10 popular plant species. An intuitive web interface was also developed for convenient searching and browsing, and analytical tools were included to help users flexibly analyze their own siRNA NGS data. Pln24NT will help the plant research community to discover and characterize 24-nt siRNAs, and may prove useful for studying the roles of siRNA in RNA-directed DNA methylation in plants.

Availability and Implementation
http://bioinformatics.caf.ac.cn/Pln24NT.

Supplementary information
Supplementary data are available at Bioinformatics online.
GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification
Authors: Szpiech Zachary A , Blant Alexandra , Pemberton Trevor J 
Published: February 2017

Abstract

Summary
Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method (Pemberton et al., 2012) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method.

Availability and Implementation
GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub (https://github.com/szpiech/garlic) under the GNU General Public License version 3.

Supplementary information
Supplementary data are available at Bioinformatics online.
Structural bounds on the dyadic effect
Authors: Cinelli Matteo , Ferraro Giovanna , Iovanella Antonio 
Published: February 2017

AbstractThe dyadic effect is a phenomenon that occurs when the number of links between nodes sharing a common feature is larger than expected if the features are distributed randomly on the network. In this article, we consider the case when nodes are distinguished by a binary characteristic. Under these circumstances, two independent parameters, namely dyadicity and heterophilicity are able to detect the presence of the dyadic effect and to measure how much the considered characteristic affects the network topology. The distribution of nodes characteristics can be investigated within a two-dimensional space that represents the feasible region of the dyadic effect, which is bound by two upper bounds on dyadicity and heterophilicity. Using some network structural arguments, we are able to improve such upper bounds and introduce two new lower bounds, providing a reduction of the feasible region of the dyadic effect as well as constraining dyadicity and heterophilicity within a specific range. Some computational experiences show the bounds effectiveness and their usefulness with regards to different classes of networks.
‘Le Renégat’ d’Albert Camus: de l’insignifiance au terrorisme
Authors: Dalmas Franck 
Published: February 2017

Résumé

La nouvelle ‘Le Renégat, ou, un esprit confus’ reste un texte peu exploré d’Albert Camus malgré de nombreuses exégèses allégoriques. Au tournant du vingt-et-unième siècle, la montée des intégrismes et la prolifération du terrorisme mondial n’ont pourtant guère suscité de regain d’intérêt. C’est notre intention de replacer ce texte ‘étrange’ dans la mouvance hypermoderne de la violence. Les angles d’étude sont multiples et rendent justice à la complexité de la nouvelle. Elle est examinée à la lumière de
L’Homme révolté
, en appréhendant les dérives fondamentalistes et en faisant retour sur la guerre d’Algérie, afin de comparer les mécanismes de la terreur et les pratiques répressives. La responsabilité de l’intellectuel derrière le phénomène terroriste est également invoquée, jusqu’à la lecture contemporaine après les réflexions de Jean Baudrillard sur les attentats du 11 septembre 2001. L’insignifiance des positions présentées par le protagoniste renégat reflète l’engagement idéologique absurde selon Camus.
Survival of undersized plaice (Pleuronectes platessa), sole (Solea solea), and dab (Limanda limanda) in North Sea pulse-trawl fisheries
Authors: van der Reijden K. J. , Molenaar P. , Chen C. , Uhlmann S. S. , Goudswaard P. C. , van Marlen B. 
Published: February 2017

Abstract
The European Commission landing obligation, including species-specific “high survival” exemptions, has established a need for accurate discard survival estimates. This study presents the first discard survival estimates on-board Dutch commercial pulse trawlers. During seven, six, and one fishing trip(s), respectively, undersized plaice (Pleuronectes platessa), sole (Solea solea), and dab (Limanda limanda) were collected, assessed for vitality and subsequently monitored up to 21 days. Uncorrected for any potential impacts from predation, tagging, research-related handling, or holding conditions overall survival for plaice (n = 349), sole (n = 226), and dab (n = 187) was assessed as 15% [95% CI: 11–19%], 29% [95% CI: 24–35%], and 16% [95% CI: 10–26%] respectively. Survival was mainly effected by water temperature and factors linked to the fishing vessel. Fish length was not found to affect survival. Catch processing time and haul duration affected plaice survival but not sole. Vitality index, which averages reflex impairment and external damage scores, correlated with survival and may be developed as a proxy for discard survival. Compared to tickler-chain beam trawlers, pulse trawlers showed relatively higher discard survival under fishing conditions pertinent to these studies.
The major threats to Atlantic salmon in Norway
Authors: Forseth Torbjørn , Barlaup Bjørn T. , Finstad Bengt , Fiske Peder , Gjøsæter Harald , Falkegård Morten , Hindar Atle , Mo Tor Atle , Rikardsen Audun H. , Thorstad Eva B. , Vøllestad Leif Asbjørn , Wennevik Vidar 
Published: February 2017

AbstractAtlantic salmon (Salmo salar) is an economically and culturally important species. Norway has more than 400 watercourses with Atlantic salmon and supports a large proportion of the world’s wild Atlantic salmon. Atlantic salmon are structured into numerous genetically differentiated populations, and are therefore managed at the population level. Long-distance migrations between freshwater and ocean habitats expose Atlantic salmon to multiple threats, and a number of anthropogenic factors have contributed to the decline of Atlantic salmon during the last decades. Knowledge on the relative importance of the different anthropogenic factors is vital for prioritizing management measures. We developed a semi-quantitative 2D classification system to rank the different anthropogenic factors and used this to assess the major threats to Norwegian Atlantic salmon. Escaped farmed salmon and salmon lice from fish farms were identified as expanding population threats, with escaped farmed salmon being the largest current threat. These two factors affect populations to the extent that they may be critically endangered or lost, with a large likelihood of causing further reductions and losses in the future. The introduced parasite Gyrodactylus salaris, freshwater acidification, hydropower regulation and other habitat alterations were identified as stabilized population threats, which have contributed to populations becoming critically endangered or lost, but with a low likelihood of causing further loss. Other impacts were identified as less influential, either as stabilized or expanding factors that cause loss in terms of number of returning adults, but not to the extent that populations become threatened. Management based on population specific reference points (conservation limits) has reduced exploitation in Norway, and overexploitation was therefore no longer regarded an important impact factor. The classification system may be used as a template for ranking of anthropogenic impact factors in other countries and as a support for national and international conservation efforts.
Allelic inflation in depleted fish populations with low recruitment
Authors: Niwa Hiro-Sato , Nashida Kazuya , Yanagimoto Takashi 
Published: February 2017

AbstractWhen the recruitment process in highly fecund species involves within-litter correlations in survival probability, the offspring-number distribution can exhibit a power law. Such reproductive skew appears to be prevalent in abundant marine species. We show that an apparent paradox arises in the reproductive skew model. In years of occasionally large recruitment, we expect to observe elevated levels of relatedness among recruits. Conversely, the effective number of alleles within the population is inflated during periods of low-recruitment. Thus, depressed fish populations have excesses of singleton offspring and thus, overexploitation may cause stock depletion but with increasing genetic diversity. Some studies have documented such a diversity paradox. It does not seem possible to explain large effective population sizes of collapsed species on the basis of normal reproduction models in the domain of attraction of the Kingman coalescent. The approach outlined here provides a novel method to examine the resilience and potential for recovery in depleted populations using short-length time-series data on recruitment.