bluuebunny/crossref_metadata_2025_split huggingface dataset:
Borrowed alleles and convergence in serpentine adaptation
Authors: Arnold Brian J. , Lahner Brett , DaCosta Jeffrey M. , Weisman Caroline M. , Hollister Jesse D. , Salt David E. , Bomblies Kirsten , Yant Levi 
Published: June 2016

Significance
Serpentine barrens are enormously hostile to plant life. Understanding how plants survive such a perfect storm of low mineral nutrient, drought prone, and toxic metal rich conditions offers a powerful model of adaptation and may help design resilient crops. Advances in genomics enable population-wide views of selection and deep insight into demographic histories. These approaches are agnostic to phenotype and can indicate which traits were most important in complex adaptations and, at the same time, provide novel candidate genes. Here, we identified candidate genes for serpentine adaptation and provide evidence that some selected alleles were borrowed from a related species, whereas others were independently involved in separate adaptation events in different species.
Mapping out spin and particle conductances in a quantum point contact
Authors: Krinner Sebastian , Lebrat Martin , Husmann Dominik , Grenier Charles , Brantut Jean-Philippe , Esslinger Tilman 
Published: June 2016

Significance
Predicting the transport properties of interacting particles in the quantum regime is challenging. A conceptually simple situation is realized by connecting two reservoirs through a quantum point contact. For noninteracting fermions, the conductance is quantized in units of the inverse of Planck’s constant, reflecting the contribution to transport of an individual quantum state. We use a cold atomic Fermi gas to map out the spin and particle conductance in a quantum point contact for increasing attractive interactions and observe remarkable effects of interactions on both spin and particle transport. Our work provides maps of conductance over a wide range of parameters and in the presence of many-body correlations, yielding new insights into the nature of strongly attractive Fermi gases.
Final Report. Supplementary comparison of 50/60 Hz energy SIM.EM-S7
Authors: Carranza R , Campos S , Castruita A , Nelson T , Ribeiro A M , So E , Spaggiari A , Slomovitz D , Izquierdo D , Postigo H , Díaz H , Sanchez H , Gonzalez J , Ramos R , Zipaquira A 
Published: June 2016

From 2010 to 2012, a key comparison of energy standards at 50/60 Hz was conducted in the SIM region.
The comparison included measurements of active and reactive energy at three frequencies, aiming at providing support to high accuracy measurement needs of reactive energy. This work presents the results of the SIM.EM-S7 supplementary comparison.

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).
Report on key comparison COOMET.AUV.A-K5: pressure calibration of laboratory standard microphones in the frequency range 2 Hz to 10 kHz
Authors: Dobrowolska D , Kosterov A 
Published: June 2016

This is the final report for regional key comparison COOMET.AUV.A-K5 on the pressure calibration of laboratory standard microphones in the frequency range from 2 Hz to 10 kHz. Two laboratories—Central Office of Measures (GUM)—the national metrology institute for Poland and the State Enterprise Scientific-Research Institute for Metrology of Measurement and Control Systems (DP NDI Systema)— the designated institute for acoustics in Ukraine took part in this comparison with the GUM as a pilot. One travelling type LS1P microphone was circulated to the participants and results in the form of regular calibration certificates were collected. The results of the DP NDI Systema obtained in this comparison were linked to the CCAUV.A-K5 key comparison through the joint participation of the GUM. The degrees of equivalence were computed for DP NDI Systema with respect to the CCAUV.A-K5 key comparison reference value.

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 CCAUV, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Availability and quality of routine morbidity data: review of studies in South Africa
Authors: Roomaney Rifqah A , Pillay-van Wyk Victoria , Awotiwon Oluwatoyin F , Nicol Edward , Joubert Jané D , Bradshaw Debbie , Hanmer Lyn A 
Published: June 2016

Objectives: Routine health information systems (RHISs) provide data that are vital for planning and monitoring individual health. Data from RHISs could also be used for purposes for which they were not originally intended, provided that the data are of sufficient quality. For example, morbidity data could be used to inform burden of disease estimations, which serve as important evidence to prioritize interventions and promote health. The objective of this study was to identify and assess published quantitative assessments of data quality related to patient morbidity in RHISs in use in South Africa.
Materials and Methods: We conducted a review of literature published between 1994 and 2014 that assessed the quality of data in RHISs in South Africa. World Health Organization (WHO) data quality components were used as the assessment criteria.
Results Of 420 references identified, 11 studies met the inclusion criteria. The studies were limited to tuberculosis and HIV. No study reported more than 3 WHO data quality components or provided a quantitative assessment of quality that could be used for burden of disease estimation.
Discussion: The included studies had limited geographical focus and evaluated different source data at different levels of the information system. All studies reported poor data quality.
Conclusion: This review confirmed concerns about the quality of data in RHISs, and highlighted the need for a comprehensive evaluation of the quality of patient-level morbidity data in RHISs in South Africa.
Acute care patient portals: a qualitative study of stakeholder perspectives on current practices
Authors: Collins Sarah A , Rozenblum Ronen , Leung Wai Yin , Morrison Constance RC , Stade Diana L , McNally Kelly , Bourie Patricia Q , Massaro Anthony , Bokser Seth , Dwyer Cindy , Greysen Ryan S , Agarwal Priyanka , Thornton Kevin , Dalal Anuj K 
Published: June 2016

Objective: To describe current practices and stakeholder perspectives of patient portals in the acute care setting. We aimed to: (1) identify key features, (2) recognize challenges, (3) understand current practices for design, configuration, and use, and (4) propose new directions for investigation and innovation.Materials and Methods: Mixed methods including surveys, interviews, focus groups, and site visits with stakeholders at leading academic medical centers. Thematic analyses to inform development of an explanatory model and recommendations.Results: Site surveys were administered to 5 institutions. Thirty interviews/focus groups were conducted at 4 site visits that included a total of 84 participants. Ten themes regarding content and functionality, engagement and culture, and access and security were identified, from which an explanatory model of current practices was developed. Key features included clinical data, messaging, glossary, patient education, patient personalization and family engagement tools, and tiered displays. Four actionable recommendations were identified by group consensus.Discussion: Design, development, and implementation of acute care patient portals should consider: (1) providing a single integrated experience across care settings, (2) humanizing the patient-clinician relationship via personalization tools, (3) providing equitable access, and (4) creating a clear organizational mission and strategy to achieve outcomes of interest.Conclusion: Portals should provide a single integrated experience across the inpatient and ambulatory settings. Core functionality includes tools that facilitate communication, personalize the patient, and deliver education to advance safe, coordinated, and dignified patient-centered care. Our findings can be used to inform a “road map” for future work related to acute care patient portals.
A Case of Meningococcal Pyomyositis in an Otherwise Healthy Adult
Authors: Barakat Monique T. , Gajurel Kiran , Fischer Katrina , Stevens Kathryn , Ozdalga Errol , Montoya José G. 
Published: June 2016

Abstract
The clinical spectrum of Neisseria meningitidis can range from nasopharyngeal colonization to life-threatening invasive diseases such as meningitis. However, its etiologic role in invasive pyomyositis (PM) has never been reported before in the English language. In this study, we report the first case of PM in the English language and the second case in the literature caused by N meningitidis.
Collective strategy for obstacle navigation during cooperative transport by ants
Authors: McCreery Helen F. , Dix Zachary A. , Breed Michael D. , Nagpal Radhika 
Published: June 2016

AbstractGroup cohesion and consensus have primarily been studied in the context of discrete decisions, but some group tasks require making serial decisions that build on one another. We examine such collective problem solving by studying obstacle navigation during cooperative transport in ants. In cooperative transport, a group of ants works together to move a large object back to their nest. We blocked cooperative transport groups ofParatrechinal longicorniswith obstacles of varying complexity, analyzing groups trajectories to infer what kind of strategy the ants employed. Simple strategies require little information, but more challenging, robust strategies succeed with a wider range of obstacles. We found that transport groups use a stochastic strategy that leads to efficient navigation around simple obstacles, and still succeeds at difficult ones. While groups navigating obstacles preferentially move directly toward the nest, they change their behavior over time; the longer the ants are obstructed, the more likely they are to move away from the nest. This increases the chance of finding a path around the obstacle. Groups rapidly changed directions and rarely stalled during navigation, indicating that these ants maintain consensus even when the nest direction is blocked. While some decisions were aided by the arrival of new ants, at many key points direction changes were initiated within the group, with no apparent external cause. This ant species is highly effective at navigating complex environments, and implements a flexible strategy that works quickly for simple obstacles and still succeeds with complex obstacles.
Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data
Authors: Feng Huijuan , Li Tingting , Zhang Xuegong 
Published: June 2016

AbstractBackgroundAlternative splicing is a ubiquitous post-transcriptional process in most eukaryotic genes. Aberrant splicing isoforms and abnormal isoform ratios can contribute to cancer development. Kinase genes are key regulators of various cellular processes. Many kinases are found to be oncogenic and have been intensively investigated in the study of cancer and drugs. RNA-Seq provides a powerful technology for genome-wide study of alternative splicing in cancer besides the conventional gene expression profiling. But this potential has not been fully demonstrated yet.MethodsHere we characterized the transcriptome profile of prostate cancer using RNA-Seq data from viewpoints of both differential expression and differential splicing, with an emphasis on kinase genes and their splicing variations. We built up a pipeline to conduct differential expression and differential splicing analysis. Further functional enrichment analysis was performed to explore functional interpretation of the genes. With focus on kinase genes, we performed kinase domain analysis to identify the functionally important candidate kinase gene in prostate cancer. We further calculated the expression level of isoforms to explore the function of isoform switching of kinase genes in prostate cancer.ResultsWe identified distinct gene groups from differential expression and splicing analysis, which suggested that alternative splicing adds another level to gene expression regulation. Enriched GO terms of differentially expressed and spliced kinase genes were found to play different roles in regulation of cellular metabolism. Function analysis on differentially spliced kinase genes showed that differentially spliced exons of these genes are significantly enriched in protein kinase domains. Among them, we found that geneCDK5has isoform switching between prostate cancer and benign tissues, which may affect cancer development by changing androgen receptor (AR) phosphorylation. The observation was validated in another RNA-Seq dataset of prostate cancer cell lines.ConclusionsOur work characterized the expression and splicing profile of kinase genes in prostate cancer and proposed a hypothetical model on isoform switching ofCDK5andARphosphorylation in prostate cancer. These findings bring new understanding to the role of alternatively spliced kinases in prostate cancer and demonstrate the use of RNA-Seq data in studying alternative splicing in cancer.
Evaluating the diagnostic utility of applying a machine learning algorithm to diffusion tensor MRI measures in individuals with major depressive disorder
Authors: Schnyer David M , Clasen Peter C. , Gonzalez Christopher , Beevers Christopher G 
Published: June 2016

AbstractUsing MRI to diagnose mental disorders has been a long-term goal. Despite this, the vast majority of prior neuroimaging work has been descriptive rather than predictive. The current study applies support vector machine (SVM) learning to MRI measures of brain white matter to classify adults with Major Depressive Disorder (MDD) and healthy controls. In a precisely matched group of individuals with MDD (n= 25) and healthy controls (n= 25), SVM learning accurately (70%) classified patients and controls across a brain map of white matter fractional anisotropy values (FA). The study revealed three main findings: 1) SVM applied to DTI derived FA maps can accurately classify MDD vs. healthy controls; 2) prediction is strongest when only right hemisphere white matter is examined; and 3) removing FA values from a region identified by univariate contrast as significantly different between MDD and healthy controls does not change the SVM accuracy. These results indicate that SVM learning applied to neuroimaging data can classify the presence versus absence of MDD and that predictive information is distributed across brain networks rather than being highly localized. Finally, MDD group differences revealed through typical univariate contrasts do not necessarily reveal patterns that provide accurate predictive information.
Compensatory responses by managers, commercial and recreational harvesters to variation in stock abundance of Lake Erie walleye (Sander vitreus vitreus)
Authors: Turgeon Katrine , Reid Kevin B. , Fryxell John M. , Nudds Thomas D. 
Published: June 2016

AbstractDelayed quota adjustments, and/or lagged fishing effort and catch by harvesters, to changes in stock abundance may induce unstable population dynamics and exacerbate the risk of fishery collapse. We examined a 39-y time series of change to quotas by managers, and to effort and catch by both commercial harvesters and anglers, in response to changes in Lake Erie walleye abundance (Sander vitreus) estimated both contemporaneously and retrospectively. Quotas, commercial effort and catch were entrained by contemporaneous estimates of stock abundance. Recreational effort and harvest were not; they had better tracked abundance, as better estimated today, than did the commercial fishery. During the 1990s, a significant mismatch developed between the quota-driven commercial harvest and stock abundance that persisted until a new assessment process obtained. The quasi-open access recreational fishery, instead, freed anglers to respond better to stock abundance. Further elaboration of adaptive risk governance processes, including multi-model inference for stock assessments, may bode well to further reduce risk to fisheries imposed by lagged adjustments to variation in stock abundance.
A signal detection theoretic demonstration of hiring rate asymmetries in competitive academic job markets
Authors: Miuccio Michael , Liu Ka-yuet , Lau Hakwan , Peters Megan A. K. 
Published: June 2016

AbstractTo get a faculty job, graduating doctoral students have to substantially outperform their peers, given the competitive nature of the academic job market. In an ideal, meritocratic world, factors such as prestige of degree-granting university ought not to play a substantial role. However, it has recently been reported that top-ranked universities produced about 2–6 times more faculty than did universities that were ranked lower (Clauset, Arbesman, and Larremore 2015), necessitating un-meritocratic factors: how could students from top-ranked universities be six times more productive than their peers from lower-ranked universities? Here we present a signal detection model to demonstrate that substantially higher rates of faculty production need not require substantially (and unrealistically) higher levels of student productivity. Instead, it is a high hiring threshold due to keen competition that causes small difference in average student productivity between universities to result in manifold differences in placement rates. Under this framework, the previously reported results are compatible with a purely meritocratic system. As a simple proof of concept, we examined the association between university ranking and the impact factors of students publications from a small selected sample of psychology departments in the U.S. The results are in agreement with our theoretical model. Whereas these results do not necessarily mean that the actual faculty hiring market is purely meritocratic, they highlight the difficulty in empirically demonstrating that it is not so.
The mutation rate in human evolution and demographic inference
Authors: Scally Aylwyn 
Published: June 2016

AbstractThe germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5 × 10−9bp−1yr−1in all human or hominin demographic analyses.
How to evaluate phase differences between trial groups in ongoing electrophysiological signals
Authors: VanRullen Rufin 
Published: June 2016

AbstractA growing number of studies endeavor to reveal periodicities in sensory and cognitive functions, by comparing the distribution of ongoing (pre-stimulus) oscillatory phases between two (or more) trial groups reflecting distinct experimental outcomes. A systematic relation between the phase of spontaneous electrophysiological signals, before a stimulus is even presented, and the eventual result of sensory or cognitive processing for that stimulus, would be indicative of an intrinsic periodicity in the underlying neural process. Prior studies of phase-dependent perception have used a variety of analytical methods to measure and evaluate phase differences, and there is currently no established standard practice in this field. The present report intends to remediate this need, by systematically comparing the statistical power of various measures of “phase opposition” between two trial groups, in a number of real and simulated experimental situations. Seven measures were evaluated: one parametric test (circular Watson-Williams test), and three distinct measures of phase opposition (phase bifurcation index, phase opposition sum and phase opposition product) combined with two procedures for non-parametric statistical testing (permutation, or a combination of z-score and permutation). While these are obviously not the only existing or conceivable measures, they have all been used in recent studies. All tested methods performed adequately on a previously published dataset (Busch, Dubois & VanRullen, 2009). On a variety of artificially constructed datasets, no single measure was found to surpass all others, but instead the suitability of each measure was contingent on several experimental factors: the time, frequency and depth of oscillatory phase modulation; the absolute and relative amplitudes of post-stimulus event-related potentials for the two trial groups; the absolute and relative trial numbers for the two groups; and the number of permutations used for non-parametric testing. The concurrent use of two phase opposition measures, the parametric Watson-Williams test and a non-parametric test based on summing inter-trial coherence values for the two trial groups, appears to provide the most satisfactory outcome in all situations tested. Matlab code is provided to automatically compute these phase opposition measures.
Aberrant prefrontal beta oscillations predict episodic memory encoding deficits in schizophrenia
Authors: Meconi Federica , Anderl-Straub Sarah , Raum Heidelore , Landgrebe Michael , Langguth Berthold , Bäuml Karl-Heinz T. , Hanslmayr Simon 
Published: June 2016

AbstractVerbal episodic memory is one of the core cognitive functions affected in patients suffering from schizophrenia (SZ). Although this verbal memory impairment in SZ is a well-known finding, our understanding about its underlying neurophysiological mechanisms is rather scarce. Here we address this issue by recording brain oscillations during a memory task in a sample of healthy controls and patients suffering from SZ. Brain oscillations represent spectral fingerprints of specific neurocognitive operations and are therefore a promising tool to identify neurocognitive mechanisms that are affected by SZ. Healthy controls showed a prominent suppression of left prefrontal beta oscillatory activity during successful memory formation, which replicates several previous oscillatory memory studies. In contrast, patients failed to exhibit such left prefrontal beta power suppression. Utilizing a new topographical pattern similarity approach, we further demonstrate that the degree of similarity between a patient's beta power decrease to that of the controls reliably predicted memory performance. This relationship between beta power decreases and memory was such that the patients' memory performance improved as they showed a more similar topographical beta desynchronization pattern compared to that of healthy controls. These findings suggest that left prefrontal beta power suppression (or lack thereof) during memory encoding is a possible biomarker for the observed encoding impairments in SZ in verbal memory. This lack of left prefrontal beta power decreases might indicate a specific semantic processing deficit of verbal material in patients with schizophrenia.