bluuebunny/crossref_metadata_2025_split huggingface dataset:
Status of the Shortnose Sturgeon Population in the Savannah River, Georgia
Authors: Bahr Derek L. , Peterson Douglas L. 
Published: December 2016

AbstractThe federally endangered Shortnose Sturgeon Acipenser brevirostrum was once abundant in all major coastal river systems from the Saint John River, Canada, to the St. Johns River, Florida. During much of the 20th century, however, populations suffered major declines throughout their range from the combined effects of overfishing, pollution, and habitat loss. Although the species was a charter member of the Endangered Species Act, quantified population assessments are still lacking for many river systems throughout their range. Because river‐specific assessments are critical for evaluating species recovery, the objective of this study was to quantify abundance and annual recruitment of Shortnose Sturgeon occupying the Savannah River, Georgia. Anchored gill nets and trammel nets fished during slack tides were used to sample juvenile and adult Shortnose Sturgeon in their summer holding areas during 2013–2015. Huggins closed‐capture models in RMark were used to derive abundance estimates for each demographic group. The best models estimated that the Savannah River contained 81 (95% CI = 27–264) age‐1 juveniles in 2013, 270 (162–468) in 2014, and 245 (104–691) in 2015. The models also estimated the river to contain 486 (198–1,273) age‐2+ juveniles in 2013, 123 (69–235) in 2014, and 187 (81–526) in 2015. Similarly, the adult population was estimated to be 1,865 (784–4,694) individuals in 2013, 1,564 (1,005–2,513) in 2014, and 940 (535–1,753) in 2015. The results of this study provide the first population estimates available for Shortnose Sturgeon in the Savannah River. Additionally, the results suggest that the Savannah River likely contains the second largest population of Shortnose Sturgeon in Georgia. Future studies are needed in the Savannah River and other South Atlantic river systems to better evaluate Shortnose Sturgeon recovery status and the effects of river‐specific anthropogenic modifications.Received June 27, 2016; accepted September 29, 2016 Published online December 2, 2016
Vincenzo Danti’s Deceits
Authors: Cole Michael , Gamberini Diletta 
Published: November 2016

AbstractThe great sculptor Vincenzo Danti wrote one of the longest poems to have survived from a Renaissance artist, but the text’s close thematic and conceptual connections to its author’s art have gone entirely unnoticed. What Danti’s poem and sculpture share, this essay argues, is a concern with mystified identity. Danti’s poetic sensibility stands at odds with the biographical frameworks that typically guide the interpretation of Renaissance art and literature. At the same time, his example shows how much there is to be gained from an investigation of how artists learned to be writers, and of what came of those efforts.
The CCL-K11 ongoing key comparison. Final report for the year 2014
Authors: Matus Michael , Gavalyugov Veselin , Tamakyarska Denita , Alqahtani Nasser , Alfohaid Mohammad , Moona Girija , Sharma Rina , Hapiddin Asep , Boynawan Ahmad Mohamad , Ranusawud Monludee , Tonmueanwai Anusorn , Hong Feng-Lei , Ishikawa Jun , Robertsson Lennart 
Published: November 2016

Lasers from four national metrological institutes (NMIs) were compared in 2014 as part of the CCL-K11 ongoing key comparison, initiated by the 13th meeting of the Comité Consultative des Longuers (CCL) in 2007. The absolute frequency of R(127) 11-5 transitions of molecular iodine was measured for these lasers following the technical protocol for CCL-K11. The results of these measurements are compiled in the present report. The comparison reports, as communicated by each participant, are included as appendices.
This document constitutes the sixth final report for the ongoing key comparison CCL-K11.

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 CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Maternal Blood Pressure Before Pregnancy and Sex of the Baby: A Prospective Preconception Cohort Study
Authors: Retnakaran Ravi , Wen Shi Wu , Tan Hongzhuan , Zhou Shujin , Ye Chang , Shen Minxue , Smith Graeme N. , Walker Mark C. 
Published: December 2016

Abstract

BACKGROUND
Population-level sociologic studies have suggested that adverse societal conditions may affect fetal viability in a sex-specific manner and thereby modify the ratio of male vs. female babies. This concept suggests that there may exist certain physiologic features in a woman that relate to her likelihood of delivering a boy or girl. We thus established a preconception cohort to prospectively evaluate the relationship between maternal pregravid health and sex of the baby.

METHODS
In this analysis nested within an observational cohort study, 1,411 newly married women in Liuyang, China, underwent pregravid cardiometabolic characterization (including anthropometry and measurement of blood pressure, cholesterol, triglycerides, and glucose) at median 26.3 weeks before a singleton pregnancy, delivering at 39.0 ± 1.3 weeks gestation.

RESULTS
Systolic blood pressure before pregnancy was higher in women who delivered a boy than in those who had a girl (112.5 ± 11.9 vs. 109.6 ± 12.0 mm Hg, P &lt; 0.0001). The prevalence of a male baby progressively increased across quintiles of pregravid systolic blood pressure (P &lt; 0.0001). After covariate adjustment, mean adjusted pregravid systolic blood pressure was higher in mothers of boys vs. girls (106.0 vs. 103.3 mm Hg, P = 0.0015). On logistic regression analysis, pregravid systolic blood pressure emerged as the only significant predictor of having a male baby (adjusted odds ratio = 1.017 per mm Hg, 95% confidence interval = 1.007–1.028). The pregravid difference in blood pressure between mothers of boys and girls was not present during any trimester of pregnancy.

CONCLUSION
Maternal blood pressure before pregnancy is a previously unrecognized factor that may be associated with the likelihood of delivering a boy or girl.
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
Authors: Leimeister Chris-André , Sohrabi-Jahromi Salma , Morgenstern Burkhard 
Published: December 2016

Abstract

Motivation
Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods.

Results
We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes.

Availability and Implementation
The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/

Supplementary information
Supplementary data are available at Bioinformatics online.
Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Authors: Jacox Edwin , Weller Mathias , Tannier Eric , Scornavacca Celine 
Published: December 2016

AbstractSummaryGene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is insufficient to determine them all. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. However finding a most parsimonious binary resolution of a non-binary tree obtained by contracting the unsupported branches is NP-hard if transfer events are considered as possible gene scale events, in addition to gene origination, duplication and loss. We propose an exact, parameterized algorithm to solve this problem in single-exponential time, where the parameter is the number of connected branches of the gene tree that show low support from the sequence alignment or, equivalently, the maximum number of children of any node of the gene tree once the low-support branches have been collapsed. This improves on the best known algorithm by an exponential factor. We propose a way to choose among optimal solutions based on the available information. We show the usability of this principle on several simulated and biological datasets. The results are comparable in quality to several other tested methods having similar goals, but our approach provides a lower running time and a guarantee that the produced solution is optimal.Availability and ImplementationOur algorithm has been integrated into the ecceTERA phylogeny package, available at http://mbb.univ-montp2.fr/MBB/download_sources/16__ecceTERA and which can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.Supplementary informationSupplementary data are available at Bioinformatics online.
pHMM-tree: phylogeny of profile hidden Markov models
Authors: Huo Luyang , Zhang Han , Huo Xueting , Yang Yasong , Li Xueqiong , Yin Yanbin 
Published: December 2016

Abstract
Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families.

Availability and Implementation
This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/

Supplementary information
Supplementary data are available at Bioinformatics online.
HIV Infection, Immunosuppression, and Age at Diagnosis of Non-AIDS-Defining Cancers
Authors: Shiels Meredith S. , Althoff Keri N. , Pfeiffer Ruth M. , Achenbach Chad J. , Abraham Alison G. , Castilho Jessica , Cescon Angela , D’Souza Gypsyamber , Dubrow Robert , Eron Joseph J. , Gebo Kelly , John Gill M. , Goedert James J. , Grover Surbhi , Hessol Nancy A. , Justice Amy , Kitahata Mari , Mayor Angel , Moore Richard D. , Napravnik Sonia , Novak Richard M. , Thorne Jennifer E. , Silverberg Michael J. , Engels Eric A. ,   for the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiologic Databases to Evaluate AIDS (IeDEA)
Published: December 2016

Abstract

Background.
It is unclear whether immunosuppression leads to younger ages at cancer diagnosis among people living with human immunodeficiency virus (PLWH). A previous study found that most cancers are not diagnosed at a younger age in people with AIDS, with the exception of anal and lung cancers. This study extends prior work to include all PLWH and examines associations between AIDS, CD4 count, and age at cancer diagnosis.

Methods.
We compared the median age at cancer diagnosis between PLWH in the North American AIDS Cohort Collaboration on Research and Design and the general population using data from the Surveillance, Epidemiology and End Results Program. We used statistical weights to adjust for population differences. We also compared median age at cancer diagnosis by AIDS status and CD4 count.

Results.
After adjusting for population differences, younger ages at diagnosis (P &lt; .05) were observed for PLWH compared with the general population for lung (difference in medians = 4 years), anal (difference = 4), oral cavity/pharynx (difference = 2), and kidney cancers (difference = 2) and myeloma (difference = 4). Among PLWH, having an AIDS-defining event was associated with a younger age at myeloma diagnosis (difference = 4; P = .01), and CD4 count &lt;200 cells/µL (vs ≥500) was associated with a younger age at lung cancer diagnosis (difference = 4; P = .006).

Conclusions.
Among PLWH, most cancers are not diagnosed at younger ages. However, this study strengthens evidence that lung cancer, anal cancer, and myeloma are diagnosed at modestly younger ages, and also shows younger ages at diagnosis of oral cavity/pharynx and kidney cancers, possibly reflecting accelerated cancer progression, etiologic heterogeneity, or risk factor exposure in PLWH.
Hepatitis C Infection and the Risk of Non-Liver-Related Morbidity and Mortality in HIV-Infected Persons in the Swiss HIV Cohort Study
Authors: Kovari Helen , Rauch Andri , Kouyos Roger , Rougemont Mathieu , Cavassini Matthias , Schmid Patrick , Stöckle Marcel , Bernasconi Enos , Weber Rainer , Ledergerber Bruno ,   for the Swiss HIV Cohort Study
Published: December 2016

Abstract

Background.
Hepatitis C virus (HCV) infection has been associated with increased non-liver-related morbidity and mortality. However, studies have yielded inconsistent results.

Methods.
The incidence of clinical events in human immunodeficiency virus (HIV)–infected HCV-seropositive and incidence density–matched HCV-seronegative participants of the Swiss HIV Cohort Study from August 1994 to December 2014 was studied. We compared (1) HCV-seropositive with HCV-seronegative participants and (2) HCV-viremic with successfully treated nonviremic patients. Poisson regression was used to assess differences between these groups.

Results.
We included 2503 HCV-seropositive participants (540 with spontaneous HCV clearance, 1294 untreated HCV RNA positive, 345 treated with sustained virologic response [SVR], 43 during treatment, and 281 treated without SVR), and 2503 HCV-seronegative controls. After a mean follow-up of 8.2 years, we observed (HCV seropositive and HCV seronegative, respectively) 107 and 18 liver events, 41 and 14 kidney events, 230 and 121 osteoporosis/fractures, 82 and 94 diabetes mellitus, 114 and 129 cardiovascular events, 119 and 147 non-AIDS malignancies, 162 and 126 Centers for Disease Control and Prevention HIV category B/C events, 106 and 10 liver-related deaths, and 227 and 218 non-liver-related deaths. Compared with HCV-negative controls, HCV-seropositive participants had an increased risk of liver events (incidence rate ratio [IRR], 6.29 [95% confidence interval {CI}, 3.52–11.22]), liver-related death (IRR, 8.24 [95% CI, 3.61–18.83]), kidney events (IRR, 2.43 [95% CI, 1.11–5.33]), and osteoporosis/fracture (IRR, 1.43 [95% CI, 1.03–2.01]). Among HCV-seropositive individuals, treated participants without SVR vs those with SVR had a higher risk of liver events (IRR, 6.79 [95% CI, 2.33–19.81]), liver-related death (IRR, 3.29 [95% CI, 1.35–8.05]), and diabetes mellitus (IRR, 4.62 [95% CI, 1.53–13.96]). Similar but not statistically significant differences were found between untreated HCV RNA–positive patients and those with SVR.

Conclusions.
While HCV exposure was associated with an increased risk of kidney disease and osteoporosis/fracture, this risk did not seem to be dependent of persistent HCV RNA. Successful HCV treatment was associated with a lower incidence of liver disease, liver-related death, and diabetes mellitus, whereas the other conditions studied were less affected.
Incidence of myocardial infarction in pregnancy: a systematic review and meta-analysis of population-based studies
Authors: Gibson Paul , Narous Mariam , Firoz Tabassum , Chou Doris , Barreix Maria , Say Lale , James Matthew ,   on behalf of the WHO Maternal Morbidity Working Group
Published: December 2016

Abstract

Aims
Cardiac disease is one of the leading causes of indirect maternal death, and myocardial infarction (MI) is one of its most common aetiologies. The objectives of this systematic review and meta-analysis were to characterize the incidence of pregnancy-associated MI (PAMI), as well as the maternal mortality and the case-fatality rates due to PAMI.

Methods and results
Articles were obtained by searching electronic databases, bibliographies and conference proceedings with no language or date restrictions. Two reviewers independently selected population-based cohort and case-control studies reporting on incidence, mortality and case-fatality rates for pregnancy-associated MI. Meta-analysis was performed to estimate pooled maternal incidence, mortality and case-fatality rates. Meta-regression was performed to explore heterogeneity. Based on 17 included studies, the pooled incidence of PAMI and maternal mortality from PAMI were 3.34 (2.09–4.58) and 0.20 (0.10–0.29) per 100 000 pregnancies, respectively. The case-fatality rate was 5.03% (3.78–6.27%). Country/region (meta-regression P = 0.006) and years of study (meta-regression P = 0.04) were potential explanations for the observed heterogeneity in the pooled incidence estimates of maternal MI and its associated mortality, with more recent studies and those conducted in the USA revealing the highest rates.

Conclusion
This article provides a global estimate of the incidence, mortality rate, and case fatality rate of pregnancy-associated MI. We identified higher rates of PAMI in the USA (relative to Canada and European countries) and rising rates over time. Further research regarding this population is needed, especially given rising maternal age and the increasing prevalence of cardiovascular risk factors.
The UCLA Health Resident Informaticist Program – A Novel Clinical Informatics Training Program
Authors: Singer Jennifer S , Cheng Eric M , Baldwin Kevin , Pfeffer Michael A ,   the UCLA Health Physician Informaticist Committee
Published: December 2016

Abstract
Few opportunities exist for physician trainees to gain exposure to, and training in, the field of clinical informatics, an Accreditation Council for Graduate Medical Education–accredited, recently board-certified specialty. Currently, 21 approved programs exist nationwide for the formal training of fellows interested in pursuing careers in this discipline. Residents and fellows training in medical and surgical fields, however, have few avenues available to gain experience in clinical informatics. An early introduction to clinical informatics brings an opportunity to generate interest for future career trajectories. At University of California Los Angeles (UCLA) Health, we have developed a novel, successful, and sustainable program, the Resident Informaticist Program, with the goals of exposing physician trainees to the field of clinical informatics and its academic nature and providing opportunities to expand the clinical informatics workforce. Herein, we provide an overview of the development, implementation, and current state of the UCLA Health Resident Informaticist Program, with a blueprint for development of similar programs.
Adaptive and Network Sampling for Inference and Interventions in Changing Populations
Authors: Thompson Steven K 
Published: December 2016

Abstract
In this paper, I discuss some of the wider uses of adaptive and network sampling designs. Three uses of sampling designs are to select units from a population to make inferences about population values, to select units to use in an experiment, and to distribute interventions to benefit a population. The most useful approaches for inference from adaptively selected samples are design-based methods and Bayesian methods. Adaptive link-tracing network sampling methods are important for sampling populations that are otherwise hard to reach. Sampling in changing populations involves temporal network or spatial sampling design processes with units selected both into and out of the sample over time. Averaging or smoothing fast-moving versions of these designs provides simple estimates of network-related characteristics. The effectiveness of intervention programs to benefit populations depends a great deal on the sampling and assignment designs used in spreading the intervention.
A Substructural Modal Logic of Utility
Authors: Anderson Gabrielle , Pym David 
Published: December 2016

Abstract
We introduce a substructural modal logic of utility that can be used to reason aboutoptimality with respect to properties of states. Our notion of state is quite general, and is able to represent resource allocation problems in distributed systems. The underlying logic is a variant of the modal logic of bunched implications, and based on resource semantics, which is closely related to concurrent separation logic. We consider a labelled transition semantics and establish conditions under which Hennessy—Milner soundness and completeness hold. By considering notions of cost, strategy and utility, we are able to formulate characterizations of Pareto optimality, best responses, and Nash equilibrium within resource semantics. We also show that our logic is able to serve as a logic for a fully featured process algebra and explain the interaction between utility and the structure of processes.
Comparision of Optical Low Coherence Reflectometry Versus Ultrasonic Biometry in High Hypermetropia
Authors: Aydin Rukiye , Karaman Erdur Sevil , Serefoglu Cabuk Kubra , Karahan Eyyup , Kaynak Suleyman 
Published: November 2016

Purpose:
To compare anterior chamber depth (ACD), axial length (AL), and lens thickness (LT) measurements obtained by the Lenstar LS 900 (Haag-Streit AG) optical low-coherence reflectometry with those obtained by the A-scan contact ultrasound among patients with moderate and high hypermetropia.

Methods:
Fifty-two eyes of 52 patients with moderate and high hypermetropia (spherical equivalent of +4 D or more) were examined in this study measurements of ACD, AL, and LT obtained by Lenstar were compared with those obtained by applanation A-scan ultrasound. All measurements were obtained by two independent examiners. The interdevice agreements were evaluated with Bland–Altman analyses.

Results:
The mean age of the patients was 54.78±12.77 years (range 18–74 years). The mean spherical equivalent refractive power was +5.16±1.12 D (+4.0 to +8.75). The mean values of ACD, AL, and LT with A-scan were 3.05±0.34, 21.55±0.75, and 4.33±0.49 mm, respectively, whereas these values were 2.99±0.45, 21.58±0.78, and 4.20±0.44 mm, respectively, with Lenstar. There was statistically significant difference of LT between the two methods (P=0.02). The mean differences (lower/upper limit of agreement) of the ACD, AL, and LT values for A-scan ultrasound and Lenstar were −0.06 (−0.594/0.474), 0.04 (−0.380/0.459), and −0.12 (−0.739/0.502), respectively.

Conclusion:
Among patients with moderate and high hypermetropia, the biometric measurements of ACD, AL, and LT by ultrasound and optical biometry were determined to be correlated and there was a high degree of agreement between contact A-scan ultrasonic biometry and Lenstar.