bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migration Trends of Sockeye Salmon at the Northern Edge of Their Distribution
Authors: Carey Michael P. , Zimmerman Christian E. , Keith Kevin D. , Schelske Merlyn , Lean Charlie , Douglas David C. 
Published: June 2017

AbstractClimate change is affecting arctic and subarctic ecosystems, and anadromous fish such as Pacific salmon Oncorhynchus spp. are particularly susceptible due to the physiological challenge of spawning migrations. Predicting how migratory timing will change under Arctic warming scenarios requires an understanding of how environmental factors drive salmon migrations. Multiple mechanisms exist by which environmental conditions may influence migrating salmon, including altered migration cues from the ocean and natal river. We explored relationships between interannual variability and annual migration timing (2003–2014) of Sockeye Salmon O. nerka in a subarctic watershed with environmental conditions at broad, intermediate, and local spatial scales. Low numbers of Sockeye Salmon have returned to this high‐latitude watershed in recent years, and run size has been a dominant influence on the migration duration and the midpoint date of the run. The duration of the migration upriver varied by as much as 25 d across years, and shorter run durations were associated with smaller run sizes. The duration of the migration was also extended with warmer sea surface temperatures in the staging area and lower values of the North Pacific Index. The midpoint date of the total run was earlier when the run size was larger, whereas the midpoint date was delayed during years in which river temperatures warmed earlier in the season. Documenting factors related to the migration of Sockeye Salmon near the northern limit of their range provides insights into the determinants of salmon migrations and suggests processes that could be important for determining future changes in arctic and subarctic ecosystems.Received October 24, 2016; accepted March 2, 2017 Published online June 8, 2017
The Role of Mindfulness Skills in Terms of Anxiety-Related Cognitive Risk Factors among College Students with Problematic Alcohol Use
Authors: Kraemer Kristen M. , O'Bryan Emily M. , Johnson Adrienne L. , McLeish Alison C. 
Published: June 2017

Background The aim of the current study was to examine the associations between the specific mindfulness skills of observing, describing, awareness, nonjudgment, and nonreactivity in terms of anxiety sensitivity (AS), distress tolerance (DT), and intolerance of uncertainty (IU) among college students with problematic alcohol use. Methods Participants were 202 (69.3% male; Mage = 18.96, SD = 2.24, range = 18–45 years) undergraduate college students with problematic alcohol use who completed self-report measures for course credit. Results Results indicated that after controlling for the effects of gender, smoking status, marijuana use status, and negative affectivity, greater use of the mindfulness skill of observing was associated with higher AS, greater describing was associated with lower AS and higher DT, greater nonjudgment was associated with lower AS and IU and higher DT, and greater nonreactivity was associated with increased DT. Awareness did not significantly predict any of the examined risk factors. Conclusions These results suggest that specific mindfulness skills are associated with a greater tolerance of physiological, emotional, and uncertain states. An important next step will be to examine whether mindfulness skills are associated with decreased problematic alcohol use due to improvements in these anxiety-related risk factors.
TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
Authors: Tappeiner Elias , Finotello Francesca , Charoentong Pornpimol , Mayer Clemens , Rieder Dietmar , Trajanoski Zlatko 
Published: June 2017

Abstract

Summary
Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from next-generation sequencing data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates and quantification of tumor immunogenicity.

Availability and implementation
TIminer is freely available at http://icbi.i-med.ac.at/software/timiner/timiner.shtml.

Supplementary information
Supplementary data are available at Bioinformatics online.
We have confidence to lead gravitational-wave science: an interview with Yueliang Wu
Authors: Jia Hepeng 
Published: June 2017

Abstract
Yueliang Wu, chief scientist of Taiji Program, is a well-known theoretical physicist and the Vice-President of the University of Chinese Academy of Sciences (UCAS). Taiji Program, initially proposed in 2008, is one of China's ambitious plans to observe gravitational waves. Obtaining his Ph.D. at the Institute of Theoretical Physics (ITP) under the Chinese Academy of Sciences (CAS) in 1987, Wu had been working at Dortmund University and Mainz University in Germany and Carnegie-Mellon University and the Ohio-State University in the USA. In 1996, he joined the ITP and became its director in 2007. He has also served as the Director of the Kavli Institute for Theoretical Physics China at the CAS since 2006. In 2007, he was elected as a CAS member.
Wu's research is focused on elementary particle physics, quantum field theory, symmetry principle and cosmophysics. In recent years, he has been proposing a gravitational quantum field theory as a new approach to reconciling the general theory of relativity and quantum mechanics. The most fundamental unanswered question of the general theory of relativity is how general relativity can be reconciled with the laws of quantum physics to produce a complete and self-consistent theory of quantum gravity. To extend the general relativity to realize the reconciliation, Wu suggested a basic gravitational field be needed in the future model.
Since 2012, he, together with Wenrui Hu, has been working as Taiji Program's chief scientist and promoting nationwide gravitational-wave research. National Science Review (NSR) spoke with Wu about the future of gravitational-wave research, the development of China's nationwide gravitational-wave studies and particularly the progress of Taiji Program.
Infants Born Preterm Demonstrate Impaired Exploration of Their Bodies and Surfaces Throughout the First 2 Years of Life
Authors: Babik Iryna , Galloway James Cole , Lobo Michele A. 
Published: June 2017

Abstract

Background
Non–object-oriented exploratory behaviors infants perform with their bodies and surfaces have been proposed to be key precursors of infants’ object exploration, early learning, and future cognitive development. Little is known about the developmental trajectories of these behaviors, especially for infants born preterm.

Objective
The purpose of the study was to longitudinally compare non–object-oriented exploratory behaviors performed by full-term and preterm infants.

Design
The study followed 24 full-term and 30 preterm infants (6 with significant brain injury) performing non–object-oriented exploratory behaviors in prone, supine, and sitting from birth through 24 months.

Methods
Infants were observed without objects or direct social interaction for 3 minutes in prone and supine (0 through 9 months) and in sitting (3 through 24 months). Behavioral coding produced data that were analyzed using hierarchical linear modeling. Developmental trajectories of behaviors were compared among full-term infants, preterm infants without significant brain injury, and preterm infants with significant brain injury.

Results
Compared to full-term peers, preterm infants showed poorer postural control (less head lifting in prone), midline behavior (holding the head in midline, holding both hands in midline), hand-to-mouth and visual-motor behaviors against gravity, and more asymmetrical one-handed fisting. Preterm infants performed fewer bouts of non–object-oriented exploratory behaviors, and their behaviors were less variable with fewer combinations.

Limitations
There was a limited sample of infants born preterm with significant brain injury.

Conclusions
Non–object-oriented exploratory behaviors are important for early perceptual-motor development. Key differences were noted in these behaviors for infants born preterm. These differences may lead to impaired reaching, object exploration, and cognition. Early intervention programs should utilize assessments and interventions that target these very early non–object-oriented exploratory behaviors.
An Initiative to Reduce the Episiotomy Rate
Authors: Zhang-Rutledge Kathy , Clark Steven L. , Denning Stacie , Timmins Audra , Dildy Gary A. , Gandhi Manisha 
Published: June 2017

OBJECTIVE:
To assess the association of education, performance feedback, and the Hawthorne effect with a reduction in the episiotomy rate in a large academic institution.

METHODS:
We describe a prospective observational study of a project conducted between March 2012 and February 2017 to assist clinicians in meeting the Leapfrog Group (www.leapfroggroup.org) target rates for episiotomy. Phases of this project included preintervention (phase 1, March 2012 to April 2014), education and provision of collective department episiotomy rates (phase 2, May 2014 to December 2014), ongoing education with emphasis on a revised Leapfrog target rate (phase 3, January 2015 to February 2016), and provision of individual episiotomy rates to practitioners on a monthly basis (phase 4, March 2016 to February 2017). We analyzed the department episiotomy rates before, during, and after these efforts. Cases of shoulder dystocia were excluded from this analysis. Statistical analysis was performed using a two-tailed Student t test and χ2 test with P<.05 considered significant.

RESULTS:
During the study period 1,176 episiotomies were performed in 16,441 vaginal deliveries (7.2%). In phase 2 (2,352 vaginal deliveries), there was a nonsignificant drop in the episiotomy rate with education alone (9.0–8.2%, P=.21). In phase 3 (4,379 vaginal deliveries), the episiotomy rate demonstrated an additional, significant drop to 5.9% (P<.001), but this reduction did not reach the new Leapfrog goal of 5%. In phase 4 (3,160 vaginal deliveries), the hospital episiotomy rate again dropped significantly from 5.9% to 4.37% (P=.007) and met the target rate of 5%. This reduction was sustained over a 12-month time period. During this same time period, the rate of operative vaginal delivery among vaginal births increased (4.5–5.4%, P=.003) and there was no significant change in the rates of third- and fourth-degree perineal laceration (3.8–3.3%, P=.19).

CONCLUSION:
Education, performance feedback, and the Hawthorne effect were associated with a reduction in the episiotomy rate in a large academic institution without a reduction in the rate of operative vaginal delivery or an increase in the rate of third- and fourth-degree lacerations.
Four Cases of Parkinson Disease Diagnosed During the Postpartum Period
Authors: Maltête David , Grangeon Lou , Le Goff Floriane , Ozel Gulden , Fetter Damien , Ahtoy Patrick , Temgoua Olivier , Rouillé Audrey , Lefaucheur Romain 
Published: June 2017

BACKGROUND:
There is little experience with the effect of pregnancy on Parkinson disease because the number of women with Parkinson disease who are of childbearing age is small. We report four cases beginning during the postpartum period and discuss the potential contribution of different factors that may influence the occurrence of Parkinson disease in this time period.

CASES:
Four women aged 29–35 years developed arm tremor, shoulder pain, dizziness, or decreased dexterity of the hand in the first few days or months after childbirth. They were initially diagnosed with postpartum depression or psychogenic parkinsonism. Finally, dopamine transporter imaging confirmed the diagnosis of young-onset Parkinson disease.

CONCLUSION:
Early-onset Parkinson disease may present in postpartum women. In women with atypical motor symptoms in addition to depression, this diagnosis should be considered.
Clinical Validation of a Test for the Diagnosis of Vaginitis
Authors: Gaydos Charlotte A. , Beqaj Sajo , Schwebke Jane R. , Lebed Joel , Smith Bonnie , Davis Thomas E. , Fife Kenneth H. , Nyirjesy Paul , Spurrell Timothy , Furgerson Dorothy , Coleman Jenell , Paradis Sonia , Cooper Charles K. 
Published: June 2017

OBJECTIVE:
Vaginitis may be diagnosed as bacterial vaginosis, vulvovaginal candidiasis, trichomoniasis, or coinfection. A new molecular test assays the vaginal microbiome and organisms that cause three common infections. The objective of the trial was to evaluate the clinical accuracy of the investigational test for vaginal swabs collected by patients (self) or clinicians. The primary and secondary outcomes were to compare the investigational test with reference methods for the three most common causes of vaginitis and compare clinician-collected with self-collected swabs.

METHODS:
We conducted a cross-sectional study in which women with symptoms of vaginitis were recruited at ten clinical centers and consented to the investigation between May and September 2015. The woman collected a vaginal swab, sheathed, and then handed it to the clinician. These swabs were to evaluate how self-collected swabs compared with clinician-collected swabs. The clinician collected an investigational test swab and reference test swabs. From 1,740 symptomatic patients, clinician-collected and self-collected vaginal swabs were evaluated by the molecular test and six tests. The reference methods for bacterial vaginosis were Nugent's score and Amsel's criteria for intermediate Nugent results. The reference methods for Candida infection were isolation of any potential Candida microorganisms from inoculation of two culture media: chromogenic and Sabouraud agar and sequencing. The reference methods for trichomoniasis were wet mount and culture.

RESULTS:
For clinician-collected swabs, by reference methods, bacterial vaginosis was diagnosed in 56.5%, vaginal candidiasis in 32.8%, trichomoniasis in 8%, and none of the three infections in 24% with a coinfection rate of 20%. The investigational test sensitivity was 90.5% (95% confidence interval [CI] 88.3–92.2%) and specificity was 85.8% (95% CI 83.0–88.3%) for bacterial vaginosis. The investigational test sensitivity was 90.9% (95% CI 88.1–93.1%) and specificity was 94.1% (95% CI 92.6–95.4%) for the Candida group. Sensitivity for Candida glabrata was 75.9% (95% CI 57.9–87.8%) and specificity was 99.7% (95% CI 99.3–99.9%). Investigational test sensitivity was 93.1% (95% CI 87.4–96.3%) and specificity was 99.3% (95% CI 98.7–99.6%) for trichomoniasis. Results from self-collected swabs were similar to clinician-collected swabs.

CONCLUSION:
A molecular-based test using vaginal swabs collected by clinicians or patients can accurately diagnose most common bacterial, fungal, and protozoan causes of vaginitis. Women and their clinicians seeking accurate diagnosis and appropriate selection of efficacious treatment for symptoms of vaginitis might benefit from this molecular test.
Postdischarge Opioid Use After Cesarean Delivery
Authors: Osmundson Sarah S. , Schornack Leslie A. , Grasch Jennifer L. , Zuckerwise Lisa C. , Young Jessica L. , Richardson Michael G. 
Published: June 2017

OBJECTIVE:
To characterize postdischarge opioid use and examine factors associated with variation in opioid prescribing and consumption.

METHODS:
We conducted a prospective observational cohort study by recruiting all women undergoing cesarean delivery during an 8-week period, excluding those with major postoperative morbidities or chronic opioid use. Starting on postoperative day 14, women were queried weekly regarding number of opioid pills used, amount remaining, and their pain experience until they had stopped opioid medication. Demographic and delivery information and in-hospital opioid use were recorded. The state Substance Monitoring Program was accessed to ascertain prescription-filling details. Morphine milligram equivalents were calculated to perform opioid use comparisons. Women in the highest quartile of opioid use (top opioid quartile use) were compared with those in the lowest three quartiles (average opioid use).

RESULTS:
Of 251 eligible patients, 246 (98%) agreed to participate. Complete follow-up data were available for 179 (71% of eligible). Most women (83%) used opioids after discharge for a median of 8 days (interquartile range 6–13 days). Of women who filled their prescriptions (165 [92%]), 75% had unused tablets (median per person 75 morphine milligram equivalents, interquartile range 0–187, maximum 630) and the majority (63%) stored tablets in an unlocked location. This amounts to an equivalent of 2,540 unused 5-mg oxycodone tablets over our study period. Women who used all prescribed opioids (n=40 [22%]) were more likely to report that they received too few tablets than women who used some (n=109 [61%]) or none (n=30 [17%]) of the prescribed opioids (33% compared with 4% compared with 5%, P<.001). The top quartile was more likely to be smokers than average users and consumed more opioid morphine milligram equivalents per hour of inpatient stay than average opioid users (1.6, interquartile range 1.1–2.3 compared with 1.0, interquartile range 0.5–1.4, P<.001).

CONCLUSION:
Most women—especially those with normal in-hospital opioid use—are prescribed opioids in excess of the amount needed.
Perinatal and Maternal Outcomes After Training Residents in Forceps Before Vacuum Instrumental Birth
Authors: Skinner Sasha , Davies-Tuck Miranda , Wallace Euan , Hodges Ryan 
Published: June 2017

OBJECTIVE:
To compare the rates of attempted and successful instrumental births, intrapartum cesarean delivery, and subsequent perinatal and maternal morbidity before and after implementing a training intervention to arrest the decline in forceps competency among resident obstetricians.

METHODS:
This retrospective cohort study examined all attempted instrumental births at Monash Health from 2005 to 2014. We performed an interrupted time-series analysis to compare outcomes of attempted instrumental births in 2005–2009 with those in 2010–2014.

RESULTS:
There were 72,490 births from 2005 to 2014 at Monash Health, of which 8,789 (12%) were attempted instrumental vaginal births. After the intervention, rates of forceps births increased [autoregressive integrated moving average coefficient (β) 1.5, 95% confidence interval (CI) 1.03–1.96; P<.001], and vacuum births decreased (β −1.43, 95% CI −2.5 to −0.37; P<.01). Rates of postpartum hemorrhage decreased (β −1.3, 95% CI −2.07 to −0.49; P=.002) and epidural use increased (β 0.03, 95% CI 0.02–0.05; P<.001). There was no change in rates of unsuccessful instrumental births (β −0.39, 95% CI −3.03 to 2.43; P=.83), intrapartum cesarean delivery (β −0.29, 95% CI −0.55 to 0.14; P=.24), third- and fourth-degree tears (β −1.04, 95% CI −3.1 to 1.00; P=.32), or composite neonatal morbidity (β −0.18, 95% CI −0.38 to 0.02, P=.08). Unsuccessful instrumental births were more likely to be in nulliparous women (P<.001), less likely to have a senior obstetrician present (P<.001), be at later gestation (P<.001), and involved larger birth weight neonates (P<.001).

CONCLUSION:
A policy of ensuring obstetric forceps competency before beginning vacuum training results in more forceps births, fewer postpartum hemorrhages, and no increase in third- and fourth-degree perineal injuries or episiotomies.
Anesthetic Cream Use During Office Pessary Removal and Replacement
Authors: Taege Susanne K. , Adams William , Mueller Elizabeth R. , Brubaker Linda , Fitzgerald Colleen M. , Brincat Cynthia 
Published: June 2017

OBJECTIVE:
To estimate the effect of lidocaine–prilocaine cream on patient pain at the time of office pessary removal and reinsertion.

METHODS:
In this double-blind, randomized placebo-controlled trial, participants undergoing routine pessary care in a urogynecology office at a tertiary referral center were randomized to application of 4 g of either lidocaine–prilocaine or placebo cream 5 minutes before pessary change. Visual analog scale pain scores were collected from the patient at baseline, after pessary removal, and after pessary reinsertion. Physicians also recorded their estimate of patient pain at pessary removal and reinsertion. The primary outcome was the participant-reported visual analog scale pain score at the time of pessary removal and reinsertion. A sample size of 26 per group (n=52) was planned to estimate an absolute mean difference in visual analog scale pain of 2.1 cm at the time of pessary removal. An analysis of covariance was used to evaluate pain at removal and reinsertion as a function of treatment assignment controlling for baseline pain.

RESULTS:
From July 2015 through February 2016, 116 women were screened and 54 were recruited: 28 in the lidocaine–prilocaine cream group and 26 in the placebo group. One patient in the lidocaine-prilocaine cream group was later withdrawn owing to vaginal erosion. The participants were all postmenopausal women, with an average age of 77.8 years. Most characteristics were similar between groups. After adjusting for baseline pain, participants randomized to the lidocaine–prilocaine group had lower pain at pessary removal when compared with those assigned to placebo (mean difference=−2.05, 95% confidence interval −3.69 to −0.41; P=.015).

CONCLUSION:
Lidocaine–prilocaine cream use at the time of office pessary removal reduces patient-reported pain. Clinicians may wish to include this simple intervention to optimize patient comfort and compliance.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, NCT02380742.
Detection of an Inherited Deletion in Products of Conception in a Patient With Recurrent Losses and Normal Karyotype
Authors: Thorne Jeffrey , Craffey Alicia , Nulsen John C. 
Published: June 2017

BACKGROUND:
Microarray analysis testing on products of conception can provide valuable information in the evaluation of recurrent pregnancy loss beyond ploidy status.

CASE:
A maternally inherited deletion on the X chromosome was detected by microarray analysis performed on products of conception in a couple with recurrent pregnancy loss. The mother had a previously demonstrated normal karyotype with standard cytogenetic analysis but was subsequently determined to have the same X chromosome deletion by oligonucleotide single-nucleotide polymorphism (SNP) microarray analysis.

CONCLUSION:
Direct testing of products of conception using oligonucleotide SNP microarray identified a maternally inherited microdeletion on the X chromosome in a patient with recurrent losses and normal karyotype. Going forward, the couple may use preimplantation genetic diagnosis testing to identify embryos free of this deletion for transfer.