bluuebunny/crossref_metadata_2025_split huggingface dataset:
L3 acquisition of English attributive adjectives
Authors: Fallah Nader , Jabbari Ali Akbar 
Published: October 2016

Abstract
This study examines three L3 transfer proposals, namely the L1 Factor (Hermas, 2010, 2014a, 2014b), the CEM (Flynn et al., 2004) and the TPM (Rothman, 2010, 2011, 2013, 2015) as well as investigates the role of the language of dominance in L3 acquisition of English attributive adjectives. Three groups of bilinguals took part in this study: L1 Mazandarani/L2 Persian, with Mazandarani as the dominant language of communication, L1 Mazandarani/L2 Persian, with Persian as the dominant language of communication and L1 Persian/L2 Mazandarani, with Persian as the dominant language of communication. The results of a grammaticality judgment task and an element rearrangement task show that the predictions of the above-mentioned L3 transfer proposals were not realized. Instead, the dominant language of communication turns out to be the main source of syntactic crosslinguistic influence at the initial stages of L3 acquisition, irrespective of its status as an L1 or L2.
Rabifier2: an improved bioinformatic classifier of Rab GTPases
Authors: Surkont Jaroslaw , Diekmann Yoan , Pereira-Leal José B 
Published: October 2016

Abstract

Summary
The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases. It is more accurate, significantly faster than the original version and is now open source, both the code and the data, allowing for community participation.

Availability and Implementation
Rabifier and RabDB are freely available through the web at http://rabdb.org. The Rabifier package can be downloaded from the Python Package Index at https://pypi.python.org/pypi/rabifier, the source code is available at Github https://github.com/evocell/rabifier.

Supplementary information
Supplementary data are available at Bioinformatics online.
Recommendations for high-risk clinical target volume definition with computed tomography for three-dimensional image-guided brachytherapy in cervical cancer patients
Authors: Ohno Tatsuya , Wakatsuki Masaru , Toita Takafumi , Kaneyasu Yuko , Yoshida Ken , Kato Shingo , Ii Noriko , Tokumaru Sunao , Ikushima Hitoshi , Uno Takashi , Noda Shin-ei , Kazumoto Tomoko , Harima Yoko ,   , the Working Group of the Gynecological Tumor Committee of the Japanese Radiation Oncology Study Group (JROSG)
Published: October 2016

Abstract
Our purpose was to develop recommendations for contouring the computed tomography (CT)-based high-risk clinical target volume (CTVHR) for 3D image-guided brachytherapy (3D-IGBT) for cervical cancer. A 15-member Japanese Radiation Oncology Study Group (JROSG) committee with expertise in gynecological radiation oncology initiated guideline development for CT-based CTVHR (based on a comprehensive literature review as well as clinical experience) in July 2014. Extensive discussions occurred during four face-to-face meetings and frequent email communication until a consensus was reached. The CT-based CTVHR boundaries were defined by each anatomical plane (cranial–caudal, lateral, or anterior–posterior) with or without tumor progression beyond the uterine cervix at diagnosis. Since the availability of magnetic resonance imaging (MRI) with applicator insertion for 3D planning is currently limited, T2-weighted MRI obtained at diagnosis and just before brachytherapy without applicator insertion was used as a reference for accurately estimating the tumor size and topography. Furthermore, utilizing information from clinical examinations performed both at diagnosis and brachytherapy is strongly recommended. In conclusion, these recommendations will serve as a brachytherapy protocol to be used at institutions with limited availability of MRI for 3D treatment planning.
On the metallicity dependance of the [Y/Mg] – age relation for solar type stars
Authors: Feltzing Sofia , Howes Louise M. , McMillan Paul J. , Stonkutė Edita 
Published: October 2016

Abstract
Several recent studies of Solar twins in the Solar neighbourhood have shown a tight correlation between various elemental abundances and age, in particular [Y/Mg]. If this relation is real and valid for other types of stars as well as elsewhere in the Galaxy it would provide a very powerful tool to derive ages of stars without the need to resort to determining their masses (evolutionary stage) very precisely. The method would also likely work if the stellar parameters have relatively large errors. The studies presented in the recent literature span a narrow range of [Fe/H]. By studying a larger sample of Solar neighbourhood dwarfs with a much larger range in [Fe/H], we find that the relation between [Y/Mg] and age depends on the [Fe/H] of the stars. Hence, it appears that the [Y/Mg] – age relation is unique to Solar analogues.
Internal Medicine Residency Program Directors’ Views of the Core Entrustable Professional Activities for Entering Residency: An Opportunity to Enhance Communication of Competency Along the Continuum
Authors: Angus Steven V. , Vu T. Robert , Willett Lisa L. , Call Stephanie , Halvorsen Andrew J. , Chaudhry Saima 
Published: October 2016

Purpose
To examine internal medicine (IM) residency program directors’ (PDs’) perspectives on the Core Entrustable Professional Activities for Entering Residency (Core EPAs)—introduced into undergraduate medical education to further competency-based assessment—and on communicating competency-based information during transitions.

Method
A spring 2015 Association of Program Directors in Internal Medicine survey asked PDs of U.S. IM residency programs for their perspectives on which Core EPAs new interns must or should possess on day 1, which are most essential, and which have the largest gap between expected and observed performance. Their views and preferences were also requested regarding communicating competency-based information at transitions from medical school to residency and residency to fellowship/employment.

Results
The response rate was 57% (204/361 programs). The majority of PDs felt new interns must/should possess 12 of the 13 Core EPAs. PDs’ rankings of Core EPAs by relative importance were more varied than their rankings by the largest gaps in performance. Although preferred timing varied, most PDs (82%) considered it important for medical schools to communicate Core EPA-based information to PDs; nearly three-quarters (71%) would prefer a checklist format. Many (60%) would be willing to provide competency-based evaluations to fellowship directors/employers. Most (> 80%) agreed that there should be a bidirectional communication mechanism for programs/employers to provide feedback on competency assessments.

Conclusions
The gaps identified in Core EPA performance may help guide medical schools’ curricular and assessment tool design. Sharing competency-based information at transitions along the medical education continuum could help ensure production of competent, practice-ready physicians.
From Communication Skills to Skillful Communication: A Longitudinal Integrated Curriculum for Critical Care Medicine Fellows
Authors: Roze des Ordons Amanda L. , Doig Christopher J. , Couillard Philippe , Lord Jason 
Published: October 2016

Problem
Communication with patients and families in critical care medicine (CCM) can be complex and challenging. A longitudinal curricular model integrating multiple techniques within classroom and clinical milieus may facilitate skillful communication across diverse settings.

Approach
In 2014–2015, the authors developed and implemented a curriculum for CCM fellows at the Cumming School of Medicine, University of Calgary, to promote the longitudinal development of skillful communication. A departmental needs assessment informed curriculum development. Five 4-hour classroom sessions were developed: basic communication principles, family meetings about goals and transitions of care, discussing patient safety incidents, addressing conflict, and offering organ donation. Teaching methods—including instructor-led presentations incorporating a consistent framework for approaching challenging conversations, simulation and clinical practice, and feedback from peers, trained facilitators, family members, and clinicians—supported integration of skills into the clinical setting and longitudinal development of skillful communication. Seven fellows participated during the first year of the curriculum.

Outcomes
CCM fellows engaged enthusiastically in the program, commented that the framework provided was helpful, and highly valued the opportunity to practice challenging communication scenarios, learn from observing their peers, and receive immediate feedback.

Next Steps
More detailed accounts of fellows’, patients’, and family members’ experiences will be obtained to guide curricular development. The curriculum will be expanded to involve other members of the multidisciplinary intensive care unit team, and faculty education initiatives will be offered to enhance the quality of the feedback provided. The impact of the curriculum on initial skill development, retention, and progression will be assessed.
Acquired Exchange Protein Directly Activated by Cyclic Adenosine Monophosphate Activity Induced by p38 Mitogen-activated Protein Kinase in Primary Afferent Neurons Contributes to Sustaining Postincisional Nociception
Authors: Matsuda Megumi , Oh-hashi Kentaro , Yokota Isao , Sawa Teiji , Amaya Fumimasa 
Published: October 2016

Abstract

Background
The molecular mechanisms responsible for sustained pain after tissue injury are largely unknown. The aim of this study was to clarify the role of exchange protein directly activated by cyclic adenosine monophosphate (EPAC) in sustained postincisional nociception, using tissue injury-induced nociceptor priming, and involvement of p38 mitogen-activated protein kinase (p38MAPK) in EPAC-mediated nociceptor priming.

Methods
Plantar incisions were made in the hind paws of Sprague–Dawley rats (n = 144). Nociceptor priming was confirmed by behavior testing followed by prostaglandin E2 injection 14 to 21 days after the incision. ESI-09, a selective EPAC inhibitor, was administered to assess its effects on nociceptor priming. Expression of two isoforms of EPAC (EPAC1/EPAC2) in dorsal root ganglions from naive rats and those 14 days after the incision was detected by immunohistochemistry and Western blotting. Separately, FR167653, a selective p38MAPK inhibitor, was administered to assess its effect on EPAC1/EPAC2 expression and the development of nociceptor priming.

Results
Prostaglandin E2 injection 14 to 21 days after the plantar incision induced persistent mechanical hyperalgesia for 7 days. EPAC1/EPAC2 expression in dorsal root ganglion neurons was trivial in naive rats (7.7 ± 4.8% for EPAC1; 6.3 ± 4.1% for EPAC2) but markedly increased 14 days after the incision (21.0 ± 9.4% and 20.1 ± 3.8%, respectively). ESI-09 treatment inhibited prostaglandin E2-induced persistent mechanical hypersensitivity but had no effect on incision-induced acute nociceptive hypersensitivity. Treatment with FR167653 before the incision inhibited the development of nociceptor priming and incision-induced EPAC1/EPAC2 expression (8.5 ± 5.4% and 7.6 ± 3.3%, respectively).

Conclusions
Transient inflammatory stimulation causes long-lasting nociceptive hypersensitivity via nociceptor priming during the subacute period after incision. Acquired EPAC activity by p38MAPK in the dorsal root ganglion neurons is a key for this event.
Intra-fetal Compared With Intra-amniotic Digoxin Before Dilation and Evacuation
Authors: White Katharine O'Connell , Nucatola Deborah L. , Westhoff Carolyn 
Published: October 2016

OBJECTIVE:
To compare the effectiveness of 1.0 mg intra-fetal or intra-amniotic digoxin to achieve fetal asystole before second-trimester surgical pregnancy termination.

METHODS:
In a randomized trial, women received 1.0 mg transabdominal intra-fetal or intra-amniotic digoxin on the day of laminaria placement before dilation and evacuation between 20 and 24 weeks of gestation. The primary outcome was incidence of fetal asystole, documented immediately before dilation and evacuation. We planned to analyze the primary outcome by original group assignment as well as by as-treated and per-protocol populations. A sample size of 270 was needed to detect an 8% difference in failure rates between groups. Prespecified secondary outcomes included the incidence of adverse events, side effects, and procedural differences.

RESULTS:
Between January 2012 and January 2013, we screened 381 women and randomized 270 women to receive intra-fetal (n=136) or intra-amniotic (n=134) digoxin. Characteristics were similar across groups; the mean gestational age was 21.6 weeks (standard deviation 1.2). The proportion of fetal asystole was higher in the intra-fetal group (128/135 [94.8%]) than the intra-amniotic group (107/130, 82.3%; relative risk of failure to achieve asystole 3.41, 95% confidence interval 1.52–7.68). Results were similar in the as-treated and per-protocol populations. There were no significant differences in adverse events or side effects and no differences in injection duration, operative time, or estimated blood loss.

CONCLUSION:
Administration of intra-fetal injection of digoxin led to a higher proportion of participants achieving fetal asystole within 24 hours than intra-amniotic injection.

CLINICAL TRIAL REGISTRATION:
ClinicalTrials.gov, https://clinicaltrials.gov, NCT01047748.
Pregnancy Outcomes in Women With a History of Previable, Preterm Prelabor Rupture of Membranes
Authors: Monson Martha A. , Gibbons Karen J. , Esplin M. Sean , Varner Michael W. , Manuck Tracy A. 
Published: October 2016

OBJECTIVE:To characterize subsequent pregnancy outcomes among women with a history of previable, preterm prelabor rupture of membranes (PROM) and assess factors associated with recurrent preterm birth.METHODS:This was a retrospective cohort study of women cared for with a history of one or more singleton pregnancy complicated by preterm PROM at less than 24 weeks of gestation between 2002 and 2013 who were cared for in two tertiary care health systems by a single group of maternal-fetal medicine specialists. Women were identified using International Classification of Diseases, 9th Revision codes and obstetric databases. Those with iatrogenic preterm PROM and those whose index preterm PROM at less than 24 weeks of gestation was preceded by advanced cervical dilation were excluded. All women with one or more pregnancies reaching the second trimester after an index previable, preterm PROM pregnancy were included. The primary outcome was recurrent preterm birth at less than 37 weeks of gestation. Data were analyzed by χ2, Fisher exact,ttest, Wilcoxon rank-sum, and logistic regression.RESULTS:Two hundred ninety-four women had one or more pregnancies complicated by previable, preterm PROM. One hundred eight of 294 (37%) had one or more subsequent pregnancies in our health care systems and 50 of 108 (46%) had two or more. In the pregnancy immediately after the index delivery, the risk of prematurity was high: 50 (46%) delivered at less than 37 weeks of gestation, 31 (30%) at less than 34 weeks of gestation, 25 (23%) at less than 28 weeks of gestation, and 18 (17%) before 24 weeks of gestation. Fewer than half (n=49 [45%]) of women received preterm birth prophylaxis (progesterone or cerclage) in a subsequent pregnancy; rates of recurrent preterm birth were similar among women who received preterm birth prophylaxis compared with those who did not. In regression models, the only factor significantly associated with recurrent preterm birth at less than 37 weeks of gestation was a history of preterm birth preceding previable, preterm PROM delivery (adjusted odds ratio 3.23, 95% confidence interval 1.32–7.93).CONCLUSION:Patients with a history of previable, preterm PROM are at high risk of recurrent preterm birth.
Laparoscopically Confirmed Endometriosis and Breast Cancer in the Nurses' Health Study II
Authors: Farland Leslie V. , Tamimi Rulla M. , Eliassen A. Heather , Spiegelman Donna , Hankinson Susan E. , Chen Wendy Y. , Missmer Stacey A. 
Published: October 2016

OBJECTIVE:
To investigate the association between laparoscopically confirmed endometriosis and the risk of breast cancer. Previous research on endometriosis and breast cancer has reported mixed results.

METHODS:
Our prospective cohort study included 116,430 women from the Nurses' Health Study II cohort followed from 1989 until 2013. Our primary analysis investigated the association between self-reported laparoscopically confirmed endometriosis and the risk of breast cancer. Breast cancer diagnosis was verified through medical records. Multivariable adjusted Cox proportional hazard models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs). Breast cancer was further classified by menopausal status at the time of diagnosis and tumor hormone receptor status verified through tissue microarrays when available and medical records.

RESULTS:
At baseline, 5,389 (5%) women reported laparoscopically confirmed endometriosis. Over 24 years of follow-up, 4,979 (3%) incident breast cancer cases were diagnosed. Women with endometriosis were not at higher risk for overall (adjusted HR 0.96, 95% CI 0.88–1.06), premenopausal (adjusted HR 1.05, 95% CI 0.89–1.23), or postmenopausal breast cancer (adjusted HR 0.93, 95% CI 0.80–1.07). However, associations varied by tumor hormone receptor status (P value, test for heterogeneity: .001), although women with endometriosis were not at increased risk of estrogen- and progesterone receptor-positive (ER+/PR+) tumors (adjusted HR 1.00, 95% CI 0.87–1.14) or ER− and PR− tumors (adjusted HR 0.90, 95% CI 0.67–1.21). Women with endometriosis reported 2.87 ER+/PR− breast cancer cases per 10,000 person-years compared with women without endometriosis (1.32/10,000 person-years), which resulted in nearly a twofold increased risk of ER+/PR− breast cancers (adjusted HR 1.90, 95% CI 1.44–2.50).

CONCLUSION:
Endometriosis was not found to be associated with overall risk of breast cancer in this study; however, endometriosis was significantly associated with an increased risk of ER+/PR− breast tumors, which should be interpreted cautiously.
Identifying Patients With Vesicovaginal Fistula at High Risk of Urinary Incontinence After Surgery
Authors: Bengtson Angela M. , Kopp Dawn , Tang Jennifer H. , Chipungu Ennet , Moyo Margaret , Wilkinson Jeffrey 
Published: October 2016

OBJECTIVE:
To develop a risk score to identify women with vesicovaginal fistula at high risk of residual urinary incontinence after surgical repair.

METHODS:
We conducted a prospective cohort study among 401 women undergoing their first vesicovaginal fistula repair at a referral fistula repair center in Lilongwe, Malawi, between September 2011 and December 2014, who returned for follow-up within 120 days of surgery. We used logistic regression to develop a risk score to identify women with a high likelihood of residual urinary incontinence, defined as incontinence grade 2–5 within 120 days of vesicovaginal fistula repair, based on preoperative clinical and demographic characteristics (age, number of years with fistula, human immunodeficiency virus status, body mass index, previous repair surgery at an outside facility, revised Goh classification, Goh vesicovaginal fistula size, circumferential fistula, vaginal scaring, bladder size, and urethral length). The sensitivity, specificity, and positive and negative predictive values of the risk score at each cut point were assessed.

RESULTS:
Overall, 11 (3%) women had unsuccessful fistula closure. Of those with successful fistula closure (n=372), 85 (23%) experienced residual incontinence. A risk score cut point of 20 had sensitivity of 82% (95% confidence interval [CI] 72–89%) and specificity 63% (95% CI 57–69%) to potentially identify women with residual incontinence. In our population, the positive predictive value for a risk score cut point of 20 or higher was 43% (95% CI 36–51%) and the negative predictive value was 91% (95% CI 86–94%). Forty-eight percent of our study population had a risk score 20 or greater and, therefore, would have been identified for further intervention.

CONCLUSION:
A risk score of 20 or higher was associated with an increased likelihood of residual incontinence with satisfactory sensitivity and specificity. If validated in alternative settings, the risk score could be used to refer women with a high likelihood of postoperative incontinence to more experienced surgeons.
Sleep-disordered breathing and the menopausal transition among participants in the Sleep in Midlife Women Study
Authors: Mirer Anna G. , Young Terry , Palta Mari , Benca Ruth M. , Rasmuson Amanda , Peppard Paul E. 
Published: October 2016

Abstract

Objective:
Menopause is widely believed to be an established cause of sleep disorders, but evidence for this theory is inconclusive. Attributing any sleep problem to normal processes of menopause may lead to underdiagnosis of treatable sleep disorders in midlife women. This study uses detailed longitudinal data on sleep and menopausal health from participants in the Sleep in Midlife Women Study to investigate whether risk and severity of sleep-disordered breathing increase with progression through menopause, accounting for changes in age and body habitus.

Methods:
A total of 219 women aged 38 to 62 years were recruited from participants in the Wisconsin Sleep Cohort Study. Menopause status was determined from daily diaries in which participants reported menstrual flow, hot flashes, and use of hormonal medications. Each participant underwent in-home polysomnography studies every 6 months, to measure the apnea-hypopnea index (AHI) (N = 1,667 studies). Linear models with empirical standard errors were fit for logarithm of AHI on menopause status and years in menopause, adjusting for age, body mass index, waist girth, and neck girth.

Results:
Compared with women in premenopause, AHI was 21% higher among participants in perimenopause (95% CI, −4 to 54), 31% higher among participants in postmenopause (95% CI, 2-68), and 41% higher among participants whose menopausal stage could not be distinguished between peri- and postmenopause (95% CI, 8-82). Among women who had begun perimenopause, each additional year in menopause was associated with 4% greater AHI (95% CI, 2-6).

Conclusions:
Progression through menopause is associated with greater sleep-disordered breathing severity. This association is independent of aging and changes in body habitus.