bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compound image segmentation of published biomedical figures
Authors: Li Pengyuan , Jiang Xiangying , Kambhamettu Chandra , Shatkay Hagit 
Published: September 2017

Abstract

Motivation
Images convey essential information in biomedical publications. As such, there is a growing interest within the bio-curation and the bio-databases communities, to store images within publications as evidence for biomedical processes and for experimental results. However, many of the images in biomedical publications are compound images consisting of multiple panels, where each individual panel potentially conveys a different type of information. Segmenting such images into constituent panels is an essential first step toward utilizing images.

Results
In this article, we develop a new compound image segmentation system, FigSplit, which is based on Connected Component Analysis. To overcome shortcomings typically manifested by existing methods, we develop a quality assessment step for evaluating and modifying segmentations. Two methods are proposed to re-segment the images if the initial segmentation is inaccurate. Experimental results show the effectiveness of our method compared with other methods.

Availability and implementation
The system is publicly available for use at: https://www.eecis.udel.edu/~compbio/FigSplit. The code is available upon request.

Supplementary information
Supplementary data are available online at Bioinformatics.
Genome-wide pre-miRNA discovery from few labeled examples
Authors: Yones C , Stegmayer G , Milone D H 
Published: September 2017

Abstract

Motivation
Although many machine learning techniques have been proposed for distinguishing miRNA hairpins from other stem-loop sequences, most of the current methods use supervised learning, which requires a very good set of positive and negative examples. Those methods have important practical limitations when they have to be applied to a real prediction task. First, there is the challenge of dealing with a scarce number of positive (well-known) pre-miRNA examples. Secondly, it is very difficult to build a good set of negative examples for representing the full spectrum of non-miRNA sequences. Thirdly, in any genome, there is a huge class imbalance (1: 10 000) that is well-known for particularly affecting supervised classifiers.

Results
To enable efficient and speedy genome-wide predictions of novel miRNAs, we present miRNAss, which is a novel method based on semi-supervised learning. It takes advantage of the information provided by the unlabeled stem-loops, thereby improving the prediction rates, even when the number of labeled examples is low and not representative of the classes. An automatic method for searching negative examples to initialize the algorithm is also proposed so as to spare the user this difficult task. MiRNAss obtained better prediction rates and shorter execution times than state-of-the-art supervised methods. It was validated with genome-wide data from three model species, with more than one million of hairpin sequences each, thereby demonstrating its applicability to a real prediction task.

Availability and implementation
An R package can be downloaded from https://cran.r-project.org/package=miRNAss. In addition, a web-demo for testing the algorithm is available at http://fich.unl.edu.ar/sinc/web-demo/mirnass. All the datasets that were used in this study and the sets of predicted pre-miRNA are available on http://sourceforge.net/projects/sourcesinc/files/mirnass.

Supplementary information
Supplementary data are available at Bioinformatics online.
Rational Growth and Almost Convexity of Higher-Dimensional Torus Bundles
Authors: Bregman Corey 
Published: September 2017

AbstractGiven a matrix $A\in SL(N,\mathbb{Z})$, form the semidirect product $G=\mathbb{Z}^N\rtimes_A \mathbb{Z}$ where the $\mathbb{Z}$-factor acts on $\mathbb{Z}^N$ by $A$. Such a $G$ arises naturally as the fundamental group of an $N$-dimensional torus bundle which fibers over the circle. In this article, we prove that if $A$ has distinct eigenvalues not lying on the unit circle, then there exists a finite index subgroup $H\leq G$ possessing rational growth series for some generating set. In contrast, we show that if $A$ has at least one eigenvalue not lying on the unit circle, then $G$ is not almost convex for any generating set.
Kac Polynomials for Canonical Algebras
Authors: Plamondon Pierre-Guy , Schiffmann Olivier 
Published: September 2017

Abstract
We prove that the number of geometrically indecomposable representations of fixed dimension vector $\mathbf{d}$ of a canonical algebra $C$ defined over a finite field $\mathbb{F}_q$ is given by a polynomial in $q$ (depending on $C$ and $\mathbf{d}$). We prove a similar result for squid algebras. Finally, we express the volume of the moduli stacks of representations of these algebras of a fixed dimension vector in terms of the corresponding Kac polynomials.
Randomized Noninferiority Trial of Telephone vs In-Person Genetic Counseling for Hereditary Breast and Ovarian Cancer: A 12-Month Follow-Up
Authors: Interrante Mary K. , Segal Hannah , Peshkin Beth N. , Valdimarsdottir Heiddis B. , Nusbaum Rachel , Similuk Morgan , DeMarco Tiffani , Hooker Gillian , Graves Kristi , Isaacs Claudine , Wood Marie , McKinnon Wendy , Garber Judy , McCormick Shelley , Heinzmann Jessica , Kinney Anita Y. , Schwartz Marc D. 
Published: September 2017

Abstract

Background
Telephone delivery of genetic counseling is an alternative to in-person genetic counseling because it may extend the reach of genetic counseling. Previous reports have established the noninferiority of telephone counseling on short-term psychosocial and decision-making outcomes. Here we examine the long-term impact of telephone counseling (TC) vs in-person counseling (usual care [UC]).

Methods
We recruited high-risk women for a noninferiority trial comparing TC with UC. Of 1057 potentially eligible women, 669 were randomly assigned to TC (n = 335) or UC (n = 334), and 512 completed the 12-month follow-up. Primary outcomes were patient-reported satisfaction with genetic testing decision, distress, and quality of life. Secondary outcomes were uptake of cancer risk management strategies.

Results
TC was noninferior to UC on all primary outcomes. Satisfaction with decision (d = 0.13, lower bound of 97.5% confidence interval [CI] = –0.34) did not cross its one-point noninferiority limit, cancer-specific distress (d = –2.10, upper bound of 97.5% CI = –0.07) did not cross its four-point noninferiority limit, and genetic testing distress (d = –0.27, upper bound of 97.5% CI = 1.46), physical function (d = 0.44, lower bound of 97.5% CI = –0.91) and mental function (d = –0.04, lower bound of 97.5% CI = –1.44) did not cross their 2.5-point noninferiority limit. Bivariate analyses showed no differences in risk-reducing mastectomy or oophorectomy across groups; however, when combined, TC had significantly more risk-reducing surgeries than UC (17.8% vs 10.5%; χ2= 4.43, P = .04).

Conclusions
Findings support telephone delivery of genetic counseling to extend the accessibility of this service without long-term adverse outcomes.
First star formation in ultralight particle dark matter cosmology
Authors: Hirano Shingo , Sullivan James M , Bromm Volker 
Published: September 2017

Abstract
The formation of the first stars in the high-redshift Universe is a sensitive probe of the small-scale, particle physics nature of dark matter (DM). We carry out cosmological simulations of primordial star formation in ultralight, axion-like particle DM cosmology, with masses of 10−22 and 10−21 eV, with de Broglie wavelengths approaching galactic scales (∼ kpc). The onset of star formation is delayed, and shifted to more massive host structures. For the lightest DM particle mass explored here, first stars form at z ∼ 7 in structures with ∼109 M⊙, compared to the standard minihalo environment within the Λ cold dark matter (ΛCDM) cosmology, where z ∼ 20–30 and ∼105–106 M⊙. Despite this greatly altered DM host environment, the thermodynamic behaviour of the metal-free gas as it collapses into the DM potential well asymptotically approaches a very similar evolutionary track. Thus, the fragmentation properties are predicted to remain the same as in ΛCDM cosmology, implying a similar mass scale for the first stars. These results predict intense starbursts in the axion cosmologies, which may be amenable to observations with the James Webb Space Telescope.
Resident Wellness Initiative to Reduce Burnout and Mitigate Stress
Authors: Wagner Brian , Nentin Farida , Ferrara Lauren 
Published: September 2017

BACKGROUND:
Burnout during residency training has gained significant attention over the past several years. High-rates of burnout, depression and anxiety have been documented in residents throughout their training and a call has been made to develop programs to help mitigate the stress of residency training. We undertook a comprehensive resident wellness initiative to assess burnout and offer residents potential interventions and coping strategies to decrease burnout and reduce stress.

METHODS:
An interventional trial was developed where we incrementally introduced multiple wellness initiatives from September 2012 through June 2016 in an OB/GYN residency program in a large urban university medical center. The wellness initiatives included increased access to program and department leadership for ongoing program improvements, formalized mindful practice training with an emphasis on stress-reduction techniques, confidential, free access to psychotherapy, group conflict mediation and peer and faculty engagement in a mentorship program. Prior to the start of the program and annually, the residents were assessed with the Maslach Burnout Inventory (MBI) and the Perceived Stress Scale. Additionally, we tracked resident satisfaction with the program through an annual online survey review of the training program.

RESULTS:
Forty-nine residents participated in the program over 3 years. At the beginning of the wellness initiative, 64% of the residents exhibited signs of burn-out as defined by two or more high-risk scores in the MBI subcategories. Perceived stress was above normative values in 61% of the residents. Within the first year the number with burn-out signs began to stabilize (62%) and improve in year 2 (51%; P<.05). This trend has been maintained through year 3 (49%). Additionally, there was a decrease in the number of residents with perceived stress scores above the norm (49%; P<.05), suggesting an improvement in coping mechanisms with additional exposure to the wellness curriculum. We saw no difference in overall number of residents reporting a “very positive” residency experience (72%, range 65%–79%) over the course of the wellness initiative.

DISCUSSION:
A comprehensive resident wellness initiative can offer a significant improvement in preventing burnout, reducing stress burdens, and potentially improve resiliency in residency through the development of useful coping mechanisms.
Improving Interprofessional Communication Utilizing Obstetric Simulation Training
Authors: Durst Jennifer , Temming Lorene , Gamboa Christine , Tuuli Methodius , Macones George , Young Omar 
Published: September 2017

BACKGROUND:
Effective interprofessional communication requires clear, concise, and respectful participation from each provider. Simulation has been shown to improve teamwork and patient safety in nonobstetric fields. Whether the benefit of interdisciplinary participation in simulation extends to the obstetric population is unknown.

METHODS:
We conducted a prospective educational trial involving obstetric residents and L&D nurses. Participants were administered a pretest examining their perception of interprofessional communication and cooperation with responses measured on a Likert scale. Participants then underwent an obstetric simulation, watched their video-taped performance, participated in a structured debrief and educational session, and then repeated the simulation. Following the simulation, they were administered a posttest to assess changes in their perception of communication and cooperation.

RESULTS:
Eighteen L&D nurses and 17 obstetric residents participated in the trial. Following simulation, participants were more likely to report that they feel respect from other providers (P=.0087), use closed-loop communication (P<.001), designate a clear leader (P=.0009), read back verbal orders (P=.0002), conduct a nonaccusatory debrief (P=.0491), and view both their communication and communication from others as clear and effective (P=.0043 and P=.0042, respectively).

DISCUSSION:
Obstetric simulation can be used to improve effective interprofessional communication and cooperation. Continued use of interdisciplinary simulation in obstetrics should be encouraged to promote a commitment to patient safety.
West Virginia University's Department of OB/GYN Resident Resiliency Curriculum: A Focus on Well-Being
Authors: Cohen Elizabeth , Matta Maria , Leonard Cassie , Rowan Shon , Hashmi Mahreen 
Published: September 2017

BACKGROUND:
Stress and burnout impact physicians at all stages of training and practice, but resident physicians are particularly at risk. Resiliency skills may protect physicians from the dangers of stress and burnout and may provide improved coping skills.

METHODS:
The Department of Obstetrics and Gynecology conducted monthly meetings with the Residents to discuss resiliency topics in an off-site, private setting without judgment, evaluation consequences, or attending participation.

RESULTS:
During the 2015–2016 academic year, 12 sessions were conducted focusing on Communication Styles, Conflict Resolution, Leadership Skills, Difficult Patient Encounters, Physician Wellness, Resiliency, and Stress/Burnout Management. After completion, residents were anonymously surveyed and sessions were evaluated for effectiveness based on a Likert scale of 1–5. Eleven of 12 sessions returned a 4 or 5 rating, corresponding with a moderately or strongly agree from 100% of the residents. Only one session revealed one resident with a neutral response, or 3.

DISCUSSION:
Sessions explored difficult patient encounters, sentinel events, and interpersonal and professional conflicts. Positive mindfulness-based resilience interventions were discussed. Resident communication about perceived failures and stressors promoted positive discussion and insight. Sessions were almost all uniformly positively scored, with the highest ratings in communication styles, leadership/team-building, and conflict resolution. Resiliency is a key coping skill for physicians to maintain well-being. A residency resiliency curriculum has shown to be well-received in our institution and should be considered as integral in curricula as medical knowledge concepts.
2016 Neonatal Nurse Practitioner Workforce Survey
Authors: Staebler Suzanne , Bissinger Robin 
Published: September 2017

The National Association of Neonatal Nurse Practitioners (NANNP) conducted its second workforce survey of certified neonatal nurse practitioners in the fall of 2016. National Association of Neonatal Nurse Practitioners partnered with the National Certification Corporation and the American Association of Nurse Practitioners to conduct this electronic survey, containing 69 questions and focusing on practice sites and total compensation packages (including benefits) and workforce deficits.
Findings indicate a rising neonatal nurse practitioners (NNPs) position vacancy rate across the country. Regional salary data indicated that the southeast had lower compensation rates for NNPs, with regions 4 and 11 (South) having the lowest rates. A promising trend indicated that new graduate NNPs with a doctorate are earning more. The study findings indicate that tailoring benefit packages to the age and years of experience for the individual NNP may aid in recruiting and retaining NNPs in practice. For experienced NNPs, altered shift lengths (shorter), higher employer matching rates in retirement plans, and less employee cost sharing for health insurance benefits are more appealing strategies.
It is critical for NNPs to continually evaluate the profession's workforce data. There are more than 205,000 nurse practitioners practicing in the United States, with neonatal NPs making up approximately 3% of the larger whole. Increased participation in future surveys will assist in creating sustainable solutions to the workforce crisis facing the profession.
Effects of a Short Video–Based Resident-as-Teacher Training Toolkit on Resident Teaching
Authors: Ricciotti Hope A. , Freret Taylor S. , Aluko Ashley , McKeon Bri Anne , Haviland Miriam J. , Newman Lori R. 
Published: September 2017

OBJECTIVE:
To pilot a short video–based resident-as-teacher training toolkit and assess its effect on resident teaching skills in clinical settings.

METHODS:
A video-based resident-as-teacher training toolkit was previously developed by educational experts at Beth Israel Deaconess Medical Center, Harvard Medical School. Residents were recruited from two academic hospitals, watched two videos from the toolkit (“Clinical Teaching Skills” and “Effective Clinical Supervision”), and completed an accompanying self-study guide. A novel assessment instrument for evaluating the effect of the toolkit on teaching was created through a modified Delphi process. Before and after the intervention, residents were observed leading a clinical teaching encounter and scored using the 15-item assessment instrument. The primary outcome of interest was the change in number of skills exhibited, which was assessed using the Wilcoxon signed-rank test.

RESULTS:
Twenty-eight residents from two academic hospitals were enrolled, and 20 (71%) completed all phases of the study. More than one third of residents who volunteered to participate reported no prior formal teacher training. After completing two training modules, residents demonstrated a significant increase in the median number of teaching skills exhibited in a clinical teaching encounter, from 7.5 (interquartile range 6.5–9.5) to 10.0 (interquartile range 9.0–11.5; P<.001). Of the 15 teaching skills assessed, there were significant improvements in asking for the learner's perspective (P=.01), providing feedback (P=.005), and encouraging questions (P=.046).

CONCLUSION:
Using a resident-as-teacher video-based toolkit was associated with improvements in teaching skills in residents from multiple specialties.
Laparoscopic Major Vascular Injury Simulation Using a Synthetic Compared With Porcine Model
Authors: Milad Magdy P. , Alvi Farah A. , Breen Michael T. , Brincat Cynthia , Frederick Peter J. , Lewicky-Gaupp Christina , Lewis Mark , Rone Bryan , Swan Kimberly , Wollschlaeger Karin 
Published: September 2017

BACKGROUND:
Major vascular injury training may improve clinical skills and reduce patient morbidity during gynecologic laparoscopy; thus, reliable models for simulation should be identified.

METHOD:
Two laparoscopic major vascular injury simulations using synthetic or live porcine models were constructed. The primary surgeon was given the opportunity to complete both simulations. After obtaining peritoneal access, the surgeon quickly encountered a major vascular injury. Degrading vital signs and estimated blood loss coupled with the replay of a human heartbeat that increased in volume and intensity were provided to heighten tension during the synthetic simulation.

EXPERIENCE:
Twenty-two gynecologic surgery educators evaluated the simulations. Educators considered the porcine model superior to the synthetic model with regard to tissue handling. The synthetic model simulation was found to be equivalent to the porcine model on how likely the simulation would be able to improve performance in a clinical setting. Educators were more likely to implement the synthetic simulation over the porcine simulation.

CONCLUSION:
The synthetic model was found to be more feasible and as effective as the porcine model to simulate and teach the initial management steps of major vascular injury at laparoscopy by gynecologic educators.
Use of Electrically Evoked Compound Action Potentials for Cochlear Implant Fitting: A Systematic Review
Authors: de Vos Johan J. , Biesheuvel Jan Dirk , Briaire Jeroen J. , Boot Pieter S. , van Gendt Margriet J. , Dekkers Olaf M. , Fiocco Marta , Frijns Johan H. M. 
Published: September 2017

Objectives:
The electrically evoked compound action potential (eCAP) is widely used in the clinic as an objective measure to assess cochlear implant functionality. During the past decade, there has been increasing interest in applying eCAPs for fitting of cochlear implants. Several studies have shown that eCAP-based fitting can potentially replace time-consuming behavioral fitting procedures, especially in young children. However, a closer look to all available literature revealed that there is no clear consensus on the validity of this fitting procedure. This study evaluated the validity of eCAP-based fitting of cochlear implant recipients based on a systematic review of the recent literature.

Design:
The Preferred Reporting Items for Systematic Reviews and Meta-Analyses were used to search the PubMed, Web of Science, and Cochrane Library databases. The term “eCAP” was combined with “cochlear implants,” “thresholds,” and “levels,” in addition to a range of related terms. Finally, 32 studies met the inclusion criteria. These studies were evaluated on the risk of bias and, when possible, compared by meta-analysis.

Results:
Almost all assessed studies suffered from some form of risk of bias. Twenty-nine of the studies based their conclusion on a group correlation instead of individual subject correlations (analytical bias); 14 studies were unclear about randomization or blinding (outcome assessment bias); 9 studies provided no clear description of the populations used, for example, prelingually or postlingually implanted subjects (selection bias); and 4 studies had a high rate of loss (>10%) for patients or electrodes (attrition bias). Meta-analysis of these studies revealed a weak pooled correlation between eCAP thresholds and both behavioral T- and C-levels (r = 0.58 and r = 0.61, respectively).

Conclusions:
This review shows that the majority of the assessed studies suffered from substantial shortcomings in study design and statistical analysis. Meta-analysis showed that there is only weak evidence to support the use of eCAP data for cochlear implant fitting purposes; eCAP thresholds are an equally weak predictor for both T- and C-levels. Based on this review, it can be concluded that research on eCAP-based fitting needs a profound reflection on study design and analysis to draw well-grounded conclusions about the validity of eCAP-based fitting of cochlear implant recipients.