bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome
Authors: Alvarez Roberto Vera , Li Shan , Landsman David , Ovcharenko Ivan 
Published: September 2017

Abstract

Summary
Addressing deleterious effects of noncoding mutations is an essential step towards the identification of disease-causal mutations of gene regulatory elements. Several methods for quantifying the deleteriousness of noncoding mutations using artificial intelligence, deep learning and other approaches have been recently proposed. Although the majority of the proposed methods have demonstrated excellent accuracy on different test sets, there is rarely a consensus. In addition, advanced statistical and artificial learning approaches used by these methods make it difficult porting these methods outside of the labs that have developed them. To address these challenges and to transform the methodological advances in predicting deleterious noncoding mutations into a practical resource available for the broader functional genomics and population genetics communities, we developed SNPDelScore, which uses a panel of proposed methods for quantifying deleterious effects of noncoding mutations to precompute and compare the deleteriousness scores of all common SNPs in the human genome in 44 cell lines. The panel of deleteriousness scores of a SNP computed using different methods is supplemented by functional information from the GWAS Catalog, libraries of transcription factor-binding sites, and genic characteristics of mutations. SNPDelScore comes with a genome browser capable of displaying and comparing large sets of SNPs in a genomic locus and rapidly identifying consensus SNPs with the highest deleteriousness scores making those prime candidates for phenotype-causal polymorphisms.

Availability and implementation
https://www.ncbi.nlm.nih.gov/research/snpdelscore/

Supplementary information
Supplementary data are available at Bioinformatics online.
Marriage, Cohabitation, and Divorce in Later Life
Authors: Brown Susan L , Wright Matthew R 
Published: September 2017

AbstractOlder adults are at the forefront of family change as a declining share experiences lifelong marriage and rates of cohabitation and divorce in later life continue to rise. The goal of this article is to review recent scholarship on marriage, cohabitation, and divorce among older adults and identify directions for future research. The varied family experiences characterizing the later life course demonstrate the importance of moving beyond marital status to capture additional dimensions of the marital biography, including transitions, timing, duration, and sequencing. Cohabitation operates as an alternative to marriage for older adults and is increasingly replacing remarriage following divorce or widowhood. The gray divorce rate has doubled in recent decades as older adults abandon marriage in favor of unmarried partnerships or singlehood. The retreat from marriage among older adults raises important questions about the ramifications of family change for health and well-being as well as access to caregivers given that spouses historically have been the primary source of care.
Experience with Kaposi Sarcoma Herpesvirus Inflammatory Cytokine Syndrome in a Large Urban HIV Clinic in the United States: Case Series and Literature Review
Authors: Cantos Valeria D , Kalapila Aley G , Ly Nguyen Minh , Adamski Marylyn , Gunthel Clifford J 
Published: September 2017

AbstractIn 2010, a new entity, characterized by the classical signs and symptoms of Kaposi sarcoma herpesvirus–associated multicentric Castleman’s disease (KSHV-MCD) in the absence of pathologic evidence of MCD, was described in individuals living with HIV. This syndrome was named KSHV inflammatory cytokine syndrome (KICS). It carries mortality rates of up to 60%. To date, there are no standard therapies. Treatment regimens studied in clinical trials for MCD disease are used in cases of KICS.
The detection rates of merging binary black holes originating from star clusters and their mass function
Authors: Fujii Michiko S. , Tanikawa Ataru , Makino Junichiro 
Published: September 2017

Abstract
Advanced LIGO (Laser Interferometer Gravitational Wave Observatory) observations achieved the first detection of the gravitational wave, which was from a merging binary black hole (BBH). In the near future, more merger events will be observed, and the mass distribution of them will become available. The mass distribution of merger events reflects the evolutionary path of BBHs: dynamical formation in dense star clusters or common envelope evolution from primordial binaries. In this paper, we estimate the detection rate of merging BBHs which dynamically formed in dense star clusters by combining the results of N-body simulations, modeling of globular clusters, and cosmic star-cluster formation history. We estimate that the merger rate density in the local universe within the redshift of 0.1 is 13–57 Gpc−3 yr−1. We find that the detection rate is 0.23–4.6 per year for the current sensitivity limit and that it would increase to 5.1–99 per year for the designed sensitivity which will be achieved in 2019. The distribution of merger rate density in the local universe as a function of redshifted chirp mass has a peak close to the low-mass end. The chirp mass function of the detected mergers, on the other hand, has a peak at the high-mass end, but is almost flat. This difference is simply because the detection range is larger for more massive BBHs.
Reliability of a Skin Diagnostic Device in Assessing Hydration and Erythema
Authors: Huimin Koh , Rowledge Alexandra M. , Borzdynski Caroline J. , Miller Charne , Frescos Nicoletta , McKenzie Gayle , Perry Elizabeth , McGuiness William 
Published: September 2017

ABSTRACT

OBJECTIVE:
To examine the reliability of a skin diagnostic device, the SD202 (Courage+Khazaka GmBH, Cologne, Germany), in assessing hydration and erythema of periwound skin and pressure injury-prone areas.

DESIGN:
Intrarater reliabilities from 3 cross-sectional and prospective studies are reported.

SETTING AND PARTICIPANTS:
Patients attending an outpatient, nurse-led wound dressing clinic (n = 16), a podiatrist-led high-risk foot clinic (n = 17), and residents (n = 38) at a single residential aged-care facility.

MAIN OUTCOME MEASURE:
Skin hydration and erythema levels assessed using the SD202.

MAIN RESULTS:
High internal consistency was maintained for consecutive skin hydration and erythema measures at a single point on the venous leg ulcer periwound (α > .996 and α > .970 for hydration and erythema, respectively) and for the pressure-prone areas of the sacrum (α > .916), right (α > .994) and left (α > .967) ischium, right (α > .989) and left (α > .916) trochanter, right (α > .985) and left (α > .992) calcaneus, and right (α > .991) and left (α > .990) lateral malleolus. High consistency was also found for the measures obtained at 4 different locations around the periwound for the venous leg ulcer (α > .935 and α > .870 for hydration and erythema, respectively). In diabetic foot ulcer assessment, acceptable internal consistency of hydration measures around the periwound was observed (α > .634). Internal consistency of erythema measures was variable, ranging from low to high reliability, particularly among predebridement measures.

CONCLUSIONS:
Using the protocols outlined in this study, the SD202 demonstrates high reliability for assessing skin hydration and erythema levels. It is possible that the SD202 can be used in clinical practice as an appropriate tool for skin hydration and erythema assessment.
Refractory Ulcerated Necrobiosis Lipoidica: Closure of a Difficult Wound with Topical Tacrolimus
Authors: Ginocchio Luke , Draghi Lisa , Darvishian Farbod , Ross Frank L. 
Published: September 2017

ABSTRACT

OBJECTIVE:
To report a case of refractory ulcerated necrobiosis lipoidica (NL) with significant response to treatment with topical tacrolimus.

SUBJECT:
A 55-year-old woman without diabetes and with a previous history of NL presented to the Helen L. and Martin S. Kimmel Hyperbaric and Advanced Wound Healing Center of NYU Langone Medical Center, New York, with bilateral lower-leg ulcerations resistant to wound healing techniques at other institutions.

MATERIALS AND METHODS:
Repeat biopsy performed at the author’s institution confirmed the diagnosis of NL. Initial therapy was based on reports of other successful treatment methods, which included collagen wound grafts and collagen-based dressings coupled with compression. These methods initially showed promising results; however, the wounds reulcerated, and any gains in wound healing were lost. Alternative options were initiated, including topical clobetasol and narrowband ultraviolet B; however, no significant improvement was observed. The patient’s lower-extremity wounds began to deteriorate. The patient also refused systemic therapy. Treatment was changed to topical 0.1% tacrolimus ointment and was applied daily for 10 months with multilayer compression wraps.

RESULTS:
Both lower-extremity ulcerations began to show significant improvement, with the ulcers progressing toward closure except for 1 very small area on the left lower extremity.

CONCLUSIONS:
Topical tacrolimus seems to be an effective treatment option for patients with refractory chronic ulcerated NL who do not want systemic oral therapy. The authors found that successful wound closure may require a multimodal approach, which promotes wound healing, but also concurrently addresses the underlying disease process.
Primum Non Nocere and the 5 Rights
Authors: Popp Gabriele , Clarke Dick , Rothstein Stephen 
Published: September 2017

ABSTRACT
Overutilization of hyperbaric oxygen therapy (HBOT) is commonplace and primarily associated with outpatient wound care. While the number of hospitals providing HBOT is at an all-time high, the number of those willing to treat patients in immediate need is at an all-time low. Huge areas of the country, including major population areas, are now completely devoid of 24/7 HBOT availability and inpatient access. Purchasers of healthcare, including the Centers for Medicare and Medicaid Services, have become increasingly concerned to the point that several strategies have been introduced to constructively deal with this issue. This commentary serves as a counterpoint to concerns that one such approach, prior authorization of elective indications, adversely delays medically necessary care. The historical evolution of HBOT practice will be described to underscore how this problem has become so widespread and, to date, largely unchecked. It will also address the paradoxical national crisis of access for emergencies.
Secondary Traumatic Stress in NICU Nurses
Authors: Beck Cheryl Tatano , Cusson Regina M. , Gable Robert K. 
Published: September 2017

Background:
Secondary traumatic stress is an occupational hazard for healthcare providers who care for patients who have been traumatized. This type of stress has been reported in various specialties of nursing, but no study to date had specifically focused on neonatal intensive care unit (NICU) nurses.

Purpose:
(1) To determine the prevalence and severity of secondary traumatic stress in NICU nurses and (2) to explore those quantitative findings in more depth through nurses' qualitative descriptions of their traumatic experiences caring for critically ill infants in the NICU.

Methods:
Members of NANN were sent e-mails with a link to the electronic survey. In this mixed-methods study, a convergent parallel design was used. Neonatal nurses completed the Secondary Traumatic Stress Scale (STSS) and then described their traumatic experiences caring for critically ill infants in the NICU. SPSS version 24 and content analysis were used to analyze the quantitative and qualitative data, respectively.

Results:
In this sample of 175 NICU nurses, 49% of the nurses' scores on the STSS indicated moderate to severe secondary traumatic stress. Analysis of the qualitative data revealed 5 themes that described NICU nurses' traumatic experiences caring for critically ill infants.

Implications for Practice:
NICU nurses need to know the signs of secondary traumatic stress that they may experience caring for their critically ill infants. Avenues for dealing with the stress should be provided.

Implications for Research:
Future research with a higher response rate to increase the external validity of the findings to the population of neonatal nurses is needed.
Notch inhibitors and their role in the treatment of triple negative breast cancer: promises and failures
Authors: Locatelli Marzia , Curigliano Giuseppe 
Published: September 2017

Purpose of review
Notch signaling is a highly evolutionarily conserved cell-to-cell communication system that is involved in a number of pivotal cellular processes, such as development, stem cell maintenance, cell fate specification, differentiation, proliferation, and death. Much progress has been made in understanding Notch signaling. This review will focus on the role of canonical Notch signaling pathway in breast cancer cause and progressing.

Recent findings
In this review, we will discuss the results of the studies using drugs, which target the Notch pathway.

Summary
Notch sustains a proliferative signaling and protects from apoptosis, favors the angiogenic switch, the chemoresistance and radioresistance, controls the cancer stemness, and induces a prometastatic phenotype. Therefore, Notch-signaling represented an interesting target in the strategy against cancer growth.
Stepwise Guided Photorefractive Keratectomy in Treatment of Irregular Astigmatism After Penetrating Keratoplasty and Deep Anterior Lamellar Keratoplasty
Authors: Sorkin Nir , Einan-Lifshitz Adi , Abelson Sagi , Boutin Tanguy , Showail Mahmood , Borovik Armand , Ashkenazy Zach , Chan Clara C. , Rootman David S. 
Published: September 2017

Purpose:
To report the outcome of stepwise ablation using topography-guided photorefractive keratectomy to treat irregular astigmatism after either penetrating keratoplasty (PKP) or deep anterior lamellar keratoplasty (DALK).

Methods:
This is a retrospective, interventional analysis including patients with irregular astigmatism after either PKP or DALK, who underwent topography-guided photorefractive keratectomy. The entire cohort was analyzed, as well as the PKP and DALK groups separately. Analysis of factors associated with a better outcome was also performed.

Results:
Thirty-four eyes of 34 patients (20 PKP patients and 14 DALK patients) aged 47.4 ± 15.9 years were included. Twenty-one patients underwent more than 1 ablation. Refractive stability and a minimal period of 5 months were required before repeat ablation. The average follow-up duration was 17.0 ± 6.0 months. Corrected distance visual acuity (CDVA) improved significantly from 0.22 ± 0.14 logarithm of the minimum angle of resolution (logMAR) to 0.14 ± 0.12 logMAR at final follow-up (P = 0.035). Uncorrected distance visual acuity (UDVA) improved significantly from 0.90 ± 0.54 logMAR to 0.57 ± 0.40 logMAR at final follow-up (P = 0.004). CDVA and UDVA improved by ≥1 Snellen lines in 54.2% and 70.8% of the eyes, respectively, and by ≥3 Snellen lines in 16.7% and 54.2% of the eyes, respectively. Statistically significant improvement was seen in optical aberrometry indices (total root mean square, higher-order aberration root mean square, defocus, coma, trefoil, and spherical aberration). The difference between PKP and DALK in either CDVA (P = 0.562) or UDVA (P = 0.384) improvement was nonsignificant.

Conclusions:
The stepwise topography-guided photorefractive keratectomy approach in cases of irregular astigmatism after PKP or DALK can help improve visual acuity outcomes. Patients should be appropriately counseled that more than 1 treatment will likely be needed.
Management of Type I and Type II laryngeal clefts: controversies and evidence
Authors: Bowe Sarah N. , Hartnick Christopher J. 
Published: September 2017

Purpose of review
To summarize the pediatric Type I and Type II laryngeal cleft literature, paying special attention to recent trends, including evolution of surgical techniques, standardization of outcome assessments, and utilization of management algorithms.

Recent findings
There are a variety of options to choose from whenever considering Type I and Type II cleft repair, including endoscopic repair, transoral robotic surgery, and injection laryngoplasty. Conservative management including feeding therapy and treatment of comorbid medical conditions is recommended prior to repair. Validated outcome measures have arisen for swallow study interpretation and timing, as well as caregiver quality-of-life assessment. In addition, a series of medical algorithms have been proposed, which provide specific recommendations for diagnosis, treatment, and follow-up.

Summary
For clefts that fail conservative management, endoscopic repair has become the gold standard. In addition, injection laryngoplasty appears to provide both a diagnostic and therapeutic option in the management of these patients. Transoral robotic-assisted endoscopic repair appears well tolerated and feasible, although broader implementation of this technology remains limited. The development and refinement of best practice algorithms can help standardize management and improve decision-making. Furthermore, incorporating validated outcome measures, recorded and followed over time, will improve both patient care and research efforts moving forward.
Relationship Between Alpha Rhythm and the Default Mode Network: An EEG-fMRI Study
Authors: Bowman Anthony D. , Griffis Joseph C. , Visscher Kristina M. , Dobbins Allan C. , Gawne Timothy J. , DiFrancesco Mark W. , Szaflarski Jerzy P. 
Published: September 2017

Purpose:
Reports of the relationship between the default mode network (DMN) and alpha power are conflicting. Our goal was to assess this relationship by analyzing concurrently obtained EEG/functional MRI data using hypothesis-independent methods.

Methods:
We collected functional MRI and EEG data during eyes-closed rest in 20 participants aged 19 to 37 (10 females) and performed independent component analysis on the functional MRI data and a Hamming-windowed fast Fourier transform on the EEG data. We correlated functional MRI fluctuations in the DMN with alpha power.

Results:
Of the six independent components found to have significant relationships with alpha, four contained DMN-associated regions: One independent component was positively correlated with alpha power, whereas all others were negatively correlated. Furthermore, two independent components with opposite relationships with alpha had overlapping voxels in the medial prefrontal cortex and posterior cingulate cortex, suggesting that subpopulations of neurons within these classic nodes within the DMN may have different relationships to alpha power.

Conclusions:
Different parts of the DMN exhibit divergent relationships to alpha power. Our results highlight the relationship between DMN activity and alpha power, indicating that networks, such as the DMN, may have subcomponents that exhibit different behaviors.
Genetic markers of ADHD-related variations in intracranial volume
Authors: Klein Marieke , Walters Raymond K. , Demontis Ditte , Stein Jason L. , Hibar Derrek P. , Adams Hieab H. , Bralten Janita , Mota Nina Roth , Schachar Russell , Sonuga-Barke Edmund , Mattheisen Manuel , Neale Benjamin M. , Thompson Paul M. , Medland Sarah E. , Børglum Anders D. , Faraone Stephen V. , Arias-Vasquez Alejandro , Franke Barbara 
Published: September 2017

ABSTRACTAttention-Deficit/Hyperactivity Disorder (ADHD) is a common and highly heritable neurodevelopmental disorder with a complex pathophysiology, where genetic risk is hypothesized to be mediated by alterations in structure and function of diverse brain networks. We tested one aspect of this hypothesis by investigating the genetic overlap between ADHD (n=55,374) and (mainly subcortical) brain volumes (n=11,221-24,704), using the largest publicly available studies. At the level of common variant genetic architecture, we discovered a significant negative genetic correlation between ADHD and intracranial volume (ICV). Meta-analysis of individual variants found significant loci associated with both ADHD risk and ICV; additional loci were identified for ADHD and amygdala, caudate nucleus, and putamen volumes. Gene-set analysis in the ADHD-ICV meta-analytic data showed significant association with variation in neurite outgrowth-related genes. In summary, our results suggest new hypotheses about biological mechanisms involved in ADHD etiology and highlight the need to study additional brain parameters.
Spreading pre-saccadic attentional resources without trade-off
Authors: Puntiroli Michael , Deubel Heiner , Szinte Martin 
Published: September 2017

SummaryWhen preparing a saccade, attentional resources are focused at the saccade target and its immediate vicinity. Here we show that this does not hold true when saccades are prepared towards a recently extinguished target. We obtained detailed maps of orientation sensitivity when participants prepared a saccade toward a target that either remained on the screen or disappeared before the eyes moved. We found that attention was mainly focused at the immediate surround of the visible target and increasingly spread to more peripheral locations as a function of the delay between the target’s disappearance and the saccade. Interestingly, this spread was accompanied by an overall increase in sensitivity, speaking against a dilution of limited resources over a larger spatial area. We hypothesize that these results reflect the behavioral consequences of the spatio-temporal dynamics of visual receptive fields in the presence and in the absence a structured visual cue.