bluuebunny/crossref_metadata_2025_split huggingface dataset:
Publishing Trends in the Field of Pediatric Emergency Medicine From 2004 to 2013
Authors: Rixe Nancy S. , Rixe Jeffrey , Glick Joshua , Lehman Erik , Olympia Robert P. 
Published: November 2016

Objective
To identify publishing trends within the field of pediatric emergency medicine between 2004 and 2013.

Methods
We conducted a MEDLINE search of pediatric emergency medicine articles, filtered by clinical trial, published between 2004 and 2013 in ten journals from the fields of pediatrics, emergency medicine, general medicine, and pediatric emergency medicine. Each article was classified by journal type, study design, results (positive or negative/equivocal), age/type of subjects, and major topic (based on the objective of the study). Articles were stratified by publication period (2004–2008 or 2009–2013) to analyze trends.

Results
A total of 464 articles were analyzed. The majority of articles were described as randomized-controlled trials (47%) with negative/equivocal findings (70%). The most common major topics were pain management, asthma, sedation, bronchiolitis, resuscitation, simulation, and ultrasound. Over time, the percentage of articles published in pediatrics and pediatric emergency medicine journals increased (P = 0.0499) and the percentage for all study designs increased except for randomized controlled trials (P = 0.0089). There were no differences between the 2 publication periods when stratified by results, age/type of subjects, and major topic.

Conclusions
By identifying these trends, we hope to encourage researchers to perform studies in the field of pediatric emergency medicine where deficiencies lie and to guide pediatric health care professionals to where published, evidence-based studies can be found in the medical literature.
Assessing Different Partner Notification Methods for Assuring Partner Treatment for Gonorrhea: Looking for the Best Mix of Options
Authors: Fleming Eleanor , Hogben Matthew 
Published: November 2016

Context:
Partner notification for gonorrhea is intended to interrupt transmission and to bring people exposed to infection to care. Partner notification may be initiated through public health professionals (disease intervention specialist: DIS referral) or patients (patient referral). In some cases, patients may carry medications or prescriptions for partners (patient-delivered partner therapy: PDPT).

Objective:
To examine how patterns of notifying and treating partners of persons with gonorrhea differ by partner notification approach.

Design:
From published literature (2005-2012), we extracted 10 estimates of patient referral data from 7 studies (3853 patients, 7490 partners) and 5 estimates of PDPT data from 5 studies (1781 patients, 3125 partners). For DIS referral estimates, we obtained 2010-2012 data from 14 program settings (4581 patients interviewed, 8301 partners). For each approach, we calculated treatment cascades based on the proportion of partners who were notified and treated. We also calculated cascades based on partners notified and treated per patient diagnosed.

Results:
Proportions of partners notified and treated were, for patient referral, 56% and 34%; for PDPT, 57% and 46%; for DIS referral, 25% and 22%. Notification and treatment estimates for patient referral and PDPT were significantly higher than for DIS referral, but DIS referral was more efficacious than the other methods in assuring treatment among those notified (all Ps < .001). The notification and treatment ratios per patient seen were, for patient referral, 0.96 and 0.61; for PDPT, 0.90 and 0.73; for DIS referral, 0.45 and 0.40.

Conclusion:
Patient-based methods had higher proportions of partners treated overall, but provider referral had the highest proportion treated among those notified. These data may assist programs to align the most efficacious strategies with the most epidemiologically or clinically important cases while assuring the best scalable standard of care for others.
Uptake of HIV Pre-Exposure Prophylaxis (PrEP) in a National Cohort of Gay and Bisexual Men in the United States
Authors: Parsons Jeffrey T. , Rendina H. Jonathon , Lassiter Jonathan M. , Whitfield Thomas H. F. , Starks Tyrel J. , Grov Christian 
Published: November 2016

Objectives:
The HIV care cascade provides milestones to track the progress of HIV-positive people from seroconversion through viral suppression. We propose a Motivational pre-exposure prophylaxis (PrEP) Cascade involving 5 stages based on the Transtheoretical Model of Change.

Methods:
We analyzed data from 995 men in One Thousand Strong, a longitudinal study of a national panel of HIV-negative gay and bisexual men in the United States.

Results:
Nearly all (89%) participants were sexually active in the past 3 months and 65% met Centers for Disease Control criteria for PrEP candidacy. Of those identified as appropriate candidates, 53% were Precontemplative (stage 1; unwilling to take or believing they were inappropriate candidates for PrEP) and 23% were in Contemplation (stage 2; willing and self-identified as appropriate candidates). Only 11% were in PrEParation (stage 3; seeing PrEP as accessible and planning to initiate PrEP) and 4% were in PrEP Action (stage 4; prescribed PrEP). Although few of those who were identified as appropriate candidates were on PrEP, nearly all PrEP users (98%) reported adhering to 4 or more doses per week and most (72%) were returning for recommended quarterly medical visits, resulting in 9% of PrEP candidates reaching Maintenance and Adherence (stage 5).

Conclusions:
The large majority of participants were appropriate candidates for PrEP, yet fewer than 1 in 10 were using and adherent to PrEP. These findings highlight the need for interventions tailored to address the unique barriers men face at each stage of the cascade, particularly at the earliest stages where the most dramatic losses were identified.
An Ultra-High Field Study of Cerebellar Pathology in Early Relapsing-Remitting Multiple Sclerosis Using MP2RAGE
Authors: Fartaria Mário João , O'Brien Kieran , Şorega Alexandra , Bonnier Guillaume , Roche Alexis , Falkovskiy Pavel , Krueger Gunnar , Kober Tobias , Bach Cuadra Meritxell , Granziera Cristina 
Published: November 2016

Objectives
The aim of this study was to study focal cerebellar pathology in early stages of multiple sclerosis (MS) using ultra-high-field magnetization-prepared 2 inversion-contrast rapid gradient-echo (7T MP2RAGE).

Materials and Methods
Twenty early-stage relapsing-remitting MS patients underwent an MP2RAGE acquisition at 7 T magnetic resonance imaging (MRI) (images acquired at 2 different resolutions: 0.58 × 0.58 × 0.58 mm3, 7T_0.58, and 0.75 × 0.75 × 0.90 mm3, 7T_0.75) and 3 T MRI (1.0 × 1.0 × 1.2 mm3, 3T_1.0). Total cerebellar lesion load and volume and mean cerebellar lesion volume were compared across images using a Wilcoxon signed-rank test. Mean T1 relaxation times in lesions and normal-appearing tissue as well as contrast-to-noise ratio (CNR) measurements were also compared using a Wilcoxon signed-rank test. A multivariate analysis was applied to assess the contribution of MRI metrics to clinical performance in MS patients.

Results
Both 7T_0.58 and 7T_0.75 MP2RAGE showed significantly higher lesion load compared with 3T_1.0 MP2RAGE (P < 0.001). Plaques that were judged as leukocortical in 7T_0.75 and 3T_1.0 MP2RAGEs were instead identified as WM lesions in 7T_0.58 MP2RAGE. Cortical lesion CNR was significantly higher in MP2RAGEs at 7 T than at 3 T. Total lesion load as well as total and mean lesion volume obtained at both 7 T and 3 T MP2RAGE significantly predicted attention (P < 0.05, adjusted R
2 = 0.5), verbal fluency (P < 0.01, adjusted R
2 = 0.6), and motor performance (P = 0.01, adjusted R
2 = 0.7).

Conclusions
This study demonstrates the value of 7 T MP2RAGE to study the cerebellum in early MS patients. 7T_0.58 MP2RAGE provides a more accurate anatomical description of white and gray matter pathology compared with 7T_0.75 and 3T_1.0 MP2RAGE, likely due to the improved spatial resolution, lower partial volume effects, and higher CNR.
Transvaginal Pelvic Floor Muscle Injection Technique: A Cadaver Study
Authors: Gupta Priyanka , Ehlert Michael , Sirls Larry T. , Peters Kenneth 
Published: November 2016

Introduction
Women with pelvic floor dysfunction can have tender areas on vaginal examination, which can be treated with trigger-point injections. There are no publications to evaluate the accuracy of pelvic floor muscle injections.

Methods
Trigger-point injections were performed on 2 fresh cadaveric pelvises using a curved nasal cannula guide and 7-in spinal needle. This was performed using our standard template of 2 sets of injections at the 1-, 3-, and 5-o'clock positions distally and proximally. The first pelvis was dissected to examine dye penetration. Based on these results, we modified our technique and repeated the injections on the second cadaver. We dissected the second pelvis and compared our findings.

Results
The 1-o'clock proximal and distal injections stained the obturator internus and externus near the insertion at the ischiopubic ramus. The 3-o'clock injections stained the midbody of the pubococcygeus and puborectalis. The distal 5-o'clock position was too deep and stained the fat of the ischiorectal space. The proximal 5-o'clock injection stained the area of the pudendal nerve. Our goal at the distal 5-o'clock position was to infuse the iliococcygeus muscle, so we shortened the needle depth from 2 to 1 cm beyond the cannula tip. In our second dissection, the distal 5-o'clock injection again stained only the fat of the ischiorectal space.

Conclusions
This is the first study to characterize the distribution of pelvic floor muscle injections in a cadaver model and confirms the ability to deliver medications effectively to the pelvic floor muscles.
The Global Avian Invasions Atlas - A database of alien bird distributions worldwide
Authors: Dyer Ellie E. , Redding David W. , Blackburn Tim M. 
Published: November 2016

AbstractThe introduction of species to locations where they do not naturally occur (termed aliens) can have far-reaching and unpredictable environmental and economic consequences. Therefore there is a strong incentive to stem the tide of alien species introduction and spread. In order to identify broad patterns and processes of alien invasions, a spatially referenced, global dataset on the historical introductions and alien distributions of a complete taxonomic group is required.Here we present the Global Avian Invasions Atlas (GAVIA) – a new spatial and temporal dataset comprising 27,723 distribution records for 971 alien bird species introduced to 230 countries and administrative areas spanning the period 6000BCE – AD2014. GAVIA was initiated to provide a unified database of records on alien bird introductions, incorporating records from all stages of invasion, including introductions that have failed as well as those that have succeeded. GAVIA represents the most comprehensive resource on the global distribution of alien species in any major taxon, allowing the spatial and temporal dynamics of alien bird distributions to be examined.
Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
Authors: O’Donnell Timothy , Christie Elizabeth L. , Ahuja Arun , Buros Jacqueline , Aksoy B. Arman , Bowtell David D. L. , Snyder Alexandra , Hammerbacher Jeff 
Published: November 2016

BackgroundPatients with highly mutated tumors, such as melanoma or smoking-related lung cancer, have higher rates of response to immune checkpoint blockade therapy, perhaps due to increased neoantigen expression. Many chemotherapies including platinum compounds are known to be mutagenic, but the impact of standard treatment protocols on mutational burden and resulting neoantigen expression in most human cancers is unknown.MethodsWe sought to quantify the effect of chemotherapy treatment on computationally predicted neoantigen expression for 12 high grade serous ovarian carcinoma (HGSC) patients with pre- and post-chemotherapy samples collected in the Australian Ovarian Cancer Study. We additionally analyzed 16 patients from the cohort with post-treatment samples only, including five primary surgical samples exposed to neoadjuvant chemotherapy. Our approach integrates tumor whole genome and RNA sequencing with class I MHC binding prediction and mutational signatures of chemotherapy exposure extracted from two preclinical studies.ResultsThe mutational signatures for cisplatin and cyclophosphamide identified in a preclinical model had significant but inexact associations with the relevant exposure in the clinical samples. In an analysis stratified by tissue type (solid tumor or ascites), relapse samples collected after chemotherapy harbored a median of 90% more expressed neoantigens than untreated primary samples, a figure that combines the effects of chemotherapy and other mutagenic processes operative during relapse. Neoadjuvant-treated primary samples showed no detectable increase over untreated samples. The contribution from chemotherapy-associated signatures was small, accounting for a mean of 5% (range 0–16) of the expressed neoantigen burden in relapse samples. In both treated and untreated samples, most neoantigens were attributed to COSMICSignature (3), associated with BRCA disruption,Signature (1), associated with a slow mutagenic process active in healthy tissue, andSignature (8), of unknown etiology.ConclusionRelapsed HGSC tumors harbor nearly double the predicted expressed neoantigen burden of primary samples, but mutations associated with chemotherapy signatures account for only a small part of this increase. The mutagenic processes responsible for most neoantigens are similar between primary and relapse samples. Our analyses are based on mutations detectable from whole genome sequencing of bulk samples and do not account for neoantigens present in small populations of cells.
SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data
Authors: Bacher Rhonda , Chu Li-Fang , Leng Ning , Gasch Audrey P. , Thomson James A. , Stewart Ron M. , Newton Michael , Kendziorski Christina 
Published: November 2016

SummaryNormalization of RNA-sequencing data is essential for accurate downstream inference, but the assumptions upon which most methods are based do not hold in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstream analyses. To address this, we introduce SCnorm for accurate and efficient normalization of scRNA-seq data.
Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin
Authors: Vergara Zaida , Sequeira-Mendes Joana , Morata Jordi , Hénaff Elizabeth , Peiró Ramón , Costas Celina , Casacuberta Josep M. , Gutierrez Crisanto 
Published: November 2016

AbstractGenomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. In spite of multiple efforts, the DNA and chromatin features that determine ORI specification are not presently known. We have generated a high-resolution genome-wide map of ORIs in cultured Arabidopsis thaliana cells that rendered a collection of 3230 ORIs. In this study we focused on defining the features associated with ORIs in heterochromatin. We found that while ORIs tend to colocalize with genes in euchromatic gene-rich regions, they frequently colocalize with transposable elements (TEs) in pericentromeric gene-poor domains. Interestingly, ORIs in TEs associate almost exclusively with retrotransposons, in particular, of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with TEs is largely limited to retrotransposons, which are defined by their transposition mechanisms based on transcription, and they occur in a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has also implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin as well as of the entire genome.
The natural selection of metabolism explains curvature in allometric scaling
Authors: Witting Lars 
Published: November 2016

AbstractI simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-specific allometry for metabolism. The estimated selection of mass specific metabolism was found to bend the metabolic allometry over time, with the strongest curvature in the placental clade. The rate of exponential increase in mass specific metabolism for placentals was estimated to 9.3 × 10−9(95% CI:7.3 × 10−9− 1.1 × 10−8) on the per generation time-scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar size.
Behavioral evidence for feedback gain control by the inhibitory microcircuit of the substantia nigra
Authors: Brown Jennifer , Martin Kathleen A. , Dudman Joshua T. 
Published: November 2016

AbstractWe recently demonstrated that the collaterals of substantia nigra (SN) projection neurons can implement divisive feedback inhibition, or gain control (Brown et al., 2014). While in vivo recordings were consistent with divisive feedback inhibition, a causal test was lacking. A gain control model of the nigral microcircuit implies behavioral effects of disrupting intranigral inhibition that are distinct from previous functional models. To test the model predictions experimentally, we develop a chemogenetic approach that can selectively suppress synaptic release within the substantial nigra without affecting the propagation of activity to extranigral targets. We observe behavioral consequences of suppressing intranigral inhibition that are uniquely consistent with a gain control model. Our data further suggest that if endogenous metabotropic signaling can modulate intranigral synapses, this would provide a circuit mechanism for an exploitation/exploration trade-off in which the timing and variability of goal-directed movements are controlled independently of changes in action.
Tuning the course of evolution on the biophysical fitness landscape of an RNA virus
Authors: Rotem Assaf , Serohijos Adrian W.R. , Chang Connie B. , Wolfe Joshua T. , Fischer Audrey E. , Mehoke Thomas S. , Zhang Huidan , Tao Ye , Ung W. Lloyd , Choi Jeong-Mo , Kolawole Abimbola O. , Koehler Stephan A. , Wu Susan , Thielen Peter M. , Cui Naiwen , Demirev Plamen A. , Giacobbi Nicholas S. , Julian Timothy R. , Schwab Kellogg , Lin Jeffrey S. , Smith Thomas J. , Pipas James M. , Wobus Christiane E. , Feldman Andrew B. , Weitz David A. , Shakhnovich Eugene I. 
Published: November 2016

ABSTRACTPredicting viral evolution remains a major challenge with profound implications for public health. Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics device, the “Evolution Chip”, which propagates millions of independent viral sub-populations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs shape viral evolution.
Enhancing clinical practice: reducing health inequalities – reflections on a clinical education and training partnership
Authors: Marshall-Tate Karina 
Published: November 2016

PurposeThe purpose of this paper is to outline a two-year project designed to reduce health inequalities and improve health outcomes of people with intellectual disabilities using health services in South London by raising awareness and increasing health staff confidence and capability.Design/methodology/approachThe project was conducted in two stages. In stage 1, a mapping exercise was undertaken to establish existing intellectual disabilities education and training availability. In stage 2, a network of stakeholders was formed and education and training materials were developed and delivered.FindingsA formal evaluation of the project is underway and this paper seeks to share information about the project. That said prima facie data appear to indicate that health staff who attended education and training events learned new knowledge and skills that they could implement in their practice, increasing confidence and capability.Research limitations/implicationsHealth staff who attended the events appeared to have an interest in intellectual disabilities and wanted to increase their knowledge and skills base. This means that there is a significant group of health staff that the project was unable to reach or who may not know that they need to know about intellectual disabilities. The results of the project have not yet been formally analysed.Practical implicationsWork-based education and training events can have a positive impact on health staff capability and confidence, however, it would appear that only those who already have an interest in the field or recognise its value to their own practice attend such events. To truly capture all health staff intellectual disabilities needs to be visibly included in all health curricula.Originality/valueThis project has not focussed on one profession or one aspect of healthcare and has embraced the values of inter professional and inter agency learning; this has enabled health staff to learn from each other and think in a “joined up” way replicating the realities of providing healthcare to people with intellectual disabilities.