bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anogenital and Physical Injuries in Adolescent Sexual Assault Patients: The Role of Victim–Offender Relationship, Alcohol Use, and Memory Impairment
Authors: Feeney Hannah , Chiaramonte Danielle , Campbell Rebecca , Greeson Megan R. , Fehler-Cabral Giannina 
Published: May 2017

ABSTRACT
Prior research has documented high rates of anogenital and physical injuries among adolescent sexual assault patients. Although a number of factors related to rates of injury detection in adolescents have been identified, there may be additional features of the assault that are disclosed in the patient history that could be important indicators of injury risk. The purpose of the current study was to expand this literature by examining whether factors that are salient in sexual assaults committed against adolescents—victim–offender relationship, substance use, and memory impairment—are associated with documented anogenital and physical injury rates. Results indicated that victim–offender relationship, substance use, and assault memory are significantly related to the number of anogenital injuries and, particularly, the number of physical injuries detected in adolescent sexual assault patients. These results highlight the importance of a comprehensive patient history, including assessment of alcohol and drug use and memory impairment, to guide the medical forensic examination.
If Background Lung Abnormalities Do Not Affect the Presentation of Spontaneous Pneumothorax, Is Lung Resection Always Justified?
Authors: Bilancia Rocco , Sharkey Annabel J. , Paik Amit , Waller David A. 
Published: May 2017

Background:
The suggestion that spontaneous pneumothorax (SP) may result from diffuse porosity rather than discrete anatomic abnormality challenges the practice of targeted bullectomy. We assessed whether underlying pulmonary abnormalities are correlated or could be predicted from the mode of presentation, with potential implications for treatment.

Methods:
We analyzed 192 consecutive video-assisted thoracoscopic surgery resections for SP (139 primary, 53 secondary) in 171 patients (115 male, age 36, range, 16 to 81). Presentation was categorized as: recurrent never drained (RND), recurrent drained, persistent air leak (PAL). Resected lung pathology was categorized as: no bleb/bulla, ruptured bleb/bulla, unruptured bleb/bulla.

Results:
No correlation between presentation and resected lung pathology was observed for primary (P=0.608) or secondary SP (P=0.597). A similar proportion of patients in each pathologic group presented with PAL or RND; ruptured bleb/bulla or no bleb/bulla was equally noted in PAL and RND group.

Conclusions:
There is lack of association between resected lung pathology and mode of presentation. This suggests that discrete anatomic abnormalities may not be responsible for the air leak leading to pneumothorax. In conjunction with favorable reported outcomes from medical thoracoscopy and talc pleurodesis alone, these findings challenge the current practice of routine video-assisted thoracoscopic surgery lung resection in these patients.
Etiological factors of chronic hepatitis in Italy: a 2014 national survey
Authors: Stroffolini Tommaso , Sagnelli Evangelista , Almasio Piero L. , Andriulli Angelo , Smedile Antonina , Pirisi Mario , Sagnelli Caterina , Russello Maurizio , Coppola Nicola , de Luca Massimo , Pisaturo Mariantonietta , Rosina Floriano , Gaeta Giovanni B. 
Published: May 2017

Background
The last Italian prevalence survey on chronic hepatitis (CH) conducted in 2001 showed that the hepatitis C virus (HCV) was the main agent associated with CH.

Aim
The aim of this study was to evaluate epidemiological changes in CH occurring after 13 years.

Patients and methods
Enrollment of 1392 CH consecutive patients referred to 16 Italian liver units in 2014 scattered all over the country (four in the North, four in the Center, four in the South, and four in the Islands) was performed.

Results
The mean age of the patients was 58.3 years, with a sex ratio (male/female) of 1.5. HCV infection (also with other etiologies) continues to be the most prevalent etiology (58.1%). However, this prevalence was lower (P<0.01) than the corresponding figure (76.5%) for 2001. The proportion of hepatitis B virus-related cases almost doubled over time from 12.2% in 2001 to 22.5% in 2014 (P<0.01), most probably biased because of the distribution of entecavir and tenofovir free of charge at outpatient hospital clinics after 2001. Patients reporting risky alcohol intake (also with other etiologies) accounted for 12.4% of cases, a figure lower than that reported in 2001: 19.2% (P<0.01). The proportion of nonalcoholic fatty liver disease cases nearly doubled over time (3.6% in 2001 and 6.2% in 2014; P<0.05), reflecting the greater attention over time devoted to this syndrome.

Conclusion
The decreasing role of HCV infection as an etiologic factor of CH in Italy is good news considering the high cost of the directly acting antiviral agents for HCV eradication. Metabolic factors warrant greater attention in the near future.
Global surgery: current evidence for improving surgical care
Authors: Fuller Jennifer C. , Shaye David A. 
Published: May 2017

Purpose of review
The field of global surgery is undergoing rapid transformation, owing to several recent prominent reports positioning it as a cost-effective means of relieving global disease burden. The purpose of this article is to review the recent advances in the field of global surgery.

Recent findings
Efforts to grow the global surgical workforce and procedural capacity have focused on innovative methods to increase surgeon training, enhance international collaboration, leverage technology, optimize existing health systems, and safely implement task-sharing. Computer modeling offers a novel means of informing policy to optimize timely access to care, equitably promote health and financial protection, and efficiently grow infrastructure. Tools and checklists have recently been developed to enhance data collection and ensure methodologically rigorous publications to inform planning, benchmark surgical systems, promote accurate modeling, track key health indicators, and promote safety. Creation of institutional partnerships and trainee exchanges can enrich training, stimulate commitment to humanitarian work, and promote the equal exchange of ideas and expertise.

Summary
The recent body of work creates a strong foundation upon which work toward the goal of universal access to safe, affordable surgical care can be built; however, further collection and analysis of country-specific data is necessary for accurate modeling and outcomes research into the efficacy of policies such as task-sharing is greatly needed.
Multiple Cranial Nerve Palsies in Giant Cell Arteritis
Authors: Ross Michael , Bursztyn Lulu , Superstein Rosanne , Gans Mark 
Published: May 2017

Abstract:
Giant cell arteritis (GCA) is a systemic vasculitis of medium and large arteries often with ophthalmic involvement, including ischemic optic neuropathy, retinal artery occlusion, and ocular motor cranial nerve palsies. This last complication occurs in 2%–15% of patients, but typically involves only 1 cranial nerve. We present 2 patients with biopsy-proven GCA associated with multiple cranial nerve palsies.
A comparison between single cell RNA sequencing and single molecule RNA FISH for rare cell analysis
Authors: Torre Eduardo , Dueck Hannah , Shaffer Sydney , Gospocic Janko , Gupte Rohit , Bonasio Roberto , Kim Junhyong , Murray John , Raj Arjun 
Published: May 2017

AbstractThe development of single cell RNA sequencing technologies has emerged as a powerful means of profiling the transcriptional behavior of single cells, leveraging the breadth of sequencing measurements to make inferences about cell type. However, there is still little understanding of how well these methods perform at measuring single cell variability for small sets of genes and what “transcriptome coverage” (e.g. genes detected per cell) is needed for accurate measurements. Here, we use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ∼2000 genes detected. A similar complexity threshold also allows for robust assignment of multi-genic cell states such as cell cycle phase. Our results provide guidelines for selecting sequencing depth and complexity thresholds for single cell RNA sequencing. More generally, our results suggest that if the number of genes whose expression levels are required to answer any given biological question is small, then greater transcriptome complexity per cell is likely more important than obtaining very large numbers of cells.
All fingers are not the same: Handling variable-length sequences in a discriminative setting using conformal multi-instance kernels
Authors: Nikumbh Sarvesh , Ebert Peter , Pfeifer Nico 
Published: May 2017

AbstractMost string kernels for comparison of genomic sequences are generally tied to using (absolute) positional information of the features in the individual sequences. This poses limitations when comparing variable-length sequences using such string kernels. For example, profiling chromatin interactions by 3C-based experiments results in variable-length genomic sequences (restriction fragments). Here, exact position-wise occurrence of signals in sequences may not be as important as in the scenario of analysis of the promoter sequences, that typically have a transcription start site as reference. Existing position-aware string kernels have been shown to be useful for the latter scenario.In this work, we propose a novel approach for sequence comparison that enables larger positional freedom than most of the existing approaches, can identify a possibly dispersed set of features in comparing variable-length sequences, and can handle both the aforementioned scenarios. Our approach,CoMIK, identifies not just the features useful towards classification but also their locations in the variable-length sequences, as evidenced by the results of three binary classification experiments, aided by recently introduced visualization techniques. Furthermore, we show that we are able to efficiently retrieve and interpret the weight vector for the complex setting of multiple multi-instance kernels.
Enhanced guide-RNA Design and Targeting Analysis for Precise CRISPR Genome Editing of Single and Consortia of Industrially Relevant and Non-Model Organisms
Authors: Mendoza Brian J. , Trinh Cong T. 
Published: May 2017

AbstractMotivationGenetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions.ResultsTo accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CASPER (CRISPR Associated Software for Pathway Engineering and Research), for identifying on- and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, p<0.05) over the conventional methods for predicting on- and off-target activities, respectively. Further we used CASPER to develop novel applications in genome editing: multitargeting analysis (i.e. simultaneous multiple-site modification on a target genome with a sole guide-RNA (gRNA) requirement) and multispecies population analysis (i.e. gRNA design for genome editing across a consortium of organisms). Our analysis on a selection of industrially relevant organisms revealed a number of non-unique target sites associated with genes and transposable elements that can be used as potential sites for multitargeting. The analysis also identified shared and unshared targets that enable genome editing of single or multiple genomes in a consortium of interest. We envision CASPER as a useful platform to enhance the precise CRISPR genome editing for metabolic engineering and synthetic biology applications.
The prevalence and benefits of admixture during species invasions: a role for epistasis?
Authors: Barker Brittany S , Cocio Janelle E , Anderson Samantha R , Braasch Joseph E , Cang F Alice , Gillette Heather D , Dlugosch Katrina M 
Published: May 2017

AbstractSpecies introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favorable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixture’s benefits should be expected to increasewith greater divergence among and lower genetic diversity within source populations. We use a literature survey to quantify the prevalence of admixture and evaluate whether it occurrs under circumstances predicted to be mostbeneficial to introduced species. We find that 39% of species are reported to be admixed when introduced. Admixed introductions come from sources with a wide range of genetic variation, but are disproportionately absent where there is high genetic divergence among native populations. We discuss multiple potential explanations for these patterns, but note that negative epistatic interactions should be expected at high divergence amongpopulations (outbreeding depression). As a case study, we experimentally cross source populations differing in divergence in the invasive plantCentaurea solstitialis. We find many positive (heterotic) interactions, but fitness benefits decline and are ultimately negative at high source divergence, with patterns suggestingcyto-nuclear epistasis. We conclude that admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, but that these conditions may be constrained by predictable negativegenetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.
Disentangling the effects of selection and loss bias on gene dynamics
Authors: Iranzo Jaime , Cuesta José A. , Manrubia Susanna , Katsnelson Mikhail I. , Koonin Eugene V. 
Published: May 2017

ABSTRACTWe combine mathematical modelling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most non-parasitic genes is low albeit positive, compatible with the observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in anti-parasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction-modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not the duplication to loss ratio, correlates with genome size, potentially explaining the increased abundance of neutral and costly elements in larger genomes.SIGNIFICANCEEvolution of microbes is dominated by horizontal gene transfer and the incessant host-parasite arms race that promotes the evolution of diverse anti-parasite defense systems. The evolutionary factors governing these processes are complex and difficult to disentangle but the rapidly growing genome databases provide ample material for testing evolutionary models. Rigorous mathematical modeling of evolutionary processes, combined with computer simulation and comparative genomics, allowed us to elucidate the evolutionary regimes of different classes of microbial genes. Only genes involved in key informational and metabolic pathways are subject to strong selection whereas most of the others are effectively neutral or even burdensome. Mobile genetic elements and defense systems are costly, supporting the understanding that their evolution is governed by the same factors.
How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects
Authors: Chandler Christopher H. , Chari Sudarshan , Kowalski Alycia , Choi Lin , Tack David , DeNieu Michael , Pitchers William , Sonnenschein Anne , Marvin Leslie , Hummel Kristen , Marier Christian , Victory Andrew , Porter Cody , Mammel Anna , Holms Julie , Sivaratnam Gayatri , Dworkin Ian 
Published: May 2017

ABSTRACTFor a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and variation across alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both thescallopedandvestigialgenes, which influence wing development inDrosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.
Dynamics of the Human Antibody Repertoire following B-cell Depletion in Systemic Sclerosis
Authors: de Bourcy Charles F. A. , Dekker Cornelia L. , Davis Mark M. , Nicolls Mark R. , Quake Stephen R. 
Published: May 2017

AbstractSystemic sclerosis with pulmonary arterial hypertension (SSc-PAH) is a debilitating and frequently lethal disease of unknown cause lacking effective treatment options. Lymphocyte anomalies and autoantibodies observed in systemic sclerosis have suggested an autoimmune character. Here we study the clonal structure of the B-cell repertoire in SSc-PAH using immunoglobulin heavy-chain sequencing before and after B-cell depletion. We found SSc-PAH to be associated with anomalies in B-cell development, namely altered VDJ rearrangement frequencies (reduced IGHV2-5 segment usage) and an increased somatic mutation-fixation probability in expanded B-cell lineages. SSc-PAH was also characterized by anomalies in B-cell homeostasis, namely an expanded IgD+proportion with reduced mutation loads and an expanded proportion of highly antibody-secreting cells. Disease signatures pertaining to IGHV2-5 segment usage, IgD proportions and mutation loads were temporarily reversed after B-cell depletion. Analyzing the time course of B-cell depletion, we find that the kinetics of naïve replenishment are predictable from baseline measurements alone, that release of plasma cells into the periphery can precede naïve replenishment and that modes of B-cell receptor diversity are highly elastic. Our findings shed light on the humoral immune basis of SSc-PAH and provide insights into the effect of B-cell depletion on the antibody repertoire.AbbreviationsSSc-PAHSystemic sclerosis with pulmonary arterial hypertensionIGHimmunoglobulin heavy-chainBCRB-cell receptorCDR3complementarity-determining region 3IgimmunoglobulinAAamino acid
STAR Chimeric Post For Rapid Detection of Circular RNA and Fusion Transcripts
Authors: Akers Nicholas K. , Schadt Eric E. , Losic Bojan 
Published: May 2017

AbstractMotivationThe biological relevance of chimeric RNA alignments is now well established. Chimera arising as chromosomal fusions are often drivers of cancer, and recently discovered circular RNA are only now being characterized. While software already exists for fusion discovery and quantitation, high false positive rates and high run-times hamper scalable fusion discovery on large datasets. Furthermore, very little software is available for circular RNA detection and quantification.ResultsHere we present STAR Chimeric Post (STARChip), a novel software package that processes chimeric alignments from the STAR aligner and produces annotated circular RNA and high precision fusions in a rapid, efficient, and scalable manner that is appropriate for high dimensional medical omics datasets.Availability and ImplementationSTARChip is available athttps://github.com/LosicLab/STARChipContactsbojan.losic@mssm.eduornicholas.kipp.akers@gmail.comSupplementary InformationSupplementary figures and tables are available online.
Performance assessment of class-E inverter for capacitive power transfer system
Authors: Yusop Yusmarnita , Md. Saat Mohd. Shakir , Husin Siti Huzaimah , Kiong Nguang Sing , Hindustan Imran 
Published: May 2017

Purpose
This paper aims to present a new wireless power transfer technique using capacitive coupling. The capacitive power transfer (CPT) system has been introduced as an attractive alternative to the traditional inductive coupling method. The CPT offers benefits such as simple topology, fewer components, better electromagnetic interference (EMI) performance and robustness to surrounding metallic elements.

Design/methodology/approach
A class-E inverter together with and without inductor capacitor (LC) matching circuit has been utilised in this work because of its ability to perform the DC-to-AC inversion efficiently with significant reduction in switching losses. The validity of the proposed concept has been verified by conducting a laboratory experiment of the CPT system.

Findings
The performances for both systems are analysed and evaluated. A 9.7 W output power is generated through a combined interface [printed circuit board (PCB) plate] capacitance of 2.82 nF at an operating frequency of 1 MHz, with 97 per cent efficiency for 0.25 mm coupling gap distance.

Originality value
An efficient CPT system with class-E LC matching topology is proposed in this paper. With this topology, the zero-voltage switching can be achieved even if the load is different by properly designing the LC matching transformation circuit.