bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Study of Untethering and Spine-Shortening Surgery for Tethered Cord Syndrome in Adults
Authors: Nakashima Hiroaki , Imagama Shiro , Matsui Hiroki , Yukawa Yasutsugu , Sato Koji , Kanemura Tokumi , Kamiya Mitsuhiro , Ito Kenyu , Matsuyama Yukihiro , Ishiguro Naoki , Kato Fumihiko 
Published: November 2015

Study Design Retrospective multicenter study. Objective Although untethering surgery has been a standard treatment in patients with adult tethered cord syndrome (TCS), spine-shortening osteotomy (SSO) has recently been performed as an alternative technique. The purpose of this study was to compare the clinical outcomes of the two procedures for TCS in adults. Methods Fourteen patients (37.7 ± 12.5 years) with TCS were enrolled at 6 hospitals. Their clinical charts, operative records, and follow-up data were reviewed. The categories of tethering lesions were tight terminal filum in 1 patient, lipoma in 5 patients, and lipomyelomeningocele in 8 patients. Eleven patients underwent untethering surgery, and 3 patients underwent SSO surgery. Results There were no significant differences in age, sex, types of preoperative symptoms, or duration of follow-up between the two groups. The preoperative duration of symptoms was significantly longer (25 ± 12.4 years) and the percentage of those with prior surgery was higher in the SSO group (66.7%). The preoperative pathology was lipomeningocele in all SSO group and lipoma or tight terminal filum in the untethering group. Cerebrospinal fluid leakage and urinary infection occurred in 1 patient each among those with untethering, and massive intraoperative bleeding occurred in 1 patient with SSO. SSO provided better clinical improvement than untethering surgery ( p = 0.003). Conclusions Based on this small retrospective case series, SSO appears to provide clinical improvement at least comparable to the untethering procedure, especially in more challenging cases.
Thromboembolic Disease after Cervical Spine Surgery: A Review of 5,405 Surgical Procedures and Matched Cohort Analysis
Authors: Sebastian Arjun S. , Currier Bradford L. , Clarke Michelle J. , Larson Dirk , Huddleston Paul M. , Nassr Ahmad 
Published: November 2015

Study Design Retrospective matched cohort analysis. Objective The majority of the literature on venous thromboembolism (VTE) after spine surgery is limited to studies of thoracolumbar surgery. Less is known regarding the incidence of VTE and associated risk factors following cervical spine surgery. Methods A total of 5,405 patients at our institution underwent cervical diskectomy, laminectomy, corpectomy, laminoplasty, or fusion between 1995 and 2012; 85 of the 5,405 patients (1.57%) suffered either a DVT (55) or pulmonary embolus (51) within 30 days postoperatively. The cases were matched 1:2 to controls based on age, sex, and date of surgery. Data regarding multiple perioperative factors, demographics, and comorbidities was collected. Results Several risk factors were identified for VTE. Significant medical comorbidities included chronic venous insufficiency (odds ratio [OR] = 3.40), atrial fibrillation (OR = 2.69), obesity (OR = 2.67), and ischemic heart disease (OR = 2.18). Staged surgery (OR = 28.0), paralysis (OR = 19.0), combined approach (OR = 7.46), surgery for infection (OR = 18.5), surgery for trauma (OR = 11.1), comorbid traumatic injuries (OR > 10), oncologic procedures (OR = 5.2), use of iliac crest autograft (OR = 4.16), two or more surgical levels (OR = 3.48), blood loss > 300 mL (OR = 1.66), and length of stay 5 days or greater (OR = 3.47) were all found to be risk factors for VTE ( p < 0.05) in univariate analysis. Multivariate analysis found staged surgery (OR = 35.7), paralysis (OR = 7.86), and nonelective surgery (OR = 6.29) to be independent risk factors for VTE. Conclusions Although the incidence of VTE following cervical spine surgery is low, we identified several risk factors that may be predictive. More aggressive approaches to prophylaxis and surveillance in certain patient populations may be warranted.
RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power
Authors: Lee Chee , Patil Snehal , Sartor Maureen A. 
Published: November 2015

Abstract
Summary: Tests for differential gene expression with RNA-seq data have a tendency to identify certain types of transcripts as significant, e.g. longer and highly-expressed transcripts. This tendency has been shown to bias gene set enrichment (GSE) testing, which is used to find over- or under-represented biological functions in the data. Yet, there remains a surprising lack of tools for GSE testing specific for RNA-seq. We present a new GSE method for RNA-seq data, RNA-Enrich, that accounts for the above tendency empirically by adjusting for average read count per gene. RNA-Enrich is a quick, flexible method and web-based tool, with 16 available gene annotation databases. It does not require a P-value cut-off to define differential expression, and works well even with small sample-sized experiments. We show that adjusting for read counts per gene improves both the type I error rate and detection power of the test.
Availability and implementation: RNA-Enrich is available at http://lrpath.ncibi.org or from supplemental material as R code.
Contact: sartorma@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Simulated diurnal pH fluctuations radically increase variance in—but not the mean of—growth in the barnacle Balanus improvisus
Authors: Eriander L. , Wrange A.-L. , Havenhand J. N. 
Published: November 2015

Abstract
Shallow coastal waters are characterized by substantial diurnal fluctuations in pH, especially in nearshore environments. The biological effects of ocean acidification in combination with these natural fluctuations have received relatively little attention to date. We exposed multiple batches (≈ different genotypes) of newly settled barnacles, Balanus improvisus, to constant pH under “control” (pH = 8.1) or “stable acidified” (pH = 7.7) conditions, as well as a treatment that simulated the maximum diurnal pH fluctuations seen in the nearshore habitats where this barnacle lives (±0.2 pH units), superimposed on the stable acidified treatment (“fluctuating acidified”; 7.5 ≤ pH ≤ 7.9). We found that fluctuating acidification had no effect on mean response in growth and shell mineralogy, but caused an ∼20-fold increase in variance of responses, compared with stable acidification. In contrast to these results, we found no effect of fluctuating acidification on variances of response ratios for barnacle survival and shell strength. Similarly, mean survival did not vary significantly with pH. However, we observed a strong negative effect of stable and fluctuating acidification on mean shell strength. Our finding that barnacles respond differently to fluctuating pH than to stable low pH indicate the importance of including fluctuating acidification treatments when studying species that live in variable environments. Importantly, because phenotypic variance is the raw material for natural selection, and thus lays at the heart of evolutionary responses to environmental variability and change, our findings also highlight the need to study changes in variance of—as well as mean—responses to changing ocean climates.
A data-driven approach for quality assessment of radiologic interpretations
Authors: Hsu William , Han Simon X , Arnold Corey W , Bui Alex AT , Enzmann Dieter R 
Published: November 2015

Abstract
Given the increasing emphasis on delivering high-quality, cost-efficient healthcare, improved methodologies are needed to measure the accuracy and utility of ordered diagnostic examinations in achieving the appropriate diagnosis. Here, we present a data-driven approach for performing automated quality assessment of radiologic interpretations using other clinical information (e.g., pathology) as a reference standard for individual radiologists, subspecialty sections, imaging modalities, and entire departments. Downstream diagnostic conclusions from the electronic medical record are utilized as “truth” to which upstream diagnoses generated by radiology are compared. The described system automatically extracts and compares patient medical data to characterize concordance between clinical sources. Initial results are presented in the context of breast imaging, matching 18 101 radiologic interpretations with 301 pathology diagnoses and achieving a precision and recall of 84% and 92%, respectively. The presented data-driven method highlights the challenges of integrating multiple data sources and the application of information extraction tools to facilitate healthcare quality improvement.
Seasonal Variation in the Presentation of Infectious Keratitis
Authors: Gorski Matthew , Genis Alina , Yushvayev Sharon , Awwad Ahmed , Lazzaro Douglas R. 
Published: November 2015

Introduction:
Infectious keratitis is a common ophthalmic disease with the potential for severe ocular morbidity. Multiple studies have described various risk factors for the development of infectious keratitis. The purpose of this study was to analyze the seasonal variation in the presentation of infectious keratitis, and also seasonal changes in its etiologies and risk factors.

Methods:
A retrospective chart review was performed on consecutive patients presenting to the emergency department at our tertiary care urban hospital center who were diagnosed with infectious keratitis from 2008 to 2013. A chi-square analysis was performed to determine whether a significant seasonal variation existed between the month, season, frequency of presentation of ulcers, and other risk factors.

Results:
A total of 155 patients—53 men and 102 women—with a mean age of 40 (range, 3–97; median, 36) diagnosed with infectious keratitis were included in the analysis. Sixty-nine (44.5%) ulcers presented in the summer, 19 (12.3%) in the fall, 34 (21.9%) in the winter, and 33 (21.3%) in the spring (P<0.0001). Seventeen (11%) patients experienced diabetes mellitus, 60 (39%) were contact lens wearers, 12 (8%) ulcers occurred in the setting of trauma, and 19 (12%) patients underwent previous ocular surgery. A total of 92 ulcers were cultured, of which 53.8% were positive in the summer, 42.9% in the fall, 55.0% in the winter, and 42.1% in the spring. A significant seasonal variation in the frequency of 1 organism, Pseudomonas aeruginosa, was identified (P=<0.0001); up to 47.6% of culture-positive ulcers in the summer were P. aeruginosa positive, whereas cultures in the remaining seasons were 0, 9.1% and 12.5% positive for this organism.

Discussion:
The summer months have a higher frequency of infectious keratitis and P. aeruginosa positivity in this study. Possible factors leading to this increased summer presentation include warmer temperatures, higher humidity, and greater ocular exposure to water. Clinicians should increase their vigilance and education to high-risk patients during these periods and potentially modify empiric treatment regimens.
Cell-type and state-dependent synchronization among rodent areas S1BF, V1, perirhinal cortex and hippocampus CA1
Authors: Vinck Martin , Bos Jeroen J. , Van Mourik-Donga Laura A. , Oplaat Krista T. , Klein Gerbrand A. , Jackson Jadin C. , Gentet Luc J. , Pennartz Cyriel M.A. 
Published: November 2015

AbstractBeta and gamma rhythms have been hypothesized to be involved in global and local coordination of neuronal activity, respectively. Here, we investigated how cells in rodent area S1BF are entrained by rhythmic fluctuations at various frequencies within the local area and in connected areas, and how this depends on behavioral state and cell type. We performed simultaneous extracellular field and unit recordings in four connected areas of the freely moving rat (S1BF, V1M, perirhinal cortex, CA1). S1BF spiking activity was strongly entrained by both beta and gamma S1BF oscillations, which were associated with deactivations and activations, respectively. We identified multiple classes of fast spiking and excitatory cells in S1BF, which showed prominent differences in rhythmic entrainment and in the extent to which phase locking was modulated by behavioral state. Using an additional dataset acquired by whole-cell recordings in head-fixed mice, these cell classes could be compared with identified phenotypes showing gamma rhythmicity in their membrane potential. We next examined how S1BF cells were entrained by rhythmic fluctuations in connected brain areas. Gamma-synchronization was detected in all four areas, however we did not detect significant gamma coherence among these areas. Instead, we only found long-range coherence in the theta-beta range among these areas. In contrast to local S1BF synchronization, we found long-range S1BF-spike to CA1-LFP synchronization to be homogeneous across inhibitory and excitatory cell types. These findings suggest distinct, cell-type contributions of low and high-frequency synchronization to intra- and inter-areal neuronal interactions.
Genome-wide expression profilingDrosophila melanogasterdeficiency heterozygotes reveals diverse genomic responses
Authors: Lee Hangnoh , Cho Dong-Yeon , Whitworth Cale , Eisman Robert , Phelps Melissa , Roote John , Kaufman Thomas , Cook Kevin , Russell Steven , Przytycka Teresa M. , Oliver Brian 
Published: November 2015

AbstractDeletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies on the left arm of chromosome2and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of changes in gene regulation due to altered nuclear architecture are rare. These rare cases includetransde-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100 bp) or within the gene body. Genome-wide effects of deficiencies are observed at genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds.Author summaryDeletions alter gene dose in heterozygotes and bring distant regions of the genome into juxtaposition. We find that the transcriptional dose response is generally varied, gene-specific, and coherently propagates into gene expression regulatory networks. Analysis of deletion heterozygote expression profiles indicates that distinct genetic pathways are weakened in adult flies bearing different deletions even though they show minimal or no overt phenotypes. While there are exceptions, breakpoints have a minimal effect on the expression of flanking genes, despite the fact that different regions of the genome are brought into contact and that important elements such as insulators are deleted. These data suggest that there is little effect of nuclear architecture and long-range enhancer and/or silencer promoter contact on gene expression in the compactDrosophilagenome.
Hotelvp: swimming with sharks
Authors: Gong Yan , Velamuri Ramakrishna , Zhao Liman , Dong Liang 
Published: November 2015

Subject area
This case is written for those people who are interested in entrepreneurship, and to generate discussions on the Lean Start-up methodology, as well as other topics related to entrepreneurship and innovation.

Study level/applicability
It can be used with senior undergraduates, MBAs, EMBAs and senior executives.

Case overview
In August 2011, Mars Ren and Gene Deng created a technology-based venture, Shanghai Tianhailu Network Information Technology Ltd. Filled with passion, they aspired to be the first “factory outlet” in China' hotel booking industry. To achieve this goal, they developed the Hotelvp app for mobile users. After 6:00 p.m. every day, users could book accommodation online in hotels above three-star standard for that same night at significant discounts. Hotels also benefited because they could sell their unsold room nights at the last minute and improve their revenue management. Ren and Deng were convinced that this win-win idea would take off. Unfortunately, it failed to fully satisfy either the users or the hotels. In spite of the founders' passion and energy, it was still acquired by a much more powerful player in the online sector, JD.com, in early 2014. This case is designed to stimulate in-depth discussions based on the question: What are the key obstacles when launching a startup and how to overcome them?

Expected learning outcomes
Through class discussion, it aims at teaching the student how to define and practice a start-up idea successfully by following the “Lean Start-up” methodology and/or take advantage of a practical tool, discovery-driven planning. Specifically, this case intends to teach students how: To identify and define a good start-up idea; To take actions based on the idea/opportunity, iterate and modify it along the way to create new start-ups, and finally lead the new start-ups to grow and succeed; To understand the key concepts, frameworks and theoretical logics of Lean Start-up methodology, and apply it in practice.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Quality of life and human rights conditions in a public psychiatric hospital in Cairo
Authors: Elnemais Fawzy Michael 
Published: November 2015

Purpose
– There is no documented evidence on service users’ perceptions of quality of care and observance of human rights in mental health residential facilities in Egypt after the new mental health law passed in 2009. The purpose of this paper is to investigate El-Abbassia Mental Health Hospital in Cairo. Special attention is paid as to the variety of human rights violations which are experienced by the users and the context in which these violations occur.

Design/methodology/approach
– A cross-sectional study was performed relying on 36 depth interviews with patients, 58 staff members and 15 family members, reviews of documents and observations by an independent assessment team consisting of the author, another psychiatrist, a nurse and a family member using the World Health Organization Quality Rights Tool Kit which uses the Convention on the Rights of Persons with Disabilities (CRPD) as its framework.

Findings
– The study reported empirical insights into how the steps taken by the hospital to address several of the themes drawn from the CRPD require either improvement or initiation to comply fully with the convention’s themes.

Research limitations/implications
– Respondents may have failed to disclose their true experiences due to fear of punishment.

Practical implications
– Users admitted to mental hospitals have often been forgotten, thus becoming victims of violence, neglect and other human rights violations.

Social implications
– An opportunity to promote public awareness of the rights of patients.

Originality/value
– The importance of this study came from being the first documented evidence on service users’ perceptions of quality of care and observance of human rights in mental health residential facilities in Egypt after the new mental health law passed in 2009.
Linking transient dynamics and life history to biological invasion success
Authors: Iles David T. , Salguero‐Gómez Roberto , Adler Peter B. , Koons David N. 
Published: November 2015

Summary

Upon arriving in a novel environment, invading populations are likely to be small and far from a stable stage structure. This unstable stage structure can cause transient (short‐term) population dynamics to differ greatly from asymptotic (long‐term) dynamics. Because the persistence of small populations depends heavily on population growth rate, short‐term dynamics may strongly influence the viability of invading populations.

We used published matrix population models to study the dynamics of small ‘invading’ populations for 105 plant species spanning a range of life histories, including species classified as both invasive and non‐invasive. We simulated the matrix population models to estimate the effect of transient dynamics on population viability (i.e. potential invasiveness) after a hypothetical seed dispersal event into a novel environment. We then evaluated the predictive power of transient and long‐term population growth rates to explain variation in population viability and identified the life‐history correlates of population dynamics that best explained establishment success.

Transient and long‐term population growth rates were positively but independently correlated with population viability across species. Minimum transient density (minimum population density attained en route to a stable stage structure) was the best transient predictor of population viability. This suggests that avoidance of severe short‐term population declines is more important during establishment than either the rate of decline or transient ability to increase in density following a decline.

Despite a negative correlation between transient density and fecundity, species with high fecundity had disproportionately favourable transient dynamics and higher long‐term population growth rates, resulting in higher population viability. Together, these results suggest that highly fecund species are better equipped to overcome the early effects of demographic stochasticity in the establishment phase than less fecund species and help explain the common empirical finding that species invasiveness is correlated with fecundity.

Synthesis. Transient and long‐term population dynamics are independent predictors of demographic performance that influence the viability of invading (i.e. small, unstable) populations subjected to strong effects of demographic stochasticity. Greater long‐term population growth rates and disproportionately favourable transient dynamics may account for the commonly observed invasiveness of highly fecund species. Given the strong dependence of population viability on population growth and the wide range of transient responses among species, transient analysis may provide critical insights into the demographic correlates of biological invasion potential.