bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atg1-mediated autophagy suppresses tissue degeneration inpink1/parkinmutants by promoting mitochondrial fission inDrosophila
Authors: Ma Peng , Yun Jina , Deng Hansong , Guo Ming 
Published: October 2018

Mitochondrial dysfunction is considered a hallmark of multiple neurodegenerative diseases, including Parkinson’s disease (PD). The PD familial genes pink1 and parkin function in a conserved pathway that regulates mitochondrial function, including dynamics (fusion and fission). Mammalian cell culture studies suggested that the pink1/parkin pathway promotes mitophagy (mitochondrial autophagy). Mitophagy through mitochondrial fission and autolysosomal recycling was considered a quality control system at the organelle level. Whether defects in this quality control machinery lead to pathogenesis in vivo in PD remains elusive. Here, we found that elevating autophagy by atg1 overexpression can significantly rescue mitochondrial defects and apoptotic cell death in pink1 and parkin mutants in Drosophila. Surprisingly, the rescue effect relied both on the autophagy–lysosome machinery and on drp1, a mitochondrial fission molecule. We further showed that Atg1 promotes mitochondrial fission by posttranscriptional increase in the Drp1 protein level. In contrast, increasing fission (by drp1 overexpression) or inhibiting fusion (by knocking down mitofusin [mfn]) rescues pink1 mutants when lysosomal or proteasomal machinery is impaired. Taken together, our results identified Atg1 as a dual-function node that controls mitochondrial quality by promoting mitochondria fission and autophagy, which makes it a potential therapeutic target for treatment of mitochondrial dysfunction–related diseases, including PD.
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Authors: Zhu Anqi , Ibrahim Joseph G , Love Michael I 
Published: October 2018

Abstract

Motivation
In RNA-seq differential expression analysis, investigators aim to detect those genes with changes in expression level across conditions, despite technical and biological variability in the observations. A common task is to accurately estimate the effect size, often in terms of a logarithmic fold change (LFC).

Results
When the read counts are low or highly variable, the maximum likelihood estimates for the LFCs has high variance, leading to large estimates not representative of true differences, and poor ranking of genes by effect size. One approach is to introduce filtering thresholds and pseudocounts to exclude or moderate estimated LFCs. Filtering may result in a loss of genes from the analysis with true differences in expression, while pseudocounts provide a limited solution that must be adapted per dataset. Here, we propose the use of a heavy-tailed Cauchy prior distribution for effect sizes, which avoids the use of filter thresholds or pseudocounts. The proposed method, Approximate Posterior Estimation for generalized linear model, apeglm, has lower bias than previously proposed shrinkage estimators, while still reducing variance for those genes with little information for statistical inference.

Availability and implementation
The apeglm package is available as an R/Bioconductor package at https://bioconductor.org/packages/apeglm, and the methods can be called from within the DESeq2 software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization
Authors: Pividori Milton , Cernadas Andres , de Haro Luis A , Carrari Fernando , Stegmayer Georgina , Milone Diego H 
Published: October 2018

Abstract

Motivation
Heterogeneous and voluminous data sources are common in modern datasets, particularly in systems biology studies. For instance, in multi-holistic approaches in the fruit biology field, data sources can include a mix of measurements such as morpho-agronomic traits, different kinds of molecules (nucleic acids and metabolites) and consumer preferences. These sources not only have different types of data (quantitative and qualitative), but also large amounts of variables with possibly non-linear relationships among them. An integrative analysis is usually hard to conduct, since it requires several manual standardization steps, with a direct and critical impact on the results obtained. These are important issues in clustering applications, which highlight the need of new methods for uncovering complex relationships in such diverse repositories.

Results
We designed a new method named Clustermatch to easily and efficiently perform data-mining tasks on large and highly heterogeneous datasets. Our approach can derive a similarity measure between any quantitative or qualitative variables by looking on how they influence on the clustering of the biological materials under study. Comparisons with other methods in both simulated and real datasets show that Clustermatch is better suited for finding meaningful relationships in complex datasets.

Availability and implementation
Files can be downloaded from https://sourceforge.net/projects/sourcesinc/files/clustermatch/ and https://bitbucket.org/sinc-lab/clustermatch/. In addition, a web-demo is available at http://sinc.unl.edu.ar/web-demo/clustermatch/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prevalence and predictors of tobacco smoking among university students in Sylhet Division, Bangladesh
Authors: Hassan Muhammad Shaikh , Hossain Md Kamrul , Khan Hafiz T A 
Published: October 2018

Abstract

Background
Among university students, large numbers are involved with smoking and suffer from many chronic diseases. This study examined tobacco smoking prevalence and potential predictors among university students in Sylhet Division, Bangladesh.

Methods
A total of 416 students were selected for face-to-face interviews. Logistic regression analysis was used to fulfil the specific objectives of the study.

Results
It was discovered that the prevalence of smoking among university students in Sylhet Division was 37% and almost half of current male students were smokers. Mother’s occupation and peer smoking status were found to be significant factors. Although data were collected using multistage sampling, the stages (type of university, universities, departments and academic levels) were insignificant with smoking status. There is a 2.1 times greater likelihood of a student becoming a smoker if a close friend is a smoker. The adjusted living expenses (>$100) was a proactive factor, though individually it was a significant factor.

Conclusions
This study and previous studies found that smoking initiation among female students is negligible, so gender-specific health promotion and intervention is needed in Bangladesh. Tobacco control awareness programs and ‘No smoking’ signage should be displayed within university campuses and sanctioned by university authorities.
Digital, digitized, and numerical humanities
Authors: Roth Camille 
Published: October 2018

AbstractThe term ‘digital humanities’ may be understood in three different ways: as ‘digitized humanities’, by dealing essentially with the constitution, management, and processing of digitized archives; as ‘numerical humanities’, by putting the emphasis on mathematical abstraction and the development of numerical and formal models; and as ‘humanities of the digital’, by focusing on the study of computer-mediated interactions and online communities. Discussing their methods and actors, we show how these three potential acceptations cover markedly distinct epistemological endeavors and, eventually, non-overlapping scientific communities.
Representing stories as interdependent dynamics of character activities and plots: A two-mode network relational event model
Authors: Chao Dingding , Kanno Taro , Furuta Kazuo , Lin Chen 
Published: October 2018

AbstractRecent advances in data science and machine learning have enhanced our ability to analyze and understand the structure of social interactions in fictional stories by using formal and quantitative approaches. However, an objective assessment of these aspects of fictional stories remains a relatively new and technically difficult field. In this brief report, we introduce our study in which we modeled story dynamics from a novel perspective. By implementing a relational event model based on a two-mode network framework in an analytical system for movie scripts, we examined the interdependence of character activities and their participation in a given plot on the basis of an analysis of more than 900 scripts from the Internet Movie Script Database.
SageBook: Toward a cross-generational social network for the Jewish sages’ prosopography
Authors: Zhitomirsky-Geffet Maayan , Prebor Gila 
Published: October 2018

Abstract
In this research we devised and implemented a semi-automatic approach for building a SageBook–a cross-generational social network of the Jewish sages from the Rabbinic literature. The proposed methodology is based on a shallow argumentation analysis leading to detection of lexical–syntactic patterns which represent different relationships between the sages in the text. The method was successfully applied and evaluated on the corpus of the Mishna, the first written work of the Rabbinic Literature which provides the foundation to the Jewish law development. The constructed prosopographical database and the network generated from its data enable a large-scale quantitative analysis of the sages and their related data, and therefore might contribute to the research of the Talmudic literature and evolution of the Jewish thought throughout the two last millennia.
Stress Exposure in Dopamine D4 Receptor Knockout Mice Induces Schizophrenia-Like Behaviors via Disruption of GABAergic Transmission
Authors: Tan Tao , Wang Wei , Williams Jamal , Ma Kaijie , Cao Qing , Yan Zhen 
Published: October 2018

Abstract
A combination of genetic and environmental risk factors has been considered as the pathogenic cause for mental disorders including schizophrenia. Here, we sought to find out whether the abnormality of the dopamine system, coupled with the exposure to modest stress, is sufficient to trigger the manifestation of schizophrenia-like behaviors. We found that exposing dopamine D4 receptor knockout (D4KO) mice with 1-week restraint stress (2 h/d) induced significant deficits in sensorimotor gating, cognitive processes, social engagement, as well as the elevated exploratory behaviors, which are reminiscent to schizophrenia phenotypes. Electrophysiological studies found that GABAergic transmission was significantly reduced in prefrontal cortical neurons from stressed D4KO mice. Additionally, administration of diazepam, a GABA enhancer, restored GABAergic synaptic responses and ameliorated some behavioral abnormalities in stressed D4KO mice. These results have revealed that the combination of 2 key genetic and environmental susceptibility factors, dopamine dysfunction and stress, is a crucial trigger for schizophrenia-like phenotypes, and GABA system in the prefrontal cortex is a downstream convergent target that mediates some behavioral outcomes.
What Is the True Catheterization Rate After Intravesical OnabotulinumtoxinA Injection?
Authors: Patel Devin N. , Jamnagerwalla Juzar , Houman Justin , Anger Jennifer T. , Eilber Karyn S. 
Published: October 2018

(Abstracted from Int Urogynecol J 2018;29:1005–1009)
Intravesical onabotulinumtoxinA (Botox) is widely used for the treatment of urinary urge incontinence and overactive bladder (OAB). One of the most common complications of intravesical onabotulinumtoxinA injection is incomplete bladder emptying requiring clean intermittent catheterization (CIC).
Cognitive Outcomes of Children Born Extremely or Very Preterm Since the 1990s and Associated Risk Factors: A Meta-analysis and Meta-regression
Authors: Twilhaar E. Sabrina , Wade Rebecca M. , de Kieviet Jorrit F. , van Goudoever Johannes B. , van Elburg Ruurd M. , Oosterlaan Jaap 
Published: October 2018

(Abstracted from JAMA Pediatr 2018;172(4):361–367)
Despite apparent progress in perinatal care, children born extremely preterm or very preterm (EP/VP) remain at high risk of cognitive deficits, and long-term morbidity rates have not decreased. Extremely preterm or very preterm birth (<32 weeks of gestation) is associated with higher risks of motor, learning, and behavior problems and, particularly, cognitive impairment.
Metformin in Gestational Diabetes: The Offspring Follow-up (MiG TOFU): Body Composition and Metabolic Outcomes at 7–9 Years of Age
Authors: Rowan Janet A. , Rush Elaine C. , Plank Lindsay D. , Lu Jun , Obolonkin Victor , Coat Suzette , Hague William M. 
Published: October 2018

(Abstracted from BMJ Open Diabetes Res Care 2018;6:e000456)
This study was a follow-up study to the prospective randomized controlled trial comparing metformin versus insulin. In particular, it compared the body composition and metabolic outcomes at 7 to 9 years of children born to women with gestational diabetes mellitus (GDM) randomized to metformin (±insulin) or insulin treatment during pregnancy.
Geographic and Patient Characteristics Associated With Election of Prophylactic Mastectomy in Young Breast Cancer Patients With Early Disease
Authors: Franc Benjamin L. , Copeland Timothy P. , Thombley Robert , Park Miran , Marafino Ben , Dean Mitzi , Boscardin W. John , Rugo Hope S. , Dudley R. Adams 
Published: October 2018

Objectives:
To examine the association between geography and utilization rates of contralateral prophylactic mastectomy (CPM) relative to patient-level factors in patients with early stage breast cancer.

Materials and Methods:
Using the Truven Health MarketScan Commercial Database, a descriptive analysis of geographic variation in genetic testing and CPM rates of 38,108 women ages 18 to 64 years treated with surgery for invasive unilateral breast cancer between 2010 and 2012 was conducted. Multivariate hierarchical analysis was used to examine the relationship between CPM likelihood and patient characteristics, with metropolitan statistical area (MSA) serving as a random effect. Patient characteristics included age group, BRCA1/2 carrier status, family history of breast cancer, breast surgery type, radiation therapy, drug therapy, and payer type. All MSAs in the United States were included, with areas outside MSAs within a given state aggregated into a single area for analytical purposes.

Results:
Descriptive analysis demonstrated significant geographic variation in rates of CPM irrespective of risk inferred from primary malignancy treatment course (P<0.01 to <0.001). Odds of CPM were higher among BRCA1/2 carriers (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.52-2.06), followed by MSA (median OR among all MSAs was 1.61; 95% CI, 1.51-1.73) and family history of breast cancer (OR, 1.49; 95% CI, 1.28-1.53), respectively. Patients who were not tested for BRCA1/2 were less likely (OR, 0.66; 95% CI, 0.61-0.71) to undergo CPM than patients with a negative BRCA test.

Conclusions:
The large geographic variation we observed in CPM indicate a need to understand and optimize clinical decision-making.
Measurement of Radioactivity in the Granites of Pakistan: A Review
Authors: Younis Hannan , Qureshi Aziz Ahmed , Manzoor Shahid , Anees Muhammad 
Published: October 2018

Abstract
All human beings are exposed to primordial radiation. The main source of primordial radiation has been naturally radioactive building materials. In Pakistan, among building materials, granites are most commonly used. This paper reviews the previous studies conducted for the estimation of natural radioactivity of granites from Rustam-Koga, Shewa-Shahbazgarhi, Bunair, Mansehra, and Nagarparkar. The techniques used for these studies include gamma spectrometry and field surveys. To assess the radiation hazards associated with granites of Pakistan, primordial radionuclides and corresponding radiation hazards have been estimated. Most of these granites are found to be safe except Rustam-Koga granite, which presents high excess lifetime cancer risk.
Outcomes of Frontalis Sling Versus Levator Resection in Patients With Monocular Elevation Deficiency Associated Ptosis
Authors: Dave Tarjani Vivek , Sharma Pranjali , Nayak Arpita , Moharana Ruby , Naik Milind N. 
Published: October 2018

Purpose:
To compare outcomes of frontalis sling (FS) silicone and levator resection (LR) in ptosis associated with monocular elevation deficiency.

Methods:
Retrospective interventional comparative case series of FS and LR in monocular elevation deficiency associated ptosis. Favorable outcome was defined as difference in margin reflex distance 1 of ≤1 mm between the 2 eyes in unilateral cases and margin reflex distance 1 of 4 mm in bilateral cases at last follow-up visit.

Results:
One hundred four eyes of 95 patients were included. Median age at surgery was 14 years, and the mean follow-up period was 19.75 ± 34.55 months. Ptosis was severe in 91 (87.5%) patients. Associated Marcus Gunn jaw-winking (MGJW) phenomenon was seen in 43 (42%) patients. Frontalis sling was performed in 76 (73%) and LR in 28 (27%). Mean pre- and postoperative margin reflex distance 1 were −1.27 ± 2.17 mm and 2.18 ± 1.49 mm (p < 0.0001). The mean improvement in margin reflex distance 1 was significantly more with FS (4.46 ± 2.19) compared with LR (1.85 + 2.5) (p < 0.0001). There were no cases of exposure keratopathy requiring reversal of surgery in either group. The number of resurgeries required was 42 (55%) in the FS group and 10 (36%) (p = 0.08) in the LR group. Favorable outcome was seen in 54 (71%) in FS group and 16 (57%) (p = 0.17) in LR group.

Conclusions:
When compared with levator resection, frontalis suspension with silicone gives a better eyelid elevation but has greater regression requiring more resurgeries. In spite of a poor Bells phenomenon, exposure keratopathy is not a concern.
Dual enkephalinase inhibitor PL265: a novel topical treatment to alleviate corneal pain and inflammation
Authors: Reaux-Le Goazigo Annabelle , Poras Hervé , Ben-Dhaou Cyrine , Ouimet Tanja , Baudouin Christophe , Wurm Michel , Melik Parsadaniantz Stéphane 
Published: October 2018

Abstract
Ocular pain is a core symptom of inflammatory or traumatic disorders affecting the anterior segment. To date, the management of chronic ocular pain remains a therapeutic challenge in ophthalmology. The main endogenous opioids (enkephalins) play a key role in pain control but exhibit only transient analgesic effects due to their rapid degradation. The aim of this study was to explore the antinociceptive and anti-inflammatory effects of topical administration of PL265 (a dual enkephalinase inhibitor) on murine models of corneal pain. On healthy corneas, chronic PL265 topical administration did not alter corneal integrity nor modify corneal mechanical and chemical sensitivity. Then, on murine models of corneal pain, we showed that repeated instillations of PL265 (10 mM) significantly reduced corneal mechanical and chemical hypersensitivity. PL265-induced corneal analgesia was completely antagonized by naloxone methiodide, demonstrating that PL265 antinociceptive effects were mediated by peripheral corneal opioid receptors. Moreover, flow cytometry (quantification of CD11b+ cells) and in vivo confocal microscopy analysis revealed that instillations of PL265 significantly decreased corneal inflammation in a corneal inflammatory pain model. Chronic PL265 topical administration also decreased Iba1 and neuronal injury marker (ATF3) staining in the nucleus of primary sensory neurons of ipsilateral trigeminal ganglion. These results open a new avenue for ocular pain treatment based on the enhancement of endogenous opioid peptides' analgesic effects in tissues of the anterior segment of the eye. Dual enkephalinase inhibitor PL265 seems to be a promising topical treatment for safe and effective alleviation of ocular pain and inflammation.
Comparing Before- and After-School Neurocognitive Performance in High School Athletes: Implications for Concussion Management
Authors: Anderson Morgan , Elbin R. J. , Schatz Philip , Henry Luke , Covassin Tracey 
Published: October 2018

Objective:
To compare before- and after-school neurocognitive performance and total symptoms in a sample of nonconcussed high school athletes.

Design:
Repeated-measures, counterbalanced design.

Setting:
Midwest high schools.

Participants:
Thirty-nine nonconcussed high school athletes.

Interventions:
The Immediate Post-Concussion Assessment and Cognitive Testing battery was administered before and after school in a counterbalanced testing order.

Main Outcome Measures:
Neurocognitive and total symptom scores.

Results:
Paired-sample t tests revealed no significant differences in verbal memory (P = 0.43), visual memory (P = 0.44), processing speed (P = 0.94), reaction time (P = 0.16), or total symptoms (P = 0.52) between before- and after-school testing sessions.

Conclusions:
The results of this study expand on best practice guidelines for baseline and postinjury concussion computerized neurocognitive testing and symptom report administration. This study suggests that sports medicine professionals can administer computerized neurocognitive testing before or after school without concern of confounding factors affecting performance or total symptoms.
Overlooked muscle cramps in patients with chronic liver disease: in relation to the prevalence of muscle cramps
Authors: Murata Ai , Hyogo Hideyuki , Nonaka Michihiro , Sumioka Akihiko , Suehiro Yosuke , Furudoi Akira , Fujimoto Yoshifumi , Aisaka Yasuyuki , Komatsu Hironao , Tokumo Hironori 
Published: October 2018

Introduction
Muscle cramps are common comorbidities in chronic liver disease (CLD). Although the prevalence of these has been reported in patients with liver cirrhosis (LC), that of CLD is unknown. In this study, we aimed to clarify the prevalence and characteristics of muscle cramps in individual CLD.

Patients and methods
A total of 432 patients with CLD who visited our hospital were enrolled. The existence of muscle cramps, frequency, time zone, duration, and the degree of pain were investigated using a medical interview questionnaire.

Results
The median age of the patients was 65 years and 48.6% of the patients were women. The prevalence of muscle cramps was 25.9%. Age, female sex, lower BMI, existence of comorbid diseases, and liver fibrosis were associated significantly with muscle cramps. In LC, muscle cramps were significantly frequent, and the severity and duration of these were significantly stronger and longer compared with chronic hepatitis. Female sex [odds ratio (OR): 2.26; P=0.014], diabetes (OR: 29.4; P<0.001), chronic kidney disease (OR: 8.33; P=0.004), and lower BMI (OR: 0.853; P<0.001) were independent factors associated with muscle cramps in CLD. Muscle mass indices were significantly lower among nonalcoholic fatty liver disease patients with muscle cramps, female patients, elderly patients, and patients with advanced fibrosis.

Conclusion
The prevalence of muscle cramps was relatively high in CLD. Female sex, comorbid diabetes, and chronic kidney disease are associated with muscle cramps in CLD. Furthermore, reduced muscle mass is related to muscle cramps in nonalcoholic fatty liver disease.