bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Prevalence of Depression and Depressive Symptoms among Eye Disease Patients: A Systematic Review and Meta-analysis
Authors: Zheng Yajing , Wu Xiaohang , Lin Xiaoming , Lin Haotian 
Published: April 2017

AbstractThe prevalence of depression among different eye disease patients varies across studies and has not been systematically reviewed. This study is to provide a summary of the prevalence of depression among eye disease patients. PubMed, Medline, Embase and Cochrane Library were searched from January, 1990 to December, 2015 to identify studies with information on the prevalence of depression among ophthalmic patients. A random/fixed-effects meta-analysis was used to estimate the pooled prevalence of depression among eye disease patients. Heterogeneity was assessed with the I2 test. 28 studies were selected from 3162 references. The overall pooled prevalence of depression or depressive symptoms with eye disease was 25% (1502/6589 individuals, 95% CI, 0.20–0.30) ranging from 5.4% to 57.0%. Regarding different disease categories, the highest prevalence was revealed for dry eye disease (DED) with 29%, followed by 25% for glaucoma patients, 24% for age-related macular degeneration (AMD) patients, 23% for cataract patients. The increased pooled prevalence of depression was identified in those with eye diseases compared with healthy controls (OR, 1.59; 95% CI, 1.40–1.81; I2 = 68.5%). Substantial heterogeneity was identified across most estimates (I2 > 75%). Further research is needed to identify effective strategies for preventing and treating depression among eye disease patients.
Low‐noise wide‐bandwidth DNA readout instrument for nanopore applications
Authors: Yun J. , Choi H. , Kim J. 
Published: April 2017

A low‐noise, wide‐bandwidth DNA readout instrument for nanopore applications is presented. Owing to hardware simplicity and reliability, a resistive‐feedback transimpedance amplifier (rf‐TIA) is adopted as the headstage for the readout instrument. However, to achieve a high gain and low input noise, its high feedback resistance induces a high parasitic capacitance, thus significantly limiting the 3 dB bandwidth. To drastically reduce the parasitic capacitance and widen the bandwidth, a novel rf‐TIA architecture is fabricated that utilises a split‐resistor technique for the high feedback resistor. This is demonstrated in a benchtop test employing an α‐haemolysin nanopore.
Giant Malignant Peripheral Nerve Sheath Tumor of Scalp in Non-neurofibromatosis Person: A Rare Case Report
Authors: Gupta Amit , Kumar Rakesh , Ojha Bal , Chandra Anil 
Published: April 2017

AbstractMalignant peripheral nerve sheath tumors (MPNSTs) are rare neoplasms, usually arising from components of nerve sheath such as perineural fibroblasts or Schwann cells. Primary scalp MPNST is an exceptionally rare entity and only few cases have been reported till date. We encountered an unusual case of giant scalp MPNST in a 70-year-old man without any history suggestive of neurofibromatosis associated with intracranial extension with underlying bone destruction. The tumor was treated with complete surgical excision followed by adjuvant radiotherapy. Histopathological examination showed hyper- and hypocellular areas of spindle cells admixed with myxoid areas and immunohistochemistry revealed positivity to vimentin and S100 on the basis of which the diagnosis of MPNST was made.
Disconnection of Ventriculoperitoneal Shunt after Mild Injury over the Catheter's Pathway: Two Cases
Authors: Lugo Claudia , Morán Miguel , Amado Andreina , Rojas Luis , Muñoz Erik , Luque Juan 
Published: April 2017

AbstractHydrocephalus is present in 1 of every 1,000 newborns treated with ventriculoperitoneal shunts (VPSs) in the majority of cases. This procedure carries a high risk of complications. One of them is the mechanical disconnection of the system that leads to dysfunction of the shunt and implies neurologic changes that the neurosurgeon has to address as soon as possible. We present two cases of congenital hydrocephalus previously treated with ventriculoperitoneal shunts. The first patient was hit on the right side of his neck. The day after the event, the patient was hypoactive and unable to communicate properly with the examiner and his parents. The radiological cervical X-ray showed disconnection of the catheter at the cervical level. The second case was of a 37-year-old man with hydrocephalus managed with VPS for the first time at the age of 14 years, who was brought to emergency due to rapid onset of symptoms apparently associated with trauma related to a blow with a soccer ball; the patient's X-ray showed fracture of the catheter's path at the thoracic level. For both cases, surgical repair was needed. Results were good, and the patients showed rapid neurologic improvement.
Role of surface and subsurface processes in scaling N2O emissions along riverine networks
Authors: Marzadri Alessandra , Dee Martha M. , Tonina Daniele , Bellin Alberto , Tank Jennifer L. 
Published: April 2017

SignificanceWe show thatN2Oemissions from riverine systems depend on river and stream size and that the primary source ofN2Oproduction shifts from the hyporheic and benthic zones in streams to the benthic and water column in rivers. This analysis also reveals the primary scaling factors governing riverineN2Oemissions. Finally, it provides a predictive tool to quantifyN2Oemissions from any riverine environment worldwide, among biomes, land-use types, and climatic conditions, using readily available reach-scale biogeochemical measurements and hydromorphological data.
Oncogene KRAS activates fatty acid synthase, resulting in specific ERK and lipid signatures associated with lung adenocarcinoma
Authors: Gouw Arvin M. , Eberlin Livia S. , Margulis Katherine , Sullivan Delaney K. , Toal Georgia G. , Tong Ling , Zare Richard N. , Felsher Dean W. 
Published: April 2017

Significance
We studied lung tumors induced by oncogene KRAS gene mutation using transgenic mice and human lung specimens. Gene expression analyses show that KRAS induces fatty acid synthase (FASN), promoting lipogenesis. Through desorption electrospray ionization MS imaging, we found specific lipid modifications in KRAS lung adenocarcinoma. Nanoimmunoassay identified specific KRAS-associated phosphoprotein signatures. We showed that KRAS activates the ERK2 protein, whereas non-KRAS lung adenocarcinoma shows elevated ERK1. We inhibited FASN by a small molecule, cerulenin, and this inhibition blocked cellular proliferation of KRAS-driven lung cancer cells. FASN inhibitors may, thus, present promising therapeutic agents for the treatment of KRAS-associated lung adenocarcinoma.
Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington’s disease
Authors: Chen Mingchen , Wolynes Peter G. 
Published: April 2017

Significance
Formation of inclusion bodies is the pathological hallmark of Huntington’s disease. Huntingtin exon 1-encoded protein fragments aggregate in inclusion bodies, causing disease onset in a length-dependent manner. Using energy landscape theory, the critical length for disease onset is predicted to be between 30 and 40.
Atlantic Sturgeon Use of the Penobscot River and Marine Movements within and beyond the Gulf of Maine
Authors: Altenritter Megan N. , Zydlewski Gayle Barbin , Kinnison Michael T. , Wippelhauser Gail S. 
Published: April 2017

Abstract
Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus were recently listed as threatened in the Gulf of Maine and endangered in the rest of their U.S. range. Continued research priorities include long-term population monitoring, identifying the species’ spawning and nursery grounds, and determining its use of estuaries and marine coastal waters. Although recent and ongoing research is filling in knowledge gaps, the Atlantic Sturgeon's life history and its severely depleted populations make this a challenging species to fully characterize. Our goal was to compile data collected over 7 years from fish captured in the Penobscot River estuary, Maine, to inform management decision making. Atlantic Sturgeon were captured (n = 199), recaptured (n = 16), and passively telemetered (n = 32 that were analyzed here) from 2006 to 2013. Captured individuals were predominantly subadults, and data from telemetry indicated repeated use of a 5-km reach of the mesohaline portion of the estuary. Subadults predictably emigrated from the river each fall (mean date ± SD, August 31 ± 43.5 d) and immigrated back each spring to early summer (May 15 ± 27.8 d), with most individuals (&gt;95% [31 of 32]) returning one or more years after tagging. Marine detections of these subadults were common (81.25% [26 of 32]) and spanned the geographic extent of both the threatened and endangered U.S. distinct population segments and into international waters, e.g., from the Hudson River, New York, to Minas Basin, Nova Scotia. However, they were more typically detected by receivers in the Gulf of Maine; 77% (20 of 26) were only detected in the Gulf of Maine when not in the river. These data indicate that, based on the temporal and spatial predictability of habitat use, the estuary of the Penobscot River is important for subadult Atlantic Sturgeon of the Gulf of Maine. The wider movement patterns emphasize the need for conservation and management across regions and international boundaries.
Identification and Characterization of Nursery Areas of Red Mullet Mullus barbatus in the Central Tyrrhenian Sea
Authors: Criscoli Alessandro , Carpentieri Paolo , Colloca Francesco , Belluscio Andrea , Ardizzone Giandomenico 
Published: April 2017

Abstract
Red Mullet Mullus barbatus is an important target of fishing activities in the central Tyrrhenian Sea, so it is essential to identify its critical habitats in order to manage this resource efficiently. Our research specifically focused on the identification and characterization of nursery areas. The use of spatial interpolation techniques enabled us to identify five nurseries that were highly persistent through time. Moreover, the estimate of juvenile density confirmed the strong aggregation effect of these nursery grounds, as a great portion of young individuals were concentrated in a relatively small surface of the study area. The environmental characterization of these areas showed that juveniles were mainly distributed on bottoms with a relatively high percentage of sand (&gt;70%; P &lt; 0.05). Shannon biodiversity index analysis indicated that the southern nurseries reached the highest values of habitat quality (P &lt; 0.0001). Multivariate analysis showed that nursery grounds were divided into three main groups, and analysis of spatial dynamics showed that two different strategies characterized Red Mullet juveniles when density changes over time. In particular, in some areas young individuals selected habitats in a density-dependent way following the basin model scheme, while in other zones they selected habitats in a density-independent way according to the proportional density model. Results also showed that juveniles followed the proportional density model strategy into nursery areas with the highest Shannon biodiversity index values.
A Bayesian group sparse multi-task regression model for imaging genetics
Authors: Greenlaw Keelin , Szefer Elena , Graham Jinko , Lesperance Mary , Nathoo Farouk S ,   Alzheimer’s Disease Neuroimaging Initiative
Published: April 2017

Abstract

Motivation
Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided. A new Bayesian method is proposed here to overcome this limitation.

Results
We develop a Bayesian hierarchical modeling formulation where the posterior mode corresponds to the estimator proposed by Wang et al. and an approach that allows for full posterior inference including the construction of interval estimates for the regression parameters. We show that the proposed hierarchical model can be expressed as a three-level Gaussian scale mixture and this representation facilitates the use of a Gibbs sampling algorithm for posterior simulation. Simulation studies demonstrate that the interval estimates obtained using our approach achieve adequate coverage probabilities that outperform those obtained from the nonparametric bootstrap. Our proposed methodology is applied to the analysis of neuroimaging and genetic data collected as part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), and this analysis of the ADNI cohort demonstrates clearly the value added of incorporating interval estimation beyond only point estimation when relating SNPs to brain imaging endophenotypes.

Availability and Implementation
Software and sample data is available as an R package ‘bgsmtr’ that can be downloaded from The Comprehensive R Archive Network (CRAN).

Supplementary information
Supplementary data are available at Bioinformatics online.
EigenTHREADER: analogous protein fold recognition by efficient contact map threading
Authors: Buchan Daniel W A , Jones David T 
Published: April 2017

AbstractMotivationProtein fold recognition when appropriate, evolutionarily-related, structural templates can be identified is often trivial and may even be viewed as a solved problem. However in cases where no homologous structural templates can be detected, fold recognition is a notoriously difficult problem (Moult et al., 2014). Here we present EigenTHREADER, a novel fold recognition method capable of identifying folds where no homologous structures can be identified. EigenTHREADER takes a query amino acid sequence, generates a map of intra-residue contacts, and then searches a library of contact maps of known structures. To allow the contact maps to be compared, we use eigenvector decomposition to resolve the principal eigenvectors these can then be aligned using standard dynamic programming algorithms. The approach is similar to the Al-Eigen approach of Di Lena et al. (2010), but with improvements made both to speed and accuracy. With this search strategy, EigenTHREADER does not depend directly on sequence homology between the target protein and entries in the fold library to generate models. This in turn enables EigenTHREADER to correctly identify analogous folds where little or no sequence homology information is.ResultsEigenTHREADER outperforms well-established fold recognition methods such as pGenTHREADER and HHSearch in terms of True Positive Rate in the difficult task of analogous fold recognition. This should allow template-based modelling to be extended to many new protein families that were previously intractable to homology based fold recognition methods.Availability and implementationAll code used to generate these results and the computational protocol can be downloaded from https://github.com/DanBuchan/eigen_scripts. EigenTHREADER, the benchmark code and the data this paper is based on can be downloaded from: http://bioinfadmin.cs.ucl.ac.uk/downloads/eigenTHREADER/.
Regulation of hematopoiesis and immune responses by long non-coding RNAs
Authors: Seo Wooseok , Taniuchi Ichiro 
Published: April 2017

Abstract
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of non-coding RNAs (ncRNAs). Although the extent to which ncRNAs are functional in vivo is still a controversial topic, there is at least a consensus that some ncRNAs are functional and that they play various roles in biology. Among the several kinds of ncRNAs, long ncRNAs (lncRNAs) in particular have received more attention because they have a larger potential to act as multifunctional regulators. Not surprisingly, researchers in the field of immunology have started to examine ncRNAs as new regulatory mechanisms. In this review, we will summarize some lncRNAs that have been reported to function in the immune system and then argue that there is still a long way to go before we can achieve a complete understanding of lncRNAs.
Theoretical study of an LAE–C iv absorption pair at z = 5.7
Authors: García L. A. , Tescari E. , Ryan-Weber E. V. , Wyithe J. S. B. 
Published: April 2017

Abstract
We present a theoretical model to predict the properties of an observed z = 5.72 Lyman α emitter galaxy–C iv absorption pair separated by 1384 comoving kpc h−1. We use the separation of the pair and an outflow velocity/time travelling argument to demonstrate that the observed galaxy cannot be the source of metals for the C iv absorber. We find a plausible explanation for the metal enrichment in the context of our simulations: a dwarf galaxy with M⋆ = 1.87 × 109 M⊙ located 119 comoving kpc h−1 away with a wind velocity of ∼100 km s−1 launched at z ∼ 7. Such a dwarf (MUV = −20.5) is fainter than the detection limit of the observed example. In a general analysis of galaxy–C iv absorbers, we find galaxies with − 20.5 &lt;MUV &lt; −18.8 are responsible for the observed metal signatures. In addition, we find no correlation between the mass of the closest galaxy to the absorber and the distance between them, but a weak anti-correlation between the strength of the absorption and the separation of galaxy–absorber pairs.
Machine learning challenges and impact: an interview with Thomas Dietterich
Authors: Zhou Zhi-Hua 
Published: April 2017

Abstract
Machine learning is the driving force of the hot artificial intelligence (AI) wave. In an interview with NSR, Prof. Thomas Dietterich, the distinguished professor emeritus of computer science at Oregon State University in the USA, the former president of Association of Advancement of Artificial Intelligence (AAAI, the most prestigious association in the field of artificial intelligence) and the founding president of the International Machine Learning Society, talked about exciting recent advances and technical challenges of machine learning, as well as its big impact on the world.
Fear of Falling in People With Multiple Sclerosis: Which Clinical Characteristics Are Important?
Authors: Khalil Hanan , Al-Shorman Alham , El-Salem Khalid , Abdo Nour , Alghwiri Alia A. , Aburub Aseel , Shalabi Sarah , Al-Mustafa Firas 
Published: April 2017

Abstract
Background. Fear of falling (FOF) is an important risk indicator for health-related outcomes and quality of life in patients with multiple sclerosis (MS). However, factors associated with FOF in MS are not well investigated.
Objectives. This study was done to explore predictors of FOF in this population.
Methods. Seventy relapsing remitting patients with MS were evaluated. Fear of falling was assessed using the Fall Efficacy Scale–International (FES-I). Motor outcomes included: 30-second chair stand test (30s-CST), Berg Balance Scale (BBS), 10-Meter Walk Test (10MWT), and 6-Minute Walk Test (6MWT). Cognitive status was determined using the Montréal Cognitive Assessment (MOCA) and Symbol Digit Modalities Test (SDMT). Affective factors including depression, fatigue, and sleep were also assessed using the Beck Depression Inventory (BDI), Modified Fatigue Impact Scale (MFIS), and Pittsburgh Sleep Quality Index (PSQI), respectively.
Results. Fear of falling was significantly correlated with all motor and affective measures used. However, a stepwise regression found that only BBS from motor measures, MOCA from cognitive measures, and sleep disorders from affective factors were significantly predictive of the FOF.
Conclusions. Fear of falling in patients with MS is multifactorial and includes motor and nonmotor factors. Thus, therapies that aim to reduce risk of falling in this population should address motor functions, cognitive abilities, and sleep quality.
Current Controversies in Prenatal Diagnosis 2: For Those Women Screened by NIPT Using Cell-Free DNA, Maternal Serum Markers Are Obsolete
Authors: Yaron Yuval , Hyett Jon , Langlois Sylvie 
Published: April 2017

(Abstracted from Prenat Diagn 2016;36:1167–1171)
Clinical prenatal care includes prenatal testing for fetal birth defects, traditionally including screening with maternal serum biochemical marker(s) to detect open neural tube defects, Down syndrome, or trisomy 18. Recent advances have led to the development of noninvasive prenatal testing using cell-free DNA (cfDNA) derived from the placenta and circulating in maternal blood.
The Hidden Value of Narrative Comments for Assessment: A Quantitative Reliability Analysis of Qualitative Data
Authors: Ginsburg Shiphra , van der Vleuten Cees P.M. , Eva Kevin W. 
Published: April 2017

Purpose
In-training evaluation reports (ITERs) are ubiquitous in internal medicine (IM) residency. Written comments can provide a rich data source, yet are often overlooked. This study determined the reliability of using variable amounts of commentary to discriminate between residents.

Method
ITER comments from two cohorts of PGY-1s in IM at the University of Toronto (graduating 2010 and 2011; n = 46–48) were put into sets containing 15 to 16 residents. Parallel sets were created: one with comments from the full year and one with comments from only the first three assessments. Each set was rank-ordered by four internists external to the program between April 2014 and May 2015 (n = 24). Generalizability analyses and a decision study were performed.

Results
For the full year of comments, reliability coefficients averaged across four rankers were G = 0.85 and G = 0.91 for the two cohorts. For a single ranker, G = 0.60 and G = 0.73. Using only the first three assessments, reliabilities remained high at G = 0.66 and G = 0.60 for a single ranker. In a decision study, if two internists ranked the first three assessments, reliability would be G = 0.80 and G = 0.75 for the two cohorts.

Conclusions
Using written comments to discriminate between residents can be extremely reliable even after only several reports are collected. This suggests a way to identify residents early on who may require attention. These findings contribute evidence to support the validity argument for using qualitative data for assessment.