bluuebunny/crossref_metadata_2025_split huggingface dataset:
State of the Art in Degenerative Cervical Myelopathy: An Update on Current Clinical Evidence
Authors: Wilson Jefferson R. , Tetreault Lindsay A. , Kim Jun , Shamji Mohammed F. , Harrop James S. , Mroz Thomas , Cho Samuel , Fehlings Michael G. 
Published: January 2017

Abstract
Degenerative cervical myelopathy (DCM) is a common cause of spinal cord dysfunction that confronts clinicians on a daily basis. Research performed over the past few decades has provided improved insight into the diagnosis, evaluation, and treatment of this disorder. We aim to provide clinicians with an update regarding the state of the art in DCM, focusing on more recent research pertaining to pathophysiology, natural history, treatment, consideration of the minimally symptomatic patient, surgical outcome prediction, and outcome measurement. Current concepts of pathophysiology focus on the combination of static and dynamic elements leading to breakdown of the blood–spinal cord barrier at the site of compression resulting in local inflammation, cellular dysfunction, and apoptosis. With respect to treatment, although there is a dearth of high-quality studies comparing surgical to nonoperative treatment, several large prospective studies have recently associated surgical management with clinically and statistically significant improvement in functional, disability, and quality of life outcome at long-term follow-up. When selecting the specific surgical intervention for a patient with DCM, anterior (discectomy, corpectomy, hybrid discectomy/corpectomy), posterior (laminectomy and fusion, laminoplasty), and combined approaches may be considered as options depending on the specifics of the patient in question; evidence supporting each of these approaches is reviewed in detail. Recently developed clinical prediction models allow for accurate forecasting of postoperative outcomes, permitting enhanced communication and management of patient expectations in the preoperative setting. Finally, an overview of outcome measures recommended for use in the assessment of DCM patients is provided.
The Continuum of Neurosurgical Care: Increasing the Neurosurgeon's Role and Responsibility
Authors: Zusman Edie E. , Benzil Deborah L. 
Published: January 2017

Abstract
The Health Care Reform Act has fostered a shift toward capitation and shared risk among providers to improve quality and reduce the escalating costs of healthcare. Like all physicians, neurosurgeons are increasingly being incentivized to participate in efforts to streamline care through the use of surgical pathways to reduce hospital length of stay and prevent readmissions. These changes have expanded the role of the neurosurgeon along the continuum of care for the neurosurgery patient. This paper predicts and advocates for a further broadening of neurosurgery participation from programs that reward physicians for helping to prevent a high-risk patient's need for surgery to management of postacute rehabilitation. It also introduces the concept of risk reduction more generally at the community level through collaborative interventions that improve health through changes to the built environment, innovations in transportation, and improved access to healthy food and recreation opportunities.
Pineoblastoma—The Experience at St. Jude Children's Research Hospital
Authors: Parikh Kara A. , Venable Garrett T. , Orr Brent A. , Choudhri Asim F. , Boop Frederick A. , Gajjar Amar J. , Klimo Paul 
Published: January 2017

Abstract

BACKGROUND: Pineoblastomas are rare, supratentorial, primitive neuroectodermal tumors.

OBJECTIVE: To document outcomes with multimodal therapy and evaluate the impact that the degree of surgical resection has on outcome.

METHODS: A departmental brain tumor database was queried to identify all patients with pathologically proven pineoblastoma who were treated from January 1997 to June 2015 at St. Jude Children's Research Hospital. For each patient, we recorded demographic, pathological, radiological, surgical, and clinical follow-up data. The effect of degree of surgical resection on survival outcomes was analyzed.

RESULTS: Forty-one patients (21 male, 20 female) treated for pineoblastoma were identified. The median age at diagnosis was 5.5 years (range 0.4-28.1) and the median follow-up was 34.5 months. Nineteen patients experienced tumor relapse with a median progression-free survival of 11.3 months, and 18 ultimately succumbed to their disease. Patients who died or experienced treatment failure were younger (median, 2.69 vs 6.5 years, P = .026) and more likely to have metastatic disease at diagnosis (12 [63.2%] vs 5 [22.7%], P = .012). When analyzing only patients 5 years of age or older with focal disease at presentation, those who had a gross total resection or near-total resection—compared with subtotal resection or biopsy—had greater overall survival (75.18 vs 48.57 months), with no patients dying as a result of their cancer.

CONCLUSION: Poor prognostic variables for children with pineoblastoma include young age, metastatic disease at presentation, and tumor relapse. For patients older than 5 years with focal disease, maximal tumor resection should be the goal.
Thirty-Day Readmission Rates Following Deep Brain Stimulation Surgery
Authors: Ramayya Ashwin G. , Abdullah Kalil G. , Mallela Arka N. , Pierce John T. , Thawani Jayesh , Petrov Dmitry , Baltuch Gordon H. 
Published: January 2017

Abstract

BACKGROUND: Deep brain stimulation (DBS) has emerged as a safe and efficacious surgical intervention for several movement disorders; however, the 30-day all-cause readmission rate associated with this procedure has not previously been documented.

OBJECT: To perform a retrospective cohort study to estimate the 30-day all-cause readmission rate associated with DBS.

METHODS: We reviewed medical records of patients over the age of 18 who underwent DBS surgery at Pennsylvania Hospital of the University of Pennsylvania between 2009 and 2014. We identified patients who were readmitted to an inpatient medical facility within 30 days from their initial discharge.

RESULTS: Over the study period, 23 (6.6%) of 347 DBS procedures resulted in a readmission to the hospital within 30 days. Causes of readmission were broadly categorized into surgery-related (3.7%): intracranial lead infection (0.6%), battery-site infection (0.6%), intracranial hematoma along the electrode tract (0.6%), battery-site hematoma (0.9%), and seizures (1.2%); and nonsurgery-related (2.9%): altered mental status (1.8%), nonsurgical-site infections (0.6%), malnutrition and poor wound healing (0.3%), and a pulse generator malfunction requiring reprogramming (0.3%). Readmissions could be predicted by the presence of medical comorbidities (P < .001), but not by age, gender, or length of stay (Ps > .15).

CONCLUSION: All-cause 30-day readmission for DBS is 6.6%. This compares favorably to previously studied neurosurgical procedures. Readmissions frequently resulted from surgery-related complications, particularly infection, seizures, and hematomas, and were significantly associated with the presence of medical comorbidities (P < .001).
Comprehensive Review of the ThinkFirst Injury Prevention Programs: A 30-Year Success Story for Organized Neurosurgery
Authors: Youngers Emily H. , Zundel Kayt , Gerhardstein Deborah , Martínez Mariela , Bertrán Carlos , Proctor Mark R. , Spatola Mark A. , Neuwelt Edward A. 
Published: January 2017

Abstract
Traumatic brain and spinal cord injuries are major public health issues causing significant death and long-term disability in the United States, with higher incidences in young and older adults. The ThinkFirst National Injury Prevention Foundation is a nonprofit organization focused on injury prevention education and awareness for people of all ages, with a particular focus on educating children, teens, and young adults. ThinkFirst chapters have evaluated the effectiveness of the ThinkFirst programs in both children and teens by demonstrating significant improvement in knowledge regarding high-risk behaviors postintervention. Here, we review the available literature studying the efficacy of the ThinkFirst National Injury Prevention Foundation programs, outline current ThinkFirst activity, and discuss future directions of the program. This review discusses the efforts of a number of ThinkFirst chapters in terms of research, legislation, and public communication. It showcases the success of ThinkFirst interventions and suggests future directions which can help improve national injury prevention efforts.
Effects of Cranioplasty on Cerebral Blood Flow Following Decompressive Craniectomy: A Systematic Review of the Literature
Authors: Halani Sameer H. , Chu Jason K. , Malcolm James G. , Rindler Rima S. , Allen Jason W. , Grossberg Jonathan A. , Pradilla Gustavo , Ahmad Faiz U. 
Published: January 2017

Abstract

BACKGROUND: Cranioplasty after decompressive craniectomy (DC) is routinely performed for reconstructive purposes and has been recently linked to improved cerebral blood flow (CBF) and neurological function.

OBJECTIVE: To systematically review all available literature to evaluate the effect of cranioplasty on CBF and neurocognitive recovery.

METHODS: A PubMed, Google Scholar, and MEDLINE search adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines included studies reporting patients who underwent DC and subsequent cranioplasty in whom cerebral hemodynamics were measured before and after cranioplasty.

RESULTS: The search yielded 21 articles with a total of 205 patients (range 3–76 years) who underwent DC and subsequent cranioplasty. Two studies enrolled 29 control subjects for a total of 234 subjects. Studies used different imaging modalities, including CT perfusion (n = 10), Xenon-CT (n = 3), single-photon emission CT (n = 2), transcranial Doppler (n = 6), MR perfusion (n = 1), and positron emission tomography (n = 2). Precranioplasty CBF evaluation ranged from 2 days to 6 months; postcranioplasty CBF evaluation ranged from 7 days to 6 months. All studies demonstrated an increase in CBF ipsilateral to the side of the cranioplasty. Nine of 21 studies also reported an increase in CBF on the contralateral side. Neurological function improved in an overwhelming majority of patients after cranioplasty.

CONCLUSION: This systematic review suggests that cranioplasty improves CBF following DC with a concurrent improvement in neurological function. The causative impact of CBF on neurological function, however, requires further study.
High-resolution spectroscopy of the extremely iron-poor post-AGB star CC Lyr
Authors: Aoki Wako , Matsuno Tadafumi , Honda Satoshi , Parthasarathy Mudumba , Li Haining , Suda Takuma 
Published: January 2017

Abstract
High-resolution optical spectroscopy was conducted for the metal-poor post-AGB star CC Lyr to determine its chemical abundances and spectral line profiles. Our standard abundance analysis confirms its extremely low metallicity ([Fe/H] &lt; −3.5) and a clear correlation between abundance ratios and the condensation temperature for 11 elements, indicating that dust depletion is the cause of the abundance anomaly of this object. The very low abundances of Sr and Ba, which are detected for the first time for this object, suggest that heavy neutron-capture elements are not significantly enhanced in this object by the s-process during its evolution through the AGB phase. The radial velocity of this object and profiles of some atomic absorption lines show variations depending on pulsation phases, which could be formed by dynamics of the atmosphere rather than by binarity or contributions of circumstellar absorption. On the other hand, the Hα emission with double peaks shows no evident velocity shift, suggesting that the emission is originating from the circumstellar matter, presumably the rotating disk around the object.
Multi-color simultaneous photometry of the T-Tauri star with planetary candidate, CVSO 30
Authors: Onitsuka Masahiro , Fukui Akihiko , Narita Norio , Hirano Teruyuki , Kusakabe Nobuhiko , Ryu Tsuguru , Tamura Motohide 
Published: January 2017

Abstract
We present three-band simultaneous observations of a weak-line T-Tauri star, CVSO 30 (PTFO 8-8695), which is one of the youngest objects having a candidate transiting planet. The data were obtained with the Multicolor Simultaneous Camera for studying Atmospheres of Transiting exoplanets (MuSCAT) on the 188 cm telescope at Okayama Astrophysical Observatory in Japan. We observed the fading event in the $g^{\prime }_2$-, $r^{\prime }_2$-, and zs, 2-bands simultaneously. As a result, we find a significant wavelength dependence of fading depths of about 3.1%, 1.7%, and 1.0% for the three bands. A cloudless H/He-dominant atmosphere of a hot Jupiter cannot explain this large wavelength dependence. Additionally, we rule out a scenario with the occultation of the gravity-darkened host star. Thus our result is in favor of the fading origin as a circumstellar dust clump or occultation of an accretion hotspot.
Exporting and Firm Performance: Evidence from a Randomized Experiment*
Authors: Atkin David , Khandelwal Amit K. , Osman Adam 
Published: January 2017

Abstract
We conduct a randomized experiment that generates exogenous variation in the access to foreign markets for rug producers in Egypt. Combined with detailed survey data, we causally identify the impact of exporting on firm performance. Treatment firms report 16–26% higher profits and exhibit large improvements in quality alongside reductions in output per hour relative to control firms. These findings do not simply reflect firms being offered higher margins to manufacture high-quality products that take longer to produce. Instead, we find evidence of learning-by-exporting whereby exporting improves technical efficiency. First, treatment firms have higher productivity and quality after controlling for rug specifications. Second, when asked to produce an identical domestic rug using the same inputs and same capital equipment, treatment firms produce higher quality rugs despite no difference in production time. Third, treatment firms exhibit learning curves over time. Finally, we document knowledge transfers with quality increasing most along the specific dimensions that the knowledge pertained to.
In vivo mutation rates and the landscape of fitness costs of HIV-1
Authors: Zanini Fabio , Puller Vadim , Brodin Johanna , Albert Jan , Neher Richard A. 
Published: January 2017

Abstract
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 × 10−5 per site per day, in agreement with the rate measured in cell cultures. We estimated the rate from G to A to be the largest, followed by the other transitions C to T, T to C, and A to G, while transversions are less frequent. At other sites, mutations tend to reduce virus replication. We estimated the fitness cost of mutations at every site in the HIV-1 genome using a model of mutation selection balance. About half of all non-synonymous mutations have large fitness costs (&gt;10 percent), while most synonymous mutations have costs &lt;1 percent. The cost of synonymous mutations is especially low in most of pol where we could not detect measurable costs for the majority of synonymous mutations. In contrast, we find high costs for synonymous mutations in important RNA structures and regulatory regions. The intra-patient fitness cost estimates are consistent across multiple patients, indicating that the deleterious part of the fitness landscape is universal and explains a large fraction of global HIV-1 group M diversity.
Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response
Authors: Alasoo Kaur , Rodrigues Julia , Mukhopadhyay Subhankar , Knights Andrew J. , Mann Alice L. , Kundu Kousik ,   HIPSCI Consortium, Hale Christine , Dougan Gordon , Gaffney Daniel J. 
Published: January 2017

AbstractNoncoding regulatory variants are often highly context-specific, modulating gene expression in a small subset of possible cellular states. Although these genetic effects are likely to play important roles in disease, the molecular mechanisms underlying context-specificity are not well understood. Here, we identify shared quantitative trait loci (QTLs) for chromatin accessibility and gene expression (eQTLs) and show that a large fraction (∼60%) of eQTLs that appear following macrophage immune stimulation alter chromatin accessibility in unstimulated cells, suggesting they perturb enhancer priming. We show that such variants are likely to influence the binding of cell type specific transcription factors (TFs), such as PU.1, which then indirectly alter the binding of stimulus-specific TFs, such as NF-κB or STAT2. Our results imply that, although chromatin accessibility assays are powerful for fine mapping causal noncoding variants, detecting their downstream impact on gene expression will be challenging, requiring profiling of large numbers of stimulated cellular states and timepoints.
TITER: predicting translation initiation sites by deep learning
Authors: Zhang Sai , Hu Hailin , Jiang Tao , Zhang Lei , Zeng Jianyang 
Published: January 2017

AbstractMotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g., GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames (uORFs) on gene expression and the mutational effects influencing translation initiation efficiency.AvailabilityTITER is available as an open-source software and can be downloaded fromhttps://github.com/zhangsaithu/titerContactlzhang20@mail.tsinghua.edu.cnandzengjy321@tsinghua.edu.cn
Heterogeneity of hypothalamic Pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Authors: Lam Brian Y. H. , Cimino Irene , Polex-Wolf Joseph , Kohnke Sara Nicole , Rimmington Debra , Iyemere Valentine , Heeley Nicholas , Cossetti Chiara , Schulte Reiner , Saraiva Luis R. , Logan Darren W. , Blouet Clemence , O’Rahilly Stephen , Coll Anthony P. , Yeo Giles S. H. 
Published: January 2017

SummaryArcuate proopiomelanocortin (POMC) neurons are critical nodes in the control of body weight. Often characterised simply as direct targets for leptin, recent data suggest a more complex architecture. Using single cell RNA sequencing, we have generated an atlas of gene expression in murine POMC neurons. Of 163 neurons, 118 expressed high levels ofPomcwith little/noAgrpexpression and were considered “canonical” POMC neurons (P+). The other 45/163 expressed low levels ofPomcand high levels ofAgrp(A+P+). Unbiased clustering analysis of P+neurons revealed four different classes, each with distinct cell surface receptor gene expression profiles. Further, only 12% (14/118) of P+neurons expressed the leptin receptor (Lepr) compared with 58% (26/45) of A+P+neurons. In contrast, the insulin receptor (Insr) was expressed at similar frequency on P+and A+P+neurons (64% and 55%, respectively). These data reveal arcuate POMC neurons to be a highly heterogeneous population.
Trait Correlates of Climatic Niche Tracking in British Birds
Authors: Rapacciuolo Giovanni , Robinson Robert A. , Gillings Simon , Purvis Andy 
Published: January 2017

ABSTRACTGrowing evidence indicates that species respond idiosyncratically when exposed to the same changes in climate. As a result, understanding the potential influence of biological traits on species’ distributional responses is a research priority. Yet, empirical support for hypothesised influences of traits on climate change responses remains equivocal.In this paper, we developed a novel approach to determine whether biological traits predict the degree of climatic niche tracking of British breeding birds in response to recent climate change. First, we quantified how well predicted positive and negative changes in probability of presence from climate-based species distribution models agreed with observed local gains and losses in species’ occupancy – our measure of climatic niche tracking. Second, we examined whether the degree of climatic niche tracking could be predicted by species’ ecological and life-history traits, as well as phylogenetic relationships.Overall, British breeding birds displayed a low degree of climatic niche tracking over the period of our study, though this varied substantially among species. Models incorporating traits and phylogeny explained a low proportion of the variation in climatic niche tracking. Nevertheless, we did find statistical evidence that species with lower lifespans tracked their climatic niches more closely, whilst species with a mixed diet displayed a lower degree of climatic niche tracking.We present here a tractable approach for quantifying the degree to which observed local range gains and losses can be related to climate redistribution and apply it to British breeding birds. Although we do not find strong evidence that traits predict the degree of climatic niche tracking, we discuss why this is likely to be a consequence of the features of our study system rather than the approach itself. We believe this approach may prove to be useful as datasets of temporal changes in species distributions become increasingly available.