bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal Gene Filtering for Single-Cell data (OGFSC)—a gene filtering algorithm for single-cell RNA-seq data
Authors: Hao Jie , Cao Wei , Huang Jian , Zou Xin , Han Ze-Guang 
Published: December 2018

Abstract

Motivation
Single-cell transcriptomic data are commonly accompanied by extremely high technical noise due to the low RNA concentrations from individual cells. Precise identification of differentially expressed genes and cell populations are heavily dependent on the effective reduction of technical noise, e.g. by gene filtering. However, there is still no well-established standard in the current approaches of gene filtering. Investigators usually filter out genes based on single fixed threshold, which commonly leads to both over- and under-stringent errors.

Results
In this study, we propose a novel algorithm, termed as Optimal Gene Filtering for Single-Cell data, to construct a thresholding curve based on gene expression levels and the corresponding variances. We validated our method on multiple single-cell RNA-seq datasets, including simulated and published experimental datasets. The results show that the known signal and known noise are reliably discriminated in the simulated datasets. In addition, the results of seven experimental datasets demonstrate that these cells of the same annotated types are more sharply clustered using our method. Interestingly, when we re-analyze the dataset from an aging research recently published in Science, we find a list of regulated genes which is different from that reported in the original study, because of using different filtering methods. However, the knowledge based on our findings better matches the progression of immunosenescence. In summary, we here provide an alternative opportunity to probe into the true level of technical noise in single-cell transcriptomic data.

Availability and implementation
https://github.com/XZouProjects/OGFSC.git

Supplementary information
Supplementary data are available at Bioinformatics online.
Deciphering the complexity of human non-coding promoter-proximal transcriptome
Authors: Mapelli Sarah N , Napoli Sara , Pisignano Giuseppina , Garcia-Escudero Ramon , Carbone Giuseppina M , Catapano Carlo V 
Published: December 2018

Abstract

Motivation
Long non-coding RNAs (lncRNAs) have gained increasing relevance in epigenetic regulation and nuclear functional organization. High-throughput sequencing approaches have revealed frequent non-coding transcription in promoter-proximal regions. However, a comprehensive catalogue of promoter-associated RNAs (paRNAs) and an analysis of the possible interactions with neighboring genes and genomic regulatory elements are missing.

Results
Integrating data from multiple cell types and experimental platforms we identified thousands of paRNAs in the human genome. paRNAs are transcribed in both sense and antisense orientation, are mostly non-polyadenylated and retained in the cell nucleus. Transcriptional regulators, epigenetic effectors and activating chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of both active promoters and enhancers. Promoters with paRNAs reside preferentially at chromatin loop boundaries, suggesting an involvement in anchor site recognition and chromatin looping. Importantly, these features are independent of the transcriptional state of neighboring genes. Thus, paRNAs may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. This study provides a comprehensive analysis of the promoter-proximal transcriptome and offers novel insights into the roles of paRNAs in epigenetic processes and human diseases.

Availability and implementation
Genomic coordinates of predicted paRNAs are available at https://figshare.com: https://doi.org/10.6084/m9.figshare.7392791.v1 and https://doi.org/10.6084/m9.figshare.4856630.v2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Health Burden, Support Adequacy, and Depressive Symptoms in Older Men With HIV
Authors: Ogletree Aaron M , Brennan-Ing Mark , Blieszner Rosemary , Karpiak Stephen E , Sands Laura P 
Published: December 2018

AbstractBackground and ObjectivesOlder adults with HIV face greater health burden than HIV-uninfected counterparts. Little is known about resources that might mediate the influence of physiological health burden on psychological well-being. Informed by the stress process model, we assessed the influence of multifaceted health burden indicators on depressive symptoms and evaluated the mediating effects of social support adequacy.Research Design and MethodsThis cross-sectional study used structural equation modeling with data from 640 older men who participated in the Research on Older Adults with HIV study in the United States. Health burden assessment included number of age-related chronic conditions, multiple HIV-related chronic conditions, and self-rated health. Perceptions of instrumental and emotional support adequacy measured support as a coping resource. Depressed mood as assessed by the 10-item Center for Epidemiologic Studies Depression Scale was the indicator of psychological well-being.ResultsHigher incidence of age-related conditions and worse self-rated health was significantly associated with more depressed mood. Self-rated health and HIV-related conditions showed a significant indirect effect on depressed mood via emotional support adequacy.Discussion and ImplicationsEach dimension of health burden demonstrated a distinct pathway to psychological well-being for men with HIV, which should be considered when prioritizing care plans. Complementing research on medical interventions for people with HIV, these findings suggest that nonpharmacological interventions may be important for improving overall well-being.
Bayesian sparse linear regression with unknown symmetric error
Authors: Chae Minwoo , Lin Lizhen , Dunson David B 
Published: December 2018

AbstractWe study Bayesian procedures for sparse linear regression when the unknown error distribution is endowed with a non-parametric prior. Specifically, we put a symmetrized Dirichlet process mixture of Gaussian prior on the error density, where the mixing distributions are compactly supported. For the prior on regression coefficients, a mixture of point masses at zero and continuous distributions is considered. Under the assumption that the model is well specified, we study behavior of the posterior with diverging number of predictors. The compatibility and restricted eigenvalue conditions yield the minimax convergence rate of the regression coefficients in $\ell _1$- and $\ell _2$-norms, respectively. In addition, strong model selection consistency and a semi-parametric Bernstein–von Mises theorem are proven under slightly stronger conditions.
Tropheryma whipplei Endocarditis: Case Presentation and Review of the Literature
Authors: McGee Michael , Brienesse Stephen , Chong Brian , Levendel Alexander , Lai Katy 
Published: December 2018

Abstract
Whipple’s disease is a rare infective condition, classically presenting with gastrointestinal manifestations. It is increasingly recognized as an important cause of culture-negative endocarditis. We present a case of Whipple’s endocarditis presenting with heart failure. A literature review identified 44 publications documenting 169 patients with Whipple’s endocarditis. The average age was 57.1 years. There is a clear sex predominance, with 85% of cases being male. Presenting symptoms were primarily articular involvement (52%) and heart failure (41%). In the majority of cases, the diagnosis was made on examination of valvular tissue. Preexisting valvular abnormalities were reported in 21%. The aortic valve was most commonly involved, and multiple valves were involved in 64% and 23% of cases, respectively. Antibiotic therapy was widely varied and included a ceftriaxone, trimethoprim, and sulfamethoxazole combination. The average follow-up was 20 months, and mortality was approximately 24%. Physician awareness is paramount in the diagnosis and management of this rare condition.
The Never-Ending Story? Or, Does the Roman Catholic Church Remain Vulnerable to Charges of Improper Handling of Clergy Child Sex Abuse?
Authors: Nash Patrick S 
Published: December 2018

Abstract
This article explores whether the Roman Catholic Church’s response to the clergy child sex abuse scandal shields it from further charges of improper handling of cases. It begins by noting the current topicality of institutionalized abuse and how several high-profile public inquiries have recently been established to investigate child sex abuse across a range of secular and religious organizational settings. Although numerous religious institutions have become embroiled in clergy child abuse crises, the Catholic Church has come in for particular scrutiny and condemnation on account of its distinctive institutional characteristics which have exacerbated its own abuse scandal in a uniquely severe way. The Church’s own understanding of this issue is that a culture of antinomianism has taken root within the clerical hierarchy and that, were canon law to be applied properly, the crisis would be resolved. This contrasts quite dramatically with the typical external understanding of the crisis which sees the canonical legal system as part of the problem, namely the Church’s refusal to cooperate fully with the secular criminal justice system and effective assumption of a criminal jurisdiction of its own. The article concludes with a final prognosis of the prospects of fundamental legal and cultural change.
Evaluation of two-stage weaning and trace mineral injection on receiving cattle growth performance and behavior
Authors: Rauch Jordan C , Stokes Rebecca S , Shike Daniel W 
Published: December 2018

Abstract
The objective was to evaluate the effects of two-stage weaning and injectable trace mineral (ITM) on receiving cattle growth performance and behavior. Angus and Simmental × Angus steers (n = 136; body weight [BW] = 200 ± 26 kg) were utilized in a 2 × 2 factorial design. Calves were blocked by source, and assigned to one of four treatments: 1) two-stage weaning and ITM (2MM), 2) two-stage weaning and saline injection (2SAL), 3) abrupt weaning and ITM (AbtMM), or 4) abrupt weaning and saline injection (AbtSAL). On d−6, calves were weighed, plastic calf weaner devices (used to prevent calf from nursing) were inserted in two-stage weaned calves, and ITM or saline injections (1 mL/45.4 kg BW) were administered. On day 0, plastic calf weaner devices were removed, and calves were weighed and shipped 272 km to Urbana, IL. Steer behavior was observed the 2 d following separation from dam. Receiving period was day 0 to 42 and growing period was day 42 to 124. Data were analyzed using the MIXED procedure of SAS and pen (six per treatment) was the experimental unit. Abruptly weaned calves had greater (P &lt; 0.01) preweaning average daily gain (ADG) than two-stage weaned calves. Treatment did not affect (P ≥ 0.16) ADG during the receiving or growing period; however, calves that received ITM tended (P 0.06) to have greater ADG from day 0 to 124. During the receiving period, abruptly weaned calves tended (P = 0.08) to eat more than two-stage calves and ITM calves ate more (P = 0.03) than calves that received saline. There was a weaning strategy × ITM interaction (P &lt; 0.01) for dry matter intake (DMI) from day 0 to 124; 2MM calves ate more (P &lt; 0.01) than 2SAL, but DMI was not different (P = 0.58) between AbtMM and AbtSAL calves. There was a weaning strategy × ITM interaction (P &lt; 0.01) for gain-to-feed ratio (G:F) from day 0 to 124; 2SAL calves had greater (P = 0.05) G:F than AbtSAL, with 2MM and AbtMM calves being intermediate and not different (P = 0.38) than each other. Two-stage weaning decreased (P ≤ 0.02) the percentage of calves walking, standing, and vocalizing, and increased (P ≤ 0.02) the percentage of calves lying and eating following separation from dam. Two-stage weaning decreased preweaning ADG and behavioral signs of stress at feedlot arrival, but had no effect on overall growth. In addition, ITM had no effect on calf BW or behavior, but increased overall DMI in two-stage weaned calves compared to abruptly weaned calves and tended to increase overall ADG regardless of weaning strategy.
The time is now: a call for action to translate recent momentum on tackling tropical snakebite into sustained benefit for victims
Authors: Harrison Robert A , Casewell Nicholas R , Ainsworth Stuart A , Lalloo David G 
Published: December 2018

Abstract
Like the other WHO-listed Neglected Tropical Diseases (NTDs), snakebite primarily affects rural, impoverished tropical communities that lack adequate health resources. The annual 138 000 deaths and 400 000 disabilities suffered by these subsistence farming communities means that snakebite is an additional cause and consequence of tropical poverty. Unlike most of the NTDs, however, snakebite is a medical emergency, and requires rapid treatment in a hospital equipped with effective antivenom, beds and appropriately trained staff. The lack of such facilities in the remote areas most affected by snakebite, and the high treatment costs, explains why most victims, particularly in sub-Saharan Africa, consult traditional healers rather than seek hospital care. Whilst affordable, there is no evidence that traditional treatments are effective. The number of snakebite victims that die, unregistered, in the community is threefold higher than hospital-recorded deaths.
After decades of inertia, WHO benefitted from advocacy interventions and the support of key agencies, including Médecins Sans Frontières, the Wellcome Trust, the Kofi Annan Foundation and the Global Snakebite Initiative, to recently institute transformative actions for reducing the public health burden of tropical snakebite. It is imperative that WHO and the other stakeholders now gain the support and investment of governments, research funders and donor agencies to ensure that this recent momentum for change is translated into sustained benefit to snakebite victims.
Choice of ANesthesia for EndoVAScular Treatment of Acute Ischemic Stroke (CANVAS): Results of the CANVAS Pilot Randomized Controlled Trial
Authors: Sun Jian , Liang Fa , Wu Youxuan , Zhao Yan , Miao Zhongrong , Zhang Li , Gelb Adrian W. , Chan Matthew T.V. , Peng Yuming , Han Ruquan 
Published: December 2018

Background:
The effect of choice of anesthesia on clinical outcome for endovascular treatment (EVT) in patients with acute ischemic stroke (AIS) remains unclear.

Methods:
We conducted a pilot trial of 43 patients with acute anterior circulation ischemic stroke having EVT. Patients were randomly allocated to receive general anesthesia or conscious sedation. We documented the rate of recruitment and rate of conversion from conscious sedation to general anesthesia. In addition, we recorded the change in National Institute of Health stroke scale (NIHSS) on day 7, the rate of successful reperfusion and measured neurological function by certified researchers using modified Rankin Score (mRS 0 to 2) at 90 days.

Results:
The recruitment rate was 31.4% and majority of patients were excluded because of delay in hospital presentation and posterior circulation stroke. The rate of conversion from conscious sedation to general anesthesia was 18.2%. This was primarily related to excessive sedation and uncontrolled movement. Change in NIHSS score, rate of successful reperfusion and functional recovery were similar between groups.

Conclusions:
It was feasible to randomize AIS patients receiving either general anesthesia or conscious sedation for EVT.
Socioeconomic Predictors of Surgical Resection and Survival for Patients With Osseous Spinal Neoplasms
Authors: Deb Sayantan , Brewster Ryan , Pendharkar Arjun Vivek , Veeravagu Anand , Ratliff John , Desai Atman 
Published: December 2018

Summary of Background Data:
Primary osseous spinal neoplasms (POSNs) include locally aggressive tumors such as osteosarcoma, chondrosarcoma, Ewing sarcoma, and chordoma. For such tumors, surgical resection is associated with improved survival for patients. Socioeconomic predictors of receiving surgery, however, have not been studied.

Objective:
To examine the independent effect of race on receiving surgery and survival probability in patients with POSN.

Study Design:
A total of 1904 patients from the SEER program at the National Cancer Institute database, all diagnosed with POSN of the spinal cord, vertebral column, pelvis, or sacrum from 2003 through 2012 were included in the study. Race was reported as white or nonwhite. Treatment included receiving surgery and no surgery.

Materials and Methods:
Multivariable logistic regression was used to determine odds of receiving surgery based on race. Survival probability based on and race and surgery status was analyzed by Cox proportional hazards model and Kaplan-Meir curves. Results were adjusted for age at diagnosis, sex, socioeconomic status (composite index), tumor size, and tumor grade. Data were analyzed with SAS version 9.4.

Results:
The study found that white patients were significantly more likely to receive surgery (odds ratio=3.076, P<0.01). Furthermore, nonwhite race was associated with significantly shorter survival time [hazard ratio (HR)=1.744, P<0.05]. Receiving surgery was associated with improved overall survival (HR=2.486, P<0.01). After adjusting for receiving surgery, white race remained significantly associated with higher survival probability (HR=2.061, P<0.05).

Conclusions:
This national study of patients with typically aggressive POSN found a significant correlation between race and the likelihood of receiving surgery. The study also found race to be a significant predictor of overall survival, regardless of receiving surgical treatment. These findings suggest an effect of race on receiving treatment and survival in patients with POSN, regardless of socioeconomic status. Further studies are required to understand reasons underlying these findings, and how they may be addressed.
Does l-Methylfolate Supplement Methylphenidate Pharmacotherapy in Attention-Deficit/Hyperactivity Disorder?
Authors: Surman Craig , Ceranoglu Atilla , Vaudreuil Carrie , Albright Brittany , Uchida Mai , Yule Amy , Spencer Andrea , Boland Heidi , Grossman Rebecca , Rhodewalt Lauren , Fitzgerald Maura , Biederman Joseph 
Published: December 2018

Abstract

Purpose/Background
Interventions for attention-deficit/hyperactivity disorder (ADHD) may be inadequate for some patients. There is evidence that supplementation with l-methylfolate augments antidepressant agent effects and thus might also augment ADHD treatment effects by a common catecholaminergic mechanism.

Methods
Forty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition diagnosis of ADHD participated in a randomized, double-blind, placebo-controlled, 12-week trial of 15 mg of l-methylfolate in combination with osmotic-release oral system methylphenidate. Osmotic-release oral system methylphenidate was dose optimized over the first 6 weeks. We evaluated the effects on ADHD symptoms, self-report on the Behavior Rating Inventory of Executive Function of executive function, methylphenidate dosing, neuropsychological test measures, the Adult ADHD Self-report scale, emotional dysregulation, social adjustment, and work productivity, as well as moderating effects of body mass index, autoantibodies to folate receptors, and select genetic polymorphisms.

Results

l-Methylfolate was well tolerated, with no significant effect over placebo except improvement from abnormal measures on the mean adaptive dimension of the ASR scale (χ2 = 4.36, P = 0.04). Methylphenidate dosing was significantly higher in individuals on l-methylfolate over time (χ2 = 7.35, P = 0.007). Exploratory analyses suggested that variation in a guanosine triphosphate cyclohydrolase gene predicted association with higher doses of methylphenidate (P < 0.001).

Conclusions

l-Methylfolate was associated with no change in efficacy on measures relevant to neuropsychiatric function in adults with ADHD, other than suggestion of reduced efficacy of methylphenidate. Further investigation would be required to confirm this effect and its mechanism and the genotype prediction of effects on dosing.
Management of pediatric low-grade glioma
Authors: de Blank Peter , Bandopadhayay Pratiti , Haas-Kogan Daphne , Fouladi Maryam , Fangusaro Jason 
Published: December 2018

Purpose of review
Pediatric low-grade gliomas (pLGGs) have been treated with similar therapies for the last 30 years. Recent biological insights have allowed a new generation of targeted therapies to be developed for these diverse tumors. At the same time, technological advances may redefine the late toxicities associated with radiation therapy. Understanding recent developments in pLGG therapy is essential to the management of these common pediatric tumors.

Recent findings
It is now well understood that aberrations of the mitogen-activated protein kinase pathway are key to oncogenesis in low-grade gliomas. This understanding, along with the development of available targeted agents, have heralded a new era of understanding and treatment for these patients. Promising, sustained responses are now being seen in early phase trials among patients with multiply recurrent/progressive disease. Also, newer and highly conformal radiation approaches such as proton beam radiotherapy maintain efficacy of radiation but limit radiation-associated toxicities.

Summary
Novel therapies offer the potential for tumor control with greatly reduced toxicities. However, late effects of these therapies are just now being explored. Improved radiation approaches and targeted agents have the potential to redefine traditional therapy for pLGG.