bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulsating ULXs: large pulsed fraction excludes strong beaming
Authors: Mushtukov Alexander A , Portegies Zwart Simon , Tsygankov Sergey S , Nagirner Dmitrij I , Poutanen Juri 
Published: December 2020

ABSTRACT
The recent discovery of pulsating ultraluminous X-ray sources (ULXs) shows that the apparent luminosity of accreting neutron stars can exceed the Eddington luminosity by a factor of 100s. The relation between the actual and apparent luminosity is a key ingredient in theoretical models of ULXs, but it is still under debate. A typical feature of the discovered pulsating ULXs is a large pulsed fraction (PF). Using Monte Carlo simulations, we consider a simple geometry of accretion flow and test the possibility of simultaneous presence of a large luminosity amplification due the geometrical beaming and a high PF. We argue that these factors largely exclude each other and only a negligible fraction of strongly beamed ULX pulsars can show PF above 10 per cent. Discrepancy between this conclusion and current observations indicates that pulsating ULXs are not strongly beamed and their apparent luminosity is close to the actual one.
Minimizing the impact of scale-dependent galaxy bias on the joint cosmological analysis of large-scale structures
Authors: Asgari Marika , Friswell Indiarose , Yoon Mijin , Heymans Catherine , Dvornik Andrej , Joachimi Benjamin , Simon Patrick , Zuntz Joe 
Published: December 2020

ABSTRACT
We present a mitigation strategy to reduce the impact of non-linear galaxy bias on the joint ‘3 × 2pt’ cosmological analysis of weak lensing and galaxy surveys. The Ψ-statistics that we adopt are based on Complete Orthogonal Sets of E/B Integrals. As such they are designed to minimize the contributions to the observable from the smallest physical scales where models are highly uncertain. We demonstrate that Ψ-statistics carry the same constraining power as the standard two-point galaxy clustering and galaxy–galaxy lensing statistics, but are significantly less sensitive to scale-dependent galaxy bias. Using two galaxy bias models, motivated by halo model fits to data and simulations, we quantify the error in a standard 3 × 2pt analysis where constant galaxy bias is assumed. Even when adopting conservative angular scale cuts, that degrade the overall cosmological parameter constraints, we find of order 1σ biases for Stage III surveys on the cosmological parameter S8 = σ8(Ωm/0.3)α. This arises from a leakage of the smallest physical scales to all angular scales in the standard two-point correlation functions. In contrast, when analysing Ψ-statistics under the same approximation of constant galaxy bias, we show that the bias on the recovered value for S8 can be decreased by a factor of ∼2, with less conservative scale cuts. Given the challenges in determining accurate galaxy bias models in the highly non-linear regime, we argue that 3 × 2pt analyses should move towards new statistics that are less sensitive to the smallest physical scales.
Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations
Authors: Pei Guangsheng , Hu Ruifeng , Dai Yulin , Manuel Astrid Marilyn , Zhao Zhongming , Jia Peilin 
Published: December 2020

AbstractAssessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise in genome-wide association studies (GWAS), and because &gt;90% of genetic variants from GWAS are located in non-coding regions. Here, we collected the largest human epigenomic map from ENCODE and Roadmap consortia and implemented a deep-learning-based convolutional neural network (CNN) model to predict the regulatory roles of genetic variants across a comprehensive list of epigenomic modifications. Our model, called DeepFun, was built on DNA accessibility maps, histone modification marks, and transcription factors. DeepFun can systematically assess the impact of non-coding variants in the most functional elements with tissue or cell-type specificity, even for rare variants or de novo mutations. By applying this model, we prioritized trait-associated loci for 51 publicly-available GWAS studies. We demonstrated that CNN-based analyses on dense and high-resolution epigenomic annotations can refine important GWAS associations in order to identify regulatory loci from background signals, which yield novel insights for better understanding the molecular basis of human complex disease. We anticipate our approaches will become routine in GWAS downstream analysis and non-coding variant evaluation.
Pseudouridine-mediated translation control of mRNA by methionine aminoacyl tRNA synthetase
Authors: Levi Ofri , Arava Yoav S 
Published: December 2020

AbstractModification of nucleotides within an mRNA emerges as a key path for gene expression regulation. Pseudouridine is one of the most common RNA modifications; however, only a few mRNA modifiers have been identified to date, and no one mRNA pseudouridine reader is known. Here, we applied a novel genome-wide approach to identify mRNA regions that are bound by yeast methionine aminoacyl tRNAMet synthetase (MetRS). We found a clear enrichment to regions that were previously described to contain pseudouridine (Ψ). Follow-up in vitro and in vivo analyses on a prime target (position 1074 within YEF3 mRNA) demonstrated the importance of pseudouridine for MetRS binding. Furthermore, polysomal and protein analyses revealed that Ψ1074 mediates translation. Modification of this site occurs presumably by Pus6, a pseudouridine synthetase known to modify MetRS cognate tRNA. Consistently, the deletion of Pus6 leads to a decrease in MetRS association with both tRNAMet and YEF3 mRNA. Furthermore, while global protein synthesis decreases in pus6Δ, translation of YEF3 increases. Together, our data imply that Pus6 ‘writes’ modifications on tRNA and mRNA, and both types of RNAs are ‘read’ by MetRS for translation regulation purposes. This represents a novel integrated path for writing and reading modifications on both tRNA and mRNA, which may lead to coordination between global and gene-specific translational responses.
Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution
Authors: Camel Benjamin R , Jose Davis , Meze Katarina , Dang Anson , von Hippel Peter H 
Published: December 2020

Abstract
In this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing circular dichroism spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. The results are interpreted in part by what we know about the topology of the binding cleft from crystallographic studies of the DNA binding domain of gp32 and provide additional insights into how gp32 can manipulate the ssDNA chain at various steps of DNA replication and other processes of genome expression.
Retrobulbar Hemangioblastomas in von Hippel-Lindau Disease: Clinical Course and Management
Authors: Alvarez Reinier , Mastorakos Panagiotis , Hogan Elizabeth , Scott Gretchen , Lonser Russell R , Wiley Henry E , Chew Emily Y , Chittiboina Prashant 
Published: December 2020

Abstract

BACKGROUND
Retrobulbar hemangioblastomas involving the optic apparatus in patients with von Hippel-Lindau disease (VHL) are rare, with only 25 reported cases in the literature.

OBJECTIVE
To analyze the natural history of retrobulbar hemangioblastomas in a large cohort of VHL patients in order to define presentation, progression, and management.

METHODS
Clinical history and imaging of 250 patients with VHL in an ongoing natural history trial and 1774 patients in a neurosurgical protocol were reviewed. The clinical course, magnetic resonance images, treatment, and outcomes were reviewed for all included patients.

RESULTS
A total of 18 patients with retrobulbar hemangioblastoma on surveillance magnetic resonance imaging met the inclusion criteria for this study. Of the 17 for whom clinical information was available, 10 patients presented with symptoms related to the hemangioblastoma, and 7 were asymptomatic. The mean tumor volume was larger for symptomatic (810.6 ± 545.5 mm3) compared to asymptomatic patients (307.6 ± 245.5 mm3; P < .05). A total of 5 of the symptomatic patients were treated surgically and all experienced improvement in their symptoms. All 3 symptomatic patients that did not undergo intervention had continued symptom progression. Long-term serial imaging on asymptomatic patients showed that these tumors can remain radiographically stable and asymptomatic for extended periods of time (101.43 ± 71 mo).

CONCLUSION
This study suggests that retrobulbar hemangioblastomas may remain stable and clinically asymptomatic for long durations. Recent growth and larger tumor volume were associated with symptom occurrence. Surgical treatment of symptomatic retrobulbar hemangioblastomas can be safe and may reverse the associated symptoms.
An updated histology recode for the analysis of primary malignant and nonmalignant brain and other central nervous system tumors in the Surveillance, Epidemiology, and End Results Program
Authors: Forjaz Gonçalo , Barnholtz-Sloan Jill S , Kruchko Carol , Siegel Rebecca , Negoita Serban , Ostrom Quinn T , Dickie Lois , Ruhl Jennifer , Van Dyke Alison , Patil Nirav , Cioffi Gino , Miller Kimberly D , Waite Kristin , Mariotto Angela B 
Published: December 2020

Abstract

Background
There are over 100 histologically distinct types of primary malignant and nonmalignant brain and other central nervous system (CNS) tumors. Our study presents recent trends in the incidence of these tumors using an updated histology recode that incorporates major diagnostic categories listed in the 2016 World Health Organization Classification of Tumours of the CNS.

Methods
We used data from the SEER-21 registries for patients of all ages diagnosed in 2000–2017. We calculated age-adjusted incidence rates and fitted a joinpoint regression to the observed data to estimate the Annual Percent Change and 95% confidence intervals over the period 2000–2017.

Results
There were 315,184 new malignant (34.2%; 107,890) and nonmalignant (65.8%; 207,294) brain tumor cases during 2004–2017. Nonmalignant meningioma represented 46.5% (146,498) of all brain tumors (malignant and nonmalignant), while glioblastoma represented 50.8% (54,832) of all malignant tumors. Temporal trends were stable or declining except for nonmalignant meningioma (0.7% per year during 2004–2017). Several subtypes presented decreases in trends in the most recent period (2013–2017): diffuse/anaplastic astrocytoma (−1.3% per year, oligodendroglioma (−2.6%), pilocytic astrocytoma (−3.8%), and malignant meningioma (−5.9%).

Conclusions
Declining trends observed in our study may be attributable to recent changes in diagnostic classification and the coding practices stemming from those changes. The recode used in this study enables histology reporting to reflect the changes. It also provides a first step toward the reporting of malignant and nonmalignant brain and other CNS tumors in the Surveillance, Epidemiology, and End Results (SEER) Program by clinically relevant histology groupings.
Rurality of Residence and Inappropriate Antibiotic Use for Acute Respiratory Infections Among Young Tennessee Children
Authors: Dantuluri Keerti L , Bruce Jean , Edwards Kathryn M , Banerjee Ritu , Griffith Hannah , Howard Leigh M , Grijalva Carlos G 
Published: December 2020

Abstract

Background
Antibiotic use is common for acute respiratory infections (ARIs) in children, but much of this use is inappropriate. Few studies have examined whether rurality of residence is associated with inappropriate antibiotic use. We examined whether rates of ARI-related inappropriate antibiotic use among children vary by rurality of residence.

Methods
We conducted a retrospective cohort study of children aged 2 months–5 years enrolled in Tennessee Medicaid between 2007 and 2017 and diagnosed with ARI in the outpatient setting. Study outcomes included ARI, ARI-related antibiotic use, and ARI-related inappropriate antibiotic use. Multivariable Poisson regression was used to measure associations between rurality of residence, defined by the US Census Bureau, and the rate of study outcomes, while accounting for other factors including demographics and underling comorbidities.

Results
A total of 805 332 children met selection criteria and contributed 1 840 048 person-years (p-y) of observation. Children residing in completely rural, mostly rural, and mostly urban counties contributed 70 369 (4%) p-y, 479 121 (26%) p-y, and 1 290 558 p-y (70%), respectively. Compared with children in mostly urban counties (238 per 1000 p-y), children in mostly rural (450 per 1000 p-y) and completely rural counties (468 per 1000 p-y) had higher rates of inappropriate antibiotic use (adjusted incidence rate ratio [aIRR] = 1.34, 95% confidence interval [CI] = 1.33–1.35 and aIRR = 1.33, 95% CI = 1.32–1.35, respectively).

Conclusions
Inappropriate antibiotic use is common among young children with ARI, with higher rates in rural compared with urban counties. These differences should inform targeted outpatient antibiotic stewardship efforts.
Viral Ribonucleic Acid Shedding and Transmission Potential of Asymptomatic and Paucisymptomatic Coronavirus Disease 2019 Patients
Authors: Samaddar Arghadip , Gadepalli Ravisekhar , Nag Vijaya Lakshmi , Misra Sanjeev , Bhardwaj Pankaj , Singh Pankaj , Meena Mahadev , Sharma Prem Prakash , Grover Malika , Kumar Garg Mahendra , Chauhan Nishant Kumar , Dutt Naveen , Niwas Ram , Kumar Deepak , Sharma Praveen , Goel Akhil Dhanesh , Kumar Gupta Manoj , Saurabh Suman , Rai Shubham , Lawdiya Chunnilal , Saini Jinesh , Singh Deepak 
Published: December 2020

Abstract
We studied the pattern and duration of viral ribonucleic acid (RNA) shedding in 32 asymptomatic and 11 paucisymptomatic coronavirus disease 2019 cases. Viral RNA shedding in exhaled breath progressively diminished and became negative after 6 days of a positive reverse-transcription polymerase chain reaction test. Therefore, the duration of isolation can be minimized to 6 days.
Bertolotti Syndrome With Articulated L5 Transverse Process Causing Intractable Back Pain: Surgical Video Showcasing a Minimally Invasive Approach for Disconnection: 2-Dimensional Operative Video
Authors: Johnson Zachary D , Aoun Salah G , Ban Vin Shen , El Ahmadieh Tarek Y , Kafka Benjamin , Wolfe Cody , Adogwa Owoicho , Bagley Carlos A , Tamimi Mazin Al 
Published: December 2020

Abstract
Bertolotti syndrome is a commonly missed cause of intractable back pain that affects 4% to 8% of the general population. It involves the congenital malformation of a transitional lumbosacral vertebra, with total or partial and unilateral or bilateral transverse process (TP) fusion or articulation to the sacrum. The pain can be debilitating, and the tethering of the spine to the sacrum can encourage deformity formation in the coronal plane and lead to early degenerative changes, especially if present only unilaterally. We present the case of a 24-yr-old woman with no notable prior medical history who presented with years of lower axial back pain radiating to her thighs, which limited her activities of daily living and was resistant to conservative management. Her imaging showed an abnormally large left L5 TP, which was articulated to the sacrum, and signs of early coronal deformity. She had responded almost completely to repeated steroid injections into the TP-sacral joint, but that effect was very transient. Informed patient consent was obtained prior to her surgery. She underwent a minimally invasive tube disconnection of the abnormal joint with partial distal resection of the TP, and her symptoms completely resolved. This case highlights the importance of correlating clinical symptoms with aberrant anatomy, and the role of selective surgery in providing symptomatic relief. This case report was written in compliance with our institutional ethical review board approval, and patient consent was waived in light of the retrospective and deidentified nature of the data presented in accordance with the University of Texas Southwestern institutional review board.
Evaluating Real-World Adherence and Effectiveness of the “Reboot Online” Program for the Management of Chronic Pain in Routine Care
Authors: Lim Derek Z , Newby Jill M , Gardner Tania , Haskelberg Hila , Schultz Regina , Faux Steven G , Shiner Christine T 
Published: December 2020

Abstract

Objective
Chronic pain is a prevalent and disabling condition. Reboot Online was developed as a multidisciplinary and widely accessible online treatment program for chronic pain. It has been shown to be effective in clinical trials, but the effectiveness of this program in routine care settings remains unknown. This study aimed to examine program adherence and effectiveness in a real-world sample of participants completing Reboot Online in the community.

Design and subjects
A retrospective cohort study was conducted using real-world data from participants referred the Reboot Online program by clinicians as part of their routine care, from April 2017 to April 2019.

Methods
Routinely collected data on program adherence, participant demography and clinical outcomes were included in the analyses. Measures included the Pain Self Efficacy Questionnaire, Brief Pain Inventory, Tampa Scale of Kinesiophobia, Pain-Disability Index, and Patient Health Questionnaire 9-item (depression). Logistic regression was used to investigate whether certain factors predict program adherence (completion versus noncompletion), and linear mixed models were used to examine effectiveness.

Results
In total, 867 participants were included in the analyses, and 583 engaged with at least one Reboot Online lesson. Of these, 42% (n = 247) completed the course in its entirety, with rurality and lower Tampa scores being significant predictors of adherence. Completers demonstrated significant improvements across all outcome measures (effect sizes ranging from 0.22 to 0.51).

Conclusions
Reboot Online is an effective treatment for chronic pain in the routine care setting. Adherence was variable (overall 42%), and could be predicted by rurality and less fear of movement at baseline.
Comparative effectiveness and persistence of TNFi and non-TNFi in juvenile idiopathic arthritis: a large paediatric rheumatology centre in the USA
Authors: Yue Xiaomeng , Huang Bin , Hincapie Ana L , Wigle Patricia R , Li Yuxiang , Qiu Tingting , Lovell Daniel J , Morgan Esi M , Guo Jeff J 
Published: December 2020

Abstract

Objective
To evaluate the persistence and effectiveness of TNF inhibitors (TNFi) vs non-TNFi among newly diagnosed JIA patients after initiation of biologic DMARD (bDMARD).

Methods
Using longitudinal patient-level data extracted from electronic medical records in a large Midwestern paediatric hospital from 2009 to 2018, we identified JIA patients initiating TNFi and non-TNFi treatment. Treatment effectiveness was assessed based on disease activity. Inverse probability of treatment weighting of propensity score was used to estimate the treatment effectiveness and Kaplan–Meier analyses were conducted to assess persistence.

Results
Of 667 JIA patients, most (92.0%) were prescribed one of the class of TNFi as their initial biologic treatment. Etanercept was the most frequently prescribed (67.1%) treatment, followed by adalimumab (27.5%). Only around 5% of patients were prescribed off-label bDMARDs as their first-course treatment; however, &gt;20% were prescribed off-label biologics as their second-course therapy. Some 7.2% of patients received four or more bDMARDs. The median persistence of the first-course bDMARD is 320 days, with TNFi being significantly longer than the non-TNFi (395 vs 320 days, P = 0.010). The clinical Juvenile Disease Activity Score (cJADAS) reduction of TNFi users (6.6, 95% CI 5.7, 7.5) was significant greater compared with non-TNFi users (3.0, 95% CI 1.5, 4.6, P &lt; 0.0001) at 6-month follow-up visit.

Conclusion
Persistence was significantly longer among patients initiating TNFi as their first biologic therapy than those receiving non-TNFi. Patients receiving TNF therapy had significant greater reduction of cJADAS at the 6-month follow-up visit compared with patients in the non-TNF cohort.
“Let’s Chat”: process evaluation of an intergenerational group chat intervention to increase cancer prevention screening among Vietnamese American families
Authors: Duong Huong T , Hopfer Suellen 
Published: December 2020

Abstract
Vietnamese Americans have a higher rate of cervical and colorectal cancer (CRC) compared to other ethnicities. Increasing CRC screening, Pap testing, and HPV vaccination is critical to preventing disproportionate cancer burden among Vietnamese families. To describe the successes and challenges of implementing a novel intergenerational family group chat intervention that encourages CRC screening, Pap testing, and HPV vaccination. Young adult Family Health Advocates (FHAs) were trained to facilitate online family group chat conversations to encourage cancer screenings. Ten families participated in a 4-week intervention. Data collection included screenshot data of family group chat conversations, family member surveys, and post-intervention FHA interviews. Intervention implementation successes included (a) cultural and language brokering, (b) active co-facilitation by family members to follow up on cancer screenings, (c) high levels of family group chat engagement, (d) high acceptability of intervention among families, and (e) accessibility of intervention curriculum. FHA challenges to implement the intervention included (a) sustaining cancer prevention conversations, (b) comfort with navigating family conversations around cancer screening, (c) relevance for all family members, and (d) missed opportunities for correcting misinformation. Researcher challenges included family recruitment and retention. The intervention made cancer-screening messages more accessible and was well accepted by Vietnamese families. Scaling up the intervention will require (a) training FHAs to monitor family conversations and build confidence in sharing medical accurate messages, (b) segmenting group chats by age and gender, and (c) employing multiple family engagement strategies.