bluuebunny/crossref_metadata_2025_split huggingface dataset:
HD 226766: a hierarchical SB3 system with two twin Am stars
Authors: Catanzaro G , Gangi M , Giarrusso M , Munari M , Leone F 
Published: May 2019

ABSTRACT
In this paper, we present a detailed revision of the orbital parameters and the first quantitative abundance analysis of the spectroscopic triple system HD 226766. By means of a simultaneous fit of the radial velocities of all the three components, we derived precise orbital parameters for the system, in particular inner pair has P(d)  =  31.9187 ± 0.0001, e  =  0.28 ± 0.01, and MA/MB  = 1.03 ± 0.03, while the C component orbits around the inner pair with a period of P(d)  =  1615 ± 59 in a very eccentric orbit (e  =  0.54 ± 0.11). From the fit of the Hβ and Hα profiles, we determined the effective temperatures and surface gravities of each component of the inner pair: Teff  =  8600 ± 500 K and log g  =  3.8 ± 0.2 for HD 226766 A and Teff  =  8500 ± 400 K and log g  =  4.0 ± 0.2 for HD 226766 B. In the hypothesis that component C is a main sequence star (log g  =  4.0) we derived Teff  =  8000 ± 500 K. Rotational velocities have been estimated by modeling the profiles of metallic lines: v sin i  =  13 ± 1 km s−1 for inner pair and v sin i  =  150 ± 20 km s−1 for the C component. We find that the inner pair is heterogeneous from the point of view of the chemical composition: both stars are very similar and show chemical anomalies typical of Am stars. With some hypothesis about the masses of the components, we estimated the orbital inclination angle for the inner binary, i = (47 ± 1)○, and for the outer orbit, i = (54 ± 19)○.
Elucidation of Codon Usage Signatures across the Domains of Life
Authors: Novoa Eva Maria , Jungreis Irwin , Jaillon Olivier , Kellis Manolis 
Published: May 2019

AbstractBecause of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being “synonymous,” these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated “optimal” codons, whereas lowly expressed genes display autocorrelated “nonoptimal” codons.
Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast
Authors: Tusso Sergio , Nieuwenhuis Bart P S , Sedlazeck Fritz J , Davey John W , Jeffares Daniel C , Wolf Jochen B W 
Published: May 2019

AbstractMutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
A long noncoding RNA cluster-based genomic locus maintains proper development and visual function
Authors: Wang Fei , Ren Dalong , Liang Xiaolin , Ke Shengwei , Zhang Bowen , Hu Bing , Song Xiaoyuan , Wang Xiangting 
Published: May 2019

AbstractLong noncoding RNAs (lncRNAs) represent a group of regulatory RNAs that play critical roles in numerous cellular events, but their functional importance in development remains largely unexplored. Here, we discovered a series of previously unidentified gene clusters harboring conserved lncRNAs at the nonimprinting regions in brain (CNIBs). Among the seven identified CNIBs, human CNIB1 locus is located at Chr 9q33.3 and conserved from Danio rerio to Homo sapiens. Chr 9q33.3-9q34.11 microdeletion has previously been linked to human nail-patella syndrome (NPS) which is frequently accompanied by developmental and visual deficiencies. By generating CNIB1 deletion alleles in zebrafish, we demonstrated the requirement of CNIB1 for proper growth and development, and visual activities. Furthermore, we found that the role of CNIB1 on visual activity is mediated through a regulator of ocular development-lmx1bb. Collectively, our study shows that CNIB1 lncRNAs are important for zebrafish development and provides an lncRNA cluster-mediated pathophysiological mechanism for human Chr 9q33.3-9q34.11 microdeletion syndrome.
Proteomic analysis of meningiomas reveals clinically distinct molecular patterns
Authors: Papaioannou Michail-Dimitrios , Djuric Ugljesa , Kao Jennifer , Karimi Shirin , Zadeh Gelareh , Aldape Kenneth , Diamandis Phedias 
Published: May 2019

Abstract

Background
Meningiomas represent one of the most common brain tumors and exhibit a clinically heterogeneous behavior, sometimes difficult to predict with classic histopathologic features. While emerging molecular profiling efforts have linked specific genomic drivers to distinct clinical patterns, the proteomic landscape of meningiomas remains largely unexplored.

Methods
We utilize liquid chromatography tandem mass spectrometry with an Orbitrap mass analyzer to quantify global protein abundances of a clinically well-annotated formalin-fixed paraffin embedded (FFPE) cohort (n = 61) of meningiomas spanning all World Health Organization (WHO) grades and various degrees of clinical aggressiveness.

Results
In total, we quantify 3042 unique proteins comparing patterns across different clinical parameters. Unsupervised clustering analysis highlighted distinct proteomic (n = 106 proteins, Welch’s t-test, P < 0.01) and pathway-level (eg, Notch and PI3K/AKT/mTOR) differences between convexity and skull base meningiomas. Supervised comparative analyses of different pathological grades revealed distinct patterns between benign (grade I) and atypical/malignant (grades II‒III) meningiomas with specific oncogenes enriched in higher grade lesions. Independent of WHO grade, clinically aggressive meningiomas that rapidly recurred (<3 y) had distinctive protein patterns converging on mRNA processing and impaired activation of the matrisome complex. Larger sized meningiomas (>3 cm maximum tumor diameter) and those with previous radiation exposure revealed perturbed pro-proliferative (eg, epidermal growth factor receptor) and metabolic as well as inflammatory response pathways (mitochondrial activity, interferon), respectively.

Conclusions
Our proteomic study demonstrates that meningiomas of different grades and clinical parameters present distinct proteomic profiles. These proteomic variations offer potential future utility in helping better predict patient outcome and in nominating novel therapeutic targets for personalized care.
Strategies to Mitigate Toxicities From Stereotactic Body Radiation Therapy for Spine Metastases
Authors: Schaub Stephanie K , Tseng Yolanda D , Chang Eric L , Sahgal Arjun , Saigal Rajiv , Hofstetter Christoph P , Foote Matthew , Ko Andrew L , Yuh William T C , Mossa-Basha Mahmud , Mayr Nina A , Lo Simon S 
Published: May 2019

Abstract
Improvements in systemic therapy are translating into more patients living longer with metastatic disease. Bone is the most common site of metastasis, where spinal lesions can result in significant pain impacting quality of life and possible neurological dysfunction resulting in a decline in performance status. Stereotactic body radiation therapy (SBRT) of the spine has emerged as a promising technique to provide durable local control, palliation of symptoms, control of oligoprogressive sites of disease, and possibly augment the immune response. SBRT achieves this by delivering highly conformal radiation therapy to allow for dose escalation due to a steep dose gradient from the planning target volume to nearby critical organs at risk. In our review, we provide an in-depth review and expert commentary regarding seminal literature that defined clinically meaningful toxicity endpoints with actionable dosimetric limits and/or clinical management strategies to mitigate toxicity potentially attributable to SBRT of the spine. We placed a spotlight on radiation myelopathy (de novo, reirradiation after conventional external beam radiation therapy or salvage after an initial course of spinal SBRT), plexopathy, vertebral compression fracture, pain flare, esophageal toxicity, myositis, and safety regarding combination with concurrent targeted or immune therapies.
Resection of Myxopapillary Ependymoma of the Filum Terminale: 2-Dimensional Operative Video
Authors: Mastorakos Panagiotis , Lynes John , Maggio Dominic , Quezado Martha M , Nduom Edjah K 
Published: May 2019

Abstract
We present the case of a 48-yr-old female who presented with persistent thigh pain and was found to have a heterogeneous mass caudal to the conus most consistent with a myxopapillary ependymoma. We performed L2-3 laminectomies for tumor resection. For this procedure, we used intraoperative ultrasound as well as neuromonitoring. This video illustrates the gross pathology of a myxopapillary ependymoma, effective circumferential blunt and sharp dissection of the cauda equina from the tumor, and identification, preparation, and sectioning of the filum terminale. This case also underlines the challenges of removing a large myxopapillary ependymoma when motor nerve rootlets are encapsulated in the tumor. In this case, we were obligated to enter the tumor capsule ventrally in order to dissect away cauda equina nerves passing through the tumor. The patient consented to be part of our research study
Flat-lining or seething beneath the surface? Two decades of changing economic inequality in the UK
Authors: Obolenskaya Polina , Hills John 
Published: May 2019

AbstractThis paper analyses what happened to economic inequalities in the United Kingdom in the two decades from 1995–6. In aggregate, inequality changes were unremarkable, especially by comparison with sharp increases in the 1980s. However, over the first decade economic outcomes improved across population groups, while over the second near-stagnation accompanied continuing high inequality. We show that the apparent stability of inequality in this period masked the way in which the nature and depth of economic inequalities changed after the economic crisis, leading to substantial differences between and within groups defined in different ways. Pervasively, younger adults lost out in the second decade compared to older ones. When population groups are defined in other ways (such as region, housing tenure, or ethnicity) patterns are more complex, but with the worst-off in particular groups often being ‘left behind’.
Court-imposed fines as a feature of the homelessness-incarceration nexus: a cross-sectional study of the relationship between legal debt and duration of homelessness in Seattle, Washington, USA
Authors: Mogk Jessica , Shmigol Valerie , Futrell Marvin , Stover Bert , Hagopian Amy 
Published: May 2019

Abstract

Background
Legal system involvement is a policy-driven risk factor for homelessness. Legal financial obligations (LFOs), such as court fees, fines and restitution, can endanger the financial security of those ensnared in the criminal justice system. In this study we measured the effect of incarceration and LFOs on duration of homelessness in Seattle, WA, USA.

Methods
To analyze the relationship between incarceration, debt and duration of homelessness, we interviewed 101 adults experiencing homelessness and living in city-sanctioned encampments and tiny house villages in Seattle, WA in 2017–18. We collected personal housing history, presence and amount of debt, and measures of legal system involvement.

Results
Our respondents experienced homelessness an average of 41 months during the current episode. Nearly two-thirds reported being convicted of a crime, and 78% had been incarcerated. More than 25% reported owing current legal fines. Individuals with legal fine debt experienced 22.9 months of additional homelessness after considering the effects of race, age, and gender.

Conclusion
We confirmed a strong association between homelessness and legal trouble. Among high-income countries, the USA has the highest rates of legal system involvement and the highest rates of homelessness; the relationship between the two may be connected.
Subglottic stenosis and endobronchial disease in granulomatosis with polyangiitis
Authors: Quinn Kaitlin A , Gelbard Alexander , Sibley Cailin , Sirajuddin Arlene , Ferrada Marcela A , Chen Marcus , Cuthbertson David , Carette Simon , Khalidi Nader A , Koening Curry L , Langford Carol A , McAlear Carol A , Monach Paul A , Moreland Larry W , Pagnoux Christian , Seo Philip , Specks Ulrich , Sreih Antoine G , Ytterberg Steven R , Merkel Peter A , Grayson Peter C 
Published: May 2019

Abstract

Objectives
To describe tracheobronchial disease in patients with granulomatosis with polyangiitis (GPA) and evaluate the utility of dynamic expiratory CT to detect large-airway disease.

Methods
Demographic and clinical features associated with the presence of subglottic stenosis (SGS) or endobronchial involvement were assessed in a multicentre, observational cohort of patients with GPA. A subset of patients with GPA from a single-centre cohort underwent dynamic chest CT to evaluate the airways.

Results
Among 962 patients with GPA, SGS and endobronchial disease were identified in 95 (10%) and 59 (6%) patients, respectively. Patients with SGS were more likely to be female (72% vs 53%, P &lt; 0.01), younger at time of diagnosis (36 vs 49 years, P &lt; 0.01), and have saddle-nose deformities (28% vs 10%, P &lt; 0.01), but were less likely to have renal involvement (39% vs 62%, P &lt; 0.01). Patients with endobronchial disease were more likely to be PR3-ANCA positive (85% vs 66%, P &lt; 0.01), with more ENT involvement (97% vs 77%, P &lt; 0.01) and less renal involvement (42% vs 62%, P &lt; 0.01). Disease activity in patients with large-airway disease was commonly isolated to the subglottis/upper airway (57%) or bronchi (32%). Seven of 23 patients screened by dynamic chest CT had large-airway pathology, including four patients with chronic, unexplained cough, discovered to have tracheobronchomalacia.

Conclusion
SGS and endobronchial disease occur in 10% and 6% of patients with GPA, respectively, and may occur without disease activity in other organs. Dynamic expiratory chest CT is a potential non-invasive screening test for large-airway involvement in GPA.
Arthritis self-efficacy beliefs and functioning among osteoarthritis and rheumatoid arthritis patients: a meta-analytic review
Authors: Jackson Todd , Xu Ting , Jia Xiaojun 
Published: May 2019

Abstract

Objectives
The Arthritis Self-Efficacy Scale (ASES) is a widely used self-report measure of beliefs reflecting confidence in one’s capacity to function despite pain and control pain or other symptoms of arthritis. Despite evidence linking higher ASES scores to lower levels of impairment, pain and emotional distress, numerous modest, non-significant associations have also been observed. In this meta-analysis, we evaluated overall associations between ASES scores and adjustment in RA and OA samples as well as potential moderators that may explain the heterogeneity in these associations.

Method
Data from 48 samples that met all 10 inclusion criteria (N = 9222 patients) were subject to analyses.

Results
ASES scores had significant medium average effect sizes with functional impairment, pain severity and emotional distress but substantial heterogeneity was evident for each association. ASES–impairment associations were moderated by the diagnosis, ASES version and ASES subscale content: significantly larger effect sizes were found for studies that included RA patients, used the original 20-item ASES and assessed subscale content reflecting the pursuit of daily activities despite pain (i.e. functional self-efficacy) than for studies based exclusively on OA patients, the eight-item ASES and ASES pain control and other symptom subscales. Relations of ASES scores with pain severity and emotional distress were moderated by ASES version and subscale content, respectively.

Conclusion
The ASES has significant overall associations with key areas of functioning. Moderator analyses of the measure provide empirically grounded suggestions for optimal use of the ASES within OA and RA patient samples.
Increased infection risk in Addison’s disease and congenital adrenal hyperplasia: a primary care database cohort study
Authors: Tresoldi Alberto S. , Sumilo Dana , Perrins Mary , Toulis Konstantinos A. , Prete Alessandro , Reddy Narendra , Wass John A.H. , Arlt Wiebke , Nirantharakumar Krishnarajah 
Published: May 2019

ABSTRACTContextMortality and infection-related hospital admissions are increased in patients with primary adrenal insufficiency (PAI). However, the risk of primary care-managed infections in patients with PAI is unknown.ObjectiveTo estimate infection risk in PAI due to Addison’s disease (AD) and congenital adrenal hyperplasia (CAH) in a primary care setting.DesignRetrospective cohort study using UK data collected from 1995 to 2018.Main outcome measuresIncidence of lower respiratory tract infections (LRTIs), urinary tract infections (UTIs), gastrointestinal infections (GIIs), and prescription counts of antimicrobials in adult PAI patients compared to unexposed controls.ResultsA diagnosis of PAI was established in 1580 AD patients (mean age 51.7 years) and 602 CAH patients (mean age 35.4 years). All AD patients and 42% of CAH patients were prescribed glucocorticoids, most frequently hydrocortisone in AD (82%) and prednisolone in CAH (50%). AD and CAH patients exposed to glucocorticoids, but not CAH patients without glucocorticoid treatment, had a significantly increased risk of LRTIs (adjusted incidence rate ratio AD 2.11 [95% confidence interval 1.64-2.69], CAH 3.23 [1.21-8.61]), UTIs (AD 1.51 [1.29-1.77], CAH 2.20 [1.43-3.34]), and GIIs (AD 3.80 [2.99-4.84], CAH 1.93 [1.06-3.52]). This was mirrored by increased prescription of antibiotics (AD 1.73 [1.69-1.77], CAH 1.77 [1.66-1.89]) and antifungals (AD 1.89 [1.74-2.05], CAH 1.91 [1.50-2.43]).ConclusionsThere is an increased risk of infections and antimicrobial use in PAI in the primary care setting at least partially linked to glucocorticoid treatment. Future studies will need to address whether more physiological glucocorticoid replacement modes could reduce this risk.PrécisUsing data from 1580 AD patients and 602 CAH patients collected in a UK primary care database from 1995 to 2018, we identified increased risk of infections and antimicrobial prescription counts.
Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop
Authors: Shade Ashley , Dunivin Taylor K. , Choi Jinlyung , Teal Tracy K. , Howe Adina C. 
Published: May 2019

AbstractHere, we report our educational approach and learner evaluations of the first five years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State University’s Kellogg Biological Station from 2014-2018. We hope this information will be useful for others who want to organize computing-intensive workshops and encourage quantitative skill development among microbiologists.ImportanceHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A week-long workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, post-doctoral scientists, faculty, and research staff).
Awake hippocampal-prefrontal replay mediates spatial learning and decision making
Authors: Shin Justin D. , Tang Wenbo , Jadhav Shantanu P. 
Published: May 2019

SUMMARYSpatial learning requires remembering and choosing paths to goals. Hippocampal place cells replay spatial paths during immobility in reverse and forward order, offering a potential mechanism. However, how replay mediates both goal-directed learning and memory-guided decision making is unclear. We therefore continuously tracked replay in the same hippocampal-prefrontal ensembles throughout learning of a spatial alternation task. We found that during pauses between behavioral trajectories, awake reverse and forward hippocampal replay consistently mediated an internal cognitive search of all available past and future possibilities, and exhibited opposing learning gradients for prediction of past and future behavioral paths, respectively. Coordinated hippocampal-prefrontal replay mediated recall of correct past paths and selection of future choices leading to reward based on the hippocampal cognitive search, executing spatial working memory rules. Our findings reveal a learning shift from hippocampal reverse-replay-based retrospective evaluation to forward-replay-based prospective planning, with prefrontal filtering of memory-guided paths for learning and decision-making.