bluuebunny/crossref_metadata_2025_split huggingface dataset:
via machinae: Searching for stellar streams using unsupervised machine learning
Authors: Shih David , Buckley Matthew R , Necib Lina , Tamanas John 
Published: November 2021

ABSTRACT
We develop a new machine learning algorithm, via machinae, to identify cold stellar streams in data from the Gaia telescope. via machinae is based on ANODE, a general method that uses conditional density estimation and sideband interpolation to detect local overdensities in the data in a model agnostic way. By applying ANODE to the positions, proper motions, and photometry of stars observed by Gaia, via machinae obtains a collection of those stars deemed most likely to belong to a stellar stream. We further apply an automated line-finding method based on the Hough transform to search for line-like features in patches of the sky. In this paper, we describe the via machinae algorithm in detail and demonstrate our approach on the prominent stream GD-1. Though some parts of the algorithm are tuned to increase sensitivity to cold streams, the via machinae technique itself does not rely on astrophysical assumptions, such as the potential of the Milky Way or stellar isochrones. This flexibility suggests that it may have further applications in identifying other anomalous structures within the Gaia data set, for example debris flow and globular clusters.
A comparison of approximate non-linear Riemann solvers for Relativistic MHD
Authors: Mattia G , Mignone A 
Published: November 2021

ABSTRACT
We compare a particular selection of approximate solutions of the Riemann problem in the context of ideal relativistic magnetohydrodynamics. In particular, we focus on Riemann solvers not requiring a full eigenvector structure. Such solvers recover the solution of the Riemann problem by solving a simplified or reduced set of jump conditions, whose level of complexity depends on the intermediate modes that are included. Five different approaches – namely the HLL, HLLC, HLLD, HLLEM, and GFORCE schemes – are compared in terms of accuracy and robustness against one – and multidimensional standard numerical benchmarks. Our results demonstrate that – for weak or moderate magnetizations – the HLLD Riemann solver yields the most accurate results, followed by HLLC solver(s). The GFORCE approach provides a valid alternative to the HLL solver being less dissipative and equally robust for strongly magnetized environments. Finally, our tests show that the HLLEM Riemann solver is not cost-effective in improving the accuracy of the solution and reducing the numerical dissipation.
Three aspects of the radius-to-frequency mapping in fast radio bursts
Authors: Tong H , Liu J , Wang H G , Yan Z 
Published: November 2021

ABSTRACT
We have explored the radius-to-frequency mapping further in cases of fast radio bursts (FRBs). We present an analytical treatment of Lyutikov (2020, ApJ, 889, 135). We obtain the frequency dependence of the drifting rate and the drifting time-scale. The aberration effect and the twist of the magnetic field lines can result in drifting in both directions. For one FRB, the burst width is larger at a lower frequency, according to the radius-to-frequency mapping. For the FRB population, the magnetic fields of the repeaters might be larger than those of the non-repeaters. Then, according to the radius-to-frequency mapping, the burst widths of the repeaters will be wider than those of the apparent non-repeaters. If a similar window function (or emission cones) as for pulsars and magnetars is also at work in the case of FRBs, then the window function might explain the single or multiple components of FRB profiles. The modelling of the radius-to-frequency mapping is, to some degree, independent of the underlying radio emission mechanism.
Dynamical ejecta of neutron star mergers with nucleonic weak processes I: nucleosynthesis
Authors: Kullmann I , Goriely S , Just O , Ardevol-Pulpillo R , Bauswein A , Janka H-T 
Published: November 2021

ABSTRACT
We present a coherent study of the impact of neutrino interactions on the r-process element nucleosynthesis and the heating rate produced by the radioactive elements synthesized in the dynamical ejecta of neutron star–neutron star (NS–NS) mergers. We have studied the material ejected from four NS–NS merger systems based on hydrodynamical simulations which handle neutrino effects in an elaborate way by including neutrino equilibration with matter in optically thick regions and re-absorption in optically thin regions. We find that the neutron richness of the dynamical ejecta is significantly affected by the neutrinos emitted by the post-merger remnant, in particular when compared to a case neglecting all neutrino interactions. Our nucleosynthesis results show that a solar-like distribution of r-process elements with mass numbers $A \gtrsim 90$ is produced, including a significant enrichment in Sr and a reduced production of actinides compared to simulations without inclusion of the nucleonic weak processes. The composition of the dynamically ejected matter as well as the corresponding rate of radioactive decay heating are found to be rather independent of the system mass asymmetry and the adopted equation of state. This approximate degeneracy in abundance pattern and heating rates can be favourable for extracting the ejecta properties from kilonova observations, at least if the dynamical component dominates the overall ejecta. Part II of this work will study the light curve produced by the dynamical ejecta of our four NS merger models.
Expression Atlas update: gene and protein expression in multiple species
Authors: Moreno Pablo , Fexova Silvie , George Nancy , Manning Jonathan R , Miao Zhichiao , Mohammed Suhaib , Muñoz-Pomer Alfonso , Fullgrabe Anja , Bi Yalan , Bush Natassja , Iqbal Haider , Kumbham Upendra , Solovyev Andrey , Zhao Lingyun , Prakash Ananth , García-Seisdedos David , Kundu Deepti J , Wang Shengbo , Walzer Mathias , Clarke Laura , Osumi-Sutherland David , Tello-Ruiz Marcela Karey , Kumari Sunita , Ware Doreen , Eliasova Jana , Arends Mark J , Nawijn Martijn C , Meyer Kerstin , Burdett Tony , Marioni John , Teichmann Sarah , Vizcaíno Juan Antonio , Brazma Alvis , Papatheodorou Irene 
Published: November 2021

Abstract
The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from &gt;4500 expression studies from &gt;65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.
Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands
Authors: Swain Monalisa , Ageeli Abeer A , Kasprzak Wojciech K , Li Mi , Miller Jennifer T , Sztuba-Solinska Joanna , Schneekloth John S , Koirala Deepak , Piccirili Joseph , Fraboni Americo J , Murelli Ryan P , Wlodawer Alexander , Shapiro Bruce A , Baird Nathan , Le Grice Stuart F J 
Published: November 2021

Abstract
Cellular and virus-coded long non-coding (lnc) RNAs support multiple roles related to biological and pathological processes. Several lncRNAs sequester their 3′ termini to evade cellular degradation machinery, thereby supporting disease progression. An intramolecular triplex involving the lncRNA 3′ terminus, the element for nuclear expression (ENE), stabilizes RNA transcripts and promotes persistent function. Therefore, such ENE triplexes, as presented here in Kaposi's sarcoma-associated herpesvirus (KSHV) polyadenylated nuclear (PAN) lncRNA, represent targets for therapeutic development. Towards identifying novel ligands targeting the PAN ENE triplex, we screened a library of immobilized small molecules and identified several triplex-binding chemotypes, the tightest of which exhibits micromolar binding affinity. Combined biophysical, biochemical, and computational strategies localized ligand binding to a platform created near a dinucleotide bulge at the base of the triplex. Crystal structures of apo (3.3 Å) and ligand-soaked (2.5 Å) ENE triplexes, which include a stabilizing basal duplex, indicate significant local structural rearrangements within this dinucleotide bulge. MD simulations and a modified nucleoside analog interference technique corroborate the role of the bulge and the base of the triplex in ligand binding. Together with recently discovered small molecules that reduce nuclear MALAT1 lncRNA levels by engaging its ENE triplex, our data supports the potential of targeting RNA triplexes with small molecules.
Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis
Authors: Guest Thomas , Haycocks James R J , Warren Gemma Z L , Grainger David C 
Published: November 2021

Abstract
Many bacteria use cyclic dimeric guanosine monophosphate (c-di-GMP) to control changes in lifestyle. The molecule, synthesized by proteins having diguanylate cyclase activity, is often a signal to transition from motile to sedentary behaviour. In Vibrio cholerae, c-di-GMP can exert its effects via the transcription factors VpsT and VpsR. Together, these proteins activate genes needed for V. cholerae to form biofilms. In this work, we have mapped the genome-wide distribution of VpsT in a search for further regulatory roles. We show that VpsT binds 23 loci and recognises a degenerate DNA palindrome having the consensus 5′-W−5R−4[CG]−3Y−2W−1W+1R+2[GC]+3Y+4W+5-3′. Most genes targeted by VpsT encode functions related to motility, biofilm formation, or c-di-GMP metabolism. Most notably, VpsT activates expression of the vpvABC operon that encodes a diguanylate cyclase. This creates a positive feedback loop needed to maintain intracellular levels of c-di-GMP. Mutation of the key VpsT binding site, upstream of vpvABC, severs the loop and c-di-GMP levels fall accordingly. Hence, as well as relaying the c-di-GMP signal, VpsT impacts c-di-GMP homeostasis.
Development of a new ultrasound scoring system to evaluate glandular inflammation in Sjögren’s syndrome: an OMERACT reliability exercise
Authors: Hočevar Alojzija , Bruyn George A , Terslev Lene , De Agustin Juan Jose , MacCarter Daryl , Chrysidis Stavros , Collado Paz , Dejaco Christian , Fana Viktoria , Filippou Georgios , Finzel Stephanie , Gandjbakhch Frederique , Hanova Petra , Hammenfors Daniel , Hernandez-Diaz Cristina , Iagnocco Annamaria , Mortada Mohamed Atia , Inanc Nevsun , Naredo Esperanza , Ohrndorf Sarah , Perko Nejc , Schmidt , Wolfgang A , Tamborrini Giorgio , Tomšič Matija , Chary-Valckenaere Isabelle , Zabotti Alen , Keen Helen I , Pineda Carlos , D’Agostino Maria-Antonietta , Jousse-Joulin Sandrine 
Published: November 2021

Abstract

Objective
The aim of this exercise from the OMERACT Ultrasound subgroup on Sjögren’s syndrome was to develop and assess the reliability of a consensus-based semiquantitative colour Doppler US scoring system for pathologic salivary gland vascularization in patients with primary Sjögren's syndrome (pSS).

Methods
Using the Delphi method, a colour Doppler semiquantitative scoring system for vascularization of bilateral parotid and submandibular glands was developed and tested in static images and on patients (9 pSS patients and 9 sonographers). Intra-reader and inter-reader reliability of grading the salivary glands were computed by weighted Cohen and Light’s kappa analysis, respectively.

Results
The consensus-based semiquantitative score was: grade 0, no visible vascular signals; grade 1, focal, dispersed vascular signals; grade 2, diffuse vascular signals detected in &lt;50% of the gland; grade 3, diffuse vascular signals in &gt;50% of the gland. In static images, the intra- and inter-reader reliability showed excellent kappa values (95% CI) of 0.90 (0.87, 0.93) and 0.80 (0.74, 0.84), respectively, for all four salivary glands together. In patients, the intra- and inter-reader reliability for all four salivary glands together was kappa = 0.84 (0.73, 0.92) and 0.70 (0.64, 0.76), respectively.

Conclusion
The consensus-based colour Doppler US scoring for the evaluation of salivary gland vascularization in pSS showed a good inter-reader reliability and excellent intra-reader reliability in static images and in patients. The clinical application of the developed scoring system should be tested in clinical settings.
Persistent Use of Prescription Opioids Following Lumbar Spine Surgery
Authors: Holmberg Siril T. , Fredheim Olav M.S. , Skurtveit Svetlana , Salvesen Øyvind O. , Nygaard Øystein P. , Gulati Agnete M. , Solberg Tore K. , Gulati Sasha 
Published: November 2021

Study Design.
Prospective pharmacoepidemiological study.

Objective.
To investigate the use of prescription opioids 2 years following degenerative lumbar spine surgery.

Summary of Background Data.
There are limited data providing details to evaluate patterns of opioid use. The number of patients is often limited and data on opioid use following some of the most common surgical procedures are lacking.

Methods.
Data from the Norwegian Registry for Spine Surgery and the Norwegian Prescription Database were linked on an individual level. The primary outcome measure was persistent opioid use the second year after surgery. Functional disability
was measured with the Oswestry disability index (ODI). Study participants were operated between 2007 and 2017.

Results.
Among 32,886 study participants, 2754 (8.4%) met criteria for persistent opioid use the second year after surgery. Among persistent opioid users in the second year after surgery, 64% met the criteria for persistent opioid use the year preceding surgery. Persistent opioid use the year preceding surgery (odds ratio [OR] 31.10, 95% confidence interval [CI] 26.9–36.0, P
= 0.001), use of high doses of benzodiazepines (OR 1.62, 95% CI 1.30–2.04, P
= 0.001), and use of high doses of z-hypnotics (OR 1.90, 95% CI 1.58–2.22, P
= 0.001) the year before surgery were associated with increased risk of persistent opioid use the second year after surgery. A higher ODI score at 1 year was observed in persistent opioid users compared with non-persistent users (41.5 vs. 18.8 points) and there was a significant difference in ODI change (–13.7 points). Patients with persistent opioid use in the year preceding surgery were less likely to achieve a minimal clinically important ODI change at 1 year compared with non-persistent users (37.7% vs. 52.6%, P
= 0.001).

Conclusion.
Patients with or at risk of developing persistent opioid should be identified and provided counseling and support to taper off opioid treatment.

Level of Evidence: 2
Disc and Vertebral Body Morphology From Birth to Adulthood
Authors: de Reuver Steven , Costa Lorenzo , van Rheenen Hanna , Tabeling Casper S. , Lemans Justin V.C. , Schlösser Tom P.C. , Kruyt Moyo C. , van Stralen Marijn , Castelein René M. 
Published: November 2021

Study Design.
Cross-sectional.

Objective.
The aim of this study was to describe the morphology of intervertebral discs and vertebral bodies during growth in asymptomatic children and adolescents.

Summary of Background Data.
Earlier studies demonstrated that spinal growth occurs predominantly in vertebral bodies. This axiom introduced a vertebral-body-focus for unravelling etiological questions and achieve growth-modulation in young spinal deformity patients. Recent studies show the importance of the intervertebral discs in the early phases and possible etiology of pediatric spinal deformities. There is presently a paucity of 3D morphometric data of spinal elements during growth.

Methods.
A database of 298 patients aged 0 to 21 that have received a computed tomography scan for indications not related to the spine was analyzed. Custom made software was used to semi-automatically measure intervertebral disc and vertebral body morphology, corrected for orientation in all 3 planes.

Results.
Vertebral body height increased from birth up to adulthood, from 4-to-14 mm in the cervical, 6 to 20 mm in the thoracic, and 9 to 28 mm in the lumbar spine. This increase was 0.70 mm/year in males, more pronounced than females with 0.62 mm/year (P = 0.001). Lumbar discs increased throughout growth from 4.4 to 9.0 mm, whereas thoracic discs only increased from 3.5 to 4.9 mm at age 4 and remained stable afterwards, similarly for cervical discs. The disc transverse surface area increased greatly and consistently throughout growth. Disc slenderness was stable in the lumbar spine during growth, but decreased in the thoracic and cervical spine. Overall, discs were more slender in females, especially around early adolescence.

Conclusion.
The spine grows predominantly in the vertebral bodies. Thoracic discs increase in height only during the first years, whereas the transverse surface area continues to increase throughout growth, thus discs slenderness decreases. Relatively, female discs remained slenderer around growth-spurt. These measurements may assist future studies on the role of disc morphology in the etiology and treatment of spinal deformity.

Level of Evidence: 4
Turner syndrome with Xp deletions and rare endometrial abnormalities
Authors: Liang Lei , Mei Libin , Shi Yingying , Huang Lingling , Su Zhiying , Zeng Yu , Gao Haijie , He Xuemei , Huang Hui , Huang Yanru , Li Ping , Chen Jing 
Published: November 2021

Abstract

Rationale:
Turner syndrome (TS) is a genetic disorder associated with abnormalities of the X chromosome related to ovarian function, but whether it is associated with endometrial abnormalities is still not clear.

Patient concerns:
We report the case of a 26-year-old Han Chinese woman with TS and Xp11.2 deletion, presenting with short final stature, ovarian hypofunction, unexplained cystic dilatation of the entire endometrium, and endometrial thickening.

Diagnoses:
The patient was diagnosed with chromosome Xp11.2 deletion through cytogenetic analysis and ultrasonic and endometrial pathology.

Interventions:
The patient was treated with conventional in vitro fertilization preimplantation genetic testing for 1 cycle.

Outcomes:
Cytogenetic examination showed karyotype 45, X, del (X) del (p11, 2). Ultrasonic examination showed uneven endometrium thickness and a full-stage cystic dilation echo. After 1 cycle of in vitro fertilization treatment, 4 eggs were obtained without forming an available embryo.

Lessons:
To our knowledge, the present case is the first report of a patient with TS with Xp deletions and ultrasound imaging endometrial abnormalities. Our findings expand the phenotypic spectrum of TS and may provide a reference for other clinicians.
High prevalence of Chlamydia trachomatis infection among women attending STD and gynecology clinics in Jiangsu province, China
Authors: Hu Haiyang , Zhou Ying , Shi Lingen , Lu Jing , Zhang Zhi , Xu Xiaoqin , Huan Xiping , Fu Gengfeng 
Published: November 2021

Abstract
Epidemics of Chlamydia trachomatis (CT) infection among women are major global public health concerns. This study examined the prevalence of CT infection and associated factors among women attending sexually transmitted disease (STD) and gynecology clinics in Jiangsu province, China.
A cross-sectional survey was conducted among women attending STD and gynecology clinics in the province during 2018 to 2019. Socio-demographic and behavioral information were collected through face-to-face questionnaire survey. Cervical swab specimens were collected to test for CT. Chi square tests were used to compare differences in CT prevalence between subgroups of characteristics. Multivariate logistic regression analysis was used to identify factors associated with CT infection.
A total of 2664 participants were enrolled. The prevalence of CT infection was 16.6% (95% confidence interval: 15.0%–18.1%). Of those, CT prevalence among participants from STD clinics (19.4%) and South Jiangsu (18.5%) were higher. Female outpatients who were service personnel (adjusted odds ratio [aOR] = 1.667, P = .004) or farmers (aOR = 1.593, P = .039), lived in South Jiangsu (aOR = 1.796, P = .004), and were from STD clinics (aOR = 1.608, P = .022) were more likely to infect CT.
Our study showed a high prevalence of CT infection among women attending STD and gynecology clinics in Jiangsu province, China. CT screening, surveillance and treatment promotion should therefore be of top priority on the CT prevention agenda.
The application value of contrast-enhanced computed tomography in cervical lymph node metastasis of oral carcinomas
Authors: Zhang Hao , Yang Shou-Kang , Jiang Xiao-Wen , Deng Guo-Lei , Li Kun-Qin , Long Yu-Fang 
Published: November 2021

Abstract

Background:
Oral carcinomas is a concerning condition around the world. Globally, it is the 11th most common form of cancer. Over 90% of oral carcinomas are squamous cell carcinomas. Smoking, tobacco intake, smokeless tobacco (snuff or chewing tobacco), excessive sunlight exposure, alcohol, betel nut consumption, human papillomavirus, and reverse end smoking are the most common causes of oral carcinomas. Oral carcinomas are prone to neck lymph mode metastasis, which has an impact on the prognosis of patients and the five-year survival rate. Thus, precise lymph node metastasis and staging of oral carcinomas are critical. With the development of nuclear medicine and molecular imaging, an increasing number of studies have found that Contrast-Enhanced Computed Tomography (CECT) has high diagnostic value for tumors.

Methods and analyses:
The reviewers will conduct a thorough search for related literature in 6 online databases, including The Cochrane Library, PubMed, WanFang database, Web of Science, Chinese biomedical literature database, and the China National Knowledge Infrastructure. The authors will obtain full text of studies deemed to be eligible to extract and synthesize data. The present systematic review will be reported in accordance with the Preferred Reporting Project (PRISMA-P) of the 2015 System Review and Meta-Analysis Protocol.

Results:
The present systematic analysis will pool the results of individual studies to assess the value of CECT in cervical lymph node metastasis of oral carcinomas.

Conclusion:
The results in the proposed research will determine whether CECT is an efficient diagnostic method for cervical lymph node metastasis of oral carcinomas.

Ethics and dissemination:
This study will utilize secondary data from pre-published studies. Therefore, an ethical clearance is not required. The research outcomes shall be disseminated in conference reports and peer-reviewed publications.

OSF registration number:
Oct 13, 2021.osf.io/k5nr9. (https://osf.io/k5nr9/).