bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the Gaia radial velocity sample selection function in its native photometry
Authors: Rybizki Jan , Rix Hans-Walter , Demleitner Markus , Bailer-Jones Coryn A L , Cooper William J 
Published: October 2020

ABSTRACT
The Gaia Data Release 2 (DR2) radial velocity sample (GDR2RVS), which provides six-dimensional phase-space information on 7.2 million stars, is of great value for inferring properties of the Milky Way. Yet a quantitative and accurate modelling of this sample is hindered without knowledge and inclusion of a well-characterized selection function. Here we derive the selection function through estimates of the internal completeness, i.e. the ratio of GDR2RVS sources compared to all Gaia DR2 sources (GDR2all). We show that this selection function or ‘completeness’ depends on basic observables, in particular the apparent magnitude GRVS and colour G − GRP, but also on the surrounding source density and on sky position, where the completeness exhibits distinct small-scale structure. We identify a region of magnitude and colour that has high completeness, providing an approximate but simple way of implementing the selection function. For a more rigorous and detailed description we provide python code to query our selection function, as well as tools and adql queries that produce custom selection functions with additional quality cuts.
Chemical diversity among A–B stars with low rotational velocities: non-LTE abundance analysis
Authors: Mashonkina L , Ryabchikova T , Alexeeva S , Sitnova T , Zatsarinny O 
Published: October 2020

ABSTRACT
We present accurate element abundance patterns based on the non-local thermodynamic equilibrium (non-LTE, NLTE) line formation for 14 chemical elements from He to Nd for a sample of nine A9 to B3-type stars with well-determined atmospheric parameters and low rotational velocities. We constructed new model atom of Zr ii–iii and updated model atoms for Sr ii and Ba ii by implementing the photoionization cross-sections from calculations with the Dirac B-spline R-matrix method. The NLTE abundances of He to Fe in the stars HD 17081, HD 32115, HD 160762, and HD 209459 are found to be consistent with the solar abundances, and HD 73666 being a Blue Straggler does not reveal deviations from chemical composition of the Praesepe cluster. Three of these stars with an effective temperature of lower than 10 500 K have supersolar abundances of Sr, Zr, Ba, and Nd, and our results suggest the presence of a positive correlation between stellar effective temperature and abundance. For each star, enhancement of Ba is higher than that for any other heavy element. We propose that the solar Ba abundance is not representative of the galactic Ba abundance at modern epoch. The status of HD 145788 was not clarified: This star has solar abundances of C to Si and enhancements of Sr to Ba similar to that for superficially normal stars of similar temperature, while Ca, Ti, and Fe are overabundant. The NLTE abundances of Vega support its status of a mild λ Bootis star.
Synthetic line and continuum observations of simulated turbulent clouds: the apparent widths of filaments
Authors: Priestley F D , Whitworth A P 
Published: October 2020

ABSTRACT
Filamentary structures are ubiquitous in observations of real molecular clouds and also in simulations of turbulent, self-gravitating gas. However, making comparisons between observations and simulations is complicated by the difficulty of estimating volume densities observationally. Here, we have post-processed hydrodynamical simulations of a turbulent isothermal molecular cloud, using a full time-dependent chemical network. We have then run radiative transfer models to obtain synthetic line and continuum intensities that can be compared directly with those observed. We find that filaments have a characteristic width of ${\sim }0.1 \, {\rm pc}$, both on maps of their true surface density and on maps of their $850\, {\rm \mu m}$ dust continuum emission in agreement with previous work. On maps of line emission from CO isotopologues, the apparent widths of filaments are typically several times larger because the line intensities are poorly correlated with the surface density. On maps of line emission from dense gas tracers such as N2H+ and HCN, the apparent widths of filaments are ${\la}0.1\, {\rm pc}$. Thus, current observations of molecular-line emission are compatible with the universal $0.1 \, {\rm pc}$ filament width inferred from Herschel observations, provided proper account is taken of abundance, optical depth, and excitation considerations. We find evidence for ${\sim}0.4 \, {\rm km \, s^{-1}}$ radial velocity differences across filaments. These radial velocity differences might be a useful indicator of the mechanism by which a filament has formed or is forming, for example the turbulent cloud scenario modelled here, as against other mechanisms such as cloud–cloud collisions.
A ‘big data’ approach to global freshwater mussel diversity (Bivalvia: Unionoida), with an updated checklist of genera and species
Authors: Graf Daniel L , Cummings Kevin S 
Published: October 2020

ABSTRACTThe objective of this review is to update our previously published checklist of Recent freshwater mussel species and genera (Graf & Cummings, 2007, J. Molluscan Stud.: 291–314) to reflect the new data and research findings that have accumulated over the last decade. The MUSSEL Project Database was developed to synthesize the available taxonomic nomenclature, species ranges and published taxonomic hypotheses on genus–species combinations and synonymy. We have found 4,988 available species-group level nominal species representing 958 valid species in 192 genera worldwide, an increase of 118 species since 2007. The current patterns of species richness are discussed with regard to both taxonomy and geography, as is the general flux in the number of species recognized over time. A checklist is provided herein, with a bibliography to key faunistic and taxonomic references. The full dataset is maintained and updated on the MUSSEL Project Web Site (http://mussel-project.net/).
A novel assay provides insight into tRNAPhe retrograde nuclear import and re-export inS. cerevisiae
Authors: Nostramo Regina T , Hopper Anita K 
Published: October 2020

AbstractIn eukaryotes, tRNAs are transcribed in the nucleus and subsequently exported to the cytoplasm where they serve as essential adaptor molecules in translation. However, tRNAs can be returned to the nucleus by the evolutionarily conserved process called tRNA retrograde nuclear import, before relocalization back to the cytoplasm via a nuclear re-export step. Several important functions of these latter two trafficking events have been identified, yet the pathways are largely unknown. Therefore, we developed an assay in Saccharomyces cerevisiae to identify proteins mediating tRNA retrograde nuclear import and re-export using the unique wybutosine modification of mature tRNAPhe. Our hydrochloric acid/aniline assay revealed that the karyopherin Mtr10 mediates retrograde import of tRNAPhe, constitutively and in response to amino acid deprivation, whereas the Hsp70 protein Ssa2 mediates import specifically in the latter. Furthermore, tRNAPhe is re-exported by Crm1 and Mex67, but not by the canonical tRNA exporters Los1 or Msn5. These findings indicate that the re-export process occurs in a tRNA family-specific manner. Together, this assay provides insights into the pathways for tRNAPhe retrograde import and re-export and is a tool that can be used on a genome-wide level to identify additional gene products involved in these tRNA trafficking events.
MASI: microbiota—active substance interactions database
Authors: Zeng Xian , Yang Xue , Fan Jiajun , Tan Ying , Ju Lingyi , Shen Wanxiang , Wang Yali , Wang Xinghao , Chen Weiping , Ju Dianwen , Chen Yu Zong 
Published: October 2020

Abstract
Xenobiotic and host active substances interact with gut microbiota to influence human health and therapeutics. Dietary, pharmaceutical, herbal and environmental substances are modified by microbiota with altered bioavailabilities, bioactivities and toxic effects. Xenobiotics also affect microbiota with health implications. Knowledge of these microbiota and active substance interactions is important for understanding microbiota-regulated functions and therapeutics. Established microbiota databases provide useful information about the microbiota-disease associations, diet and drug interventions, and microbiota modulation of drugs. However, there is insufficient information on the active substances modified by microbiota and the abundance of gut bacteria in humans. Only ∼7% drugs are covered by the established databases. To complement these databases, we developed MASI, Microbiota—Active Substance Interactions database, for providing the information about the microbiota alteration of various substances, substance alteration of microbiota, and the abundance of gut bacteria in humans. These include 1,051 pharmaceutical, 103 dietary, 119 herbal, 46 probiotic, 142 environmental substances interacting with 806 microbiota species linked to 56 diseases and 784 microbiota–disease associations. MASI covers 11 215 bacteria-pharmaceutical, 914 bacteria-herbal, 309 bacteria-dietary, 753 bacteria-environmental substance interactions and the abundance profiles of 259 bacteria species in 3465 patients and 5334 healthy individuals. MASI is freely accessible at http://www.aiddlab.com/MASI.
Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR)
Authors: Siau Jia Wei , Nonis Samuel , Chee Sharon , Koh Li Quan , Ferrer Fernando J , Brown Christopher J , Ghadessy Farid J 
Published: October 2020

Abstract
Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interacting protein–peptide pair. Escherichia coli cells co-expressing protein–peptide pairs can directly be used in polymerase chain reactions to determine relative interaction strengths by the measurement of amplicon yields. Conditional polymerase activity is further used to link genotype to phenotype of interacting protein–peptide pairs co-expressed in E. coli using the compartmentalized self-replication directed evolution platform. We validate this approach, termed compartmentalized two-hybrid replication, by selecting for high-affinity peptides that bind two model protein partners: SpyCatcher and the large fragment of NanoLuc luciferase. We further demonstrate directed co-evolution by randomizing both protein and peptide components of the SpyCatcher–SpyTag pair and co-selecting for functionally interacting variants.
Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations
Authors: Giardine Belinda M , Joly Philippe , Pissard Serge , Wajcman Henri , K. Chui David H , Hardison Ross C , Patrinos George P 
Published: October 2020

Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is a widely-used locus-specific database (LSDB) launched 20 years ago by a multi-center academic effort to provide timely information on the numerous genomic variants leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Here, we report several advances for the database. We made clinically relevant updates of HbVar, implemented as additional querying options in the HbVar query page, allowing the user to explore the clinical phenotype of compound heterozygous patients. We also made significant improvements to the HbVar front page, making comparative data querying, analysis and output more user-friendly. We continued to expand and enrich the regular data content, involving 1820 variants, 230 of which are new entries. We also increased the querying potential and expanded the usefulness of HbVar database in the clinical setting. These several additions, expansions and updates should improve the utility of HbVar both for the globin research community and in a clinical setting.
Constitutional Conventions and the Judiciary
Authors: Stephenson Scott 
Published: October 2020

Abstract
Analyses of constitutional conventions tend not to include those conventions that concern relations between the judiciary and other arms of government. The focus is generally on the conventions concerning the monarch, executive and legislature. This article argues that a study of the constitutional conventions relating to the judiciary reveals three insights about the nature of constitutional conventions and the nature of the judiciary. First, significant aspects of the judiciary’s authority, independence and impartiality are often secured by means of constitutional convention. Second, these conventions help understand the simultaneous strength and fragility of the judiciary’s constitutional position. Third, they highlight that, contrary to suggestions in the literature on democratic decay, it is not always problematic for constitutional conventions to be modified or even destroyed. To illustrate these insights, the article compares the executive’s duty to defend the judiciary from public attack in Australia, the UK and the United States.
Incidence of extra-articular manifestations in ankylosing spondylitis, psoriatic arthritis and undifferentiated spondyloarthritis: results from a national register-based cohort study
Authors: Bengtsson Karin , Forsblad-d'Elia Helena , Deminger Anna , Klingberg Eva , Dehlin Mats , Exarchou Sofia , Lindström Ulf , Askling Johan , Jacobsson Lennart T H 
Published: October 2020

Abstract

Objectives
To estimate the incidence and strength of association of extra-articular manifestations [EAMs, here: anterior uveitis (AU), IBD and psoriasis] in patients with AS, undifferentiated SpA (uSpA) and PsA, compared with controls.

Methods
Three mutually exclusive cohorts of patients aged 18–69 years with AS (n = 8517), uSpA (n = 10 245) and PsA (n = 22 667) were identified in the Swedish National Patient Register 2001–2015. Age-, sex- and geography-matched controls were identified from the Swedish Population Register. Follow-up began 1 January 2006, or six months after the first SpA diagnosis, whichever occurred later, and ended at the first date of the EAM under study, death, emigration, 70 years of age, and 31 December 2016. Incidence rates (IRs) and incidence rate ratios were calculated for each EAM, and stratified by sex and age.

Results
Incidence rate ratios for incident AU, IBD and psoriasis were significantly increased in AS (20.2, 6.2, 2.5), uSpA (13.6, 5.7, 3.8) and PsA (2.5, 2.3, n.a) vs controls. Men with AS and uSpA had significantly higher IRs per 1000 person-years at risk for incident AU than women with AS (IR 15.8 vs 11.2) and uSpA (IR 10.1 vs 6.0), whereas no such sex difference was demonstrated in PsA or for the other EAMs.

Conclusions
AU, followed by IBD and psoriasis, is the EAM most strongly associated with AS and uSpA. Among the SpA subtypes, AS and uSpA display a largely similar pattern of EAMs, whereas PsA has a considerably weaker association with AU and IBD.
Procedure-specific and patient-specific pain management for ambulatory surgery with emphasis on the opioid crisis
Authors: Raeder Johan 
Published: October 2020

Purpose of review
Postoperative pain is frequent while, on the other hand, there is a grooving general concern on using effective opioid pain killers in view of the opioid crisis and significant incidence of opioid abuse. The present review aims at describing nonopioid measures in order to optimize and tailor perioperative pain management in ambulatory surgery.

Recent findings
Postoperative pain should be addressed both preoperatively, intraoperatively and postoperatively. The management should basically be multimodal, nonopioid and procedure-specific. Opioids should only be used when needed on top of multimodal nonopioid prophylaxis, and then limited to a few days at maximum, unless strict control is applied. The individual patient should be screened preoperatively for any risk factors for severe postoperative pain and/or any abuse potential.

Summary
Basic multimodal analgesia should start preoperatively or peroperatively and include paracetamol, cyclo-oxygenase (COX)-2 specific inhibitor or conventional nonsteroidal anti-inflammatory drug (NSAID) and in most cases dexamethasone and local anaesthetic wound infiltration. If any of these basic analgesics are contraindicated or there is an extra risk of severe postoperative pain, further measures may be considered: nerve-blocks or interfascial plane blocks, gabapentinnoids, clonidine, intravenous lidocaine infusion or ketamine infusion. In the abuse-prone patient, a preferably nonopioid perioperative approach should be aimed at.
Association Between Symbolic Play and Language: A Comparison Between Typically Developing Children and Children with Down Syndrome
Authors: Joginder Singh Susheel , Gan Brenda , Chu Shin Ying 
Published: October 2020

ABSTRACT:

Objective:
Language and symbolic play require the same underlying symbolic ability and develop parallel to one another. The aim of this study was to determine the association between symbolic play and vocabulary in typically developing children and children with Down syndrome in Malaysia.

Methods:
Twenty-five typically developing children and 25 children with Down syndrome aged between 12 and 36 months were involved in this study. They were recruited from an early intervention center and various kindergartens from the West Coast of Peninsular Malaysia. Their play skills were assessed using the Symbolic Play Test Second Edition, and information about their vocabulary was obtained through the MacArthur Bates Communicative Development Inventories that was filled out by their parents.

Results:
There was a significant difference in the vocabulary and symbolic play scores of children with Down syndrome compared with typically developing children. There was also a positive correlation between symbolic play scores and receptive and expressive vocabulary scores for both groups of children.

Conclusion:
When providing intervention, speech-language pathologists need to promote the development of symbolic play in addition to language, given the association between the two. They should also look into introducing an augmentative and alternative communication system to the children who demonstrate age-appropriate symbolic play skills but have trouble with symbolic language production.
Poor Graft and Patient Survival After Liver Transplantation in Sarcoidosis
Authors: Thuluvath Avesh J. , Savva Yulia , Chen Po-Hung 
Published: October 2020

Goals and Background:
There are limited data on post-liver transplantation (LT) outcomes of patients with sarcoidosis.

Study:
We examined the clinical characteristics and post-LT outcomes of patients with sarcoidosis using the United Network for Organ Sharing database from 1985 to 2016 and compared them to patients (entire cohort as well as age, gender, and year of LT-matched counterparts) with primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). For the matched design, a conditional logistic regression was used for categorical variables and marginal generalized estimating equation regression models for continuous variables. Survival functions were constructed using the Kaplan-Meier estimator.

Results:
A total of 206 patients with sarcoidosis, transplanted during the study period, were compared with 3933 patients with PBC and 5323 with PSC. In total, 197 patients with sarcoidosis were compared with 576 with PBC and 576 with PSC in the 1:3 matched analysis. The sarcoidosis group had a higher proportion of blacks (53.3%) and a higher prevalence of obesity and type II diabetes mellitus. The graft and patient survival for sarcoidosis patients were lower when compared with unmatched PBC and PSC patients. The results remained unchanged in the matched analysis. At 5-year, patient survival was ~15% lower for the sarcoidosis group when compared with PBC and PSC. In multivariate analysis using matched data, hazard ratios (HRs) for graft (HR=1.68, 95% confidence interval=1.03-2.75, P=0.04), and patient (HR=2.01, confidence interval=1.22-3.34, P<0.01) survival were higher for sarcoidosis.

Conclusions:
Patients who underwent LT for sarcoidosis had a lower graft and patient survival when compared with those with PBC or PSC. That being said, 66% of patients survived 5 years after transplantation, suggesting that LT is an acceptable option in this population.
The interconnection between lipoprotein(a), lipoprotein(a) cholesterol and true LDL-cholesterol in the diagnosis of familial hypercholesterolemia
Authors: Yeang Calvin , Willeit Peter , Tsimikas Sotirios 
Published: October 2020

Purpose of review
Elevated levels of lipoprotein(a) [Lp(a)] are present in 30–50% of patients with familial hypercholesterolemia. The contribution of Lp(a) towards risk stratification of patients with familial hypercholesterolemia has been recently recognized, with studies showing a significantly worse prognosis if Lp(a) is elevated. However, the role of elevated Lp(a) in diagnosis of familial hypercholesterolemia is less well defined or accepted.

Recent findings
An important confounder in the diagnosis of familial hypercholesterolemia is the significant contribution of the cholesterol content on Lp(a) (Lp(a)-C) in individuals with elevated Lp(a). Because Lp(a)-C is incorporated into all clinical LDL-C measurements, it can contribute significantly to the cholesterol threshold diagnostic criteria for familial hypercholesterolemia used in most clinical algorithms.

Summary
In this review, we discuss the interrelationship of Lp(a), Lp(a)-C and correct LDL-C in the diagnosis and prognosis of familial hypercholesterolemia. Future studies of accurately measuring correct LDL-C or in using apoB-100 and Lp(a) criteria may overcome the limitations of using estimated LDL-C in the diagnosis of familial hypercholesterolemia in individuals with concomitant elevation of Lp(a).
Predictors of surgical management for paediatric orbital subperiosteal abscesses
Authors: Appachi Swathi , Bedwell Joshua R. 
Published: October 2020

Purpose of review
Many paediatric orbital subperiosteal abscesses (SPA) are effectively managed conservatively with systemic antibiotics, but surgical drainage is required in some patients. This review aims to summarize the current literature to determine predictors of surgical intervention.

Recent findings
Nearly all the data regarding this topic come from analysis of retrospective case series. There is consensus that large volume SPAs require surgical drainage; however, the cutoff for volume differs between studies. Proptosis more than 5 mm, superior location of SPA and patient age more than 9 years are also all factors that may predispose towards surgical treatment.

Summary
A conservative approach may be trialled in younger patients with medial, smaller volume SPAs. Larger volume SPA, presence of proptosis, superior location of SPA and patient age more than 9 years should lower the threshold for considering surgical intervention. Given that many studies have been retrospective, future studies should be prospective and specifically aim to determine a cutoff for SPA volume.