bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring the total infrared light from galaxy clusters at z = 0.5–1.6: connecting stellar populations to dusty star formation
Authors: Alberts Stacey , Lee Kyoung-Soo , Pope Alexandra , Brodwin Mark , Chiang Yi-Kuan , McKinney Jed , Xue Rui , Huang Yun , Brown Michael , Dey Arjun , Eisenhardt Peter R M , Jannuzi Buell T , Popescu Roxana , Ramakrishnan Vandana , Stanford Spencer A , Weiner Benjamin J 
Published: October 2020

ABSTRACT
Massive galaxy clusters undergo strong evolution from z ∼ 1.6 to z ∼ 0.5, with overdense environments at high-z characterized by abundant dust-obscured star formation and stellar mass growth which rapidly give way to widespread quenching. Data spanning the near- to far-infrared (IR) can directly trace this transformation; however, such studies have largely been limited to the massive galaxy end of cluster populations. In this work, we present ‘total light’ stacking techniques spanning $3.4\!-\!500\, \mu$m aimed at revealing the total cluster emission, including low-mass members and potential intracluster dust. We detail our procedures for WISE, Spitzer, and Herschel imaging, including corrections to recover the total stacked emission in the case of high fractions of detected galaxies. We apply our techniques to 232 well-studied log$\, M_{200}/\mathrm{M}_{\odot }\sim 13.8$ clusters in multiple redshift bins, recovering extended cluster emission at all wavelengths. We measure the averaged IR radial profiles and spectral energy distributions (SEDs), quantifying the total stellar and dust content. The near-IR profiles are well described by an NFW model with a high (c ∼ 7) concentration. Dust emission is similarly concentrated, albeit suppressed at $r\lesssim 0.3\,$Mpc. The measured SEDs lack warm dust, consistent with the colder SEDs of low-mass galaxies. We derive total stellar masses consistent with the theoretical Mhalo−M⋆ relation and specific star formation rates that evolve strongly with redshift, echoing that of log$\, M_{\star }/\mathrm{M}_{\odot }\gtrsim 10$ cluster galaxies. Separating out the massive population reveals the majority of cluster far-IR emission ($\sim 70\!-\!80{{\ \rm per\ cent}}$) is provided by the low-mass constituents, which differs from field galaxies. This effect may be a combination of mass-dependent quenching and excess dust in low-mass cluster galaxies.
Prestellar grain-surface origins of deuterated methanol in comet 67P/Churyumov–Gerasimenko
Authors: Drozdovskaya Maria N , Schroeder I Isaac R H G , Rubin Martin , Altwegg Kathrin , van Dishoeck Ewine F , Kulterer Beatrice M , De Keyser Johan , Fuselier Stephen A , Combi Michael 
Published: October 2020

ABSTRACT
Deuterated methanol is one of the most robust windows astrochemists have on the individual chemical reactions forming deuterium-bearing molecules and the physicochemical history of the regions where they reside. The first-time detection of mono- and di-deuterated methanol in a cometary coma is presented for comet 67P/Churyumov–Gerasimenko using Rosetta–ROSINA data. D-methanol (CH3OD and CH2DOH combined) and D2-methanol (CH2DOD and CHD2OH combined) have an abundance of 5.5 ± 0.46 and 0.00069 ± 0.00014 per cent relative to normal methanol. The data span a methanol deuteration fraction (D/H ratio) in the 0.71−6.6 per cent range, accounting for statistical corrections for the location of D in the molecule and including statistical error propagation in the ROSINA measurements. It is argued that cometary CH2DOH forms from CO hydrogenation to CH3OH and subsequent H–D substitution reactions in CH3–R. CHD2OH is likely produced from deuterated formaldehyde. Meanwhile, CH3OD and CH2DOD could form via H–D exchange reactions in OH–R in the presence of deuterated water ice. Methanol formation and deuteration is argued to occur at the same epoch as D2O formation from HDO, with formation of mono-deuterated water, hydrogen sulphide, and ammonia occurring prior to that. The cometary D-methanol/methanol ratio is demonstrated to agree most closely with that in prestellar cores and low-mass protostellar regions. The results suggest that cometary methanol stems from the innate cold (10–20 K) prestellar core that birthed our Solar system. Cometary volatiles individually reflect the evolutionary phases of star formation from cloud to core to protostar.
From ArrayExpress to BioStudies
Authors: Sarkans Ugis , Füllgrabe Anja , Ali Ahmed , Athar Awais , Behrangi Ehsan , Diaz Nestor , Fexova Silvie , George Nancy , Iqbal Haider , Kurri Sandeep , Munoz Jhoan , Rada Juan , Papatheodorou Irene , Brazma Alvis 
Published: October 2020

Abstract
ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes
Authors: Csizmadia Georgina , Erdős Gábor , Tordai Hedvig , Padányi Rita , Tosatto Silvio , Dosztányi Zsuzsanna , Hegedűs Tamás 
Published: October 2020

Abstract
Protein and lipid membrane interactions play fundamental roles in a large number of cellular processes (e.g. signalling, vesicle trafficking, or viral invasion). A growing number of examples indicate that such interactions can also rely on intrinsically disordered protein regions (IDRs), which can form specific reversible interactions not only with proteins but also with lipids. We named IDRs involved in such membrane lipid-induced disorder-to-order transition as MemMoRFs, in an analogy to IDRs exhibiting disorder-to-order transition upon interaction with protein partners termed Molecular Recognition Features (MoRFs). Currently, both the experimental detection and computational characterization of MemMoRFs are challenging, and information about these regions are scattered in the literature. To facilitate the related investigations we generated a comprehensive database of experimentally validated MemMoRFs based on manual curation of literature and structural data. To characterize the dynamics of MemMoRFs, secondary structure propensity and flexibility calculated from nuclear magnetic resonance chemical shifts were incorporated into the database. These data were supplemented by inclusion of sentences from papers, functional data and disease-related information. The MemMoRF database can be accessed via a user-friendly interface at https://memmorf.hegelab.org, potentially providing a central resource for the characterization of disordered regions in transmembrane and membrane-associated proteins.
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes
Authors: Garczarek Laurence , Guyet Ulysse , Doré Hugo , Farrant Gregory K , Hoebeke Mark , Brillet-Guéguen Loraine , Bisch Antoine , Ferrieux Mathilde , Siltanen Jukka , Corre Erwan , Le Corguillé Gildas , Ratin Morgane , Pitt Frances D , Ostrowski Martin , Conan Maël , Siegel Anne , Labadie Karine , Aury Jean-Marc , Wincker Patrick , Scanlan David J , Partensky Frédéric 
Published: October 2020

Abstract
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
Co-Operative Pain Education and Self-management (COPES) Expanding Treatment for Real-World Access (ExTRA): Pragmatic Trial Protocol
Authors: Heapy Alicia A , Driscoll Mary A , Buta Eugenia , LaChappelle Kathryn M , Edmond Sara , Krein Sarah L , Piette John D , Mattocks Kristin , Murphy Jennifer L , DeBar Lynn , MacLean R Ross , Ankawi Brett , Kawecki Todd , Martino Steve , Wagner Todd , Higgins Diana M 
Published: October 2020

Abstract

Background
Given access barriers to cognitive behavioral therapy for chronic pain (CBT-CP), this pragmatic superiority trial will determine whether a remotely delivered CBT-CP intervention that addresses these barriers outperforms in-person and other synchronous forms of CBT-CP for veterans with musculoskeletal pain.

Design
This pragmatic trial compares an asynchronous form of CBT-CP that uses interactive voice response (IVR) to allow patients to participate from their home (IVR CBT-CP) with synchronous CBT-CP delivered by a Department of Veterans Affairs (VA) clinician. Veterans (n=764; 50% male) with chronic musculoskeletal pain throughout nine VA medical centers will participate. The primary outcome is pain interference after treatment (4 months). Secondary outcomes, including pain intensity, depression symptom severity, sleep, self-efficacy, and global impression of change, are also measured after treatment. Where possible, outcomes are collected via electronic health record extraction, with remaining measures collected via IVR calls to maintain blinding. Quantitative and qualitative process evaluation metrics will be collected to evaluate factors related to implementation. A budget impact analysis will be performed.

Summary
This pragmatic trial compares the outcomes, cost, and implementation of two forms of CBT-CP as delivered in the real-world setting. Findings from the trial can be used to guide future policy and implementation efforts related to these interventions and their use in the health system. If one of the interventions emerges as superior, resources can be directed to this modality. If both treatments are effective, patient preferences and health care system factors will take precedence when making referrals. Implications of COVID-19 on treatment provision and trial outcomes are discussed.
Charging of overseas visitors in England and universal health coverage: a cross-sectional analysis of NHS trusts
Authors: Dobbin Joanna , Milner Adrienne , Dobbin Alexander , Potter Jessica 
Published: October 2020

Abstract

Background
In 2017, new regulations in England introduced upfront charging for non-urgent care within the National Health Service (NHS). Individuals from outside the European Economic Area who have not paid the immigration surcharge are chargeable for NHS care at 150% of cost.

Methods
A freedom of information (FOI) request was sent to 135 acute non-specialist NHS trusts in England to create a database of overseas visitors charges. This was analysed using multiple linear regression to explore the relationship between sex, age, nationality, ethnicity, urgency and the cost of healthcare.

Results
Of 135 acute non-specialist trusts in England 64 replied, providing a data set of 13 484 patients. Women were found to be invoiced higher amounts than men (P = 0.002). Patients were more likely to be women (63 versus 37% men), and within this group, almost half of patients were of reproductive age, with 47.9% (3165) aged 16–40 years old. Only seven trusts supplied data on urgency, and within these trusts the urgency of treatment was significantly related to cost, with the most urgent (immediately necessary) treatment costing the most (P &lt; 0.001).

Conclusion
This research reflects that that migrant women, and particularly undocumented women, are disproportionately impacted by the NHS charging policies in England.
The convergence of social media and other communication technologies in the promotion of illicit and controlled drugs
Authors: Al-Rawi Ahmed 
Published: October 2020

Abstract
Some social media platforms have strict regulations regarding the promotion of illicit and controlled drug on their sites. This study attempts to examine whether social media outlets like Twitter, Flickr and Tumblr have implemented practical measures to stop the active promotion of such drugs. We examined over 2.6 million social media posts taken from these three platforms. By focusing on keyword searches around mobile apps and communication means, we found evidence of ongoing opioid drug promotion, especially on Twitter followed by Flickr and Tumblr; we discuss our approach which effectively identifies posts related to the promotion of opioids and controlled drugs.
Childhood Sjögren syndrome: features of an international cohort and application of the 2016 ACR/EULAR classification criteria
Authors: Basiaga Matthew L , Stern Sara M , Mehta Jay J , Edens Cuoghi , Randell Rachel L , Pomorska Anna , Irga-Jaworska Ninela , Ibarra Maria F , Bracaglia Claudia , Nicolai Rebecca , Susic Gordana , Boneparth Alexis , Srinivasalu Hemalatha , Dizon Brian , Kamdar Ankur A , Goldberg Baruch , Knupp-Oliveira Sheila , Antón Jordi , Mosquera Juan M , Appenzeller Simone , O’Neil Kathleen M , Protopapas Stella A , Saad-Magalhães Claudia , Akikusa Jonathan D , Thatayatikom Akaluck , Cha Seunghee , Nieto-González Juan Carlos , Lo Mindy S , Treemarcki Erin Brennan , Yokogawa Naoto , Lieberman Scott M ,   for the Childhood Arthritis and Rheumatology Research Alliance and the International Childhood Sjögren Syndrome Workgroup
Published: October 2020

Abstract

Objective
Sjögren syndrome in children is a poorly understood autoimmune disease. We aimed to describe the clinical and diagnostic features of children diagnosed with Sjögren syndrome and explore how the 2016 ACR/EULAR classification criteria apply to this population.

Methods
An international workgroup retrospectively collected cases of Sjögren syndrome diagnosed under 18 years of age from 23 centres across eight nations. We analysed patterns of symptoms, diagnostic workup, and applied the 2016 ACR/EULAR classification criteria.

Results
We identified 300 children with Sjögren syndrome. The majority of patients n = 232 (77%) did not meet 2016 ACR/EULAR classification criteria, but n = 110 (37%) did not have sufficient testing done to even possibly achieve the score necessary to meet criteria. Even among those children with all criteria items tested, only 36% met criteria. The most common non-sicca symptoms were arthralgia [n = 161 (54%)] and parotitis [n = 140 (47%)] with parotitis inversely correlating with age.

Conclusion
Sjögren syndrome in children can present at any age. Recurrent or persistent parotitis and arthralgias are common symptoms that should prompt clinicians to consider the possibility of Sjögren syndrome. The majority of children diagnosed with Sjögren syndromes did not meet 2016 ACR/EULAR classification criteria. Comprehensive diagnostic testing from the 2016 ACR/EULAR criteria are not universally performed. This may lead to under-recognition and emphasizes a need for further research including creation of paediatric-specific classification criteria.
A hierarchical model for interpersonal verbal communication
Authors: Jiang Jing , Zheng Lifen , Lu Chunming 
Published: October 2020

Abstract
The ability to use language makes us human. For decades, researchers have been racking their minds to understand the relation between language and the human brain. Nevertheless, most previous neuroscientific research has investigated this issue from a ‘single-brain’ perspective, thus neglecting the nature of interpersonal communication through language. With the development of modern hyperscanning techniques, researchers have begun probing the neurocognitive processes underlying interpersonal verbal communication and have examined the involvement of interpersonal neural synchronization (INS) in communication. However, in most cases, the neurocognitive processes underlying INS are obscure. To tentatively address this issue, we propose herein a hierarchical model based on the findings from a growing amount of hyperscanning research. We suggest that three levels of neurocognitive processes are primarily involved in interpersonal verbal communication and are closely associated with distinctive patterns of INS. Different levels of these processes modulate each other bidirectionally. Furthermore, we argued that two processes (shared representation and interpersonal predictive coding) might coexist and work together at each level to facilitate successful interpersonal verbal communication. We hope this model will inspire further innovative research in several directions within the fields of social and cognitive neuroscience.
Risk Characterization of Environmental Samples UsingIn VitroBioactivity and Polycyclic Aromatic Hydrocarbon Concentrations Data
Authors: Chen Zunwei , Lloyd Dillon , Zhou Yi-Hui , Chiu Weihsueh A , Wright Fred A , Rusyn Ivan 
Published: October 2020

AbstractMethods to assess environmental exposure to hazardous chemicals have primarily focused on quantification of individual chemicals, although chemicals often occur in mixtures, presenting challenges to the traditional risk characterization framework. Sampling sites in a defined geographic region provide an opportunity to characterize chemical contaminants, with spatial interpolation as a tool to provide estimates for non-sampled sites. At the same time, the use of in vitro bioactivity measurements has been shown to be informative for rapid risk-based decisions. In this study, we measured in vitro bioactivity in 39 surface soil samples collected immediately after flooding associated with Hurricane Harvey in Texas in a residential area known to be inundated with polycyclic aromatic hydrocarbon (PAH) contaminants. Bioactivity data were from a number of functional and toxicity assays in 5 human cell types, such as induced pluripotent stem cell-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as human umbilical vein endothelial cells. Data on concentrations of PAH in these samples were also available and the combination of data sources offered a unique opportunity to assess the joint spatial variation of PAH components and bioactivity. We found significant evidence of spatial correlation of a subset of PAH contaminants and of cell-based phenotypes. In addition, we show that the cell-based bioactivity data can be used to predict environmental concentrations for several PAH contaminants, as well as overall PAH summaries and cancer risk. This study’s impact lies in its demonstration that cell-based profiling can be used for rapid hazard screening of environmental samples by anchoring the bioassays to concentrations of PAH. This work sets the stage for identification of the areas of concern and direct quantitative risk characterization based on bioactivity data, thereby providing an important supplement to traditional individual chemical analyses by shedding light on constituents that may be missed from targeted chemical monitoring.
Repeatability and agreement of total corneal and sublayer pachymetry with 2 different algorithms of Fourier-domain optical coherence tomography in myopic and postphotorefractive keratectomy eyes
Authors: Latifi Golshan , Mohammadi S.Saeed 
Published: October 2020

Purpose:
To investigate repeatability and agreement of total corneal and sublayer pachymetry with 2 different algorithms of Fourier-domain optical coherence tomography (OCT) in myopic and postphotorefractive keratectomy (PRK) eyes.

Setting:
Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran.

Design:
Prospective observational study.

Methods:
Total corneal, epithelial, and stromal thicknesses were measured using RTVue-XR OCT with Pachymetry + Cpwr (6.0 mm algorithm) and PachymetryWide (9.0 mm algorithm) scan patterns. The repeatability of 25 zones of 9.0 mm map and 17 zones of 6.0 mm map and the agreement between measurements of these 2 algorithms were calculated.

Results:
Ninety-five myopic and 117 post-PRK patients were evaluated. By the 9.0 mm algorithm, coefficient of variation (CoV) for total cornea was 2.33% or lesser and 2.49% or lesser and for epithelium was 5.14% or lesser and 5.18% or lesser; and by the 6.0 mm algorithm, CoV for total cornea was 1.80% or lesser and 2.59% or lesser and for epithelial thickness was 3.08% or lesser and 4.80% or lesser in myopic and post-PRK eyes, respectively. Bland-Altman mean difference for epithelial thickness was 0.69 or lesser and 1.16 or lesser and 95% limits of agreement for epithelial thickness was 6.81 or lesser and 8.56 or lesser in myopic and post-PRK eyes, respectively.

Conclusions:
Good repeatability was seen in measurements of total corneal, stromal, and epithelial thicknesses by both algorithms. Agreement of the 2 algorithms in central zone was also good. However, large range of variation in paracentral thickness measurements did not allow us to consider these algorithms as interchangeable.