bluuebunny/crossref_metadata_2025 huggingface dataset:
Arrhythmogenic potential of myocardial disarray in hypertrophic cardiomyopathy: genetic basis, functional consequences and relation to sudden cardiac death
Authors: Finocchiaro Gherardo , Sheikh Nabeel , Leone Ornella , Westaby Joe , Mazzarotto Francesco , Pantazis Antonis , Ferrantini Cecilia , Sacconi Leonardo , Papadakis Michael , Sharma Sanjay , Sheppard Mary N , Olivotto Iacopo
Published: October 2020

Myocardial disarray is defined as disorganized cardiomyocyte spatial distribution, with loss of physiological fibre alignment and orientation. Since the first pathological descriptions of hypertrophic cardiomyopathy (HCM), disarray appeared as a typical feature of this condition and sparked vivid debate regarding its specificity to the disease and clinical significance as a diagnostic marker and a risk factor for sudden death. Although much of the controversy surrounding its diagnostic value in HCM persists, it is increasingly recognized that myocardial disarray may be found in physiological contexts and in cardiac conditions different from HCM, raising the possibility that central focus should be placed on its quantity and distribution, rather than a mere presence. While further studies are needed to establish what amount of disarray should be considered as a hallmark of the disease, novel experimental approaches and emerging imaging techniques for the first time allow ex vivo and in vivo characterization of the myocardium to a molecular level. Such advances hold the promise of filling major gaps in our understanding of the functional consequences of myocardial disarray in HCM and specifically on arrhythmogenic propensity and as a risk factor for sudden death. Ultimately, these studies will clarify whether disarray represents a major determinant of the HCM clinical profile, and a potential therapeutic target, as opposed to an intriguing but largely innocent bystander.
A Path toward SARS-CoV-2 Attenuation: Metabolic Pressure on CTP Synthesis Rules the Virus Evolution
Authors: Ou Zhihua , Ouzounis Christos , Wang Daxi , Sun Wanying , Li Junhua , Chen Weijun , Marlière Philippe , Danchin Antoine
Published: October 2020

In the context of the COVID-19 pandemic, we describe here the singular metabolic background that constrains enveloped RNA viruses to evolve toward likely attenuation in the long term, possibly after a step of increased pathogenicity. Cytidine triphosphate (CTP) is at the crossroad of the processes allowing SARS-CoV-2 to multiply, because CTP is in demand for four essential metabolic steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope, it is a critical building block of the host transfer RNAs synthesis and it is required for synthesis of dolichol-phosphate, a precursor of viral protein glycosylation. The CCA 3′-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. This unique metabolic setup allowed us to highlight and provide a raison d’être to viperin, an enzyme of innate antiviral immunity, which synthesizes 3ʹ-deoxy-3′,4ʹ-didehydro-CTP as an extremely efficient antiviral nucleotide.
Assuring Quality in Nursing Homes: The Black Box of Administrative and Clinical Leadership—A Scoping Review
Authors: Siegel Elena O , Young Heather M
Published: October 2020

Background and Objectives

Licensed nursing home administrators (NHA) and directors of nursing (DON) are responsible for nursing home quality and assuring optimal performance and job satisfaction/retention of their nursing home workforce. NHA/DON-focused studies have generated important foundational knowledge over the last three decades; yet, targeted research is needed to understand and apply the complexities of the black box of this top management team. This scoping review identifies, reviews, synthesizes, and maps the topical areas of research in NHA/DON positions in U.S. nursing homes.

Research Design and Methods

We conducted searches of 5 databases, yielding 3,479 records; screening/review yielded 88 unique records. We used thematic analysis to code the primary foci of the studies and the variables associated with the concepts of interest.

Results

Most papers (n = 40) focused on role characteristics, 23 examined approaches to management and leadership, 24 focused on perceptions about the role, and the remaining 12 examined role structure. The role-related themes linked to outcomes (n = 42), processes (n = 27), and structures (n = 30).

Discussion and Implications

We highlight important gaps for future research and offer a call to action for research, policy, practice, and education collaborations to accelerate the rate of research and translate the findings into best practices for NHA/DON to lead and manage the nursing home workforce and build capacity to ensure person-centered, high-quality care. Based on foundational descriptive studies, it is time to use what is known to design and implement interventions that enhance the capacity of NHA/DON to improve the structures, processes, and outcomes of nursing homes.
Focusing joint inversion of gravity and magnetic data using a clustering stabilizer in a space of weighted parameters
Authors: Xu Zhengwei , Zou Guangui , Wei Qianqian , Tian Junqi , Yuan Hemin
Published: October 2020

This paper develops a minimum-support focusing stabilizer to perform a joint inversion of the vertical components of gravity and magnetic data using fuzzy c-means clustering (FCM) with the regularized Newton method in a space of weighted parameters. Not only does this joint inversion technology arrive at the conditionally well-posed traditional potential field inversion, but it also increases the structural correlation between multiple inverted models. The FCM and the focusing stabilizer make it possible to balance the convergence of the data space (D) and the model space (M), guiding multimodal geophysical parameters toward assigned petrophysical values, which makes the results more stable and realistic. Two model studies are presented to illustrate the method, a simple synthetic model with two rectangular bodies in a homogenous background and a realistic model of the Volcanogenic Massive Sulfide (VMS) deposits in northeastern New Brunswick, Canada. These models demonstrate that the new focusing joint inversion algorithm produces better images than traditional methods because the FCM function uses the structural correlation of density contrast and magnetic susceptibility as constraints.
Criminal Law
Authors: Allen Michael , Edwards Ian
Published: October 2020

Course-focused and comprehensive, the Textbook
on series provides an accessible overview of the key areas on the law curriculum. Textbook on Criminal
Law has been providing students of criminal law with a readable and reliable introduction to the subject for the past 28 years. This is the fifteenth edition, which has been updated to include all of the latest case law and statutory changes. Topics covered include actus reus, mens rea, negligence and strict liability, and capacity and incapacitating conditions. It also examines general defences, parties to crime, inchoate offences, and homicide. Towards the end of the book chapters consider non-fatal offences, sexual offences, offences under the Theft Acts 1968 and 1978, fraud, and criminal damage.
In patients undergoing valve-sparing aortic root replacement, is reimplantation superior to remodelling?
Authors: Maskell Perry , Brimfield Matthew , Ahmed Amna , Harky Amer
Published: October 2020

A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was: in patients undergoing valve-sparing aortic root replacement, is reimplantation superior to remodelling? The purpose of this best evidence topic was to re-review the updated evidence that has become available in the near decade since the previous review published in 2011. Altogether more than 300 papers were found using the reported search, of which 8 papers represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. The included studies have significant limitations relating to low-level evidence study design, variable outcome collection and limited significance testing with direct comparison. Long-term outcomes such as survival, recurrence of aortic regurgitation and valve reintervention were largely equal between the two procedures across the studies. This review, updated from the previous best evidence topic, continues to suggest that there are no clear recommendations or even consensus to guide clinical decision-making when choosing between remodelling or reimplantation approaches to valve-sparing aortic root replacement. To date, no study provides strong clinical benefit to favour either procedure in terms of perioperative outcomes, medium–long term survival or reintervention of the aortic valve. As such, procedure selection should be based upon patient factors and valve evaluation, combined with surgeon preference and experience.
Intrusive tech-enabled surveillance and ‘National Security’ secrecy: mounting concerns of mass snooping amid informational asymmetry
Authors: Babele Aryan
Published: October 2020

The onset of technological innovations such as Big Data and Analytics is changing the ways in which law enforcement agencies police and investigate crimes in India. Pervasive technologies like smartphones, closed-circuit cameras, etc, coupled with such innovations have augmented abilities of law enforcement to identify, monitor and predict suspicious individuals and activities. However, the expansive adoption of intrusive technologies for law enforcement challenge the statutory and the constitutional limits on mass surveillance. Also, the government has not been forthcoming in disclosing details about the extent and the ambition of such surveillance technologies. The secrecy has resulted in an informational asymmetry between the people and the government which raises profound concerns of mistrust, transparency and public-accountability. This article examines the feasibility of the ‘national security’ argument that law enforcement agencies normatively use to justify such secrecy of their surveillance powers. They argue that such disclosures may negatively affect their investigational strategies and render them susceptible to circumvention, such that it may be a risk to ‘national security’. The article analyses such ‘national security’ secrecy claims that currently exist without any proper surveillance law and external oversight. The article seeks to recommend meaningful approaches to limit the over-broad ‘national security’ secrecy claims and initiate an informed public conversation on expansive tech-enabled surveillance practices of the Indian government.
Nevirapine pharmacokinetics in HIV-infected persons receiving rifapentine and isoniazid for TB prevention
Authors: Podany A T , Leon-Cruz J , Hakim J , Supparatpinyo K , Omoz-Oarhe A , Langat D , Mwelase N , Kanyama C , Gupta A , Benson C A , Chaisson R E , Swindells S , Fletcher C V ,   the AIDS Clinical Trials Group A5279 Team, Kim Peter , Johnson Daniel , Moran Laura , Andersen Janet , Bao Yajing , Wu Shirley , Blanchard-Horan Christina , Walawander Ann , Shin Katherine , Ebiasah Ruth , Holland David , JeanJuste Marc Antoine , Nuermberger Eric , Pillay Sandy , Sanne Ian , Nicotera Janet , Shugarts David , Shali Amina , Tutko Jimi , Demers Brigitte , Maroni Marilyn , Sanchez Jorge L , Iglesias David , Lama Javier , Matoga Mitch , do Amaral Calvet Guilherme , Tonui Ronald Kibet , Modise Taolo , Kasaro Margaret , Naidoo Kogieleum , Kadam Deelip , Burman William
Published: October 2020

Background

The use of rifamycin antibiotics for TB prevention carries a risk of detrimental drug–drug interactions with concomitantly used ART.

Objectives

To evaluate the interaction of the antiretroviral drug nevirapine in combination with 4 weeks of daily rifapentine and isoniazid for TB prevention in people living with HIV.

Methods

Participants were individuals enrolled in the BRIEF-TB study receiving nevirapine and randomized to the rifapentine/isoniazid arm of the study. Participants provided sparse pharmacokinetic (PK) sampling at baseline and weeks 2 and 4 for trough nevirapine determination. Nevirapine apparent oral clearance (CL/F) was estimated and the geometric mean ratio (GMR) of CL/F prior to and during rifapentine/isoniazid was calculated.

Results

Seventy-eight participants had evaluable PK data: 61 (78%) female, 51 (65%) black non-Hispanic and median (range) age of 40 (13–66) years. Median (IQR) nevirapine trough concentrations were: week 0, 7322 (5266–9302) ng/mL; week 2, 5537 (3552–8462) ng/mL; and week 4, 5388 (3516–8243) ng/mL. Sixty out of 78 participants (77%) had nevirapine concentrations ≥3000 ng/mL at both week 2 and 4. Median (IQR) nevirapine CL/F values were: week 0 pre-rifapentine/isoniazid, 2.03 (1.58–2.58) L/h; and during rifapentine/isoniazid, 2.62 (1.81–3.42) L/h. The GMR (90% CI) for nevirapine CL/F was 1.30 (1.26–1.33).

Conclusions

The CL/F of nevirapine significantly increased with concomitant rifapentine/isoniazid. The decrease in nevirapine trough concentrations during rifapentine/isoniazid therapy suggests induction of nevirapine metabolism, consistent with known rifapentine effects. The magnitude of this drug–drug interaction suggests daily rifapentine/isoniazid for TB prevention should not be co-administered with nevirapine-containing ART.
Two-dose emtricitabine/tenofovir alafenamide plus bictegravir prophylaxis protects macaques against SHIV infection
Authors: Bekerman Elena , Cox Stephanie , Babusis Darius , Campigotto Federico , Das Moupali , Barouch Dan H , Cihlar Tomas , Callebaut Christian
Published: October 2020

Objectives

Current prophylaxis options for people at risk for HIV infection include two US FDA-approved daily pre-exposure prophylaxis (PrEP) regimens and guidelines for a 2-1-1 event-driven course specifically for men who have sex with men. Despite this, PrEP use rates remain suboptimal, and additional PrEP options may help to improve uptake among diverse populations. Here, we evaluated protective efficacy of two-dose PrEP and two-dose postexposure prophylaxis (PEP) schedules with emtricitabine (FTC)/tenofovir alafenamide (TAF) with or without bictegravir (BIC) in an SHIV macaque model.

Methods

Macaques received one oral dose of 200 mg emtricitabine, 25 mg tenofovir alafenamide and 25-100 mg of bictegravir to establish pharmacokinetic profiles of each drug either in the plasma or the peripheral blood mononuclear cells. Protective efficacy of multiple two-dose PrEP and PEP schedules with FTC/TAF with or without bictegravir was then assessed in two repeat low-dose rectal SHIV challenge studies.

Results

The data revealed over 95% per-exposure risk reduction with FTC/TAF PrEP initiated 2 h before the exposure, but a loss of significant protection with treatment initiation postexposure. In contrast, FTC/TAF plus BIC offered complete protection as PrEP and greater than 80% per-exposure risk reduction with treatment initiation up to 24 h postexposure.

Conclusions

Together, these results demonstrate that two-dose schedules can protect macaques against SHIV acquisition and highlight the protective advantage of adding the integrase inhibitor bictegravir to the reverse transcriptase inhibitors emtricitabine and tenofovir alafenamide as part of event-driven prophylaxis.
African Junta and Defence Spending: A Capture Effect or Self-preservation?
Authors: Kodila-Tedika Oasis , Khalifa Sherif
Published: October 2020

This paper examines the effect of the presence of a military ruler on military expenditure using a panel of sub-Saharan Africa countries. The paper also explores whether the relationship reflects a capture effect, is an outcome of the confrontational climate of the cold war or is a self-preservation effort by military rulers. The panel data estimations show that the presence of a military ruler has a statistically significant negative effect on military spending as a percentage of GDP. The coefficients are also not significantly different before or after the end of the cold war era. This implies that the negative relationship is driven by an effort by military rulers to preempt the ability of their peers to overthrow them from power. We also attempt to deal with potential endogeneity and consider the possibility of persistence in military spending. The paper uses the Arellano and Bond (1991) estimation technique that shows a negative but insignificant effect of the presence of a military ruler on military expenditure, while military spending shows a high degree of persistence.
Method Matters: Comparing Cancer-Related Adjustment of Siblings to Norms and Well-matched Peers
Authors: Tomatsu Saori C , Stanley Caroline , Conroy Rowena , Alderfer Melissa A
Published: October 2020

Objective 

The purpose of this study was to better understand conflicting findings in the literature regarding the adjustment of siblings of children with cancer by examining, in a single sample, differences in patterns of results as a function of reporter and comparator used (i.e., population norms, demographically matched classmates).

Method 

Self- and parent-report standardized measures of depression, anxiety, and behavioral problems were collected for 67 siblings and 67 demographically matched classmates. Comparisons were made to norms and controls.

Results 

Siblings consistently demonstrated poorer psychosocial functioning than their demographically matched peers across all measures but their scores did not differ from norms. A significantly greater percentage of siblings fell outside the normal range than that expected in the general population for parent-reported total and internalizing problems, but not for externalizing problems or the self-report measures.

Conclusions 

Findings regarding the psychological adjustment of siblings of children with cancer differ according to the research methods used. It is important to use rigorous methods such as demographically matched peer comparisons when investigating the impact of childhood cancer on siblings.
COVID-19 Pandemic Preparedness in a UK Tertiary and Quaternary Children’s Hospital: Tales of the Unexpected
Authors: Alders Nele , Penner Justin , Grant Karlie , Patterson Charlotte , Hassell Jane , MacDermott Nathalie , Pincott Sian , Bamford Alasdair , du Pré Pascale , Johnson Mae , Moshal Karyn
Published: October 2020

We describe the adaptive coping strategies required in the management of a heterogeneous group of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pediatric patients. The diverse range of presentations, presenting in distinct phenotypic waves, exemplified the importance of preparedness for the unknown. Lessons learned will be essential in planning for a likely second wave of SARS-CoV-2.
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

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

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

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

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

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.
Death
Authors: Chrystal Paul
Published: October 2020

Life and death is a vast subject, potentially taking in a massive chunk of the published output of Greco-Roman scholarship since the time of Homer and his contemporaries. So, some serious restriction of extent is required: this article will focus on life and death and how the two interrelate throughout the Greek and Roman periods. “Death” will cover eschatology, funeral and burial rites, funerary epigraphy, as well as different forms of death such as suicide, death in war and in the arena, death through disease, and murder. Poisonings, toxicology, osteoarchaeology, and forensics are also covered. “Life” will take in life where death impinges on it in whatever form. As with any culture and civilization, life and death were inextricably linked in ancient Greece and Rome: how one led one’s life was dictated to a large degree by belief in and expectations of a further life in the afterworld; similarly, the kind of afterlife one might expect was thought to be predicated on how one conducted oneself during life. The Greek tragedies underscore the absolute necessity for proper burial rites in Greek society while the Romans too had strict rules relating to funerary protocol and ritual. Epigraphy takes in military inscriptions and the formulaic praise, particularly of wives, husbands, children and mothers. We will see much on necromancy, communion with the dead, the underworld journey, underworld topography, and denizens of Hades and Tartarus such as Charon. The section on Postmortem Studies takes in works on memories of the departed, mourning, commemoration of the dead, the Parentalia, dining with the deceased, death pollution, corpse abuse, and cremations that went badly wrong. War death covers military and civilian death in battle and siege, disasters, and atrocities while suicide gives us Lucretia, euthanasia, and depictions of suicide in art. Finally, from murder, toxicology, and forensics we find studies on the effects of lead poisoning, the patricide of Verginia, three infamous women poisoners, and amateur toxicologists—Mithridates and Cleopatra. The citations range from Homer to late Roman, from the Greek polis to the Roman Empire at its widest extent and to its fall; they take in all available types of evidence as found in journal articles, books, visual arts, epigraphy, archaeology, architecture, science, and online sources.
Intellectual Virtues
Authors: Crerar Charlie , Allen Teresa , Battaly Heather
Published: October 2020

Intellectual virtues are qualities that make us excellent thinkers. There are different analyses of exactly which qualities count as intellectual virtues: virtue responsibilists have emphasized praiseworthy character traits, such as open-mindedness and intellectual humility, while virtue reliabilists have emphasized reliable skills and faculties, such as vision, memory, and skills of logic. Importantly, all agree that intellectual virtues are (i) excellences, as opposed to defects; and (ii) distinctively intellectual and not, or not simply, moral. In other words, intellectual virtues are qualities that make us excellent (and not defective) as thinkers, not (or not simply) as people in general. This bibliography provides an overview of philosophical work on the intellectual virtues. It includes articles and books addressing responsibilist and reliabilist analyses of the structure of intellectual virtue; analyses of individual intellectual virtues; the application of intellectual virtue to education and other professional fields; the role of intellectual virtues in epistemology; and, finally, the structure of intellectual vice. It also includes some historical sources on intellectual virtue, though its focus is contemporary. Analyses of intellectual virtue (and of individual intellectual virtues) have developed in tandem with the epistemological subfield of virtue epistemology, which employs the notion of intellectual virtue in an account of knowledge. These analyses also frequently draw on virtue ethics, especially in the Aristotelian tradition. Some of the sources cited touch upon connections between intellectual virtue and these fields, though a fuller treatment of these topics can be found in the corresponding bibliographies on Virtue Epistemology and Virtue Ethics.
Boko Haram
Authors: Warner Jason , Chapin Ellen
Published: October 2020

When referring to the terrorist group known as “Boko Haram,” observers are broadly pointing to a violent, Salafist-jihadist group (in its various incarnations and often encompassing its offshoots) based in northeastern Nigeria, which seeks to establish a caliphate ruled by sharia law in northeastern Nigeria and its environs. The group that served as its predecessor was founded in 2002 in Maiduguri, Nigeria, by Mohammed Yusuf, and was named “Jama’atu Ahil as-Sunna li ad-Da’wa wa al-Jihad,” or “People Committed to the Propagation of the Prophet’s Teachings and Jihad” (JAS). By the time that the group became violent in 2009—also the year that Yusuf died and the group was taken over by Abubakar Shekau—observers had begun to refer to the group as “Boko Haram,” broadly meaning “Western education is sinful” or “forbidden.” Even after the group pledged allegiance to the Islamic State and became the Islamic State’s West Africa Province (ISWAP) in March 2015, and later faced the breakaway of a splinter group in 2016, observers have still referred to these iterations as “Boko Haram.” In other words, this article, which is ostensibly about “Boko Haram,” is more generally about the various incarnations of the above-referenced group, the nature of its violence, its cycles of leadership, its shifting global and regional affiliations, and the offshoot groups which it has engendered, all of which continue to be referred to by more casual observers as “Boko Haram,” even though none of the above iterations of the group referred to themselves as such, at least formally. While this article is one that seeks to provide an overview of the best literature available on the emergence, evolution, and current activities of the “Boko Haram” phenomenon, given the multi- and interdisciplinary study of the group—most commonly undertaken by scholars of political science, history, religion, and conflict and security—there is no singular, unifying intellectual framework by which to study the group. Instead, writings on Boko Haram have occurred across disciplines, and as we articulate in the subsections below, have been defined by two general approaches. On one hand, scholars of Boko Haram have often written comprehensive histories of the group, attempting to understand the organization writ large, while on the other, others have written about particular facets of the group relating to Boko Haram’s emergence, ideology, patterns of violence, treatment of gender and age, and interactions with global jihadist organizations, and impact on communities in which it operates. In the pages below, we detail what we view to be the most rigorous pieces written to date in each of these two broad categories, keeping in mind that given space restrictions, we were not able to include sections on every facet of the Boko Haram insurgency.
Young Children's Working Theories
Authors: Hedges Helen
Published: October 2020

Ways children make sense of their lives in their families, communities, and cultures are of immense interest to parents, teachers, and researchers internationally. “Working theories” originated as an holistic outcome of Te Whāriki, the Aotearoa New Zealand (NZ) early childhood curriculum (Ministry of Education 1996, Ministry of Education 2017). The term describes the provisional and exploratory ideas and understandings children—and adults—develop as they participate in learning. Working theories help children and adults with meaning making, explanation, prediction, and problem solving. The term therefore has wide educational relevance beyond NZ. Working theories have connections with, but are not the same as, knowledge development or a focus on learning academic concepts. Developing accurate knowledge is not necessarily a goal for young children. In contrast, theories frequently persist in the face of contrary evidence and involve both progression and retrogression in understandings as children attempt to meld new ideas and experiences with their prior, albeit limited, knowledge and experience—rather curiosity and inquiry into personally interesting and meaningful understandings motivates children. More than a focus on cognitive and knowledge development, working theories include all of children’s embodied, linguistic, communicative, and social efforts to learn. The goal of such efforts is to participate and contribute more effectively and competently in their families, communities, and cultures. Consequently, there is an expectation that adults will engage with and support children’s working theory development in respectful, reciprocal, and responsive interactions. Most related literature is at present from NZ; international interest is more recent and growing. Scope for future research includes specific topics of children’s theorizing, especially topics adults might struggle to understand or respond to; ways to document working theories and working theory development over time; exploration and application of Māori concepts and examples given the bicultural aim of Te Whāriki; and ways curriculum might be designed around working theories. The following bibliography has four sections. The first section is literature that has worked on Understanding the Concept of Working Theories. The second section offers examples of working theories from research undertaken with children, adults in teaching roles, and families. The third section describes teacher understandings of the concept of working theories and ways these might drive curriculum, and the fourth section has examples of pedagogical strategies and responses. Naturally there are overlaps between sections 2 through 4 and section assignment does not mean the selected literature does not address material in other sections.
Organizational Climate
Authors: Ehrhart Mark , Kuenzi Maribeth
Published: October 2020

The study of organizational climate has had a long history that in many ways mirrors the development of the fields of organizational psychology and organizational behavior, and demonstrates the critical role of the environment in individual and organizational effectiveness. High levels of interest in organizational climate, largely coming from researchers in psychology, contributed to the initial rise and early progress in our understanding of the construct in the late 1960s through the 1970s. A variety of concerns related to the definition and measurement of climate, along with the rise in interest in climate’s sibling construct of organizational culture, resulted in waning interest through the 1980s and much of the 1990s. However, with increasing sophistication in and understanding of multilevel theory and measurement in the late 1990s through the 2000s came a rebirth of interest in climate, with a particular emphasis on focused climates (e.g., safety climate or service climate) that continues to this day. This bibliography provides an overview of research on organizational climate, including climate measurement, the most common types of climate that are found in the research literature, and the major research findings on organizational climate.
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

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.

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

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 < 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

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

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.