bluuebunny/crossref_metadata_2025_split huggingface dataset:
Family networks and voluntary sector participation in the care of people with intellectual disability
Authors: Raghavan Raghu , Jones Keir 
Published: November 2023

Abstract
The role of family in the lives of people with intellectual disability is often central to their sense of identity and well-being. Families often hold caring and advocacy roles for their loved ones with an intellectual disability throughout their lives. Understanding this relationship and the challenges faced by people with intellectual disability and their families is therefore important. As in many fields of medical and sociological research, most published material on this topic is focused on the Global North (the economically developed countries of Europe, North America, Australia, and Israel). The relative lack of research focusing on the Global South (economically less stable countries of Africa, India, China, South East Asia, and Central and South America) means that the experiences of families in these areas are poorly understood and many of the strengths and challenges they may face are not shared more widely. This chapter presents some of the research literature from the Global South and North that focuses on the role of the family. It considers some key themes that emerge from this review and compares and contrasts some of the strengths and challenges faced in different parts of the world. It also considers how services provided by the voluntary sector may differ in response to these differing cultural perspectives.
People with intellectual disability in the criminal justice system
Authors: Amiola Ayomipo J. , Boer Harm , Manju Chikkanna , Srikumar Sowmya , Alexander Regi T. 
Published: November 2023

Abstract
Cultural attitudes to crime in general and criminal activity by those with mental disorders and intellectual disability vary across the world. While the relationship between crime and intellectual disability is curvilinear, people with intellectual disability may be over-represented at different stages of the criminal justice process. This may be related to the heterogeneity of studies and inconsistent research methodologies. Several screening instruments to establish the presence of intellectual disability are now available. Cultural attitudes and legislative structures affect pathways of care through the criminal justice system for people with intellectual disability.
Intellectual Disability Services in the United Kingdom and Ireland
Authors: Tromans Samuel J. , Chester Verity , Hiremath Avinash , Gumber Rohit 
Published: November 2023

Abstract
In the United Kingdom (UK) and Ireland, the psychiatry of intellectual disability (ID) is treated as a speciality, with a linked training pathway. This is subsequently linked to dedicated secondary care services, which provide care for those only with ID. This prompts debates around the strengths and weaknesses of specialization, versus mainstreaming, whereby those with ID are supported to access generic services. This chapter describes the care and treatment of those with ID in the UK and Ireland both historically and the present day. Furthermore, research detailing epidemiology, quality of life factors such as employment and social contact, service provision, and the future of care for this population are discussed.
Intellectual disability services in the Middle East (with a focus on Iran)
Authors: Alaghband-Rad Javad , Motamed Mahtab , Al-Uzri Mohammed 
Published: November 2023

Abstract
This chapter describes services for people with intellectual disability in the Middle East, with particular focus on Iran. While Iran is advanced in terms of having legislations in support of people with intellectual disability and autism, there are significant shortcomings in policymaking and resource allocation at various levels. There are many long-standing challenges to adequate care provision for this population. In particular, services are inadequate in terms of offering holistic and individually tailored social care and healthcare. The situation is no better in many countries in the Middle East, especially those that suffered significant population displacement due to conflict. The situation is compounded by inaccurate information about prevalence, stigma, poor understanding of needs, lack of supportive legislations, and limited services. This adds to the suffering of this vulnerable group of society, with families bearing the brunt of caring for them.
Intellectual disability services in the Indian subcontinent
Authors: Amiola Ayomipo J. , Zia Asif , Hewage Chandanie G. , Punnoose Varghese , Gangadharan Satheesh Kumar , Alexander Regi T. 
Published: November 2023

Abstract
The Indian subcontinent, also called South Asia, comprises countries with similar cultural backgrounds with broad similarities on the perception of intellectual disability and how people with intellectual disability are supported. Prevalence rates vary widely although they are consistently higher in developing countries compared to high-income countries. Cultural factors related to care include delay in seeking specialist care due to superstitious beliefs, an emphasis on community care often provided by family members especially women, and normalization. There are several local/national legislations in the region in addition to global legislations that promote the rights and inclusion of those with intellectual disabilities, and services are provided based on internationally accepted concepts involving community and hospital-based healthcare teams, education services, social services, non-governmental organizations, and parent associations.
Effects of Gynecomastia Surgery on Readiness and Return to Duty in an Active Duty Military Population
Authors: Zhang Bobby , Podszus Brendan , Williams James , Palmerton Hannah , Pak Grace , Roedel Erik , Bingham Jason , McClellan John 
Published: November 2023

ABSTRACT

Introduction
Simple mastectomies are routinely performed in the military health care system as gynecomastia can cause significant pain and discomfort when wearing body armor. Postoperative recovery negatively impacts personnel readiness. In this study, we sought to study time to return to duty in active duty service members who undergo surgery for gynecomastia.

Methods and Materials
We conducted a single-center retrospective review of active duty patients undergoing a surgical operation for gynecomastia from July 2020—June 2022. A total of 96 patients were included. Our primary outcome of interest was time from surgery to return to duty. A multivariate analysis was performed to assess for factors independently associated with surgical complications including patient demographics and operative techniques.

Results
The median number of days to return to duty after surgery was 28 days (IQR 13-37). The median loss of duty days because of gynecomastia without surgery was 19 days (IQR 10-21), which was different on the Mann–Whitney U test. Surgical complications were observed in 19 patients (19.7%) with the most common complications being seroma (11), hematoma (4), nipple-areolar complex necrosis (2), and infection (2). Patients with a complication have significantly more time to return to duty (28 vs. 49 days, P &lt; .001). Risk factors associated with an increased risk of complication include ranks E1-E4, behavioral health diagnosis, “open” vs. “combined” technique with liposuction, length of operation greater than 58 minutes, and excised breast mass greater than 17.9 g.

Conclusions
Gynecomastia surgery is associated with a detriment to personnel readiness. Surgery should be reserved for patients with severe symptoms that prevent the performance of daily duties. Furthermore, factors associated with an increased risk for complications include ranks E1-E5, behavioral health diagnosis, length of operation &gt;58 minutes, and excised breast mass &gt;17.9 g. The operating surgeon should be mindful of these factors.
Post-giant impact planetesimals sustaining extreme debris discs
Authors: Watt Lewis , Leinhardt Zoë M , Carter Philip J 
Published: November 2023

ABSTRACT
Extreme debris discs can show short-term behaviour through the evolution and clearing of small grains produced in giant impacts, and potentially a longer period of variability caused by a planetesimal population formed from giant impact ejecta. In this paper, we present results of numerical simulations to explain how a planetesimal populated disc can supply an observed extreme debris disc with small grains. We simulated a sample of giant impacts from which we form a planetesimal population. We then use the N-body code rebound to evolve the planetesimals spatially and collisionally. We adopt a simplistic collision criteria in which we define destructive collisions to be between planetesimals with a mutual impact velocity that exceeds two times the catastrophic disruption threshold, V*. We find that for some configurations, a planetesimal populated disc can produce a substantial amount of dust to sustain an observable disc. The semimajor axis at which the giant impact occurs changes the mass added to the observed disc substantially, while the orientation of the impact has less of an effect. We determine how the collision rate at the collision point changes over time and show that changes in semimajor axis and orientation only change the initial collision rate of the disc. Collision rates across all discs evolve at a similar rate.
Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction
Authors: Femerling Georgette , van Oosterhout Cock , Feng Shaohong , Bristol Rachel M , Zhang Guojie , Groombridge Jim , P. Gilbert M Thomas , Morales Hernán E 
Published: November 2023

Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
Historic Museum Samples Provide Evidence for a Recent Replacement of Wolbachia Types in European Drosophila melanogaster
Authors: Strunov Anton , Kirchner Sandra , Schindelar Julia , Kruckenhauser Luise , Haring Elisabeth , Kapun Martin 
Published: November 2023

Abstract
Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host–symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster, which is naturally infected with at least 5 different variants among which wMel and wMelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that wMelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant wMel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90 to 200 yr ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host–symbiont interactions. However, we also identified contamination with DNA from crickets that resulted in co-contamination with cricket-specific Wolbachia in several samples. These results underpin the need for rigorous quality assessments of museomic data sets to account for contamination as a source of error that may strongly influence biological interpretations if it remains undetected.
PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful
Authors: Pastrello Chiara , Kotlyar Max , Abovsky Mark , Lu Richard , Jurisica Igor 
Published: November 2023

AbstractPathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all sources, separate sources or by combining specific pathway subsets; they can select the types of sources to use or the types of pathways for the analysis, reducing the number of resulting generic pathways or pathways not related to users’ research question; users can use API. All pathways have been mapped to seven representative types. The results of pathway enrichment can be summarized through knowledge-based pathway consolidation. All curated pathways were mapped to 53 pathway ontology-based categories. In addition to genes, pathDIP 5 now includes metabolites. We updated existing databases, included two new sources, PathBank and MetabolicAtlas, and removed outdated databases. We enable users to analyse their results using Drugst.One, where a drug-gene network is created using only the user's genes in a specific pathway. Interpreting the results of any analysis is now improved by multiple charts on all the results pages. PathDIP 5 is freely available at https://ophid.utoronto.ca/pathDIP.
Europe PMC in 2023
Authors: Rosonovski Summer , Levchenko Maria , Bhatnagar Rajat , Chandrasekaran Umamageswari , Faulk Lynne , Hassan Islam , Jeffryes Matt , Mubashar Syed Irtaza , Nassar Maaly , Jayaprabha Palanisamy Madhumiethaa , Parkin Michael , Poluru Jagadeeswararao , Rogers Frances , Saha Shyamasree , Selim Mohamed , Shafique Zunaira , Ide-Smith Michele , Stephenson David , Tirunagari Santosh , Venkatesan Aravind , Xing Lijun , Harrison Melissa 
Published: November 2023

Abstract
Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.
A single fiber view of the nucleosome organization in eukaryotic chromatin
Authors: Boltengagen Mark , Verhagen Daan , Wolff Michael Roland , Oberbeckmann Elisa , Hanke Matthias , Gerland Ulrich , Korber Philipp , Mueller-Planitz Felix 
Published: November 2023

Abstract
Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this stereotypic organization describes the nucleosome organization in Saccharomyces cerevisiae using Fiber-Seq, a long-read sequencing technique that maps entire nucleosome arrays on individual chromatin fibers in a high throughput manner. With each fiber coming from a different cell, Fiber-Seq uncovers cell-to-cell heterogeneity. The long reads reveal the nucleosome architecture even over repetitive DNA such as the ribosomal DNA repeats. The absolute nucleosome occupancy, a parameter that is difficult to obtain with conventional sequencing approaches, is a direct readout of Fiber-Seq. We document substantial deviations from the stereotypical nucleosome organization with unexpectedly long linker DNAs between nucleosomes, gene bodies missing entire nucleosomes, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays and irregular nucleosome spacing. Nucleosome array structures are indistinguishable throughout the gene body and with respect to the direction of transcription arguing against transcription promoting array formation. Acute nucleosome depletion destroyed most of the array organization indicating that nucleosome remodelers cannot efficiently pack nucleosomes under those conditions. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity uncovered by Fiber-Seq provides much needed information to understand chromatin structure and function.
A novel HPV16 splicing enhancer critical for viral oncogene expression and cell immortalization
Authors: Jönsson Johanna , Wang Lianqing , Kajitani Naoko , Schwartz Stefan 
Published: November 2023

Abstract
High-risk carcinogenic human papillomaviruses (HPVs), e.g. HPV16, express the E6 and E7 oncogenes from two mRNAs that are generated in a mutually exclusive manner by splicing. The HPV16 E7 mRNA, also known as the E6*I/E7 mRNA, is produced by splicing between splice sites SD226 and SA409, while E6 mRNAs retain the intron between these splice sites. We show that splicing between HPV16 splice sites SD226 and SA409 is controlled by a splicing enhancer consisting of a perfect repeat of an adenosine-rich, 11 nucleotide sequence: AAAAGCAAAGA. Two nucleotide substitutions in both 11 nucleotide sequences specifically inhibited production of the spliced E6*I/E7 mRNA. As a result, production of E7 protein was reduced and the ability of HPV16 to immortalize human primary keratinocytes was abolished. The splicing-enhancing effect was mediated by the cellular TRAP150/THRAP3 protein that also enhanced splicing of other high-risk HPV E6*I/E7 mRNAs, but had no effect on low-risk HPV mRNAs. In summary, we have identified a novel splicing enhancer in the E6 coding region that is specific for high-risk HPVs and that is critically linked to HPV16 carcinogenic properties.
Modular cytosine base editing promotes epigenomic and genomic modifications
Authors: Weischedel Julian , Higgins Laurence , Rogers Sally , Gramalla-Schmitz Anna , Wyrzykowska Paulina , Borgoni Simone , MacCarthy Thomas , Chahwan Richard 
Published: November 2023

Abstract
Prokaryotic and eukaryotic adaptive immunity differ considerably. Yet, their fundamental mechanisms of gene editing via Cas9 and activation-induced deaminase (AID), respectively, can be conveniently complimentary. Cas9 is an RNA targeted dual nuclease expressed in several bacterial species. AID is a cytosine deaminase expressed in germinal centre B cells to mediate genomic antibody diversification. AID can also mediate epigenomic reprogramming via active DNA demethylation. It is known that sequence motifs, nucleic acid structures, and associated co-factors affect AID activity. But despite repeated attempts, deciphering AID’s intrinsic catalytic activities and harnessing its targeted recruitment to DNA is still intractable. Even recent cytosine base editors are unable to fully recapitulate AID’s genomic and epigenomic editing properties. Here, we describe the first instance of a modular AID-based editor that recapitulates the full spectrum of genomic and epigenomic editing activity. Our ‘Swiss army knife’ toolbox will help better understand AID biology per se as well as improve targeted genomic and epigenomic editing.
A COVID-19 monitoring process for healthcare workers utilizing occupational health
Authors: Crosby J C , Lee R A , McGwin G , Heath S L , Burkholder G A , Gravett R M , Overton E T , Locks G , Fleece M E , Franco R , Nafziger S 
Published: November 2023

Abstract

Background
Hospital-based occupational health (HBOH) is uniquely positioned to not only prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, but to care for healthcare workers (HCWs) sick with coronavirus disease 2019 (COVID-19).

Aims
The primary objective of this study is to describe a system where HBOH services were adapted to provide a monitoring programme whereby HCWs with SARS-CoV-2 received daily evaluations and treatment options in order to improve access to care, and to report the clinical outcomes and predictors of hospitalization in HCWs enrolled in the programme. A secondary objective is to compare clinical outcomes to data on national HCWs with COVID-19.

Methods
This retrospective cohort study used survey data collected on HCWs at a university health system with COVID-19 from 1 March 2020 through 1 December 2021. A firth regression model was used to examine the unadjusted and adjusted association between clinical factors and hospitalization.

Results
The study cohort included 4814 HCWs with COVID-19. Overall hospitalizations were 119 (2%), and there were six deaths (0.12%). Predictors of hospitalization include several co-morbidities and symptoms. A total of 1835 HCWs monitored before vaccine or monoclonal antibody availability were compared with data on U.S. HCWs in a similar time period. The monitored HCWs had a lower rate of co-morbidities (19% versus 44%, P &lt; 0.001), a lower hospitalization rate (3% versus 8% P &lt; 0.001) and case-fatality rate (0.11% versus 0.95% P &lt; 0.001).

Conclusions
This monitoring strategy for COVID-19 may be feasible for HBOH systems to implement and improve access to care, but more data are needed to determine if it improves outcomes.