bluuebunny/crossref_metadata_2025_split huggingface dataset:
119 A Descriptive Epidemiological Study of Clinical Trials, Comparing Trials Targeted At Older People to Adults of All Ages
Authors: Renton J P , McAllister D 
Published: March 2021

Abstract

Introduction
Fewer clinical trials are carried out in older people. It is unclear how representative and applicable clinical trials carried out exclusively in older people are. We compared clinical trials recruiting older people exclusively “older trials” to those recruiting adults of all ages “all age trials”, using anti-hypertensives acting on the renin-angiotensin aldosterone system (RAAS drugs) as an exemplar.

Method
We searched the US clinical trials register 1, to identify all trials carried out exclusively in those aged over 60. From these we selected trials of RAAS drugs. These were matched in a 2:1 ratio to trials carried out in adults of all ages. Data regarding baseline characteristics, adverse events and eligibility criteria were collected from clinical trial reports and clinicaltrials.gov. Estimated associations were calculated for age, sex and adverse events. Eligibility criteria were described and ICD- 10 coded, as appropriate.

Results
71 clinical trials were carried out exclusively in older people.13 related to RAAS drugs. Participants in “Older trials” had higher mean age (73.1 and 55.9 respectively), mean difference 16.17 (CI 15.31–17.02). Older trials had fewer male participants. Participants in older trials had lower mean body mass index (BMI). A higher rate of participants in older trials experienced serious adverse events. (2.07, CI 1.55–2.75.) Few older trials had upper age limits (23.1% V 27% all age trials). All trials had exclusion criteria in multiple ICD blocks. Concurrent medications were a more common exclusion criterion in older trials (61.5% v 40.9%).

Conclusions
Clinical trials carried out exclusively in older people are representative in terms of age, serious adverse events and eligibility. Although there are multiple exclusion criteria for clinical trial participation in both groups, this is not prohibitive. This supports carrying out more trials exclusively in older people. References 1. NIH, US national library of medicine.ClinicalTrials.gov Available at https://clinicaltrials.gov/
129 “Pop-Up” Specialist End of Life Ward For COVID-19—The Nottingham Experience
Authors: Arnott R , Lewis A , Berbecila D , Deery J , Wells L , Poon M H 
Published: March 2021

Abstract

Background
Our hospital trust anticipated an increased need for palliation and end of life care (EoLC) in patients with Covid-19 who were not appropriate for escalation and mechanical ventilation.

Intervention
A dedicated ward was opened as part of the trust-wide Covid-19 admissions pathway, led by geriatricians with palliative care input and staffed by relocated nursing and auxiliary personnel. Retrospective data was collected for consecutive patients admitted to the ward between 3rd April and 26th May 2020 and qualitative data regarding staff experience using a questionnaire.

Result
Of the 168 patients (55% male) admitted, 31.5% came directly from Emergency Department, 17.3% from admission areas and the remainder from inpatient wards. Time spent on the ward ranged from 10 minutes to 17 days (median length of stay 43 hours). 75% had Clinical Frailty Scale score of 6 or more. 150 died with 75% naming Covid-19 as primary cause or contributing factor. Ward staff, who were not palliative care specialists, reported increased confidence in many aspects of palliation including assessing comfort, relieving symptoms, prescribing and administering anticipatory medications and in supporting and communicating with relatives. Staff apprehension about working on a Covid ward eased once the ward was established. Qualitative themes emerging from staff feedback included: professional competency, communication, prioritisation, team work, emotional response, care and consistency in a time of change.

Discussion
The pathway and referral system ensured that our ward cared for appropriate older patients living with frailty. The formation of a specialist unit over a short period of time created a series of logistical and management challenges. The emotional burden felt by staff was also prominent in feedback. These challenges were outweighed by the personal and professional development of staff coupled with the strong sense of teamwork, pride and enthusiasm felt in providing high quality care.
134 A Quality Improvement Project—Physiotherapy Caseload Management on the Older Person’s Unit
Authors: Snape C , Triteos N , Wood C A , Robert G , Jones J 
Published: March 2021

Abstract

Introduction
Complex health issues, co-morbidities and the number of patients living with frailty are critical concerns associated with the ageing population (Kojima et al, 2019). In this wider context, there is an emphasis on targeting resources efficaciously within the NHS. A consequence of capacity constraints, inpatient physiotherapy teams across the OPU at a large urban teaching hospital, prioritise their patient caseload, but lack evidence-based guidance on dosage and frequency of physiotherapy intervention, to inform the process. The aim of the quality improvement project was to design and deliver a staff education and training package to facilitate implementation of a newly-developed, evidence-based prioritisation resource.

Method
Plan-Do-Study-Act cycles and the Com-B model to influence behaviour changes were employed between October 2019 and March 2020. Stakeholders were engaged throughout the design process. Training to all 11 physiotherapists consisted of familiarisation with the resource through content discussion and “mock-use” training sessions to ensure intra/inter-rater-reliabilty. Physiotherapist staff knowledge and confidence of prioritisation was evaluated by questionnaire. Accuracy of use of the prioritisation tool was determined by comparison of staff prioritisation decision with expert opinion.

Results
From the 11 questionnaire responses, pre to post intervention physiotherapy knowledge of the prioritisation categories increased (43% to 100%), physiotherapist rated confidence using the prioritisation tool increased (mean score, 6.9 to 8.2/10) and accuracy of prioritisation of patients improved (mean 42.1% to 92.3%).

Conclusion
The education and training package developed to support implementation of the prioritisation tool resulted in improved staff knowledge and confidence of patient prioritisation and increased the accuracy of OPU physiotherapy targeting. This project has highlighted the importance of staff training in resource allocation to ensure that decisions regarding which patients receive physiotherapy intervention are efficacious. This has increased relevance in a department with a large number of rotational staff.
Comparison of Nuclear Grade, Necrosis, and Histologic Subtype Between Biopsy and Resection in Pleural Malignant Mesothelioma: An International Multi-Institutional Analysis
Authors: Schulte Jefree J , Chapel David B , Attanoos Richard , Brcic Luka , Burn Juliet , Butnor Kelly J , Chang Nina , Chen Heather , Dacic Sanja , De Perrot Marc , Fukuoka Junya , Galateau-Salle Francoise , Godschachner Theresa , Hiroshima Kenzo , Klebe Sonja , Krausz Thomas , Litzky Leslie , Marchevsky Alberto M , Mueller Jeffrey , Nabeshima Kazuki , Nicholson Andrew G , Pal Prodipto , Roden Anja C , Rorvig Sara , Santoni-Rugiu Eric , Tazelaar Henry , Tsao Ming-Sound , Walts Ann E , Weynand Birgit , Zaizen Yoshiaki , Zhang Yu Zhi , Husain Aliya N 
Published: March 2021

Abstract

Objectives
Numerous studies on malignant mesothelioma (MM) highlight the prognostic importance of histologic subtype, nuclear grade, and necrosis. This study compares these parameters in paired biopsy and resection specimens of pleural MM.

Methods
Histologic subtype, percentage of epithelioid morphology, nuclear grade, and the presence or absence of necrosis were compared in 429 paired biopsies and resection specimens of pleural MM from 19 institutions.

Results
Histologic subtype was concordant in 81% of cases (κ = 0.58). When compared with resection specimens, epithelioid morphology at biopsy had a positive predictive value (PPV) of 78.9% and a negative predictive value (NPV) of 93.5%; sarcomatoid morphology showed high PPV (92.9%) and NPV (99.3%), and biphasic morphology PPV was 89.7% and NPV was 79.7%. Agreement of the percentage of epithelioid morphology was fair (κ = 0.27). Nuclear grade and necrosis were concordant in 75% (κ = 0.59) and 81% (κ = 0.53) of cases, respectively. Nuclear grade showed moderate (κ = 0.53) and substantial (κ = 0.67) agreement from patients with and without neoadjuvant therapy, respectively, and necrosis showed moderate (κ = 0.47 and κ = 0.60) agreement, respectively, in the same subsets of paired specimens.

Conclusions
Paired biopsy-resection specimens from pleural MM show overall moderate agreement in pathologic parameters. These findings may help guide postbiopsy management and triage of patients with MM.
Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris)
Authors: Schmidt Nicola , Seibt Kathrin M , Weber Beatrice , Schwarzacher Trude , Schmidt Thomas , Heitkam Tony 
Published: March 2021

AbstractBackground and AimsEndogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence.MethodsUsing next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization.Key ResultsFull-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4–7.2 million years ago.ConclusionsOur study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
Direct evidence of cytosolic PNGase activity in Arabidopsis thaliana: in vitro assay system for plant cPNGase activity
Authors: Shirai Sahoko , Uemura Ryota , Maeda Megumi , Kajiura Hiroyuki , Misaki Ryo , Fujiyama Kazuhito , Kimura Yoshinobu 
Published: March 2021

ABSTRACT
Cytosolic peptide:N-glycanase (cPNGase), which occurs ubiquitously in eukaryotic cells, is involved in the de-N-glycosylation of misfolded glycoproteins in the protein quality control system. In this study, we aimed to provide direct evidence of plant cPNGase activity against a denatured glycoprotein using a crude extract prepared from a mutant line of Arabidopsis thaliana lacking 2 acidic PNGase genes.
Song type and song type matching are important for joint territorial defense in a duetting songbird
Authors: Wheeldon Amie , Szymański Paweł , Surmacki Adrian , Osiejuk Tomasz S 
Published: March 2021

Abstract
Birds have a diverse acoustic communication system, with species-specific repertoires facilitating more complex behaviors in terms of both within- and between-pair communications. Certain song types are produced for specific functions, such as aggressive encounters. In addition, song matching behaviors, whereby neighboring individuals match song types, can be used in aggressive interactions as a sophisticated acoustic behavior. In this study, we examined the functions of song types, in a duet context, of male yellow-breasted boubous (Laniarius atroflavus), an Afromontane bush-shrike with a vocal sexual dimorphism. We aimed at assessing whether, structurally, certain song types elicited a heightened reaction than others and also whether song matching affected response behavior. A dual speaker playback procedure was performed for 18 pairs of boubous, each pair being exposed to duets with three different male song types. We found differences in response toward the different duet types but these differences resulted from the amount at which males matched different song types. Pairs responded stronger when a focal male matched the playback type, and matching was significantly more often found in cases where the rarest type of male song was used. We found no sex differences in terms of response strength to playback type. Our results indicate a two-level way of coding aggression toward intruding pairs. The yellow-breasted boubous utilize their repertoires, linking matching with structure in order to show aggression in terms of territory defense and sexual conflict. This study also confirms joint territorial defense as a main function of duets in this species.
The conspecific avoidance strategies of adult female-calf humpback whales
Authors: Indeck Katherine L , Noad Michael J , Dunlop Rebecca A 
Published: March 2021

Abstract
During migration, humpback whale (Megaptera novaeangliae) adult females and their calves use acoustic calling to help maintain contact. The signals produced by these pairs, however, may unintentionally attract nearby breeding males, which can result in interactions that have negative physical and physiological effects on the calf. Therefore, maternal females must choose the vocal and/or behavioral strategy that most effectively balances intra-pair communication with male avoidance. Here, we analyzed differences in adult female-calf vocal activity and movement behavior according to the presence of, and distance to, singing whales and other groups likely to contain males. The results of this study found that these pairs make only minimal changes to their vocal behavior in response to nearby males, suggesting that they have instead evolved calls that are naturally difficult to detect (i.e., produced at significantly lower rates and acoustic levels than other whale groups, resulting in a restricted active space). In addition, they maintain spatial separation from nearby groups by moving to shallower, inshore waters, increasing their proportion of time spent near the surface, and favoring a direct migratory course. This combination of cryptic strategies balances avoidance of unwanted conspecific interaction with the necessity of continued contact between maternal female humpback whales and their calves.
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
Authors: Sánchez Juan A , Gil-Martinez Ana L , Cisterna Alejandro , García-Ruíz Sonia , Gómez-Pascual Alicia , Reynolds Regina H , Nalls Mike , Hardy John , Ryten Mina , Botía Juan A 
Published: March 2021

Abstract

Motivation
Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behavior for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single &lt;gene, function, cell type&gt; for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks.

Results
We applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets &lt;gene, function, cell type&gt; by 46.73%. Moreover, GMSCA predicts that the SNCA gene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes.

Availabilityand implementation
The tool is available at GitHub, https://github.com/drlaguna/GMSCA as open-source software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Fast and sensitive taxonomic assignment to metagenomic contigs
Authors: Mirdita M , Steinegger M , Breitwieser F , Söding J , Levy Karin E 
Published: March 2021

Abstract

Summary
MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig’s taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2–18× faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.

Availability and implementation
MMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
Highly variable sperm morphology in the masked finch (Poephila personata) and other estrildid finches
Authors: Mccarthy Elise , Mcdiarmid Callum S , Hurley Laura L , Rowe Melissah , Griffith Simon C 
Published: March 2021

AbstractSpermatozoa exhibit remarkable levels of morphological diversification among and within species. Among the passerine birds, the zebra finch (Taeniopygia guttata) has become a model system for studies of sperm biology, yet studies of closely related Estrildidae finches remain scarce. Here, we examine sperm morphology in the masked finch (Poephila personata) and place the data into the broader context of passerine sperm morphology using data for an additional 189 species. The masked finch exhibited high levels of within- and among-male variation in total sperm length and in specific sperm components. Furthermore, among-male variance in sperm length was significantly greater in estrildid (N = 12) compared with non-estrildid species (N = 178). We suggest that the high variation in sperm morphology in the masked finch and other estrildid species is likely to be linked to low levels of sperm competition, hence relaxed or weak selection on sperm length, in the clade. Our findings highlight that the highly variable sperm of the masked finch and widely studied zebra finch are ‘typical’ for estrildid species and stress the relevance of studying groups of closely related species. Finally, we suggest that further studies of Estrildidae will enhance our understanding of sperm diversity and avian diversity more generally.
Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda)
Authors: Cortez Thainá , Amaral Rafael V , Sobral-Souza Thadeu , Andrade Sónia C S 
Published: March 2021

Abstract
An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.
Securitizing the Colour Revolution: Assessing the Political Role of Triads in Hong Kong’s Umbrella Movement
Authors: Lo T Wing , Kwok Sharon Ingrid , Garrett Daniel 
Published: March 2021

Abstract
In Hong Kong’s Umbrella Movement, the use of Chinese triads to attack protestors has attracted international attention, forcing the regime to constrain further acts of grand illegitimate violence. Research suggests that triads were used as ‘thugs-for-hire’ by the regime to achieve political ends. The present study aims to examine why the triads were hired and what their specific roles and motivations were. It concludes that triads acted as non-state securitization actors, agent provocateurs or extralegal protectors depending on several factors, such as financial incentives, being stakeholders in occupied sites, business interests in mainland China and individuals’ political ideology. It suggests that triads were used as vigilantes against the threats of Western-instigated Color Revolution and hybrid warfare targeting China.