cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Risk factors for foot ulceration in adults with end-stage renal disease on dialysis: a prospective observational cohort study
Creators: name: Kaminski, Michelle
name: Lambert, Katrina
name: Raspovic, Anita
name: LP McMahon
name: Erbas, Bircan
name: PF Mount
name: PG Kerr
name: Landorf, Karl
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Background: Dialysis patients experience high rates of foot ulceration. Although risk factors for ulceration have been extensively studied in patients with diabetes, there is limited high-quality, longitudinal evidence in the dialysis population. Therefore, this study investigated risk factors for foot ulceration in a stable dialysis cohort. Methods: We prospectively collected clinical, demographic, health status, and foot examination information on 450 adults with end-stage renal disease from satellite and home-therapy dialysis units in Melbourne, Australia over 12 months. The primary outcome was foot ulceration. Cox proportional hazard modelling and multinomial regression were used to investigate risk factors. Results: Among 450 dialysis patients (mean age, 67.5 years; 64.7% male; 94% hemodialysis; 50.2% diabetes), new cases of foot ulceration were identified in 81 (18%) participants. Overall, risk factors for foot ulceration were neuropathy (HR 3.02; 95% CI 1.48 to 6.15) and previous ulceration (HR 2.86; CI 1.53 to 5.34). In those without history of ulceration, nail pathology (RR 3.85; CI 1.08 to 13.75) and neuropathy (RR 2.66; CI 1.04 to 6.82) were risk factors. In those with history of ulceration, neuropathy (RR 11.23; CI 3.16 to 39.87), peripheral arterial disease (RR 7.15; CI 2.24 to 22.82) and cerebrovascular disease (RR 2.08; CI 1.04 to 4.16) were risk factors. There were 12 (2.7%) new amputations, 96 (21.3%) infections, 24 (5.3%) revascularizations, 42 (9.3%) foot-related hospitalizations, and 52 (11.6%) deaths. Conclusions: Neuropathy and previous ulceration are major risk factors for foot ulceration in dialysis patients. Risk factors differ between those with and without prior ulceration. The risk factors identified will help to reduce the incidence of ulceration and its associated complications.
Illuminating meanings of thriving for persons living in nursing homes
Creators: name: Baxter, Rebecca
name: Per-Olof Sandman
name: Björk, Sabine
name: Qarin Lood
name: Edvardsson, David
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © 2019 The Author(s). Published by Oxford University Press on behalf of The Gerontological Society of America. Background and Objectives: Thriving has been described as a multidimensional concept that can be used to explore place-related well-being; however, there has been limited research into the meaning of thriving in aged care. This study aimed to illuminate meanings of thriving as narrated by persons living in nursing homes. Research Design and Methods: Narrative interviews were conducted with 21 persons residing in a rural Australian nursing home. The interviews were audio-recorded, transcribed, and interpreted using a phenomenological hermeneutic approach. Results: Meanings of thriving could be understood as: Striving toward acceptance of being in a nursing home while maintaining a positive outlook; Feeling supported and cared for while maintaining a sense of independence; Balancing opportunities for solitude and company while living with others; and, Feeling a sense of home while residing in an institutional environment. The meanings of thriving, as presented through the interpretive lens of Gaston Bachelard's "Poetics of Space,"encompassed having access to literal, metaphorical, and symbolic doors, as well as having the freedom to open, close, and use these doors however the person wishes. Discussion: Exploring meanings of thriving in nursing homes could contribute towards understanding and implementing positive life-world constructs in research and practice. These findings could be used to inform and enhance person-centered care practices by maximizing opportunities for persons residing in nursing homes to have options and choices, and the agency to make decisions where possible, in relation to their everyday care and living environment.
Modern Beijing sublineage of Mycobacterium tuberculosis shift macrophage into a hyperinflammatory status
Creators: name: Tong, Jingfeng
name: Meng, Lu
name: Bei, Cheng
name: Liu, Qingyun
name: Wang, Min
name: Yang, TingTing
name: Takiff, Howard E.
name: Zhang, Shuye
name: Gao, Qian
name: Wang, Chuan
name: Yan, Bo
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences

description: The high prevalence of the modern Beijing sublineage of Mycobacterium tuberculosis may be related to increased virulence, although the responsible mechanisms remain poorly understood. We previously described enhanced triacylglycerol accumulation in modern Beijing strains. Here we show that modern Beijing strains grow faster in vitro and trigger a vigorous immune response and pronounced macrophage infiltration. Transcriptomic analysis of bone marrow derived macrophages infected with modern Beijing lineage strains revealed a significant enrichment of infection, cholesterol homeostasis and amino acid metabolic pathways. The upregulation of proinflammatory / bactericidal cytokines was confirmed by RT-PCR analysis, which is also in consistent with the reduced bacterial burden in modern strains infected macrophages. These results suggest that modern Beijing strains elicit a hyperinflammatory response which might indicate a stronger virulence and contribute to their extensive global prevalence.
Emergence, Prevalence, and Evolution of H5N8 Avian Influenza Viruses in Central China, 2020
Creators: name: Li, Xiang
name: Lv, Xinru
name: Li, Yi
name: Xie, Linhong
name: Peng, Peng
name: An, Qing
name: Fu, Tian
name: Qin, Siyuan
name: Cui, Yuan
name: Zhang, Chengbo
name: Qin, Rongxiu
name: Qu, Fengyi
name: Zhao, Zhenliang
name: Wang, Meixi
name: Xu, Qiuzi
name: Li, Yong
name: Yang, Guoxiang
name: Chen, Guang
name: Zhang, Jun
name: Zheng, Hesong
name: Ma, Enda
name: Zhou, Ruifang
name: Zeng, Xiangwei
name: Wang, Yulong
name: Hou, Zhijun
name: Wang, Yajun
name: Chu, Dong
name: Li, Yanbing
name: Chai, Hongliang
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Highly pathogenic influenza A(H5N8) viruses have caused several worldwide outbreaks in birds and are able cross the species barrier to infect humans, posing a substantial threat to public health. After the first detection of H5N8 viruses in deceased swans in Inner Mongolia, we performed early warning and active monitoring along swan migration routes in central China. We isolated and sequenced 42 avian influenza viruses, including 40 H5N8 viruses, 1 H5N2 virus, and 1 H9N2 virus, in central China. Our H5N8 viruses isolated in swan stopover sites and wintering grounds showed high nucleotide homologies in the whole genome, revealing a common evolutionary source. Phylogenetic analysis revealed that the H5 viruses of clade 2.3.4.4b prevalent in 2020 have further diverged into two sub-clades: b1 and b2. The phylogeographic analysis also showed that the viruses of sub-clade b2 most likely originated from poultry in Russia. Notably, whooper swans were found to be responsible for the introduction of sub-clade b2 viruses in central China; whooper and tundra swans play a role in viral spread in the Yellow River Basin and the Yangtze River Basin, respectively. Our findings highlight swans as an indicator species for transborder spreading and monitoring of the H5N8 virus.
Obatoclax inhibits SARS-CoV-2 entry by altered endosomal acidification and impaired cathepsin and furin activity in vitro
Creators: name: Mao, Binli
name: Le-Trilling, Vu Thuy Khanh
name: Wang, Kai
name: Mennerich, Denise
name: Hu, Jie
name: Zhao, Zhenyu
name: Zheng, Jiaxin
name: Deng, Yingying
name: Katschinski, Benjamin
name: Xu, Shilei
name: Zhang, Guiji
name: Cai, Xuefei
name: Hu, Yuan
name: Wang, Jianwei
name: Lu, Mengji
name: Huang, Ailong
name: Tang, Ni
name: Trilling, Mirko
name: Lin, Yong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Coronavirus disease 2019 (COVID-19) caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has set off a global pandemic. There is an urgent unmet need for safe, affordable, and effective therapeutics against COVID-19. In this regard, drug repurposing is considered as a promising approach. We assessed the compounds that affect the endosomal acidic environment by applying human angiotensin-converting enzyme 2 (hACE2)- expressing cells infected with a SARS-CoV-2 spike (S) protein-pseudotyped HIV reporter virus and identified that obatoclax resulted in the strongest inhibition of S protein-mediated virus entry. The potent antiviral activity of obatoclax at nanomolar concentrations was confirmed in different human lung and intestinal cells infected with the SARS-CoV-2 pseudotype system as well as clinical virus isolates. Furthermore, we uncovered that obatoclax executes a double-strike against SARS-CoV-2. It prevented SARS-CoV-2 entry by blocking endocytosis of virions through diminished endosomal acidification and the corresponding inhibition of the enzymatic activity of the endosomal cysteine protease cathepsin L. Additionally, obatoclax impaired the SARS-CoV-2 S-mediated membrane fusion by targeting the MCL-1 protein and reducing furin protease activity. In accordance with these overarching mechanisms, obatoclax blocked the virus entry mediated by different S proteins derived from several SARS-CoV-2 variants of concern such as, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Taken together, our results identified obatoclax as a novel effective antiviral compound that keeps SARS-CoV-2 at bay by blocking both endocytosis and membrane fusion. Our data suggested that obatoclax should be further explored as a clinical drug for the treatment of COVID-19.
DS_10.1177_0022034520962751 – Supplemental material for Dental Research Waste in Design, Analysis, and Reporting: A Scoping Review
Creators: name: N. Pandis
name: P.S. Fleming
name: C. Katsaros
name: J.P.A. Ioannidis
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 110599 Dentistry not elsewhere classified
subject: FOS: Clinical medicine
subject: 91299 Materials Engineering not elsewhere classified
subject: FOS: Materials engineering

description: Supplemental material, DS_10.1177_0022034520962751 for Dental Research Waste in Design, Analysis, and Reporting: A Scoping Review by N. Pandis, P.S. Fleming, C. Katsaros and J.P.A. Ioannidis in Journal of Dental Research
Understanding traditional and modern eating: the TEP10 framework
Creators: name: Sproesser, G
name: Ruby, Matthew
name: Arbit, N
name: Akotia, CS
name: Alvarenga, MDS
name: Bhangaokar, R
name: Furumitsu, I
name: Hu, X
name: Imada, S
name: Kaptan, G
name: Kaufer-Horwitz, M
name: Menon, U
name: Fischler, C
name: Rozin, P
name: Schupp, HT
name: Renner, B
Publisher: name: La Trobe
Year: 2022
Subjects: classificationCode: 300699
subject: Food sciences not elsewhere classified
classificationCode: 321099
subject: Nutrition and dietetics not elsewhere classified
classificationCode: 420699
subject: Public health not elsewhere classified

description: Across the world, there has been a movement from traditional to modern eating, including a movement of traditional eating patterns from their origin culture to new cultures, and the emergence of new foods and eating behaviors. This trend toward modern eating is of particular significance because traditional eating has been related to positive health outcomes and sustainability. Yet, there is no consensus on what constitutes traditional and modern eating. The present study provides a comprehensive compilation of the various facets that seem to make up traditional and modern eating. Specifically, 106 facets were mentioned in the previous literature and expert discussions, combining international and interdisciplinary perspectives. The present study provides a framework (the TEP10 framework) systematizing these 106 facets into two major dimensions, what and how people eat, and 12 subdimensions. Hence, focusing only on single facets of traditional and modern eating is an oversimplification of this complex phenomenon. Instead, the multidimensionality and interplay between different facets should be considered to gain a comprehensive understanding of the trends, consequences, and underlying factors of traditional and modern eating.
Additional file 1 of The use of technology to improve medication adherence in heart failure patients: a systematic review of randomised controlled trials
Creators: name: Cheng, Chloe
name: Donovan, Gemma
name: Al-Jawad, Naseer
name: Jalal, Zahraa
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1: Table S1. Example search strategy- EMBASE. Table S2. Other clinical outcomes and their effects.
Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides
Creators: name: Zhang, Wen
name: Li, ZhiFei
name: Sun, Yufan
name: Cui, Peng
name: Liang, Jianhua
name: Xing, Qinghe
name: Wu, Jing
name: Xu, Yanhui
name: Zhang, Wenhong
name: Zhang, Ying
name: He, Lin
name: Gao, Ning
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis (Mtb). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with D. radiodurans (Dra) ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for Mtb remains elusive since the Mtb ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the Mtb ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 (E. coli numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel syn-conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C–H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.
sj-pdf-1-jhs-10.1177_1753193420968040 - Supplemental material for Challenging the dogma: severely angulated neck fractures of the fifth metacarpal must be treated surgically
Creators: name: Boeckstyns, Michel E. H.
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 110314 Orthopaedics
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine
subject: FOS: Health sciences
subject: 110323 Surgery

description: Supplemental material, sj-pdf-1-jhs-10.1177_1753193420968040 for Challenging the dogma: severely angulated neck fractures of the fifth metacarpal must be treated surgically by Michel E. H. Boeckstyns in Journal of Hand Surgery (European Volume)
sj-pdf-1-cep-10.1177_0333102420966581 - Supplemental material for Characterization and preclinical evaluation of a protease activated receptor 2 (PAR2) monoclonal antibody as a preventive therapy for migraine
Creators: name: Kopruszinski, Caroline M
name: Thornton, Peter
name: Arnold, Joanne
name: Newton, Philip
name: Lowne, David
name: Navratilova, Edita
name: Swiokla, Juliana
name: Dodick, David W
name: Dobson, Claire
name: Gurrell, Ian
name: Chessell, Iain Patrick
name: Porreca, Frank
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 110904 Neurology and Neuromuscular Diseases
subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: Neuroscience

description: Supplemental material, sj-pdf-1-cep-10.1177_0333102420966581 for Characterization and preclinical evaluation of a protease activated receptor 2 (PAR2) monoclonal antibody as a preventive therapy for migraine by Caroline M Kopruszinski, Peter Thornton, Joanne Arnold, Philip Newton, David Lowne, Edita Navratilova, Juliana Swiokla, David W Dodick, Claire Dobson, Ian Gurrell, Iain Patrick Chessell and Frank Porreca in Cephalalgia
Omicron variant showed lower neutralizing sensitivity than other SARS-CoV-2 variants to immune sera elicited by vaccines after boost
Creators: name: Ai, Jingwen
name: Zhang, Haocheng
name: Zhang, Yi
name: Lin, Ke
name: Zhang, Yanliang
name: Wu, Jing
name: Wan, Yanming
name: Huang, Yanfang
name: Song, Jieyu
name: Fu, Zhangfan
name: Wang, Hongyu
name: Guo, Jingxin
name: Jiang, Ning
name: Fan, Mingxiang
name: Zhou, Yang
name: Zhao, Yuanhan
name: Zhang, Qiran
name: Liu, Qiang
name: Lv, Jing
name: Li, Peiyao
name: Qiu, Chao
name: Zhang, Wenhong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Physiology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The emerging new VOC B.1.1.529 (Omicron) variant has raised serious concerns due to multiple mutations, reported significant immune escape, and unprecedented rapid spreading speed. Currently, studies describing the neutralization ability of different homologous and heterologous booster vaccination against Omicron are still lacking. In this study, we explored the immunogenicity of COVID-19 breakthrough patients, BBIBP-CorV homologous booster group and BBIBP-CorV/ZF2001 heterologous booster group against SARS-CoV-2 pseudotypes corresponding to the prototype, Beta, Delta, and the emergent Omicron variant. Notably, at 14 days post two-dose inactivated vaccines, pVNT titre increased to 67.4 GMTs against prototype, 8.85 against Beta and 35.07 against Delta, while neutralization activity against Omicron was below the lower limit of quantitation in 80% of the samples. At day 14 post BBIBP-CorV homologous booster vaccination, GMTs of pVNT significantly increased to 285.6, 215.7, 250.8, 48.73 against prototype, Beta, Delta, and Omicron, while at day 14 post ZF2001 heterologous booster vaccination, GMTs of pVNT significantly increased to 1436.00, 789.6, 1501.00, 95.86, respectively. Post booster vaccination, 100% samples showed positive neutralization activity against Omicron, albeit illustrated a significant reduction (5.86- to 14.98-fold) of pVNT against Omicron compared to prototype at 14 days after the homologous or heterologous vaccine boosters. Overall, our study demonstrates that vaccine-induced immune protection might more likely be escaped by Omicron compared to prototypes and other VOCs. After two doses of inactivated whole-virion vaccines as the “priming” shot, a third heterologous protein subunit vaccine and a homologous inactivated vaccine booster could improve neutralization against Omicron.
HIV self-testing intervention experiences and kit usability: results from a qualitative study among men who have sex with men in the SELHPI (Self-Testing Public Health Intervention) randomized controlled trial in England and Wales
Creators: name: TC Witzel
name: Bourne, Adam
name: FM Burns
name: AJ Rodger
name: L McCabe
name: MM Gabriel
name: M Gafos
name: D Ward
name: Y Collaco-Moraes
name: DT Dunn
name: A Speakman
name: C Bonell
name: R Pebody
name: FC Lampe
name: J Harbottle
name: AN Phillips
name: S McCormack
name: P Weatherburn
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © 2019 The Authors. HIV Medicine published by John Wiley & Sons Ltd on behalf of British HIV Association Objectives: SELPHI (HIV Self-Testing Public Health Intervention) is the largest randomized controlled trial (RCT) of HIV self-testing (HIVST) in a high-income setting to date, and has recruited 10 000 men who have sex with men (cis- and transgender) and transgender women who have sex with men. This qualitative substudy aimed to explore how those utilizing self-tests experience HIVST and the implications for further intervention development and scale-up. This is the first qualitative study in Europe investigating experiences of HIVST among intervention users, and the first globally examining the experience of using blood-based HIVST. Methods: Thirty-seven cisgender MSM SELPHI participants from across England and Wales were purposively recruited to the substudy, in which semi-structured interviews were used to explore testing history, HIVST experiences and intervention preferences. Interviews were audio-recorded, transcribed and analysed through a framework analysis. Results: Men accessed the intervention because HIVST reduced barriers related to convenience, stigma and privacy concerns. Emotional responses had direct links to acceptability. Supportive intervention components increased engagement with testing and addressed supportive concerns. HIVST facilitated more frequent testing, with the potential to reduce sexually transmitted infection (STI) screening frequency. Substudy participants with an HIV-positive result (n = 2) linked to care promptly and reported very high acceptability. Minor adverse outcomes (n = 2; relationship discord and fainting) did not reduce acceptability. Ease of use difficulties were with the lancet and the test processing stage. Conclusions: Intervention components shaped acceptability, particularly in relation to overcoming a perceived lack of support. The intervention was broadly acceptable and usable; participants expressed an unexpected degree of enthusiasm for HIVST, including those with HIV-positive results and individuals with minor adverse outcomes.
Reviewer_2_v.1 – Supplemental material for Clinical characteristics and risk factors for severity of COVID-19 outside Wuhan: a double-center retrospective cohort study of 213 cases in Hunan, China
Creators: name: Hu, Xingsheng
name: Hu, Chunhong
name: Yang, Yong
name: Chen, Juan
name: Zhong, Ping
name: Wen, Yajing
name: Chen, Xiangyu
Publisher: name: SAGE Journals
Year: 2020
Subjects: Aged Health Care
Pharmacology and Pharmaceutical Sciences not elsewhere classified
Respiratory Diseases

description: Supplemental material, Reviewer_2_v.1 for Clinical characteristics and risk factors for severity of COVID-19 outside Wuhan: a double-center retrospective cohort study of 213 cases in Hunan, China by Xingsheng Hu, Chunhong Hu, Yong Yang, Juan Chen, Ping Zhong, Yajing Wen and Xiangyu Chen in Therapeutic Advances in Respiratory Disease
Bioinformatic analysis of eosinophil activity and its implications for model and target species
Creators: name: Jenvey, Caitlin
name: Alenizi, Dalal Sader H
name: Fazel Almasi
name: Cairns, Callum
name: A Holmes
name: Sloan, Sarah
name: Stear, Michael
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Copyright © The Author(s), 2019. Published by Cambridge University Press. Eosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.
online_supp-Supplementary_Information_file_Selective_Exposure_to_Multimodal_Communication – Supplemental material for Selection in a Snapshot? The Contribution of Visuals to the Selection and Avoidance of Political News in Information-Rich Media Settings
Creators: name: Powell, Thomas E.
name: Hameleers, Michael
name: Meer, Toni G. L. A. Van Der
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 200199 Communication and Media Studies not elsewhere classified
subject: FOS: Media and communications
subject: 160607 International Relations
subject: FOS: Political science

description: Supplemental material, online_supp-Supplementary_Information_file_Selective_Exposure_to_Multimodal_Communication for Selection in a Snapshot? The Contribution of Visuals to the Selection and Avoidance of Political News in Information-Rich Media Settings by Thomas E. Powell, Michael Hameleers and Toni G. L. A. van der Meer in The International Journal of Press/Politics
Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile (Crocodylus porosus)
Creators: name: Sarker, Subir
name: Isberg, SR
name: Moran, JL
name: Araujo, RD
name: Elliott, N
name: Melville, L
name: Beddoe, Travis
name: Helbig, Karla
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3107
subject: Microbiology

description: © 2019 by the authors. Saltwater crocodilepox virus (SwCRV), belonging to the genus Crocodylidpoxvirus, are large DNA viruses posing an economic risk to Australian saltwater crocodile (Crocodylus porosus) farms by extending production times. Although poxvirus-like particles and sequences have been confirmed, their infection dynamics, inter-farm genetic variability and evolutionary relationships remain largely unknown. In this study, a poxvirus infection dynamics study was conducted on two C. porosus farms. One farm (Farm 2) showed twice the infection rate, and more concerningly, an increase in the number of early- to late-stage poxvirus lesions as crocodiles approached harvest size, reflecting the extended production periods observed on this farm. To determine if there was a genetic basis for this difference, 14 complete SwCRV genomes were isolated from lesions sourced from five Australian farms. They encompassed all the conserved genes when compared to the two previously reported SwCRV genomes and fell within three major clades. Farm 2's SwCRV sequences were distributed across all three clades, highlighting the likely mode of inter-farm transmission. Twenty-four recombination events were detected, with one recombination event resulting in consistent fragmentation of the P4c gene in the majority of the Farm 2 SwCRV isolates. Further investigation into the evolution of poxvirus infection in farmed crocodiles may offer valuable insights in evolution of this viral family and afford the opportunity to obtain crucial information into natural viral selection processes in an in vivo setting.
Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile (Crocodylus porosus)
Creators: name: Sarker, Subir
name: SR Isberg
name: JL Moran
name: RD Araujo
name: N Elliott
name: L Melville
name: Beddoe, Travis
name: Helbig, Karla J
Publisher: name: La Trobe
Year: 2020
Subjects: Uncategorized

description: © 2019 by the authors. Saltwater crocodilepox virus (SwCRV), belonging to the genus Crocodylidpoxvirus, are large DNA viruses posing an economic risk to Australian saltwater crocodile (Crocodylus porosus) farms by extending production times. Although poxvirus-like particles and sequences have been confirmed, their infection dynamics, inter-farm genetic variability and evolutionary relationships remain largely unknown. In this study, a poxvirus infection dynamics study was conducted on two C. porosus farms. One farm (Farm 2) showed twice the infection rate, and more concerningly, an increase in the number of early- to late-stage poxvirus lesions as crocodiles approached harvest size, reflecting the extended production periods observed on this farm. To determine if there was a genetic basis for this difference, 14 complete SwCRV genomes were isolated from lesions sourced from five Australian farms. They encompassed all the conserved genes when compared to the two previously reported SwCRV genomes and fell within three major clades. Farm 2's SwCRV sequences were distributed across all three clades, highlighting the likely mode of inter-farm transmission. Twenty-four recombination events were detected, with one recombination event resulting in consistent fragmentation of the P4c gene in the majority of the Farm 2 SwCRV isolates. Further investigation into the evolution of poxvirus infection in farmed crocodiles may offer valuable insights in evolution of this viral family and afford the opportunity to obtain crucial information into natural viral selection processes in an in vivo setting.
Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain
Creators: name: Betts, Natalie S
name: Dockter, Christoph
name: Berkowitz, Oliver
name: Collins, Helen M
name: Hooi, Michelle
name: Qiongxian Lu
name: Burton, Rachel A
name: Bulone, Vincent
name: Skadhauge, Birgitte
name: Whelan, James
name: Fincher, Geoffrey B
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. Mobilization of reserves in germinated cereal grains is critical for early seedling vigour, global crop productivity, and hence food security. Gibberellins (GAs) are central to this process. We have developed a spatio-temporal model that describes the multifaceted mechanisms of GA regulation in germinated barley grain. The model was generated using RNA sequencing transcript data from tissues dissected from intact, germinated grain, which closely match measurements of GA hormones and their metabolites in those tissues. The data show that successful grain germination is underpinned by high concentrations of GA precursors in ungerminated grain, the use of independent metabolic pathways for the synthesis of several bioactive GAs during germination, and a capacity to abort bioactive GA biosynthesis. The most abundant bioactive form is GA1, which is synthesized in the scutellum as a glycosyl conjugate that diffuses to the aleurone, where it stimulates de novo synthesis of a GA3 conjugate and GA4. Synthesis of bioactive GAs in the aleurone provides a mechanism that ensures the hormonal signal is relayed from the scutellum to the distal tip of the grain. The transcript data set of 33 421 genes used to define GA metabolism is available as a resource to analyse other physiological processes in germinated grain.
Mapping cross-variant neutralizing sites on the SARS-CoV-2 spike protein
Creators: name: Xu, Shiqi
name: Wang, Yifan
name: Wang, Yanxing
name: Zhang, Chao
name: Hong, Qin
name: Gu, Chenjian
name: Xu, Rong
name: Wang, Tingfeng
name: Yang, Yong
name: Zang, Jinkai
name: Zhou, Yu
name: Li, Zuyang
name: Liu, Qixing
name: Zhou, Bingjie
name: Bai, Lulu
name: Zhu, Yuanfei
name: Deng, Qiang
name: Wang, Haikun
name: Lavillette, Dimitri
name: Wong, Gary
name: Xie, Youhua
name: Cong, Yao
name: Huang, Zhong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The emergence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of currently approved vaccines and authorized therapeutic monoclonal antibodies (MAbs). It is hence important to continue searching for SARS-CoV-2 broadly neutralizing MAbs and defining their epitopes. Here, we isolate 9 neutralizing mouse MAbs raised against the spike protein of a SARS-CoV-2 prototype strain and evaluate their neutralizing potency towards a panel of variants, including B.1.1.7, B.1.351, B.1.617.1, and B.1.617.2. By using a combination of biochemical, virological, and cryo-EM structural analyses, we identify three types of cross-variant neutralizing MAbs, represented by S5D2, S5G2, and S3H3, respectively, and further define their epitopes. S5D2 binds the top lateral edge of the receptor-binding motif within the receptor-binding domain (RBD) with a binding footprint centred around the loop477–489, and efficiently neutralizes all variant pseudoviruses, but the potency against B.1.617.2 was observed to decrease significantly. S5G2 targets the highly conserved RBD core region and exhibits comparable neutralization towards the variant panel. S3H3 binds a previously unreported epitope located within the evolutionarily stable SD1 region and is able to near equally neutralize all of the variants tested. Our work thus defines three distinct cross-variant neutralizing sites on the SARS-CoV-2 spike protein, providing guidance for design and development of broadly effective vaccines and MAb-based therapies.
Hello old friend- Plantago ovata
Creators: name: Matharu, Mandeep
Publisher: name: Zenodo
Year: 2022

description: Abstract of conference oral presentation on Hello old friend- Plantago ovata by Herbarium Curator (digitiser) Mandeep Matharu of Herbarium Curator (digitiser) Royal Horticultural Society Gardens Surrey United Kingdom for SPNHC2022 Conference, Edinburgh. June 5-10th 2022.
sj-pdf-1-ajr-10.1177_1945892420964169 - Supplemental material for TRPV4-Mediated Epithelial Junction Disruption in Allergic Rhinitis Triggered by House Dust Mites
Creators: name: Kijeong Lee
name: Junhyoung Byun
name: Byoungjae Kim
name: Jiwoo Yeon
name: Junhu Tai
name: Lee, Sang Hag
name: Kim, Tae Hoon
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 110315 Otorhinolaryngology
subject: FOS: Clinical medicine

description: Supplemental material, sj-pdf-1-ajr-10.1177_1945892420964169 for TRPV4-Mediated Epithelial Junction Disruption in Allergic Rhinitis Triggered by House Dust Mites by Kijeong Lee MD, Junhyoung Byun MS, Byoungjae Kim PhD, Jiwoo Yeon MS, Junhu Tai MD, Sang Hag Lee MD, PhD, Tae Hoon Kim MD, PhD in American Journal of Rhinology & Allergy
Obatoclax inhibits SARS-CoV-2 entry by altered endosomal acidification and impaired cathepsin and furin activity in vitro
Creators: name: Mao, Binli
name: Le-Trilling, Vu Thuy Khanh
name: Wang, Kai
name: Mennerich, Denise
name: Hu, Jie
name: Zhao, Zhenyu
name: Zheng, Jiaxin
name: Deng, Yingying
name: Katschinski, Benjamin
name: Xu, Shilei
name: Zhang, Guiji
name: Cai, Xuefei
name: Hu, Yuan
name: Wang, Jianwei
name: Lu, Mengji
name: Huang, Ailong
name: Tang, Ni
name: Trilling, Mirko
name: Lin, Yong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Coronavirus disease 2019 (COVID-19) caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has set off a global pandemic. There is an urgent unmet need for safe, affordable, and effective therapeutics against COVID-19. In this regard, drug repurposing is considered as a promising approach. We assessed the compounds that affect the endosomal acidic environment by applying human angiotensin-converting enzyme 2 (hACE2)-expressing cells infected with a SARS-CoV-2 spike (S) protein-pseudotyped HIV reporter virus and identified that obatoclax resulted in the strongest inhibition of S-protein-mediated virus entry. The potent antiviral activity of obatoclax at nanomolar concentrations was confirmed in different human lung and intestinal cells infected with the SARS-CoV-2 pseudotype system as well as clinical virus isolates. Furthermore, we uncovered that obatoclax executes a double-strike against SARS-CoV-2. It prevented SARS-CoV-2 entry by blocking endocytosis of virions through diminished endosomal acidification and the corresponding inhibition of the enzymatic activity of the endosomal cysteine protease cathepsin L. Additionally, obatoclax impaired the SARS-CoV-2 S-mediated membrane fusion by targeting the MCL-1 protein and reducing furin protease activity. In accordance with these overarching mechanisms, obatoclax blocked the virus entry mediated by different S proteins derived from several SARS-CoV-2 variants of concern such as, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Taken together, our results identified obatoclax as a novel effective antiviral compound that keeps SARS-CoV-2 at bay by blocking both endocytosis and membrane fusion. Our data suggested that obatoclax should be further explored as clinical drug for the treatment of COVID-19.
Informing COVID-19 Response and Health Equity Agenda: Collection of Public Health Reports Articles on Emerging Viral Epidemics in the United States, 1878-2021
Creators: name: Harada, Noelle M.
name: Dean, Hazel D.
name: Kuzmichev, Andrey
name: Dembek, Zygmunt F.
name: Ising, Amy I.
Publisher: name: SAGE Publications
Year: 2023

description:
OBJECTIVE: Public Health Reports (PHR) is the oldest public health journal in the United States and has reported on viral epidemics since the 19th century. We describe the creation and analysis of a collection of historic PHR articles on emerging viral epidemics in the United States to inform public health response to COVID-19 and future epidemics. METHODS: We searched databases from 1878 through 2021 using custom search strings and conducted a manual search for articles published under previously used names for PHR. We evaluated all articles based on inclusion/exclusion criteria and coded the final list for virus/disease, article type, public health emergency preparedness and response capabilities from the Centers for Disease Control and Prevention (CDC), and PubMed citation count. RESULTS: We identified 349 relevant articles including 130 commentaries/reviews/editorials, 79 epidemiologic reports, 75 research articles, and 65 case study/practice articles. The collection focused on influenza (n = 244), COVID-19 (n = 75), dengue (n = 14), and other emerging viruses, such as Zika and Ebola (n = 25). The collection included 48 articles on health disparities/health of various disadvantaged populations, highlighting such disparities as race and ethnicity (n = 22), socioeconomic status (n = 17), and age (n = 15). When we categorized articles by CDC public health emergency preparedness and response capabilities, we found that 207 addressed surveillance and epidemiologic investigation, 36 addressed community preparedness, and 28 addressed medical countermeasure dispensing and administration. The articles addressing surveillance and epidemiologic investigation, nonpharmaceutical interventions, and community preparedness had the most PubMed citations (799, 334, and 308, respectively). CONCLUSIONS: PHR's historic articles on US emerging viral epidemics covered a range of virus/disease types, emergency preparedness and response capabilities, and contribution types and were widely cited in the scholarly literature. This publicly available and continuously updated collection is a valuable resource for pandemic planning and response.
Direct neuronal infection of SARS-CoV-2 reveals cellular and molecular pathology of chemosensory impairment of COVID-19 patients
Creators: name: Lyoo, Kwang-Soo
name: Kim, Hyeon Myeong
name: Lee, Bina
name: Che, Young Hyun
name: Kim, Seong-Jae
name: Song, Daesub
name: Hwang, Woochang
name: Lee, Sun
name: Park, Jae-Hoon
name: Na, Woonsung
name: Yun, Seung Pil
name: Kim, Yong Jun
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: Information Systems not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Direct neuronal infection of SARS-CoV-2 reveals cellular and molecular pathology of chemosensory impairment of COVID-19 patients
Additional file 2 of Genome wide transcriptome analysis provides bases on hepatic lipid metabolism disorder affected by increased dietary grain ratio in fattening lambs
Creators: name: Mi, Hui
name: Hu, Fan
name: Gebeyew, Kefyalew
name: Cheng, Yan
name: Du, Ruiping
name: Gao, Min
name: He, Zhixiong
name: Tan, Zhiliang
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: Table S2 Primer sequences used for real-time quantitative PCR
Antibiotic resistance in hospital-acquired ESKAPE-E infections in low- and lower-middle-income countries: a systematic review and meta-analysis
Creators: name: Ayobami, Olaniyi
name: Brinkwirth, Simon
name: Eckmanns, Tim
name: Markwart, Robby
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Antimicrobial resistance (AMR) and hospital-acquired infections (HAIs) are global health challenges. The burden of antibiotic resistance in HAIs is still unclear in low- and lower-middle-income countries (L-LMICs). This study summarizes recent data on antibiotic resistance in priority HAIs (ESKAPE-E) in L-LMICs and compares them with data from high-income countries (HICs). EMBASE, Web of Science, and Global Index Medicus were searched for studies on AMR patterns in HAIs published from 01/2010 to 10/2020. Random-effects meta-analyses were performed to obtain pooled estimates. In total, 163 eligible studies were included in the review and meta-analysis. The pooled methicillin resistance proportion in Staphylococcus aureus was 48.4% (95% confidence interval [95%CI] 41·7-55·2, n = 80). Pooled carbapenem resistance proportions were high in Gram-negative pathogens: Escherichia coli: 16·6% (95%CI 10·7-23·4, n = 60); Klebsiella pneumoniae: 34·9% (95%CI 24·6-45·9, n = 50); Pseudomonas aeruginosa: 37.1% (95%CI 24·6-45·9, n = 56); Enterobacter spp.: 51·2% (95%CI 27·5-74·7, n = 7); and Acinetobacter baumannii (complex): 72·4% (95%CI 62·1-81·7%, n = 36). A higher resistance proportions were observed for third-generation cephalosporins: Klebsiella pneumoniae: 78·7% (95%CI 71·5-85·2, n = 46); Escherichia coli: 78·5% (95%CI 72·1-84·2%, n = 58); and Enterobacter spp.: 83·5% (95%CI 71·9-92·8, n = 8). We observed a high between-study heterogeneity (I2 > 80%), which could not be explained by our set of moderators. Pooled resistance proportions for Gram-negative pathogens were higher in L-LMICs than regional and national estimates from HICs. Patients in resource-constrained regions are particularly affected by AMR. To combat the high resistance to critical antibiotics in L-LMICs, and bridge disparities in health, it is crucial to strengthen local surveillance and the health systems in general.
Herbarium as an object for conservation. Ethical background to decision making on conservation treatments
Creators: name: Grenda-Kurmanow, Magdalena
Publisher: name: Zenodo
Year: 2022

description: Abstract of conference oral presentation on Herbarium as an object for conservation. Ethical background to decision making on conservation treatments by Assistant Professor Magdalena Grenda-Kurmanow of Assistant Professor Academy of Fine Arts in Warsaw, Faculty of Conservation and Restoration of Works of Art Warszawa Polska for SPNHC2022 Conference, Edinburgh. June 5-10th 2022.
Proteomic Insights into Endometrial Receptivity and Embryo‐Endometrial Epithelium Interaction for Implantation Reveal Critical Determinants of Fertility
Creators: name: Evans, Jemma
name: Hutchison, Jennifer
name: Salamonsen, Lois A
name: Greening, David
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim In vitro fertilization has overcome infertility issues for many couples. However, achieving implantation of a viable embryo into the maternal endometrium remains a limiting step in optimizing pregnancy success. The molecular mechanisms which characterize the transient state of endometrial receptivity, critical in enabling embryo-endometrial interactions, and proteins which underpin adhesion at the implantation interface, are limited in humans despite these temporally regulated processes fundamental to life. Hence, failure of implantation remains the “final frontier” in infertility. A human coculture model is utilized utilizing spheroids of a trophectoderm (trophoblast stem) cell line, derived from pre-implantation human embryos, and primary human endometrial epithelial cells, to functionally identify “fertile” versus “infertile” endometrial epithelium based on adhesion between these cell types. Quantitative proteomics identified proteins associated with human endometrial epithelial receptivity (“epithelial receptome”) and trophectoderm adhesion (“adhesome”). As validation, key “epithelial receptome” proteins (MAGT-1/CDA/LGMN/KYNU/PC4) localized to the epithelium of receptive phase (mid-secretory) endometrium obtained from fertile, normally cycling women but is largely absent from non-receptive (proliferative) phase tissues. Factors involved in embryo-epithelium interaction in successive temporal stages of endometrial receptivity and implantation are demonstrated and potential targets for improving fertility are provided, enhancing potential to become pregnant either naturally or in a clinical setting.