cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ioustinos, Chariton, Charito, Euelpistos, Hierax, Paion, Liberianos and their companions, martyrs of Rome
Creators: name: Admin, CSLA
Publisher: name: University of Oxford
Year: 2016
Subjects: History

description: All evidence related to Ioustinos, Chariton, Charito, Euelpistos, Hierax, Paion, Liberianos and their companions, martyrs of Rome.
Non-verbal skills in auditory word processing: implications for typical and dyslexic readers
Creators: name: Jhilal, Soufiane
name: Molinaro, Nicola
name: Klimovich-Gray, Anastasia
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Dyslexia presents with poor phonological skills and atypical neural responses to text and speech stimuli, while non-verbal intelligence remains unaffected. However, the impact of non-verbal intelligence on language-evoked neural responses in dyslexia is underexplored. This study examines non-verbal intelligence’s effects on neural responses to auditory words in typical and dyslexic readers. Participants completed IQ tests, reading and phonological assessments, and underwent magnetoencephalography recordings while listening to words. Event-related brain field responses at different stages of auditory word processing (100, 200, and 400 ms) were analysed in relation to non-verbal IQ scores. Higher non-verbal IQ in typical readers yielded earlier right hemisphere perceptual responses (100 ms). Dyslexic readers showed no IQ-related latency effects but those with lower non-verbal IQ displayed amplified left hemisphere response amplitudes at 100 ms. These findings confirm the link between non-verbal cognitive abilities and early auditory word processing in adults, highlighting distinct effects in dyslexia and controls.
Enhanced replication fitness of MERS-CoV clade B over clade A strains in camelids explains the dominance of clade B strains in the Arabian Peninsula
Creators: name: Te, Nigeer
name: Rodon, Jordi
name: Pérez, Mónica
name: Segalés, Joaquim
name: Vergara-Alert, Júlia
name: Bensaid, Albert
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Middle East respiratory syndrome coronavirus (MERS-CoV) continues infecting humans and dromedary camels. While MERS-CoV strains from the Middle East region are subdivided into two clades (A and B), all the contemporary epidemic viruses belong to clade B. Thus, MERS-CoV clade B strains may display adaptive advantages over clade A in humans and/or reservoir hosts. To test this hypothesis in vivo, we compared an early epidemic clade A strain (EMC/2012) with a clade B strain (Jordan-1/2015) in an alpaca model monitoring virological and immunological parameters. Further, the Jordan-1/2015 strain has a partial amino acid (aa) deletion in the double stranded (ds) RNA binding motif of the open reading frame ORF4a protein. Animals inoculated with the Jordan-1/2015 variant had higher MERS-CoV replicative capabilities in the respiratory tract and larger nasal viral shedding. In the nasal mucosa, the Jordan-1/2015 strain caused an early IFN response, suggesting a role for ORF4a as a moderate IFN antagonist in vivo. However, both strains elicited maximal transcription of antiviral interferon stimulated genes (ISGs) at the peak of infection on 2 days post inoculation, correlating with subsequent decreased in tissular viral loads. Genome alignment analysis revealed several clade B specific amino acid substitutions occurring in the replicase and the S proteins, which could explain a better adaptation of clade B strains in camelid hosts. Differences in replication and shedding reported herein indicate a better fitness and transmission capability of MERS-CoV clade B strains than their clade A counterparts.
Cognitive load of three levels of object categories in reading tasks: evidence from eye movements
Creators: name: Li, Jing
name: Luo, Chuanwei
name: Xiao, Jiao
name: Wang, Yimeng
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Neuroscience
Biotechnology
Biological Sciences not elsewhere classified
Science Policy
Mental Health

description: To evaluate the cognitive load of Chinese basic-level categories, eye movement measures of naturalistic reading and proofreading tasks were used. 36 participants completed two reading tasks, each involving 21 groups of sentences containing category terms of varying levels. The results indicate that the difficulty of reading tasks does not influence initial category processing, but only affects late overall processing. The cognitive economy of basic-level categories appears as the difficulty and complexity of reading tasks increase. Specifically, in the proofreading task, the cognitive load of basic-level categories is lower than that of the subordinate categories. The processing difficulty of basic-level categories in naturalistic reading is equivalent to that of the superordinate category in the overall processing. Furthermore, generalisation plays the same role as gestalt in the judgment of category cognitive economy. It results in smaller differences in processing difficulty and cognitive load between the superordinate and basic-level categories in local processing.
Additional file 7 of Immune profiling of SARS-CoV-2 epitopes in asymptomatic and symptomatic pediatric and adult patients
Creators: name: Tornesello, Anna Lucia
name: Botti, Chiara
name: Micillo, Alberto
name: Labonia, Francesco
name: Arpino, Sergio
name: Isgrò, Maria Antonietta
name: Meola, Serena
name: Russo, Luigi
name: Cavalcanti, Ernesta
name: Sale, Silvia
name: Nicastro, Carmine
name: Atripaldi, Luigi
name: Starita, Noemy
name: Cerasuolo, Andrea
name: Reimer, Ulf
name: Holenya, Pavlo
name: Buonaguro, Luigi
name: Buonaguro, Franco M.
name: Tornesello, Maria Lina
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 7: Fig.S2. A) Percentage of patients in each group, which reacted against peptides of S protein. B) Percentage of patients in each group, which reacted against peptides of M protein.
A standardized assay for the quantitative detection of serum HBV RNA in chronic hepatitis B patients
Creators: name: Yu, Guangxin
name: Chen, Ran
name: Zheng, Sujun
name: Liu, Yanna
name: Zou, Jun
name: Gu, Zhiqiang
name: Jiang, Bei
name: Gao, Qi
name: Dai, Lizhong
name: Peng, Jie
name: Wang, Jie
name: Lu, Fengmin
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Serum hepatitis B virus (HBV) pregenomic RNA (pgRNA) is a surrogate marker for reflecting the transcriptional activity of covalently closed circular DNA. However, there is still no standardized assay for the quantitative detection of serum HBV RNA in chronic hepatitis B patients. In this study, quantitative polymerase chain reactions for detecting the preC/C-RNA (preC/C region HBV pgRNA), SF-RNA (splicing variants-free pgRNA) and XR-RNA (X region remained pgRNA) regions were set up. The dynamic changes of serum pgRNA splicing variants and 3′ terminal truncations were analysed in three retrospective cohorts: 35 treatment-naive chronic HBV-infected patients (cohort A), 52 chronic hepatitis B (CHB) patients who received nucleos(t)ide analogs (NAs) therapy for 48 weeks (cohort B) and eight CHB patients who are under long-term NAs treatment (cohort C). The accuracy and sensitivity of HBV RNA detection were assessed by the National Standard of HBV RNA. We confirmed that high proportions of pgRNA splicing variants and 3′ terminal truncations were present and significantly affect the quantitative detection of serum HBV RNA in both treatment-naive and NAs-treated CHB patients. To achieve the higher accuracy and sensitivity on the detection of HBV RNA level, the primers and probes should be designed at the 5′ terminal region of HBV genome and outside the mainly spliced sequence of pgRNA, especially for CHB patients under long-term NAs treatment. This study would help to better understand the significance of the pgRNA splicing variants and 3′ terminal truncations, and further guide the clinical detection of serum HBV RNA.
Cytonemes, their formation, regulation, and roles in signaling and communication in tumorigenesis
Creators: name: S Casas-Tintó
name: Portela-Esteban, Marta
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © 2019 by the authors. Licensee MDPI, Basel, Switzerland. Increasing evidence during the past two decades shows that cells interconnect and communicate through cytonemes. These cytoskeleton-driven extensions of specialized membrane territories are involved in cell–cell signaling in development, patterning, and differentiation, but also in the maintenance of adult tissue homeostasis, tissue regeneration, and cancer. Brain tumor cells in glioblastoma extend ultralong membrane protrusions (named tumor microtubes, TMs), which contribute to invasion, proliferation, radioresistance, and tumor progression. Here we review the mechanisms underlying cytoneme formation, regulation, and their roles in cell signaling and communication in epithelial cells and other cell types. Furthermore, we discuss the recent discovery of glial cytonemes in the Drosophila glial cells that alter Wingless (Wg)/Frizzled (Fz) signaling between glia and neurons. Research on cytoneme formation, maintenance, and cell signaling mechanisms will help to better understand not only physiological developmental processes and tissue homeostasis but also cancer progression.
Success and failure of compositional generalisation in distributional models of language
Creators: name: Mao, Shufan
name: Huebner, Philip
name: Willits, Jon
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Are distributional learning mechanisms capable of complex linguistic inferences requiring compositional generalisation? This question has become contentious with the development of large language models, which mimic human language abilities in many ways, but which struggle with compositional generalisation. We investigated a set of qualitatively different distributional models (word co-occurrence models, graphical models, recurrent neural networks, and Transformers), by training them on a carefully controlled artificial language containing combinatorial dependencies involving multiple words, and then testing them on novel sequences containing distributionally overlapping combinatorial dependencies. In this work, we show that graphical network models and Transformers, but not co-occurrence space models and recurrent neural networks, were able to perform compositional generalisation. This work demonstrates that the kinds of distributional models that can perform compositional generalisation are those that can represent words both individually and as a part of the phrases in which they participate.
Overcoming expectations: Electrophysiological effects of inhibitory control demands in a non-linguistic task on subsequent semantic relatedness judgements
Creators: name: Rataj, Karolina
name: Kakuba, Patrycja
name: van Heuven, Walter J. B.
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Marine Biology
subject: Science Policy
subject: Mental Health

description: This event-related potentials study focussed on whether extensive practice of inhibitory control in a conflict task affects semantic processing/decisions in a subsequent language task. Participants took part in two 40-min sessions of the Simon task with either low or high inhibitory demands, each followed by a relatedness judgement task with strongly related, weakly related, and unrelated word pairs. The N400 in the relatedness judgement task was unaffected by inhibitory control demands of the preceding Simon task. However, the late frontal positivity for weakly related pairs was enhanced relative to the other two conditions only after the low inhibitory demands Simon task, indicating a difference in the inhibition of the expected strongly related words between the two sessions. This suggests that the mechanisms underlying semantic facilitation for weakly related pairs operate at the decision stage and these can be modulated by inhibitory control demands in a preceding non-linguistic conflict task.
Two novel human coronavirus OC43 genotypes circulating in hospitalized children with pneumonia in China
Creators: name: Zhang, Zhaoyong
name: Liu, Wenkuan
name: Zhang, Shengnan
name: Wei, Peilan
name: Zhang, Lu
name: Chen, Dehui
name: Qiu, Shuyan
name: Li, Xiaobo
name: Zhao, Jingxian
name: Shi, Yongxia
name: Zhou, Rong
name: Wang, Yanqun
name: Zhao, Jincun
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Pharmacology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.
Harbor Porpoise Time Machine: mounting a small cetacean to gain insights into how old specimens were prepared.
Creators: name: Desjardins, Becky
Publisher: name: Zenodo
Year: 2022

description: Abstract of conference oral presentation on Harbor Porpoise Time Machine: mounting a small cetacean to gain insights into how old specimens were prepared. by Senior Preparator Becky Desjardins of Senior Preparator Naturalis Biodiversity Center Leiden Netherlands for SPNHC2022 Conference, Edinburgh. June 5-10th 2022.
Two novel human coronavirus OC43 genotypes circulating in hospitalized children with pneumonia in China
Creators: name: Zhang, Zhaoyong
name: Liu, Wenkuan
name: Zhang, Shengnan
name: Wei, Peilan
name: Zhang, Lu
name: Chen, Dehui
name: Qiu, Shuyan
name: Li, Xiaobo
name: Zhao, Jingxian
name: Shi, Yongxia
name: Zhou, Rong
name: Wang, Yanqun
name: Zhao, Jincun
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Pharmacology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.
sj-pdf-1-pec-10.1177_0301006620967641 - Supplemental material for Reduced contrast sensitivity function in central and peripheral vision by disability glare
Creators: name: Wu, Di
name: Liu, Na
name: Xu, Pengbo
name: Sun, Kewei
name: Xiao, Wei
name: Li, Chenxi
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: Psychology not elsewhere classified
subject: Psychiatry (incl. Psychotherapy)

description: Supplemental material, sj-pdf-1-pec-10.1177_0301006620967641 for Reduced contrast sensitivity function in central and peripheral vision by disability glare by Di Wu, Na Liu, Pengbo Xu, Kewei Sun, Wei Xiao and Chenxi Li in Perception
Genomic epidemiology and characterisation of penicillin-sensitive Staphylococcus aureus isolates from invasive bloodstream infections in China: an increasing prevalence and higher diversity in genetic typing be revealed
Creators: name: Jin, Ye
name: Zhou, Wangxiao
name: Zhan, Qing
name: Chen, Yunbo
name: Luo, Qixia
name: Shen, Ping
name: Xiao, Yonghong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Many countries have reported increasing rates of penicillin-susceptible methicillin-sensitive Staphylococcus aureus (MSSA-PENS). To date, there is relatively little known about the current situation and molecular characteristics of MSSA-PENS in China. In this study, we carried out a laboratory-based multi-region retrospective study to investigate the genomic epidemiology and characterisation of MSSA-PENS isolated from invasive bloodstream infections (BSIs) across 17 provinces. The prevalence of MSSA-PENS isolates increased significantly over the 6-year period, with the proportion increasing from 3.51% in 2014 to 8.80% in 2019, an average relative increase of 22.14% per year (95% confidence interval 9.67%-34.61%, P for trend <0.001), suggesting that China is experiencing a resurgence of MSSA-PENS. Phylogenetic analysis showed a higher strain diversity occurred; the most frequent clonal complexes (CCs) identified were CC188 (17.14%), CC398 (15.71%) and CC5 (15.71%). Over half of MSSA-PENS strains were pan-susceptible, with erythromycin the most frequent resistance observed. Moreover, 25 isolates were identified as immune evasion cluster negative, including CC15, CC188 and CC1, and 6 strains encoded the Panton-Valentine leucocidin gene. Importantly, virulence assays showed that MSSA-PENS exhibited a level of virulence comparable to that of penicillin-resistant MSSA (MSSA-PENR), indicating that more-sensitive strains should not be mistaken for lacking aggressiveness in vivo. Furthermore, 11 of these isolates were confirmed as blaZ positive but phenotype sensitive, with different amino acid changes in blaZ. Our data support the recommendation to clinicians regarding the usage of penicillin in invasive BSIs caused by MSSA-PENS, which might create a novel opportunity for better antimicrobial stewardship in the future.
Additional file 1 of Potential of Exogenous Treatment with Dehydroascorbate to Control Root-knot Nematode Infection in Rice
Creators: name: Chavan, Satish Namdeo
name: Tumpa, Farzana Haque
name: Khokon, Md. Atiqur Rahman
name: Kyndt, Tina
Publisher: name: figshare
Year: 2024
Subjects: subject: Plant Biology
subject: FOS: Biological sciences

description: Additional File 1: Supplementary Figure S1. Experimental set up of lab nematode infection. Supplementary Figure S2. Experimental set up of pot study. Supplementary Figure S3. Experimental set up of field study. Supplementary Figure S4. In vitro bioassay showing (a) live (healthy and moving) and (b) dead nematodes (second-stage juveniles, J2s of Meloidogyne graminicola) from control and DHA solutions, respectively. Supplementary Figure S5. Effect of dehydroascorbate (DHA) on rice susceptibility to Meloidogyne graminicola.
B cell Receptor Signatures Associating with Strong and Poor SARS-CoV-2 Vaccine Response
Creators: name: Lin, Ke
name: Zhou, Yawen
name: Ai, Jingwen
name: Wang, Yan A.
name: Zhang, Senxin
name: Qiu, Chao
name: Lian, Chaoyang
name: Gao, Bo
name: Liu, Tingting
name: Wang, Hongyu
name: Zhang, Haocheng
name: Zhang, Yi
name: Fu, Zhangfan
name: Li, Dan
name: Jiang, Ning
name: Guo, Jingxin
name: Wu, Jing
name: Wang, Yan O.
name: Song, Shusen
name: Li, Qiang
name: Yin, Yanan
name: Xia, Jia
name: Xu, Yingjie
name: Yeap, Leng-Siew
name: Zheng, Xiaoqi
name: Gu, Ye
name: Liu, Hongyan
name: Zhang, Wenhong
name: Meng, Fei-Long
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Breakthrough infection of SARS-CoV-2 is a serious challenge, as increased cases of infections were documented in fully-vaccinated individuals. Recipients with poor antibody response are highly vulnerable to reinfection, whereas those with strong antibody response achieve sterilizing immunity. Thus far, biomarkers associated with levels of vaccine-elicited antibody response are still lacking. Here, we studied the antibody response of an age- and gender-controlled healthy cohort who received inactivated SARS-CoV-2 vaccines, and profiled the B cell receptor repertoires in longitudinally consecutive samples. Upon vaccination, all vaccinated individuals displayed a convergent antibody response with shared common antibody clones and public neutralizing antibodies. Strikingly, poor vaccine-responders are distinguishable from strong vaccine-responders by a biased V-usage before vaccination and IgG to IgM mRNA ratio. These findings reveal molecular signatures associated with the different levels of vaccine-induced antibody response, which could be further developed into biomarkers for the design of vaccination strategies.
Omicron variant susceptibility to neutralizing antibodies induced in children by natural SARS-CoV-2 infection or COVID-19 vaccine
Creators: name: Chen, Lin-Lei
name: Chua, Gilbert T.
name: Lu, Lu
name: Chan, Brian Pui-Chun
name: Wong, Joshua Sung-Chih
name: Chow, Calvin Chit-Kwong
name: Yu, Tak-Ching
name: Leung, Agnes Sze-Yin
name: Lam, Shu-Yan
name: Wong, Tak-Wai
name: Tsang, Hing-Wai
name: Wong, Ian Chi-Kei
name: Chan, Kwok-Hung
name: Yuen, Kwok-Yung
name: Ip, Patrick
name: Kwan, Mike Yat-Wah
name: To, Kelvin Kai-Wang
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The novel SARS-CoV-2 Omicron variant may increase the risk of re-infection and vaccine breakthrough infections as it possesses key mutations in the spike protein that affect neutralizing antibody response. Most studies on neutralization susceptibility were conducted using specimens from adult COVID-19 patients or vaccine recipients. However, since the paediatric population has an antibody response to SARS-CoV-2 infection that is distinct from the adult population, it is critical to assess the neutralization susceptibility of pediatric serum specimens. This study compared the neutralization susceptibility of serum specimens collected from 49 individuals of <18 years old, including 34 adolescent BNT162b2 (Pfizer-BioNTech) vaccine recipients, and 15 recovered COVID-19 patients aged between 2 and 17. We demonstrated that only 38.2% of BNT162b2 vaccine recipients and 26.7% of recovered COVID-19 patients had their serum neutralization titre at or above the detection threshold in our live virus microneutralization assay. Furthermore, the neutralizing antibody titer against the Omicron variant was substantially lower than those against the ancestral virus or the Beta variant. Our results suggest that vaccine recipients and COVID-19 patients in the pediatric age group will likely be more susceptible to vaccine breakthrough infections or reinfections due to the Omicron variant than previous variants.
Additional file 1 of Kawasaki disease (KD) and multisystem inflammatory syndrome in children (MIS-C) in a Middle Eastern patient cohort
Creators: name: Yavuz, Lemis
name: AlHamdani, Sarmad
name: Alasrawi, Samah
name: Wafadari, Deena
name: Al-Fraihat, Ali
name: Bebars, Marwa A.
name: Nath, Jaidev
name: Arango, Diego
name: Pallavidino, Marco
name: Jain, Ruchi
name: Yavuz, Sinan
name: AlAwadhi, Mohamed
name: Alkhayat, Abdulla
name: Tayoun, Ahmad Abou
name: Abuhammour, Walid Mohammad
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Supplementary Material 1
Supplementary_Data_2 – Supplemental material for PD-L1 expression with respect to driver mutations in non-small cell lung cancer in an Asian population: a large study of 1370 cases in China
Creators: name: Li, Caichen
name: Liu, Jun
name: Xie, Zhanhong
name: Zhu, Feng
name: Cheng, Bo
name: Liang, Hengrui
name: Li, Jianfu
name: Xiong, Shan
name: Chen, Zisheng
name: Liu, Zhichao
name: Zhao, Yi
name: Ou, Limin
name: Zhong, Ran
name: Wang, Wei
name: Huang, Jun
name: Sun, Jinyun
name: Zhang, Chunya
name: Weng, Landong
name: He, Jianxing
name: Liang, Wenhua
name: Pan, Zhenkui
Publisher: name: SAGE Journals
Year: 2020
Subjects: Oncology and Carcinogenesis not elsewhere classified
Aged Health Care
Pharmacology and Pharmaceutical Sciences not elsewhere classified
Respiratory Diseases

description: Supplemental material, Supplementary_Data_2 for PD-L1 expression with respect to driver mutations in non-small cell lung cancer in an Asian population: a large study of 1370 cases in China by Caichen Li, Jun Liu, Zhanhong Xie, Feng Zhu, Bo Cheng, Hengrui Liang, Jianfu Li, Shan Xiong, Zisheng Chen, Zhichao Liu, Yi Zhao, Limin Ou, Ran Zhong, Wei Wang, Jun Huang, Jinyun Sun, Chunya Zhang, Landong Weng, Jianxing He, Wenhua Liang and Zhenkui Pan in Therapeutic Advances in Medical Oncology
DS_10.1177_0363546520962774 – Supplemental material for Application of Autogenous Urine-Derived Stem Cell Sheet Enhances Rotator Cuff Healing in a Canine Model
Creators: name: Chen, Yang
name: Xu, Yan
name: Li, Muzhi
name: Shi, Qiang
name: Chen, Can
Publisher: name: SAGE Journals
Year: 2020
Subjects: Orthopaedics
Sports Medicine
Surgery

description: Supplemental material, DS_10.1177_0363546520962774 for Application of Autogenous Urine-Derived Stem Cell Sheet Enhances Rotator Cuff Healing in a Canine Model by Yang Chen, Yan Xu, Muzhi Li, Qiang Shi and Can Chen in The American Journal of Sports Medicine
Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein
Creators: name: Jiang, Sheng
name: Wu, Shuting
name: Zhao, Gan
name: He, Yue
name: Guo, Xinrong
name: Zhang, Zhiyu
name: Hou, Jiawang
name: Ding, Yuan
name: Cheng, Alex
name: Wang, Bin
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development, and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus-neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. This study predicted several potential T cell epitopes with web-based analytic tools and narrowed them down from several potential MHC-I and MHC-II epitopes by ELIspot and cytolytic assays to a conserved MHC-I epitope. The epitope is highly conserved in current viral variants and compatible with a presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.
Additional file 1 of Bacterial findings in patients referred to hospital for the treatment of acute tonsillitis with or without peritonsillar phlegmon
Creators: name: Andersen, Camilla
name: Greve, Thomas
name: Reinholdt, Kasper Basse
name: Kjaerulff, Ann Marlene Gram
name: Udholm, Nichlas
name: Khalid, Vesal
name: Madzak, Adnan
name: Duez, Christophe
name: Münch, Henrik
name: Pauli, Søren
name: Danstrup, Christian Sander
name: Petersen, Niels Krintel
name: Klug, Tejs Ehlers
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1. Clinical and biochemical characteristics of 64 patients with or without follow up cultures. Additional file 2. Methods used for identification of bacteria.
The H2O2 Concentration-Dependent Kinetics of Gene Expression: Linking the Intensity of Oxidative Stress and Mycobacterial Physiological Adaptation
Creators: name: Wu, Mengying
name: Shan, Wenyan
name: Zhao, Guo-Ping
name: Lyu, Liang-Dong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Defense against oxidative stress is crucial for Mycobacterium tuberculosis to survive and replicate within macrophages. Mycobacteria have evolved multilayer antioxidant systems, including scavenging enzymes, iron homeostasis, repair pathways and metabolic adaptation, for coping with oxidative stress. How these systems are coordinated to enable the physiological adaptation to different intensities of oxidative stress, however, remains unclear. To address this, we investigated the expression kinetics of the well-characterized antioxidant genes at bacteriostatic H2O2 concentrations ranging from 1 mM to 10 mM employing Mycolicibacterium smegmatis as a model. Our results showed that most of the selected genes were expressed in a H2O2 concentration-dependent manner, whereas a subset exhibited sustained induction or repression without dose-effect, reflecting H2O2 concentration-dependent physiological adaptations. Through analyzing the dynamics of coordinated gene expression, we demonstrated that the expression of the H2O2 scavenging enzymes, DNA damage response and Fe-S cluster repair function was strikingly correlated to the intensity of oxidative stress. The sustained induction of mbtB, irtA and dnaE2 indicated that mycobacteria might deploy increased iron acquisition and error-prone lesion bypass function as fundamental strategies to counteract oxidative damages, which is distinct from the defense tactics of Escherichia coli characterized by shrinking the iron pool and delayed DNA repair. Moreover, the distinct gene expression kinetics among the tricarboxylic acid cycle, glyoxylate shunt and methylcitrate cycle suggested that mycobacteria could dynamically redirect its metabolic fluxes according to the intensity of oxidative stress. This work defines the H2O2 concentration-dependent gene expression kinetics and provides unique insights into mycobacterial antioxidant defense strategies.
Omicron variant susceptibility to neutralizing antibodies induced in children by natural SARS-CoV-2 infection or COVID-19 vaccine
Creators: name: Chen, Lin-Lei
name: Chua, Gilbert T.
name: Lu, Lu
name: Chan, Brian Pui-Chun
name: Wong, Joshua Sung-Chih
name: Chow, Calvin Chit-Kwong
name: Yu, Tak-Ching
name: Leung, Agnes Sze-Yin
name: Lam, Shu-Yan
name: Wong, Tak-Wai
name: Tsang, Hing-Wai
name: Wong, Ian Chi-Kei
name: Chan, Kwok-Hung
name: Yuen, Kwok-Yung
name: Ip, Patrick
name: Kwan, Mike Yat-Wah
name: To, Kelvin Kai-Wang
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The novel SARS-CoV-2 Omicron variant may increase the risk of reinfection and vaccine breakthrough infections as it possesses key mutations in the spike protein that affect neutralizing antibody response. Most studies on neutralization susceptibility were conducted using specimens from adult COVID-19 patients or vaccine recipients. However, since the pediatric population has an antibody response to SARS-CoV-2 infection that is distinct from the adult population, it is critical to assess the neutralization susceptibility of pediatric serum specimens. This study compared the neutralization susceptibility of serum specimens collected from 49 individuals of <18 years old, including 34 adolescent BNT162b2 (Pfizer-BioNTech) vaccine recipients, and 15 recovered COVID-19 patients aged between 2 and 17. We demonstrated that only 38.2% of BNT162b2 vaccine recipients and 26.7% of recovered COVID-19 patients had their serum neutralization titer at or above the detection threshold in our live virus microneutralization assay. Furthermore, the neutralizing antibody titer against Omicron variant was substantially lower than those against the ancestral virus or the Beta variant. Our results suggest that vaccine recipients and COVID-19 patients in the pediatric age group will likely be more susceptible to vaccine breakthrough infections or reinfections due to Omicron variant.
Harnessing the power of community science to digitize, transcribe and import preparation information into a collections management database system
Creators: name: Levitt-Bussian, Carolyn
Publisher: name: Zenodo
Year: 2022

description: Abstract of conference oral presentation on Harnessing the power of community science to digitize, transcribe and import preparation information into a collections management database system by Carolyn Levitt-Bussian of Natural History Museum Of Utah (UMNH) Salt Lake City United States for SPNHC2022 Conference, Edinburgh. June 5-10th 2022.
Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein
Creators: name: Jiang, Sheng
name: Wu, Shuting
name: Zhao, Gan
name: He, Yue
name: Guo, Xinrong
name: Zhang, Zhiyu
name: Hou, Jiawang
name: Ding, Yuan
name: Cheng, Alex
name: Wang, Bin
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development, and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus-neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. This study predicted several potential T cell epitopes with web-based analytic tools and narrowed them down from several potential MHC–I and MHC–II epitopes by ELIspot and cytolytic assays to a conserved MHC–I epitope. The epitope is highly conserved in current viral variants and compatible with a presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.
A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)
Creators: name: Andrés, Cristina
name: Piñana, Maria
name: Borràs-Bermejo, Blanca
name: González-Sánchez, Alejandra
name: García-Cehic, Damir
name: Esperalba, Juliana
name: Rando, Ariadna
name: Zules-Oña, Ricardo-Gabriel
name: Campos, Carolina
name: Codina, Maria Gema
name: Blanco-Grau, Albert
name: Colomer-Castell, Sergi
name: Martín, Maria Carmen
name: Castillo, Carla
name: García-Comuñas, Karen
name: Vásquez-Mercado, Rodrigo
name: Martins-Martins, Reginaldo
name: Saubi, Narcís
name: Campins-Martí, Magda
name: Pumarola, Tomàs
name: Quer, Josep
name: Antón, Andrés
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Herein, we describe the genetic diversity of circulating SARS-CoV-2 viruses by whole-genome sequencing (WGS) in Barcelona city (Catalonia, Spain) throughout the first four pandemic waves. From weeks 11/2020–24/2021, SARS-CoV-2-positive respiratory samples were randomly selected per clinical setting (80% from primary care or 20% from the hospital), age group, and week. WGS was performed following the ARTICv3 protocol on MiSeq or NextSeq2000 Illumina platforms. Nearly complete consensus sequences were used for genetic characterization based on GISAID and PANGOLIN nomenclatures. From 2475 samples, 2166 (87%) were fully sequenced (78% from primary care and 22% from hospital settings). Multiple genetic lineages were co-circulating, but four were predominant at different periods. While B.1.5 (50.68%) and B.1.1 (32.88%) were the major lineages during the first pandemic wave, B.1.177 (66.85%) and B.1.1.7 (83.80%) were predominant during the second, third, and fourth waves, respectively. Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants. But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage. The fact that a predominant lineage was observed in each pandemic wave suggests advantageous properties over other contemporary co-circulating variants. This genetic variability should be monitored, especially when a massive vaccination campaign is ongoing because the potential selection and emergence of novel antigenic SARS-CoV-2 strains related to immunological escapement events.
Plant roots and deep-banded nutrient-rich amendments influence aggregation and dispersion in a dispersive clay subsoil
Creators: name: Xiaojuan Wang
name: Sale, Peter
name: H Hayden
name: Caixian Tang
name: Clark, Gary
name: Armstrong, Roger
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: © 2019 The ameliorating effect of deep banding of nutrient-rich organic amendments, termed subsoil manuring, on improving physical structure of sodic high-clay subsoils, has been often attributed to organic amendments per se. However, this cannot explain the transformation of soil physical properties between the rip-lines, away from the amendments. This study assessed the effect of deep-banding nutrient-rich amendments on aggregation and dispersion of a clay subsoil in the presence and absence of wheat (Triticum aestivum) roots under controlled environment conditions. A specially-designed dual-column was set up to simulate a soil profile where a well-structured topsoil overlaid a sodic clay subsoil with an exchangeable sodium percentage (ESP) of 21%. The five amendments include a control (zero amendments), fertilizer nutrients (NPKS), wheat straw + fertilizer nutrients (straw/NPKS), poultry litter (PL) and poultry litter + controlled-release fertilizer (PL/mac). All amendments were added to the centre of the subsoil, 6 cm below the base of the topsoil. Our results showed that the presence of deep-placed nutrient-rich amendments, such as straw/NPKS and PL/mac, greatly enhanced deep root proliferation in this sodic clay subsoil, and resulted in the rapid build-up of large (>2000 μm) water-stable macroaggregates. There was a significant (P < 0.05) positive linear relationship between the root length density and the formation of large macroaggregates in the subsoil adjacent to and below the amendment. The stimulation of microbial growth by root exudates or by mucilage, as indicated by a significantly higher bacterial and fungal abundance (P < 0.05) in the planted than unplanted soils, is likely to have contributed to the formation of these macroaggregates. The effectiveness of wheat straw/NPKS in promoting the formation of macroaggregates in the unplanted soil could be attributed to the ‘straw effect’ which induced a marked increase in fungal growth (P < 0.05). Soil electrical conductivity (EC) and aggregate size were the key determinants of clay dispersion in the aggregated subsoil. Plant roots showed a contrasting effect on clay dispersion: increasing clay dispersion by reducing soil EC while suppressing clay dispersion via root-induced increases in large macroaggregates. We argue that the degree of slaking or disaggregation is likely to determine the net effect of roots on clay dispersion, and that root effect on increasing dispersion of macroaggregates in wet subsoil is limited. The major finding of the study is that increased aggregation in a dispersive clay subsoil can occur when wheat roots grow actively in these layers, in response to deep-placed nutrient-rich amendments.
Additional file 1 of Lack of alignment between orthopaedic surgeon priorities and patient expectations in total joint arthroplasty
Creators: name: Shah, Harsh N.
name: Barrett, Andrew A.
name: Le, Patrick H.
name: Arora, Prerna
name: Kamal, Robin N.
name: Amanatullah, Derek F.
Publisher: name: figshare
Year: 2024
Subjects: Medicine
Mental Health

description: Additional file 1.
Ploutarchos, Herakleides, Heron, Herais, Serenos, pupils of Origen and martyrs of Alexandria
Creators: name: Admin, CSLA
Publisher: name: University of Oxford
Year: 2016
Subjects: History

description: All evidence related to Ploutarchos, Herakleides, Heron, Herais, Serenos, pupils of Origen and martyrs of Alexandria.
Pharmacologically induced endolysosomal cholesterol imbalance through clinically licensed drugs itraconazole and fluoxetine impairs Ebola virus infection in vitro
Creators: name: Kummer, Susann
name: Lander, Angelika
name: Goretzko, Jonas
name: Kirchoff, Norman
name: Rescher, Ursula
name: Schloer, Sebastian
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Ebola virus disease (EVD) is a severe and frequently lethal disease caused by Ebola virus (EBOV). The latest occasional EVD outbreak (2013–2016) in Western African, which was accompanied by a high fatality rate, showed the great potential of epidemic and pandemic spread. Antiviral therapies against EBOV are very limited, strain-dependent (only antibody therapies are available) and mostly restricted to symptomatic treatment, illustrating the urgent need for novel antiviral strategies. Thus, we evaluated the effect of the clinically widely used antifungal itraconazole and the antidepressant fluoxetine for a repurposing against EBOV infection. While itraconazole, similar to U18666A, directly binds to and inhibits the endosomal membrane protein Niemann-Pick C1 (NPC1), fluoxetine, which belongs to the structurally unrelated group of weakly basic, amphiphile so-called “functional inhibitors of acid sphingomyelinase” (FIASMA) indirectly acts on the lysosome-residing acid sphingomyelinase via enzyme detachment leading to subsequent lysosomal degradation. Both, the drug-induced endolysosomal cholesterol accumulation and the altered endolysosomal pH, might interfere with the fusion of viral and endolysosomal membrane, preventing infection with EBOV. We further provide evidence that cholesterol imbalance is a conserved cross-species mechanism to hamper EBOV infection. Thus, exploring the endolysosomal host-pathogen interface as a suitable antiviral treatment may offer a general strategy to combat EBOV infection.