bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual Neuromuscular Training Among Physically Active Young Adults: A Feasibility Study
Authors: Magliato Samantha N. , Wingerson Mathew J. , Smulligan Katherine L. , Little Casey C. , Lugade Vipul , Wilson Julie C. , Howell David R. 
Published: October 2024

Context: Evidence indicates a 2 to 3 times increased risk of musculoskeletal injury after return to play from concussion. Undetected neuromuscular control deficits at return to play may relate to increased musculoskeletal injury risk. Rehabilitation to improve neuromuscular control may benefit patients with concussion, but access to rehabilitation professionals and/or poor adherence may limit efficacy. Our purpose was to determine the feasibility of an 8-week virtual neuromuscular training (NMT) program administered through a novel smartphone application among physically active, uninjured adults. Design: Feasibility trial. Methods: Participants were instructed to complete an NMT program administered via a smartphone application and returned for follow-up questionnaires 8 weeks later. They were instructed to complete 3 asynchronous self-guided workouts per week during the 8-week intervention period. Workouts included balance, plyometrics, strengthening, and dual-task exercises. The application provided instructions for each exercise using video, text, and audio descriptions. Our primary feasibility measure was participant adherence, calculated as the percentage of workouts completed out of the total possible 24 workouts. We recorded the average duration of each workout using start/stop/advance features within the application. Results: Twenty participants were enrolled, of which 15 (age = 26.3 [2.7] y, 67% female) returned for follow-up (75% retention). Participant adherence was 57.2% (25.0%; range: 16.7%–91.7%). Participants spent 17.3 (8.0) minutes per workout (range: 7.4–37.9 min). There were no adverse reactions or injuries. Most participants (60%) reported time availability as a primary barrier to intervention completion. Conclusions: Participants were moderately (>50%) adherent to a virtual NMT program, without any reported injuries. We identified several barriers to participation and pathways for improved adherence in the future. The virtual NMT program completed by uninjured adults provides evidence of its feasibility and future scalability to those with a recent concussion to address neuromuscular control deficits and reduce future injury risk.
An Imperfect List of Eminent Sport and Exercise Psychology Researchers
Authors: Smolinski Allison , McIntyre Olivia , Martin Drew , Martin Jeffrey J. 
Published: October 2024

The purpose of the present study was to identify eminent sport and exercise psychology researchers, based on citation count, and their most highly cited papers. Men (n = 121) and women (n = 32) from 17 different countries (e.g., the United States n = 47 to Ireland n = 1) were identified. Researchers were selected if their h-index was 60 or greater for Google Scholar and Web of Science combined. This criterion reflects Hirsch’s (2005) characterization as follows based on h-index: a successful scientist (20), an outstanding scientist (40), and truly unique (60), for one database. Our criteria of 60 for two databases are equivalent to a designation halfway between successful and outstanding. The results indicate an h-index mean of 103, median of 94, mode of 105, and range of 60–346. Top-cited publications leaned toward more sport psychology than exercise psychology topics. Prominent journals included the Journal of Sport and Exercise Psychology (n = 24) and Psychology of Sport and Exercise (n = 15). Other publications were in related fields (e.g., Psychology and Health). In summary, we have identified the most highly cited researchers in sport and exercise psychology and their single most-cited papers. We hope this information is of both heuristic and practical value to readers.
Bridging The Gap: Promoting Faculty Diversity to Align With Student Demographics
Authors: Malek Moh H. , Mache Melissa A. , Jerome Gerald J. , Miller Matthew W. , Aiken Christopher A. 
Published: October 2024

In many kinesiology and health care science departments in the United States, there is a mismatch between the demographic composition of the student population and the faculty cohort. That is, although student populations are more diverse, the faculty cohort does not reflect this same diversity. The purpose of this paper is threefold: (a) Provide background information on the faculty–student mismatch, (b) discuss reactive strategies to increase diversity among a faculty cohort, and (c) discuss proactive strategies to increase diversity among a faculty cohort. Our approach is pragmatic and concise, which will give the reader various strategies they can incorporate to increase diversity in their faculty cohort.
SARS-CoV-2 nsp13 suppresses hepatitis B virus replication by targeting cccDNA transcription
Authors: Li Aixin , Zhao Kaitao , Duan Yurong , Zhang Bei , Zheng Yingcheng , Zhu Chengliang , Chen Qiongrong , Liu Wen-Bo , Hui Lixia , Xia Yuchen , Cheng Xiaoming 
Published: October 2024

ABSTRACT

SARS-CoV-2 nonstructural protein 13 (nsp13) has been shown to selectively suppress the transcription of episomal DNA while sparing chromosomal DNA. Hepatitis B Virus (HBV) harbors covalently closed circular DNA (cccDNA), a form of viral episomal DNA found within infected hepatocyte nuclei. The persistence of cccDNA is the major cause of chronic HBV infection. In this study, we investigated the impact of SARS-CoV-2 nsp13 on HBV replication, particularly in the context of cccDNA. Our findings demonstrate that nsp13 effectively hinders HBV replication by suppressing the transcription of HBV cccDNA, both
in vitro
and
in vivo
. Additionally, we observed that SARS-CoV-2 nsp13 binds to HBV cccDNA and its NTPase and helicase activities contribute significantly to inhibiting HBV replication. Furthermore, our screening identified the interaction between nsp13 and structural maintenance of chromosomes 4, opening new avenues for future mechanistic inquiries. This study presents the evidence suggesting the potential utilization of SARS-CoV-2 nsp13 as a strategy to impede HBV replication by specifically targeting cccDNA. These findings provide a proof of concept for exploring nsp13 as a prospective approach in combating HBV infection.

IMPORTANCE
To effectively combat hepatitis B virus (HBV), it is imperative to develop potent antiviral medications targeting covalently closed circular DNA (cccDNA). Our investigation aimed to assess the impact of SARS-CoV-2 nsp13 on HBV replication across diverse HBV models, confirming its ability to significantly reduce several HBV replication markers. Additionally, our identification of the interaction between nsp13 and SMC4 opens the door for further mechanistic exploration. This marks a paradigm shift in our approach to HBV antiviral therapy, introducing an entirely novel perspective. Our findings propose a novel strategy for developing anti-HBV drugs that specifically target HBV cccDNA.
Dosage constraint of the ribosome-associated molecular chaperone drives the evolution and fates of its duplicates in bacteria
Authors: Wan Tianyu , Zhuo Li , Pan Zhuo , Chen Rui-yun , Ma Han , Cao Ying , Wang Jianing , Wang Jing-jing , Hu Wei-feng , Lai Ya-jun , Hayat Muhammad , Li Yue-zhong 
Published: October 2024

ABSTRACT

Gene duplication events happen prevalently during evolution, and the mechanisms governing the loss or retention of duplicated genes are mostly elusive. Our genome scanning analysis revealed that trigger factor (TF), the one and only bacterial ribosome-associated molecular chaperone, is singly copied in virtually every bacterium except for a very few that possess two or more copies. However, even in these exceptions, only one complete TF copy exists, while other homologs lack the N-terminal domain that contains the conserved ribosome binding site (RBS) motif. Consistently, we demonstrated that the overproduction of the N-terminal complete TF proteins is detrimental to the cell, which can be rescued by removing the N-terminal domain. Our findings also indicated that TF overproduction leads to a decrease in protein productivity and profile changes in proteome due to its characteristic ribosome binding and holdase activities. Additionally, these N-terminal deficient TF homologs in bacteria with multiple TF homologs partition the function of TF via subfunctionalization. Our results revealed that TF is subjected to a dosage constraint that originates from its own intrinsic functions, which may drive the evolution and fates of duplicated TFs in bacteria.

IMPORTANCE

Gene duplication events presumably occur in
tig
, which encodes the ribosome-associated molecular chaperone trigger factor (TF). However, TF is singly copied in virtually every bacterium, and these exceptions with multiple TF homologs always retain only one complete copy while other homologs lack the N-terminal domain. Here, we reveal the manner and mechanism underlying the evolution and fates of TF duplicates in bacteria. We discovered that the mutation-to-loss or retention-to-sub/neofunctionalization of TF duplicates is associated with the dosage constraint of N-terminal complete TF. The dosage constraint of TF is attributed to its characteristic ribosome binding and substrate-holding activities, causing a decrease in protein productivity and profile changes in cellular proteome.
Epitranscriptomic m
6
A modifications during reactivation of HIV-1 latency in CD4
+
T cells
Authors: Mishra Tarun , Phillips Stacia , Zhao Yutao , Wilms Bethany , He Chuan , Wu Li 
Published: October 2024

ABSTRACT

Despite effective antiretroviral therapy reducing HIV-1 viral loads to undetectable levels, the presence of latently infected CD4
+
T cells poses a major barrier to HIV-1 cure.
N
6
-methyladenosine (m
6
A) modification of viral and cellular RNA has a functional role in regulating HIV-1 infection. m
6
A modification of HIV-1 RNA can affect its stability, translation, and splicing in cells and suppresses type-I interferon induction in macrophages. However, the function of m
6
A modification in regulating HIV-1 latency reactivation remains unknown. We used the Jurkat T cell line-derived HIV-1 latency model (J-Lat cells) to investigate changes in m
6
A levels of cellular RNA in response to latency reversal. We observed a significant increase in m
6
A levels of total cellular RNA upon reactivation of latent HIV-1 in J-Lat cells. This increase in m
6
A levels was transient and returned to steady-state levels despite continued high levels of viral gene expression in reactivated cells compared to control cells. Upregulation of m
6
A levels occurred without significant changes in the protein expression of m
6
A writers or erasers that add or remove m
6
A, respectively. Knockdown of m
6
A writers in J-Lat cells significantly reduced HIV-1 reactivation. Treatment with an m
6
A writer inhibitor reduced cellular RNA m
6
A levels, along with a reduction in HIV-1 reactivation. Furthermore, using m
6
A-specific sequencing, we identified cellular RNAs that are differentially m
6
A-modified during HIV-1 reactivation in J-Lat cells. Knockdown of identified m
6
A-modified RNA validates these results with an established primary CD4
+
T cell model of HIV-1 latency. These results show the importance of m
6
A RNA modification in HIV-1 latency reversal.

IMPORTANCE

RNA m
6
A modification is important for regulating gene expression and innate immune responses to HIV-1 infection. However, the functional significance of m
6
A modification during HIV-1 latency reactivation is unknown. To address this important question, in this study, we used established cellular models of HIV-1 latency, m
6
A-specific sequencing at single-base resolution, and functional assays. We demonstrate that HIV-1 latency reversal leads to increased levels of cellular m
6
A modification, correlates with cellular m
6
A levels, and is dependent on the catalytic activity of the m
6
A methyltransferase enzyme. We also identified cellular genes that are differentially m
6
A-modified during HIV-1 reactivation, as well as the sites of m
6
A within HIV-1 RNA. Our novel findings point toward a significant role for m
6
A modification in HIV-1 latency reversal.
Aedes aegypti
adiponectin receptor-like protein signaling facilitates Zika virus infection
Authors: Chen Tse-Yu , Marín-López Alejandro , Raduwan Hamidah , Fikrig Erol 
Published: October 2024

ABSTRACT

The
Aedes aegypti
mosquito plays a critical role in the transmission of viral diseases, including Zika virus, which poses significant public health challenges. Understanding the complex interactions between mosquitoes and viruses is paramount for the development of effective control strategies. In this study, we demonstrate that silencing the
A. aegypti
adiponectin receptor-like protein (AaARLP) results in a reduction of Zika virus infection. Transcriptomic analysis identified alterations in several trypsin genes and further revealed that
AaARLP
-knockdown mosquitoes had diminished trypsin activity. Moreover, silencing of selected
trypsins
resulted in a similar delay in Zika virus infection in mosquitoes, further highlighting the connection between the AaARLP and trypsin. Overall, our findings demonstrate that AaARLP signaling is important for Zika virus infection of
A. aegypti
.

IMPORTANCE

Arboviruses pose a significant threat to public health, with mosquitoes, especially
Aedes aegypti
, being a major vector for their transmission. Gaining insight into the complex interaction between mosquitoes and viruses is essential to build successful control strategies. In this study, we identified a novel pathway connecting the
A. aegypti
adiponectin receptor-like protein and its association with trypsin, key enzymes involved in blood digestion. Furthermore, we demonstrated the significance of signaling via the adiponectin receptor-like protein in virus infection within the mosquito. Together, our discoveries illuminate mosquito metabolic pathways essential in viral infection.
Metagenomes and metagenome assembled genomes from anaerobic digesters at three Canadian pulp and paper mills
Authors: Nesbø Camilla L. , Yang Minqing Ivy , Sharan Anupama Achal , Meyer Torsten , Edwards Elizabeth A. 
Published: October 2024

ABSTRACT

We present a dataset of six metagenomes and 323 metagenome assembled genomes (MAGs) describing the microbial community of anaerobic digesters at three Canadian pulp and paper mills. Our objective was to assess the coding potential of the microbial community and obtain draft genomes of key organisms in the digesters.
Draft genome sequence analysis of multidrug-resistant
Salmonella enterica
subsp.
enterica
serovar Mbandaka harboring colistin resistance gene
mcr
-
9.1
isolated from foals in Kentucky, USA
Authors: Helmy Yosra A. , Kabir Ajran , Saleh Mohamed , Kennedy Laura A. , Burns Logan , Johnson Beth 
Published: October 2024

ABSTRACT

Horses play a significant role in the direct or indirect transmission of
Salmonella
to humans. Here, we report the draft genomes of multidrug-resistant
Salmonella enterica
subsp.
enterica
serovar Mbandaka YAH-F68 isolated from foals in Kentucky, USA belonging to sequence type 413 and harboring the mobile colistin resistance gene
mcr
-
9.1
.
A novel method for the preparation of reproducible, stable, and non-infectious quality control materials for
Chlamydia trachomatis
nucleic acid detection
Authors: Li Jing , Zhang Kuo , Han Yanxi , Peng Rongxue , Li Lin , Li Jinming , Lin Guigao 
Published: October 2024

ABSTRACT

Chlamydia trachomatis
(CT) is a significant sexually transmitted pathogen known to evoke severe complications, including infertility. Nucleic acid amplification tests (NAATs) are recommended by the World Health Organization to detect CT infection. Furthermore, the establishment of methods, performance validation, internal quality control, and external quality assessment for CT NAATs necessitate the utilization of quality control materials (QCs). QCs are specimens or solutions that are analyzed for quality control purposes in a test system. In this study, we established a novel cell line that stably integrates CT amplification target sequences for producing QCs for CT NAATs. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, we integrated the CT plasmid-mediated sequence (comprising the full length of the cryptic plasmid and the major outer membrane protein gene, 9,136 bp) into the
MUC4
gene of HEK293T cells. Positive clones were screened through flow cytometric sorting, single-cell culture, and PCR-based identification, followed by the establishment of stable cell lines. These cells were then processed using optimized cell preservation procedures to prepare QCs. The sequence insertion copy number was confirmed by real-time quantitative PCR. This novel CT QCs demonstrate excellent clinical applicability, non-infectiousness, quantifiability, and stability. With an integrated sequence exceeding 9 kb in length, it offers exceptional flexibility for adapting to new kit developments. Furthermore, maintaining a well-defined copy number and stable shelf life, the QCs closely aligns with the quality control requirements of CT NAATs. This study presents an innovative method for preparing QCs for CT nucleic acid detection, making a valuable contribution to improving the performance of CT NAATs.

IMPORTANCE
Untreated CT infections impose significant burdens on individuals and communities, underscoring the importance of early and accurate testing via CT NAATs for disease control. QCs are instrumental in identifying testing process issues. Hence, we developed a cell line integrating CT-amplified target sequences as readily accessible non-infectious QCs. These QCs boast several advantages: the integration of over 9 kb of CT sequence allows for broad applicability, allowing flexible adaptation to the development of new kits. Confirming the CT sequence copy number provides a reliable basis for QC concentration preparation and kit detection limit evaluation. Optimized preservation protocol enhances QC stability during storage, facilitating convenient shipment to clinical laboratories at ambient temperatures. In summary, our novel CT QCs offer a powerful tool for improving CT NAAT performance and present a fresh perspective on QC preparation for detecting nucleic acids from intracellular parasitic pathogens.
Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the
Embecovirus
subgenus
Authors: Zehr Jordan D. , Kosakovsky Pond Sergei L. , Shank Stephen D. , McQueary Holly , Grenier Jennifer K. , Whittaker Gary R. , Stanhope Michael J. , Goodman Laura B. 
Published: October 2024

ABSTRACT

There are several examples of coronaviruses in the Betacoronavirus subgenus
Embecovirus
that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and
Embecovirus
-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major
Embecovirus
member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.

IMPORTANCE

The Betacoronavirus subgenus
Embecovirus
contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.