bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Practical Procedure for Fatigue Assessment of Mooring Line Chains With Pitting Corrosion
Authors: Rezende Filipe A. , Videiro Paulo M. , Sagrilo Luis V. S. 
Published: February 2024

Abstract
Chain link fatigue failures in mooring lines have recently aroused the interest of the technical community in developing new design and monitoring methodologies focused on considering the effects of local corrosion. Experimental breakage test results evidenced that the effects of mean tension, pitting corrosion, and surface roughness may influence the fatigue strength of chain links. A recently-developed methodology here denoted as corrosion grade considers the effects of mean tension and local corrosion through a visual assessment of the chain. The present work proposes a parametric correction factor to be used in the current S–N fatigue design methodology for considering local corrosion in studless chains. The parametric model is developed by means of finite element-based modeling of various pit shapes in the chain. The correction factor is fitted as a function of the pit aspect ratio. The proposed correction factor is combined with the corrosion grade methodology to obtain a final formula that considers the mean tension and the local corrosion. Results from both corrosion grade and the proposed correction factor are compared in three corroded experimental test samples. The proposed correction factor is capable of estimating the fatigue life of the corroded components analyzed with conservatism.
An Overview of Physical Activity Research Evolution in Africa: The Global Observatory for Physical Activity—GoPA!
Authors: Oyeyemi Adewale L. , Ramirez Varela Andrea , Lambert Estelle V. , Kohn Eduardo Ribes , Hallal Pedro C. , Pratt Michael 
Published: February 2024

Objective: To describe the evolution of physical activity (PA) research in Africa, examine income and gender inequalities, and discuss future possibilities. Methods: A secondary analyses of the Global Observatory for Physical Activity data on PA research in Africa (1950–2019). Results: We identified 514 PA articles from 47 African countries in the past 70 years. Majority (83.1%) of the articles were published between 2012 and 2019. Fifteen countries had no publications. Six countries (South Africa [n = 156], Nigeria [n = 85], Ethiopia [n = 44], Ghana [n = 41], Kenya [n = 39], and Cameroon [n = 20]) accounted for about 75% of the publications. Most articles were observational (92.4%), single-country studies (78.4%), with male first (58.4%) and last authors (68%), and were classified as surveillance studies (45.1%). Few studies addressed interventions (5.8%) and policy (3.5%) or used device-based PA measurement (14.0%). The number of articles per country was positively related to human population level (r = .552, P = .000) and gross domestic product % spent on research and development (r = .301, P = .040). The publication rate per 100,000 people was positively related with the human development index (r = .349, P = .016) and negatively with the gender inequality index (r = −.360, P = .019). Conclusions: Our results provide an overview and status of PA research in Africa, highlighting country differences and gender inequalities in authorship. The findings may be used to benchmark the evolution of research in the region and to inform areas for improvement. There is an urgent need for more PA interventions and policy studies in Africa.
The History of Physical Activity Promotion in Physical Education and Suggestions for Moving Forward
Authors: Centeio Erin E. , Brusseau Timothy A. 
Published: February 2024

Physical activity (PA) is an essential component of the physical education classroom, whether it is used to practice motor skills, increase motor competence, or provide experience and opportunities to nurture lifelong PA participation. This chapter outlines the history of PA in the school setting, beginning with physical education and expanding through a Comprehensive School Physical Activity Program model including PA during the school day (e.g., recess and classroom-based activity), PA before and after school (including active commuting), staff involvement, and family and community engagement. We begin by discussing the theoretical underpinnings of PA in the school setting and then outline previous research around PA implications. Ideas and suggestions for how the field of physical education and PA in schools can move the field forward together to embrace PA during the school day while being culturally and socially just are presented. Finally, future directions and implications for research are discussed.
Coxiella burnetii
infection persistence in a goat herd during seven kidding seasons after an outbreak of abortions: the effect of vaccination
Authors: Zendoia Ion I. , Barandika Jesús F. , Cevidanes Aitor , Hurtado Ana , García-Pérez Ana L. 
Published: February 2024

ABSTRACT

Coxiella burnetii
infection was monitored during seven kidding seasons (2017–2023) in a dairy goat herd that after an outbreak of Q fever abortions was vaccinated with an inactivated phase I vaccine. Due to the high infection rate just after the outbreak, only the replacement stock was vaccinated during the first three kidding seasons, and when the average herd immunity had decreased (fourth kidding season onwards), the whole herd was vaccinated. Vaginal swabs, feces, and milk were analyzed by PCR to monitor infection, and dust and aerosols were analyzed to measure
C. burnetii
environmental contamination. One year after the onset of the outbreak, a significant reduction in
C. burnetii
shedding loads was observed, but the percentage of shedding animals remained high until the third kidding season. By the seventh kidding season, no shedders were detected. The bacterial load excreted was significantly lower in vaccinated compared with unvaccinated animals, and in yearlings compared with multiparous.
C. burnetii
was detected by PCR in aerosols collected inside the animal premises throughout the study period except in the last season; whereas, aerosols collected outdoors tested negative in the last three kidding seasons. Viable
C. burnetii
was detectable in environmental dust collected inside the barn until the third kidding season following the outbreak. These results indicate that after an outbreak of Q fever, the risk of infection for humans and susceptible animals can remain high for at least three kidding seasons when the number of
C. burnetii
animal shedders is still high, even when bacterial excretion is low.

IMPORTANCE

Q fever is a zoonosis distributed worldwide. Ruminants are the main reservoir, and infection can cause high rates of abortion. After entering a farm,
Coxiella burnetii
infection can persist in the animal population over several lambing/kidding periods. Once infection is established in a herd, vaccination with the inactivated Phase I vaccine significantly reduces bacterial shedding, but although at low levels, excretion may continue to occur for several lambing/kidding seasons. The time that
C. burnetii
remains viable in the farm environment after an outbreak of Q fever determines the period when risk of infection is high for the people in close contact. This work showed that this period extends at least three kidding seasons after the outbreak. These results provided valuable information on the epidemiology of
C. burnetii
infection in goat herds and may help to develop guidelines for controlling the disease and reducing infection risk for susceptible people and animals.
A prototrophic suppressor of a
Vibrio fischeri
D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF)
Authors: Coppinger Macey N. , Laramore Kathrin , Popham David L. , Stabb Eric V. 
Published: February 2024

ABSTRACT

Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in
Vibrio fischeri
and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic
murI racD
mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >10
11
cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses
proB
to a gene encoding a putative
b
road-
s
pectrum
r
acemase of

V.
f
ischeri

,
bsrF
. An engineered
bsrF
allele lacking the putative secretion signal (ΔSS-
bsrF
) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-
bsrF
allele similarly suppressed the D-alanine auxotrophy of an
alr
mutant and restored prototrophy to a
murI alr
double mutant auxotrophic for both D-ala and D-glu. The ΔSS-
bsrF
allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in
V. fischeri
that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance.

IMPORTANCE

D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in
Vibrio fischeri
, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.
RBM14 inhibits the replication of porcine epidemic diarrhea virus by recruiting p62 to degrade nucleocapsid protein through the activation of autophagy and interferon pathway
Authors: Wang Xiaoquan , Tong Wu , Yang Xinyu , Zhai Huanjie , Qin Wenzhen , Liu Changlong , Zheng Hao , Yu Hai , Tong Guangzhi , Zhang Zhendong , Kong Ning , Shan Tongling 
Published: February 2024

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) results in PED, which is an infectious intestinal disease with the representative features of diarrhea, vomiting, and dehydration. PEDV infects neonatal piglets, causing high mortality rates. Therefore, elucidating the interaction between the virus and host in preventing and controlling PEDV infection is of immense significance. We found a new antiviral function of the host protein, RNA-binding motif protein 14 (RBM14), which can inhibit PEDV replication via the activation of autophagy and interferon (IFN) signal pathways. We found that RBM14 can recruit cargo receptor p62 to degrade PEDV nucleocapsid (N) protein through the RBM14-p62-autophagosome pathway. Furthermore, RBM14 can also improve the antiviral ability of the hosts through interacting with mitochondrial antiviral signaling protein to induce IFN expression. These results highlight the novel mechanism underlying RBM14-induced viral restriction. This mechanism leads to the degradation of viral N protein via the autophagy pathway and upregulates IFN for inhibiting PEDV replication; thus, offering new ways for preventing and controlling PED.

IMPORTANCE
Porcine epidemic diarrhea virus (PEDV) is a vital reason for diarrhea in neonatal piglets, which causes high morbidity and mortality rates. There is currently no effective vaccine or drug to treat and prevent infection with the PEDV. During virus infection, the host inhibits virus replication through various antiviral factors, and at the same time, the virus antagonizes the host’s antiviral reaction through its own encoded protein, thus completing the process of virus replication. Our study has revealed that the expression of RNA-binding motif protein 14 (RBM14) was downregulated in PEDV infection. We found that RBM14 can recruit cargo receptor p62 to degrade PEDV N protein via the RBM14-p62-autophagosome pathway and interacted with mitochondrial antiviral signaling protein and TRAF3 to activate the interferon signal pathway, resulting in the inhibition of PEDV replication.
Nsp1 facilitates SARS-CoV-2 replication through calcineurin-NFAT signaling
Authors: Lui Wai-Yin , Ong Chon Phin , Cheung Pak-Hin Hinson , Ye Zi-Wei , Chan Chi-Ping , To Kelvin Kai-Wang , Yuen Kit-San , Jin Dong-Yan 
Published: February 2024

ABSTRACT

SARS-CoV-2, the causative agent of COVID-19, has been intensely studied in search of effective antiviral treatments. The immunosuppressant cyclosporine A (CsA) has been suggested to be a pan-coronavirus inhibitor, yet its underlying mechanism remained largely unknown. Here, we found that non-structural protein 1 (Nsp1) of SARS-CoV-2 usurped CsA-suppressed nuclear factor of activated T cells (NFAT) signaling to drive the expression of cellular DEAD-box helicase 5 (DDX5), which facilitates viral replication. Nsp1 interacted with calcineurin A (CnA) to displace the regulatory protein regulator of calcineurin 3 (RCAN3) of CnA for NFAT activation. The influence of NFAT activation on SARS-CoV-2 replication was also validated by using the Nsp1-deficient mutant virus. Calcineurin inhibitors, such as CsA and VIVIT, inhibited SARS-CoV-2 replication and exhibited synergistic antiviral effects when used in combination with nirmatrelvir. Our study delineated the molecular mechanism of CsA-mediated inhibition of SARS-CoV-2 replication and the anti-SARS-CoV-2 action of calcineurin inhibitors.

IMPORTANCE
Cyclosporine A (CsA), commonly used to inhibit immune responses, is also known to have anti-SARS-CoV-2 activity, but its mode of action remains elusive. Here, we provide a model to explain how CsA antagonizes SARS-CoV-2 through three critical proteins: DDX5, NFAT1, and Nsp1. DDX5 is a cellular facilitator of SARS-CoV-2 replication, and NFAT1 controls the production of DDX5. Nsp1 is a viral protein absent from the mature viral particle and capable of activating the function of NFAT1 and DDX5. CsA and similar agents suppress Nsp1, NFAT1, and DDX5 to exert their anti-SARS-CoV-2 activity either alone or in combination with Paxlovid.
The
Caenorhabditis elegans
proteome response to two protective
Pseudomonas
symbionts
Authors: Pees Barbara , Peters Lena , Treitz Christian , Hamerich Inga K. , Kissoyan Kohar A. B. , Tholey Andreas , Dierking Katja 
Published: February 2024

ABSTRACT

The
Caenorhabditis elegans
natural microbiota isolates
Pseudomonas lurida
MYb11 and
Pseudomonas fluorescens
MYb115 protect the host against pathogens through distinct mechanisms. While
P. lurida
produces an antimicrobial compound and directly inhibits pathogen growth,
P. fluorescens
MYb115 protects the host without affecting pathogen growth. It is unknown how these two protective microbes affect host biological processes. We used a proteomics approach to elucidate the
C. elegans
response to MYb11 and MYb115. We found that both
Pseudomonas
isolates increase vitellogenin protein production in young adults, which confirms previous findings on the effect of microbiota on
C. elegans
reproductive timing. Moreover, the
C. elegans
responses to MYb11 and MYb115 exhibit common signatures with the response to other vitamin B
12
-producing bacteria, emphasizing the importance of vitamin B
12
in
C. elegans
-microbe metabolic interactions. We further analyzed signatures in the
C. elegans
response specific to MYb11 or MYb115. We provide evidence for distinct modifications in lipid metabolism by both symbiotic microbes. We could identify the activation of host-pathogen defense responses as an MYb11-specific proteome signature and provide evidence that the intermediate filament protein IFB-2 is required for MYb115-mediated protection. These results indicate that MYb11 not only produces an antimicrobial compound but also activates host antimicrobial defenses, which together might increase resistance to infection. In contrast, MYb115 affects host processes such as lipid metabolism and cytoskeleton dynamics, which might increase host tolerance to infection. Overall, this study pinpoints proteins of interest that form the basis for additional exploration into the mechanisms underlying
C. elegans
microbiota-mediated protection from pathogen infection and other microbiota-mediated traits.

IMPORTANCE

Symbiotic bacteria can defend their host against pathogen infection. While some protective symbionts directly interact with pathogenic bacteria, other protective symbionts elicit a response in the host that improves its own pathogen defenses. To better understand how a host responds to protective symbionts, we examined which host proteins are affected by two protective
Pseudomonas
bacteria in the model nematode
Caenorhabditis elegans
. We found that the
C. elegans
response to its protective symbionts is manifold, which was reflected in changes in proteins that are involved in metabolism, the immune system, and cell structure. This study provides a foundation for exploring the contribution of the host response to symbiont-mediated protection from pathogen infection.
Draft genome sequence of
Bacillus velezensis
strains AOA1 and AKS2, the potential plant growth-promoting rhizobacteria
Authors: Babalola Olubukola Oluranti , Akanmu Akinlolu Olalekan , Ayangbenro Ayansina Segun 
Published: February 2024

ABSTRACT

This report describes the draft genome sequence of
Bacillus velezensis
strains AOA1 and AKS2 isolated from maize rhizosphere soil in South Africa.
Bacillus velezensis
plays important biological roles as plant growth promoting rhizobacterium (PGPR).
Bacillus velezensis
strains also exhibit numerous biotechnological application potentials in agriculture and diverse industrial settings.
Draft genome sequences of 21
Pedobacter
strains isolated from amphibian specimens
Authors: Zumkeller Celine M. , Bletz Molly C. , Rakotoarison Andolalao , Sabino-Pinto Joana , Reiter Silke , Spohn Marius , Schwengers Oliver , Goesmann Alexander , Vences Miguel , Mihajlovic Sanja , Schäberle Till F. 
Published: February 2024

ABSTRACT

The genomes of 21
Pedobacter
strains isolated from the European salamander
Salamandra salamandra
and different Madagascan frog species were sequenced using Illumina sequencing. Here, we report their draft genome sequences (~4.7–7.2 Mbp in size) to allow comparative genomics and taxonomic assignment of these strains.
Development of a duplex droplet digital PCR assay for the detection of
Burkholderia cepacia
complex and
Stenotrophomonas maltophilia
in bloodstream infections
Authors: Liu Chunmei , He Ziqiang , Kong Mimi , Jin Dong 
Published: February 2024

ABSTRACT

Burkholderia cepacia
complex (BCC) and
Stenotrophomonas maltophilia
are nosocomial pathogens that cause various infections and exhibit high resistance to multiple antimicrobial agents. In this study, we aimed to develop a duplex droplet digital PCR (ddPCR) assay for detecting BCC and
S. maltophilia
in bloodstream infections. We optimized the experimental conditions by setting the annealing temperature to 51°C and determining the optimal concentrations of primers and probes, as well as the thermal cycle numbers. The feasibility of the duplex ddPCR reaction system with the optimal conditions was established and verified through parallel reactions with reference strains of BCC and
S. maltophilia
. The specificity of the assay, tested with 33 reference strains, was found to be 100%. The duplex ddPCR assay demonstrated good repeatability and could detect as low as 5.35 copies/reaction of BCC and 7.67 copies/reaction of
S. maltophilia
. This level of sensitivity was consistent in the simulated blood and blood bottle samples. We compared nucleic acid extraction methods and found that the Chelex-100 boiling method and kit extraction method exhibited similar detection sensitivity, suggesting the potential application of the Chelex-100 boiling method in the ddPCR assay. In the clinical samples, the duplex ddPCR assay accurately detected BCC and
S. maltophilia
in 58 cases. In conclusion, our study successfully developed a duplex ddPCR assay that provides accurate and convenient detection of BCC and
S. maltophilia
in bloodstream infections.

IMPORTANCE

Burkholderia cepacia
complex (BCC) and
Stenotrophomonas maltophilia
are implicated in a wide range of infections, including bloodstream infections (BSIs), pneumonia, and meningitis, and often exhibit high intrinsic resistance to multiple antimicrobial agents, limiting therapeutic options. The gold standard for diagnosing bloodstream infections remains blood culture. However, current blood culture detection and positivity rates do not meet the “rapid diagnosis” required for the diagnosis and treatment of critically ill patients with BSIs. The digital droplet PCR (ddPCR) method is a potentially more powerful tool in the diagnosis of BSIs compared to other molecular methods due to its greater sensitivity, specificity, accuracy, and reproducibility. In this study, a duplex ddPCR assay for the detection of BCC and
S. maltophilia
in BSIs was developed.
Clinical characteristics and outcomes of pleural aspergillosis: a review of 13 cases
Authors: Zhang Jing , Gao Xing-Lin , Wu Jian , Chen Jing-Jing 
Published: February 2024

ABSTRACT

Aspergillus pleurisy is a rare complication of invasive pulmonary aspergillosis (IPA), which mostly occurs in the immunocompromised host. The clinical condition is critical, especially to those who develop bronchopleural fistula. This study aimed to assess the characteristics and the prognosis of aspergillus pleurisy. Clinical data from 13 patients diagnosed with aspergillus pleurisy in our hospital from January 2000 to December 2022 were retrospectively studied. Thirteen patients with
Aspergillus
pleurisy were included. There were 10 males and 3 females, with a median age of 65 (range: 18–79) years. Bronchopleural fistula was present in eight patients. A proven diagnosis of
Aspergillus
pleurisy was based on positive pleural fluid culture in seven cases and histopathological examination of pleural biopsies in six cases. Four patients refused further treatment and were discharged from the hospital against medical advice. Nine cases recovered and were discharged after multiple antifungal treatments (systemic and topical antifungal therapies, pleural drainage and irrigation, and surgical repair). During follow-up, one patient, who suffered underlying bronchiectasis, died of massive hemoptysis 2 years after discharge. The remaining eight cases are still under close follow-up, with a median follow-up of 5.4 (range: 1.3–18.9) years. The prognosis of aspergillus pleurisy complicated with bronchopleural fistula is poor. Thoracic surgery, especially lung resection, is a risk factor associated with the incidence of
Aspergillus
pleurisy. Systemic antifungal therapy and adequate pleural irrigation could improve the prognosis.

IMPORTANCE
Aspergillus pleurisy is a rare complication of invasive pulmonary aspergillosis (IPA), associated with a poor prognosis. The morbidity and mortality of this condition have not been thoroughly studied, and recent research on this topic is limited. The current study included 13 patients diagnosed with Aspergillus pleurisy, with the majority presenting concomitantly with a bronchopleural fistula. Among these patients, nine had a history of thoracic surgery, including lung transplantation and lobectomy. Four patients refused further treatment and were discharged against medical advice, while one patient succumbed to massive hemoptysis 2 years after discharge. This case series provides essential insights into Aspergillus pleurisy and evaluates the therapeutic strategy based on a limited cohort.