bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Emergence of Cat‐Transmitted Sporotrichosis Driven by Sporothrix brasiliensis in Piauí, Brazil
Authors: Pinheiro Raizza Eveline Escórcio , Santana Clara Cecília Azevedo , Martins Liline Maria Soares , Veloso Dilbert Silva , Luz Jardenio Assis dos Santos , Lima Oriana Bezerra , Santos Namir Clementino , Gonsales Fernanda Fidelis , de Carvalho Jamile Ambrósio , Rodrigues Anderson Messias 
Published: November 2024

ABSTRACTIntroductionIn Brazil, the emergence of feline sporotrichosis, a neglected subcutaneous mycosis primarily transmitted by cats and caused by the fungus Sporothrix brasiliensis, has been monitored via molecular tools. This approach underscores the geographic expansion of this disease and highlights the critical role of molecular surveillance in understanding its epidemiology and guiding public health interventions.MethodsWe investigated three domestic cats (Felis catus) with multiple skin lesions in Picos, Piauí, Brazil. The cats were examined, and samples were collected for laboratory diagnosis, including cytological evaluation, fungal culture, and molecular characterisation. The molecular analysis involved a one‐tube multiplex probe‐based qPCR assay for the diagnosis of Sporothrix species, mating‐type determination, and amplified fragment length polymorphism (AFLP, EcoRI‐GA/MseI‐AG) to assess genetic similarity and potential origin.ResultsAll three cats were diagnosed with sporotrichosis caused by the hypervirulent S. brasiliensis. A probable case of zoonotic transmission has been reported in a 12‐year‐old girl who developed Parinaud oculoglandular syndrome after contact with one of the cats with sporotrichosis. The molecular analysis revealed that the cat isolates were MAT 1‐2 and formed a single cluster according to the AFLP analysis, suggesting direct transmission (cat‐cat) and a potential founder effect. The isolates were also closely related to strains from Pernambuco and Southeast Brazil, indicating a possible introduction from these regions.ConclusionsIdentifying S. brasiliensis in Piauí emphasises the need for increased awareness and control measures to prevent further spread. The predominance of the MAT1‐2 idiomorphs and the genetic similarity among outbreak isolates suggest clonal expansion, which could have significant implications for public health and veterinary practices. Considering its zoonotic potential and environmental adaptability, a One Health approach is crucial for managing and controlling the spread of cat‐transmitted sporotrichosis.
A Better Way to Visualize the Cervix: A Low-Cost Cervical Cancer Screening Device for LMIC Settings
Authors: Barsukova Anita Dey , Jebran Ahmad Mujtaba , Lynch Naomi , Galgali Amit , Moncada Andrea , Sakerka Lauren , Cotner Cody , Davey Sonya , Nimgaonkar Vivek , Ying Binbin , Mendez Keegan , Traverso Giovanni 
Published: November 2024

Abstract
Cervical cancer is a leading cause of cancer-related mortality worldwide, killing over 300,000 women annually. Lack of resources to perform screening and treatment of cervical cancer in low- and middle-income countries (LMICs) as well as the stigma associated with screening has led to high mortality rates in these regions. Specifically, the speculum—a duck bill-shaped device used to open the vaginal canal for visualization of the cervix by a clinician—does not always provide a clear line of sight to the cervix and can cause patient discomfort due to the concentrated stress it exerts on the vaginal canal. To overcome these barriers, we developed a low-cost screening device for use in LMIC settings that enables better visualization of the cervix at low cervical angles and exerts less pressure on the vaginal walls compared to a speculum in finite element (FE) models.
Numerical Analysis of Gas Generation and Migration in a Radioactive Waste Disposal Cell of a Deep Geological Repository
Authors: Sun Lan , Qiu Liyan 
Published: November 2024

Abstract
In a deep geological repository (DGR) for the long-term disposal of radioactive waste, gases (e.g., hydrogen (H2), carbon dioxide (CO2) and methane (CH4)) can be generated through a number of processes, such as corrosion of various metals and alloys and degradation of organic materials. If gas induced pressure exceeds the containment capacity of the engineered barrier systems (EBS) or the host rock, the gases could migrate through these barriers and potentially expose people and the environment to radiation. Therefore, a good understanding on the long-term performance of these barriers against gas migration is an important component in DGR design and safety assessment. In the present work, a numerical model has been developed to simulate the diffusion of CO2 (one of the gas species) in the near field of a DGR with the generation from related chemical reactions. The generation of CO2 was investigated to determine if it is a critical factor to impact the DGR safety under Canadian geological formations. A commercial computational fluid dynamics (CFD) code, ANSYS Fluent was used for the calculations. The model considered pH and temperature effects on CO2 migration under Canadian DGR geochemistry conditions.
Development of Large-Diameter Hybrid Film-Riding Seals for Supercritical Carbon Dioxide Turbines
Authors: Bidkar Rahul A. , Kumar Uttara , Trivedi Deepak , Zhang Xiaohua , Rambacher Collin , Rimpel Aaron , Kerr Thomas , Johnson Jeremy 
Published: November 2024

Abstract
Compared to traditional labyrinth seals, large-diameter (about 24 in or 609.6 mm) film-riding face seals are worth 0.55–0.65% points efficiency for utility-scale supercritical carbon dioxide (sCO2) turbines. Conventional dry gas seals (DGS) that rely on aerodynamic spiral grooves cannot be used at such large diameters due to manufacturability limitations and mechanical deformations. Hybrid film-riding face seals are excellent compromise candidates that can operate at large diameters with slightly increased albeit leakier films. This paper presents the development and test data for a hybrid face seal developed for the utility-scale sCO2 turbine application. A high-level overview of the seal design considerations is presented followed by test data on three seals—a small-size seal (5.7 in or 144.8 mm diameter), an intermediate-size seal (14 in or 355.6 mm diameter), and two full-size seals (24 in or 609.6 mm diameter) tested over a range of pressures and temperatures with both air and CO2 as the working fluid. This paper presents nondimensional seal film thickness and seal leakage (effective clearance) data as a function of the pressure ratios, speed, and temperature. The film thickness measurements presented in this paper agree well with the computational fluid dynamics (CFD)-based film thickness predictions. The measured seal effective clearance for the seals was around 0.001 in (0.0254 mm) effective clearance, which is better than published data on aerostatic face seals and less risky compared to conventional DGS. Rotating test data across all three length scales presented in this work show successful laboratory-scale seal operation for the newly design hybrid face seals.
Who Wants To Be a Physical Education Teacher? Identity Development
Authors: Simon Eitan , Weissblueth Eyal 
Published: November 2024

Purpose: This article delves into analyzing professional identity development among Israeli physical education preservice teachers (PSTs), examining shifts in training programs mandated by the Ministry of Education. Method: One hundred and twenty-three physical education PSTs in three different years answered a validated teacher’s professional identity questionnaire. Two-way analysis of variance was used to detect significant differences between subgroups. Results: Analysis revealed variations among PSTs based on an academic year, with third-year students showing higher levels of commitment and identity. Discussion/Conclusion: The results trace how identity evolves dynamically over 3 years, emphasizing how interactions with stakeholders shape and underscore the importance of these early stages in fostering future professional competence and values, underlining the significance of gradual training. We suggest that teacher educators should acknowledge this dynamic process and consistently support PSTs throughout their training.
Mutant prevention concentrations,
in vitro
resistance evolution dynamics, and mechanisms of resistance to imipenem and imipenem/relebactam in carbapenem-susceptible
Klebsiella pneumoniae
isolates showing ceftazidime/avibactam resistance
Authors: Blanco-Martín Tania , González-Pinto Lucía , Aja-Macaya Pablo , Rodríguez-Pallares Salud , Sánchez-Peña Lucía , Gato Eva , Fernández-López María del Carmen , Outeda-García Michelle , Rodríguez-Coello Arianna , Pedraza-Merino Rosa , Alonso-García Isaac , Vázquez-Ucha Juan Carlos , Martínez-Martínez Luis , Arca-Suárez Jorge , Beceiro Alejandro , Bou Germán 
Published: November 2024

ABSTRACT

Klebsiella pneumoniae
carbapenemase (KPC) variants selected during ceftazidime/avibactam treatment usually develop susceptibility to carbapenems and carbapenem/β-lactamase inhibitors, such as imipenem and imipenem/relebactam. We analyzed imipenem and imipenem/relebactam single-step mutant frequencies, resistance development trajectories and differentially selected resistance mechanisms using two representative
K. pneumoniae
isolates that had developed ceftazidime/avibactam resistance during therapy (ST512/KPC-31 and ST258/KPC-35). Mutant frequencies and mutant prevention concentrations were measured in Mueller–Hinton agar plates containing incremental concentrations of imipenem or imipenem/relebactam. Resistance dynamics were determined after incubation for 7 days in 10 mL MH tubes containing incremental concentrations of each antibiotic or combination, up to 64 times their baseline MIC. Two colonies per strain from each experiment were characterized by antimicrobial susceptibility testing and whole genome sequencing. The impact of KPC variants identified in resistant mutants on β-lactam resistance was investigated by cloning experiments. Imipenem/relebactam suppressed the emergence of resistant mutants at lower concentrations than imipenem, slowed down resistance development for both strains, and the resulting mutants yielded lower MICs of carbapenems and carbapenem/β-lactamase inhibitors than those selected with imipenem alone. Characterization of resistant mutants revealed that imipenem resistance was mainly caused by inactivation of OmpK36 and mutations in the KPC β-lactamase. Imipenem/relebactam-resistant mutants also maintained OmpK36 alterations, but mutations in KPC were much less frequent compared with those selected with imipenem alone. Genetic and biochemical characterization of the KPC derivatives identified in the resistant mutants confirmed their role in carbapenem resistance. Our data positions imipenem/relebactam as an attractive therapeutic option for combating ceftazidime/avibactam-resistant KPC-producing
K. pneumoniae
infections.
The extended recovery ring-stage survival assay is a scalable alternative for artemisinin susceptibility phenotyping of fresh
Plasmodium falciparum
isolates
Authors: Okitwi Martin , Shoue Douglas A. , Checkley Lisa A. , Orena Stephen , Ceja Frida G. , Taremwa Yoweri , Tumwebaze Patrick K. , Katairo Thomas , Byaruhanga Oswald , Sievert Mackenzie A.C. , Garg Shreeya , Kreutzfeld Oriana K. , Legac Jennifer , Bailey Jeffrey A. , Nsobya Sam L. , Conrad Melissa D. , Rosenthal Philip J. , Ferdig Michael T. , Cooper Roland A. 
Published: November 2024

ABSTRACT

Artemisinin partial resistance (ART-R) has emerged in eastern Africa, necessitating regular surveillance of susceptibility of
Plasmodium falciparum
to artemisinins. The microscopy-based ring-stage survival assay (RSA) provides a laboratory correlate of ART-R but is limited by low throughput and subjectivity of microscopic counts of viable parasites. The extended recovery ring-stage survival assay (eRRSA) replaces microscopy with efficient quantitative PCR (qPCR) readouts but has been studied only with culture-adapted
P. falciparum
clones. We measured susceptibility to dihydroartemisinin (DHA) after a 6-h incubation with 700-nM DHA, followed by culture without drug, by comparing survival with that of untreated controls by microscopy (the RSA) or qPCR (the eRRSA) and also performed standard growth inhibition (half-maximal inhibitory concentration [IC
50
]) assays for 122
P. falciparum
isolates freshly collected in eastern and northern Uganda from March to July 2022. The median values for RSA survival, eRRSA fold change, and DHA IC
50
were 3.0%, 46.2, and 3.2 nM, respectively. RSA percent survival and eRRSA fold changes correlated strongly (Spearman correlation coefficient [
r

s

] = −0.7411,
P
< 0.0001), with modest associations between the presence of validated
P. falciparum
Kelch13 ART-R mutations (C469Y or A675V) and RSA (median survival 2.6% for wild type [WT] vs 4.1% for mutant,
P
= 0.01), or eRRSA (median fold change 63.4 for WT vs 30.9 for mutant,
P
= 0.003) results. Significant correlations were also observed between DHA IC
50
values and both RSA percent survival (

r
s

= 0.4235,
P
< 0.0001) and eRRSA fold changes (

r
s

= −0.4116,
P
< 0.0001). The eRRSA is a scalable alternative for phenotyping fresh
P. falciparum
isolates, providing similar results with improved throughput.
Design of ancestral mammalian alkaline phosphatase bearing high stability and productivity
Authors: Hagiwara Yusuke , Mihara Yasuhiro , Motoyama Tomoharu , Ito Sohei , Nakano Shogo 
Published: November 2024

ABSTRACT

Mammalian alkaline phosphatase (AP) is widely used in diagnostics and molecular biology but its widespread use is impaired because it is difficult to express in
Escherichia coli
and has low thermostability. To overcome these challenges, we employed sequence-based protein redesign methods, specifically full consensus design (FCD) and ancestral sequence reconstruction (ASR), to create APs with enhanced properties. Biochemical analyses revealed that these newly designed APs exhibited improved levels of expression in their active form and increased thermostability compared to bovine intestinal AP isozyme II (bIAPII), without impeding enzymatic activity. Notably, the activity in culture broth of the designed APs was an order of magnitude higher than that of bIAPII, and their thermal stability increased by 13°C–17°C (measured as
T
50
). We also assessed 28 single-point mutants of bIAPII to identify regions influencing thermostability and expression level; these mutations were common in the engineered APs but not in bIAPII. Specific mutations, such as T413E and G402S, enhanced thermostability, whereas increasing the expression level required multiple mutations. This suggests that a synergistic effect is required to enhance the expression level. Mutations enhancing thermostability were located in the crown domain, while those improving expression were close to the dimer interface, indicating distinct mechanisms underpinning these enhancements.

IMPORTANCE

Sequence-based protein redesign methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR), have the potential to construct new enzymes utilizing protein sequence data registered in a rapidly expanding sequence database. The high thermostability of these enzymes would expand their application in diagnostics and molecular biology. These enzymes have also demonstrated a high level of active expression by
Escherichia coli
. These characteristics make these APs attractive candidates for industrial application. In addition, different amino acid residues are primarily responsible for thermal stability and active expression, suggesting important implications for strategies for designing enzymes by FCD and ASR.
Laboratory detection of carbapenemases among Gram-negative organisms
Authors: Simner Patricia J. , Pitout Johann D. D. , Dingle Tanis C. 
Published: November 2024

SUMMARY

The carbapenems remain some of the most effective options available for treating patients with serious infections due to Gram-negative bacteria. Carbapenemases are enzymes that hydrolyze carbapenems and are the primary method driving carbapenem resistance globally. Detection of carbapenemases is required for patient management, the rapid implementation of infection prevention and control (IP&C) protocols, and for epidemiologic purposes. Therefore, clinical and public health microbiology laboratories must be able to detect and report carbapenemases among predominant Gram-negative organisms from both cultured isolates and direct from clinical specimens for treatment and surveillance purposes. There is not a “one size fits all” laboratory approach for the detection of bacteria with carbapenemases, and institutions need to determine what fits best with the goals of their antimicrobial stewardship and IP&C programs. Luckily, there are several options and approaches available for clinical laboratories to choose methods that best suits their individual needs. A laboratory approach to detect carbapenemases among bacterial isolates consists of two steps, namely a screening process (
e.g.
, not susceptible to ertapenem, meropenem, and/or imipenem), followed by a confirmation test (
i.e.
, phenotypic, genotypic or proteomic methods) for the presence of a carbapenemase. Direct from specimen testing for the most common carbapenemases generally involves detection
via
rapid, molecular approaches. The aim of this article is to provide brief overviews on Gram-negative bacteria carbapenem-resistant definitions, types of carbapenemases, global epidemiology, and then describe in detail the laboratory methods for the detection of carbapenemases among Gram-negative bacteria. We will specifically focus on the
Enterobacterales, Pseudomonas aeruginosa
, and
Acinetobacter baumannii
complex.
Enriching the future of public health microbiology with hybridization bait capture
Authors: Beaudry Megan S. , Bhuiyan Mohammad Imtiaj Uddin , Glenn Travis C. 
Published: November 2024

SUMMARY
Public health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.
Performance evaluation of the Specific Reveal system for rapid antibiotic susceptibility testing from positive blood cultures containing Gram-negative pathogens
Authors: Ostermann Greta , Körber-Irrgang Barbara , Krüger Alexander , Singh Pragya , Vo Kenny , Gielen Jörg , Aurbach Ute , Wisplinghoff Hilmar , Jazmati Nathalie 
Published: November 2024

ABSTRACT

Rapid antimicrobial drug administration is crucial for the efficient treatment of sepsis or septic shock, but empirical therapy is limited by the increasing prevalence of multidrug-resistant bacteria. Thus, rapid and reliable antimicrobial susceptibility testing (AST) is needed to start appropriate antimicrobial drug administration as quickly as possible. In the present study, we evaluated the performance of the Reveal rapid AST system. From February to April 2021, 102 positive blood culture bottles (BCBs) from hospitalized patients with bacteremia caused by Gram-negative bacteria were included in the study. All isolates were tested by the Reveal system directly from the positive BCBs in comparison to the DxM MicroScan WalkAway. Essential agreement (EA) and category agreement (CA) were high with 98.5% and 97.1%, respectively. We also determined the susceptibility of 10 highly resistant CDC & FDA AR strains in duplicate. Here, EA was 99.6% and CA 97.9%. The average time to result by Reveal was 5.4 h ± 1.2 h compared to an average of 16 h by DxM MicroScan WalkAway for clinical strains and 3.8 h ± 1.2 h for more resistant CDC & FDA AR strains. Susceptibility determination with the Reveal rapid AST system directly from positive BCBs is for the frequently represented bug-drug combinations a reliable and accurate approach, meeting the European ISO guideline for the performance of AST systems. Moreover, AST directly from blood cultures performed with the Reveal system saves time when compared to the conventional AST, as no subculturing is needed and time to result is very short.
Exosome-mediated viral nucleic acid presentation in a crustacean expounds innate immunity from a novel perspective
Authors: Gong Yi , Hu Hang , Zhao Xinshan , Wei Weiqian , Zhang Ming , Tran Ngoc Tuan , Ma Hongyu , Zhang Yueling , Chan Kok-Gan , Li Shengkang 
Published: November 2024

ABSTRACT

As an enduring hot topic in the field of innate immunity, apoptosis is widely considered an effective approach to eliminate pathogenic microbes and plays a crucial role during host–pathogen interactions. Recently, researchers have found that the virus-containing host cells could transmit apoptotic signals to the surrounding uninfected cells during infection, but the mechanism remains unclear. Here, we found that exosomes secreted by WSSV-infected mud crab hemocytes contain viral nucleic acid wsv277, which could be transported to the recipient cells and further expressed viral protein with phosphokinase activity. Besides, by using transcriptome, proteome, ChIP-seq, and coIP techniques, the results revealed that wsv277 could activate the transcription and translation of apoptotic genes via interacting with CBF and EF-1α so as to suppress the spread of virus infection by inducing apoptosis of the surrounding cells. Therefore, for the first time, our study proved that the components of DNA virus could be encapsulated into exosomes and elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosomes.

IMPORTANCE
Our study revealed that the components of DNA virus could be packaged and transmitted through the exosomes of lower invertebrates, which strongly demonstrated the diversity of exosome-mediated viral immunity and its universality in animals. Furthermore, we elucidated the mechanism of apoptotic signal transduction between cells from the perspective of exosomes and revealed a novel strategy for the host to cope with viral infection.