bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topology-Agnostic Graph U-Nets for Scalar Field Prediction on Unstructured Meshes
Authors: Ferguson Kevin , Chen Yu-hsuan , Chen Yiming , Gillman Andrew , Hardin James , Burak Kara Levent 
Published: October 2024

Abstract
Machine-learned surrogate models to accelerate lengthy computer simulations are becoming increasingly important as engineers look to streamline the product design cycle. In many cases, these approaches offer the ability to predict relevant quantities throughout a geometry, but place constraints on the form of the input data. In a world of diverse data types, a preferred approach would not restrict the input to a particular structure. In this paper, we propose topology-agnostic graph U-Net (TAG U-Net), a graph convolutional network that can be trained to input any mesh or graph structure and output a prediction of a target scalar field at each node. The model constructs coarsened versions of each input graph and performs a set of convolution and pooling operations to predict the node-wise outputs on the original graph. By training on a diverse set of shapes, the model can make strong predictions, even for shapes unlike those seen during training. A 3D additive manufacturing dataset is presented, containing laser powder bed fusion simulation results for thousands of parts. The model is demonstrated on this dataset, and it performs well, predicting both 2D and 3D scalar fields with a median R2&gt;0.85 on test geometries.
Pain Reduction in Medial Tibial Stress Syndrome With Extracorporeal Shockwave Therapy: A Critically Appraised Topic
Authors: Perrero Elizabeth , Uriegas Nancy A. , Adams Morgan , Fraley Amy L. 
Published: October 2024

In active populations with medial tibial stress syndrome (MTSS), is extracorporeal shockwave therapy an effective treatment to reduce pain? A computerized search was conducted in October 2021. Inclusion criteria consisted of participants 18+ years old with diagnosed MTSS for 21+ days, where pain was in the posterior medial aspect of the tibia. Exclusion criteria involved patients with tibial fractures, compartment syndrome, and prior treatment of MTSS with extracorporeal shockwave therapy. Results were measured by the number of days athletes could complete the running protocol pain-free according to the Likert scale (p = .008), visual analog scale (p = .001), and Roles and Maudsley scale (RMS; p = .002). The third study showed no statistical significance in pain reduction or self-perception of change in symptoms on the Numerical Rating Scale (NRS; p = .05). Using the Strengthening the Reporting of Observational studies in Epidemiology scale, one study received a 17/22 since no biases were addressed, lack of participant status in each stage of the study, no numbers or analysis reported in each group, and no explanation of external validity or funding. The single-blind randomized controlled trial received a 10/11 using the Physiotherapy Evidence Database scale and one level of evidence. The double-blind sham randomized controlled trial received an 11/11 and one level of evidence (LOE). The research appraised would mostly agree the use of extracorporeal shockwave therapy could reduce pain in MTSS in active populations. The strength of recommendation is B.
Does a Single Session of Cupping Therapy Increase Range of Motion in Individuals With Limited Hamstring Flexibility? A Critically Appraised Topic
Authors: Arganbright Dwight , Russ Anne , Mansell Jamie , Tierney Ryan 
Published: October 2024

Context: Improving hamstring tightness is a common therapeutic goal to maintain performance and reduce injury risk. How effective is a single session of therapeutic cupping on improving hamstring flexibility? Methods: PubMed was searched in the Summer of 2023 using the search terms: cupping and range of motion (ROM). Included studies were intervention studies that evaluated cupping and flexibility within the lower extremity during a single treatment session. Hip flexion ROM was measured with the passive or active straight leg test. Means, SDs, 95% CI, and effect sizes were calculated. Results: Three articles were screened. Warren et al. reported a statistically significant increase in ROM from pre- to posttest of 4.42° using a digital inclinometer during the passive straight leg test. However, this is below a reported minimal detectable difference for the passive straight leg test (10°). Schafer et al. and Williams et al. reported no significant cupping effect over time between groups. Conclusions: There is consistent evidence that a single session of cupping therapy does not increase lower-extremity ROM in patients with limited hamstring flexibility.
Identifying Trajectories of Change in Burnout Symptoms of Gaelic Games Athletes Over Two Consecutive Seasons
Authors: Woods Siobhán , Dunne Simon , Gallagher Pamela , McCarren Andrew 
Published: October 2024

Athlete burnout is conceptualized as an enduring multidimensional syndrome, and longitudinal research is essential to understanding its development over time. However, much of the existing work has been limited to a small number of timepoints (≤3) or short intervals between waves (≤3 weeks), which fail to account for the chronic and complex nature of the syndrome. This study aimed to address these limitations by tracking burnout in adult athletes at 6 timepoints over a 21-month period for the first time. Data from 207 Gaelic games athletes were included in latent growth analysis to compare burnout trajectories of increasing complexity. A linear model best described all burnout symptoms. On average over the 21-month period, feelings of exhaustion declined, sport devaluation increased, and reduced accomplishment remained stable. Findings provide important insight into potential high-risk periods in the season and can help to inform targeted intervention or prevention efforts.
PBP4 is required for serum-induced cell wall thickening and antibiotic tolerance in
Staphylococcus aureus
Authors: Ledger Elizabeth V. K. , Massey Ruth C. 
Published: October 2024

ABSTRACT

The bacterial pathogen
Staphylococcus aureus
responds to the host environment by synthesizing a thick peptidoglycan cell wall, which protects the bacterium from membrane-targeting antimicrobials and the immune response. However, the proteins required for this response were previously unknown. Here, we demonstrate by three independent approaches that the penicillin-binding protein PBP4 is crucial for serum-induced cell wall thickening. First, mutants lacking various non-essential cell wall synthesis enzymes were tested, revealing that a mutant lacking
pbp4
was unable to generate a thick cell wall in serum. This resulted in reduced serum-induced tolerance of the
pbp4
mutant toward the last resort antibiotic daptomycin relative to wild-type cells. Second, we found that serum-induced cell wall thickening occurred in each of a panel of 134 clinical bacteremia isolates, except for one strain with a naturally occurring mutation that results in an S140R substitution in the active site of PBP4. Finally, inhibition of PBP4 with cefoxitin prevented serum-induced cell wall thickening and the resulting antibiotic tolerance in the USA300 strain and clinical MRSA isolates. Together, this provides a rationale for combining daptomycin with cefoxitin, a PBP4 inhibitor, to potentially improve treatment outcomes for patients with invasive MRSA infections.
sll1019
and
slr1259
encoding glyoxalase II improve tolerance of
Synechocystis
sp. PCC 6803 to methylglyoxal- and ethanol- induced oxidative stress by glyoxalase pathway
Authors: Ji Kai , Zhang Yihang , Zhang Tianyuan , Li Daixi , Yuan Yuan , Wang Li , Huang Qiaoyun , Chen Wenli 
Published: October 2024

ABSTRACT

The glyoxalase pathway is the primary detoxification mechanism for methylglyoxal (MG), a ubiquitous toxic metabolite that disrupts redox homeostasis. In the glyoxalase pathway, glyoxalase II (GlyII) can completely detoxify MG. Increasing the activity of the glyoxalase system can enhance the resistance of plants or organisms to abiotic stress, but the relevant mechanism remains largely unknown. In this study, we investigated the physiological functions of GlyII genes (
sll1019
and
slr1259
) in
Synechocystis
sp. PCC 6803 under MG or ethanol stress based on transcriptome and metabolome data. High-performance liquid chromatography (HPLC) results showed that proteins Sll1019 and Slr1259 had GlyII activity. Under stress conditions,
sll1019
and
slr1259
protected the strain against oxidative stress by enhancing the activity of the glyoxalase pathway and raising the contents of antioxidants such as glutathione and superoxide dismutase. In the photosynthetic system,
sll1019
and
slr1259
indirectly affected the light energy absorption by strains, synthesis of photosynthetic pigments, and activities of photosystem I and photosystem II, which was crucial for the growth of the strain under stress conditions. In addition,
sll1019
and
slr1259
enhanced the tolerance of strain to oxidative stress by indirectly regulating metabolic networks, including ensuring energy acquisition, NADH and NADPH production, and phosphate and nitrate transport. This study reveals the mechanism by which
sll1019
and
slr1259
improve oxidative stress tolerance of strains by glyoxalase pathway. Our findings provide theoretical basis for breeding, seedling, and field production of abiotic stress tolerance-enhanced variety.

IMPORTANCE

The glyoxalase system is present in most organisms, and it is the primary pathway for eliminating the toxic metabolite methylglyoxal. Increasing the activity of the glyoxalase system can enhance plant resistance to environmental stress, but the relevant mechanism is poorly understood. This study revealed the physiological functions of glyoxalase II genes
sll1019
and
slr1259
in
Synechocystis
sp. PCC 6803 under abiotic stress conditions and their regulatory effects on oxidative stress tolerance of strains. Under stress conditions,
sll1019
and
slr1259
enhanced the activity of the glyoxalase pathway and the antioxidant system, maintained photosynthesis, ensured energy acquisition, NADH and NADPH production, and phosphate and nitrate transport, thereby protecting the strain against oxidative stress. This study lays a foundation for further deciphering the mechanism by which the glyoxalase system enhances the tolerance of cells to abiotic stress, providing important information for breeding, seedling, and selection of plants with strong stress resistance.
Identification, characterization, and distribution of novel amidase gene
aphA
in sphingomonads conferring resistance to amphenicol antibiotics
Authors: Qian Yingying , Lai Lin , Cheng Minggen , Fang Hua , Fan Dandan , Zylstra Gerben J. , Huang Xing 
Published: October 2024

ABSTRACT

Amphenicol antibiotics, such as chloramphenicol (CHL), thiamphenicol (TAP), and florfenicol (Ff), are high-risk emerging pollutants. Their extensive usage in aquaculture, livestock, and poultry farming has led to an increase in bacterial antibiotic resistance and facilitated the spread of resistance genes. Yet, limited research has been conducted on the co-resistance of CHL, TAP, and Ff. Herein, a novel amidase AphA was identified from a pure cultured strain that can concurrently mediate the hydrolytic inactivation of CHL, TAP, and Ff, yielding products
p
-nitrophenylserinol, thiamphenicol amine (TAP-amine), and florfenicol amine (Ff-amine), respectively. The antibacterial activity of these antibiotic hydrolysates exhibited a significant reduction or complete loss in comparison to the parent compounds. Notably, AphA shared less than 26% amino acid sequence identity with previously reported enzymes and exhibited high conservation within the sphingomonad species. Through enzymatic kinetic analysis, the AphA exhibited markedly superior affinity and catalytic activity toward Ff in comparison to CHL and TAP. Site-directed mutagenesis analysis revealed the indispensability of catalytic triad residues, particularly serine 153 and histidine 277, in forming crucial hydrogen bonds essential for AphA’s hydrolytic activity. Comparative genomic analysis showed that
aphA
genes in some species are closely adjacent to various transposable elements, indicating that there is a high potential risk of horizontal gene transfer (HGT). This study established a hydrolysis resistance mechanism of amphenicol antibiotics in sphingomonads, which offers theoretical guidance and a novel marker gene for assessing the prevalent risk of amphenicol antibiotics in the environment.

IMPORTANCE

Amphenicol antibiotics are pervasive emerging contaminants that present a substantial threat to ecological systems. Few studies have elucidated resistance genes or mechanisms that can act on CHL, TAP, and Ff simultaneously. The results of this study fill this knowledge gap and identify a novel amidase AphA from the bacterium
Sphingobium yanoikuyae
B1, which mediates three typical amphenicol antibiotic inactivation, and the molecular mechanism is elucidated. The diverse types of transposable elements were identified in the flanking regions of the
aphA
gene, indicating the risk of horizontal transfer of this antibiotic resistance genes (ARG). These findings offer new insights into the bacterial resistance to amphenicol antibiotics. The gene reported herein can be utilized as a novel genetic diagnostic marker for monitoring the environmental fate of amphenicol antibiotics, thereby enriching risk assessment efforts within the context of antibiotic resistance.
Approaches to developing and implementing a molecular diagnostics stewardship program for infectious diseases: an ASM Laboratory Practices Subcommittee report
Authors: Valencia-Shelton Frances , Anderson Neil , Palavecino Elizabeth L. , Navas Maria E. , Larkin Paige M. K. , She Rosemary , Filkins Laura M. 
Published: October 2024

ABSTRACT

Diagnostic stewardship (DxS) for infectious disease testing requires a multi-disciplinary approach to optimize test selection, performance, interpretation and patient treatment. Nucleic acid amplification-based tests for the diagnosis of infectious diseases, or “molecular microbiology tests,” have rapidly expanded over the past two decades. With the increased availability and complexity of these tests, there is also an increased need for collaborative approaches to optimize test use to promote positive impacts on patient care, while mitigating potential negative impact or resource waste. In this review, we provide recommendations on building collaborative DxS teams, including microbiologists and the diverse stakeholders that use and interpret molecular microbiology tests. We then detail approaches to identify high-priority molecular microbiology tests that may need utilization assessment, select appropriate diagnostic stewardship interventions, and monitor the impact of implemented interventions. This strategic process may be employed by laboratories to realize optimal testing for selected tests at their institution.
Updated ASM Curriculum Guidelines describe core microbiology content to modernize the framework for microbiology education
Authors: Boury Nancy , Siegesmund Amy , Kushner David B. , Smyth Davida S. , Allen Mary E. , Frazier Adronisha , Gillette-Ferguson Illona , Markum Miriam , Patriquin Glenn , Reynolds Sara E. , Rosario Sarah , Steel J. Jordan , Horak Rachel 
Published: October 2024

ABSTRACT

Curricular guidelines promote standardized approaches to coverage of essential knowledge and skills in undergraduate education. The American Society for Microbiology (ASM) Curriculum Guidelines for Undergraduate Microbiology were developed in 2012. Continuous, rapid growth of knowledge in science and a dynamic, changing world necessitate updates to these guidelines. As such, ASM formed a task force in the summer of 2022. The task force assessed the 2012 ASM Curriculum Guidelines considering advancements in technology, an understanding of an expanded role of microbes, and a broader scope addressing relevant social and environmental aspects of microbiology. Language in the updated guidelines was also modified to better include eukaryotic microbes, viruses, and other acellular microbes. The task force formed working groups, each aimed at revising specific sections of the 2012 ASM Curriculum Guidelines. The revisions to the ASM Curriculum Guidelines were reviewed by subject matter experts and education stakeholders. Feedback from this peer review was incorporated into the updated guidelines, and further comments were solicited from the ASM Conference of Undergraduate Educators (ASMCUE) attendees in November 2023 before these guidelines were finalized. In this article, we describe the rationale and development of updated ASM Curriculum Guidelines which identify foundational concepts that will serve to improve microbial literacy and that can be expanded upon to address more advanced and specialized topics.
A measles virus collective infectious unit that caused lethal human brain disease includes many locally restricted and few widespread copy-back defective genomes
Authors: Taye Biruhalem , Yousaf Iris , Navaratnarajah Chanakha K. , Schroeder Declan C. , Pfaller Christian K. , Cattaneo Roberto 
Published: October 2024

ABSTRACT

During virus replication in cultured cells, copy-back defective viral genomes (cbDVGs) can arise. CbDVGs are powerful inducers of innate immune responses
in vitro
, but their occurrence and impact on natural infections of human hosts remain poorly defined. We asked whether cbDVGs were generated in the brain of a patient who succumbed to subacute sclerosing panencephalitis (SSPE) about 20 years after acute measles virus (MeV) infection. Previous analyses of 13 brain specimens of this patient indicated that a collective infectious unit (CIU) drove lethal MeV spread. In this study, we identified 276 replication-competent cbDVG species, each present in over 100 copies in the brain. Six species were detected in multiple forebrain locations, implying that they travelled long-distance with the CIU. The cbDVG to full-length genomes ratio was often close to 1 (0.6–1.74). Most cbDVGs were 324–2,000 bases in length, corresponding to 2%–12% of the full-length genome; all are predicted to have complementary terminal sequences. If improperly encapsidated, these sequences have the potential to form double-stranded structures that can induce innate immune responses. To assess this, we examined the transcriptome of all brain specimens. Several interferon and inflammatory response genes were upregulated, but upregulation levels did not correlate with cbDVG levels in the specimens. Thus, the CIU that drove MeV pathogenesis in this brain includes, in addition to two complementary full-length genome populations, many locally restricted and few widespread cbDVG species. The widespread cbDVG species may have been positively selected but how they impacted pathogenesis remains to be determined.

IMPORTANCE

Copy-back defective viral genomes (cbDVGs) can drive virus–host interactions. They can suppress virus replication directly, by competing with full-length genomes, or indirectly by stimulating antiviral immunity.
In vitro
, cbDVG can slow down infections and promote persistence, but there is limited documentation of their presence in human hosts or of their impact on disease. We had the unique opportunity to analyze the brain of a patient who succumbed to subacute sclerosing panencephalitis, a rare but lethal consequence of measles. We detected more than 270 distinct cbDVG species; most were restricted to one specimen, but several reached all lobes of the forebrain, suggesting positive selection. Our analyses provide the missing knowledge of the diversity of cbDVG in a natural infection of a human host. They also reveal that a collective infectious unit that caused lethal human brain disease includes few widespread cbDVG, in addition to two ubiquitous complementary full-length genome populations.
Draft genome sequence of
Pseudomona
s sp. ZS001 isolated from peanut plantation soil
Authors: Peng Chenchen , Li Dandan , Yang Haoyu , Wu Xiaoyan , Zhao Xinyue , Qin Jie 
Published: October 2024

ABSTRACT

Pseudomonas
sp. ZS001 is a bacterium potentially degrading soluble starch isolated from peanut plantation soil sprayed with starch-based material in Dasi Town, Tianjin. Reporting the genome sequence of strain ZS001 can help us understand the genome composition, potential functional characteristics, and application value of
Pseudomonas
members at the genetic level.
Complete genome sequence of
Bacillus cereus
NBNZ-2162, isolated from citrus rhizosphere soil
Authors: Chen Wei , Chen Ling , Cheng Xiyu , Liu Xiaoyan , Zhu Lei 
Published: October 2024

ABSTRACT

Plant rhizosphere microorganisms are an important source for discovering beneficial microorganisms in crops. Here we presented the complete genome of
Bacillus cereus
NBNZ-2162 isolated from citrus rhizosphere soil, of which the total length is 5,395,922 bp and possesses 5,368 CDS.
Complete genome sequences of feline astroviruses from asymptomatic stray cats in Japan
Authors: Kitashin Ichika , Kumano Hitomi , Nakagawa Keisuke 
Published: October 2024

ABSTRACT

We determined the complete genome sequences of two feline astroviruses (FAstVs) in non-diarrheic stool samples from apparently healthy stray cats in 2020 in Japan. Information on the complete genome sequence of FAstV from asymptomatic cats has great potential for a better understanding of the ecology of FAstV in cats.
Genome sequence of an extremely halophilic archaeon isolated from Permian Period halite, Salado Formation in New Mexico, USA:
Halobacterium
sp. strain NMX12-1
Authors: Soto Leonardo , DasSarma Priya , Anton Brian P. , Vincze Tamas , Verma Ishita , Eralp Bora , Powers Dennis W. , Dozier Brian Lee , Roberts Richard J. , DasSarma Shiladitya 
Published: October 2024

ABSTRACT

Halobacterium
sp. strain NMX12-1, an extremely halophilic Archaeon, was isolated from 250 million-year-old Salado Formation salt crystal in Carlsbad, New Mexico. Single-molecule real-time sequencing revealed a 3.2-Mbp genome with a 2.6-Mbp chromosome and five plasmids (234, 211, 119, 21, and 1.6-kbp). The GC-rich genome encodes an acidic proteome, characteristic of Haloarchaea.