bluuebunny/crossref_metadata_2025_split huggingface dataset:
Creating and Performing Educational Gymnastics Using Computational Thinking Skills
Authors: Chen YuChun , Jacques Lorraine A. 
Published: September 2024

Purpose: This study examined how physical education majors used computational thinking (CT) skills in a movement concept course. Method: Twenty-two physical education majors were tasked to create two gymnastics routines (i.e., algorithm design), analyze their routines (i.e., decomposition and abstraction), create and follow a personalized fitness plan (i.e., abstract), revise the routines (i.e., debugging), and perform the routines at the end of the semester. Data were analyzed as a single case study with embedded units using structural coding. Results: The participants demonstrated strengths with debugging and algorithm design; however, they struggled with decomposition and abstraction, which was congruent with previous research regarding these two concepts as the most difficult and important CT skills to master. Discussion/Conclusions: The findings underscore the value of CT skills in a non-STEM (i.e., science, technology, engineering, and mathematics) course, expending the instructional appropriateness to expose CT to undergraduate students with little to no interest or previous experience in STEM.
Prevalence of the cefazolin inoculum effect (CzIE) in nasal colonizing methicillin-susceptible
Staphylococcus aureus
in patients from intensive care units in Colombia and use of a modified rapid nitrocefin test for detection
Authors: Carvajal Lina P. , Rincon Sandra , Gomez Villegas Sara I. , Matiz-Gonzalez J. Manuel , Ordoñez Karen , Santamaria Alejandra , Ospina Navarro Leonardo , Beltran Jaime , Guevara Fredy , Mendez Yardany R. , Salcedo Soraya , Porras Alexandra , Valencia-Moreno Albert , Greenia Haley , Deyanov Alexander , Baptista Rodrigo , Tam Vincent H. , Panesso Diana , Tran Truc T. , Miller William R. , Arias Cesar A. , Reyes Jinnethe 
Published: September 2024

ABSTRACT

The cefazolin inoculum effect (CzIE) has been associated with poor clinical outcomes in patients with methicillin-susceptible
Staphylococcus aureus
(MSSA) infections. We aimed to investigate the point prevalence of the CzIE among nasal colonizing MSSA isolates from ICU patients in a multicenter study in Colombia (2019–2023). Patients underwent nasal swabs to assess for
S. aureus
colonization on admission to the ICU, and some individuals had follow-up swabs. We performed cefazolin MIC by broth microdilution using standard and high inoculum and developed a modified nitrocefin-based rapid test to detect the CzIE. Whole-genome sequencing was carried out to characterize BlaZ types and allotypes, phylogenomics, and Agr-typing. A total of 352 patients were included; 46/352 (13%) patients were colonized with
S. aureus
and 22% (10/46) and 78% (36/46) with MRSA and MSSA, respectively. Among 36 patients who contributed with 43 MSSA colonizing isolates, 21/36 (58%) had MSSA exhibiting the CzIE. BlaZ type A and BlaZ-2 were the predominant type and allotype in 56% and 52%, respectively. MSSA belonging to CC30 were highly associated with the CzIE, and single-nucleotide polymorphism (SNP) analyses supported possible transmission of MSSA exhibiting the CzIE among some patients of the same unit. The modified nitrocefin rapid test had 100%, 94.4%, and 97.7% sensitivity, specificity, and accuracy, respectively. We found a high point prevalence of the CzIE in MSSA colonizing the nares of critically ill patients in Colombia. A modified rapid test was highly accurate in detecting the CzIE in this patient population.
The foundation for the microbiology laboratory’s essential role in diagnostic stewardship: an ASM Laboratory Practices Subcommittee report
Authors: Dumm Rebekah E. , Marlowe Elizabeth M. , Patterson Logan , Larkin Paige M. K. , She Rosemary C. , Filkins Laura M. 
Published: September 2024

ABSTRACT

Diagnostic stewardship (DxS) has gained traction in recent years as a cross-disciplinary method to improve the quality of patient care while appropriately managing resources within the healthcare system. Clinical microbiology laboratorians have been highly engaged in DxS efforts to guide best practices with conventional microbiology tests and more recently with molecular infectious disease diagnostics. Laboratories can experience resistance to their role in DxS, especially when the clinical benefits, motivations for interventions, and underlying regulatory requirements are not clearly conveyed to stakeholders. Clinical laboratories must not only ensure ethical practices but also meet obligatory requirements to steward tests responsibly. In this review, we aim to support clinical microbiology laboratorians by providing the background and resources that demonstrate the laboratory’s essential role in DxS. The heart of this review is to collate regulatory and accreditation requirements that, in essence, mandate DxS practices as a long-standing, core element of high-quality laboratory testing to deliver the best possible patient care. While examples of the clinical impact of DxS are plentiful in the literature, here, we focus on the operational and regulatory justification for the laboratory’s role in stewardship activities.
Rare BK polyomavirus subtype III detected in hematopoietic cell transplant recipient
Authors: Walder Tiana A. , Odegard Elizabeth A. , Meeds Heidi L. , Kleiboeker Steven B. , Ziady Assem , Sabulski Anthony , Jodele Sonata , Seif Alix E. , Davies Stella M. , Laskin Benjamin L. , Blackard Jason T. 
Published: September 2024

ABSTRACT

BK polyomavirus (BKPyV) is associated with disease in transplant patients. BKPyV genomic diversity is thought to contribute to functional differences in virulence factors. Here, we present the near full-length BKPyV genome sequence from a patient who underwent hematopoietic cell transplant and was infected with subtype III, a rare subtype.
Microevolution of
Bartonella grahamii
driven by geographic and host factors
Authors: Xu Ailing , Lu Liang , Zhang Wen , Song Xiuping , Li Guichang , Miao Yu , Li Ruixiao , Chen Min , Liu Qiyong , Li Dongmei 
Published: September 2024

ABSTRACT

Bartonella grahamii
is one of the most prevalent
Bartonella
species in wild rodents and has been associated with human cases of neuroretinitis. The structure and distribution of genomic diversity in natural
B. grahamii
is largely unexplored. Here, we have applied a comprehensive population genomic and phylogenomic analysis to 172 strains of
B. grahamii
to unravel the genetic differences and influencing factors that shape its populations. The findings reveal a remarkable genomic diversity within the species, primarily in the form of single- nucleotide polymorphisms. The open pangenome of
B. grahamii
indicates a dynamic genomic evolution influenced by its ecological niche. Whole-genome data allowed us to decompose
B. grahamii
diversity into six phylogroups, each characterized by a unique “mosaic pattern” of hosts and biogeographic regions. This suggests a complex interplay between host specificity and biogeography. In addition, our study suggests a possible origin of European strains from Asian lineages, and host factors have a more significant impact on the genetic differentiation of
B. grahamii
than geographical factors. These insights contribute to understanding the evolutionary history of this pathogen and provide a foundation for future epidemiological research and public health strategies.

IMPORTANCE

Bartonella grahamii
has been reported worldwide and shown to infect humans. Up to now, an effective transmission route of
B. grahamii
to humans has not been confirmed. The genetic evolution of
B. grahamii
and the relationship between
B. grahamii
and its host need to be further studied. The factors driving the genetic diversity of
B. grahamii
are still controversial. The results showed that the European isolates shared a common ancestor with the Chinese isolates. Host factors were shown to play an important role in driving the genetic diversity of
B. grahamii
. When host factors were fixed, geographic barriers drove
B. grahamii
microevolution. Our study emphasizes the importance of characterizing isolate genomes derived from hosts and geographical locations and provides a new reference for the origin of
B. grahamii
.
Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages
Authors: Zeng Tao , Cao Yongqing , Yin Jianmei , Feng Peishi , Tian Yong , Sun Hanxue , Gu Tiantian , Zong Yibo , Ma Xueying , Zhao Zelong , Chen Li , Xu Wenwu , Han Wei , Lu Lizhi 
Published: September 2024

ABSTRACT

Tibetan animals have several unique advantages owing to the harsh ecological conditions under which they live. However, compared to Tibetan mammals, understanding of the advantages and underlying mechanisms of the representative high-latitude bird, the Tibetan chicken (
Gallus gallus
, TC), remains limited. The gut microbiota of animals has been conclusively shown to be closely related to both host health and host environmental adaptation. This study aimed to explore the relationships between the cecal microbiome and the advantages of TCs based on comparisons among three populations: native TCs residing on the plateau, domestic TCs living in the plain, and one native plain species. Metatranscriptomic sequencing revealed a significant enrichment of active Bacteroidetes but a loss of active Firmicutes in native TCs. Additionally, the upregulated expression of genes in the cecal microbiome of native TCs showed enriched pathways related to energy metabolism, glycan metabolism, and the immune response. Furthermore, the expression of genes involved in the biosynthesis of short-chain fatty acids (SCFAs) and secondary bile acids (SBAs) was upregulated in the cecal microbiome of native TCs. Data from targeted metabolomics further confirmed elevated levels of certain SCFAs and SBAs in the cecum of native TCs. Based on the multi-omics association analysis, we proposed that the higher ratio of active Bacteroidetes/Firmicutes may be attributed to the efficient energy metabolism and stronger immunological activity of native TCs. Our findings provide a better understanding of the interactions between gut microbiota and highland adaptation, and novel insights into the mechanisms by which Tibetan chickens adapt to the plateau hypoxic environment.

IMPORTANCE
The composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.
Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques
Authors: Brochu Hayden N. , Smith Elise , Jeong Sangmi , Carlson Michelle , Hansen Scott G. , Tisoncik-Go Jennifer , Law Lynn , Picker Louis J. , Gale Michael , Peng Xinxia 
Published: September 2024

ABSTRACT

Rhesus cytomegalovirus expressing simian immunodeficiency virus (RhCMV/SIV) vaccines protect ~59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is unknown. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here, we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post-challenge and were profiled using 16S rRNA based microbiome analysis. We identified ~2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, by using newly developed compositional data analysis techniques, we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.

IMPORTANCE
The human immunodeficiency virus (HIV) has infected millions of people worldwide. Unfortunately, still there is no vaccine that can prevent or treat HIV infection. A promising pre-clinical HIV vaccine based on rhesus cytomegalovirus (RhCMV) expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) provides sustained, durable protection against SIV challenge in ~59% of vaccinated rhesus macaques. There is an urgent need to understand the cause of this protection vs non-protection outcome. In this study, we profiled the gut microbiomes of 45 RhCMV/SIV vaccinated rhesus macaques and identified gut microbial signatures that were predictive of RhCMV/SIV vaccination groups and vaccine protection outcomes. These vaccine protection-associated microbial features were significantly correlated with early vaccine-induced host immune signatures in whole blood from the same animals. These findings show that the gut microbiome may be involved in RhCMV/SIV vaccine-induced protection, warranting further research into the impact of the gut microbiome in human vaccine trials.
Acute stress and multicellular development alter the solubility of the
Dictyostelium
Sup35 ortholog ERF3
Authors: Williams Felicia N. , Travis Kanesha L. , Haver Holly N. , Umano Anna D. , Guerra-Hernandez Yaneli , Scaglione K. Matthew 
Published: September 2024

ABSTRACT

Among sequenced organisms, the genome of
Dictyostelium discoideum
is unique in that it encodes for a massive amount of repeat-rich sequences in the coding region of genes. This results in the
Dictyostelium
proteome encoding for thousands of repeat-rich proteins, with nearly 24% of the
Dictyostelium
proteome encoding Q/N-rich regions that are predicted to be prion like in nature. To begin investigating the role of prion-like proteins in
Dictyostelium
, we decided to investigate ERF3, the
Dictyostelium
ortholog of the well-characterized yeast prion protein Sup35. ERF3 lacks the Q/N-rich region required for prion formation in yeast, raising the question of whether this protein aggregates and has prion-like properties in
Dictyostelium
. Here, we found that ERF3 formed aggregates in response to acute cellular stress. However, unlike
bona fide
prions, we were unable to detect transmission of aggregates to progeny. We further found that aggregation of this protein is driven by the ordered C-terminal domain independently of the disordered N-terminal domain. Finally, we also observed aggregation of ERF3 under conditions that induce multicellular development, suggesting that this phenomenon may play a role in
Dictyostelium
development. Together, these findings suggest a role for regulated protein aggregation in
Dictyostelium
cells under stress and during development.

IMPORTANCE

Prion-like proteins have both beneficial and deleterious effects on cellular health, and many organisms have evolved distinct mechanisms to regulate the behaviors of these proteins. The social amoeba
Dictyostelium discoideum
contains the highest proportion of proteins predicted to be prion like and has mechanisms to suppress their aggregation. However, the potential roles and regulation of these proteins remain largely unknown. Here, we demonstrate that aggregation of the
Dictyostelium
translation termination factor ERF3 is induced by both acute cellular stress and by multicellular development. These findings imply that protein aggregation may have a regulated and functional role in the
Dictyostelium
stress response and during multicellular development.
Building allied health professions’ leadership self-efficacy through authentic experiential learning: a participatory evaluation of allied health professions leadership fellow secondments
Authors: Harding Deborah , Lycett Helen , Avery Leila , Kumaresan Tania , Madden Venus 
Published: September 2024

BackgroundNHS England’s Chief Allied Health Profession’s Officer has called for investment in allied health professions (AHPs) leaders and the need to address limited leadership development opportunities for AHPs. We report the evaluation of a small-scale leadership initiative in a UK National Health Service (NHS) provider where part-time, fixed term, project focused AHP leadership fellow posts were established.AimTo gain insights about the implementation and benefits of an AHP leadership fellow initiative and to identify learning to inform future AHP leadership development.MethodA participatory evaluative approach was adopted, involving the associate director for AHPs who established the initiative and the first cohort of AHP leadership fellows.FindingsThere is evidence of organisational value and benefits for AHP leadership fellows which map to mid-career leadership opportunities described in NHS guidance.ConclusionAHP leadership fellow posts provide innovative experiential opportunities for authentic and meaningful strategic leadership development consistent with NHS guidance. While small scale, with limited representation from just two of the AHPs recognised in the NHS, there are indications of positive outcomes for both aspiring AHP leaders and employers. The approach could be replicated across healthcare systems, in different settings and with wider representation from other AHPs.
Planar decomposition of the HOMFLY polynomial for bipartite knots and links
Authors: Anokhina A. , Lanina E. , Morozov A. 
Published: September 2024

AbstractThe theory of the Kauffman bracket, which describes the Jones polynomial as a sum over closed circles formed by the planar resolution of vertices in a knot diagram, can be straightforwardly lifted from $$\mathfrak {sl}(2)$$

sl
(
2
)

to $$\mathfrak {sl}(N)$$

sl
(
N
)

at arbitrary N – but for a special class of bipartite diagrams made entirely from the antiparallel lock tangle. Many amusing and important knots and links can be described in this way, from twist and double braid knots to the celebrated Kanenobu knots for even parameters – and for all of them the entire HOMFLY polynomials possess planar decomposition. This provides an approach to evaluation of HOMFLY polynomials, which is complementary to the arborescent calculus, and this opens a new direction to homological techniques, parallel to Khovanov–Rozansky generalizations of the Kauffman calculus. Moreover, this planar calculus is also applicable to other symmetric representations beyond the fundamental one, and to links which are not fully bipartite what is illustrated by examples of Kanenobu-like links.
Deflection of charged signals in a dipole magnetic field in Kerr background
Authors: Li Zonghai , Jia Junji 
Published: September 2024

AbstractThis paper investigates charged particle deflection in a Kerr spacetime background with a dipole magnetic field, focusing on the equatorial plane and employing the weak field approximation. We employ the Jacobi–Randers metric to unify the treatment of the gravitational and electromagnetic effects on charged particles. Furthermore, we utilize the Gauss–Bonnet theorem to calculate the deflection angle through curvature integrals. The difference between the prograde and retrograde deflection angles is linked to the non-reversibility of metrics and geodesics in Finsler geometry, revealing that this difference can be considered a Finslerian effect. We analyze the impact of both gravitomagnetic field and dipole magnetic field on particle motion and deflection using the Jacobi–Randers magnetic field. The model considered in this paper exhibits interesting features in the second-order approximation of (M/b), i.e., the ratio between the spacetime mass and impact parameters. When $$q\mu =2MaE$$

q
μ
=
2
M
a
E

, where $$q,\,E$$

q
,

E

are the charge and asymptotic energy of the charged particle and $$\mu ,\,a$$

μ
,

a

are the dipole magnetic moment and spacetime spin, the Jacobi–Randers metric possesses reversible geodesics, leading to equal prograde and retrograde deflection angles. In this case, the gravitomagnetic field and dipole magnetic field cancel each other out, distinguishing it from scenarios involving only the gravitomagnetic field or the dipole magnetic field. We also explore the magnetic field’s impact on gravitational lensing of charged particles.
On the Feasibility and Benefits of Extensive Evaluation
Authors: Hui Yujie , Yu Miao , Qi Hao , Gan Yifan , Li Tianxi , Li Yuke , Ren Xueyuan , Ma Sixiang , Lu Xiaoyi , Wang Yang 
Published: September 2024

Benchmark and system parameters often have a significant impact on performance evaluation, which raises a long-lasting question about which settings we should use.
This paper studies the feasibility and benefits of extensive evaluation. A full extensive evaluation, which tests all possible settings, is usually too expensive. This work investigates whether it is possible to sample a subset of the settings and, upon them, generate observations that match those from a full extensive evaluation. Towards this goal, we have explored the incremental sampling approach, which starts by measuring a small subset of random settings, builds a prediction model on these samples using the popular ANOVA approach, adds more samples if the model is not accurate enough, and terminates otherwise.
To summarize our findings: 1) Enhancing a research prototype to support extensive evaluation mostly involves changing hard-coded configurations, which does not take much effort. 2) Some systems are highly predictable, which means that they can achieve accurate predictions with a low sampling rate, but some systems are less predictable. 3) We have not found a method that can consistently outperform random sampling + ANOVA. Based on these findings, we provide recommendations to improve artifact predictability and strategies for selecting parameter values during evaluation.