bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of laboratory‐based and non‐laboratory‐based cardiovascular risk prediction tools in rural India
Authors: Birhanu Mulugeta Molla , Zengin Ayse , Evans Roger G. , Kim Joosup , Olaiya Muideen T. , Riddell Michael A. , Kalyanram Kartik , Kartik Kamakshi , Suresh Oduru , Thomas Nihal , Srikanth Velandai K. , Thrift Amanda G.
Published: December 2024

Background

Non‐laboratory‐based cardiovascular risk prediction tools are feasible alternatives to laboratory‐based tools in low‐ and middle‐income countries. However, their effectiveness compared to their laboratory‐based counterparts has not been adequately tested.

Aim

We compared estimates from laboratory‐based and non‐laboratory‐based risk prediction tools in a low‐ and middle‐income country setting.

Methods

Using a cross‐sectional design, residents of the Rishi Valley region, Andhra Pradesh, India, were surveyed from 2012 to 2015. Ten‐year absolute risk was compared for laboratory‐based and non‐laboratory‐based Framingham Risk Score (FRS), World Health Organization‐Risk Score (WHO‐RS) and risk prediction tool for global populations (Globorisk). An agreement was assessed using ordinary least‐products (OLP) regression (for RS) and quadratic weighted kappa (κw, for risk band).

Results

Among 2847 participants aged 40–74 years, the mean age was 54.0 years. Cardiovascular RS increased with age and was greater in men than women in each age group. For all tools, regardless of whether laboratory or non‐laboratory‐based, over 80% of the participants were classified in the same risk band. There was strong agreement between laboratory‐based and non‐laboratory‐based tools, greatest for the WHO‐RS tools (OLP slope = 0.96, κw = 0.93) and least for the FRS (OLP slope = 0.84, κw = 0.88). The level of agreement was greater among women than men, less in those with hypercholesterolaemia or hypertension than those without, and was particularly poor among those with diabetes.

Conclusions

Non‐laboratory‐based Framingham, WHO‐RS and Globorisk tools performed relatively well compared with their laboratory‐based counterparts in rural India. However, they may be less useful for risk stratification when applied to individuals with diabetes.
How Do Scientists Think? Contributions Toward a Cognitive Science of Science
Authors: Nersessian Nancy J.
Published: December 2024

Scientific thinking is one of the most creative expressions of human cognition. This paper discusses my research contributions to the cognitive science of science. I have advanced the position that data on the cognitive practices of scientists drawn from extensive research into archival records of historical science or collected in extended ethnographic studies of contemporary science can provide valuable insight into the nature of scientific cognition and its relation to cognition in ordinary contexts. I focus on contributions of my research on analogy, model‐based reasoning, and conceptual change and on how scientists enhance their natural cognitive capacities by creating modeling environments that integrate cognitive, social, material, and cultural resources. I provide an outline of my trajectory from a physicist to a philosopher of science to a hybrid cognitive scientist in my quest to understand the nature of scientific thinking.
Unlocking regeneration potential: harnessing morphogenic regulators and small peptides for enhanced plant engineering
Authors: Youngstrom Christopher , Wang Kan , Lee Keunsub
Published: December 2024

Plant genetic transformation is essential for understanding gene functions and developing improved crop varieties. Traditional methods, often genotype‐dependent, are limited by plants' recalcitrance to gene delivery and low regeneration capacity. To overcome these limitations, new approaches have emerged that greatly improve efficiency and genotype flexibility. This review summarizes key strategies recently developed for plant transformation, focusing on groundbreaking technologies enhancing explant‐ and genotype flexibility. It covers the use of morphogenic regulators (MRs), stem cell‐based methods, and in planta transformation methods. MRs, such as maize Babyboom (BBM) with Wuschel2 (WUS2), and GROWTH‐REGULATING FACTORs (GRFs) with their cofactors GRF‐interacting factors (GIFs), offer great potential for transforming many monocot species, including major cereal crops. Optimizing BBM/WUS2 expression cassettes has further enabled successful transformation and gene editing using seedling leaves as starting material. This technology lowers the barriers for academic laboratories to adopt monocot transformation systems. For dicot plants, tissue culture‐free or in planta transformation methods, with or without the use of MRs, are emerging as more genotype‐flexible alternatives to traditional tissue culture‐based transformation systems. Additionally, the discovery of the local wound signal peptide Regeneration Factor 1 (REF1) has been shown to enhance transformation efficiency by activating wound‐induced regeneration pathways in both monocot and dicot plants. Future research may combine these advances to develop truly genotype‐independent transformation methods.
Rapid and efficient in planta genome editing in sorghum using foxtail mosaic virus‐mediated sgRNA delivery
Authors: Baysal Can , Kausch Albert P. , Cody Jon P. , Altpeter Fredy , Voytas Daniel F.
Published: December 2024

The requirement of in vitro tissue culture for the delivery of gene editing reagents limits the application of gene editing to commercially relevant varieties of many crop species. To overcome this bottleneck, plant RNA viruses have been deployed as versatile tools for in planta delivery of recombinant RNA. Viral delivery of single‐guide RNAs (sgRNAs) to transgenic plants that stably express CRISPR‐associated (Cas) endonuclease has been successfully used for targeted mutagenesis in several dicotyledonous and few monocotyledonous plants. Progress with this approach in monocotyledonous plants is limited so far by the availability of effective viral vectors. We engineered a set of foxtail mosaic virus (FoMV) and barley stripe mosaic virus (BSMV) vectors to deliver the fluorescent protein AmCyan to track viral infection and movement in Sorghum bicolor. We further used these viruses to deliver and express sgRNAs to Cas9 and Green Fluorescent Protein (GFP) expressing transgenic sorghum lines, targeting Phytoene desaturase (PDS), Magnesium‐chelatase subunit I (MgCh), 4‐hydroxy‐3‐methylbut‐2‐enyl diphosphate reductase, orthologs of maize Lemon white1 (Lw1) or GFP. The recombinant BSMV did neither infect sorghum nor deliver or express AmCyan and sgRNAs. In contrast, the recombinant FoMV systemically spread throughout sorghum plants and induced somatic mutations with frequencies reaching up to 60%. This mutagenesis led to visible phenotypic changes, demonstrating the potential of FoMV for in planta gene editing and functional genomics studies in sorghum.
The importin α proteins IMPA1, IMPA2, and IMPA4 play redundant roles in suppressing autoimmunity in Arabidopsis thaliana
Authors: Mori Airi , Nakagawa Shitomi , Suzuki Toshiyuki , Suzuki Takamasa , Gaudin Valérie , Matsuura Takakazu , Ikeda Yoko , Tamura Kentaro
Published: December 2024

Proteins in the importin α (IMPA) family play pivotal roles in intracellular nucleocytoplasmic transport. Arabidopsis thaliana possesses nine IMPA members, with diverse tissue‐specific expression patterns. Among these nine IMPAs, IMPA1, IMPA2, and IMPA4 cluster together phylogenetically, suggesting potential functional redundancy. To explore this redundancy, we analyzed single and multiple T‐DNA mutants for these genes and discovered severe growth defects in the impa1 impa2 impa4 triple knockout mutant but not in the single or double mutants. Complementation with IMPA1, IMPA2, or IMPA4 fused to green fluorescent protein (GFP) rescued the growth defects observed in the impa1 impa2 impa4 mutant, indicating the functional redundancy of these three IMPAs. The IMPA‐GFP fusion proteins were localized in the nucleus and nuclear envelope, suggesting their involvement in nucleocytoplasmic transport processes. Comparative transcriptomics revealed that salicylic acid (SA)‐responsive genes were significantly upregulated in the impa1 impa2 impa4 triple mutant. Consistent with this observation, impa1 impa2 impa4 mutant plants accumulated SA and reactive oxygen species to high levels compared with wild‐type plants. We also found enhanced resistance to the anthracnose pathogen Colletotrichum higginsianum in the impa1 impa2 impa4 mutants, suggesting that defense responses were constitutively activated in the impa1 impa2 impa4 mutant. Our findings shed light on the redundant roles of IMPA1, IMPA2, and IMPA4 in suppressing the autoimmune responses and suggest avenues of research to clarify their potentially unique roles.
Elicitron: A Large Language Model Agent-Based Simulation Framework for Design Requirements Elicitation
Authors: Ataei Mohammadmehdi , Cheong Hyunmin , Grandi Daniele , Wang Ye , Morris Nigel , Tessier Alexander
Published: December 2024

Requirement elicitation, a critical, yet time-consuming and challenging step in product development, often fails to capture the full spectrum of user needs. This may lead to products that fall short of user expectations. This article introduces a novel framework that leverages large language models (LLMs) to automate and enhance the requirement elicitation process. LLMs are used to generate a vast array of simulated users (LLM agents), enabling the exploration of a much broader range of user needs and unforeseen use cases. These agents engage in product experience scenarios, explaining their actions, observations, and challenges. Subsequent agent interviews and analysis uncover valuable user needs, including latent ones. We validate our framework with three experiments. First, we explore different methodologies for the challenge of diverse agent generation, discussing their advantages and shortcomings. We measure the diversity of identified user needs and demonstrate that context-aware agent generation leads to greater diversity. Second, we show how our framework effectively mimics empathic lead user interviews, identifying a greater number of latent needs than conventional human interviews. Third, we show that LLMs can be used to analyze interviews, capture needs, and classify them as latent or not. Our work highlights the potential of using LLMs to accelerate early-stage product development with minimal costs and increase innovation.
The role of acoustic cues in the checked-unchecked tone merging of the Qixian Jin dialect
Authors: Liu Kangdi , Liang Lei , Qin Quentin Zhen
Published: December 2024

The weakening/loss of the stop coda in checked tone syllables (also known as “Ru syllable opening”) may lead to a subsequent merger of tonal contrasts in Chinese. This study examined the role of acoustic cues in checked-unchecked tone merging in the Qixian Jin dialect by comparing three age groups. Results showed that duration served as a robust cue for the tonal contrast regardless of age, whereas glottalization did not. The F0 contour signaled the tone merging process with variations across age groups. The findings have implications for modeling complex F0 (falling-rising) contours to enable further cross-dialect comparisons from a phonetic perspective.
Malate or Not? Acute Effects of L-Citrulline Versus Citrulline Malate on Neuromuscular Performance in Young, Trained Adults: A Randomized, Double-Blind, Placebo-Controlled Crossover Trial
Authors: Martín-Olmedo Juan J. , Miras-Moreno Sergio , Cuadra-Montes Kevin , García-Ramos Amador , Ruiz Jonatan R. , Jurado-Fasoli Lucas
Published: December 2024

L-citrulline (CIT) supplementation seems to improve resistance training performance; yet, whether malate has additive ergogenic effects when combined with CIT is unknown. This randomized, double-blind, placebo-controlled crossover trial aimed to compare the acute effects of CIT versus citrulline malate (CMA) supplementation on neuromuscular performance and exertion and emotional perceptions in young, trained men and women. 43 (21 women; 24.2 ± 3.7 years) participants ingested a placebo, CIT (5.3 g of CIT), or CMA (5.3 g of CIT, 2.7 g of malate) 45 min before three experimental sessions in a counterbalanced manner. We evaluated the upper and lower limb maximal neuromuscular and ballistic performance through the two-point method and countermovement jump. Strength-endurance was assessed across three sets of 10 repetitions in the squat and bench press exercises. Exertion and emotional perceptions were evaluated before and after the assessment and during the strength-endurance assessment. CIT and CMA supplementation did not enhance maximal neuromuscular performance (all p ≥ .061, ), or ballistic strength (all p ≥ .348, ). Neither CIT nor CMA supplementation improved strength-endurance as observed in the total number of repetitions (all p ≥ .590, ), repetitions before reaching velocity loss threshold (all p ≥ .623, ), mean velocity (all p ≥ .792, ), mean velocity decline (all p ≥ .293, ), and mean velocity maintenance (all p ≥ .393 ), or exertion and emotional perceptions (both p ≥ .306, ). In conclusion, CIT and CMA supplementation may not increase the neuromuscular performance during low- to moderate-volume resistance training sessions in young, trained adults. This trial was registered at ClinicalTrials.gov (No. NCT05183893).
Association Between Anthropometry and Motor Performance With Competitive Indicators of Women Athletes in the Capoeira World Games: A Cross-Sectional Study
Authors: Barros Lorrana K.S. , Oliveira Ariel C. , Vale Thamires S. , dos Santos Geovani A. , Moreira Débora Vitória S. , Pinheiro Anderson S. , dos Santos Rafael G. , da Silva Ilma Sabrina B. , de Souza Thales Alessandro V.M. , Ribeiro Davi L. , da Silva Priscila , Moreira Sérgio R.
Published: December 2024

Objective: This study aimed to verify the association of anthropometric and motor variables with the competitive indicators of female athletes in the ABADÁ-Capoeira (Associação Brasileira de Apoio e Desenvolvimento da Arte Capoeira) World Games. Methods: Forty-two capoeira athletes from 15 countries (capoeira experience = 15.1 [7.9] y, age = 32.1 [8.8] y, body mass = 63.2 [6.3] kg, and height = 161.8 [4.4] cm) were recruited for anthropometric and motor evaluation of sit and reach, push-up, trunk flexion, countermovement jump (CMJ), and quadrant jump (QDJ). Each athlete’s ranking and stage scores in the competition were obtained as indicators of competitive performance. Results: There were inverse correlations between abdominal circumference, body mass index, body fat percentage, and endomorphy with motor variables (rho = −.36 to −.46; P < .05). Positive correlations of motor performance with competitive performance indicators were evidenced, being between the average increment score with the CMJ (rho = .33; P < .05) and the QDJ (rho = .35; P < .05), and between the competition score with the CMJ (rho = .32; P < .05) and the QDJ (rho = .32; P < .05). Additionally, the motor performance of trunk flexion (β = 0.11; odds ratio = 1.126; 95% CI, 1.025–1.238), QDJ (β = 0.21; odds ratio = 1.239; 95% CI, 1.022–1.503), and CMJ (β = 0.20; odds ratio = 1.230; 95% CI, 1.029–1.471) predicted competition stage advancement. Conclusions: Associations occurred between anthropometry and motor performance, and this was predictive of competitive indicators of female capoeira athletes in international competition. Such information may contribute to an optimized and effective training process aimed at the integral improvement of capoeira practitioners’ body composition and motor skills, especially to improve localized muscular endurance of the upper limbs and abdomen, as well as agility and power of the lower limbs.
Examining a Successful High-Performance Triathlon Environment From the Coaching Team Perspective
Authors: Andronikos Georgios , Westbury Tony , Souglis Athanasios , Travlos Antonios , Martindale Russell J.J.
Published: December 2024

This research aims to investigate an environment designed by a head coach with a track record of both highly successful talent development and world-class performance outcomes in the sport of triathlon. A qualitative approach involving semistructured interviews with the head coach, the psychologist, and the nutritionist was used. Key considerations regarding the selection of athletes were discussed, providing evidence for the key role of psychology and prolonged trials that allowed thorough understanding of the athlete, and insight into development capacity, as well as their contribution to the wider squad. In addition, a coaching team was embedded utilizing a multidisciplinary approach, and significant others were actively incorporated in the development process. Furthermore, the complexities of managing long-term development were highlighted, and the use of challenge as a mechanism of development was evident.
From Early Explorers to Restricted Practitioners: A Qualitative Analysis of Coaches’ Development, Context, and Practices Within U.K. Mixed Martial Arts
Authors: Kirk Christopher , Cronin Colum , Langan-Evans Carl , Clark David R. , Morton James P.
Published: December 2024

Despite its growing popularity and participation rates, mixed martial arts (MMA) coaching has not been the subject of much critical scholarly analysis. Accordingly, knowledge of this activity is limited, and inadequate, as a means of understanding this MMA context, and supporting those coaches who practice in it. To begin to address this gap, we report an initial exploration based upon three interviews with four experienced U.K.-based MMA coaches (12 interviews in total). Via a reflexive thematic analysis we generated four themes: (1) MMA coaches developed their practice via experiential and peer learning; (2) MMA coaches have dual aims of producing competitive athletes while appealing to paying, recreational participants; (3) private event promoters dictate competition dates, meaning preparation time may be suboptimal; and (4) MMA coaches rely on “coach’s eye” and subjective feedback to enact practices in relation to training load, fatigue, and skill development. Coupled with theoretical sensemaking, this novel exploration reveals MMA practices that are grounded in “folk pedagogies,” and shaped by economic imperatives and powerful actors. These findings provide an original and significant analysis of an increasingly prevalent coaching. This approach supplements existing quantitative training studies, thus enabling a pragmatic understanding of the U.K. MMA coaching, while also providing direction for future in-depth studies.
Impact of Reach Height on Estimated Rotator Cuff Compression Risk in Manual Wheelchair Users With Spinal Cord Injury
Authors: Schaffer Kylee M. , Madansingh Stefan I. , Fortune Emma , Morrow Melissa M. , Zhao Kristin D. , Cloud-Biebl Beth A.
Published: December 2024

Reaching is a common daily activity requiring a range of humeral elevation that contributes to rotator cuff compression. The purpose of this study was to estimate supraspinatus and infraspinatus tendon compression risk relative to the acromion and coracoacromial ligament during reaching by manual wheelchair users with spinal cord injury. A cross-sectional design was used to evaluate 8 participants (7 males, median [range] age 36 y [23–61]). Electromagnetic motion capture recorded shoulder kinematics while participants reached for a can at 2 heights: low (0.91 m) and high (1.37 m). Using 1 set of computed tomographic-based bone models and individual glenohumeral kinematics, compression risk was evaluated as the percentage of the reach activity and number of seconds that tendon insertions were less than 5 mm from scapular landmarks. Reach conditions were compared using a Wilcoxon signed-rank test (α = .05). Although not statistically significant, the supraspinatus and infraspinatus relative to the acromion had approximately 40% of the activity duration or 0.8 seconds more time under 5 mm in low versus high reach, indicating increased risk of compression. Compression risk estimates were consistent with prior publications on planar arm movements. Estimating the risk of tendon compression using absolute time may help with understanding cumulative exposure during day-to-day activity.
Individualization of Footwear for Optimizing Running Economy: A Theoretical Framework
Authors: Connick Mark J. , Lichtwark Glen A.
Published: December 2024

Advanced footwear technologies contain thicker, lightweight, and more resilient midsoles and are associated with improved running economy (RE) compared with traditional footwear. This effect is highly variable with some individuals gaining a greater RE benefit, indicating that biomechanics plays a mediating role with respect to the total effect. Indeed, the energy generated by contractile elements and the elastic energy recovered from stretched tendons and ligaments in the legs and feet are likely to change with footwear. Therefore, if RE is to be maximized according to individual characteristics, an individualized approach to footwear selection is required. However, current theoretical frameworks hinder this approach. Here, we introduce a framework that describes causal relationships between footwear properties, biomechanics, and RE. The framework proposes that RE changes with footwear due to (1) a direct effect of footwear properties—for example, increased or decreased energy return—and (2) a mediating effect of footwear on ankle and foot biomechanics and the spring-mass system. By describing the total effect as 2 complementary pathways, the framework facilitates research that aims to separately quantify direct and mediating effects of footwear. This may permit the development of footwear materials that can separately target the direct and individual mediating effects.
Professional Identity of Physical Education Teachers: What Are the Key Components?
Authors: Park Junhyuk , Yun Sanga , Choi Euichang
Published: December 2024

Purpose: Professional identity (PI) has gained significant attention from professional education programs as this concept underscores the professional values and qualities that professionals should internalize alongside their professional skills and knowledge. This study aims to explore the PI components formed by Korean secondary school physical education (PE) teachers. Methods: Twelve PE teachers participated in this qualitative study, selected through maximum variation sampling. Data collection methods included open-ended questionnaires, semistructured individual interviews, and documentation. Results: Eighteen PI components were identified and categorized into nine domains based on three identity dimensions (competence, knowledge, and disposition) and three task areas (teaching, student, and administration) of the professional identity matrix for physical education teachers framework. Discussion/Conclusions: The PI components, reflecting the professionalism instilled in PE teachers, emphasize the importance of embodying the qualities necessary to act, think, and feel like a PE teacher, which help visualize the educational outcomes of PE teacher education programs.
Prevalence and features of hypervirulent
Klebsiella pneumoniae
in respiratory specimens at a US hospital system
Authors: McElheny Christi L. , Iovleva Alina , Chen Nathalie , Woods Dominic , Pradhan Akansha , Sonnabend Jonah L. , Matunis Aidan R. , Raabe Nathan J. , Lee Janet S. , Trevejo-Nuñez Giraldina , Van Tyne Daria , Doi Yohei
Published: December 2024

Hypervirulent
Klebsiella pneumoniae
(hvKp) strains are considered to be relatively rare in the United States, but cases are increasingly reported. We prospectively and serially collected
K. pneumoniae
clinical isolates identified in respiratory specimens at a health system in Western Pennsylvania between 2020 and 2022. A total of 273
K
.
pneumoniae
isolates from 216 unique patients were analyzed for markers of hypervirulence by both string test for a hypermucoid phenotype and multiplex PCR to detect isolates carrying cardinal virulence genes
rmpA
,
rmpA2
,
iutA
, and
iro
. Of the 273 isolates, 13 (4.8%) tested positive by string test including 11 nonduplicate
K. pneumoniae
isolates, and two of these (0.7%) were positive by PCR for virulence genes
rmpA
,
rmpA2
,
iutA
, and
iro
. The latter two putative hvKp strains, belonging to sequence types ST23-K1 and ST86-SLV-K2, possessed pLVPK-like plasmids, and were collected from community-associated infections in individuals without known travel histories. Both putative hvKp strains and two additional string test-positive strains were resistant to killing by human serum. The hvKp strains caused significant pneumonia in mice infected by oropharyngeal aspiration, with significantly higher weight loss and increased bacterial burden in the lungs of mice infected with the KL1 (ST23) strain compared to the KL2 (ST86-SLV) strain. We also observed decreased survival of mice infected with the KL1 strain compared to the KL2 strain. These findings add to the growing body of evidence suggesting that hvKp strains, once considered endemic to Asia, may now be circulating in North America.

IMPORTANCE

Certain lineages of
Klebsiella pneumoniae
are increasingly recognized to cause severe community-associated infection, but information on their prevalence in the United States is limited. In a prospective, sequential cohort of 273
K
.
pneumoniae
respiratory isolates, we identified two of them as genetically defined hypervirulent
K. pneumoniae
. The isolates were from local residents who developed community-onset pneumonia, suggesting that hypervirulent
K. pneumoniae
may already be present in the community.
An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase function
Authors: Emam Elhassan Ali Fathi , Roy Koyel , Singh Devendra Pratap , Saini Deepak K. , Varshney Umesh
Published: December 2024

MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyze 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harboring the Nudix box motif, and a C-terminal domain (CTD) harboring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to the corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK-
Pi
) intermediate. Recently, we showed that NDK-
Pi
converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT-deficient
Escherichia coli
. We now show that both
Mycobacterium tuberculosis
MutT1 and
Mycobacterium smegmatis
MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK-
Pi
and prevent it from catalyzing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that
Msm
MutT1 decreases A to C mutations in
E. coli
under the conditions of
Eco
NDK overexpression.

IMPORTANCE

MutT proteins, having a Nudix box domain, hydrolyze the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobacterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK-
Pi
) intermediate and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK-
Pi
levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in
Escherichia coli
under the conditions of NDK overexpression.
Lipid a remodeling modulates outer membrane vesicle biogenesis by
Porphyromonas gingivalis
Authors: Alaei Sarah R. , King Alisa J. , Banani Karim , Reddy Angel , Ortiz Joshua , Knight Alexa L. , Haldeman Jessica , Su Thet Hnin , Park Hana , Coats Stephen R. , Jain Sumita
Published: December 2024

Outer membrane vesicles (OMVs) are small membrane enclosed sacs released from bacteria which serve as carriers of biomolecules that shape interactions with the surrounding environment. The periodontal pathogen,
Porphyromonas gingivalis
, is a prolific OMV producer. Here, we investigated how the structure of lipid A, a core outer membrane molecule, influences
P. gingivalis
OMV production, OMV-dependent TLR4 activation, and biofilm formation. We examined mutant strains of
P. gingivalis
33277 deficient for enzymes that alter lipid A phosphorylation and acylation status. The lipid A C4′-phosphatase (
lpxF
)-deficient strain and strains bearing inactivating point mutations in the LpxF active site displayed markedly reduced OMV production relative to WT. In contrast, strains deficient for either the lipid A C1-phosphatase (
lpxE
) or the lipid A deacylase (PGN_1123;
lpxZ
) genes did not display alterations in OMV abundance compared to WT. These data indicate that lipid A C4′-phosphate removal is required for typical OMV formation. In addition, OMVs produced by
ΔlpxF
and
ΔlpxZ
strains, possessing only penta-acylated lipid A, stimulated robust TLR4 activation, whereas OMVs obtained from WT and
ΔlpxE
strains, containing predominantly tetra-acylated lipid A, did not. Hence, lipid A remodeling modulates the capacity of OMVs to engage host TLR4-dependent immunity. Finally, we demonstrate an inverse relationship between OMV abundance and biofilm density, with the
∆lpxF
mutants forming denser biofilms than either WT,
ΔlpxE
, or
ΔlpxZ
strains. Therefore, OMVs may also contribute to pathogenesis by regulating biofilm formation and dispersal.

IMPORTANCE

Porphyromonas gingivalis
is a bacterium strongly associated with periodontitis.
P. gingivalis
exports lipids, proteins, and other biomolecules that contribute to the bacterium’s ability to persist in inflammatory conditions encountered during disease. These biomolecules are exported through several mechanisms, including via outer membrane vesicles (OMVs). Despite their ubiquity, the mechanisms that drive outer membrane vesicle production vary among bacteria and are not fully understood. In this study, we report that C4′ dephosphorylation of lipid A, a major outer membrane molecule, is required for robust outer membrane vesicle production and biological function in
P. gingivalis
. This finding adds to the growing body of evidence that lipid A structure is an important factor in outer membrane vesicle biogenesis in diverse bacterial species.
The histidine kinase NahK regulates denitrification and nitric oxide accumulation through RsmA in
Pseudomonas aeruginosa
Authors: Guercio Danielle , Boon Elizabeth
Published: December 2024

Pseudomonas aeruginosa
have a versatile metabolism; they can adapt to many stressors, including limited oxygen and nutrient availability. This versatility is especially important within a biofilm where multiple microenvironments are present. As a facultative anaerobe,
P. aeruginosa
can survive under anaerobic conditions utilizing denitrification. This process produces nitric oxide (NO) which has been shown to result in cell elongation. However, the molecular mechanism underlying this phenotype is poorly understood. Our laboratory has previously shown that NosP is a NO-sensitive hemoprotein that works with the histidine kinase NahK to regulate biofilm formation in
P. aeruginosa
. In this study, we identify NahK as a novel regulator of denitrification under anaerobic conditions. Under anaerobic conditions, deletion of
nahK
leads to a reduction of growth coupled with reduced transcriptional expression and activity of the denitrification reductases. Furthermore, during stationary phase under anaerobic conditions, Δ
nahK
does not exhibit cell elongation, which is characteristic of
P. aeruginosa
. We determine the loss of cell elongation is due to changes in NO accumulation in Δ
nahK
. We further provide evidence that NahK may regulate denitrification through modification of RsmA levels.

IMPORTANCE

Pseudomonas aeruginosa
is an opportunistic multi-drug resistance pathogen that is associated with hospital-acquired infections.
P. aeruginosa
is highly virulent, in part due to its versatile metabolism and ability to form biofilms. Therefore, better understanding of the molecular mechanisms that regulate these processes should lead to new therapeutics to treat
P. aeruginosa
infections. The histidine kinase NahK has been previously shown to be involved in both nitric oxide (NO) signaling and quorum sensing through RsmA. The data presented here demonstrate that NahK is responsive to NO produced during denitrification to regulate cell morphology. Understanding the role of NahK in metabolism under anaerobic conditions has larger implications in determining its role in a heterogeneous metabolic environment such as a biofilm.
2-Thiouridine formation in
Escherichia coli
: a critical review
Authors: Leimkühler Silke
Published: December 2024

Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability, and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in prokaryotes and eukaryotes. The s
2
group of s
2
U34 stabilizes anticodon structure, confers ribosome-binding ability to tRNA, and improves reading frame maintenance. In particular, specific enzymes catalyze the biosynthesis of sulfur-containing nucleosides of s
2
U34, such as the L-cysteine desulfurase IscS and the tRNA thiouridylase MnmA in
Escherichia coli
. Until recently, the mechanism of sulfur transfer in
E. coli
was considered to involve persulfide chemistry; however, a newly proposed mechanism suggests the involvement of a [4Fe–4S] cluster bound to MnmA. This review provides a critical appraisal of recent evidence for [4Fe–4S]-dependent or [4Fe–4S]-independent tRNA thiolation in 2-thiouridine formation.
Underappreciated layers of antibody-mediated immune synapse architecture and dynamics
Authors: Goldberg Benjamin S. , Ackerman Margaret E.
Published: December 2024

The biologic activities of antibody drugs are dictated by structure-function relationships—emerging from the kind, composition, and degree of interactions with a target antigen and with soluble and cellular antibody receptors of the innate immune system. These activities are canonically understood to be both modular: antigen recognition is driven by the heterodimeric antigen-binding fragment, and innate immune recruitment by the homodimeric constant/crystallizable fragment. The model that treats these domains with a high degree of independence has served the field well but is not without limitations. Here, we consider how new insights, particularly from structural studies, complicate the model of neat biophysical separation between these domains and shape our understanding of antibody effector functions. The emerging model endeavors to explain the phenotypic impact of both antibody intrinsic characteristics and extrinsic features—fitting them within a spatiotemporal paradigm that better accounts for observed antibody activities. In this review, we will use insights from recent models of classical complement complexes and T cell immune synapse formation to explore how structural differences in antibody-mediated immune synapses may relate to their functional diversity.
Efn1 and Efn2 are extracellular 5'-nucleotidases induced during the fission yeast response to phosphate starvation
Authors: Innokentev Aleksei , Sanchez Ana M. , Monetti Mara , Schwer Beate , Shuman Stewart
Published: December 2024

The fission yeast
PHO
regulon genes
pho1
,
pho84
, and
tgp1
—encoding a cell surface-associated acid phosphatase (Pho1), a plasma membrane inorganic phosphate transporter (Pho84), and a plasma membrane glycerophosphocholine transporter (Tgp1)—are strongly upregulated in response to acute phosphate starvation, as are the
SPBPB2B2.06c
and
SPAC1039.02
genes that encode putative 5'-nucleotidase paralogs of the binuclear metallophosphoesterase enzyme superfamily. Via proteomic analysis of the medium harvested from phosphate-replete and phosphate-starved fission yeast, we define a starvation secretome that includes SPBPB2B2.06c (renamed Efn1, for
e
xtracellular
f
ive-prime
n
ucleotidase), SPAC1039.02 (henceforth Efn2), and Pho1 among the most abundant exported proteins elaborated by phosphate-starved cells. We demonstrate and characterize a 5'-nucleotidase activity secreted into the medium of phosphate-starved
efn1
+
efn2
+
cells, which is eliminated by simultaneous deletion of
efn1
and
efn2
. By singly deleting
efn1
and
efn2
, we find that Efn1 contributes the greater share of secreted 5'-nucleotidase activity. Efn1 and Efn2 catalyze the release of inorganic phosphate from all four standard ribonucleoside monophosphates, in order of preference: CMP > UMP > AMP > GMP. Whereas
efn1
+
efn2
+
cells can use extracellular CMP as a source of phosphate during phosphate starvation,
efn1
∆
efn2
∆ cells cannot. The secretion of 5'-nucleotidase enzymes during phosphate limitation is a newly appreciated facet of fission yeast phosphate homeostasis.

IMPORTANCE

Schizosaccharomyces pombe
adapts to phosphate starvation by upregulating the expression of a cell surface acid phosphatase that mobilizes inorganic phosphate from the extracellular milieu, as well as transmembrane transporters that take up inorganic phosphate and glycerophosphocholine. This study identifies two paralogous extracellular 5'-nucleotidase enzymes, Efn1 and Efn2, encoded by genes that are highly transcriptionally induced during acute phosphate starvation, as major proteins secreted into the medium by phosphate-starved fission yeast cells. Secreted Efn1 and Efn2 catalyze the release of inorganic phosphate from all ribonucleoside monophosphates, with a preference for CMP. Secretion of Efn1 and Efn2 enables phosphate-starved fission yeast to thrive by using extracellular CMP as a source of inorganic phosphate. The starvation-induced production of extracellular 5'-nucleotidases adds a new layer of pro-adaptive function during phosphate limitation.
What do women experiencing domestic violence expect from healthcare professionals? A qualitative study in Sri Lanka
Authors: Silva Tharuka , Rathnayake Abey , Evans Maggie , Knipe Duleeka , Rajapakse Thilini , Agampodi Thilini
Published: December 2024

Objectives

For healthcare professionals (HCPs) to provide optimal support for women experiencing domestic violence (DV), it is important to understand what type of support women expect from HCPs. The objective of this study was to explore what kind of support women who experienced DV in Sri Lanka expect from HCPs.

Design

A qualitative descriptive design was used.

Setting

This study was conducted in two gender-based violence centres (Mithuru Piyasa centres) and a toxicology unit, situated in hospitals in the Central Province of Sri Lanka.

Participants

Twenty women who had experienced DV and presented to health services were purposefully recruited using the maximum variation sampling technique, ensuring diversity of age and socio-economic variables. In-depth interviews were conducted with women who consented.

Results

Women who have experienced DV expect varying assistance from HCPs, including changing their abusive partner’s behaviour, resolving their issues or restoring family and marital harmony. Women expect HCPs to intervene in different ways, such as by conversing with both parties or offering support to help the abusive partner overcome alcohol or drug addiction. Women also recommend community-based programmes that concentrate on enhancing marital and family cohesion. Financial and instrumental social support also emerged as key expectations. They anticipate emotional support from HCPs, whom they expect to maintain confidentiality, exhibit empathy, listen attentively and give more importance to DV disclosures. A few women requested referrals to other support services.

Conclusions

A multisectoral approach including a proper referral system and social support between health and other social services is a timely recommendation, given the women’s requests for financial and instrumental social support, which go beyond the health sector. The women’s requests for HCPs to talk with both women and their partners to resolve their issues is a more complex and new finding, which warrants further exploration.
Socioeconomic inequality in cervical cancer screening uptake among women in sub-Saharan Africa: a decomposition analysis of Demographic and Health Survey data
Authors: Asgedom Yordanos Sisay , Kassie Gizachew Ambaw , Habte Aklilu , Ketema Daniel Bekele , Aragaw Fantu Mamo
Published: December 2024

Objective

To examine socioeconomic inequalities in the use of cervical cancer screening among women in sub-Saharan Africa.

Design

Secondary data from the Demographic and Health Survey data in sub-Saharan Africa.

Setting

Sub-Saharan Africa.

Participants

Women aged 15–64 years.

Outcome measures

Socioeconomic inequalities in cervical cancer screening uptake and the pooled prevalence of cervical cancer screening.

Results

The pooled prevalence of cervical cancer screening among women in sub-Saharan African countries was 10.51% (95% CI: 7.54% to 13.48%). Cervical cancer screening uptake showed a significant pro-rich distribution of wealth-related inequalities, with a weighted Erreygers normalised concentration index of 0.084 and an SE of 0.003 (p value <0.0001). This finding suggests that disparities in cervical cancer screening uptake among women are related to wealth. Decomposition analysis revealed that the wealth index, educational status, place of residence and media exposure were the most important factors contributing to this pro-rich socioeconomic inequality in cervical cancer screening.

Conclusion

This study emphasises the importance of addressing modifiable factors such as improving educational opportunities, increasing media exposure accessibility in households and improving the country’s economy to reduce wealth disparities and improve cervical cancer screening uptake among women.
Environmental multiple sclerosis (MS) risk factors, genetic MS risk, and brain development in a general paediatric population
Authors: de Mol Casper Louk , Lamballais Sander , Muetzel Ryan , Duijts Liesbeth , Smolders Joost , White Tonya , Neuteboom Rinze Frederik
Published: December 2024

Background

Neuroaxonal loss occurs in the early stages of multiple sclerosis (MS), but whether it results from early inflammatory brain damage or an ongoing neurodegenerative process remains unclear. We hypothesise that genetic and childhood environmental risk factors for MS may already have an impact on neurodevelopment before the typical age of onset for MS in the general population.

Methods

We examined associations and interactions of genetic and environmental risk factors for MS with brain MRI outcomes, including volumetric (n=5350) and diffusion data (n=5649), at ages 9 and 13 years in a large, population-based childhood cohort without MS diagnoses. Polygenic risk scores (PRSs) were used to assess genetic burden, with rs10191329 as a marker of MS severity. Environmental factors at age 5 included Epstein-Barr virus (EBV) serology, vitamin D status, body mass index, duration of outdoor activities, and household parental smoking.

Results

Genetic data were available for 2817 and 2970 participants with volumetric and diffusion data, respectively. The MS-PRS was positively associated with EBV viral capsid antigen titres among EBV-positive children (β=0.15, p=2.98×10−6). A negative association was observed between the MS-PRS and subcortical grey matter volume (β=−0.03, p=0.014). Interaction between the MS-PRS and household parental smoking was negatively linked to total brain (β=−0.21, p=0.025) and thalamic volumes (β=−0.22, p=0.003), where a higher MS-PRS and household smoking were associated with lower volumes. No associations were observed for rs10191329 with brain outcomes.

Conclusions

Genetic and environmental risk factors for MS interact to influence brain volumes in childhood, suggesting a potential window for preventing MS in genetically susceptible individuals by reducing exposure to household smoking.
An improved method to predict man-made slope failure using machine learning tools
Authors: Ng C.W.W. , Liu Y. , Kwan J.S.H. , Cheung R.W.M. , Zhang Q.
Published: December 2024

Landslide hazards associated with man-made slopes are increasing due to ageing and extreme weather conditions under a changing climate. To effectively mitigate landslide risks, the implementation of regional landslide early warning systems is desirable, albeit challenging, if not impossible, due to the scarcity of reliable landslide data and suitable predictive tools. In this paper, a thorough analysis has been conducted on reasonably reliable and substantial amounts of historical rainfall data, slope features, and landslide inventory of man-made slope failures in Hong Kong. Four different machine learning methods, namely logistic regression (LR), decision tree (DT), random forest (RF), and extreme gradient boosting (XGBoost), have been employed. The predicted number of landslides from the machine learning methods is compared with the predictions made by the current Landslip Warning System in Hong Kong. The effects of rainfall parameters and slope features on model performance are also investigated. The analysed results show that dynamic rainfall conditions are identified as the most influential factors for predicting man-made slope landslide. A combination of 1 and 12 h maximal rolling rainfall (MRR) demonstrates superior performance compared to relying solely on the 24 h MRR. Therefore, this combination is recommended for predicting man-made slope failures in Hong Kong.
Influence of lake volume on food web metrics in a freshwater fish assemblage across a small range of ecosystem sizes
Authors: Andersen Alyssa M. , Blanchfield Paul J. , Heuvel Cecilia E. , McCann Kevin S. , McMeans Bailey C. , Ridgway Mark S. , Fisk Aaron T.
Published: December 2024

Lake size effects on food webs have been most clearly demonstrated for predator fish across large gradients in ecosystem size and species richness. We isolated the influence of lake size to assess food web metrics in six fish species with diverse ecologies across five lakes with similar lake characteristics in Algonquin Provincial Park (Ontario, Canada) using δ13C, δ15N, and δ34S. Lake volume was a significant factor influencing food web metrics across most fish species. However, relationships between lake volume and food web metrics (trophic position, littoral carbon use, δ34S, and niche area) were weak. For most species, trophic position decreased with lake volume, opposite from previous studies that included a wider range of lake sizes and biodiversity. Littoral carbon use and δ34S showed negative and positive relationships with lake volume, respectively, suggesting a shift to pelagic offshore energy in larger lakes. Albeit weak, our results highlight that multiple co-occurring fish species within a community can have similar responses in littoral carbon use, trophic position, δ34S, and niche area across a small range of lake sizes.