bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequencing analysis of the pncA, rpsA and panD genes responsible for pyrazinamide resistance of Mycobacterium tuberculosis from Indonesian isolates
Authors: Rukmana Andriansjah , Nurfadillah Mifa , Gozali Cynthia , Kiranasari Ariyani 
Published: October 2024

AbstractBackgroundDeveloping the most suitable treatment against tuberculosis based on resistance profiles is imperative to effectively cure tuberculosis patients. Whole‐genome sequencing is a molecular method that allows for the rapid and cost‐effective detection of mutations in multiple genes associated with anti‐tuberculosis drug resistance. This sequencing approach addresses the limitations of culture‐based methods, which may not apply to certain anti‐TB drugs, such as pyrazinamide, because of their specific culture medium requirements, potentially leading to biased resistance culture results.MethodsThirty‐four M. tuberculosis isolates were subcultured on a Lowenstein–Jensen medium. The genome of these bacteria was subsequently isolated using cetyltrimethylammonium bromide. Genome sequencing was performed with Novaseq Illumina 6000 (Illumina), and the data were analysed using the GenTB and Mykrobe applications. We also conducted a de novo analysis to compare the two methods and performed mutation analysis of other genes encoding pyrazinamide resistance, namely rpsA and panD.ResultsThe results revealed mutations in the pncA gene, which were identified based on the databases accessed through GenTB and Mykrobe. Two discrepancies between the drug susceptibility testing and sequencing results may suggest potential instability in the drug susceptibility testing culture, specifically concerning PZA. Meanwhile, the results of the de novo analysis showed the same result of pncA mutation to the GenTB or Mykrobe; meanwhile, there were silent mutations in rpsA in several isolates and a point mutation; no mutations were found in the panD gene. However, the mutations in the genes encoding pyrazinamide require further and in‐depth study to understand their relationship to the phenotypic profile.ConclusionsCompared to the conventional culture method, the whole‐genome sequencing method has advantages in determining anti‐tuberculosis resistance profiles, especially in reduced time and bias.
Allelic variants confer Arabidopsis adaptation to small regional environmental differences
Authors: Wijfjes Raúl Y. , Boesten René , Becker Frank F. M. , Theeuwen Tom P. J. M. , Snoek Basten L. , Mastoraki Maria , Verheijen Jelle J. , Güvencli Nuri , Denkers Lissy‐Anne M. , Koornneef Maarten , van Eeuwijk Fred A. , Smit Sandra , de Ridder Dick , Aarts Mark G. M. 
Published: October 2024

SUMMARYNatural populations of Arabidopsis thaliana provide powerful systems to study the adaptation of wild plant species. Previous research has predominantly focused on global populations or accessions collected from regions with diverse climates. However, little is known about the genetics underlying adaptation in regions with mild environmental clines. We have examined a diversity panel consisting of 192 A. thaliana accessions collected from the Netherlands, a region with limited climatic variation. Despite the relatively uniform climate, we identified evidence of local adaptation within this population. Notably, semidwarf accessions, due to mutation of the GIBBERELLIC ACID REQUIRING 5 (GA5) gene, occur at a relatively high frequency near the coast and these displayed enhanced tolerance to high wind velocities. Additionally, we evaluated the performance of the population under iron deficiency conditions and found that allelic variation in the FE SUPEROXIDE DISMUTASE 3 (FSD3) gene affects tolerance to low iron levels. Moreover, we explored patterns of local adaptation to environmental clines in temperature and precipitation, observing that allelic variation at LA RELATED PROTEIN 1C (LARP1c) likely affects drought tolerance. Not only is the genetic variation observed in a diversity panel of A. thaliana collected in a region with mild environmental clines comparable to that in collections sampled over larger geographic ranges but it is also sufficiently rich to elucidate the genetic and environmental factors underlying natural plant adaptation.
A gene cluster for polyamine transport and modification improves salt tolerance in tomato
Authors: Yang Jie , Zhang Zhonghui , Li Xianggui , Guo Langchen , Li Chun , Lai Jun , Han Yige , Ye Weizhen , Miao Yuanyuan , Deng Meng , Cao Peng , Zhang Yueran , Ding Xiangyu , Zhang Jianing , Yang Jun , Wang Shouchuang 
Published: October 2024

SUMMARYPolyamines act as protective compounds directly protecting plants from stress‐related damage, while also acting as signaling molecules to participate in serious abiotic stresses. However, the molecular mechanisms underlying these effects are poorly understood. Here, we utilized metabolome genome‐wide association study to investigate the polyamine content of wild and cultivated tomato accessions, and we discovered a new gene cluster that drove polyamine content during tomato domestication. The gene cluster contains two polyphenol oxidases (SlPPOE and SlPPOF), two BAHD acyltransferases (SlAT4 and SlAT5), a coumaroyl‐CoA ligase (Sl4CL6), and a polyamine uptake transporter (SlPUT3). SlPUT3 mediates polyamine uptake and transport, while the five other genes are involved in polyamine modification. Further salt tolerance assays demonstrated that SlPPOE, SlPPOF, and SlAT5 overexpression lines showed greater phenolamide accumulation and salt tolerance as compared with wild‐type (WT). Meanwhile, the exogenous application of Spm to SlPUT3‐OE lines displayed salt tolerance compared with WT, while having the opposite effect in slput3 lines, confirms that the polyamine and phenolamide can play a protective role by alleviating cell damage. SlPUT3 interacted with SlPIP2;4, a H2O2 transport protein, to maintain H2O2 homeostasis. Polyamine‐derived H2O2 linked Spm to stress responses, suggesting that Spm signaling activates stress response pathways. Collectively, our finding reveals that the H2O2‐polyamine‐phenolamide module coordinately enhanced tomato salt stress tolerance and provide a foundation for tomato stress‐resistance breeding.
Tubings, chord diagrams, and Dyson–Schwinger equations
Authors: Balduf Paul‐Hermann , Cantwell Amelia , Ebrahimi‐Fard Kurusch , Nabergall Lukas , Olson‐Harris Nicholas , Yeats Karen 
Published: October 2024

AbstractWe give series solutions to single insertion place propagator‐type systems of Dyson–Schwinger equations using binary tubings of rooted trees. These solutions are combinatorially transparent in the sense that each tubing has a straightforward contribution. The Dyson–Schwinger equations solved here are more general than those previously solved by chord diagram techniques, including systems and noninteger values of the insertion parameter . We remark on interesting combinatorial connections and properties.
Children’s involvement in the development and evaluation of parent-focused mental health interventions: a scoping review protocol
Authors: Nowland Rebecca , Christian Danielle L. , Aspinall Georgia , Berzins Kathryn , Khalid Sundus , Ahuja Shalini , Gallagher Lucy , Gee Brioney , Mickleburgh Ella , Fernandes Blossom , Kelsall Afra , Randell Becca , Michelson Daniel 
Published: October 2024

Objective:
This review will i) describe methods used to involve children in the development and/or evaluation of parent-focused interventions to prevent or treat child mental health problems; ii) summarize the perspectives of children or adults about these methods; iii) highlight any reported enablers and barriers; and iv) identify guidance and make recommendations for further research.

Introduction:
Parent-focused interventions (where children are not primarily involved or are excluded) have been implemented to address various child mental health outcomes. However, it is unclear to what extent, and to what end, children have been involved in developing and evaluating such interventions. Engaging children in formative research activities, with or without their parents, has the potential to improve quality and implementation of the interventions.

Inclusion criteria:
Eligible studies will involve children (5–12 years) in the development and/or evaluation of parent-focused interventions aimed at preventing or treating common child mental health problems (eg, anxiety, depression, ADHD, disruptive behavior) delivered in any setting (eg, school, community, home, health facility). Eligible interventions may include one or more psychosocial practice elements targeting behavioral, cognitive, emotional, interpersonal, social, and/or environmental factors implicated in the onset and maintenance of child mental health problems.

Methods:
Comprehensive searches will be conducted in 5 electronic databases (PsycINFO, MEDLINE, CINAHL, Embase, and Scopus). Gray literature will be sourced using Google as well as through searches of key organization websites and via notifications on social media. Only English-language primary studies will be considered. Findings across a range of methodologies will be charted and combined into a narrative synthesis.

Review registration:
Open Science Framework https://osf.io/x9376/
Predicting Leidenfrost Temperature and Effects of Impact Conditions on Droplet Size Distribution in Film-Boiling Regime
Authors: Patwary Mohammad F. F. , Isik Doruk , Kong Song-Charng , Mayhew Eric , Kim Kenneth S. , Kweon Chol-Bum M. 
Published: October 2024

Abstract
The interaction of a droplet with a solid wall is relevant in various engineering applications. The properties of the resulting secondary droplets are determined by the wall temperature, ambient pressure, impact momentum, and impact angle. This paper presents a comprehensive characterization of drop–wall interactions and the subsequent atomization as a function of the combined effects of such parameters. A drop–wall interaction model is derived for F-24 liquid fuel droplets using smoothed particle hydrodynamics (SPH). F-24 is a derivative of Jet-A aviation fuel with military additives, and it is the focus of this study due to its common use in military applications. The model can predict different impact outcome regimes (deposition, rebound, contact-splash, and film-splash) for different ambient pressures, wall temperatures, and impact parameters. The model also addresses the effect of ambient pressure on the Leidenfrost behavior. Size distributions of secondary droplets are compared for vertical and nonvertical impacts of F-24 droplets on superheated surfaces in the film-boiling regime. The nondimensional Sauter mean diameter (SMD) of the secondary droplets varies based on the position in the impact plane for all the nonvertical impacts but remains almost unchanged for vertical impacts. The zone of leading direction for nonvertical impact consists of larger secondary droplets, and the size decreases toward the zone of trailing direction. An empirical relation is proposed to represent this trend. This research sheds light on successive droplet impacts by studying the effects of impact frequency on SMD evolution. The results are compared to single droplet impact cases for different fuels and Weber numbers. The size of secondary droplets for successive impacts is observed to be nearly indistinguishable from that of single droplet vertical impacts.
The Bressesque Surface: Distribution of Screw Pitch
Authors: Dooner David , Garcia-Garcia Ricardo , Rico José M. 
Published: October 2024

Abstract
Presented is an overview of the T-N interpretation of the famous planar Euler–Savary formula. The T-N spatial analog interpretation consists of two components: the established axial component along with a new transverse component. The axial component entails the spatial Euler–Savary relation involving the Disteli axis and motion parallel to the instantaneous screw axis (ISA). The transverse component emulates the classical planar Euler–Savary relation involving motion perpendicular to the ISA. Within the T-N interpretation is an inflection surface together with a family of Bressesque surfaces. Traditionally, a Bresse circle is a planar motion concept defined by points with zero tangential acceleration. Here, the Bressesque surfaces do not consider accelerations akin to the planar scenario. Instead, the Bressesque surfaces are defined as a linear combination of two axes of the inflection surface. These two axes are used to establish a skew axis gear set where the axodes are tangent along a generator of the Bressesque surface. This tangency is the ISA for the gear set. What is new is the screw pitch for each generator of the hyperboloidal Bressesque surface. Two graphs are shown: the first graph is the variation in screw pitch in terms of the ray angle and the second graph is the variation in speed ratio of the skew axes gear set in terms of the ray angle.
A Comparative Analysis Among Dynamics Modeling Approaches for Space Manipulator Systems
Authors: Tantravahi Santosh 
Published: October 2024

Abstract
This paper presents a comparative analysis on the space manipulator systems dynamics modeling approaches, namely, the standard approach (SA) and the dual quaternion based dynamics modeling approach. A detailed analysis supported by the results from numerical simulations, comparing the two approaches in terms of operational count and execution time, has been presented to determine which approach is computationally and temporally efficient.
Epsilon-Greedy Thompson Sampling to Bayesian Optimization
Authors: Do Bach , Adebiyi Taiwo , Zhang Ruda 
Published: October 2024

Abstract
Bayesian optimization (BO) has become a powerful tool for solving simulation-based engineering optimization problems thanks to its ability to integrate physical and mathematical understandings, consider uncertainty, and address the exploitation–exploration dilemma. Thompson sampling (TS) is a preferred solution for BO to handle the exploitation–exploration tradeoff. While it prioritizes exploration by generating and minimizing random sample paths from probabilistic models—a fundamental ingredient of BO–TS weakly manages exploitation by gathering information about the true objective function after it obtains new observations. In this work, we improve the exploitation of TS by incorporating the ε-greedy policy, a well-established selection strategy in reinforcement learning. We first delineate two extremes of TS, namely the generic TS and the sample-average TS. The former promotes exploration, while the latter favors exploitation. We then adopt the ε-greedy policy to randomly switch between these two extremes. Small and large values of ε govern exploitation and exploration, respectively. By minimizing two benchmark functions and solving an inverse problem of a steel cantilever beam, we empirically show that ε-greedy TS equipped with an appropriate ε is more robust than its two extremes, matching or outperforming the better of the generic TS and the sample-average TS.
Machine Learning in Wear Prediction
Authors: Shah Raj , Pai Nikhil , Thomas Gavin , Jha Swarn , Mittal Vikram , Shirvni Khosro , Liang Hong 
Published: October 2024

Abstract
As modern devices and systems continue to advance, device wear remains a key factor in limiting their performance and lifetime, as well as environmental and health effects. Traditional approaches often rely on wear prediction based on physical models, but due to device complexity and uncertainty, these methods often fail to provide accurate predictions and accurate wear identification. Machine learning, as a data-driven approach based on its ability to discover patterns and correlations in complex systems, has enormous potential for monitoring and predicting device wear. Here, we review recent advances in applying machine learning for predicting the wear of mechanical components. Machine learning for wear prediction shows significant potential in optimizing material selection, manufacturing processes, and equipment maintenance, ultimately enhancing productivity and resource efficiency. Successful implementation relies on careful data collection, standardized evaluation methods, and the selection of effective algorithms, with artificial neural networks (ANNs) frequently demonstrating notable success in predictive accuracy.
Women Movement Behaviors During Pregnancy and 2 Years After Childbirth: Physical Activity, Sedentary Time, Sleep, and Rhythm Changes in a Brazilian Birth Cohort
Authors: Wendt Andrea , Costa Martins Rafaela , Kramer Fiala Machado Adriana , Ricardo Luiza I.C. , Ginar da Silva Shana , Gonçalves Cordeiro da Silva Bruna , Mielke Gregore I. , Rodrigues Domingues Marlos , Hallal Pedro C. , Crochemore-Silva Inácio 
Published: October 2024

Objective: To describe physical activity (PA), sleep, and rhythm patterns during 24-hr cycles from the second trimester of pregnancy up to 2 years after childbirth. Methods: This longitudinal study used data from mothers of the 2015 Pelotas Birth Cohort (Brazil). Women were invited to wear the accelerometer during 7 days on the nondominant wrist during the second trimester of pregnancy and 2 years after childbirth. Data collected included PA, sleep, and rhythm variables. We compared the means/medians of variables during the pregnancy and 2 years after the childbirth. We also describe the shape of acceleration across the day in the two evaluated periods and stratified this curve according to covariables. Results: This study includes data from 1,293 women with valid accelerometer data for both periods. The nonbouted moderate-to-vigorous PA average was 94 min during pregnancy and increased to 122 min 2 years after childbirth (p < .001). Sleep decreased by 11 min (388–377 min; p < .001) in the evaluated period. The pattern of acceleration across the day did not change in the evaluated period with two marked spikes of activity at 10 a.m. and 6 p.m. The amount of activity, however, increased. Conclusions: These findings may be helpful to better understand changes in PA and sleep during this specific period of life and assist in planning recommendations.
Low penicillin susceptibility in
Streptococcus mitis/oralis
from bloodstream infections in pediatric populations
Authors: Zhou Jian-Ming , Wu Cai-Yu , Li Jian-Ping , Ye Yi-Hua , Fang Chao , Zhou Ming-Ming 
Published: October 2024

ABSTRACT

Streptococcus mitis/oralis
can cause invasive diseases, including bloodstream infections. However, existing research primarily focuses on specific populations, and limited studies have been conducted on the prevalence of bloodstream infection caused by
S. mitis/oralis
across the entire pediatric population. Therefore, clinical data of
S. mitis/oralis
isolated from blood samples at Children’s Hospital, Zhejiang University School of Medicine, during the period 2019–2023 were collected retrospectively to provide a comprehensive understanding of the clinical characteristics and drug resistance patterns associated with bloodstream infections caused by
S. mitis/oralis
in pediatric populations. There were 57 (43.5%) instances of contamination across various departments, indicating a relatively dispersed pattern. Bloodstream infections caused by
S. mitis/oralis
are notably prevalent among pediatric patients with hematological diseases and tumors. The susceptibility rates of the 74
S. mitis/oralis
isolates to different antibiotics were as follows: penicillin (23%), ceftriaxone (74.3%), levofloxacin (86.5%), chloramphenicol (89.2%), erythromycin (27%), clindamycin (67.6%), linezolid (100%), and vancomycin (100%). Notably, 21.6% of the isolates exhibited multi-drug resistance (MDR). The predominant mode of MDR in
S. mitis/oralis
infections was identified as resistance to β-lactams, erythromycin, and clindamycin. The observed low susceptibility rate to penicillin, coupled with the emergence of MDR strains, underscores the imperative for continuous monitoring of the evolving antimicrobial resistance in
S. mitis/oralis
.

IMPORTANCE

Existing research primarily focuses on specific populations, such as those with hematopathy or tumors, who experience
Streptococcus mitis/oralis
bacteremia. Limited studies have been conducted on the prevalence of bloodstream infections caused by
S. mitis/oralis
across the entire pediatric population. It was found that the contamination rate of
S. mitis/oralis
isolated from blood cultures was notably high in our study. Therefore, this study evaluated the clinical characteristics and drug resistance patterns of bloodstream infections caused by
S. mitis/oralis
across the entire pediatric populations, explicitly excluding cases of blood culture contamination. The observed low susceptibility rate to penicillin, coupled with the emergence of multi-drug-resistant strains, underscores the imperative for continuous monitoring of the evolving antimicrobial resistance in
S. mitis/oralis
.
Strength of viscous subduction interfaces: A global compilation
Authors: Abila Ana Lorena , Behr Whitney M. , Ruh Jonas 
Published: October 2024

Abstract
The long- and short-term dynamics of subduction zones are strongly affected by interface rheology. Current estimates of interface viscosity are based on endmember flow laws or simple mixing models, but the variation of possible materials on the subduction interface theoretically permits viscosity variations of up to five orders of magnitude. To better constrain the range of strength along deep/viscous subduction interfaces, we compiled a global database of rock types and block-and-matrix distributions in exhumed deep subduction interface mélange shear zones. We applied numerical shear experiments to each shear zone to quantify their bulk shear strengths/viscosities. Our results show that natural subduction shear zones have viscosities ranging from ~1018 to 1020 Pa·s and shear strengths of ~1–100 MPa. The variation among them is dominantly controlled by temperature, but even for shear zones deformed at the same temperature, variations of up to a factor of 50 are observed. These variations are attributed to differences in matrix composition, shear zone width, and block distributions. Our results are consistent with paleopiezometric and force-balance–derived estimates of interface strength, and they confirm the importance of variation in geological inputs and their spatial distribution along the interface for subduction dynamics.