bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of avaC from Human Gut Microbial Isolates that Converts 5AVA to 2-Piperidone
Authors: Zhou Qiudi , Feng Lihui 
Published: June 2024

Abstract2-piperidone is a crucial industrial raw material of high-value nylon-5 and nylon-6,5. Currently, a major bottleneck in the biosynthesis of 2-piperidone is the identification of highly efficient 2-piperidone synthases. In this study, we aimed to identify specific strains among 51 human gut bacterial strains capable of producing 2-piperidone and to elucidate its synthetic mechanism. Our findings revealed that four gut bacterial strains, namely Collinsella aerofaciens LFYP39, Collinsella intestinalis LFYP54, Clostridium bolteae LFYP116, and Clostridium hathewayi LFYP18, could produce 2-piperidone from 5-aminovaleric acid (5AVA). Additionally, we observed that 2-piperidone could be synthesized from proline through cross-feeding between Clostridium difficile LFYP43 and one of the four 2-piperidone producing strains, respectively. To identify the enzyme responsible for catalyzing the conversion of 5AVA to 2-piperidone, we utilized a gain-of-function library and identified avaC (5-aminovaleric acid cyclase) in C. intestinalis LFYP54. Moreover, homologous genes of avaC were validated in the other three bacterial strains. Notably, avaC were found to be widely distributed among environmental bacteria. Overall, our research delineated the gut bacterial strains and genes involved in 2-piperidone production, holding promise for enhancing the efficiency of industrial biosynthesis of this compound.
Implication of homoplasy in hypervariable region (HVR) of mitochondrial DNA in a population of marbled flounder Pseudopleuronectes yokohamae: consideration for conducting population genetic analyses using the HVR
Authors: Yamamoto Yuki , Takanashi Airi , Yokosawa Yuji , Ikeda Minoru 
Published: June 2024

AbstractThe hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy.
Suppression of HIV-TAT and cocaine-induced neurotoxicity and inflammation by cell penetrable itaconate esters
Authors: Cui B. Celia , Aksenova Marina , Sikirzhytskaya Aliaksandra , Odhiambo Diana , Korunova Elizaveta , Sikirzhytski Vitali , Ji Hao , Altomare Diego , Broude Eugenia , Frizzell Norma , Booze Rosemarie , Wyatt Michael D. , Shtutman Michael 
Published: June 2024

AbstractHIV-associated neurological disorder (HAND) is a serious complication of HIV infection marked by neurotoxicity induced by viral proteins like Tat. Substance abuse exacerbates neurocognitive impairment in people living with HIV. There is an urgent need for therapeutic strategies to combat HAND comorbid with Cocaine Use Disorder (CUD). Our analysis of HIV and cocaine-induced transcriptomes in primary cortical cultures revealed significant overexpression of the macrophage-specific gene aconitate decarboxylase 1 (Acod1). The ACOD1 protein converts the tricarboxylic acid intermediate cis-aconitate into itaconate during the activation of inflammation. Itaconate then facilitates cytokine production and activates anti-inflammatory transcription factors, shielding macrophages from infection-induced cell death. However, the immunometabolic function of itaconate was unexplored in HIV and cocaine-exposed microglia. We assessed the potential of 4-octyl-itaconate (4OI), a cell-penetrable ester form of itaconate known for its anti-inflammatory properties. When primary cortical cultures exposed to Tat and cocaine were treated with 4OI, microglial cell number increased and the morphological altercations induced by Tat and cocaine were reversed. Microglial cells also appeared more ramified, resembling the quiescent microglia. 4OI treatment inhibited secretion of the proinflammatory cytokines IL-1α, IL-1β, IL-6, and MIP1-α induced by Tat and cocaine. Transcriptome profiling determined that Nrf2 target genes were significantly activated in Tat and 4OI treated cultures relative to Tat alone. Further, genes associated with cytoskeleton dynamics in inflammatory microglia were downregulated by 4OI treatment. Together, the results strongly suggest 4-octyl-itaconate holds promise as a potential candidate for therapeutic development to treat HAND coupled with CUD comorbidities.
Graphical Abstract
Model of 4OI-mediated neuroprotection against Tat-Cocaine toxicity. Tat and Tat-Cocaine treatment induce neuronal damage, which is mitigated by 4OI through microglia cells. This cartoon shows the reduction of harmful effects such as pro-inflammatory cytokine release, upregulation of P2R, PDE, and Acod1 by the presence of 4OI. This ester modified itaconate triggers anti-inflammatory responses and activates antioxidant pathways
Accurate and affordable detection of rifampicin and isoniazid resistance in Tuberculosis sputum specimens by multiplex PCR-multiple probes melting analysis
Authors: Xie Long , Zhu Xiao-Ya , Xu Li , Xu Xiao-Xie , Ruan Ze-Fan , Huang Ming-Xiang , Chen Li , Jiang Xi-Wen 
Published: June 2024

Abstract
Background
Escalating cases of multidrug-resistant tuberculosis (MDR-TB) pose a major challenge to global TB control efforts, necessitating innovative diagnostics to empower decentralized detection of gene mutations associated with resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis (M. tuberculosis) in resource-constrained settings.

Methods
Combining multiplex fluorescent PCR and Multiple Probes Melting Analysis, we identified mutations in the rpoB, katG, ahpC and inhA genes from sputum specimens. We first constructed a reference plasmid library comprising 40 prevalent mutations in the target genes’ resistance determining regions and promoters, serving as positive controls. Our assay utilizes a four-tube asymmetric PCR method with specifically designed molecular beacon probes, enabling simultaneous detection of all 40 mutations. We evaluated the assay’s effectiveness using DNA isolated from 50 clinically confirmed M. tuberculosis sputum specimens, comparing our results with those obtained from Sanger sequencing and retrospective validation involving bacteriological culture and phenotypic drug susceptibility testing (pDST). We also included the commercial Xpert MTB/RIF assay for accuracy comparison.

Results
Our data demonstrated remarkable sensitivity in detecting resistance to RIF and INH, achieving values of 93.33% and 95.24%, respectively, with a specificity of 100%. The concordance between our assay and pDST was 98.00%. Furthermore, the accuracy of our assay was comparable to both Sanger sequencing and the Xpert assay. Importantly, our assay boasts a 4.2-h turnaround time and costs only $10 per test, making it an optimal choice for peripheral healthcare settings.

Conclusion
These findings highlight our assay’s potential as a promising tool for rapidly, accurately, and affordably detecting MDR-TB.
Early Exposure of Medical Students to a Formal Research Program Promotes Successful Scholarship in a Multi-Campus Medical School
Authors: Conover Gloria M. , Monk Mikayla B. , Nigli Selina , Awalt Avery 
Published: June 2024

Abstract
Objectives
Many physicians today struggle to learn the complexities of the biological basis for evidence-based medicine. To bridge this gap, the Medical Scholar Research Pathway Program (MSRPP) founded in 2019 prepares medical students for analytical reasoning and critical thinking while engaging in faculty-mentored research projects in a community-based public medical school.

Methods
MSRPP is an application-based extracurricular research program, designed for novice and experienced medical students. Three distinct pathways offer ample opportunities for pre-clinical and clinical students to participate in research on a flexible schedule. The program director guides students in one-on-one coaching meetings to set achievable goals with their faculty mentor, and plan their research deliverables, considering their interests and residency plans.

Results
We report the implementation of a multi-year and multi-campus research training program for medical students across five campuses. Our results show that five class cohorts (2021–2025) of MSRPP students were twice as likely to seek formal research support than students not in the program. MSRPP students continuously growth their self-confidence to disseminate their research by practicing oral communication in monthly Launch talk research reports and bi-annual research conferences. Moreover, students report they learn technical communication skills and feel inspired to participate in research by interacting with invited faculty seminars. MSRPP students have a significantly higher scholarship output as compared to non-MSRPP students. Early indicators show that students that participate in formal research programs have a measurable difference for matching into competitive residencies.

Conclusions
MSRPP students report that they have gained research competencies and technical skills to establish a baseline to promote their future research engagement. This study provides other peer medical schools with strategies to create the infrastructure to support and promote medical student research.
Feasibility of Biochar from Seaweed for Ferroalloy Production
Authors: Senanu Samuel , Sandquist Judit , Skjermo Jorunn , Rørvik Stein , Windfeldt Magnus 
Published: June 2024

AbstractBiochar from seaweed, specifically sugar kelp, cultivated on the Norwegian coastline has been investigated as a possible biocarbon source for the metal industry to reduce the dependency on terrestrial biomass. Pre-processing of the biomass prior to pyrolysis is needed to reduce the water and ash content and was performed by water and acid washing followed by drying. The three types of biochar were obtained after pyrolysis at a temperature of 550 °C. Characterization of the three batches of biochars showed that pre-processing of the seaweed as was done during the water and acid washing, plays an important role on the removal of ash content. Due to the enormous amount of woody biomass needed for example in the ferroalloy industry to replace fossil coal, replacing only parts of the woody biomass with kelp biochar could have a significant impact. Water washing combined with acid washing had the best results considering the ash and fixed carbon contents. Microstructural analysis of the seaweed biochars showed a very porous material with the crystal structure resembling that of charcoal, albeit a lower degree of crystallinity.
Graphical Abstract
Identifying missing data handling methods with text mining
Authors: Boros Krisztián , Kmetty Zoltán 
Published: June 2024

AbstractMissing data is an inevitable aspect of every empirical research. Researchers developed several techniques to handle missing data to avoid information loss and biases. Over the past 50 years, these methods have become more and more efficient and also more complex. Building on previous review studies, this paper aims to analyze what kind of missing data handling methods are used among various scientific disciplines. For the analysis, we used nearly 50.000 scientific articles published between 1999 and 2016. JSTOR provided the data in text format. We utilized a text-mining approach to extract the necessary information from our corpus. Our results show that the usage of advanced missing data handling methods, such as Multiple Imputation or Full Information Maximum Likelihood estimation, is steadily growing in the examination period. Additionally, simpler methods, like listwise and pairwise deletion, are still in widespread use.
Factors Associated with STEM Career Expectations of Greek 15-Year-Old Students
Authors: Pagkratidou Marianna , Michaelides Michalis P. , Pitsia Vasiliki , Karakolidis Anastasios 
Published: June 2024

Abstract
Science, technology engineering, and mathematics (STEM) professions offer competitive earnings, tend to be compatible with technological advances, and are predicted to remain in high demand in the future. Many countries, including Greece, have prioritised STEM education on their educational agendas, aiming to prepare students for careers in these fields. In this study, we investigated factors that may predict Greek students’ STEM career expectations through analysing data from the 2015 cycle of the Programme for International Student Assessment (PISA). In doing so, we categorised the responses of 4910 15-year-old students to the question “What kind of job do you expect to have when you are about 30 years old?” into STEM and non-STEM professions, following a wide approach that included health and medical professions in the STEM category and a narrow approach that excluded these professions from the STEM category. Binary logistic regression results showed that student enjoyment of science, instrumental motivation, interest towards broad science topics, and their science performance were associated with their career expectations across both approaches; family economic, social, and cultural status was associated with students’ career expectations within the wide approach only, while gender and achievement motivation were associated with students’ career expectations within the narrow approach only. The differences in the factors predicting students’ career expectations between the two approaches indicate that transparency in the definitions and operationalisations of STEM is needed within the relevant research.
Stress and Strain Characteristics in Flexible Pavement Using Three-Dimensional Nonlinear Finite Element Analysis
Authors: Nega Ainalem , Gedafa Daba , Nikraz Hamid 
Published: June 2024

AbstractA new numerical simulation was developed to obtain various structural parameters by employing a nonlinear finite element method using ABAQUS: stress, strain, and the displacement response of five layers on the flexible pavement. The primary purpose of this study was to develop a new simulation that can accurately and effectively characterize stress and strain problems in flexible pavement. New constitutive model equations were developed based on Hooke’s law the three-dimensional model for stress and strain. 40 kN wheel load was used to represent a set of dual tires, assuming a uniformly distributed contact area between the tire-pavement surfaced using linear viscoelastic and nonlinear viscoelastic materials. Four tire-inflation pressures were used 380, 490, 630, and 700 kPa. Results indicated that each flexible pavement layer created with a nonlinear viscoelastic material exhibited a 40% vertical plastic strain reduction compared to linear viscoelastic materials after 7000 s and repeated for 30,000 cyclic loadings. The implication of this newly developed constitutive model was verified against published experimental data. Analyses were completed to simplify the results model results considering the effects of stress and strain on flexible pavement layers. The newly developed constitutive model for solving stress and strain characterization problems can predict the effects on flexible pavement layers and various types of observed flexible pavement failure.
Simulation of large plausible tsunami scenarios associated with the 2019 Durres (Albania) earthquake source and adjacent seismogenic zones
Authors: Xhafaj Edlira , Hassan Hany M. , Scaini Chiara , Peresan Antonella 
Published: June 2024

AbstractWe present an analysis of the hazards of potential earthquake-generated tsunamis along the Albanian–Adriatic coast. The study adopts a case study approach to model plausible tsunamigenic events associated with the 2019 Mw 6.4 Durres (Albania) earthquake source zone. The approach combines current findings on regional tectonics and scenario-based calculations of potential tsunami impacts. The study’s goal is to analyse the propagation of tsunami waves generated by identified seismogenic sources (namely ALCS002 [Lushnje] and ALCS018 [Shijak]) and determine the tsunami risk assessment for Durres City on the Albanian–Adriatic coast. The sources can generate earthquakes with maximum moment magnitudes of Mw 7.5 and Mw 6.8, which are likely to trigger tsunamis that could cause significant impacts in the region. The modelling is performed deterministically with the NAMI DANCE numerical code, including scenarios associated with the largest plausible earthquake. The model integrates bathymetry and topography datasets of large and medium resolutions. Each tsunami scenario simulation is based on the solution of the non-linear shallow water equations used to generate maximum positive wave amplitudes (water elevation), travel time, and tsunami inundation maps. In Durres City, modelling indicates that medium-sized waves could reach up to 2.5 m inland, posing a significant danger to the city’s low-lying areas. The most substantial tsunami waves are expected to impact the area within the first 10 to 20 min. Combining inundation maps and information on exposed assets allows for identifying areas where damages can be expected. In terms of human impact, a preliminary analysis shows that the study area is prone to tsunami threat, with more than 138,000 inhabitants living in vulnerable urban areas of Durres City by 2036. The model’s capacity to capture details related to the presence of buildings is limited due to constraints posed by the resolution of bathymetry and topography datasets available during this study. If refined with high-resolution bathymetry and topography datasets, our results can be considered a backbone for exposure and resilience assessment features to be integrated into preparedness or new urban development plans.
Prison Violence in Latin America: Criminal Governance and an Absent State
Authors: Fondevila Gustavo , Vilalta-Perdomo Carlos 
Published: June 2024

AbstractUsing a survey applied to incarcerated populations in Latin American countries, this study aims to examine the factors that determine the existence of violence in prisons and explain why some penitentiaries are more violent than others by studying variables such as inmate age, sentence length, and crime type. A quantitative examination is used to determine the effect of these variables on prison violence (property theft and beatings), and whether it is a result of the living conditions within the prisons. The results indicate that the most overpopulated prisons, with the worst living conditions, have the lowest levels of violence (in Brazil and El Salvador). The lower rates of violence observed in certain Latin American prisons appear to be explained by the existence of criminal governments within penitentiary systems, organized and run by a dominant prison gang.
Optimizing HAR Systems: Comparative Analysis of Enhanced SVM and k-NN Classifiers
Authors: Shdefat Ahmed Younes , Mostafa Nour , Al-Arnaout Zakwan , Kotb Yehia , Alabed Samer 
Published: June 2024

AbstractThis research addresses the accuracy issues in IoT-based human activity recognition (HAR) applications, essential for health monitoring, elderly care, gait analysis, security, and Industry 5.0. This study uses 12 machine learning approaches, split equally between support vector machine (SVM) and k-nearest neighbor (k-NN) models. Data from 102 individuals, aged 18–43, were used to train and test these models. The researchers aimed to detect twelve daily activities, such as sitting, walking, and cycling. Results showed k-NN models achieved slightly higher accuracy (97.08%) compared to SVM models (95.88%), though SVM had faster processing times. The improved machine learning approaches proved effective in accurately classifying daily activities, with k-NN models outperforming SVM models marginally. The paper provides significant contributions to the field of HAR by enhancing the performance of SVM and k-NN classifiers, optimizing them for higher accuracy and faster processing. Through robust testing with samples of real-world data, the study provides a detailed comparative analysis that highlights strengths and weaknesses of each classifier model, specifically within IoT-based systems. This work not only advances the theoretical understanding and practical applications of HAR systems in areas, such as healthcare and industrial automation, but also sets the stage for future research that could explore hybrid models or further enhancements, consequently improving the efficiency and functionality of IoT devices based on activity recognition.
Skepticism and physics: epistemic beliefs of Norwegian physics students compared with other student groups
Authors: Kjelsberg Ronny 
Published: June 2024

AbstractThe purpose of this study is to examine how physics students position themselves compared to other student groups on various attitudes and opinions relevant to the tradition of “scientific skepticism”. Previous research has shown physics students identifying and having mindsets in line with the epistemic ideas from this philosophical tradition, promoting disbelief in epistemically unfounded ideas, and skeptical inquiry as a tool for evaluating claims. In this, we employ quantitative constructs testing conspiracy beliefs and supernatural beliefs along with established psychological constructs for social dominance orientation, and the conspiracy mentality questionnaire that have previously been shown to have interconnectedness. After showing several direct comparisons between different student groups, the paper also examines other elements that can influence “scientific skepticism”, like education level, education type, and gender via multivariate regression analysis. The results suggest physics students tend to position themselves to the end of the spectrum on several constructs connected to scientific skepticism, both compared to students from the humanities and social sciences, and students from other STEM (science, technology, engineering, and mathematics) fields, and the regression analysis finds being a physics student contributes a statistically significant contribution along the tested dimensions. The paper discusses possible reasons for this and what this tells us about physics students and physics education.