bluuebunny/crossref_metadata_2025_split huggingface dataset:
XX sex chromosome complement modulates immune responses to heat-killed Streptococcus pneumoniae immunization in a microbiome-dependent manner
Authors: Amato-Menker Carly J. , Hopen Quinn , Pettit Andrea , Gandhi Jasleen , Hu Gangqing , Schafer Rosana , Franko Jennifer 
Published: March 2024

Abstract
Background
Differences in male vs. female immune responses are well-documented and have significant clinical implications. While the immunomodulatory effects of sex hormones are well established, the contributions of sex chromosome complement (XX vs. XY) and gut microbiome diversity on immune sexual dimorphisms have only recently become appreciated. Here we investigate the individual and collaborative influences of sex chromosome complements and gut microbiota on humoral immune activation.

Methods
Male and female Four Core Genotype (FCG) mice were immunized with heat-killed Streptococcus pneumoniae (HKSP). Humoral immune responses were assessed, and X-linked immune-related gene expression was evaluated to explain the identified XX-dependent phenotype. The functional role of Kdm6a, an X-linked epigenetic regulatory gene of interest, was evaluated ex vivo using mitogen stimulation of B cells. Additional influences of the gut microbiome on sex chromosome-dependent B cell activation was also evaluated by antibiotically depleting gut microbiota prior to HKSP immunization. Reconstitution of the depleted microbiome with short-chain fatty acid (SCFA)-producing bacteria tested the impact of SCFAs on XX-dependent immune activation.

Results
XX mice exhibited higher HKSP-specific IgM-secreting B cells and plasma cell frequencies than XY mice, regardless of gonadal sex. Although Kdm6a was identified as an X-linked gene overexpressed in XX B cells, inhibition of its enzymatic activity did not affect mitogen-induced plasma cell differentiation or antibody production in a sex chromosome-dependent manner ex vivo. Enhanced humoral responses in XX vs. XY immunized FCG mice were eliminated after microbiome depletion, indicating that the microbiome contributes to the identified XX-dependent immune enhancement. Reconstituting microbiota-depleted mice with select SCFA-producing bacteria enhanced fecal SCFA concentrations and increased humoral responses in XX, but not XY, FCG mice. However, exposure to the SCFA propionate alone did not enhance mitogenic B cell stimulation in ex vivo studies.

Conclusions
FCG mice have been used to assess sex hormone and sex chromosome complement influences on various sexually dimorphic traits. The current study indicates that the gut microbiome impacts humoral responses in an XX-dependent manner, suggesting that the collaborative influence of gut bacteria and other sex-specific factors should be considered when interpreting data aimed at delineating the mechanisms that promote sexual dimorphism.
Advancing material property prediction: using physics-informed machine learning models for viscosity
Authors: Chew Alex K. , Sender Matthew , Kaplan Zachary , Chandrasekaran Anand , Chief Elk Jackson , Browning Andrea R. , Kwak H. Shaun , Halls Mathew D. , Afzal Mohammad Atif Faiz 
Published: March 2024

AbstractIn materials science, accurately computing properties like viscosity, melting point, and glass transition temperatures solely through physics-based models is challenging. Data-driven machine learning (ML) also poses challenges in constructing ML models, especially in the material science domain where data is limited. To address this, we integrate physics-informed descriptors from molecular dynamics (MD) simulations to enhance the accuracy and interpretability of ML models. Our current study focuses on accurately predicting viscosity in liquid systems using MD descriptors. In this work, we curated a comprehensive dataset of over 4000 small organic molecules’ viscosities from scientific literature, publications, and online databases. This dataset enabled us to develop quantitative structure–property relationships (QSPR) consisting of descriptor-based and graph neural network models to predict temperature-dependent viscosities for a wide range of viscosities. The QSPR models reveal that including MD descriptors improves the prediction of experimental viscosities, particularly at the small data set scale of fewer than a thousand data points. Furthermore, feature importance tools reveal that intermolecular interactions captured by MD descriptors are most important for viscosity predictions. Finally, the QSPR models can accurately capture the inverse relationship between viscosity and temperature for six battery-relevant solvents, some of which were not included in the original data set. Our research highlights the effectiveness of incorporating MD descriptors into QSPR models, which leads to improved accuracy for properties that are difficult to predict when using physics-based models alone or when limited data is available.
Graphical Abstract
Operational strategies for achieving comprehensive cancer center community outreach and engagement objectives: impact and logic models
Authors: Odedina Folakemi T. , Salinas Manisha , Albertie Monica , Murrell Doug , Munoz Kristin 
Published: March 2024

Abstract
Background
The National Cancer Institute’s (NCI) Cancer Center Support Grants (CCSGs) encourages Cancer Centers to address health disparities and reduce the cancer burden in their Catchment Area (CA) through an organized Community Outreach and Engagement (COE) structure. This paper shares the development of two guide models that fosters the operations of the Mayo Clinic Comprehensive Cancer Center (MCCCC) COE Office and programs, the MCCCC COE Impact Model and the MCCCC COE Logic Model.

Methods
Following a less than stellar CCSG rating for COE in 2018, the MCCCC developed a transition team to specifically address the critique and create a transformative plan for engaging communities to address cancer burden in the CA. A qualitative research approach was employed, focusing on organizing and displaying the relationship between MCCCC COE processes and outcomes through impact and logic models. An impact model was developed to illustrate the components of the CCSG and connect those components to short- and long-term COE outcomes. A logic model was developed to track and monitor activities for continuous process improvement for all COE activities.

Results
The impact and logic model serve as a roadmap to monitor progress towards short- and long-term COE goals of the MCCCC. The COE operational strategies draw upon bidirectional partnership, evidence-based practices, and research facilitation to respond to the CCSG critique.

Conclusion
These strategies demonstrate successful practices in addressing cancer burden, promoting health equity and eliminating cancer disparities in the MCCCC CA.
Adaptive capability and socioecological traps: a bioenergy case in communities of Irapuato, Guanajuato, Mexico
Authors: Reyes-Santiago María del Rosario , Maruri Montes de Oca Ana Elizabeth , Olalde Portugal Victor , Hernández-Rosales Maribel 
Published: March 2024

Abstract
Background
Energy poverty, which is the deprivation of a series of energy services that satisfy human needs, affects over 2 billion individuals who rely on the combustion of biomass and other solid fuels to fulfill their energy needs. While certain communities address their energy shortfall by harnessing local natural resources, these alternatives fail to provide access to more advantageous and sustainable conditions, thus leading to what are commonly referred to as socioecological traps.

Results
This research studies the relationships between the energy alternatives that two communities have developed, the bioenergy capability that would allow the system to access more desirable and sustainable states, and the costs and benefits that are perceived from this new use of their residues and resources. A quantitative methodology was employed by designing and applying a structured questionnaire applied to 207 households in two energy-poor communities in the municipality of Irapuato, Guanajuato, Mexico: San Agustín de los Tordos and El Comedero Grande. We have inferred that the alternatives generated by the communities function as socioecological traps. On the one hand, these options generate adverse effects on the health of people and the environment, while discouraging the construction of bioenergy capabilities; on the other hand, they allow them to cover some training costs, at least in the short term. These discoveries suggest that the system is currently in an advantageous phase of the cultivation of new capabilities.

Conclusions
The outcomes of this study contribute significantly to enhancing our comprehension of socioecological traps and capabilities within the realm of energy, thereby offering valuable insights for the effective management of successful bioenergy implementation initiatives. Moreover, these findings enable the development of frameworks for theoretical interpretation and methodological application within specific contexts, exemplified in our case by rural communities in Irapuato, Guanajuato Mexico. The holistic approach reveals that while individuals may have alternatives to fulfill their energy requirements, many of these alternatives can inadvertently become socioecological traps. For instance, the use of firewood as a short-term solution for household energy needs can generate adverse health and environmental consequences in the long run. In the light of these considerations, a study of their nature becomes imperative and relevant as it delves deeply into the intricate relationship between compensatory alternatives and capacities. Simultaneously, it scrutinizes the community’s perception of bioenergy in terms of costs and benefits, with the overarching goal of transitioning toward a sustainable energy system.
Analysis of inappropriate prophylactic use of proton pump inhibitors during the perioperative period: an observational study
Authors: Liu Pengpeng , Li Guangyao , Wu Qian , Han Mei , Zhang Chao 
Published: March 2024

Abstract
Background
The prevalence and characteristics of inappropriate use of proton pump inhibitors (PPIs) to prevent stress-related mucosal disease (SRMD) during the perioperative period and its associated factors are rarely reported. This study aimed to investigate the prevalence and characteristics of inappropriate prophylactic use of proton pump inhibitors (PPIs) during the perioperative period and identify its associated factors in a tertiary care and academic teaching hospital in China and to provide evidence for regulation authorities and pharmacists to take targeted measures to promote rational drug use.

Methods
Inpatients who underwent surgical operations and received prophylactic use of PPIs from June 2022 to November 2022 were included in this retrospective study. The appropriateness of perioperative prophylactic use of PPIs was evaluated by clinical pharmacists. Associated factors with inappropriate perioperative prophylactic use of PPIs were analyzed by univariable and multivariable logistic regression.

Results
Four-hundred seventy-two patients were finally included in this study, of which 131 (27.75%) patients had at least one problem with inappropriate perioperative prophylactic use of PPIs. The three most common problems were drug use without indication (52.0%), inappropriate usage and dosage (34.6%), and inappropriate duration of medication (6.7%). Multiple logistic regression analysis showed that oral dosage form of PPIs [OR = 18.301, 95% CI (7.497, 44.671), p < 0.001], discharge medication of PPIs [OR = 11.739, 95% CI (1.289, 106.886), p = 0.029], and junior doctors [OR = 9.167, 95% CI (3.459, 24.299), p < 0.001] were associated with more inappropriate prophylactic use of PPIs. Antithrombotics [OR = 0.313, 95% CI (0.136, 0.721), p = 0.006] and prolonged postoperative hospital stay (longer than 15 days) [OR = 0.262, 95% CI (0.072, 0.951), p = 0.042] were associated with less inappropriate prophylactic use of PPIs.

Conclusions
The inappropriate prophylactic use of PPIs during the perioperative period is common. Regulation authorities and pharmacists should take more targeted measures to promote the rational prophylactic use of PPIs during the perioperative period.
Global gene expression profiling of perirenal brown adipose tissue whitening in goat kids reveals novel genes linked to adipose remodeling
Authors: Zhao Le , Yang Haili , Li Minhao , Xiao Min , Li Xingchun , Cheng Lei , Cheng Wenqiang , Chen Meixi , Zhao Yongju 
Published: March 2024

Abstract
Background
Brown adipose tissue (BAT) is known to be capable of non-shivering thermogenesis under cold stimulation, which is related to the mortality of animals. In the previous study, we observed that goat BAT is mainly located around the kidney at birth, and changes to white adipose tissue (WAT) in the perirenal adipose tissue of goats within one month after birth. However, the regulatory factors underlying this change is remain unclear. In this study, we systematically studied the perirenal adipose tissue of goat kids in histological, cytological, and accompanying molecular level changes from 0 to 28 d after birth.

Results
Our study found a higher mortality rate in winter-born goat kids, with goat birthing data statistics. Then we used thermal imaging revealing high temperature in goat hips at postnatal 0 d and gradually decrease during 28 d. This is consistent with the region of perirenal BAT deposition and highlights its critical role in energy expenditure and body temperature regulation in goat kids. Additionally, we found a series of changes of BAT during the first 28 d after birth, such as whitening, larger lipid droplets, decreased mitochondrial numbers, and down-regulation of key thermogenesis-related genes (UCP1, DIO2, UCP2, CIDEA, PPARGC1a, C/EBPb, and C/EBPa). Then, we used RNA-seq found specific marker genes for goat adipose tissue and identified 12 new marker genes for BAT and 10 new marker genes for WAT of goats. Furthermore, 12 candidate genes were found to potentially regulate goat BAT thermogenesis. The mechanism of the change of this biological phenomenon does not involve a large-scale death of brown adipocytes and subsequent proliferation of white adipocytes. While apoptosis may play a limited role, it is largely not critical in this transition process.

Conclusions
We concluded that perirenal BAT plays a crucial role in thermoregulation in newborn goat kids, with notable species differences in the expression of adipose tissue marker genes, and we highlighted some potential marker genes for goat BAT and WAT. Additionally, the change from BAT to WAT does not involve a large-scale death of brown adipocytes and subsequent proliferation of white adipocytes.
Not a passive learner but an active one: a focus on the efficacy of philosophy-based language instruction and its consequences on EFL learners’ critical thinking, engagement, and academic achievement
Authors: Li Lingxi , Ismail Sayed M. , Patra Indrajit , Lami Desta 
Published: March 2024

AbstractThis study investigates the impact of Philosophy-Based Language Teaching (PBLT) on the critical thinking skills and learner engagement of English as a Foreign Language (EFL) students. A concurrent mixed-methods approach, including semi-structured interviews, document analysis, and academic achievement tests, was employed with an experimental group (EG) exposed to PBLT and a control group (CG) receiving traditional instruction. The results reveal a substantial positive effect of PBLT on the critical thinking abilities of EFL learners, as evidenced by thematic analyses of interviews and document content. Themes include heightened critical thinking awareness, collaborative knowledge construction, and increased learner engagement. Academic achievement tests further demonstrate significant improvement in the experimental group’s performance. A comparison with existing literature underscores the novelty of our mixed-methods approach. Implications for language teachers, materials developers, syllabus designers, and policy-makers are discussed, highlighting the potential of PBLT in cultivating critical thinking and learner engagement.
The scientific analysis of the bronze mous excavated from Wushan, Chongqing, China: new perspectives from alloy composition analysis and proteomic method
Authors: Tan Liwei , Fan Xiaopan , Rao Huiyun , Zhang Hui , Yang Yimin 
Published: March 2024

Abstract
The bronze mou was an important artifact commonly used in the Ba-Shu region (now in Chongqing and Sichuan Province) during the Spring and Autumn Period and the Han Dynasty. Although extensive archaeological study of the bronze mou has been conducted, scientific analysis of the bronze mou has been limited, and no organic residue analysis has been performed on the bronze mou. In this study, four bronze mous dated to the Han dynasty (206 BC–220 AD) with organic residues unearthed in three archaeological sites in Wushan, Chongqing, were selected for analysis by portable X-ray fluorescent spectrometer (P-XRF) and liquid chromatograph-tandem mass spectrometry (LC/MS/MS). The results of the alloy composition indicated that all the samples are copper-tin-lead ternary alloys. The proteomic analysis results confirmed that the bronze mou had been used as cooking utensils or containers. At the Tuchengpo Cemetery, soybeans were found in both bronze mou M32:27 and M38:39, and vigna was discovered in M32:27. No useful protein was discovered in the bronze mou from the Shennvmiao Cemetery. Proteins of ginkgo and chicken were found in M16:12 at the Gaotangguan Cemetery. The discovery indicated that residents in Wushan, Chongqing, had access to a diverse range of food sources around 2000 years ago. Furthermore, this study demonstrates that proteomic analysis is highly effective in studying archaeological organic residues.
Food insecurity is associated with low diet quality and unhealthy cooking and eating habits in Iranian women
Authors: Kohanmoo Ali , Hashemzadeh Maral , Teymouri Maryam , Zare Morteza , Akhlaghi Masoumeh 
Published: March 2024

Abstract
Background
Food insecurity affects diet and nutrition intakes. We explored the relationship between food insecurity and dietary intakes in a group of Iranian women.

Methods
The cross-sectional study was performed on 190 healthy females aged 20–55 years attending primary healthcare centers in Shiraz. Food insecurity was evaluated by Household Food Insecurity Access Scale, which is a validated tool for assessing food insecurity in developing countries. Diet was assessed using a food frequency questionnaire. The association of dietary patterns and food insecurity was assessed by linear regression.

Results
Assessment of dietary intakes revealed that consumption of red meat, poultry, fish, dairy, fruits, non-starchy vegetables, and nuts decreased whereas that of grains, processed meats, potato, and sugary foods increased with increasing food insecurity. Among nutrients, carbohydrates, fiber, vitamin A, vitamin C, folic acid, potassium, calcium, and magnesium decreased while fat and sodium increased as food insecurity increased. Three major dietary patterns were detected. Healthy dietary patterns showed inverse associations with food insecurity in the crude (β = -0.422 and − 0.435, P < 0.001) and adjusted (adjusted for age, marital status, and educational level) (β = -0.475 and − 0.341, P < 0.001) models of regression analysis but unhealthy pattern did not show an association with food insecurity. Compared to food secure participants, a higher percentage of food insecure individuals indicated unhealthy eating habits, such as skipping breakfast, lower snack ingestion, more fast and fried food consumption, and using unhealthy cooking methods.

Conclusion
Overall, this study showed that food insecurity was associated with less healthy diet and unhealthy cooking and eating habits.
H3K4 methylation regulates development, DNA repair, and virulence in Mucorales
Authors: Osorio-Concepción Macario , Lax Carlos , Lorenzo-Gutiérrez Damaris , Cánovas-Márquez José Tomás , Tahiri Ghizlane , Navarro Eusebio , Binder Ulrike , Nicolás Francisco Esteban , Garre Victoriano 
Published: March 2024

AbstractMucorales are basal fungi that opportunistically cause a potentially fatal infection known as mucormycosis (black fungus disease), which poses a significant threat to human health due to its high mortality rate and its recent association with SARS-CoV-2 infections. On the other hand, histone methylation is a regulatory mechanism with pleiotropic effects, including the virulence of several pathogenic fungi. However, the role of epigenetic changes at the histone level never has been studied in Mucorales. Here, we dissected the functional role of Set1, a histone methyltransferase that catalyzes the methylation of H3K4, which is associated with the activation of gene transcription and virulence. A comparative analysis of the Mucor lusitanicus genome (previously known as Mucor circinelloides f. lusitanicus) identified only one homolog of Set1 from Candida albicans and Saccharomyces cerevisiae that contains the typical SET domain. Knockout strains in the gene set1 lacked H3K4 monomethylation, dimethylation, and trimethylation enzymatic activities. These strains also showed a significant reduction in vegetative growth and sporulation. Additionally, set1 null strains were more sensitive to SDS, EMS, and UV light, indicating severe impairment in the repair process of the cell wall and DNA lesions and a correlation between Set1 and these processes. During pathogen-host interactions, strains lacking the set1 gene exhibited shortened polar growth within the phagosome and attenuated virulence both in vitro and in vivo. Our findings suggest that the histone methyltransferase Set1 coordinates several cell processes related to the pathogenesis of M. lusitanicus and may be an important target for future therapeutic strategies against mucormycosis.
Discordance in Recommendation Between Next-Generation Sequencing Test Reports and Molecular Tumor Boards in India
Authors: Mathew Aju , Davis Sissmol , Boby Jeffrey Mathew , R I Anu , Suryavanshi Moushumi , Dawood Shaheenah S. , Panda Pankaj Kumar , Nag Shona Milon , Das Arunangshu , Rohatgi Nitesh , Popat Sanjay , Shah Riyaz N.H. , Thampy Cherian , Parikh Aparna Raj , Yadav Siddhartha , Mehta Prashant , Singh Randeep , Mukherji Deborah , Shilpakar Ramila , Mullapally Sujith Kumar , Sirohi Bhawna 
Published: March 2024

PURPOSE Accurate understanding of the genomic and transcriptomic data provided by next-generation sequencing (NGS) is essential for the effective utilization of precision oncology. Molecular tumor boards (MTBs) aim to translate the complex data in NGS reports into effective clinical interventions. Often, MTB treatment recommendations differ from those in the NGS reports. In this study, we analyze the discordance between these recommendations and the rationales behind the discordances, in a non–high-income setting, with international input to evaluate the necessity of MTB in clinical practice. METHODS We collated data from MTB that were virtually hosted in Chennai, India. We included patients with malignancies who had NGS reports on solid tissue or liquid biopsies, and excluded those with incomplete data. MTB forms and NGS reports of each clinical case were analyzed and evaluated for recommendation concordance. Concordance was defined as an agreement between the first recommendation in the MTB forms and the therapeutic recommendations suggested in the NGS report. Discordance was the absence of the said agreement. The rationales for discordance were identified and documented. RESULTS Seventy MTB reports were analyzed with 49 cases meeting the inclusion criteria. The recommendation discordance was 49% (24 of 49). Discordant recommendations were mainly due to low level of evidence for the drug (75% of cases). CONCLUSION The discordance between MTB and NGS vendor recommendations highlights the clinical utility of MTB. The educational experiences provided by this initiative are an example of how virtual academic collaborations can enhance patient care and provider education across geographic borders.