bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taeniasis impacts human gut microbiome composition and function
Authors: Mu Wenjie , Ma Pingping , Wang Yugui , Li Yaqi , Ding Yingying , Zou Yang , Pu Lixia , Yan Qi , Kong Haoyue , Guo Xiaola , Guo Aijiang , Li Hailong , Wang Shuai 
Published: October 2024

Abstract
Human taeniasis, caused by Taenia tapeworms, is a global parasitic disease with significant implications for public health and food safety. These tapeworms can grow to considerable sizes and potentially impact the microecology of the host gut. Despite their importance, the effects of Taenia infection on host gut microbiota haven’t been thoroughly investigated. In this study, we conducted a cross-sectional analysis of the gut microbiome in patients infected with Taenia asiatica (n = 87) compared to healthy controls (n = 79) in the Dali cohort, China. We also performed a longitudinal assessment of microbial changes following deworming in a subset of patients (n = 24). Our findings reveal a significant shift in gut microbial composition, characterized by increased alpha-diversity and an enrichment of Prevotella-driven enterotypes in infected patients compared to healthy controls. The stability of these microbial features post-deworming varied widely among individuals and was lower in those with lower initial alpha diversity and Prevotella-enterotype before deworming. We observed a significant depletion of Bifidobacterium species in infected individuals, regardless of enterotypes, and these prebiotics did not recover post-deworming. Metabolic network analysis and in vitro experiments suggest that the reduction of Bifidobacterium was linked to metabolic competition for ecological niches or nutrients, particularly stachyose, from other microbes rather than the parasitism itself. Furthermore, our machine learning analysis demonstrated that taxa associated with Bifidobacterium in stachyose metabolism could robustly predict infection but could not predict deworming. This study highlights the substantial impact of taeniasis on the human gut microbiome and overall gut health.
Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement
Authors: Bustos-Caparros Esteban , Viver Tomeu , Gago Juan F , Rodriguez-R Luis M , Hatt Janet K , Venter Stephanus N , Fuchs Bernhard M , Amann Rudolf , Bosch Rafael , Konstantinidis Konstantinos T , Rossello-Mora Ramon 
Published: October 2024

Abstract
To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (~36% salts) ~230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the most prevalent species, Haloquadratum walsbyi and Salinibacter ruber, either increased in dominance by replacing less competitive populations (for D20, moderate stress conditions), or severely decreased in abundance and were eventually replaced by other congeneric species better adapted to the higher osmotic stress (for D13, strong stress conditions). Congeneric species replacement was commonly observed within additional abundant genera in response to changes in environmental or biological conditions (e.g. phage predation) within the same system and under a controlled perturbation of a relevant environmental parameter. Therefore, a genus is an ecologically important level of diversity organization, not just a taxonomic rank, that persists in the environment based on congeneric species replacement due to relatively high functional overlap (gene sharing), with important consequences for the success of the lineage, and similar to the success of a species via strain-replacement. Further, our results showed that successful species were typically accompanied by the emergence of their own viral cohorts, whose intra-cohort diversity appeared to strongly covary with, and likely drive, the intra-host diversity. Collectively, our results show that brine communities are ecologically resilient and continuously adapting to changing environments by transitioning to alternative stable states.
Current Concepts in Molecular Breast Imaging
Authors: Patel Miral M , Adrada Beatriz E , Guirguis Mary S , Whitman Gary , Moseley Tanya W , Rauch Gaiane M 
Published: October 2024

Abstract
Molecular breast imaging (MBI) is a functional imaging modality that utilizes technetium 99m sestamibi radiotracer uptake to evaluate the biology of breast tumors. Molecular breast imaging can be a useful tool for supplemental screening of women with dense breasts, for breast cancer diagnosis and staging, and for evaluation of treatment response in patients with breast cancer undergoing neoadjuvant systemic therapy. In addition, MBI is useful in problem-solving when mammography and US imaging are insufficient to arrive at a definite diagnosis and for patients who cannot undergo breast MRI. Based on the BI-RADS lexicon, a standardized lexicon has been developed to aid radiologists in MBI reporting. In this article, we review MBI equipment, procedures, and lexicon; clinical indications for MBI; and the radiation dose associated with MBI.
Geranylgeranyl diphosphate synthase inhibition impairs osteoclast differentiation, morphology, and resorptive activity
Authors: Muehlebach Molly E , Haney Staci L , Chhonker Yashpal S , Rashid Mamunur , Murry Daryl J , Talmon Geoffrey , Holstein Sarah A 
Published: October 2024

Abstract
Nitrogen bisphosphonates, such as zoledronic acid, target the enzyme farnesyl diphosphate synthase (FDPS) in the isoprenoid biosynthetic pathway (IBP), and are the frontline treatment for osteolytic bone diseases. A strong affinity of these agents for bone limits their distribution out of the skeleton. Geranylgeranyl diphosphate synthase (GGDPS) is directly downstream to FDPS in the IBP and novel GGDPS inhibitors such as RAM2061 have been shown to have key drug-like features including prolonged half-life, metabolic stability, and systemic distribution. Furthermore, RAM2061 exerts anti-neoplastic benefits in mouse models of multiple myeloma and Ewing sarcoma. Therefore, we are interested in determining the potential impact of RAM2061 on osteoclast biology and bone remodeling. Studies utilizing undifferentiated RAW264.7 cells demonstrated that treatment with RAM2061 depletes cells of geranylgeranyl diphosphate, impairs protein geranylgeranylation, and induces markers of the unfolded protein response pathway and apoptosis. Differentiation of RAW264.7 cells to mature osteoclasts is disrupted by RAM2061, resulting in decreased numbers of mature osteoclasts, altered morphology, and decreased tartrate-resistant acid phosphatase activity. Treatment of fully differentiated RAW264.7 cells with RAM2061 led to decreased resorptive activity. Confocal microscopy studies revealed that RAM2061 disrupts Cdc42 localization, inhibiting proper actin ring formation in osteoclasts. No significant impact on bone turnover markers or bone histomorphology was observed following a 3-week treatment of CD-1 mice with RAM2061, although decreased numbers of osteoclasts were observed. Liquid chromatography-tandem mass spectrometry studies confirmed accumulation of RAM2061 in bone from the in vivo studies as well as hydroxyapatite binding in vitro. In conclusion, these studies are the first to demonstrate the anti-osteoclastic activity of GGDPS inhibitor treatment and support future studies exploring the therapeutic benefit of this novel therapy in the setting of pathological bone remodeling.
Comparative ecological analysis and predictive modeling of tick-borne pathogens
Authors: Manley William , Tran Tam , Prusinski Melissa , Brisson Dustin 
Published: October 2024

Abstract
Tick-borne diseases constitute the predominant vector-borne health threat in North America. Recent observations have noted a significant expansion in the range of the black-legged tick (Ixodes scapularis Say, Acari: Ixodidae), alongside a rise in the incidence of diseases caused by its transmitted pathogens: Borrelia burgdorferi Johnson (Spirochaetales: Spirochaetaceae), Babesia microti Starcovici (Piroplasmida: Babesiidae), and Anaplasma phagocytophilium Zhu (Rickettsiales: Anaplasmataceae), the causative agents of Lyme disease, babesiosis, and anaplasmosis, respectively. Prior research identified environmental features that influence the ecological dynamics of I. scapularis and B. burgdorferi that can be used to predict the distribution and abundance of these organisms, and thus Lyme disease risk. In contrast, there is a paucity of research into the environmental determinants of B. microti and A. phagocytophilium. Here, we use over a decade of surveillance data to model the impact of environmental features on the infection prevalence of these increasingly common human pathogens in ticks across New York State (NYS). Our findings reveal a consistent northward and westward expansion of B. microti in NYS from 2009 to 2019, while the range of A. phagocytophilum varied at fine spatial scales. We constructed biogeographic models using data from over 650 site-year visits and encompassing more than 250 environmental variables to accurately forecast infection prevalence for each pathogen to a future year that was not included in model training. Several environmental features were identified to have divergent effects on the pathogens, revealing potential ecological differences governing their distribution and abundance. These validated biogeographic models have applicability for disease prevention efforts.
Impacts of nitrogen deposition on Zanthoxylum bungeanum and intercropped plants: assessing growth, chlorophyll fluorescence and yields across diverse cultivation systems
Authors: Li Zilong , Pan Kaiwen , Li Xiyang , Wang Sizhong , Tan Xue , Huang Dan 
Published: October 2024

Abstract
The study aimed to thoroughly investigate the effects of nitrogen deposition on the growth, chlorophyll fluorescence and yield of Zanthoxylum bungeanum Maxim. in both monoculture and intercropping systems with Capsicum annuum L. and Glycine max. The research provided a detailed evaluation of how nitrogen deposition influenced soil and plant parameters within these intercropping systems. Key findings include: (i) In the Z. bungeanum monoculture, nitrogen deposition led to a 346.5% increase in soil NO3− levels, significantly affecting chlorophyll fluorescence parameters and decreasing soil pH. (ii) In the Z. bungeanum–C. annuum intercropping system, nitrogen deposition influenced the growth and chlorophyll fluorescence of both crops and resulted in a 261.5% increase in the root length of C. annuum. (iii) In the Z. bungeanum–G. max system, nitrogen deposition negatively impacted the chlorophyll fluorescence of G. max, reduced Z. bungeanum yields by 89.3% and altered its chlorophyll fluorescence parameters. These changes likely hindered the nitrogen-fixing capacity of G. max due to altered soil conditions. Overall, the Z. bungeanum–C. annuum system showed superior performance by enhancing soil NO3−-N content. In contrast, the Z. bungeanum–G. max system experienced reduced yields due to the adverse effects of nitrogen deposition on symbiotic nitrogen fixation. These findings are crucial for developing agricultural strategies aimed at improving crop adaptability and yield in response to environmental changes.
Studying Chinese immigrants’ spatial distribution in the Raleigh–Durham area by linking survey and commercial data using romanized names
Authors: Bai Eric A , Ju Botao , Beckner Madeleine , Reiter Jerome P , Merli M Giovanna , Mouw Ted 
Published: October 2024

Abstract
Many population surveys do not provide information on respondents’ residential addresses, instead offering coarse geographies like zip code or higher aggregations. However, fine resolution geography can be beneficial for characterizing neighbourhoods, especially for relatively rare populations such as immigrants. One way to obtain such information is to link survey records to records in auxiliary databases that include residential addresses by matching on variables common to both files. We present an approach based on probabilistic record linkage that enables matching survey participants in the Chinese Immigrants in Raleigh–Durham Study to records from InfoUSA, an information provider of residential records. The two files use different Chinese name romanization practices, which we address through a novel and generalizable strategy for constructing records’ pairwise comparison vectors for romanized names. Using a fully Bayesian record linkage model, we characterize the geospatial distribution of Chinese immigrants in the Raleigh–Durham area of North Carolina.
ECBD: European chemical biology database
Authors: Škuta Ctibor , Müller Tomáš , Voršilák Milan , Popr Martin , Epp Trevor , Skopelitou Katholiki E , Rossella Federica , Herzog Katja , Stechmann Bahne , Gribbon Philip , Bartůněk Petr 
Published: October 2024

Abstract
The European Chemical Biology Database (ECBD, https://ecbd.eu) serves as the central repository for data generated by the EU-OPENSCREEN research infrastructure consortium. It is developed according to FAIR principles, which emphasize findability, accessibility, interoperability and reusability of data. This data is made available to the scientific community following open access principles. The ECBD stores both positive and negative results from the entire chemical biology project pipeline, including data from primary or counter-screening assays. The assays utilize a defined and diverse library of over 107 000 compounds, the annotations of which are continuously enriched by external user supported screening projects and by internal EU-OPENSCREEN bioprofiling efforts. These compounds were screened in 89 currently deposited datasets (assays), with 48 already being publicly accessible, while the remaining will be published after a publication embargo period of up to 3 years. Together these datasets encompass ∼4.3 million experimental data points. All public data within ECBD can be accessed through its user interface, API or by database dump under the CC-BY 4.0 license.
20 years of the Bio-Analytic Resource for Plant Biology
Authors: Sullivan Alexander , Lombardo Michael N , Pasha Asher , Lau Vincent , Zhuang Jian Yun , Christendat Ashley , Pereira Bruno , Zhao Tianhui , Li Youyang , Wong Rachel , Qureshi Faisal Z , Provart Nicholas J 
Published: October 2024

Abstract
The Bio-Analytic Resource for Plant Biology (‘the BAR’, at https://bar.utoronto.ca) is celebrating its 20th year in operation in 2025. The BAR encompasses and provides visualization tools for large ‘omics data sets from plants. The BAR covers data from Arabidopsis, tomato, wheat, barley and 29 other plant species (with data for 2 others to be released soon). These data include nucleotide and protein sequence data, gene expression data, protein-protein and protein–DNA interactions, protein structures, subcellular localizations, and polymorphisms. The data are stored in more than 200 relational databases holding 186 GB of data and are presented to the researchers via web apps. These web apps provide data analysis and visualization tools. Some of the most popular tools are eFP (‘electronic fluorescent pictograph’) Browsers, ePlants and ThaleMine (an Arabidopsis-specific instance of InterMine). The BAR was designated a Global Core Biodata Resource in 2023. Like other GCBRs, the BAR has excellent operational stability, provides access without login requirement, and provides an API for researchers to be able to access BAR data programmatically. We present in this update a new overarching search tool called Gaia that permits easy access to all BAR data, powered by machine learning and artificial intelligence.
MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights
Authors: Lu Yao , Hui Fiona , Zhou Guangyan , Xia Jianguo 
Published: October 2024

Abstract
The growing volumes of microbiome studies over the past decade have revealed a wide repertoire of microbial associations under diverse conditions. Microbes produce small molecules to interact with each other as well as to modulate their environments. Their metabolic profiles hold the key to understanding these association patterns for translational applications. Based on this concept, we developed MicrobiomeNet, a comprehensive database that integrates microbial associations with their metabolic profiles for mechanistic insights. It currently contains a total of ∼5.8 million known microbial associations, coupled with &gt;12 400 genome-scale metabolic models (GEMs) covering ∼6000 microbial species. Users can intuitively explore microbial associations and compare their corresponding metabolic profiles. Our case studies show that MicrobiomeNet can provide mechanistic insights that are consistent with the literature. MicrobiomeNet is freely available at https://www.microbiomenet.com/.
Nutritional Psychology: Review the Interplay Between Nutrition and Mental Health
Authors: Horovitz Omer 
Published: October 2024

Abstract
Nutritional psychology is a burgeoning field that examines the intricate relationship between nutrition and mental health. This concept, its historical development, and its current significance in understanding the complex interplay between diet and psychological well-being are explored in this article. The influence of various nutrients on mental health, the role of dietary patterns, and the impact of nutrition on specific mental disorders are examined. Highlighted are the potential mechanisms underlying the nutrition-mental health connection, and the implications for clinical practice and public health interventions are discussed. The discussion in this article underscores the importance of considering nutrition as essential in mental health promotion and treatment.
26 Culturally informed developmental paediatric care: A qualitative study
Authors: McLeod Scott , Huie Michelle , Francois Katilyn 
Published: October 2024

Abstract

Background
Paediatricians provide developmental care through developmental surveillance, identification and management of specific developmental disorders, and health advocacy. Despite being one of the most common reasons to visit a paediatrician, the provision of care in this field is challenging as it intersects with medical, mental health, and educational systems. Additionally, the rise of international migration, inequities in health systems, and unique culturally based concepts of child development require paediatricians to have unique skills for culturally informed care provision in this area.

Objectives
A qualitative study was conducted to describe the perceptions of paediatricians on providing culturally informed developmental paediatric care to diverse populations.

Design/Methods
Semi-structured interviews were completed with paediatricians who primarily provide developmental care to understand the challenges, opportunities, and potential educational enhancements to improve culturally informed care for developmental paediatrics. Thematic analysis was used to analyze the transcribed interviews using inductive and deductive approaches.

Results
Three major themes emerged from 18 individual semi-structured interviews. The first theme, “cultural translation,” described language differences, interpretation, and trust-building between discordant physician/family dyads. The second theme, “inequity,” described systemic barriers that diverse populations experience, power distance in healthcare relationships, and pandemic-related amplifications of inequity. The third theme, “educational opportunities,” highlighted reflective practice opportunities, immersive experiences in diverse settings, and building a community of practice for paediatricians to build their knowledge base. Paediatricians practicing developmental paediatric care highlighted unique elements to the practice which may benefit from practice changes and curricular reform. Integration of meaningful training in the use of interpretation services, multicultural health brokers, and care coordination teams is a recommended intervention which is transferable to many disciplines. Peer-mentorship from colleagues of differing cultural backgrounds may help reduce race-based stereotypes and enhance perspective taking.

Conclusion
Paediatricians had a variety of perspectives on the provision of developmental paediatric care to diverse populations within Canada. There were a range of perceived opportunities for improvements in care noted on individual and systems levels. The development of infrastructure to build capacity in culturally informed developmental paediatric care to reduce culturally based health gaps is a needed future direction for developmental paediatrics.
59 Enhancing career development in paediatrics residency: A needs assessment
Authors: Cooper Jessica , Veale Pamela 
Published: October 2024

Abstract

Background
Mentorship is a cornerstone of professional growth within medical training, yet the role of formal mentorship in career advising for medical residents remains understudied. In 2020, our Paediatrics Residency program introduced the role of faculty advisors as part of the Competence by Design framework, with a mission to guide academic growth, professional development, and excellence in patient care. However, it is unclear to what extent career advising is occurring in this advisor-advisee relationship.

Objectives
The primary aim of this study was to complete a needs assessment for Paediatric residents to inform faculty advisor roles and responsibilities and effectively support paediatric residents in their career development. This included examination of the current state, identification of the ideal state, followed by a gap analysis and recommendations to create a comprehensive advising program.

Design/Methods
This study utilized a mixed methods approach, using quantitative and qualitative survey methodologies. The survey questions (n=20) were designed from background literature and pilot testing. An anonymous survey was administered through the Qualtrics platform to the Paediatrics residents (n=59). The protocol was submitted for REB review and was granted an exemption as a quality improvement project. Thematic analysis of the qualitative content was completed by two investigators, utilizing the Braun & Clarke six-phase framework.

Results
The response rate for the survey reached 34% (n=20) with the final sample including 16% PGY1, 42% PGY2, 16% PGY3, and 26% PGY4 residents. Alarmingly, most residents (63%) did not have a well-defined plan for monitoring career goals. No residents claimed to have sufficient career mentorship at present (0%), with majority (84%) expressing their interest in regular career planning sessions. A significant proportion (79%) also underscored the importance of considering life context when setting career goals. Our thematic analysis revealed that career advising currently follows a non-formal, self-initiated process, with time constraints as the primary obstacle. Primary themes elicited emphasized career exploration (n=15), networking (n=7) including discussions around life context (n=6), mentorship (n=6), and advisor role clarity (n=6).

Conclusion
Our findings affirm a compelling need for enhanced career development within our Paediatrics Residency program. In response, we propose a multi-faceted approach advocating for structured formal career development. This entails scheduled information sessions, resident goal setting, and formal mentorship. We recommend creating opportunities for networking to enable personalized career development considerations. Exploring an adjunctive role to faculty advisors may be necessary to ensure the success of these recommendations in optimizing resident career education.