bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Mosquito Salivary Antigens Demonstrate Promise as Biomarkers of Recent Exposure to Plasmodium falciparum–Infected Mosquito Bites
Authors: Lapidus Sarah , Goheen Morgan M , Sy Mouhamad , Deme Awa B , Ndiaye Ibrahima Mbaye , Diedhiou Younous , Mbaye Amadou Moctar , Hagadorn Kelly A , Sene Seynabou Diouf , Pouye Mariama Nicole , Thiam Laty Gaye , Ba Aboubacar , Guerra Noemi , Mbengue Alassane , Raduwan Hamidah , Gagnon Jacqueline , Vigan-Womas Inés , Parikh Sunil , Ko Albert I , Ndiaye Daouda , Fikrig Erol , Chuang Yu-Min , Bei Amy K 
Published: October 2024

Abstract

Background
Measuring malaria transmission intensity using the traditional entomological inoculation rate is difficult. Antibody responses to mosquito salivary proteins like SG6 have been used as biomarkers of exposure to Anopheles mosquito bites. Here, we investigate 4 mosquito salivary proteins as potential biomarkers of human exposure to mosquitoes infected with Plasmodium falciparum: mosGILT, SAMSP1, AgSAP, and AgTRIO.

Methods
We tested population-level human immune responses in longitudinal and cross-sectional plasma from individuals with known P falciparum infection from low- and moderate-transmission areas in Senegal using a multiplexed magnetic bead–based assay.

Results
AgSAP and AgTRIO were the best indicators of recent exposure to infected mosquitoes. Antibody responses to AgSAP, in a moderate-endemicity area, and to AgTRIO in both low- and moderate-endemicity areas, were significantly higher than nonendemic controls. No antibody responses significantly differed between low- and moderate-transmission areas, or between equivalent groups during and outside the malaria transmission seasons. AgSAP and AgTRIO reactivity peaked 2–4 weeks after clinical P falciparum infection and declined 3 months after infection.

Conclusions
Reactivity to AgSAP and AgTRIO reflects exposure to infectious mosquitoes or recent bites rather than general mosquito exposure, highlighting their promise for incorporation into multiplexed assays for serosurveillance of population-level changes in P falciparum–infected mosquito exposure.
Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession
Authors: Wang Haocai , Wang Hang , Crowther Thomas W , Isobe Kazuo , Reich Peter B , Tateno Ryunosuke , Shi Weiyu 
Published: October 2024

Abstract
There is growing awareness of the need for regenerative practices in the fight against biodiversity loss and climate change. Yet, we lack a mechanistic understanding of how microbial community composition and functioning are likely to change alongside transition from high-density tillage to large-scale vegetation restoration. Here, we investigated the functional dynamics of microbial communities following a complete vegetation successional chronosequence in a subtropical zone, Southwestern China, using shotgun metagenomics approaches. The contents of total soil phosphorus (P), available P, litter P, and microbial biomass P decreased significantly during vegetation succession, indicating that P is the most critical limiting nutrient. The abundance of genes related to P-uptake and transport, inorganic P-solubilization, organic P-mineralization, and P-starvation response regulation significantly increased with successional time, indicating an increased microbial “mining” for P under P limitation. Multi-analysis demonstrated microbial P limitation strongly inhibits carbon (C) catabolism potential, resulting in a significant decrease in carbohydrate-active enzyme family gene abundances. Nevertheless, over successional time, microorganisms increased investment in genes involved in degradation-resistant compounds (lignin and its aromatic compounds) to acquire P resources in the litter. Our study provides functional gene-level insights into how P limitation during vegetation succession in subtropical regions inhibits soil microbial C metabolic processes, thereby advancing our understanding of belowground C cycling and microbial metabolic feedback during forest restoration.
Isolation and biogeography of the oligotrophic ocean diazotroph, Crocosphaera waterburyi nov. sp
Authors: Cleveland Catie S , Turk-Kubo Kendra A , Zhao Yiming , Zehr Jonathan P , Webb Eric A 
Published: October 2024

Abstract
Marine N2-fixing cyanobacteria, including the unicellular genus Crocosphaera, are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen and carbon, which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one pelagic, oligotrophic, phycoerythrin-rich species, Crocosphaera watsonii, has ever been identified and characterized as widespread. Herein, we present a new species, named Crocosphaera waterburyi, enriched from the North Pacific Ocean. C. waterburyi was found to be phenotypically and genotypically distinct from C. watsonii, active in situ, distributed globally, and preferred warmer temperatures in culture and the ocean. Additionally, C. waterburyi was detectable in 150- and 4000-meter sediment export traps, had a relatively larger biovolume than C. watsonii, and appeared to aggregate in the environment and laboratory culture. Therefore, it represents an additional, previously unknown link between atmospheric CO2 and N2 gas and deep ocean carbon and nitrogen export and sequestration.
Equitable community-based participatory research engagement with communities of color drives All of Us Wisconsin genomic research priorities
Authors: Thareja Suma K , Yang Xin , Upama Paramita Basak , Abdullah Aziz , Torres Shary Pérez , Cocroft Linda Jackson , Bubolz Michael , McGaughey Kari , Lou Xuelin , Kamaraju Sailaja , Ahamed Sheikh Iqbal , Madiraju Praveen , Kwitek Anne E , Whittle Jeffrey , Franco Zeno 
Published: October 2024

Abstract

Objective
The NIH All of Us Research Program aims to advance personalized medicine by not only linking patient records, surveys, and genomic data but also engaging with participants, particularly from groups traditionally underrepresented in biomedical research (UBR). This study details how the dialogue between scientists and community members, including many from communities of color, shaped local research priorities.

Materials and Methods
We recruited area quantitative, basic, and clinical scientists as well as community members from our Community and Participant Advisory Boards with a predetermined interest in All of Us research as members of a Special Interest Group (SIG). An expert community engagement scientist facilitated 6 SIG meetings over the year, explicitly fostering openness and flexibility during conversations. We qualitatively analyzed discussions using a social movement framework tailored for community-based participatory research (CBPR) mobilization.

Results
The SIG evolved through CBPR stages of emergence, coalescence, momentum, and maintenance/integration. Researchers prioritized community needs above personal academic interests while community members kept discussions focused on tangible return of value to communities. One key outcome includes SIG-driven shifts in programmatic and research priorities of the All of Us Research Program in Southeastern Wisconsin. One major challenge was building equitable conversations that balanced scientific rigor and community understanding.

Discussion
Our approach allowed for a rich dialogue to emerge. Points of connection and disconnection between community members and scientists offered important guidance for emerging areas of genomic inquiry.

Conclusion
Our study presents a robust foundation for future efforts to engage diverse communities in CBPR, particularly on healthcare concerns affecting UBR communities.
isoAsp-Quest: workflow development for isoAsp identification using database searches
Authors: Sakaue Hiroaki , Kuno Atsushi 
Published: October 2024

Abstract
A recent study reported that isomerization of aspartyl residues (Asp) occurs in various tissues and proteins in vivo. For a comprehensive analysis of post-translational modifications, the mass spectrometry (MS)-based proteomic approach is a straightforward method; however, the isomerization of Asp does not alter its molecular weight. Therefore, a unique method is required to analyse Asp isomers using MS. Herein, we present a novel strategy, isoAsp-Quest, which is a database search-oriented isoAsp identification method. isoAsp is specifically converted to 18O-labelled Lα-Asp by the enzymatic reaction of protein L-isoaspartyl-O-methyltransferase (PIMT) in 18O water with a mass shift of 2 Da, which, in principle, enables us to distinguish Asp isomers. However, in practise, a labelled Lα-Asp signal overlaps with that of endogenous Lα-Asp, making detection challenging. Therefore, degradation of the endogenous Lα-Asp peptide by AspN and subsequent removal of AspN were performed prior to the PIMT reaction. This strategy was applied to bovine lens α-crystallin. Consequently, several Asp isomerization sites, consistent with human αA-crystallin, were identified in bovine αA-crystallin, indicating that this strategy is also effective for biological proteins. Therefore, isoAsp-Quest enables the analysis of Lβ-Asp in a straightforward and rapid workflow, which may be useful for the quality control of protein products and biomarker discovery.
Burosumab in adults with X-linked hypophosphatemia: real-world experience from a retrospective study in Sydney
Authors: Kumar Shejil , Girgis Christian M , Tran Brian , Alvarez Malu , Clifton-Bligh Roderick J 
Published: October 2024

Abstract
X-linked hypophosphatemia (XLH) is a chronic disabling hereditary musculoskeletal disorder associated with inactivating PHEX mutations and elevated circulating FGF-23 concentrations. In a placebo-controlled trial of adults with XLH, burosumab (anti-FGF-23 antibody) demonstrated durable improvements in phosphate concentrations, and self-reported stiffness and physical limitation. However, real-world data regarding burosumab efficacy and tolerability in adults with XLH is lacking.
A retrospective audit was performed of patients (age ≥ 18-years) who commenced four-weekly subcutaneous burosumab for XLH at Royal North Shore and Westmead Hospitals, Sydney, between January 2021 and June 2024. Patients were managed per standard clinical care and burosumab dose adjusted as necessary according to manufacturer instructions. Electronic medical records were reviewed to collate data regarding patient demographics, XLH-related complications and prior treatment, burosumab dosage and side effects, and pre- and post-burosumab biochemistry and Western Ontario and McMaster Universities Arthritis Index (WOMAC) scores.
Of thirteen adults with XLH, all had hypophosphatemia before commencing burosumab (mean 0.64 ± 0.08 mmol/L). Mean WOMAC scores demonstrated baseline impairments in stiffness, pain and physical limitation. Burosumab was administered for median 15 months during follow-up (median dose 70 mg). Hypophosphatemia resolved in all patients within three months of burosumab (mean 1.03 ± 0.38 mmol/L). Two patients developed hyperphosphatemia two weeks after commencing burosumab requiring dose reduction. One patient ceased burosumab in the setting of hypercalcaemia and constipation secondary to pre-existing tertiary hyperparathyroidism. Adverse events were mild, including transient musculoskeletal discomfort (n = 4), restless legs (n = 2), injection site reaction (n = 2) and headache (n = 1). Repeat WOMAC within 12 months of commencing burosumab (n = 9) demonstrated clinically meaningful improvements in stiffness (-33.3 ± 12.5, P&lt;.001) and physical function (-14.3 ± 16.2, P=.029).
This study reports real-world outcomes of adults with XLH treated with burosumab. Clinical experience from two centres in Sydney support trial findings that burosumab is well-tolerated and associated with improved serum phosphate concentrations and self-reported stiffness and physical function.
Granulomatosis with polyangiitis with lacrimal gland enlargement and pancreatic swelling: A case report and a literature review
Authors: Kawajiri Tetsuya , Iwata Shigeru , Tanaka Katsunori , Sonoda Takeru , Nishikawa Mizuki , Iwamoto Ryuta , Takahashi Yuichi , Kojima Fumiyoshi , Fujii Takao 
Published: October 2024

ABSTRACT
A 62-year-old man had bilateral eyelid swelling for 4 months. Two months before admission, he developed fatigue and lost 5 kg of body weight. Further examination revealed elevated serum C-reactive protein, normal angiotensin-converting enzyme, elevated proteinase-3 antineutrophil cytoplasmic antibody (PR3-ANCA), and normal immunoglobulin (Ig)G4 concentration. Chest X-ray and computed tomography showed no enlarged hilar lymph nodes, but positron emission tomography-computed tomography showed fluorodeoxyglucose accumulation in both lacrimal glands, in lung nodules, and in the pancreas. Tissue biopsies of the lacrimal glands and pulmonary nodules showed granuloma with giant cells, but no IgG4-positive cells or fibrosis. Pancreatic tissue showed no findings of autoimmune pancreatitis. In the 2022 American College of Rheumatology/European Alliance of Associations for Rheumatology classification criteria for granulomatosis with polyangiitis, the total score was 10 points. Final comprehensive diagnosis was granulomatosis with polyangiitis, based on the negative results of differential diseases, such as IgG4-related diseases and sarcoidosis. Prednisolone 60 mg/day was started on Day 8, and rituximab 500 mg/body/week on Day 12. After beginning treatment, general malaise and lacrimal gland enlargement were resolved, PR3-ANCA and C-reactive protein became negative, and the nodular shadow in the lungs disappeared. This is the first report of granulomatosis with polyangiitis presenting both lacrimal gland and pancreatic lesions.
GTSF1 is required for transposon silencing in the unicellular eukaryote Paramecium tetraurelia
Authors: Wang Chundi , Lyv Liping , Solberg Therese , Zhang Haoyue , Wen Zhiwei , Gao Feng 
Published: October 2024

Abstract
The PIWI-interacting RNA (piRNA) pathway is crucial for transposon repression and the maintenance of genomic integrity. Gametocyte-specific factor 1 (GTSF1), a PIWI-associated protein indispensable for transposon repression, has been recently shown to potentiate the catalytic activity of PIWI in many metazoans. Whether the requirement of GTSF1 extends to PIWI proteins beyond metazoans is unknown. In this study, we identified a homolog of GTSF1 in the unicellular eukaryote Paramecium tetraurelia (PtGtsf1) and found that its role as a PIWI-cofactor is conserved. PtGtsf1 interacts with PIWI (Ptiwi09) and Polycomb Repressive Complex 2 and is essential for PIWI-dependent DNA elimination of transposons during sexual development. PtGtsf1 is crucial for the degradation of PIWI-bound small RNAs that recognize the organism's own genomic sequences. Without PtGtsf1, self-matching small RNAs are not degraded and results in an accumulation of H3K9me3 and H3K27me3, which may disturb transposon recognition. Our results demonstrate that the PIWI–GTSF1 interaction also exists in unicellular eukaryotes with a role in transposon silencing.
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Authors: Li Yinhu , Feng Xikang , Chen Xuhua , Yang Shuo , Zhao Zicheng , Chen Yu , Li Shuai Cheng 
Published: October 2024

Abstract
Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They contain diverse functional elements and are capable of horizontal gene transfer among hosts. While existing plasmid databases have archived plasmid sequences isolated from individual microorganisms or natural environments, there is a need for a comprehensive, standardized, and annotated plasmid database to address the vast accumulation of plasmid sequences. Here, we propose PlasmidScope (https://plasmid.deepomics.org/), a plasmid database offering comprehensive annotations, automated online analysis, and interactive visualization. PlasmidScope harbors a substantial collection of 852 600 plasmids curated from 10 repositories. Along with consolidated background information, PlasmidScope utilizes 12 state-of-the-art tools and provides comprehensive annotations for the curated plasmids, covering genome completeness, topological structure, mobility, host source, tRNA, tmRNA, signal peptides, transmembrane proteins and CRISPR/Cas systems. PlasmidScope offers diverse functional annotations for its 25 231 059 predicted genes from 9 databases as well as corresponding protein structures predicted by ESMFold. In addition, PlasmidScope integrates online analytical modules and interactive visualization, empowering researchers to delve into the complexities of plasmids.
CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening
Authors: Du Hongyan , Zhang Xujun , Wu Zhenxing , Zhang Odin , Gu Shukai , Wang Mingyang , Zhu Feng , Li Dan , Hou Tingjun , Pan Peichen 
Published: October 2024

Abstract
The rational design of targeted covalent inhibitors (TCIs) has emerged as a powerful strategy in drug discovery, known for its ability to achieve strong binding affinity and prolonged target engagement. However, the development of covalent drugs is often challenged by the need to optimize both covalent warhead and non-covalent interactions, alongside the limitations of existing compound libraries. To address these challenges, we present CovalentInDB 2.0, an updated online database designed to support covalent drug discovery. This updated version includes 8303 inhibitors and 368 targets, supplemented by 3445 newly added cocrystal structures, providing detailed analyses of non-covalent interactions. Furthermore, we have employed an AI-based model to profile the ligandability of 144 864 cysteines across the human proteome. CovalentInDB 2.0 also features the largest covalent virtual screening library with 2 030 192 commercially available compounds and a natural product library with 105 901 molecules, crucial for covalent drug screening and discovery. To enhance the utility of these compounds, we performed structural similarity analysis and drug-likeness predictions. Additionally, a new user data upload feature enables efficient data contribution and continuous updates. CovalentInDB 2.0 is freely accessible at http://cadd.zju.edu.cn/cidb/.
A new framework for SubtiWiki, the database for the model organism Bacillus subtilis
Authors: Elfmann Christoph , Dumann Vincenz , van den Berg Tim , Stülke Jörg 
Published: October 2024

Abstract
Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism.
Mediterranean Diet and Risk of Hip Fracture: A Systematic Review and Dose-Response Meta-Analysis
Authors: Fa-Binefa Manel , Clara Albert , Lamas Claudia , Elosua Roberto 
Published: October 2024

Abstract

Context
Hip fractures are a major public health concern. Understanding their epidemiologic and biological links with diet and cardiovascular risk may have important implications for prevention.

Objective
To assess the dose-response association of Mediterranean diet (MD) adherence with the risk of hip fracture.

Data Sources
A systematic search was conducted in the PubMed, Scopus, and Web of Science databases for prospective studies. Search terms were “Mediterranean Diet” and “Fracture.”

Data extraction
Data were extracted from 8 studies, encompassing 15 cohorts that included 503 174 individuals. Methodological quality was assessed using the Risk of Bias in Nonrandomized Studies of Interventions.

Data Analysis
The “meta” and “dosresmeta” packages were used in R Studio Software. The results demonstrated that high and moderate MD adherence were associated with a reduced risk of hip fracture (relative risk [RR] = 0.71 [95% CI, 0.55-0.91]; and RR = 0.78[(95% CI, 0.65-0.93], respectively). The effect of the association was similar in men and women. The dose-response pattern of the association was linear: each point increase in MD adherence was associated with a 5.25% reduction in hip fracture risk.

Conclusions
Adherence to MD is associated with a reduction in hip fracture risk, following a linear dose-response pattern. This supports the promotion of this dietary pattern for improving bone health.

Systematic Review Registration
PROSPERO registration no. CRD42023402284.
10 Optimizing implementation and continuous monitoring of a newborn screening program for severe combined immunodeficiency
Authors: Ngan Abigail Netanya , Hildebrand Kyla , Turvey Stuart , James Elliot , Cook Victoria , Cameron Scott , Setiadi Audi , Vallance Hilary , Rakic Bojana , Sinclair Graham , Biggs Catherine M 
Published: October 2024

Abstract

Background
Severe Combined Immunodeficiency (SCID) is an inborn error of immunity characterized by severely low T cell levels and function. Early diagnosis is essential to prevent serious infections and improve outcomes. Newborn screening (NBS) for SCID provides a way to detect SCID and other conditions associated with T cell lymphopenia in the neonatal period.

Objectives
1) Optimize the implementation of a NBS program for SCID in British Columbia (BC), Canada; and 2) create a systematic method for monitoring the diagnoses and outcomes of infants with a positive screen to facilitate continuous improvement of the NBS program.

Design/Methods
An interdisciplinary working group comprised of immunologists, biochemical geneticists, and hematopathologists met at regular intervals prior to and after implementing NBS for SCID in BC. We developed an algorithm for the evaluation and initial management of infants with an abnormal NBS for SCID based on literature review and local expert consensus. Using a REDCap database, we tracked the prevalence, evaluation, diagnoses and outcomes of infants with a positive NBS. The database also monitored diagnoses and outcomes of children referred to Immunology outside of the NBS program. Plan-do-study-act cycles included creation of clinical and educational guidelines on SCID, optimization of abnormal NBS cut-off values, and reflex chromosomal microarray (CMA) testing of infants with confirmed T cell lymphopenia.

Results
Between October 3, 2022 and June 16, 2023, 28,816 initial samples were tested, and 30 infants had a positive screen for SCID. Of the 30 infants, 10 were ultimately diagnosed with conditions associated with T cell lymphopenia. Diagnosis led to avoidance of live viral vaccines and implementation of infection precaution measures. No infants experienced complications related to live viral vaccine administration, compared to 1 case in the preceding 12 months prior to NBS implementation. In February 2023, the threshold for an abnormal NBS was adjusted to achieve the goal positive screen frequency of 0.1%. Performing reflex CMA testing on infants with confirmed T cell lymphopenia led to rapid diagnosis of chromosomal microdeletion syndromes, avoiding unnecessary second tier testing. Since implementing NBS for SCID in BC, there have been no cases of SCID diagnosed outside of the NBS program.

Conclusion
Establishing an interdisciplinary working group and clinical database facilitated the smooth integration and continuous improvement of NBS for SCID in BC. This model can be applied to other healthcare systems to support teams and ensure the best possible outcomes for affected patients.