bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital tools and technologies used in food fortification: A scoping review
Authors: Vasta Florencia C. , Friesen Valerie M. , Jungjohann Svenja , Nyangaresi Annette M. , Mkambula Penjani , Morrison Taylor , Walsh Fiona , Mbuya Mduduzi N. N. 
Published: January 2025

AbstractFood fortification (i.e., industrial fortification and biofortification) increases the micronutrient content of foods to improve population nutrition. Implementing effective fortification programs requires the generation and use of data to inform decision making. The use of digital tools and technologies (DTTs) for such purposes in broader nutrition programs is growing; however, there is limited consolidation of those used in fortification. This scoping review aimed to identify and describe DTTs used in fortification programs. We searched peer‐reviewed and gray literature and conducted 17 stakeholder surveys. We then mapped DTTs identified against the fortification and nutrition data value chains. Of 11,741 articles identified, 158 met the inclusion criteria. From the included articles and stakeholder surveys, 125 DTTs were identified across three categories: software and tooling (n = 58), data and information lifecycle (n = 50), and hardware and infrastructure (n = 17). Gaps were identified in processing, post‐harvest storage, aggregation, and transport nodes of the fortification value chain, and data prioritization, translation/dissemination, and decision‐making nodes of the nutrition data value chain. DTTs have the potential to address challenges faced by fortification stakeholders to generate and use data to improve program decision making and nutritional impact. Further work is needed to standardize terminology, identify relevant DTTs from other sectors, and explore stakeholder needs.
Math‐anxious people suffer more in math‐related events: The perspective of reward processing on motivated behavior
Authors: Cui Fang , Dai Luwei , He Hao , Liu Jie 
Published: January 2025

AbstractIndividuals with high math anxiety (HMA) demonstrate a tendency to avoid math‐related tasks, a behavior that perpetuates a detrimental cycle of limited practice, poor performance, increased anxiety, and further avoidance. This study delves into the cognitive and neural bases of math avoidance behavior in HMA through the lens of reward processing. In Experiment 1, participants reported their satisfaction level in response to the reward provided after solving an arithmetic problem. In Experiment 2, participants weighed the economic benefits against the cognitive costs of solving a calculation problem. This decision‐making process was framed in terms of either retaining or losing some monetary reward, creating positive or negative contexts, respectively. Experiment 1 showed that HMA participants were more punishment‐sensitive and less satisfied with incorrect answers. Experiment 2 revealed that HMA individuals were less willing to tackle math challenges when their satisfaction dipped after errors. HMAs exhibited increased math avoidance and a notably reduced P3 amplitude in negative contexts, a response unique to the HMA group. HMAs also displayed an elevated feedback‐related negativity amplitude in both contexts. This study suggests a potential impairment in reward processing in negative contexts and under negative appraisal among those with high math anxiety.
Root Development of Tomato Plants Infected by the Cacao Pathogen Moniliophthora perniciosa Is Affected by Limited Sugar Availability
Authors: Paschoal Daniele , Cazetta Laura , Mendes João V. O. , Dias Nathália C. F. , Ometto Vitor , Carrera Esther , Rossi Mônica L. , Aricetti Juliana A. , Mieczkowski Piotr , Carvalho Gabriel G. , Cesarino Igor , da Silva Simone F. , Ribeiro Rafael V. , Teixeira Paulo J. P. L. , da Silva Eder M. , Figueira Antonio 
Published: January 2025

ABSTRACTMoniliophthora perniciosa is the causal agent of the witches' broom disease of cacao (Theobroma cacao), and it can infect the tomato (Solanum lycopersicum) ‘Micro‐Tom’ (MT) cultivar. Typical symptoms of infection are stem swelling and axillary shoot outgrowth, whereas reduction in root biomass is another side effect. Using infected MT, we investigated whether impaired root growth derives from hormonal imbalance or sink competition. Intense stem swelling coincided with a reduction in root biomass, predominantly affecting lateral roots. RNA‐seq analyses of root samples identified only a few differentially expressed genes involved in hormone metabolism, and root hormone levels were not expressively altered. Inoculation of the auxin highly‐sensitive entire mutant genotype maintained the impaired root phenotype; in contrast, the low‐cytokinin MT transgenic line overexpressing CYTOKININ OXIDASE‐2 (35S::AtCKX2) with fewer symptoms did not exhibit root growth impairment. Genes involved in cell wall, carbohydrate, and amino acid metabolism were downregulated, accompanied by lower levels of carbohydrate and amino acid in roots, suggesting a reduction in metabolite availability. 13CO2 was supplied to MT plants, and less 13C was detected in the roots of infected MT but not in those of 35S::AtCKX2 line plants, suggesting that cytokinin‐mediated sugar sink establishment at the infection site may contribute to impaired root growth. Exogenous sucrose application to roots of infected MT plants partially restored root growth. We propose that the impairment of lateral root development is likely attributed to disrupted sugar signalling and photoassimilate supply by establishing a strong sugar sink at the infected stem.
Chickpea displays a temporal growth response to Mesorhizobium strains under well‐watered and drought conditions
Authors: Iqbal Nasir , Brien Chris , Jewell Nathaniel , Berger Bettina , Zhou Yi , Denison R. Ford , Denton Matthew D. 
Published: January 2025

AbstractThe relative performance of rhizobial strains could depend on their resource allocation, environmental conditions, and host genotype. Here, we used a high‐throughput shoot phenotyping to investigate the effects of Mesorhizobium strain on the growth dynamics, nodulation and bacteroid traits with four chickpea (Cicer arietinum) varieties grown under different water regimes in an experiment including four nitrogen sources (two Mesorhizobium strains, and two uninoculated controls: nitrogen fertilised and unfertilised) under well‐watered and drought conditions. We asked three questions. Does the impact of rhizobial strains on chickpea growth change with well‐watered versus drought conditions? Do Mesorhizobium strains differ in their ability to influence biomass and nodule traits of chickpea varieties under well‐watered and drought conditions? Are bacteroid size and amount of polyhydroxybutyrate modified by Mesorhizobium strain, chickpea variety, water availability and their interactions? Under well‐watered conditions, chickpea inoculated with CC1192 showed higher shoot growth rates than M075 and accumulated high plant biomass at harvest. Under drought conditions, however, the shoot growth rate was comparable between CC1192 and M075, with no significant difference in plant biomass and symbiotic effectiveness at harvest. Across sources of variation, plant biomass varied 3.0‐fold, nodules per plant 3.9‐fold, nodule dry weight 3.0‐fold, symbiotic effectiveness 1.5‐fold, bacteroid size 1.4‐fold and bacteroid polyhydroxybutyrate 1.4‐fold. Plant biomass was negatively correlated with both bacteroid size and allocation to polyhydroxybutyrate under well‐watered conditions, suggesting a trade‐off between plant and rhizobial fitness. This study demonstrates the need to reassess rhizobial strain effectiveness across diverse environments, recognising the dynamic nature of their interaction with host plants.
A robust and powerful metric for distributional homogeneity
Authors: Chen Yanzhou , Ding Tianxuan , Wang Xiufang , Zhang Yaowu 
Published: January 2025

AbstractAssessing the homogeneity of two random vectors is a fundamental task in statistical inference. In this work, we introduce a weighted multivariate Cramér‐von Mises type metric that transforms each variable through a marginal mixture distribution function and integrates the squared difference in probability functions of these transformed variables. Notably, our metric exhibits scale invariance, rendering it robust against outliers and heterogeneity. The expression for our metric is straightforward and possesses a closed‐form representation. It is non‐negative and attains a value of zero if and only if the two random vectors are identically distributed. Moreover, our metric employs an ‐norm expression, which significantly enhances its effectiveness in high‐dimensional scenarios compared to traditional methods relying on the ‐norm. We validate the efficacy of our proposed approach through extensive simulation studies and empirical data analysis.
Identification of the Novel HLA‐B*38:01:26 Allele by Next‐Generation Sequencing
Authors: Cheranev Valery , Evgrafova Natalia , Smirnova Darya , Loginova Maria , Korostin Dmitry 
Published: January 2025

ABSTRACTThe new HLA‐B*38:01:26 allele showed one synonymous nucleotide difference compared to the HLA‐B*38:01:01:01 allele in codon 101.
Validity of the Diabetic Wound Assessment Learning Tool
Authors: Selim Omar , Dueck Andrew D. , Kulasegaram Kulamakan M. , Brydges Ryan , Walsh Catharine M. , Okrainec Allan 
Published: January 2025

ABSTRACTPurposeThe development of the Diabetic Wound Assessment Learning Tool (DiWALT) has previously been described. However, an examination of its application to a larger, more heterogeneous group of participants is lacking. In order to allow for a more robust assessment of the psychometric properties of the DiWALT, we applied it to a broader group of participants.Materials and MethodsWe built validity evidence for the tool by assessing 74 clinician participants' during two simulated wound care scenarios: Two assessors independently rated each participant using our tool, with a total of five raters providing scores. We evaluated validity evidence using generalizability theory analyses and by comparing performance scores across the three experience levels using ANOVA.ResultsThe tool differentiated between novices and the other two groups well (p < 0.01) but not between intermediates and experts (p = 0.34). Our generalizability coefficient was 0.87, and our phi coefficient was 0.87.ConclusionThe accumulated validity evidence suggests our tool can be used to assess novice clinicians' competence in initial diabetic wound management during simulated cases. Further work is required to clarify the DiWALT's performance in a broader universe of generalisation and to examine evidence for its extrapolation and implications inferences.
Engaging Students in a Dialysis Unit: A Pilot Study
Authors: Couser Sarah K. , Schuh Meredith P. , Herrmann Lisa E. 
Published: January 2025

ABSTRACTBackgroundSeeking to provide early paediatric nephrology exposure to medical students in the United States, we implemented the Kids In Dialysis, Nephrology Exposure and Education (KIDNEE) club. This club served as an educational intervention in which preclinical medical students were paired with paediatric dialysis patients, as patient buddies.ApproachStudents were recruited for involvement in the club through the medical school Paediatric Interest Group. For the 2022–2023 academic year, seven first‐year students were paired with seven paediatric dialysis patients. Students met with their patient match weekly to play games, watch movies and to act as a friend.EvaluationThe evaluation aimed at assessing the feasibility and acceptability of this intervention as well as influence on student interest in paediatric chronic disease and paediatric nephrology. We developed and distributed surveys to patients, unit staff, and students after programme implementation. From October 2022 to April 2023, medical students collectively spent ~173 h in the dialysis unit. Staff and patients/families unanimously reported that they would recommend the KIDNEE club to other families. Students objectively reported an increased interest in paediatric nephrology and chronic disease and subjectively reported an increased understanding of the patient experience.ImplicationsThe KIDNEE club pilot was both feasible and acceptable for patients/families, staff and students. It holds the potential to increase student interest in the field of paediatric nephrology. As our results are limited by small sample size given the pilot nature of the programme, future studies are needed to assess programme expansion and longitudinal influence on students' career paths.
Iron deficiency and infection risk in Danish blood donors
Authors: Brøns Nanna , Kaspersen Kathrine Agergård , Bay Jakob Thaning , Dowsett Joseph , Erikstrup Christian , Hjalgrim Henrik , Aagaard Bitten , Mikkelsen Christina , Mikkelsen Susan , Pedersen Ole Birger , Rostgaard Klaus , Schwinn Michael , Sørensen Erik , Rigas Andreas Stribolt , Glenthøj Andreas , Ostrowski Sisse Rye 
Published: January 2025

AbstractBackgroundWe aimed to investigate if iron deficiency was associated with infection susceptibility in a large cohort of healthy individuals.Study Design and MethodsThe Danish Blood Donor Study is a national ongoing prospective study of blood donors. We included 94,628 donors with 338,290 ferritin measurements from March 2010 to October 2022. We performed sex‐stratified multivariable Cox regression to estimate the risk of infection for iron‐deficient donors compared with iron‐replete donors. Infection was defined as either a filled prescription of antibiotics registered in the Danish National Prescription Registry (NPR), or a hospital contact with infection registered in the Danish National Patient Registry (DNPR).ResultsIron deficiency was associated with an overall increased risk of infection (defined as prescriptions of antibiotics) for women (hazard ratio [HR] 1.08, 95% confidence interval [CI] 1.02–1.15). Subgroup analyses showed an increased risk of respiratory tract infections (HR 1.16, 95% CI 1.05–1.28) and urinary tract infections (HR 1.16, 95% CI 1.04–1.29). Iron deficiency was not associated with overall risk of infection for men (HR 1.02, 95% CI 0.82–1.28). For both men and women, no association was found between iron deficiency and hospital contacts for infections.ConclusionIron deficiency was associated with an increased risk of infection in female blood donors. However, effect sizes were small, and there was no association between iron deficiency and hospital contacts for infection. Consequently, risk of infection should not be considered an apprehension regarding blood donation. These findings support the role of iron in immune function and monitorization of iron stores in female blood donors.
Nonclinical and clinical characterization of the absorption, metabolism, and excretion of islatravir
Authors: Fillgrove Kerry L. , Matthews Randolph P. , Lu Bing , Liang Yuexia , Patel Munjal , Liu Wen , Matthews Catherine Z. , Liu Yang , Stoch S. Aubrey , Sanchez Rosa I. , Iwamoto Marian 
Published: January 2025

ABSTRACT

The development of new and improved antiretroviral therapies that allow for alternative dosing schedules is needed for people living with HIV-1. Islatravir is a deoxyadenosine analog in development for the treatment of HIV-1 that suppresses HIV-1 replication via multiple mechanisms of action, including reverse transcriptase translocation inhibition and delayed chain termination. Islatravir is differentiated from other HIV-1 antiretrovirals by its high potency, long
t
½
, broad tissue distribution, and favorable drug resistance profile. A comprehensive evaluation was performed to provide data on the mass balance, absorption, metabolism, and excretion of islatravir through studies in nonclinical species, and in adults without HIV-1 infection, using radiolabeled islatravir. Islatravir was well absorbed in both nonclinical species and humans following oral administration. The elimination of islatravir occurs primarily by a combination of oxidative deamination to 4′-ethynyl-2-fluoro-2′-deoxyinosine and renal excretion of unchanged islatravir. Islatravir and 4′-ethynyl-2-fluoro-2′-deoxyinosine are the major circulating drug components in all species assessed. Islatravir is readily taken up into cells with efficient phosphorylation to the mono-, di-, and triphosphate forms. The pharmacologically active islatravir triphosphate is the most abundant intracellular phosphorylated species, as shown by the results of
ex vivo
studies. This characterization of the absorption, metabolism, and elimination of islatravir in humans and nonclinical species supports its further development for the treatment of HIV-1.
Grass carp reovirus VP4 manipulates TOLLIP to degrade STING for inhibition of IFN production
Authors: Wang Yang-Yang , Wang Xue-Li , Li Zhuo-Cong , Zhang Can , Xu Xiao , Cui Bao-Jie , Tian Meng-Ze , Zhou Chu-Jing , Xu Na , Wu Yue , Yang Xiao-Li , Chen Dan-Dan , Lu Long-Feng , Li Shun 
Published: January 2025

ABSTRACT

Although fish possess an effective interferon (IFN) system to defend against viral infection, grass carp reovirus (GCRV) still causes epidemic hemorrhagic disease and tremendous economic loss in grass carp. Therefore, it is necessary to investigate the immune escape strategies employed by GCRV. In this study, we show that the structural protein VP4 of GCRV (encoded by the S6 segment) significantly restricts IFN expression by degrading stimulator of IFN genes (STING) through the autophagy-lysosome-dependent pathway. First, overexpression of VP4 inhibited the expression of IFN induced by GCRV and polyinosinic-polycytidylic acid (poly I:C) at both the promoter and mRNA levels. Second, VP4 was found to associate with STING, and the N-terminal transmembrane domain is essential for this interaction. Additionally, VP4 dramatically blocked STING-induced IFN expression and weakened its antiviral capacity. Further mechanistic studies revealed that VP4 degrades STING via the autophagy-lysosome pathway in a dose-dependent manner. Interestingly, toll-interacting protein (TOLLIP), a selective autophagy receptor, was found to interact with VP4 and reduce VP4-mediated STING degradation after
tollip
knockdown. Finally, overexpression of VP4 facilitated GCRV proliferation, while its depletion had the opposite effect. These findings indicate that GCRV VP4 recruits TOLLIP to degrade STING and achieve immune escape. This enhances our comprehension of aquatic virus pathogenesis.

IMPORTANCE
Upon virus invasion, fish cells employ a multitude of strategies to defend against infection. Consequently, viruses have evolved a plethora of tactics to evade host antiviral mechanisms. To date, fewer studies have been conducted on the immune evasion mechanism of grass carp reovirus (GCRV). In this study, we demonstrate that VP4 of GCRV-873 inhibits interferon expression by interacting with stimulator of IFN gene and degrading it in an autophagy-lysosome-dependent manner through the manipulation of the selective autophagy receptor toll-interacting protein. The findings of this study contribute to our understanding of the novel evasion mechanisms of GCRV and widen our knowledge of the virus-host interactions in lower vertebrates.
phylotypr: an R package for classifying DNA sequences
Authors: Schloss Patrick D. 
Published: January 2025

ABSTRACT

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.
A genome-annotated bacterial collection of the plant food system microbiota
Authors: Pietrantonio Laura , Devers-Lamrani Marion , Thorpe Peter , Arnton Catherine , Robertson-Albertyn Senga , Savojardo Castrense , Hartmann Alain , Martin-Laurent Fabrice , Abbott James , Bulgarelli Davide 
Published: January 2025

ABSTRACT

This study reports draft genomes of 30 bacteria representative of the plant food system microbiota and isolated from different sources in Italy and France. Individual genomes were reconstructed using PacBIO DNA sequencing: taxonomic classification and distribution of genes involved in microbe-environment interactions are reported to facilitate strains' characterization and utilization.
Antiviral defense systems in the rumen microbiome
Authors: Sáenz Johan S. , Rios-Galicia Bibiana , Seifert Jana 
Published: January 2025

ABSTRACT

The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage–host interaction.

IMPORTANCE
Phages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the “pan-immune system” model, which appears to be common across different environments.