bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D U-Net for automated detection of multiple sclerosis lesions: utility of transfer learning from other pathologies
Authors: Wahlig Stephen G. , Nedelec Pierre , Weiss David A. , Rudie Jeffrey D. , Sugrue Leo P. , Rauschecker Andreas M. 
Published: October 2023

Background and purposeDeep learning algorithms for segmentation of multiple sclerosis (MS) plaques generally require training on large datasets. This manuscript evaluates the effect of transfer learning from segmentation of another pathology to facilitate use of smaller MS-specific training datasets. That is, a model trained for detection of one type of pathology was re-trained to identify MS lesions and active demyelination.Materials and methodsIn this retrospective study using MRI exams from 149 patients spanning 4/18/2014 to 7/8/2021, 3D convolutional neural networks were trained with a variable number of manually-segmented MS studies. Models were trained for FLAIR lesion segmentation at a single timepoint, new FLAIR lesion segmentation comparing two timepoints, and enhancing (actively demyelinating) lesion segmentation on T1 post-contrast imaging. Models were trained either de-novo or fine-tuned with transfer learning applied to a pre-existing model initially trained on non-MS data. Performance was evaluated with lesionwise sensitivity and positive predictive value (PPV).ResultsFor single timepoint FLAIR lesion segmentation with 10 training studies, a fine-tuned model demonstrated improved performance [lesionwise sensitivity 0.55 ± 0.02 (mean ± standard error), PPV 0.66 ± 0.02] compared to a de-novo model (sensitivity 0.49 ± 0.02, p = 0.001; PPV 0.32 ± 0.02, p &lt; 0.001). For new lesion segmentation with 30 training studies and their prior comparisons, a fine-tuned model demonstrated similar sensitivity (0.49 ± 0.05) and significantly improved PPV (0.60 ± 0.05) compared to a de-novo model (sensitivity 0.51 ± 0.04, p = 0.437; PPV 0.43 ± 0.04, p = 0.002). For enhancement segmentation with 20 training studies, a fine-tuned model demonstrated significantly improved overall performance (sensitivity 0.74 ± 0.06, PPV 0.69 ± 0.05) compared to a de-novo model (sensitivity 0.44 ± 0.09, p = 0.001; PPV 0.37 ± 0.05, p = 0.001).ConclusionBy fine-tuning models trained for other disease pathologies with MS-specific data, competitive models identifying existing MS plaques, new MS plaques, and active demyelination can be built with substantially smaller datasets than would otherwise be required to train new models.
Adoption and implementation of produce prescription programs for under-resourced populations: clinic staff perspectives
Authors: Folta Sara C. , Li Zhongyu , Cash Sean B. , Hager Kurt , Zhang Fang Fang 
Published: October 2023

BackgroundProduce prescription programs represent a promising intervention strategy in the healthcare setting to address disparities in diet quality and diet-related chronic disease. The objective of this study was to understand adoption and implementation factors related to these programs that are common across contexts and those that are context-specific.MethodsIn this qualitative case comparison study, we conducted qualitative interviews with eight clinic staff from five primary care “safety net” clinics, identified by a partnering non-profit organization that operated the programs, in April–July 2021.ResultsAcross clinics, the ability to provide a tangible benefit to patients was a key factor in adoption. Flexibility in integrating into clinic workflows was a facilitator of implementation. Fit with usual operations varied across clinics. Common challenges were the need for changes to the workflow and extra staff time. Clinic staff were skeptical about the sustainability of both the benefits to patients and the ability to continue the program at their clinics.DiscussionThis study adds to a growing body of knowledge on the adoption and implementation of produce prescription programs. Future research will further this understanding, providing the evidence necessary to guide adopting clinics and to make informed policy decisions to best promote the growth and financial sustainability of these programs.
Impact of food-based fortification on nutritional outcomes and acceptability in older adults: systematic literature review
Authors: Geny Alexia , Petitjean Maité , Van Wymelbeke-Delannoy Virginie , Sulmont-Rossé Claire 
Published: October 2023

Background“Do it yourself” (DIY) food-based fortification involves adding fortificants into everyday foods. It is a flexible solution that allows older people with reduced appetite to meet their nutritional needs.ObjectivesThe aims of the systematic review are (a) to describe DIY fortified recipes, (b) to evaluate their acceptability, and (c) to evaluate whether they are effective levers to improve nutritional outcomes in older people.MethodsA systematic search of 3 databases (Web of Science, PubMed, Scopus, last searched on January 2022) was undertaken. Main eligibility criteria include older adults aged ≥60 years living at home, in an institution or in hospital. Studies carried out for a specific medical condition or targeting only micronutrient fortification were excluded. After reviewing all titles/abstracts then full-text papers, key data were extracted and synthesized narratively. The quality of included studies was assessed using Kmet et al.ResultsOf 21,493 papers extracted, 44 original studies were included (3,384 participants), with 31 reporting nutritional outcomes, 3 reporting acceptability outcomes and 10 reporting both nutritional and acceptability outcomes. The review highlighted a wide variety of DIY fortified recipes, with additional energy ranging from 23 to 850 kcal/d (M = 403; SE = 62) and/or protein ranging from 4 to 40 g/d (M = 19; SE = 2). Compared to a standard diet, DIY fortification seems to be a valuable strategy for increasing energy and protein intake in older people. However, no strong evidence was observed on the nutritional status.Implication for futureFurther acceptability studies are crucial to ensure that DIY fortified foods are palatable and thus have a significant impact on the nutritional status. In addition, it would be useful for studies to better describe DIY recipes. This information would result in a better understanding of the factors that maximize the impact of DIY fortification on nutritional outcomes. Study registration: PROSPERO no. CRD42021244689.Systematic review registration: PROSPERO: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021244689.
Probiotics for the prevention and treatment of COVID-19: a rapid systematic review and meta-analysis
Authors: Sohail Aruba , Cheema Huzaifa Ahmad , Mithani Maidah Sohail , Shahid Abia , Nawaz Ahmad , Hermis Alaa Hamza , Chinnam Sampath , Nashwan Abdulqadir J. , Cherrez-Ojeda Ivan , Awan Rehmat Ullah , Ahmad Sharjeel 
Published: October 2023

BackgroundAlthough numerous modalities are currently in use for the treatment and prophylaxis of COVID-19, probiotics are a cost-effective alternative that could be used in diverse clinical settings. Hence, we conducted a meta-analysis to investigate the role of probiotics in preventing and treating COVID-19 infection.MethodsWe searched several databases from inception to 30 May 2023 for all randomized controlled trials (RCTs) and comparative observational studies that evaluated probiotics (irrespective of the regimen) for the treatment or prevention of COVID-19. We conducted our meta-analysis using RevMan 5.4 with risk ratio (RR) and mean difference (MD) as the effect measures.ResultsA total of 18 studies (11 RCTs and 7 observational studies) were included in our review. Probiotics reduced the risk of mortality (RR 0.40; 95% CI: 0.25–0.65, I2 = 0%). Probiotics also decreased the length of hospital stay, rate of no recovery, and time to recovery. However, probiotics had no effect on the rates of ICU admission. When used prophylactically, probiotics did not decrease the incidence of COVID-19 cases (RR 0.65; 95% CI: 0.37–1.12; I2 = 66%). The results for all outcomes were consistent across the subgroups of RCTs and observational studies (P for interaction &gt;0.05).ConclusionThe results of this meta-analysis support the use of probiotics as an adjunct treatment for reducing the risk of mortality or improving other clinical outcomes in patients with COVID-19. However, probiotics are not useful as a prophylactic measure against COVID-19. Large-scale RCTs are still warranted for determining the most efficacious and safe probiotic strains.Systematic Review RegistrationPROSPERO (CRD42023390275: https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=390275).
Remission and long-term remission of pediatric-onset systemic lupus erythematosus
Authors: Chen Yi-Chieh , Hsu Chiann-Yi , Tsai Ming-Chin , Fu Lin-Shien , Huang Yung-Chieh 
Published: October 2023

ObjectivesSystemic lupus erythematosus (SLE) is a chronic autoimmune disease with diverse clinical presentations and prognoses. Remission can be achieved with or without glucocorticoid (GC) use, and several recent studies have suggested that long-term remission can be achieved in a small portion of patients. Nevertheless, few studies have investigated remission or long-term remission in the pediatric-onset SLE subgroup. This study analyzed the characteristics and factors associated with long-term remission and GC use in pediatric-onset SLE.MethodsWe enrolled 226 patients aged &lt;18 years who received a diagnosis of SLE between January 2006 and December 2016. Three remission condition groups were defined: (A) complete remission, (B) clinical remission off GCs, and (C) clinical remission on GCs. Long-term remission was defined as remission for more than 5 years. We analyzed the treatment durations before remission, durations of remission, and risk factors for non-remission with persistent GC use.ResultsDuring follow-up, 8 patients (3.5%) achieved complete remission, 35 patients (15.5%) achieved clinical remission off GCs, and 93 patients (41.2%) achieved clinical remission on GCs. In groups A, B, and C, 12.5%, 68.6%, and 65.6% of patients, respectively, remained in remission for &gt;1 year.ConclusionThis study assessed remission of pediatric-onset SLE. Up to 60.2% of patients had clinical remission after treatment, and 19% of patients achieved remission off GCs. Long-term remission is rarer in pediatric-onset SLE than in adult-onset SLE.
Global expression patterns of R-genes in tomato and potato
Authors: von Dahlen Janina K. , Schulz Kerstin , Nicolai Jessica , Rose Laura E. 
Published: October 2023

IntroductionAs key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question.MethodsIn this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants.ResultsWe found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes.DiscussionThese results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.
Plant species identity and mycorrhizal type explain the root-associated fungal pathogen community assembly of seedlings based on functional traits in a subtropical forest
Authors: Li Yongning , Xie Yan , Liu Zhengjiao , Shi Liuqing , Liu Xubing , Liang Minxia , Yu Shixiao 
Published: October 2023

IntroductionAs a crucial factor in determining ecosystem functioning, interaction between plants and soil-borne fungal pathogens deserves considerable attention. However, little attention has been paid into the determinants of root-associated fungal pathogens in subtropical seedlings, especially the influence of different mycorrhizal plants.MethodsUsing high-throughput sequencing techniques, we analyzed the root-associated fungal pathogen community for 19 subtropical forest species, including 10 ectomycorrhizal plants and 9 arbuscular mycorrhizal plants. We identified the roles of different factors in determining the root-associated fungal pathogen community. Further, we identified the community assembly process at species and mycorrhizal level and managed to reveal the drivers underlying the community assembly.ResultsWe found that plant species identity, plant habitat, and plant mycorrhizal type accounted for the variations in fungal pathogen community composition, with species identity and mycorrhizal type showing dominant effects. The relative importance of different community assembly processes, mainly, homogeneous selection and drift, varied with plant species identity. Interestingly, functional traits associated with acquisitive resource-use strategy tended to promote the relative importance of homogeneous selection, while traits associated with conservative resource-use strategy showed converse effect. Drift showed the opposite relationships with functional traits compared with homogeneous selection. Notably, the relative importance of different community assembly processes was not structured by plant phylogeny. Drift was stronger in the pathogen community for ectomycorrhizal plants with more conservative traits, suggesting the predominant role of stochastic gain and loss in the community assembly.DiscussionOur work demonstrates the determinants of root-associated fungal pathogens, addressing the important roles of plant species identity and plant mycorrhizal type. Furthermore, we explored the community assembly mechanisms of root-associated pathogens and stressed the determinant roles of functional traits, especially leaf phosphorus content (LP), root nitrogen content (RN) and root tissue density (RTD), at species and mycorrhizal type levels, offering new perspectives on the microbial dynamics underlying ecosystem functioning.
Realized genomic selection across generations in a reciprocal recurrent selection breeding program of Eucalyptus hybrids
Authors: Simiqueli Guilherme Ferreira , Resende Rafael Tassinari , Takahashi Elizabete Keiko , de Sousa João Edesio , Grattapaglia Dario 
Published: October 2023

IntroductionGenomic selection (GS) experiments in forest trees have largely reported estimates of predictive abilities from cross-validation among individuals in the same breeding generation. In such conditions, no effects of recombination, selection, drift, and environmental changes are accounted for. Here, we assessed the effectively realized predictive ability (RPA) for volume growth at harvest age by GS across generations in an operational reciprocal recurrent selection (RRS) program of hybrid Eucalyptus.MethodsGenomic best linear unbiased prediction with additive (GBLUP_G), additive plus dominance (GBLUP_G+D), and additive single-step (HBLUP) models were trained with different combinations of growth data of hybrids and pure species individuals (N = 17,462) of the G1 generation, 1,944 of which were genotyped with ~16,000 SNPs from SNP arrays. The hybrid G2 progeny trial (HPT267) was the GS target, with 1,400 selection candidates, 197 of which were genotyped still at the seedling stage, and genomically predicted for their breeding and genotypic values at the operational harvest age (6 years). Seedlings were then grown to harvest and measured, and their pedigree-based breeding and genotypic values were compared to their originally predicted genomic counterparts.ResultsGenomic RPAs ≥0.80 were obtained as the genetic relatedness between G1 and G2 increased, especially when the direct parents of selection candidates were used in training. GBLUP_G+D reached RPAs ≥0.70 only when hybrid or pure species data of G1 were included in training. HBLUP was only marginally better than GBLUP. Correlations ≥0.80 were obtained between pedigree and genomic individual ranks. Rank coincidence of the top 2.5% selections was the highest for GBLUP_G (45% to 60%) compared to GBLUP_G+D. To advance the pure species RRS populations, GS models were best when trained on pure species than hybrid data, and HBLUP yielded ~20% higher predictive abilities than GBLUP, but was not better than ABLUP for ungenotyped trees.DiscussionWe demonstrate that genomic data effectively enable accurate ranking of eucalypt hybrid seedlings for their yet-to-be observed volume growth at harvest age. Our results support a two-stage GS approach involving family selection by average genomic breeding value, followed by within-top-families individual GS, significantly increasing selection intensity, optimizing genotyping costs, and accelerating RRS breeding.
Simple cryopreservation protocol for Luffa pollen: enhancing breeding efficiency
Authors: Nagar Arvind , Gowthami Ravi , Sureja Amish Kumar , Munshi Anilabha Das , Verma Manjusha , Singh Awani Kumar , Mallick Niharika , Singh Jogendra , Chander Subhash , Shankar Muthusamy , Pathania Pooja , Rajkumar Subramani 
Published: October 2023

This study aimed to develop a long-term pollen storage protocol for Luffa species (L. acutangula, L. cylindrica, L. echinata, and L. graveolens) and assess its potential for crop improvement. The optimal medium for in vitro pollen germination varied by species, with Brewbaker and Kwack (BK) medium with 10% sucrose suitable for L. acutangula, L. cylindrica, and L. echinata, and BK medium with 3% sucrose ideal for L. graveolens. Overestimation in staining tests compared to in vitro pollen germination was observed. The best results for cryopreservation were achieved with desiccation periods of 20, 30, and 40 min, maintaining moisture content between 14.04% and 18.55%. Pollen viability was negatively correlated with storage temperature (25, 4, and −20°C) and duration. Cryopreserved pollen at −196°C exhibited the highest viability over a prolonged period (2 months) and was comparable to fresh pollen in terms of germination, ovule fertilization, and fruit and seed set. This study presents a simple and reproducible pollen cryopreservation protocol applicable across Luffa species, facilitating long-term storage and its use in crop improvement efforts.
Comparative transcriptome provides insights into gene regulation network associated with the resistance to Fusarium wilt in grafted wax gourd Benincasa hispida
Authors: Zhu Baibi , Li Chunqiang , Wang Min , Chen Jianjun , Hu Yanping , Huang Wenfeng , Wang Huifang 
Published: October 2023

IntroductionWilt is a soil-borne disease caused by Fusarium that has become a serious threat to wax gourd production. Disease-resistant graft wax gourds are an effective treatment for Fusarium wilt. However, there are few reports on the defense mechanism of graft wax gourd against wilt diseases.MethodsIn the present study, disease and growth indices were compared between grafted and original wax gourds after infection with Fusarium. High level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. RNA-seq was performed to identify the differentially expressed genes (DEGs) between the adjacent treatment time points in the grafted and original wax gourds, respectively. Then a comparative temporal analysis was performed and a total of 1,190 genes were identified to show different gene expression patterns between the two wax gourd groups during Fusarium infection.Result and discussionHere, high level of disease resistance was observed in the grafted wax gourd, with a lower disease index and low impacts on growth after infection. The DEG number was higher in grafted group than original group, and the enriched functional categories and pathways of DEGs were largely inconsistent between the two groups. These genes were enriched in multiple pathways, of which the mitogen-activated protein kinase (MAPK) signaling pathway enhanced the early defense response, and cutin, suberin, and wax biosynthesis signaling pathways enhanced surface resistance in grafted wax gourd in comparison to original group. Our study provides insights into the gene regulatory mechanisms underlying the resistance of grafted wax gourds to Fusarium wilt infection, which will facilitate the breeding and production of wilt-resistant rootstocks.
Risks of passive use of social network sites in youth athletes: a moderated mediation analysis
Authors: Zhang Weipeng , Jiang Feng , Zhu Yuanjiao , Zhang Qiang 
Published: October 2023

BackgroundWith the popularity of social media platforms, the use of social networks challenges the well-being and mental health of athletes.MotivationDespite ongoing scholarly discussions about the effects of passive use of social network sites, few studies have examined the relationship between the passive use of social network sites and mental health in young athletes from a social comparison perspective.HypothesisTo address this research gap, we draw on the social comparison and developmental systems theories to explore the mediating effect of upward social comparison on passive social network site use and mental health, as well as the moderating effects of positive psychological capital.MethodsWe analyzed data about 350 young athletes from professional Chinese sports universities.ResultsAs predicted, passive use of social network sites by young athletes increased anxiety (β = 0.26, p &lt; 0.001) and decreased subjective well-being (β = −0.35, p &lt; 0.001). Upward social comparisons had positive (β = 0.22, p &lt; 0.001) and negative (β = −0.34, p &lt; 0.001) mediating effects in passive social network site use and anxiety/subjective well-being. Positive psychological capital played a moderating effect between upward social comparison and anxiety (β = −0.28, p &lt; 0.001), and subjective well-being (β = 0.24, p &lt; 0.001); the moderated mediation effect was also supported.ConclusionOur study informs the current research by highlighting the importance of upward social comparison as a critical mechanism and positive psychological capital as a boundary condition. We suggest actively maintaining and enhancing positive psychological capital to mitigate the adverse effects of upward social comparison.