bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotype-based association mapping of genomic regions associated with Zymoseptoria tritici resistance using 217 diverse wheat genotypes
Authors: Radecka-Janusik Magdalena , Piechota Urszula , Piaskowska Dominika , Słowacki Piotr , Bartosiak Sławomir , Czembor Paweł 
Published: July 2024

Abstract
Background
Septoria tritici blotch (STB) is considered to be one of the most destructive foliar wheat diseases and is caused by Zymoseptoria tritici. The yield losses are severe and in Northwestern Europe can reach up to 50%. The efficacy of fungicides is diminishing due to changes in the genetic structure of the pathogen. Therefore, resistance breeding is the most effective strategy of disease management. Recently, genome-wide association studies (GWAS) have become more popular due to their robustness in dissecting complex traits, including STB resistance in wheat. This was made possible by the use of large mapping populations and new sequencing technologies. High-resolution mapping benefits from historical recombination and greater allele numbers in GWAS.

Results
In our study, 217 wheat genotypes of diverse origin were phenotyped against five Z. tritici isolates (IPO323, IPO88004, IPO92004, IPO86036 and St1-03) and genotyped on the DArTseq platform. In polytunnel tests two disease parameters were evaluated: the percentage of leaf area covered by necrotic lesions (NEC) and the percentage of leaf area covered by lesions bearing pycnidia (PYC). The disease escape parameters heading date (Hd) and plant height (Ht) were also measured. Pearson’s correlation showed a positive effect between disease parameters, providing additional information. The Structure analysis indicated four subpopulations which included from 28 (subpopulation 2) to 79 genotypes (subpopulation 3). All of the subpopulations showed a relatively high degree of admixture, which ranged from 60% of genotypes with less than 80% of proportions of the genome attributed to assigned subpopulation for group 2 to 85% for group 4. Haplotype-based GWAS analysis allowed us to identify 27 haploblocks (HBs) significantly associated with analysed traits with a p-value above the genome-wide significance threshold (5%, which was –log10(p) > 3.64) and spread across the wheat genome. The explained phenotypic variation of identified significant HBs ranged from 0.2% to 21.5%. The results of the analysis showed that four haplotypes (HTs) associated with disease parameters cause a reduction in the level of leaf coverage by necrosis and pycnidia, namely: Chr3A_HB98_HT2, Chr5B_HB47_HT1, Chr7B_HB36_HT1 and Chr5D_HB10_HT3.

Conclusions
GWAS analysis enabled us to identify four significant chromosomal regions associated with a reduction in STB disease parameters. The list of valuable HBs and wheat varieties possessing them provides promising material for further molecular analysis of resistance loci and development of breeding programmes.
Discovery of crucial cytokines associated with deep vein thrombus formation by protein array analysis
Authors: Wang Qitao , Chi Junyu , Zeng Wenjie , Xu Fang , Li Xin , Wang Zhen , Qu Ming 
Published: July 2024

Abstract
Background
Expanding the number of biomarkers is imperative for studying the etiology and improving venous thromboembolism prediction. In this study, we aimed to identify promising biomarkers or targeted therapies to improve the detection accuracy of early-stage deep vein thrombosis (DVT) or reduce complications.

Methods
Quantibody Human Cytokine Antibody Array 440 (QAH-CAA-440) was used to screen novel serum-based biomarkers for DVT/non-lower extremity DVT (NDVT). Differentially expressed proteins in DVT were analyzed using bioinformatics methods and validated using a customized array. Diagnostic accuracy was calculated using receiver operating characteristics, and machine learning was applied to establish a biomarker model for evaluating the identified targets. Twelve targets were selected for validation.

Results
Cytokine profiling was conducted using a QAH-CAA-440 (RayBiotech, USA) quantimeter array. Cross-tabulation analysis with Venn diagrams identified common differential factors, leading to the selection of 12 cytokines for validation based on their clinical significance. These 12 biomarkers were consistent with the results of previous array analysis: FGF-6 (AUC = 0.956), Galectin-3 (AUC = 0.942), EDA-A2 (AUC = 0.933), CHI3L1 (AUC = 0.911), IL-1 F9 (AUC = 0.898), Dkk-4 (AUC = 0.88), IG-H3 (AUC = 0.876), IGFBP (AUC = 0.858), Gas-1 (AUC = 0.858), Layilin (AUC = 0.849), ULBP-2 (AUC = 0.813)and FGF-9 (AUC = 0.773). These cytokines are expected to serve as biomarkers, targets, or therapeutic targets to differentiate DVT from NDVT.

Conclusions
EDA-A2, FGF-6, Dkk-4, IL-1 F9, Galentin-3, Layilin, Big-h3, CHI3L1, ULBP-2, Gas-1, IGFBP-5, and FGF-9 are promising targets for DVT diagnosis and treatment.
Evaluating strategies to recruit health researchers to participate in online survey research
Authors: Stevens Elizabeth R. , Cleland Charles M. , Shunk Amelia , El Shahawy Omar 
Published: July 2024

Abstract
Background
Engaging researchers as research subjects is key to informing the development of effective and relevant research practices. It is important to understand how best to engage researchers as research subjects.

Methods
A 24 factorial experiment, as part of a Multiphase Optimization Strategy, was performed to evaluate effects of four recruitment strategy components on participant opening of an emailed survey link and survey completion. Participants were members of three US-based national health research consortia. A stratified simple random sample was used to assign potential survey participants to one of 16 recruitment scenarios. Recruitment strategy components were intended to address both intrinsic and extrinsic sources of motivation, including: $50 gift, $1,000 raffle, altruistic messaging, and egoistic messaging. Multivariable generalized linear regression analyses adjusting for consortium estimated component effects on outcomes. Potential interactions among components were tested. Results are reported as adjusted odds ratios (aOR) with 95% confidence intervals (95% CI).

Results
Surveys were collected from June to December 2023. A total of 418 participants were included from the consortia, with final analytical sample of 400 eligible participants. Out of the final sample, 82% (341) opened the survey link and 35% (147) completed the survey. Altruistic messaging increased the odds of opening the survey (aOR 2.02, 95% CI: 1.35–2.69, p = 0.033), while egoistic messaging significantly reduced the odds of opening the survey (aOR 0.56, 95%CI 0.38–0.75, p = 0.08). The receipt of egoistic messaging increased the odds of completing the survey once opened (aOR 1.81, 95%CI: 1.39–2.23, p < 0.05). There was a significant negative interaction effect between the altruistic appeal and egoistic messaging strategies for survey completion outcome. Monetary incentives did not a have a significant impact on survey completion.

Conclusion
Intrinsic motivation is likely to be a greater driver of health researcher participation in survey research than extrinsic motivation. Altruistic and egoistic messaging may differentially impact initial interest and survey completion and when combined may lead to improved rates of recruitment, but not survey completion. Further research is needed to determine how to best optimize message content and whether the effects observed are modified by survey burden.
Dietary characteristics of urban community-dwelling older adults with low muscle mass: the bunkyo health study: a cross-sectional study
Authors: Muroga Yukiko , Kaga Hideyoshi , Bui Thu Hien , Sugimoto Mari , Someya Yuki , Kakehi Saori , Tabata Hiroki , Naito Hitoshi , Abudurezake Abulaiti , Shi Huicong , Otsuka Hikaru , Yoshizawa Yasuyo , Kawamori Ryuzo , Watada Hirotaka , Tamura Yoshifumi 
Published: July 2024

Abstract
Background
With the aging of the population worldwide, extending healthy life expectancy is an urgent issue. Muscle mass has been reported to be associated with physical independence and longevity. This study aimed to investigate the characteristics of food intake in urban community-dwelling older adults with low muscle mass.

Methods
This cross-sectional study used baseline data from the Bunkyo Health Study, which included 1618 urban community-dwelling older adults aged 65–84 years. All participants underwent measurement of body composition using bioelectrical impedance analysis and evaluation of nutrient and food intake using the brief-type self-administered diet history questionnaire. Participants were stratified by sex and divided into robust or low skeletal muscle mass index (SMI) groups according to the Asian Working Group for Sarcopenia criteria to compare differences in nutrient and food intake.

Results
The mean age and body mass index were 73.1 ± 5.4 years and 22.6 ± 3.1 kg/m2, respectively. The prevalence of low SMI was 31.1% in men and 43.3% in women. In men, all food intake, including total energy intake, was similar between the low SMI group and the robust group. In women, the low SMI group had less total energy intake, and consumed lower amounts of energy-producing nutrients (protein, fat, and carbohydrates), but there were only small differences in the intake of specific foods.

Conclusions
There were sex differences in food intake characteristics between urban community-dwelling older adults with low SMI and those who were robust. Advising women to increase their energy intake may be important in preventing muscle loss, and further research is needed in men.
Risk factors for residual fibroglandular breast tissue following a mastectomy - an overview and retrospective cohort study
Authors: Christine Deutschmann , Christian Singer F. , Ricarda Korbatits , Christine Kraus , Daphne Gschwantler-Kaulich , Carmen Leser , Alaa Marzogi , Baltzer Pascal A.T. , Thomas Helbich H. , Georg Pfeiler , Paola Clauser 
Published: July 2024

Abstract
Background
Residual fibroglandular breast tissue (RFGT) following a mastectomy is associated with the remaining of occult breast cancer at the time of mastectomy as well as an increased local recurrence risk thereafter. Despite its oncologic implications, data on measures to prevent RFGT are lacking. Therefore, in a first step knowledge of risk factors for RFGT is of uttermost importance in order to allow identification of patients at risk and subsequently adaption of the surgical treatment and potentially prevention of RFGT a priori.

Methods
We performed a systematic literature review in PubMed using the MESH terms [residual fibroglandular breast tissue], [residual breast tissue], [mastectomy] and [risk factor] followed by a retrospective data analysis including all patients with a mastectomy treated at the Department of Obstetrics and Gynecology of the Medical University of Vienna, Austria, between 01.01.2015 and 26.02.2020 in order to identify risk factors of RFGT following a mastectomy. The primary aim of the study was to assess a potential difference in RFGT volume between the different types of mastectomy. The secondary objectives of the study were to identify other potential risk factors for RFGT as well as to compare the skin and subcutaneous fat tissue thickness pre- to postoperatively.

Results
Significantly higher RFGT volumes were observed following a nipple-sparing mastectomy (NSM) compared to a skin-sparing mastectomy (SSM) and radical mastectomy (RME) (p < .001). Furthermore, RFGT volume was significantly associated with the variables: reconstruction (p = .012), acellular dermal matrix (ADM) or mesh (p = .031), patient age (p = .022), preoperative fibroglandular tissue (FGT) volume (p = .012) and preoperative whole breast volume (including the skin envelope and nipple-areola-complex) (p = .030). The reduction in the postoperative compared to preoperative skin envelope thickness measured medially and laterally reached statistical significance in the NSM-cohort (medial p < .001, lateral p = .001) and showed a numerical difference in the RME and SSM-cohort.

Conclusion
Mastectomy type, reconstruction, ADM or mesh, patient age, preoperative FGT volume and whole breast volume were identified as risk factors for RFGT in univariable analysis. The observed reduction in the post- compared to preoperative skin envelope thickness should be avoided considering the known associated increase in risk for ischemic complications.
Assessment of imaging risks for recurrence after stereotactic radiosurgery for brain metastases (IRRaS-BM)
Authors: Roh Yun Hwa , Park Ji Eun , Park Seo Young , Cho Young Hyun , Kim Young-Hoon , Song Sang Woo , Yoon Shinkyo , Kim Ho Sung 
Published: July 2024

Abstract
Background
The identification of viable tumors and radiation necrosis after stereotactic radiosurgery (SRS) is crucial for patient management. Tumor habitat analysis involving the grouping of similar voxels can identify subregions that share common biology and enable the depiction of areas of tumor recurrence and treatment-induced change. This study aims to validate an imaging biomarker for tumor recurrence after SRS for brain metastasis by conducting tumor habitat analysis using multi-parametric MRI.

Methods
In this prospective study (NCT05868928), patients with brain metastases will undergo multi-parametric MRI before SRS, and then follow-up MRIs will be conducted every 3 months until 24 months after SRS. The multi-parametric MRI protocol will include T2-weighted and contrast-enhanced T1-weighted imaging, diffusion-weighted imaging, and dynamic susceptibility contrast imaging. Using k-means voxel-wise clustering, this study will define three structural MRI habitats (enhancing, solid low-enhancing, and nonviable) on T1- and T2-weighted images and three physiologic MRI habitats (hypervascular cellular, hypovascular cellular, and nonviable) on apparent diffusion coefficient maps and cerebral blood volume maps. Using RANO-BM criteria as the reference standard, via Cox proportional hazards analysis, the study will prospectively evaluate associations between parameters of the tumor habitats and the time to recurrence. The DICE similarity coefficients between the recurrence site and tumor habitats will be calculated.

Discussion
The tumor habitat analysis will provide an objective and reliable measure for assessing tumor recurrence from brain metastasis following SRS. By identifying subregions for local recurrence, our study could guide the next therapeutic targets for patients after SRS.

Trial registration
This study is registered at ClinicalTrials.gov (NCT05868928).
The relationship between quality of life and some mental problems in women with gestational diabetes mellitus (GDM): a cross-sectional study
Authors: Nazarpour Soheila , Simbar Masoumeh , Kiani Zahra , Khalaji Neda , Khorrami Khargh Mobina , Naeiji Zahra 
Published: July 2024

Abstract
Background
Women with medical problems during pregnancy, including women with Gestational Diabetes Mellitus (GDM), experience an increased prevalence of mental health disorders which can affect their quality of life. This study aimed to assess the relationship between GDM-related quality of life and depression, anxiety, and stress.

Methods
This analytical cross-sectional study was performed on 150 women with GDM. The participants were selected using a multi-stage sampling including quota and then randomized method from maternal care centers affiliated with Shahid Beheshti University of Medical Sciences, Tehran-Iran. The data were collected using a personal information questionnaire, the GDM-related quality of life questionnaire (GDMQoL-36), and the depression, anxiety, and stress scale (DASS). The data were analyzed using SPSS-23 software and statistical tests of coefficient Spearman’s correlation, t-test, analysis of variance, and multiple linear regression.

Results
The mean ± SD score for the GDM-related quality of life and the DASS scale were 55.51 ± 8.87 and 27.12 ± 19.43%, respectively. Different degrees of depression, anxiety, and stress were present in 40, 61.3, and 42% of women, respectively. The total score of GDM-related quality of life had a significant negative correlation with the total score of DASS and the scores of the subscales including depression, anxiety, and stress (P < 0.001). There were significant correlations between the total score of GDM-related quality of life with age, BMI, length of marriage, educational level of the woman and her spouse, the occupation of the woman and her spouse, income, and economic class of the family. Multiple linear regression revealed that depression, education, and job are predictive factors for GDM-related quality of life.

Conclusion
GDM-related quality of life is related to some mental disorders. Therefore, it is important to consider the mental health promotion of pregnant women with GDM in future prenatal health programs to improve their quality of life. This also shows the importance of integrating mental health promotion strategies to enhance the quality of life of pregnant women with GDM.
Factors associated with a better treatment efficacy among psoriasis patients: a study based on decision tree model and logistic regression in Shanghai, China
Authors: Shen Fanlingzi , Duan Zhen , Li Siyuan , Gao Zhongzhi , Zhang Rui , Gao Xiangjin , Li Bin , Wang Ruiping 
Published: July 2024

Abstract
Background
Many effective therapies for psoriasis are being applied in clinical practice in recent years, however, some patients still can’t achieve satisfied effect even with biologics. Therefore, it is crucial to identify factors associated with the treatment efficacy among psoriasis patients. This study aims to explore factors influencing the treatment efficacy of psoriasis patients based on decision tree model and logistic regression.

Methods
We implemented an observational study and recruited 512 psoriasis patients in Shanghai Skin Diseases Hospital from 2021 to 2022. We used face-to-face questionnaire interview and physical examination to collect data. Influencing factors of treatment efficacy were analyzed by using logistic regression, and decision tree model based on the CART algorithm. The receiver operator curve (ROC) was plotted for model evaluation and the statistical significance was set at P < 0.05.

Results
The 512 patients were predominately males (72.1%), with a median age of 47.5 years. In this study, 245 patients achieved ≥ 75% improvement in psoriasis area and severity index (PASI) score in week 8 and was identified as treatment success (47.9%). Logistic regression analysis showed that patients with senior high school and above, without psoriasis family history, without tobacco smoking and alcohol drinking had higher percentage of treatment success in patients with psoriasis. The final decision tree model contained four layers with a total of seventeen nodes. Nine classification rules were extracted and five factors associated with treatment efficacy were screened, which indicated tobacco smoking was the most critical variable for treatment efficacy prediction. Model evaluation by ROC showed that the area under curve (AUC) was 0.79 (95%CI: 0.75 ~ 0.83) both for logistic regression model (0.80 sensitivity and 0.69 specificity) and decision tree model (0.77 sensitivity and 0.73 specificity).

Conclusion
Psoriasis patients with higher education, without tobacco smoking, alcohol drinking and psoriasis family history had better treatment efficacy. Decision tree model had similar predicting effect with the logistic regression model, but with higher feasibility due to the nature of simple, intuitive, and easy to understand.
Attitudes toward and preparedness for lung transplantation among individuals with cystic fibrosis in the era of highly effective modulators
Authors: Burdis Nora , Kapnadak Siddhartha G. , Bartlett Lauren E. , McElvaney Oliver , Milinic Tijana , Wai Travis Hee , Lange Allison V. , Reid Nick , Dunitz Jordan M. , Billings Joanne L. , Pilewski Joseph M. , Saavedra Milene , Goss Christopher H. , Hartzler Andrea L. , Ramos Kathleen J. 
Published: July 2024

Abstract
Background
Outcomes for individuals with cystic fibrosis (CF) have improved due to highly effective modulator therapy (HEMT). However, lung transplant (LTx) remains an important treatment for people with advanced lung disease. This study assessed attitudes and knowledge about LTx in the HEMT era.

Methods
All patients from the University of Washington CF clinic were surveyed March 25-May 30, 2020. Questions addressed self-rated LTx preparedness and knowledge, as well as barriers and facilitators to discussing LTx. Demographic and clinical data were extracted from the electronic health record.

Results
There were 159/224 (71%) responses. Respondents had a median forced expiratory volume in one second (FEV1) of 70%, and 142 (89%) were on modulatory therapy. One hundred thirteen (71%) respondents felt that it was moderately or very important to be prepared to make decisions about LTx, though only 56 (35%) felt moderately or very prepared. Only 83 (30%) and 47 (52%) participants correctly answered questions about life expectancy and improved quality of life after LTx, respectively. Respondents with Medicaid insurance less frequently answered questions correctly. The most common barriers to discussing LTx were fear of being a burden on loved ones for 58 respondents (36%) and cost of LTx for 46 (29%). Most participants (94%) trusted their CF doctor, and 75% of participants selected trust as a facilitator for LTx discussions.

Conclusions
Many individuals with CF, especially those with lower socioeconomic status, lacked knowledge and did not feel very prepared for decisions about LTx. Earlier education and discussions about LTx represent an area for improvement in CF care.
The effect of USM-IAM-based counselling vs standard counselling on insulin adherence, FBS and HbA1c among patients with uncontrolled type 2 diabetes mellitus (T2DM): a randomised controlled trial
Authors: Zainudin Aida Maziha , Rasool Aida Hanum Ghulam , Yaacob Najib Majdi , Muhamad Rosediani , Mohamed Wan Mohd Izani Wan 
Published: July 2024

AbstractBackgroundMany patients with T2DM on insulin are not optimally controlled despite receiving standard diabetes education counselling. Poor insulin adherence may be a contributing factor. We developed and evaluated a new module [Universiti Sains Malaysia-Insulin Adherence Module (USM-IAM)] on insulin-treated patients with poorly controlled diabetes.MethodsEligibility criteria are those diagnosed with T2DM, aged between 18 and 65 years, with HbA1c between 8 and 15% and on insulin therapy for 1 year. Patients were randomly allocated to receive either the USM-IAM-based counselling or the standard counselling (SC) at baseline and the second visit. Patients were instructed to adjust insulin doses based on blood glucose levels. Outcomes were changes in adherence score, FBS and HbA1c levels from baseline to 3 months and baseline to sixth month.ResultsNinety patients were randomised to each group. The baseline sociodemographic and clinical characteristics were homogenous among groups. Ninety patients were analysed for each group. Adherence score changes between baseline to 3 months were − 8.30 (− 11.47, − 5.14) in USM-IAM-based counselling group (USM-IAM) and − 7.64 (− 10.89, − 4.40) in standard counselling group (SCG), between baseline to sixth month were − 10.21 (− 13.40, − 7.03) in USM-IAM and − 10.79 (− 14.64, − 6.97) in SCG. FBS changes between baseline to 3 months were 1.374 (0.25, 2.50) in USM-IAM and 0.438 (− 0.66, 1.54) in SCG, and between baseline to sixth month were 1.713 (0.473, 2.95) in USM-IAM and 0.998 (− 0.02, 2.01) in SCG. HbA1c changes between baseline to 3 months were 1.374 (0.25, 2.50) in USM-IAM and 0.547 (0.12, 0.98) in SCG, and between baseline to sixth month were 1.03 (0.65, 1.41) in USM-IAM and 0.617 (0.20, 1.03) in SCG. Between-subjects effects for all outcomes were not statistically significant.ConclusionBoth groups had significant improvements in adherence score and HbA1c with time, with higher improvement in patients receiving the USM-IAM. FBS reductions were significant in the intervention group but not in the control group.Trial registrationThis study protocol is registered withClicaltrials.govwith ID NCT05125185 dated 17th November 2021.