bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics
Authors: Shah Labiba Riyaz , Ahmed Nazeer , Hussain Khursheed , Mansoor Sheikh , Khan Tamana , Khan Imran , Narayan Sumati , Afroza Baseerat , Murtaza Imtiyaz , Shikari Asif Bashir , Bhat Basharat , Masoodi Khalid Z. 
Published: January 2024

AbstractThe cold stress susceptibility of tomato (Solanum lycopersicum) curtails its cultivation, with significant impact in temperate regions and on cropping seasons. To unravel genomic regions responsible for cold stress resilience, a diverse set of fifty genotypes encompassing cultivated, wild species, and landraces were genotyped using genotyping-by-sequencing. Over two years and six trials employing both early and late sowing, these lines were evaluated. Illumina-based next-generation sequencing produced up to 3 million reads per sample from individually sequenced library pools. The Tassel pipeline yielded 10,802 variants, subsequently filtered to 3,854 SNPs for genome-wide association analysis (GWAS). Employing clustering methods (population structure) via TASSEL, SNPhylo, and Kinship matrix, the fifty genotypes clustered into four distinct gene pools. The GWAS for cold tolerance in tomato integrated key traits including yield. Using six independent phenotypic datasets representing various environments, the study identified 4,517 significant marker-trait associations for cold tolerance traits. Notably, pivotal variations (> 10%) in cold stress tolerance, particularly proline content, were linked to marker-trait associations. Additionally, 5,727 significant marker-trait associations for yield and yield-related traits were unveiled, shedding light on fruit yield and directly associated attributes. The investigation pinpointed 685 candidate genes across all examined traits, including 60 genes associated with biological processes within these genomic regions. Remarkably, 7 out of the 60 genes were directly linked to abiotic stress tolerance, functioning as stress-responsive genes either directly or indirectly. The identified genes, particularly those associated with stress response, could hold the key to enhancing cold tolerance and overall crop productivity in tomato cultivation.
Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce
Authors: Hung Tin Hang , Wu Ernest T. Y. , Zeltiņš Pauls , Jansons Āris , Ullah Aziz , Erbilgin Nadir , Bohlmann Joerg , Bousquet Jean , Birol Inanc , Clegg Sonya M. , MacKay John J. 
Published: January 2024

AbstractConifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and βglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of βglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of βglu-1 and Ugt5 genes. We observed very large copy numbers of βglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of βglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.
Genome-wide identification and expression characterization of the GH3 gene family of tea plant (Camellia sinensis)
Authors: Wang Xinge , Jia Chunyu , An Lishuang , Zeng Jiangyan , Ren Aixia , Han Xin , Wang Yiqing , Wu Shuang 
Published: January 2024

AbstractTo comprehensively understand the characteristics of the GH3 gene family in tea plants (Camellia sinensis), we identified 17 CsGH3 genes and analyzed their physicochemical properties, phylogenetic relationships, gene structures, promoters, and expression patterns in different tissues. The study showed that the 17 CsGH3 genes are distributed on 9 chromosomes, and based on evolutionary analysis, the CsGH3 members were divided into three subgroups. Gene duplication analysis revealed that segmental duplications have a significant impact on the amplification of CsGH3 genes. In addition, we identified and classified cis-elements in the CsGH3 gene promoters and detected elements related to plant hormone responses and non-biotic stress responses. Through expression pattern analysis, we observed tissue-specific expression of CsGH3.3 and CsGH3.10 in flower buds and roots. Moreover, based on predictive analysis of upstream regulatory transcription factors of CsGH3, we identified the potential transcriptional regulatory role of gibberellin response factor CsDELLA in CsGH3.14 and CsGH3.15. In this study, we found that CsGH3 genes are involved in a wide range of activities, such as growth and development, stress response, and transcription. This is the first report on CsGH3 genes and their potential roles in tea plants. In conclusion, these results provide a theoretical basis for elucidating the role of GH3 genes in the development of perennial woody plants and offer new insights into the synergistic effects of multiple hormones on plant growth and development in tea plants.
Enhancing nitrogen use efficiency and yield of maize (Zea mays L.) through Ammonia volatilization mitigation and nitrogen management approaches
Authors: Dawar Khadim , Dawar Atif , Tariq Muhammad , Mian Ishaq Ahmad , Muhammad Asim , Farid Laiba , Khan Shadman , Khan Kashif , Fahad Shah , Danish Subhan , Al-Ghamdi Abdullah Ahmed , Elshikh Mohamed S. , Tahzeeb-ul-Hassan Muhammad 
Published: January 2024

AbstractManagement of nitrogen (N) fertilizer is a critical factor that can improve maize (Zea mays L.) production. On the other hand, high volatilization losses of N also pollute the air. A field experiment was established using a silt clay soil to examine the effect of sulfur-coated urea and sulfur from gypsum on ammonia (NH3) emission, N use efficiency (NUE), and the productivity of maize crop under alkaline calcareous soil. The experimental design was a randomized complete block (RCBD) with seven treatments in three replicates: control with no N, urea150alone (150 kg N ha−1), urea200alone (200 kg N ha−1), urea150 + S (60 kg ha−1 S from gypsum), urea200 + S, SCU150(sulfur-coated urea) and SCU200. The results showed that the urea150 + S and urea200 + S significantly reduced the total NH3by (58 and 42%) as compared with the sole application urea200. The NH3emission reduced further in the treatment with SCU150and SCU200by 74 and 65%, respectively, compared to the treatment with urea200. The maize plant biomass, grain yield, and total N uptake enhanced by 5–14%, 4–17%, and 7–13, respectively, in the treatments with urea150 + s and urea200 + S, relative to the treatment with urea200alone. Biomass, grain yield, and total N uptake further increased significantly by 22–30%, 25–28%, and 26–31%, respectively, in the treatments with SCU150and SCU200, relative to the treatment with urea200alone. The applications of SCU150enhanced the nitrogen use efficiency (NUE) by (72%) and SCU200by (62%) respectively, compared with the sole application of urea200alone. In conclusion, applying S-coated urea at a lower rate of 150 kg N ha−1compared with a higher rate of 200 kg N ha−1may be an effective way to reduce N fertilizer application rate and mitigate NH3emission, improve NUE, and increase maize yield. More investigations are suggested under different soil textures and climatic conditions to declare S-coated urea at 150 kg N ha−1as the best application rate for maize to enhance maize growth and yield.
Bayesian Mendelian randomization with an interval causal null hypothesis: ternary decision rules and loss function calibration
Authors: Zou Linyi , Fazia Teresa , Guo Hui , Berzuini Carlo 
Published: January 2024

AbstractWe enhance the Bayesian Mendelian Randomization (MR) framework of Berzuini et al. (Biostatistics 21(1):86–101, 2018) by allowing for interval null causal hypotheses, where values of the causal effect parameter that fall within a user-specified interval of “practical equivalence” (ROPE) (Kruschke, Adv Methods Pract Psychol Sci 1(2):270–80, 2018) are regarded as equivalent to “no effect”. We motivate this move in the context of MR analysis. In this approach, the decision over the hypothesis test is taken on the basis of the Bayesian posterior odds for the causal effect parameter falling within the ROPE. We allow the causal effect parameter to have a mixture prior, with components corresponding to the null and the alternative hypothesis. Inference is performed via Markov chain Monte Carlo (MCMC) methods. We speed up the calculations by fitting to the data a simpler model than the intended, "true", one. We recover a set of samples from the “true” posterior distribution by weighted importance resampling of the MCMC-generated samples. From the final samples we obtain a simulation consistent estimate of the desired posterior odds, and ultimately of the Bayes factor for the interval-valued null hypothesis, $$H_0$$H0, vs$$H_1$$H1. In those situations where the posterior odds is neither large nor small enough, we allow for anuncertainoutcome of the test decision, thereby moving to a ternary decision logic. Finally, we present an approach to calibration of the proposed method via loss function. We illustrate the method with the aid of a study of the causal effect of obesity on risk of juvenile myocardial infarction based on a unique prospective dataset.
Health estimate differences between six independent web surveys: different web surveys, different results?
Authors: Schnell Rainer , Klingwort Jonas 
Published: January 2024

AbstractMost general population web surveys are based on online panels maintained by commercial survey agencies. Many of these panels are based on non-probability samples. However, survey agencies differ in their panel selection and management strategies. Little is known if these different strategies cause differences in survey estimates. This paper presents the results of a systematic study designed to analyze the differences in web survey results between agencies. Six different survey agencies were commissioned with the same web survey using an identical standardized questionnaire covering factual health items. Five surveys were fielded at the same time. A calibration approach was used to control the effect of demographics on the outcome. Overall, the results show differences between probability and non-probability surveys in health estimates, which were reduced but not eliminated by weighting. Furthermore, the differences between non-probability surveys before and after weighting are larger than expected between random samples from the same population.
A comparison between different patient groups for diabetes management during phases of the COVID-19 pandemic: a retrospective cohort study in Ontario, Canada
Authors: Senthinathan A. , Tu K. , Stephenson E. , O’Neill B. , Lipscombe L. , Ji C. , Butt D. A. , Apajee J. , Train A. , Crampton N. 
Published: January 2024

Abstract
Background
With the onset of the COVID-19 pandemic and the large uptake in virtual care in primary care in Canada, the care of patients with type 2 diabetes has been greatly affected. This includes decreased in-person visits, laboratory testing and in-person assessments such as blood pressure (BP). No studies have investigated if these changes persisted with pandemic progression, and it is unclear if shifts impacted patient groups uniformly. The purpose of this paper was to examine changes in diabetes care pre, early, and later pandemic across different patient groups.

Methods
A repeated cross-sectional design with an open cohort was used to investigate diabetes care in adults with type 2 diabetes for a 6-month interval from March 14 to September 13 over three consecutive years: 2019 (pre-pandemic period), 2020 (early pandemic period), and 2021 (later pandemic period). Data for this study were abstracted from the University of Toronto Practice-Based Research Network (UTOPIAN) Data Safe Haven, a primary care electronic medical records database in Ontario, Canada. Changes in diabetes care, which included primary care total visits, in-person visits, hemoglobin A1c (HbA1c) testing, and BP measurements were evaluated across the phases of the pandemic. Difference in diabetes care across patient groups, including age, sex, income quintile, prior HbA1c levels, and prior BP levels, were assessed.

Results
A total of 39,401 adults with type 2 diabetes were included in the study. Compared to the 6-month pre-pandemic period, having any in-person visits decreased significantly early pandemic (OR = 0.079 (0.076–0.082)), with a partial recovery later pandemic (OR = 0.162 (95% CI: 0.157–0.169). Compared to the pre-pandemic period, there was a significant decrease early pandemic for total visits (OR = 0.486 (95% CI: 0.470–0.503)), HbA1c testing (OR = 0.401 (95% CI: 0.389–0.413)), and BP measurement (OR = 0.121 (95% CI: 0.116–0.125)), with partial recovery later pandemic.

Conclusions
All measures of diabetes care were substantially decreased early pandemic, with a partial recovery later pandemic across all patient groups. With the increase in virtual care due to the COVID-19 pandemic, diabetes care has been negatively impacted over 1-year after pandemic onset.
The association between C-reactive protein levels and the risk of kidney stones: a population-based study
Authors: Liang Dan , Liu Chang , Yang Mei 
Published: January 2024

Abstract
Objectives
The relationship between C-reactive protein (CRP) and the risk of developing kidney stones is unclear, and we aimed to assess the association between CRP and kidney stones in US adults.

Methods
We used data from NHANES 2007–2010, and we excluded participants who were under 18 years of age and lacked data on CRP and kidney stones. Finally, we included a total of 11,033 participants and performed weighted multivariate regression analysis and subgroup analysis to assess the independent relationship between CRP and kidney stones.

Results
The mean prevalence of kidney stones among the participants was 9.8%. Notably, as CRP levels increased, the prevalence of kidney stones exhibited a corresponding rise across quartiles (Kidney stones: Quartile 1: 7.59%; Quartile 2: 8.77%; Quartile 3: 9.64%; Quartile 4: 10.89%). CRP was positively associated with the risk of kidney stones (Model 1: OR = 1.09, 95% CI: 1.01–1.18, p = 0.03; Model 2: OR = 1.09, 95% CI: 1.00–1.18, p = 0.03, Model 3: OR = 1.14, 95%CI: 1.02–1.26, p = 0.04). Participants in the highest CRP quartile experienced a 69% increased risk of kidney stones compared to those in the lowest quartile (OR = 1.64, 95% CI: 1.04–2.59, p = 0.03). Notably, interaction tests revealed that gender, BMI, diabetes, hypertension, CKD and smoking or alcohol consumption status did not significantly influence the association between CRP and kidney stones.

Conclusions
Our findings reveal a significant association between higher CRP levels and an increased risk of kidney stones. In clinical practice, heightened awareness of CRP as a potential biomarker could aid in risk assessment and management strategies for kidney stone patients.
Exploring the link between self-management of migraine and emotional wellbeing: a cross-sectional study of community-dwelling migraine sufferers
Authors: Filzmoser Nicola , Webber Iman , Kerr Gabriele , Alaa Aos , El Asmar Marie Iine , Karki Manisha , Riboli-Sasco Eva , El-Osta Austen 
Published: January 2024

Abstract
Background
Globally, an estimated 14% of adults live with migraine disease which impacts their physical, emotional and social wellbeing. To target the disease comprehensively, research recommends a multidisciplinary approach to migraine management. Yet, at present, migraine management primarily centers around pharmaceutical treatments. The aim of this study was to investigate the extent to which emotional awareness could influence the uptake of self-care behaviours of community-dwelling adults with migraine.

Methods
A cross-sectional online survey explored personal experiences with migraine disease and strategies or behaviours to manage migraine attacks. Chi-squared tests were used to investigate differences in ratings of migraine prevention and management strategies between users and non-users of the strategies. Univariable logistic regressions were used to assess the effectiveness of self-care behaviours to manage or prevent migraine attacks.

Results
We surveyed 170 community-dwelling adults with migraine in the United Kingdom, Austria, Germany and the United States. Most (85%) respondents had experienced migraine for over five years, where 42% of attacks usually lasted several days. Whereas we did not differentiate between diagnosis by a neurologist or self-diagnosis, the most common diagnoses in the cohort were migraine without aura (38.9%) and migraine with aura (29%). Staying hydrated was the most popular preventative strategy (87%), 70.2% used prescription medication and 64.9% changed their diet and/or supplements. Almost all ( 92.4%) respondents stated that their mood or emotions could trigger their migraine attacks. Keeping a headache or mood diary was the lowest-rated prevention strategy and was rated as "probably ineffective" or causing "no change" in preventing migraine attacks. Over a third (39.7%) kept track of their physical wellbeing and symptoms. Reasons stated for tracking symptoms included to identify triggers (65.8%), show reports to a healthcare professional (59.6%), understand when they must take medication (48.1%), track improvements (67.3%) or deteriorations (67.3%).

Conclusions
Migraine management is dominated by pharmaceutical management for acute pain attacks and lifestyle changes for managing migraine long-term. Perception of the effectiveness of those techniques is high, whereas perception of interventions that target the emotional or psychological components of chronic pain management (keeping a mood diary, and mental health support) is mixed. There exists a gap between the recommended biopsychosocial approach and the current state of migraine management.

Graphical Abstract
Preimplantation genetic testing in couples with balanced chromosome rearrangement: a four-year period real world retrospective cohort study
Authors: Zhou Fan , Ren Jun , Li Yutong , Keqie Yuezhi , Peng Cuiting , Chen Han , Chen Xinlian , Liu Shanling 
Published: January 2024

Abstract
Background
Couples with balanced chromosome rearrangement (BCR) are at high risk of recurrent miscarriages or birth defects due to chromosomally abnormal embryos. This study aimed to provide real-world evidence of the euploidy rate of blastocysts from couples with BCR using preimplantation genetic testing (PGT) and to guide pretesting genetic counselling.

Methods
A continuous four-year PGT data from couples with BCR were retrospectively analyzed. Biopsied trophectoderm cells were amplified using whole genome amplification, and next-generation sequencing was performed to detect the chromosomal numerical and segmental aberrations. Clinical data and molecular genetic testing results were analyzed and compared among the subgroups.

Results
A total of 1571 PGT cycles with 5942 blastocysts were performed chromosomal numerical and segmental aberrations detection during the four years. Of them, 1034 PGT cycles with 4129 blastocysts for BCR couples were included; 68.96% (713/1034) PGT cycles had transferable euploid embryos. The total euploidy rate of blastocysts in couples carrying the BCR was 35.29% (1457/4129). Couples with complex BCR had euploid blastocyst rates similar to those of couples with non-complex BCR (46.15% vs. 35.18%, P > 0.05). Chromosome inversion had the highest chance of obtaining a euploid blastocyst (57.27%), followed by Robertsonian translocation (RobT) (46.06%), and the lowest in reciprocal translocation (RecT) (30.11%) (P < 0.05). Couples with males carrying RobT had higher rates of euploid embryo both in each PGT cycles and total blastocysts than female RobT carriers did, despite the female age in male RobT is significant older than those with female RobT (P < 0.05). The proportions of non-carrier embryos were 52.78% (95/180) and 47.06% (40/85) in euploid blastocysts from couples with RecT and RobT, respectively (P > 0.05). RecT had the highest proportion of blastocysts with translocated chromosome-associated abnormalities (74.23%, 1527/2057), followed by RobT (54.60%, 273/500) and inversion (30.85%, 29/94) (P < 0.05).

Conclusions
In couples carrying BCR, the total euploidy rate of blastocysts was 35.29%, with the highest in inversion, followed by RobT and RecT. Even in couples carrying complex BCR, the probability of having a transferable blastocyst was 46.15%. Among the euploid blastocysts, the non-carrier ratios in RecT and RobT were 52.78% and 47.06%, respectively. RecT had the highest proportion of blastocysts with translocated chromosome-associated abnormalities.
Early newborn bathing practice and its determinants among postpartum women in Ethiopia: a systematic review and meta-analysis
Authors: Eyeberu Addis , Getachew Tamirat , Kebad Ayenachew , Debella Adera 
Published: January 2024

Abstract
Background
Early baby bathing has a major negative impact on the newborn's health. Even though early newborn bathing has numerous detrimental effects on neonatal health, evidence has provided little attention on the current level of practice. Furthermore, there is a dearth of data regarding the overall effects of early newborn bathing in Ethiopia, which would be helpful to program and policy designers. This meta-analysis aimed to ascertain the level of early bathing practice and its determinants among postpartum women in Ethiopia.

Methods
All articles were searched from the Web of Sciences, CINAHL (EBOSCO), Science Direct, MEDLINE, PubMed, Google Scholar, and Google websites from inception to October 10, 2023. The meta-analysis was performed using Stata version 18. The summary estimates with 95% CI were estimated using the random effect model with the Der Simonian Liard method. Heterogeneity was explored using Galbraith plot, Cochrane Q statistics, I2 statistics, and test of theta. To deal with the observed heterogeneity, subgroup analysis, sensitivity analysis, and meta-regression were done.

Results
This meta-analysis included a total of 2787 postpartum women. The pooled level of early newborn bathing practice among postpartum women in Ethiopia was 55% [95% CI: 38–71]. Based on subgroup analysis by region, the highest level of early newborn bathing practice was among studies conducted in the Afar region which was 73% (95% CI: 69–77). There is a significant association between maternal level of education and early newborn bathing practice among postpartum women in Ethiopia (AOR = 0.51, 95% CI: 0.24, 0.78).

Conclusions
In this meta-analysis, the overall estimate illustrates that more than half of postpartum women practice early newborn bathing in Ethiopia. Maternal level of education was significantly associated with early newborn bathing practice. Thus, both the government and all the concerned stakeholders should take coordinated action to boost information dissemination and awareness creation among postpartum women thereby reducing the practice of early newborn bathing and alleviating consequences of early newborn bathing.