bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China
Authors: Liu Ying , Fu Bisheng , Zhang Qiaofeng , Cai Jin , Guo Wei , Zhai Wenling , Wu Jizhong 
Published: July 2024

Abstract
Background
Wheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.

Results
To understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.

Conclusions
A core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.
Integrated transcriptome and microRNA analysis reveals molecular responses to high-temperature stress in the liver of American shad (Alosa sapidissima)
Authors: Liu Ying , Liang Zhengyuan , Li Yulin , Zhu Wenbin , Feng Bingbing , Xu Wei , Fu Jianjun , Wei Panpan , Luo Mingkun , Dong Zaijie 
Published: July 2024

Abstract
Background
Fish reproduction, development and growth are directly affected by temperature, investigating the regulatory mechanisms behind high temperature stress is helpful to construct a finer molecular network. In this study, we systematically analyzed the transcriptome and miRNA information of American shad (Alosa sapidissima) liver tissues at different cultivation temperatures of 24 ℃ (Low), 27 ℃ (Mid) and 30 ℃ (High) based on a high-throughput sequencing platform.

Results
The results showed that there were 1594 differentially expressed genes (DEGs) and 660 differentially expressed miRNAs (DEMs) in the LowLi vs. MidLi comparison group, 473 DEGs and 84 DEMs in the MidLi vs. HighLi group, 914 DEGs and 442 DEMs in the LowLi vs. HighLi group. These included some important genes and miRNAs such as calr, hsp90b1, hsp70, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p. The DEGs were mainly enriched in the protein folding, processing and export pathways of the endoplasmic reticulum; the target genes of the DEMs were mainly enriched in the focal adhesion pathway. Furthermore, the association analysis revealed that the key genes were mainly enriched in the metabolic pathway. Interestingly, we found a significant increase in the number of genes and miRNAs involved in the regulation of heat stress during the temperature change from 24 °C to 27 °C. In addition, we examined the tissue expression characteristics of some key genes and miRNAs by qPCR, and found that calr, hsp90b1 and dre-miR-125b-2-3p were significantly highly expressed in the liver at 27 ℃, while novel-m0481-5p, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p had the highest expression in the heart at 30℃. Finally, the quantitative expression trends of 10 randomly selected DEGs and 10 DEMs were consistent with the sequencing data, indicating the reliability of the results.

Conclusions
In summary, this study provides some fundamental data for subsequent in-depth research into the molecular regulatory mechanisms of A. sapidissima response to heat stress, and for the selective breeding of high temperature tolerant varieties.
CRISPR-Cas3 and type I restriction-modification team up against blaKPC-IncF plasmid transfer in Klebsiella pneumoniae
Authors: Yang Yang , Zhou Peiyao , Tian Dongxing , Wang Weiwen , Zhou Ying , Jiang Xiaofei 
Published: July 2024

Abstract
Objective
We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks.

Methods
932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems.

Results
We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity.

Conclusions
Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.
Trunk distortion weakens the tree productivity revealed by half-sib progeny determination of Pinus yunnanensis
Authors: Li Zhongmu , Gao Chengjie , Che Fengxian , Li Jin , Wang Lu , Cui Kai 
Published: July 2024

AbstractTwisted trunks are not uncommon in trees, but their effects on tree growth are still unclear. Among coniferous tree species, the phenomenon of trunk distortion is more prominent in Pinus yunnanensis. To expand the germplasm of genetic resources, we selected families with excellent phenotypic traits to provide material for advanced generation breeding. The progeny test containing 93 superior families (3240 trees) was used as the research material. Phenotypic measurements and estimated genetic parameters (family heritability, realistic gain and genetic gain) were performed at 9, 15, and 18 years of age, respectively. The genetic evaluation yielded the following results (1) The intra-family variance component of plant height (PH) was greater than that of the inter-family, while the inter-family variance components of other traits (diameter at breast height (DBH), crown diameter (CD), height under branches (HUB), degree of stem-straightness (DS)) were greater than that of the intra-family, indicating that there was abundant variation among families and potential for selection. (2) At half rotation period (18 years old), there was a significant correlation among the traits. The proportion of trees with twisted trunks (level 1–3 straightness) reached 48%. The DS significantly affected growth traits, among which PH and DBH were the most affected. The volume loss rate caused by twisted trunk was 18.06-56.75%, implying that trunk distortion could not be completely eliminated after an artificial selection. (3) The influence of tree shape, crown width, and trunk on volume increased, and the early-late correlation between PH, DBH and volume was extremely significant. The range of phenotypic coefficient of variation, genetic variation coefficient and family heritability of growth traits (PH, DBH, and volume) were 44.29-127.13%, 22.88-60.87%, and 0.79–0.83, respectively. (4) A total of 21 superior families were selected by the method of membership function combined with independent selection. Compared with the mid-term selection (18 years old), the accuracy of early selection (9 years old) reached 77.5%. The selected families’ genetic gain and realistic gain range were 5.79-19.82% and 7.12-24.27%, respectively. This study can provide some useful reference for the breeding of coniferous species.
Severe CSF immune cell alterations in cryptococcal meningitis gradually resolve during antifungal therapy
Authors: Dambietz Christine , Heming Michael , Brix Tobias J. , Schulte-Mecklenbeck Andreas , Tepasse Phil-Robin , Gross Catharina C. , Trebicka Jonel , Wiendl Heinz , Meyer zu Hörste Gerd 
Published: July 2024

Abstract
Cryptococcal meningitis (CM) is a severe fungal disease in immunocompromised patients affecting the central nervous system (CNS). Host response and immunological alterations in the cerebrospinal fluid (CSF) after invasion of Cryptococcus neoformans to the central nervous system have been investigated before but rigorous and comprehensive studies examining cellular changes in the CSF of patients with cryptococccal meningitis are still rare. We retrospectively collected CSF analysis and flow cytometry data of CSF and blood in patients with CM (n = 7) and compared them to HIV positive patients without meningitis (n = 13) and HIV negative healthy controls (n = 7). Within the group of patients with CM we compared those with HIV infection (n = 3) or other immunocompromised conditions (n = 4). Flow cytometry analysis revealed an elevation of natural killer cells and natural killer T cells in the CSF and blood of HIV negative patients with CM, pointing to innate immune activation in early stages after fungal invasion. HIV positive patients with CM exhibited stronger blood-CSF-barrier disruption. Follow-up CSF analysis over up to 150 days showed heterogeneous cellular courses in CM patients with slow normalization of CSF after induction of antifungal therapy.
Growth charts for children aged 6–17 years in Shanxi, China: comparison with other cities of China and WHO
Authors: Hou Guoqiang , Li Kunkun , Cao Wenjun , Tao Mengmeng , Tian Wei , Chang Ruimin 
Published: July 2024

Abstract
Background
Growth charts are an important method for evaluating a child’s health, growth, and nutritional status. It is essential to monitor the growth of children and adolescents using growth charts.

Objectives
To present body mass index (BMI)-for-age references reflecting children’s growth in Shanxi. We also compare our new data with growth references of other cities of China and World Health Organization (WHO) growth standards.

Methods
A stratified cluster random sampling method was used to recruit 5461 children and adolescents aged 6–17 years. Height and weight were measured and BMI was calculated. The LMS method was used to calculate the percentile values of body mass index by sex and age. Smoothed BMI-for-age growth curves were presented for both sexes and compared with reference data from other cities of China and WHO.

Results
BMI centiles increased with age but with different patterns in both boys and girls. The centile curves from the 3rd to the 50th had a slight increase, while a sharp increase was seen from 11 to 17 years in boys and from 6 to 14 years in girls in the higher centiles. In comparison with other cities of China, the values for the 50th percentile are higher than those reported for children from China 2009, Shanghai, Changsha and China 2010 in both sexes. In comparison with WHO growth references, Chinese girls and boys had higher values in all percentiles, whereas curves of girls look roughly the same. The medians for BMI in Shanxi increase linearly from 6 to 17 years in boys.

Conclusions
The BMI percentiles of children aged 6–17 years in Shanxi differed significantly from the growth reference curves of other cities of China and WHO. Recommending the provision of BMI reference curves for local children and adolescents to assess their growth and development and monitor their nutritional status.
Early detection of overweight and obesity in children provides a scientific basis for the prevention and control of overweight and obesity in children.
Experiences from patients in mental healthcare accessing their electronic health records: results from a cross-national survey in Estonia, Finland, Norway, and Sweden
Authors: Fagerlund A.J. , Bärkås Annika , Kharko A. , Blease C.R. , Hagström J. , Huvila I. , Hörhammer I. , Kane B. , Kristiansen E. , Kujala S. , Moll J. , Rexhepi H. , Scandurra I. , Simola S. , Soone H. , Wang B. , Åhlfeldt R.M. , Hägglund M. , Johansen M.A. 
Published: July 2024

Abstract
Background
Patients’ online record access (ORA) enables patients to read and use their health data through online digital solutions. One such solution, patient-accessible electronic health records (PAEHRs) have been implemented in Estonia, Finland, Norway, and Sweden. While accumulated research has pointed to many potential benefits of ORA, its application in mental healthcare (MHC) continues to be contested. The present study aimed to describe MHC users’ overall experiences with national PAEHR services.

Methods
The study analysed the MHC-part of the NORDeHEALTH 2022 Patient Survey, a large-scale multi-country survey. The survey consisted of 45 questions, including demographic variables and questions related to users’ experiences with ORA. We focused on the questions concerning positive experiences (benefits), negative experiences (errors, omissions, offence), and breaches of security and privacy. Participants were included in this analysis if they reported receiving mental healthcare within the past two years. Descriptive statistics were used to summarise data, and percentages were calculated on available data.

Results
6,157 respondents were included. In line with previous research, almost half (45%) reported very positive experiences with ORA. A majority in each country also reported improved trust (at least 69%) and communication (at least 71%) with healthcare providers. One-third (29.5%) reported very negative experiences with ORA. In total, half of the respondents (47.9%) found errors and a third (35.5%) found omissions in their medical documentation. One-third (34.8%) of all respondents also reported being offended by the content. When errors or omissions were identified, about half (46.5%) reported that they took no action. There seems to be differences in how patients experience errors, omissions, and missing information between the countries. A small proportion reported instances where family or others demanded access to their records (3.1%), and about one in ten (10.7%) noted that unauthorised individuals had seen their health information.

Conclusions
Overall, MHC patients reported more positive experiences than negative, but a large portion of respondents reported problems with the content of the PAEHR. Further research on best practice in implementation of ORA in MHC is therefore needed, to ensure that all patients may reap the benefits while limiting potential negative consequences.
Nutritional status and dietary intake among Nigerian adolescent: a systematic review
Authors: Abubakar Hadiza Abdullahi , Shahril Mohd Razif , Mat Sumaiyah 
Published: July 2024

Abstract
Introduction
The prevailing nutritional conditions and the triple challenge of malnutrition faced by adolescents have adverse consequences for both the present and future generations’ health and nutrition. Summarizing the available research on the nutritional status and dietary habits of adolescents in Nigeria is crucial.

Objective
This study aims to systematically evaluate available literature on the nutritional status of adolescent aged 10 to 19years in Nigeria.

Methodology
A systematic search using PRISMA guideline was conducted. Three electronic databases were searched i.e., PubMed, Web of Science and Scopus using specific terms and keywords for online articles published between 2013 and 2023. After applying specified inclusion and exclusion criteria, 51 articles were selected for data extraction, synthesis and quality assessment.

Results
Of the 51 included studies, 78.4% were conducted in the Southern Nigeria, 11.8% in the Northern Nigeria and 9.8% included both regions. The prevalence of overweight ranged between 0.8 and 31% and obesity ranged between 0.1 and 14%. The prevalence of thinness, stunting and underweight ranged between 3 and 31%, 0.4 to 41.6%, 0.3 to 73.3% respectively. The review also identified an inadequate intake of essential nutrients including iron, zinc, calcium, vitamin A, C, D, niacin, thiamin, riboflavin, cobalamin, and folate, with vitamin A deficiency prevalence ranges from 44 to 96%. The dietary patterns were characterized by a high consumption of cereals grains and starchy foods, low animal proteins, fast-food with soft drinks, and limited consumption of fruits and vegetables along with meal skipping.

Conclusion
These findings portray a complex picture of the nutritional challenges faced by this demographic group, highlighting both undernutrition and overnutrition, poor eating behaviour and micronutrient deficiency as significant concerns. The review revealed regional disparities in research representation, with a concentration of studies in Southern Nigeria. This highlights the importance of directing research efforts toward the northern regions, where the prevalence of nutritional issues is equally severe, but less studied.

Systematic review registration number
PROSPERO CRD42023481095.
Period poverty, reuse needs, and depressive symptoms among refugee menstruators in Jordan’s camps: a cross-sectional study
Authors: Muhaidat Nadia , Karmi Joud Al , Karam Abdulrahman M. , Abushaikha Farah , Alshrouf Mohammad Ali 
Published: July 2024

Abstract
Background
Period poverty is a significant issue that impacts the physical and psychological well-being of menstruators worldwide which can further contribute to poor mental health outcomes. For menstruators living in refugee camps, access to menstrual hygiene products is often limited or non-existent, leading to increased anxiety, shame, and embarrassment. Therefore, this study aimed to assess the prevalence of the period poverty and to comprehensively analyze the association between period poverty, reusing menstrual products, and depressive symptoms among menstruators living in refugee camps in Jordan.

Methods
A cross-sectional study surveyed refugee menstruators living in camps in Jordan, aged post-menarche to pre-menopause. Data collection included socio-demographics, menstrual practices, and depressive symptoms using the Patient Health Questionnaire (PHQ-9). Period poverty was assessed through affordability and frequency of struggles with menstrual products. Chi-squared test, independent sample t-test, One Way Analysis of variance (ANOVA) followed by Post hoc, and logistic regression models were used in the analysis.

Results
The study included a diverse sample of 386 refugee menstruators living in camps in Jordan (mean age 32.43 ± 9.95, age range 13–55). Period poverty was highly prevalent, with 42.0% reporting monthly struggles to afford menstrual products, and 71.5% reusing menstrual products. Univariate analysis revealed that experiencing period poverty was significantly associated with a younger age of marriage, increased number of children, lower education level, lower mother and father education levels, unemployment, decreased monthly income, absence of health insurance, lower reuse need score, and increased PHQ-9 score (p < 0.05). Menstruators experiencing monthly period poverty were 2.224 times more likely to report moderate to severe depression compared to those without period poverty (95% CI 1.069–4.631, P = 0.033).

Conclusion
This study highlights a significant association between period poverty and depressive symptoms among refugee menstruators in living in camps in Jordan, as high rates of period poverty were associated with a 2.2-fold increased likelihood of reporting moderate to severe depression. Addressing period poverty in refugee settings is crucial for mitigating depression risks and enhancing overall well-being.
Optimization of the extraction process for Shenshou Taiyi powder based on Box-Behnken experimental design, standard relation, and FAHP-CRITIC methods
Authors: Jiang Mengcheng , Qiu Zhidong , Diao Yuanyuan , Shi Yuwen , Liu Weipeng , Li Na , Jia Ailing 
Published: July 2024

Abstract
Background
Ancient classic prescription play a crucial role in the preservation and advancement of traditional Chinese medicine (TCM) theories. They represent a significant milestone in the ongoing development and transmission of TCM knowledge and practices and are considered one of the breakthroughs in the development of TCM inheritance. In the process of developing ancient classic prescriptions, many problems may still arise in ensuring quality consistency between traditional methods and modern production processes, among which the extraction process poses major challenges. This paper introduces a practical approach extracting an ancient classic prescription using a modern extraction process. The technique is demonstrated through the study of the extraction process of Shenshou Taiyi powder (STP).

Methods
This study focuses on optimising the STP extraction process to ensure consistency in the quality of the product obtained through ancient and modern processes using the standard relation and fuzzy analytic hierarchical process (FAHP) and criteria importance through intercriteria correlation (CRITIC) method integrated weights combined with the Box-Behnken response surface test. Using the contents of rosmarinic acid, isoimperatorin, puerarin, as well as the extract yield and fingerprint similarity as evaluation indexes of STP, the Box-Behnken response surface method was employed to examine the varying extraction parameters, including water addition ratio, extraction duration, and number of extractions. The weighted coefficients for each parameter were calculated by combining the benchmark correlation and FAHP-CRITIC method, deriving a comprehensive score.

Results
The optimal extraction process for STP consisted of a two extractions, each using at a tenfold quantity of water, performed for one hour. Process verification across three separate batches yielded a comprehensive score of 94.7, with a relative standard deviation of 0.76%.

Conclusions
The application of the Box-Behnken response surface method combined with standard relation and FAHP-CRITIC approach proved to be stable and feasible for optimising the extraction process of STP.