bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond urinalysis: evaluation of various clinical and laboratory reflex criteria to warrant urine culture collection in the emergency department
Authors: Alateeq Nada M. , Mohammed Manal B. , Alsubaie Albandari T. , Alshehri Amal A. , Attallah Dalya , Agabawi Salem , Thabit Abrar K. 
Published: June 2024

Abstract
Background
Clinical criteria are essential for diagnosing urinary tract infections (UTIs) followed by urine testing, including urinalysis (UA). No study has evaluated the potential related factors that may guide the appropriate collection of urine cultures. Therefore, we aimed to assess the factors that may guide the appropriate collection of urine cultures.

Methods
This was a case-control study of patients for whom a urine culture and a UA were ordered in the emergency department (ED) between February 2018 and December 2022. The cases included patients with positive cultures, whereas the controls included patients without growth. Patients were excluded if they were pregnant, underwent any urological procedure, received antibiotics within 3 days before ED presentation, or before culture collection.

Results
Of the 263 patients, 123 had growth and 140 did not have growth in urine cultures. In the univariate analysis, female gender, urinary symptoms, urinary white blood cell (WBC) count > 5 cells/hpf, and nitrite in urine were significantly associated with growth (P < 0.05). However, only female gender (aOR, 1.86; 95% CI, 1.06–3.24), urinary WBC count > 5 cells/hpf (aOR, 4.60; 95% CI, 2.21–9.59), and positive nitrite in urine (aOR, 21.90; 95% CI, 2.80–171.00) remained significant in the multivariable analysis. These factors also remained significant in the subgroup of patients with urinary symptoms, except for the female gender.

Conclusion
A high urinary WBC count and positive nitrite in UA should be utilized as a guide to collect urine culture, particularly in female patients, to limit the unnecessary ordering of urine culture in the ED. These factors can be used as evidence-based UA reflex criteria as an antimicrobial stewardship intervention.
Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium
Authors: Stege Paul B. , Schokker Dirkjan , Harders Frank , Kar Soumya K. , Stockhofe Norbert , Perricone Vera , Rebel Johanna M. J. , de Jong Ingrid C. , Bossers Alex 
Published: June 2024

AbstractModern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.
Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding
Authors: Li Xiaochang , Lan Fangren , Chen Xiaoman , Yan Yiyuan , Li Guangqi , Wu Guiqin , Sun Congjiao , Yang Ning 
Published: June 2024

Abstract
Background
The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding.

Results
In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight.

Conclusions
In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.
The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L
Authors: Kulesza Evelyn , Thomas Patrick , Prewitt Sarah F. , Shalit-Kaneh Akiva , Wafula Eric , Knollenberg Benjamin , Winters Noah , Esteban Eddi , Pasha Asher , Provart Nicholas , Praul Craig , Landherr Lena , dePamphilis Claude , Maximova Siela N. , Guiltinan Mark J. 
Published: June 2024

Abstract
Background
Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.

Results
We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3–5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues.

Conclusion
The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
Soil salinity regulates spatial-temporal heterogeneity of seed germination and seedbank persistence of an annual diaspore-trimorphic halophyte in northern China
Authors: Wang Zhaoren , Baskin Jerry M , Baskin Carol C , Liu Guofang , Ye Xuehua , Yang Xuejun , Huang Zhenying 
Published: June 2024

Abstract
Background and aims
Seed heteromorphism is a plant strategy that an individual plant produces two or more distinct types of diaspores, which have diverse morphology, dispersal ability, ecological functions and different effects on plant life history traits. The aim of this study was to test the effects of seasonal soil salinity and burial depth on the dynamics of dormancy/germination and persistence/depletion of buried trimorphic diaspores of a desert annual halophyte Atriplex centralasiatica.

Methods
We investigated the effects of salinity and seasonal fluctuations of temperature on germination, recovery of germination and mortality of types A, B, C diaspores of A. centralasiatica in the laboratory and buried diaspores in situ at four soil salinities and three depths. Diaspores were collected monthly from the seedbank from December 2016 to November 2018, and the number of viable diaspores remaining (not depleted) and their germinability were determined.

Results
Non-dormant type A diaspores were depleted in the low salinity “window” in the first year. Dormant diaspore types B and C germinated to high percentages at 0.3 and 0.1 mol L-1 soil salinity, respectively. High salinity and shallow burial delayed depletion of diaspore types B and C. High salinity delayed depletion time of the three diaspore types and delayed dormancy release of types B and C diaspores from autumn to spring. Soil salinity modified the response of diaspores in the seedbank by delaying seed dormancy release in autum and winter and by providing a low-salt concentration window for germination of non-dormant diaspores in spring and early summer.

Conclusions
Buried trimorphic diaspores of annual desert halophyte A. centralasiatica exhibited diverse dormancy/germination behavior in respond to seasonal soil salinity fluctuation. Prolonging persistence of the seedbank and delaying depletion of diaspores under salt stress in situ primarily is due to inhibition of dormancy-break. The differences in dormancy/germination and seed persistence in the soil seedbank may be a bet-hadging strategy adapted to stressful temporal and spatial heterogeneity, and allows A. centralasiatica to persist in the unpredictable cold desert enevironment.
Microplastics increase cadmium absorption and impair nutrient uptake and growth in red amaranth (Amaranthus tricolor L.) in the presence of cadmium and biochar
Authors: Roy Rana , Hossain Akram , Sultana Shirin , Deb Biplob , Ahmod Md. Moudud , Sarker Tanwne 
Published: June 2024

AbstractMicroplastic (MP) pollution in terrestrial ecosystems is gaining attention, but there is limited research on its effects on leafy vegetables when combined with heavy metals. This study examines the impact of three MP types—polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS)—at concentrations of 0.02, 0.05, and 0.1% w/w, along with cadmium (Cd) and biochar (B), on germination, growth, nutrient absorption, and heavy metal uptake in red amaranth (Amaranthus tricolor L.). We found that different MP types and concentrations did not negatively affect germination parameters like germination rate, relative germination rate, germination vigor, relative germination vigor, and germination speed. However, they increased phytotoxicity and decreased stress tolerance compared to an untreated control (CK1). The presence of MPs, particularly the PS type, reduced phosphorus and potassium uptake while enhancing Cd uptake. For example, treatments PS0.02CdB, PS0.05CdB, and PS0.1CdB increased Cd content in A. tricolor seedlings by 158%, 126%, and 44%, respectively, compared to the treatment CdB (CK2). Additionally, MP contamination led to reduced plant height, leaf dry matter content, and fresh and dry weights, indicating adverse effects on plant growth. Moreover, the presence of MPs increased bioconcentration factors and translocation factors for Cd, suggesting that MPs might act as carriers for heavy metal absorption in plants. On the positive side, the addition of biochar improved several root parameters, including root length, volume, surface area, and the number of root tips in the presence of MPs, indicating potential benefits for plant growth. Our study shows that the combination of MPs and Cd reduces plant growth and increases the risk of heavy metal contamination in food crops. Further research is needed to understand how different MP types and concentrations affect various plant species, which will aid in developing targeted mitigation strategies and in exploring the mechanisms through which MPs impact plant growth and heavy metal uptake. Finally, investigating the potential of biochar application in conjunction with other amendments in mitigating these effects could be key to addressing MP and heavy metal contamination in agricultural systems.
Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote
Authors: Cheng Shaobo , Su Lihong , Guo Xin , Shao Dalong , Qin Yanmei , Liu Xuanxuan , Chu Qianwen , Zhou Xiaoting , He Zhongqun 
Published: June 2024

Abstract
Background
Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far.

Results
In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine.

Conclusions
These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.
Primary surgical repair of tetralogy of fallot at the Uganda Heart Institute: a ten-year review of 30day mortality and morbidity
Authors: Khainza Rebecca Esther , Oketcho Michael , Aliku Twalib , Namuyonga Judith , Ndagire Emma , Mwambu Tom , Muhoozi Rwakaryebe Mbagga , Obongnyinge Bernard , Tumwebaze Hilda , Mbabazi Nestor , Akech Teddy , Nakato Aisha , Killen Angelline , Ofumbi Geoffrey Oburu , Lwabi Peter , Omagino John , Lubega Sulaiman 
Published: June 2024

Abstract
Background
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease (CHD) worldwide. It accounts for 7% of CHD cases in Uganda and leads to fatal outcomes in the long term without surgery. Surgery is often delayed in developing countries like Uganda due to limited resources.

Objective
This study aimed to determine the early surgical outcomes of patients with TOF who underwent primary intracardiac repair at the Uganda Heart Institute (UHI) and to identify factors associated.

Methodology
This retrospective chart review evaluated outcomes of primary TOF repair patients at UHI from February 2012 to October 2022. Patient outcomes were assessed from surgery until 30 days post-operation.

Results
Out of the 104 patients who underwent primary TOF repair at UHI, records of 88 patients (84.6%) were available for review. Males accounted for 48.9% (n = 43). The median age at the time of operation was 4 years (with an interquartile range of 2.5-8.0 years), ranging from 9 months to 16 years. Genetic syndromes were present in 5/88 (5.7%). These included 2 patients with trisomy 21, 2 with Noonan’s, and 1 with 22q11.2 deletion syndrome. Early postoperative outcomes for patients included: residual ventricular septal defects in 35/88 (39.8%), right ventricular dysfunction in 33/88 (37.5%), residual pulmonary regurgitation in 27/88 (30.7%), residual right ventricular outflow tract obstruction in 27/88 (30.0%), pleural effusion in 24/88 (27.3%), arrhythmias in 24/88(27.3%), post-operative infections in 23/88(26.1%) and left ventricular systolic dysfunction in 9/88 (10.2%). Out of the children who underwent surgery after one year of age, 8% (7 children) died within the first 30 days. There was a correlation between mortality and post-operative ventilation time, cardiopulmonary bypass (CPB) time, aortic cross-clamp time, preoperative oxygen saturations, RV and LV dysfunction and the operating team.

Conclusion
The most frequent outcomes after surgery were residual ventricular septal defects and right ventricular failure. In our study, the 30-day mortality rate following TOF repair was 8%. Deceased patients had lower pre-operative oxygen levels, longer CPB and cross-clamp times, longer post-operative ventilation, RV/LV dysfunction, and were more likely operated by the local team.
The non-invasive serum biomarkers contributes to indicate liver fibrosis staging and evaluate the progress of chronic hepatitis B
Authors: Zeng Shaoxiong , Liu Zhenzhen , Ke Bilun , Zhang Yiwang , Wang Qian , Tan Siwei 
Published: June 2024

Abstract
Background
This study aimed to evaluate the diagnostic abilities of the non-invasive serum biomarkers to predict liver fibrosis staging and evaluate the progress of hepatitis B.

Methods
We enrolled 433 patients with chronic HBV infection had complete medical data available for the study, who underwent percutaneous liver biopsy. The extent of fibrosis was assessed using the modified METAVIR score. The predictive values of the non-invasive serum biomarkers were evaluated by the areas under the receiving operator characteristics curves (AUROCs) with 95% confidence intervals.

Results
The proportion of males with progressive stages of liver fibrosis was relatively larger, and the average age of patients with cirrhosis stages is older than the non-cirrhotic stages. We found PLT, GGT, ALP, TB, FIB4 and GPR to be significantly associated with liver fibrosis in our cohort. GGT showed a sensitivity of 71.4% and specificity of 76.7% in distinguishing cirrhosis (F4) from non-cirrhotic stages (F1-3), with an AUROC of 0.775 (95%CI 0.711–0.840).The AUROCs of the GPR in distinguishing cirrhosis (F4) from non-cirrhotic stages (F1-3) was 0.794 (95%CI 0.734–0.853), but it had a lower sensitivity of 59.2%. Additionally, GGT, FIB4, and GPR could differentiate advanced fibrosis (F3-4) from non-advanced fibrosis (F1-2) among individuals with chronic hepatitis B, with AUROCs of 0.723 (95%CI 0.668–0.777), 0.729 (95%CI 0.675–0.782), and 0.760 (95%CI: 0.709–0.811) respectively.

Conclusions
GGT was a better biomarker to distinguish cirrhosis (F4) from non-cirrhotic stages (F1-3), while GPR was a better biomarker to identify advanced fibrosis (F3-4) and non-advanced fibrosis (F1-2) in patients with chronic hepatitis B.
Recent increase in atypical presentations of invasive meningococcal disease in France
Authors: Taha Samy , Deghmane Ala-Eddine , Taha Muhamed-Kheir 
Published: June 2024

Abstract
Background
Invasive meningococcal disease (IMD) cases declined upon the implementation of non-pharmaceutical interventions (NPI) (social distancing and mask wearing) to control the COVID-19 pandemic but rebounded in 2022 in numbers with genotypical changes of the strains. We explored here associated modifications in the clinical presentations of IMD.

Methods
We conducted a retrospective descriptive study using the Database of the French National Reference Centre for meningococci and Haemophilus influnezae for IMD cases between 2015 and 2022. We scored serogroups, sex, age groups, clinical presentations and clonal complexes of the corresponding patients and isolates.

Findings
Non-meningeal forms of IMD increased significantly upon easing of NPI, such as bacteremic meningococcal pneumonia and bacteremic abdominal forms. They represented 6% and 8% of all IMD forms and were significantly linked to serogroups Y and W respectively, to older adults for bacteremic pneumonia and to young adults for bacteremic abdominal presentations. These forms were significantly associated with more early mortality and clonal complexes 23, 11 and 9316.

Interpretation
The increase in atypical IMD forms may lead to higher burden of IMD due to delayed diagnosis and management. Updating prevention may be needed through by adapting the current vaccination strategies to epidemiological changes.