bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments
Authors: Tessema Biructawit B. , Raffo Miguel A. , Guo Xiangyu , Svane Simon F. , Krusell Lene , Jensen Jens Due , Ruud Anja Karine , Malinowska Marta , Thorup-Kristensen Kristian , Jensen Just 
Published: January 2024

AbstractBackgroundIn drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors.ResultsThe estimated heritabilities ($${\widehat{h}}^{2}$$h^2) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ($$GCV$$GCV) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest$$GCV$$GCVobserved for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2.ConclusionsThe significant$$GCV$$GCVand the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments.
Assessing data analysis techniques in a high-throughput meiosis-like induction detection system
Authors: Cook Tanner M. , Biswas Eva , Dutta Somak , Aboobucker Siddique I. , Hazinia Sara , Lübberstedt Thomas 
Published: January 2024

Abstract
Background
Strategies to understand meiotic processes have relied on cytogenetic and mutant analysis. However, thus far in vitro meiosis induction is a bottleneck to laboratory-based plant breeding as factor(s) that switch cells in crops species from mitotic to meiotic divisions are unknown. A high-throughput system that allows researchers to screen multiple candidates for their meiotic induction role using low-cost microfluidic devices has the potential to facilitate the identification of factors with the ability to induce haploid cells that have undergone recombination (artificial gametes) in cell cultures.

Results
A data analysis pipeline and a detailed protocol are presented to screen for plant meiosis induction factors in a quantifiable and efficient manner. We assessed three data analysis techniques using spiked-in protoplast samples (simulated gametes mixed into somatic protoplast populations) of flow cytometry data. Polygonal gating, which was considered the “gold standard”, was compared to two thresholding methods using open-source analysis software. Both thresholding techniques were able to identify significant differences with low spike-in concentrations while also being comparable to polygonal gating.

Conclusion
Our study provides details to test and analyze candidate meiosis induction factors using available biological resources and open-source programs for thresholding. RFP (PE.CF594.A) and GFP (FITC.A) were the only channels required to make informed decisions on meiosis-like induction and resulted in detection of cell population changes as low as 0.3%, thus enabling this system to be scaled using microfluidic devices at low costs.
The regulation of plasma gelsolin by DNA methylation in ovarian cancer chemo-resistance
Authors: Manzoor Hafiza Bushra , Asare-Werehene Meshach , Pereira Satyajit Dey , Satyamoorthy Kapaettu , Tsang Benjamin K. 
Published: January 2024

Abstract
Background
Ovarian cancer (OVCA) is the most lethal gynecologic cancer and chemoresistance remains a major hurdle to successful therapy and survival of OVCA patients. Plasma gelsolin (pGSN) is highly expressed in chemoresistant OVCA compared with their chemosensitive counterparts, although the mechanism underlying the differential expression is not known. Also, its overexpression significantly correlates with shortened survival of OVCA patients. In this study, we investigated the methylation role of Ten eleven translocation isoform-1 (TET1) in the regulation of differential pGSN expression and chemosensitivity in OVCA cells.

Methods
Chemosensitive and resistant OVCA cell lines of different histological subtypes were used in this study to measure pGSN and TET1 mRNA abundance (qPCR) as well as protein contents (Western blotting). To investigate the role of DNA methylation specifically in pGSN regulation and pGSN-induced chemoresistance, DNMTs and TETs were pharmacologically inhibited in sensitive and resistant OVCA cells using specific inhibitors. DNA methylation was quantified using EpiTYPER MassARRAY system. Gain-and-loss-of-function assays were used to investigate the relationship between TET1 and pGSN in OVCA chemoresponsiveness.

Results
We observed differential protein and mRNA expressions of pGSN and TET1 between sensitive and resistant OVCA cells and cisplatin reduced their expression in sensitive but not in resistant cells. We observed hypomethylation at pGSN promoter upstream region in resistant cells compared to sensitive cells. Pharmacological inhibition of DNMTs increased pGSN protein levels in sensitive OVCA cells and decreased their responsiveness to cisplatin, however we did not observe any difference in methylation level at pGSN promoter region. TETs inhibition resulted in hypermethylation at multiple CpG sites and decreased pGSN protein level in resistant OVCA cells which was also associated with enhanced response to cisplatin, findings that suggested the methylation role of TETs in the regulation of pGSN expression in OVCA cells. Further, we found that TET1 is inversely related to pGSN but positively related to chemoresponsiveness of OVCA cells.

Conclusion
Our findings broaden our knowledge about the epigenetic regulation of pGSN in OVCA chemoresistance and reveal a novel potential target to re-sensitize resistant OVCA cells. This may provide a future therapeutic strategy to improve the overall OVCA patient survival.
The high impact of zinc chromium oxide nanocombs on development of larvicidal and antimicrobial performance
Authors: Mostafa Wageha A. , Elshanawany Soad A. , Otaif Khadejah D. , khalifa Mona , Elgazzar Elsayed 
Published: January 2024

AbstractZinc chromium oxide (Cr/ZnO, 5wt.%) was prepared by a facile chemical co-precipitation route. The structure, composition, and chemical bonding were analyzed using X-ray diffraction (XRD), Energy dispersive X-ray spectroscopy (EDX), and Fourier-transform infrared spectroscopy (FTIR) indicating that chromium ions were integrated the host framework to form Cr/ZnO nanocomposite. Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM) micrographs showed comb-shaped nanoparticles with an average size 20 nm and large surface area. The energy gap of the thin films was estimated from T% and R% measurements which exhibit a strong optical absorption edge close to the visible spectrum. The insecticidal activity of the synthesized nanocombs againstC. pipienslarvae was evaluated with LC50(30.15 ppm) and LC90(100.22 ppm). Besides, the nanocomposite showed high antibacterial performance against gram-positive bacteria (Bacillus subtilis) and gram-negative bacteria (Proteus vulgaris) with inhibition zones 21.9 and 19 mm, respectively.
Sex-dependent circadian alterations of both central and peripheral clock genes expression and gut–microbiota composition during activity-based anorexia in mice
Authors: Salaün Colin , Courvalet Marine , Rousseau Léna , Cailleux Kévin , Breton Jonathan , Bôle-Feysot Christine , Guérin Charlène , Huré Marion , Goichon Alexis , do Rego Jean-Claude , Déchelotte Pierre , Ribet David , Achamrah Najate , Coëffier Moïse 
Published: January 2024

Abstract
Rationale
Patients with anorexia nervosa (AN) often present sleep disorders and circadian hormonal dysregulation. The role of the microbiota–gut–brain axis in the regulation of feeding behavior has emerged during the last decades but its relationships with the circadian rhythm remains poorly documented. Thus, we aimed to characterize the circadian clock genes expression in peripheral and central tissues in the activity-based anorexia mouse model (ABA), as well as the dynamics of the gut–microbiota composition.

Methods
From day 1 to day 17, male and female C57Bl/6 mice were submitted or not to the ABA protocol (ABA and control (CT) groups), which combines a progressive limited access to food and a free access to a running wheel. At day 17, fasted CT and ABA mice were euthanized after either resting (EoR) or activity (EoA) phase (n = 10–12 per group). Circadian clock genes expression was assessed by RT-qPCR on peripheral (liver, colon and ileum) and central (hypothalamic suprachiasmatic nucleus or SCN) tissues. Cecal bacterial taxa abundances were evaluated by qPCR. Data were compared by two-way ANOVA followed by post-tests.

Results
ABA mice exhibited a lower food intake, a body weight loss and an increase of diurnal physical activity that differ according with the sex. Interestingly, in the SCN, only ABA female mice exhibited altered circadian clock genes expression (Bmal1, Per1, Per2, Cry1, Cry2). In the intestinal tract, modification of clock genes expression was also more marked in females compared to males. For instance, in the ileum, female mice showed alteration of Bmal1, Clock, Per1, Per2, Cry1, Cry2 and Rev-erbα mRNA levels, while only Per2 and Cry1 mRNAs were affected by ABA model in males. By contrast, in the liver, clock genes expression was more markedly affected in males compared to females in response to ABA. Finally, circadian variations of gut–bacteria abundances were observed in both male and female mice and sex-dependent alteration were observed in response to the ABA model.

Conclusions
This study shows that alteration of circadian clock genes expression at both peripheral and central levels occurs in response to the ABA model. In addition, our data underline that circadian variations of the gut–microbiota composition are sex-dependent.
Respiratory particles: from analytical estimates to disease transmission
Authors: Ferreira J. A. , de Oliveira Paula , da Silva P. M. 
Published: January 2024

AbstractRespiratory particles containing infectious pathogens are responsible for a large number of diseases. To define health politics and save lives, it is important to study their transmission mechanisms, namely the path of particles once expelled. This path depends on several driving factors as intrinsic properties of particles, environmental aspects and morphology of the scenario. Following physical arguments and taking into account the results of experimental works, we consider a mathematical drift model for the mixture composed by two phases: air and particles. The relative motion between the two phases is described by a kinematic constitutive relation. We prove the stability of the model for fixed times and establish an a priori estimate for the total number of infectious particles. The upper bound of this estimate exhibits sound physical dependencies on the driving factors, in agreement with the experimental literature and mounting epidemiological evidences. Namely, we establish that the amount of particles expelled and their emission rate can explain why some people are superspreaders. Several numerical simulations illustrate the theoretical results.
Innovative approaches for mycotoxin detection in various food categories
Authors: Boshra Marina H. , El-Housseiny Ghadir S. , Farag Mohammed M. S. , Aboshanab Khaled M. 
Published: January 2024

AbstractMycotoxins (MTs), produced by filamentous fungi, represent a severe hazard to the health of humans and food safety, affecting the quality of various agricultural products. They can contaminate a wide range of foods, during any processing phase before or after harvest. Animals and humans who consume MTs-contaminated food or feed may experience acute or chronic poisoning, which may result in serious pathological consequences. Accordingly, developing rapid, easy, and accurate methods of MTs detection in food becomes highly urgent and critical as a quality control and to guarantee food safety and lower health hazards. In this review, we highlighted and discussed innovative approaches like biosensors, fluorescent polarization, capillary electrophoresis, infrared spectroscopy, and electronic noses for MT identification pointing out current challenges and future directions. The limitations, current challenges, and future directions of conventional detection methods versus innovative methods have also been highlighted and discussed.
Some variants of the hybrid extragradient algorithm in Hilbert spaces
Authors: Arfat Yasir , Kumam Poom , Khan Muhammad Aqeel Ahmad , Seangwattana Thidaporn , Iqbal Zaffar 
Published: January 2024

AbstractThis paper provides convergence analysis of some variants of the hybrid extragradient algorithm (HEA) in Hilbert spaces. We employ the HEA to compute the common solution of the equilibrium problem and split fixed-point problem associated with the finite families of $\Bbbk $
k
-demicontractive mappings. We also incorporate appropriate numerical results concerning the viability of the proposed variants with respect to various real-world applications.
Comparative analysis of COVID-19 and influenza prevalence among Egyptian pilgrims returning from Hajj and Umrah in 2022: epidemiology, clinical characteristics, and genomic sequencing
Authors: Kandeel Amr , Fahim Manal , Deghedy Ola , BahaaEldin Hala , Roshdy Wael H. , Khalifa Mohamed Kamal , Kandeil Ahmed , El Shesheny Rabeh , Naguib Amel , AbdelFatah Mohamad , Afifi Salma , Abdel Ghaffar Khaled 
Published: January 2024

Abstract
Purpose
To describe the changes that occurred in the SARS-CoV-2 and influenza Prevalence, epidemiology, clinical picture, and prevalent genotypes among the Egyptian pilgrims returning from Hajj and Umrah 2022 seasons.

Methods
Pilgrims were contacted at the airport and invited to participate in the survey. Pilgrims who consented were interviewed using a standardized line list that included participant demographics, respiratory symptoms if any, previous COVID-19 infection, influenza vaccination whereas COVID-19 vaccination information were collected from vaccination cards. Participants were asked to provide throat and nasopharyngeal swabs for SARS-CoV-2 and influenza testing using RT-PCR and a subset of isolates were sequenced. Descriptive data analysis was performed to describe the epidemiology and clinical symptoms of SARS-CoV-2 and influenza. Prevalence rates of SARS-CoV-2 and influenza during Hajj were calculated and compared to Umrah surveys using chi2 and t-test with a significance level < 0.05.

Results
Overall, 3,862 Egyptian pilgrims enrolled, their mean age was 50.5 ± 47 years, half of them were > 50 years of age and 58.2% were males. Of them, 384 (9.9%) tested positive for SARS-CoV-2 and 51 (1.3%) for influenza viruses. Prevalence of SARS-CoV-2 infections (vaccine breakthrough) increased significantly between the Umrah and Hajj surveys (6.7% vs. 9.9%, p < 0.001), and variants of the virus varied considerably. Whereas no significant difference was found in influenza prevalence, vaccine coverage and vaccine breakthrough infection rates (11.7 vs. 9.2%, 26.9 vs. 26.8%, and 1.4 vs. 1.1% respectively).

Conclusions
SARS-CoV-2 prevalence among Egyptian pilgrims returning from Hajj in July increased with reduced vaccine effectiveness compared to Umrah in March 2022 suggesting a possible wave of SARS-CoV-2 in the upcoming winter.
Perspectives of healthcare workers on the integration of overdose detection technologies in acute care settings
Authors: Rioux William , Kilby Kyle , Jones Stephanie , Joshi Pamela , Vandenberg Stephanie , Ghosh S. Monty 
Published: January 2024

Abstract
Background
People who use drugs (PWUD) face disproportionately high rates of hospitalizations and patient-initiated discharge (leaving against medical advice), explained by a combination of stigma, withdrawal, judgment, blame, and improper pain management. In addition, evidence has shown that despite abstinence-based policies within healthcare settings, PWUD continue to use their substances in healthcare environments often hidden away from hospital staff, resulting in fatalities. Various novel overdose detection technologies (ODTs) have been developed with early adoption in a few settings to reduce the morbidity and mortality from risky substance use patterns within healthcare environments. Our study aimed to gain the perspectives of healthcare workers across Canada on implementing ODTs within these settings.

Method
We used purposive and snowball sampling to recruit 16 healthcare professionals to participate in semi-structured interviews completed by two evaluators. Interview transcripts were analyzed using thematic analysis to identify key themes and subthemes.

Results
Participants recognized ODTs as a potentially feasible solution for increasing the safety of PWUD in healthcare settings. Our results suggest the mixed ability of these services to decrease stigma and build rapport with PWUD. Participants further highlighted barriers to implementing these services, including pre-established policies, legal recourse, and coordination of emergency responses to suspected overdoses. Lastly, participants highlight that ODTs should only be one part of a multifaceted approach to reducing harm in healthcare settings and could currently be integrated into discharge planning.

Conclusion
Healthcare professionals from across Canada found ODTs to be an acceptable intervention, but only as part of a larger suite of harm reduction interventions to reduce the harms associated with illicit drug use in healthcare settings. In contrast, participants noted institutional policies, stigma on behalf of healthcare workers and leadership would present significant challenges to their uptake and dissemination.
Antioxidants and the risk of stroke: results from NHANES and two-sample Mendelian randomization study
Authors: Chen Rundong , Liu Hanchen , Zhang Guanghao , Zhang Qian , Hua Weilong , Zhang Lei , Lv Nan , Zhang Yilei , Dai Dongwei , Zhao Rui , Li Qiang , Huang Qinghai , Xu Yi , Yang Pengfei , Liu Jianmin , Zuo Qiao 
Published: January 2024

Abstract
Background
Stroke is the second leading cause of death worldwide, and observational studies have suggested a correlation between antioxidants and reduced stroke risk. However, it remains unclear whether causal relationships exist.

Methods
This study first performed a cross-sectional study of the association between the Composite Dietary Antioxidant Index (CDAI) and stroke using data from the National Health and Nutrition Examination Survey (NHANES) 2007–2018. Second, a two-sample univariable Mendelian Randomization (MR) was performed to analyze the causal effect of circulating levels of antioxidants on different subtypes of stroke.

Results
The cross-sectional study included a total of 24,892 participants representing more than 200 million US non-institutionalized residents, a multivariable logistic regression model revealed that the risk of stroke decreased by 3.4% for each unit increase in CDAI (P = 0.017), with a non-linear association found, indicating a reduction in stroke risk before an inflection point of 3.078. MR analysis revealed that genetically determined levels of retinol had a suggestive protective effect on subarachnoid hemorrhage (SAH) (OR = 0.348, P = 0.025), and genetically determined levels of selenium had a suggestive protective effect against SAH (OR = 0.826, P = 0.007). However, no causal relationship was found between antioxidants and ischemic stroke or intracranial hemorrhage risk.

Conclusions
Evidence suggests that diet-derived antioxidants may reduce the risk of stroke, as indicated by the protective effects of retinol and selenium against SAH. However, more research is needed to fully understand how antioxidants prevent stroke.
Effect of Fiber Orientation on the Fatigue Behavior of Steel Fiber-Reinforced Concrete Specimens by Performing Wedge Splitting Tests and Computed Tomography Scanning
Authors: González Dorys C. , Mena-Alonso Álvaro , Mínguez Jesús , Martínez José A. , Vicente Miguel A. 
Published: January 2024

AbstractThis paper shows the relationship, in steel fiber-reinforced concrete, between fiber orientation and fatigue response through the combined use of computed tomography (CT), digital image processing (DIP) software and wedge splitting test (WST). The WST cubes were extracted from conventional 150 × 150× 600 concrete prisms and a groove and notch were carved on different faces in such a way that in half of the test specimens the fibers are oriented mostly perpendicular to the breaking surface and, in the other half, the fibers are mostly oriented parallel to the breaking surface. Fiber orientation was obtained using a CT device and DIP software from a miniprism extracted from the previously mentioned concrete prisms. The results show that there is a strong correlation between the crack-sewing fiber orientation on the one hand and fatigue life and crack opening rate per cycle on the other hand. Cubes with a higher percentage of fibers perpendicular to the crack surface (i.e., with a higher efficiency index) show a longer fatigue life and a lower crack opening rate per cycle, while cubes with a lower efficiency index show a shorter fatigue life and a higher crack opening rate per cycle.