bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multigenerational inheritance of breathing deficits following perinatal exposure to titanium dioxide nanoparticles in the offspring of mice
Authors: Boulain Marie , Morin Didier , Juvin Laurent 
Published: January 2024

Abstract
Background
The utilization of titanium dioxide nanoparticles (TIO2NPs) has experienced a significant surge in recent decades, and these particles are now commonly found in various everyday consumer products. Due to their small size, TIO2NPs can penetrate biological barriers and elicit adverse interactions with biological tissues. Notably, exposure of pregnant females to TIO2NPs during the perinatal period has been shown to disrupt the growth of offspring. Furthermore, this exposure induces epigenetic modifications in the DNA of newborns, suggesting the possibility of multigenerational effects. Thus, perinatal exposure to TIO2NPs may induce immediate metabolic impairments in neonates, which could be transmitted to subsequent generations in the long term.

Results
In this study, we utilized perinatal exposure of female mice to TIO2NPs through voluntary food intake and observed impaired metabolism in newborn male and female F1 offspring. The exposed newborn mice exhibited reduced body weight gain and a slower breathing rate compared to non-exposed animals. Additionally, a higher proportion of exposed F1 newborns experienced apneas. Similar observations were made when the exposure was limited to the postnatal period, highlighting lactation as a critical period for the adverse effects of TIO2NPs on postnatal metabolism. Importantly, the breathing deficits induced by TIO2NPs were transmitted from F1 females to the subsequent F2 generation. Moreover, re-exposure of adult F1 females to TIO2NPs exacerbated the breathing deficits in newborn F2 males.

Conclusions
Our findings demonstrate that perinatal exposure to TIO2NPs disrupts postnatal body weight gain and respiration in the offspring, and these deficits are transmissible to future generations.
Outcome and predictors of failure of abdominal surgical repair of high vesico-vaginal and vesico-uterine fistulae at Gezira Hospital for Renal Disease and Surgery
Authors: Yousif Muzafr Shakir Ali , Mohamad Ismail Gareeballah Alhag , Ahmed Mohamed Elimam Mohamed , Osman Yassin Mohammed , Yousif Ahmed Shakir Ali , Omran Mustafa 
Published: January 2024

Abstract
Background
Urogenital fistula can arise from various causes, leading to the development of diverse surgical procedures. The prevention and treatment of obstetric fistula continue to pose challenges in low-income countries.

Aim
To assess the outcomes and predictors of failure of surgical repair for urogenital fistulas, specifically high vesico-vaginal fistula (VVF) and vesico-uterine fistula (VUF), within our context.

Methods
Conducted a prospective hospital-based study involving 100 female patients with urogenital fistula (95 VVF and 5 VUF) who underwent abdominal surgical repair at Gezira Hospital for Renal Diseases and Surgery from 2018 to 2023. Collected data encompassing demographics, obstetric history, fistula etiologies, Swab test, cystoscopy findings, urine diversion, ureteric re-implantation, and repair outcomes.

Results
The majority of women were aged 20–29 years (39%), illiterate (62%), and had a low socio-economic status (87%). Lack of antenatal care was noted in 77% of patients. Fistula etiologies were predominantly obstetric (70%), mainly due to spontaneous vaginal delivery (SVD), with the remaining 30% attributed to gynecological causes (hysterectomy). In terms of fistula characteristics, all patients had a high-level fistula, 95% had a single fistula, and 69% had a posterior wall fistula. Successful closure was achieved in 84% of cases, with 11% experiencing ureteric involvements. The analysis of failures pointed to recurrent fistulae (50%), larger fistula size (31%), and the presence of multiple fistulae (19%) as notable predictors of unsuccessful repair.

Conclusion
VVF was the prevalent type of urogenital fistula in our population. Risk factors included being in the third decade of life, illiteracy, low socioeconomic status, and a lack of prenatal care. Obstetric causes, particularly prolonged and obstructed labor through SVD, dominated the etiology. Surgical procedures resulted in successful closure in 84% of cases. Recurrent fistulae, larger size, and multiple occurrences emerged as predictors of surgical repair failure.
The EU Communication on ensuring availability and affordability of fertilisers—a milestone for sustainable nutrient management or a missed opportunity?
Authors: Garske Beatrice , Heyl Katharine , Ekardt Felix 
Published: January 2024

AbstractThe global mineral fertiliser crisis increased the pressure on the EU agricultural sector. In response, the EU Commission released a Communication on ensuring availability and affordability of fertilisers in November 2022. This Policy Brief discusses the Fertiliser Communication and critically questions whether (1) the proposed measures can contribute to combat the fertiliser crisis, and (2) whether they can make the EU agricultural sector more resilient and sustainable to comply with the Paris Agreement and the Aichi Targets to the Convention on Biological Diversity. Results show that the Fertiliser Communication falls short on both challenges. It relies on existing, insufficient policies and public support measures and fails to propose innovative and effective solutions. Moreover, existing fertiliser and fossil fuel import dependencies are maintained and shifted. To overcome these shortcomings and to comply with legally binding climate and biodiversity goals, a comprehensive governance approach for nutrient management and sustainable agriculture by economic instruments that apply to livestock husbandry and fossil fuels is introduced.
A novel approach toward optimal workflow selection for DNA methylation biomarker discovery
Authors: Nazer Naghme , Sepehri Mohammad Hossein , Mohammadzade Hoda , Mehrmohamadi Mahya 
Published: January 2024

AbstractDNA methylation is a major epigenetic modification involved in many physiological processes. Normal methylation patterns are disrupted in many diseases and methylation-based biomarkers have shown promise in several contexts. Marker discovery typically involves the analysis of publicly available DNA methylation data from high-throughput assays. Numerous methods for identification of differentially methylated biomarkers have been developed, making the need for best practices guidelines and context-specific analyses workflows exceedingly high. To this end, here we propose TASA, a novel method for simulating methylation array data in various scenarios. We then comprehensively assess different data analysis workflows using real and simulated data and suggest optimal start-to-finish analysis workflows. Our study demonstrates that the choice of analysis pipeline for DNA methylation-based marker discovery is crucial and different across different contexts.
Genomic characterization of WRKY transcription factors related to secoiridoid biosynthesis in Gentiana macrophylla
Authors: Yin Yangyang , Fu Huanhuan , Mi Fakai , Yang Ye , Wang Yaomin , Li Zhe , He Yihan , Yue Zhenggang 
Published: January 2024

AbstractGentiana macrophylla is one of Chinese herbal medicines in which 4 kinds of iridoids or secoiridoids, such as loganic acid, sweroside, swertiamarin, and gentiopicroside, are identified as the dominant medicinal secondary metabolites. WRKY, as a large family of transcription factors (TFs), plays an important role in the synthesis of secondary metabolites in plants. Therefore, WRKY genes involved in the biosynthesis of secoiridoids in G. macrophylla were systematically studied. First, a comprehensive genome-wide analysis was performed, and 42 GmWRKY genes were identified, which were unevenly distributed in 12 chromosomes. Accordingly, gene structure, collinearity, sequence alignment, phylogenetic, conserved motif and promoter analyses were performed, and the GmWRKY proteins were divided into three subfamilies based on phylogenetic and multiple sequence alignment analyses. Moreover, the enzyme-encoding genes of the secoiridoid biosynthesis pathway and their promoters were then analysed, and the contents of the four secoiridoids were determined in different tissues. Accordingly, correlation analysis was performed using Pearson′s correlation coefficient to construct WRKY gene-enzyme-encoding genes and WRKY gene–metabolite networks. Meanwhile, G. macrophylla seedlings were treated with methyl jasmonate (MeJA) to detect the dynamic change trend of GmWRKYs, biosynthetic genes, and medicinal ingredient accumulation. Thus, a total of 12 GmWRKYs were identified to be involved in the biosynthesis of secoiridoids, of which 8 (GmWRKY1, 6, 12, 17, 33, 34, 38 and 39) were found to regulate the synthesis of gentiopicroside, and 4 (GmWRKY7, 14, 26 and 41) were found to regulate the synthesis of loganic acid. Taken together, this study systematically identified WRKY transcription factors related to the biosynthesis of secoiridoids in G. macrophylla, which could be used as a cue for further investigation of WRKY gene functions in secondary metabolite accumulation.
Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola
Authors: Jia Min , Ni Yunxia , Zhao Hui , Liu Xintao , Yan Wenqing , Zhao Xinbei , Wang Jing , He Bipo , Liu Hongyan 
Published: January 2024

Abstract
Background
Corynespora leaf spot is a common leaf disease occurring in sesame, and the disease causes leaf yellowing and even shedding, which affects the growth quality of sesame. At present, the mechanism of sesame resistance to this disease is still unclear. Understanding the resistance mechanism of sesame to Corynespora leaf spot is highly important for the control of infection. In this study, the leaves of the sesame resistant variety (R) and the sesame susceptible variety (S) were collected at 0–48 hpi for transcriptome sequencing, and used a combined third-generation long-read and next-generation short-read technology approach to identify some key genes and main pathways related to resistance.

Results
The gene expression levels of the two sesame varieties were significantly different at 0, 6, 12, 24, 36 and 48 hpi, indicating that the up-regulation of differentially expressed genes in the R might enhanced the resistance. Moreover, combined with the phenotypic observations of sesame leaves inoculated at different time points, we found that 12 hpi was the key time point leading to the resistance difference between the two sesame varieties at the molecular level. The WGCNA identified two modules significantly associated with disease resistance, and screened out 10 key genes that were highly expressed in R but low expressed in S, which belonged to transcription factors (WRKY, AP2/ERF-ERF, and NAC types) and protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, and RLK-Pelle_WAK types). These genes could be the key response factors in the response of sesame to infection by Corynespora cassiicola. GO and KEGG enrichment analysis showed that specific modules could be enriched, which manifested as enrichment in biologically important pathways, such as plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione metabolism, MAPK and other stress-related pathways.

Conclusions
This study provides an important resource of genes contributing to disease resistance and will deepen our understanding of the regulation of disease resistance, paving the way for further molecular breeding of sesame.
Quality assessment of flax advanced breeding lines varying in seed coat color and their potential use in the food and industrial applications
Authors: Abtahi Mozhgan , Mirlohi Aghafakhr 
Published: January 2024

Abstract
Background
With the increasing consumer awareness of the strong relationship between food and health, flax became a promising functional food due to its bioactive nutraceutical composition. Intra-specific crosses of eight contrasting flax genotypes were performed previously, and within segregating F6 progeny families, we investigated a close-up composition of phytochemicals derived from whole seeds.

Results
The considerable genetic variation among the flax F6 families suggested that intra-specific hybridization is essential in flax breeding to obtain and broaden genetic variability and largely affirmed the opportunity for selecting promising lines. Also, significant variations in the targeted metabolite contents and antioxidant properties were observed among brown and yellow-seeded families. Notably, brown-seeded families expressed the highest average values of saturated fatty acids, protein, fiber, tocopherol, phenolics, SDG, and SECO lignans. Yellow-seeded families represented the highest average content of unsaturated fatty acids and mucilage. The cultivation year significantly affects flaxseed’s composition and functional properties, presumably due to temperature, humidity, and sunshine time differences. Interestingly, the seeds obtained in warmer conditions were more potent and had more chemical constituents. The favorable genetic correlations among all evaluated traits suggest the possibility of joint genetic selection for several nutritional and phytochemical characteristics in flax. The current study highlights the importance and utilization of 19 top families as their seeds and oil play imperative roles in the pharmaceuticals and food industries. The antioxidant capacity of the seeds showed that families 84B, 23B, 35Y, 95Y, 30B, 88B, and 78B serve as a natural source of dietary antioxidants beneficial to human health. To increase the oxidative stability of the flaxseed oil, the quality evaluation identified some families with low levels of linolenic acid.

Conclusions
These findings are essential to improving flaxseed’s nutritional quality and therapeutic properties through a bulk breeding program.
Alleviation of salinity stress by EDTA chelated-biochar and arbuscular mycorrhizal fungi on maize via modulation of antioxidants activity and biochemical attributes
Authors: Huang Ping , Huang Shoucheng , Ma Yuhan , Danish Subhan , Hareem Misbah , Syed Asad , Elgorban Abdallah M. , Eswaramoorthy Rajalakshmanan , Wong Ling Shing 
Published: January 2024

AbstractSalinity stress adversely affects agricultural productivity by disrupting water uptake, causing nutrient imbalances, and leading to ion toxicity. Excessive salts in the soil hinder crops root growth and damage cellular functions, reducing photosynthetic capacity and inducing oxidative stress. Stomatal closure further limits carbon dioxide uptake that negatively impact plant growth. To ensure sustainable agriculture in salt-affected regions, it is essential to implement strategies like using biofertilizers (e.g. arbuscular mycorrhizae fungi = AMF) and activated carbon biochar. Both amendments can potentially mitigate the salinity stress by regulating antioxidants, gas exchange attributes and chlorophyll contents. The current study aims to explore the effect of EDTA-chelated biochar (ECB) with and without AMF on maize growth under salinity stress. Five levels of ECB (0, 0.2, 0.4, 0.6 and 0.8%) were applied, with and without AMF. Results showed that 0.8ECB + AMF caused significant enhancement in shoot length (~ 22%), shoot fresh weight (~ 15%), shoot dry weight (~ 51%), root length (~ 46%), root fresh weight (~ 26%), root dry weight (~ 27%) over the control (NoAMF + 0ECB). A significant enhancement in chlorophyll a, chlorophyll b and total chlorophyll content, photosynthetic rate, transpiration rate and stomatal conductance was also observed in the condition 0.8ECB + AMF relative to control (NoAMF + 0ECB), further supporting the efficacy of such a combined treatment. Our results suggest that adding 0.8% ECB in soil with AMF inoculation on maize seeds can enhance maize production in saline soils, possibly via improvement in antioxidant activity, chlorophyll contents, gas exchange and morphological attributes.
Point-of-care testing and antibiotics prescribing in out-of-hours general practice: a register-based study in Denmark
Authors: Christensen Line Due , Vestergaard Claus Høstrup , Keizer Ellen , Bech Bodil Hammer , Bro Flemming , Christensen Morten Bondo , Huibers Linda 
Published: January 2024

Abstract
Background
Point-of-care testing may reduce diagnostic uncertainty in case of suspicion of bacterial infection, thereby contributing to prudent antibiotic prescribing. We aimed to study variations in the use of point-of-care tests (C-reactive protein test, rapid streptococcal antigen detection test, and urine dipstick) among general practitioners (GPs) and the potential association between point-of-care testing and antibiotic prescribing in out-of-hours general practice.

Methods
We conducted a population-based observational register-based study, based on patient contacts with out-of-hours general practice in the Central Denmark Region in 2014–2017. The tendency of GPs to use point-of-care testing was calculated, and the association between the use of point-of-care testing and antibiotic prescribing was evaluated with the use of binomial regression.

Results
Out-of-hours general practice conducted 794,220 clinic consultations from 2014 to 2017, of which 16.1% resulted in an antibiotic prescription. The GP variation in the use of point-of-care testing was largest for C-reactive protein tests, with an observed variation (p90/p10 ratio) of 3.0; this means that the GPs in the 90th percentile used C-reactive protein tests three times as often as the GPs in the 10th percentile. The observed variation was 2.1 for rapid streptococcal antigen detection tests and 1.9 for urine dipsticks. The GPs who tended to use more point-of-care tests prescribed significantly more antibiotics than the GPs who tended to use fewer point-of-care tests. The GPs in the upper quintile of the tendency to use C-reactive protein test prescribed 22% more antibiotics than the GPs in the lowest quintile (21% for rapid streptococcal antigen detection tests and 8% for urine dipsticks). Up through the quintiles, this effect exhibited a positive linear dose–response correlation.

Conclusion
The GPs varied in use of point-of-care testing. The GPs who tended to perform more point-of-care testing prescribed more antibiotics compared with the GPs who tended to perform fewer of these tests.
Daily activity patterns in older adults receiving initial support: the association between daily steps and sitting in bouts of at least 60 min
Authors: Niklasson Joakim , Fagerström Cecilia , Backåberg Sofia , Lindberg Terese , Bergman Patrick 
Published: January 2024

Abstract
Background
Aging has a significant impact on health, underlining the importance of maintaining physical function and reducing time spent sitting among older adults. To understand how to reduce prolonged sitting or increase physical activity, factors related to the daily living and observed daily activity patterns should be explored. This study aimed to investigate the association between daily steps, self-rated health, physical activity, sedentary behavior, motivation to exercise and fear of falling among older adults receiving initial support.

Method
Cross-sectional design with total population questionnaire data from adults aged ≥ 60 years (n = 917), living at home with initial support from municipal care in southern Sweden. The older adults were offered to participate in a follow-up study measuring daily activity patterns with accelerometers (n = 72). Linear regression was used to analyze associations between daily steps and possible predictors.

Results
The linear model ($$ {R}^{2}= $$0.478) showed that sitting in unbroken bouts of > 60 min (β = -0.313, p < 0.05), walking independently outdoors (β = 0.301, p < 0.05), intending to increase physical activity (β = -0.294, p < 0.05), sex (β = 0.279, p < 0.05), relative autonomy index (β = 0.258, p < 0.05), fear of falling (β = -0.238, p < 0.05), and self-rated health (β = 0.213, p < 0.05) predicted daily steps.

Conclusion
The model of predictors brings new understanding regarding daily steps among community-dwelling older adults. The association between sitting in bouts of > 60 min and daily steps is interesting as 35% of participants had a number of sitting bouts that on average, showed 30% less steps taken. Minimizing long sitting bouts and maintaining physical functioning to promote independence when walking outdoors can be tools for clinical practitioners devising interventions to break prolonged sitting among community-dwelling older adults. Future research should prioritize studying older adults’ outdoor walking independence, including its relation to walking with or without assistive devices and its impact on physical activity and sedentary behavior.
Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis
Authors: Munawar Wan Amirul Syazwan Wan Ahmad , Elias Marjanu Hikmah , Addnan Faizul Helmi , Hassandarvish Pouya , AbuBakar Sazaly , Roslan Nuruliza 
Published: January 2024

Abstract
Background
The Coronavirus disease 2019 (COVID-19) pandemic occurred due to the dispersion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe symptoms can be observed in COVID-19 patients with lipid-related comorbidities such as obesity and diabetes. Yet, the extensive molecular mechanisms of how SARS-CoV-2 causes dysregulation of lipid metabolism remain unknown.

Methods
Here, an advanced search of articles was conducted using PubMed, Scopus, EBSCOhost, and Web of Science databases using terms from Medical Subject Heading (MeSH) like SARS-CoV-2, lipid metabolism and transcriptomic as the keywords. From 428 retrieved studies, only clinical studies using next-generation sequencing as a gene expression method in COVID-19 patients were accepted. Study design, study population, sample type, the method for gene expression and differentially expressed genes (DEGs) were extracted from the five included studies. The DEGs obtained from the studies were pooled and analyzed using the bioinformatics software package, DAVID, to determine the enriched pathways. The DEGs involved in lipid metabolic pathways were selected and further analyzed using STRING and Cytoscape through visualization by protein-protein interaction (PPI) network complex.

Results
The analysis identified nine remarkable clusters from the PPI complex, where cluster 1 showed the highest molecular interaction score. Three potential candidate genes (PPARG, IFITM3 and APOBEC3G) were pointed out from the integrated bioinformatics analysis in this systematic review and were chosen due to their significant role in regulating lipid metabolism. These candidate genes were significantly involved in enriched lipid metabolic pathways, mainly in regulating lipid homeostasis affecting the pathogenicity of SARS-CoV-2, specifically in mechanisms of viral entry and viral replication in COVID-19 patients.

Conclusions
Taken together, our findings in this systematic review highlight the affected lipid-metabolic pathways along with the affected genes upon SARS-CoV-2 invasion, which could be a potential target for new therapeutic strategies study in the future.