bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of native species richness on reproduction of invasive Bidens pilosa vary with nutrient supply
Authors: Gao Fang-Lei , Roiloa Sergio , Xia Jiangbao , Ren Jiayun , Zou Meiling , Zhao Ximei , Yu Fei-Hai 
Published: June 2024

Abstract
Background
Both increasing native species diversity and reducing nutrient availability can increase the ability of native plant communities to resist alien plant invasions. Furthermore, native species diversity and nutrient availability may interact to influence alien plant invasions. So far, however, little is known about the interactive effect of species diversity and nutrient availability on reproduction of alien invasive plants. We constructed native plant communities with one, four or eight species under low and high nutrient supply and then let them be invaded by the invasive alien plant Bidens pilosa.

Results
At both high and low nutrient supply, increasing native species richness significantly increased aboveground biomass of the native plant community and decreased aboveground biomass and biomass proportion of the invader B. pilosa. Reproductive biomass of B. pilosa decreased significantly with increasing native species richness under high nutrient supply, but this effect was not observed under low nutrient supply. Net biodiversity effect on seed mass of B. pilosa decreased significantly with increasing native species diversity under high nutrient supply, but not under low nutrient supply. This was mainly because the selection effect became dominant with increasing species richness under high nutrient supply.

Conclusions
Our study suggest that native species richness and nutrient supply can interact to influence reproduction of invasive alien plant species and that measures to help maintain a high level of native species richness and to reduce nutrient supply could be useful for efficient invasive plant control.
Understanding the spread of antibiotic resistance in vegetables cultivated with sewage sludge: implications for food safety and human health
Authors: Patra Mrinmoy , Dubey Suresh Kumar 
Published: June 2024

AbstractThe conventional practice of using sewage treatment plant (STP) derived sludge as a fertilizer poses significant negative impacts on agroecosystems. Since sludge has diverse contaminants, including heavy metals (HMs), antibiotics (ABs) and antibiotic resistance genes (ARGs), its application in the agricultural fields contaminates the food and hence causes human health risks via the food chain. The transfer of ABs and ARGs from sludge to soil and then to plants can influence the development of antibiotic resistance (AR) in plant endophytes, and leads to variations in their characteristics. In a pot experiment, vegetable carrot (Daucus carota) and spinach (Spinacia oleracea) were amended with sludge samples from three sewage treatment plants (STPs) with varying treatment capacities and both above and below-ground parts of the plants were analysed for the presence of specific ABs (amoxicillin, azithromycin, chloramphenicol, ciprofloxacin, tetracycline), ARGs (blaCTX-M, blaGES, blaNDM, ermF, qnrS, Sul1), and mobile genetic elements (MGEs) (intl1, IS26). Among the characterized culturable endophytic bacteria (EB), 22 exhibited resistance to various antibiotics (highest against ampicillin, ciprofloxacin, chloramphenicol) and heavy metals (highest against lead, nickel, and chromium). Most importantly, seven multiple antibiotic-resistant endophytic bacteria (MAREB) exhibited resistance to all tested heavy metals (HMs). Additionally, all MAREB tested positive for biofilm production, and a notable proportion (72.72%) of these endophytes displayed mobility, with strong auto-aggregation ranging from 16.67 to 92.61%. The biofilm formation dynamics among these MAREB exhibited a Gaussian distribution pattern, increasing with higher antibiotic concentrations. Notably, five MAREB demonstrated survival at clarithromycin concentrations up to 150 µg ml−1. The study revealed the presence of ABs (µg kg−1) and ARGs (copies kg−1) in all parts of both vegetables, ranging from 2.87 to 314.88 and 1 × 105 to 3.2 × 1010, respectively. MAREB displayed various advantageous features to support plant growth under different stress conditions. Moreover, 51.09% of the identified EBs were reported as both plant and human-associated pathogens, and 9.09% were solely human pathogens. Transfer factor (TF), translocation factor (TLF), and bioconcentration factor (BCF) values were correlated with higher ABs and ARGs abundance in the root and shoot compartments of both vegetables. The risk assessment for ABs and ARGs highlighted children are particularly vulnerable to prolonged adverse health risks from consuming these vegetables. Therefore, this research is imperative for understanding the co-selection mechanisms, the need for improvement of the existing treatment systems in contaminants removal, and the evaluation of the presence of ABs and ARGs in sludge before its application in agricultural fields.
Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization
Authors: Zhang Ke , He Chong , Wang Lei , Suo Langda , Guo Mengmeng , Guo Jiazhong , Zhang Ting , Xu Yangbin , Lei Yu , Liu Gongwei , Qian Quan , Mao Yunrui , Kalds Peter , Wu Yujiang , Cuoji Awang , Yang Yuxin , Brugger Daniel , Gan Shangquan , Wang Meili , Wang Xiaolong , Zhao Fangqing , Chen Yulin 
Published: June 2024

Abstract
Background
Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.

Results
A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host’s species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.

Conclusions
By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins.
Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice
Authors: Romaní-Pérez Marina , López-Almela Inmaculada , Bullich-Vilarrubias Clara , Evtoski Zoran , Benítez-Páez Alfonso , Sanz Yolanda 
Published: June 2024

Abstract
Background
The metabolic disturbances of obesity can be mitigated by strategies modulating the gut microbiota. In this study, we sought to identify whether innate or adaptive immunity mediates the beneficial metabolic effects of the human intestinal bacterium Bacteroides uniformis CECT 7771 in obesity.

Methods
We evaluated the effects of orally administered B. uniformis on energy homeostasis, intestinal immunity, hormone levels, and gut microbiota in wild-type and Rag1-deficient mice with diet-induced obesity. We also assessed whether B. uniformis needed to be viable to exert its beneficial effects in obesity and to directly induce immunoregulatory effects.

Results
The administration of B. uniformis to obese mice improved glucose tolerance and insulin secretion, restored the caloric intake suppression after an oral glucose challenge, and reduced hyperglycemia. The pre- and post-prandial glucose-related benefits were associated with restoration of the anti-inflammatory tone mediated by type 2 macrophages and regulatory T cells (Tregs) in the lamina propria of the small intestine. Contrastingly, B. uniformis administration failed to improve glucose tolerance in obese Rag1-/- mice, but prevented the increased body weight gain and adiposity. Overall, the beneficial effects seemed to be independent of enteroendocrine effects and of major changes in gut microbiota composition. B. uniformis directly induced Tregs generation from naïve CD4+ T cells in vitro and was not required to be viable to improve glucose homeostasis but its viability was necessary to prevent body weight gain in diet-induced obese wild-type mice.

Conclusions
Here we demonstrate that B. uniformis modulates the energy homeostasis in diet-induced obese mice through different mechanisms. The bacterium improves oral glucose tolerance by adaptive immunity-dependent mechanisms that do not require cell viability and prevents body weight gain by adaptive immunity-independent mechanisms which require cell viability.
The relationship between unpredictability in childhood and depression among college students: the mediating roles of coping style and resilience
Authors: Ye Chengxiu , Ye Baojuan , Zhang Zheng 
Published: June 2024

Abstract
Background
According to previous studies, unpredictability in childhood could significantly increase the risk of depression in adulthood. Only a few studies have explored the relationship between these two variables in China. This paper aims to explore the relationship between unpredictability in childhood and depression and examine the mediating roles of coping styles and resilience.

Methods
We investigated 601 college students, who had an average age of 19.09 (SD = 2.78) years. Participants completed questionnaires regarding unpredictability in childhood, coping style, resilience, and depression. We analyzed survey data using the bias-corrected bootstrap method.

Results
The findings revealed a significant positive association between unpredictability in childhood and depression among college students. Mature coping style, immature coping style, and resilience were found to mediate this relationship independently. Furthermore, the study unveiled a serial mediation process, wherein both mature and immature coping styles, followed by resilience, sequentially mediate the relationship between unpredictability in childhood and depression, underscoring the complex interplay between these variables.

Conclusions
The results indicated that the risk of depression among college students who have experienced unpredictable childhood should be valued. Attention to coping styles and resilience should be paid to decrease depression among college students who have experienced unpredictable childhood.
Climate-induced shift of deep-sea benthic foraminifera at the onset of the mid-Brunhes dissolution interval in the northeast tropical Indian Ocean
Authors: Takata Hiroyuki , Ikehara Minoru , Seto Koji , Asahi Hirofumi , Lim Hyoun Soo , Hyun Sangmin , Khim Boo-Keun 
Published: June 2024

AbstractThe mid-Brunhes dissolution interval (MBDI; Marine Isotope Stage (MIS) 13 to 7; ~ 533–191 ka) is characterized by various paleoclimatic/paleoceanographic events in the world. We investigated fossil deep-sea benthic foraminifera and sediment geochemistry at the onset of the MBDI (~ 670–440 ka) using Ocean Drilling Program (ODP) Site 758 and core GPC03 in the northeast tropical Indian Ocean (TIO), primarily focusing on the relationship between the paleoceanographic conditions of the surface and deep oceans. Based on multi-dimensional scaling, MDS axis 1 is related to the specific depth habitats of benthic foraminiferal fauna, possibly at the trophic level. In MDS axis 1, the difference between the two core sites was smaller from ~ 610 to 560 ka, whereas it was larger from ~ 560 to 480 ka. In contrast, MDS axis 2 may be related to the low food supply at episodic food pulses/relatively stable and low food fluxes. MDS axis 2 showed generally similar stratigraphic variations between the two cores during ~ 610–560 ka, but was different during ~ 560–480 ka. The proportion of lithogenic matter to biogenic carbonate was relatively low from ~ 610 to 530 ka under the highstand when sediment transport to the study area was reduced. Thus, both the depth gradient in the distribution of benthic foraminiferal fauna and the lithogenic supply between the two cores changed coincidently across the MIS 15/14 (~ 570–540 ka) transition. Such paleoceanographic conditions across MIS 15/14 transition were attributed to the long-term weakening of the wind-driven mixing of surface waters, which might have been caused by the weakening of the Indian summer monsoon in the northeast TIO, possibly with the northward displacement of the InterTropical Convergence Zone in the Northern Hemisphere. In particular, the depth gradient in the distributions of benthic foraminiferal faunas represents the paleoceanographic linkage between the surface and deep oceans through particulate organic matter ballasting by calcareous plankton skeletons in addition to lithogenic matter, which changed transiently and significantly across MIS 15/14 transition close to the onset of the MBDI.
National chlorhexidine coverage and factors associated with newborn umbilical cord care in Bangladesh and Nepal: a cross-sectional analysis using household data
Authors: Singh Kavita , Simmons Elizabeth , Garriga Bliss , Hoover Grace , Ijdi Rashida E. , KC Ashish 
Published: June 2024

Abstract
Background
Preventable newborn deaths are a global tragedy with many of these deaths concentrated in the first week and day of life. A simple low-cost intervention, chlorhexidine cleansing of the umbilical cord, can prevent deaths from omphalitis, an infection of the umbilical cord. Bangladesh and Nepal have national policies promoting chlorhexidine use, as well as routinely collected household survey data, which allows for an assessment of coverage and predictors of the intervention.

Methods
We used data from the 2017–2018 Bangladesh Demographic and Health Survey and the 2016 Nepal Demographic and Health Survey, two large-scale nationally representative household surveys. We studied coverage of single application of chlorhexidine to the umbilical cord of newborns born in the past year using descriptive, bivariate and multivariable analyses. Key predictors of newborns receiving chlorhexidine cleansing, including socio-economic factors, healthcare related factors and the application of harmful and nonharmful substances, were explored in this study.

Results
Coverage of chlorhexidine cleansing was 15.0% in Bangladesh and 50.7% in Nepal, while the application of a harmful substance was 16.9% in Bangladesh and 22.6% in Nepal. Results from the multivariable analyses indicated that delivery in a health facility was strongly associated with a newborn’s receipt of chlorhexidine in both countries (Bangladesh: OR = 2.23, p = 0.002; Nepal: OR = 5.01, p = 0.000). In Bangladesh, delivery by Cesarean section and application of another non-harmful substance were significantly and positively associated with the receipt of chlorhexidine. In Nepal antenatal care was significantly and positively associated with chlorhexidine, while application of a harmful substance was significantly and negatively associated with receipt of chlorhexidine. Maternal education, urban/rural residence, religion and sex were not significant in the multivariable analysis. Wealth was not a significant factor in Bangladesh, but in Nepal newborns in the two highest wealth quintiles were significantly less likely to receive chlorhexidine than newborns in the lowest wealth quintile.

Conclusion
As Bangladesh and Nepal continue to scale-up chlorhexidine for newborn umbilical cord care, additional focus on newborns born in non-facility environments may be warranted. Chlorhexidine cleansing may have the potential to be an equitable intervention, as newborns from the poorest wealth quintiles and whose mothers had less education were not disadvantaged in receiving the intervention in these two settings.
Quantification of 11 metabolites in rat urine after exposure to organophosphates
Authors: Leninsky Michael A. , Sobolev Vladislav E. , Sokolova Margarita O. , Voitenko Natalya G. , Skvortsov Nikita V. 
Published: June 2024

Abstract
Background
The aim of the study was to develop a technique for quantitative determination of rat urine metabolites by HPLC–MS/MS, which can be used to search for biomarkers of acute intoxication with organophosphates (OPs).

Results
The content of metabolites in the urine of rats exposed to a single dose of paraoxon (POX1x); interval, twice daily administration of paraoxon (POX2x); exposure to 2-(o-cresyl)-4H-1, 3, 2-benzodioxaphosphorin-2-oxide and paraoxon (CBPOX) was investigated. New data were obtained on the content in the urine of intact rats as well as rats in 3 models of OP poisoning: 3-methylhistidine, threonine, creatine, creatinine, lactic acid, acetylcarnitine, inosine, hypoxanthine, adenine, 3-hydroxymethyl-butyrate and 2-hydroxymethyl-butyrate.

Conclusions
The proposed assay procedure is a simple and reliable tool for urine metabolomic studies. Within 1–3 days after OP exposure in all three models of acute intoxication, the concentration of metabolites in rat urine, with the exception of adenine, changes similarly and symmetrically, regardless of the method of poisoning modeling, in all three models of acute intoxication. Further studies are needed to determine the specificity and reliability of using urinary metabolite concentration changes as potential biomarkers of acute organophosphate intoxication.

Graphical Abstract
Editorial: Management of PJI/SSI after joint arthroplasty
Authors: Cao Li , Parvizi Javad , Zhang Xiaogang , Liu Xianzhe , Zijlstra Wierd P. , Tarabichi Saad 
Published: June 2024

AbstractThe management of periprosthetic joint infection (PJI) and surgical site infection (SSI) after joint arthroplasty poses a major challenge in orthopedic surgery. This Editorial provides an overview of the studies published in the special issue “Management of PJI/SSI after Joint Arthroplasty”, summarizing the key findings from these studies, which cover a wide range of topics, including stringent preventive strategies, comprehensive diagnostic methods, and personalized treatment modalities. The authors concluded the editorial with their perspectives regarding the status quo of research in this field and future directions for research, such as the development of novel antibiotics, biofilm research, patient-specific risk factors, and the integration of technological advancements (such as machine learning and artificial intelligence) into clinical practice. The authors emphasized the need for continued research, interdisciplinary collaboration, and the application of innovative technologies to enhance patient outcomes and mitigate the burden of these infections on healthcare systems.
Prevalence of Potentially Pathogenic Germline Variants Among Adult Patients in the Philippines With Solid Malignancies Who Underwent Tumor Genomic Profiling
Authors: Franco Paula Isabel , Andal Jose Jasper , Ang Daphne Chua , Que Frances Victoria 
Published: June 2024

PURPOSE In high-income countries, 2%-10% of tumor genomic profiling (TGP) reports reveal incidental pathogenic germline variants. A third of these patients would not qualify for genetic testing on the basis of current guidelines. Our study determined the prevalence of potentially pathogenic germline variants (PPGVs) in TGP results of adult patients with solid malignancies in the Philippines. METHODS Annotated reports of patients with solid cancers who underwent TGP using FoundationOne or FoundationOne Heme between January 2021 and July 2023 were reviewed. PPGV criteria include having a variant allele frequency of >30% and were categorized as (1) high penetrance gene (HP), founder variant (FV), or variant associated with clinical presentation (VA). Pathogenicity was crosschecked through the ClinVar database. RESULTS Of 446 patients, 13 PPGV variants were found in 50 (11.2%) patients at a median age of 60.5 years. Of them, 28 (56%) had HP ( BRCA1, BRCA2, MSH2, MSH6, MLH1, RAD51C, RAD51D), 25 (50%) patients had VA ( APC, SMAD4, CDH1, CDKN2A, PTEN), and two patients with lung cancer had a FV ( EGFR p.Thr790Met). Six patients had more than one PPGV. PPGVs were primarily found in patients with colorectal (42% of 50 patients with PPGVs), breast (16%), ovarian (6%), and lung (6%) cancer ( P < .001). HP genes were mostly found in female patients (71.4%; P = .03). CONCLUSION With a PPGV prevalence of 11% in this study, it is important to recognize PPGVs as it can prompt genetic counseling and confirmatory germline testing.