bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic association and transferability for urinary albumin-creatinine ratio as a marker of kidney disease in four Sub-Saharan African populations and non-continental individuals of African ancestry
Authors: Brandenburg Jean-Tristan , Chen Wenlong Carl , Boua Palwende Romuald , Govender Melanie A. , Agongo Godfred , Micklesfield Lisa K. , Sorgho Hermann , Tollman Stephen , Asiki Gershim , Mashinya Felistas , Hazelhurst Scott , Morris Andrew P. , Fabian June , Ramsay Michèle 
Published: May 2024

BackgroundGenome-wide association studies (GWAS) have predominantly focused on populations of European and Asian ancestry, limiting our understanding of genetic factors influencing kidney disease in Sub-Saharan African (SSA) populations. This study presents the largest GWAS for urinary albumin-to-creatinine ratio (UACR) in SSA individuals, including 8,970 participants living in different African regions and an additional 9,705 non-resident individuals of African ancestry from the UK Biobank and African American cohorts.MethodsUrine biomarkers and genotype data were obtained from two SSA cohorts (AWI-Gen and ARK), and two non-resident African-ancestry studies (UK Biobank and CKD-Gen Consortium). Association testing and meta-analyses were conducted, with subsequent fine-mapping, conditional analyses, and replication studies. Polygenic scores (PGS) were assessed for transferability across populations.ResultsTwo genome-wide significant (P &lt; 5 × 10−8) UACR-associated loci were identified, one in the BMP6 region on chromosome 6, in the meta-analysis of resident African individuals, and another in the HBB region on chromosome 11 in the meta-analysis of non-resident SSA individuals, as well as the combined meta-analysis of all studies. Replication of previous significant results confirmed associations in known UACR-associated regions, including THB53, GATM, and ARL15. PGS estimated using previous studies from European ancestry, African ancestry, and multi-ancestry cohorts exhibited limited transferability of PGS across populations, with less than 1% of observed variance explained.ConclusionThis study contributes novel insights into the genetic architecture of kidney disease in SSA populations, emphasizing the need for conducting genetic research in diverse cohorts. The identified loci provide a foundation for future investigations into the genetic susceptibility to chronic kidney disease in underrepresented African populations Additionally, there is a need to develop integrated scores using multi-omics data and risk factors specific to the African context to improve the accuracy of predicting disease outcomes.
Efficacy of novel bacterial consortia in degrading fipronil and thiobencarb in paddy soil: a survey for community structure and metabolic pathways
Authors: Faridy Nastaran , Torabi Ehssan , Pourbabaee Ahmad Ali , Osdaghi Ebrahim , Talebi Khalil 
Published: May 2024

IntroductionFipronil (FIP) and thiobencarb (THIO) represent widely utilized pesticides in paddy fields, presenting environmental challenges that necessitate effective remediation approaches. Despite the recognized need, exploring bacterial consortia efficiently degrading FIP and THIO remains limited.MethodsThis study isolated three unique bacterial consortia—FD, TD, and MD—demonstrating the capability to degrade FIP, THIO, and an FIP + THIO mixture within a 10-day timeframe. Furthermore, the bioaugmentation abilities of the selected consortia were evaluated in paddy soils under various conditions.ResultsSequencing results shed light on the consortia’s composition, revealing a diverse bacterial population prominently featuring Azospirillum, Ochrobactrum, Sphingobium, and Sphingomonas genera. All consortia efficiently degraded pesticides at 800 µg/mL concentrations, primarily through oxidative and hydrolytic processes. This metabolic activity yields more hydrophilic metabolites, including 4-(Trifluoromethyl)-phenol and 1,4-Benzenediol, 2-methyl-, for FIP, and carbamothioic acid, diethyl-, S-ethyl ester, and Benzenecarbothioic acid, S-methyl ester for THIO. Soil bioaugmentation tests highlight the consortia’s effectiveness, showcasing accelerated degradation of FIP and THIO—individually or in a mixture—by 1.3 to 13-fold. These assessments encompass diverse soil moisture levels (20 and 100% v/v), pesticide concentrations (15 and 150 µg/g), and sterile conditions (sterile and non-sterile soils).DiscussionThis study offers an understanding of bacterial communities adept at degrading FIP and THIO, introducing FD, TD, and MD consortia as promising contenders for bioremediation endeavors.
The microbiome of the pregnant uterus in Holstein dairy heifers and cows assessed by bacterial culture and 16S ribosomal RNA gene sequencing
Authors: Moraes Joao G. N. , Gull Tamara , Ericsson Aaron C. , Poock Scott E. , Caldeira Monica O. , Lucy Matthew C. 
Published: May 2024

IntroductionThe possibility that there is a resident and stable commensal microbiome within the pregnant uterus has been supported and refuted by a series of recent studies. One element of most of the initial studies was that they were based primarily on 16S rRNA gene sequencing from bacteria. To account for this limitation, the current study performed both bacterial culture and 16S rRNA gene sequencing in a side-by-side manner (e.g., same tissues isolated from the same animal).MethodsThe uteruses of 10 mid-pregnant (156 ± 5 d of gestation) Holstein heifers and cows were collected following slaughter. The external surface of the reproductive tract (positive control for contamination during tissue collection) as well as tissues within the pregnant uterus (placentome, inter-cotyledonary placenta, inter-caruncular endometrium, amnionic fluid, allantoic fluid, fetal abomasum content, and fetal meconium) were sampled for bacterial culture and 16S rRNA gene sequencing.ResultsThere were 87 unique bacterial species cultured from the external surface of the pregnant reproductive tract (contamination control) and 12 bacterial species cultured from pregnancy tissues. Six out of 10 cattle (60%) exhibited bacterial growth in at least one location within the pregnant uterus. For the metataxonomic results (16S rRNA gene sequencing), a low targeted microbial biomass was identified. Analyses of the detected amplicon sequence variants (ASV) revealed that there were: (1) genera that were prevalent on both the external surface and within the pregnant uterus; (2) genera that were prevalent on the external surface but either not detected or had very low prevalence within the pregnant uterus; and (3) genera that were either not detected or had low prevalence on the external surface but found with relatively high prevalence within the pregnant uterus.ConclusionThere are a small number of viable bacteria in the pregnant uterus. The 16S rRNA gene sequencing detected a microbial community within the pregnant uterus but with a low biomass. These results are consistent with recent studies of the pregnant bovine uterus and leave open the question of whether there is adequate microbial mass to significantly affect the biology of the normal healthy bovine pregnancy.
Gut microbiome alterations during gastric cancer: evidence assessment of case–control studies
Authors: Zhang Ruimin , Wu Yingxin , Ju Wantao , Wang Senlin , Liu Yanjun , Zhu Hongmei 
Published: May 2024

ObjectivesThe study aims to systematically identify the alterations in gut microbiota that observed in gastric cancer through comprehensive assessment of case–control studies.MethodsThe systematic literature search of PubMed, Embase, Cochrane Library, and Web of Science was conducted to identify case–control studies that compared the microbiomes of individuals with and without gastric cancer. Quality of included studies was evaluated with the Newcastle-Ottawa Quality Assessment Scale (NOS). Meta-analyses utilized a random-effects model, and subgroup and sensitivity analyses were performed to assess study heterogeneity. All data analyses were performed using the “metan” package in Stata 17.0, and the results were described using log odds ratios (log ORs) with 95% confidence intervals (CIs).ResultsA total of 33 studies involving 4,829 participants were eligible for analysis with 29 studies provided changes in α diversity and 18 studies reported β diversity. Meta-analysis showed that only the Shannon index demonstrated statistical significance for α-diversity [−5.078 (−9.470, −0.686)]. No significant differences were observed at the phylum level, while 11 bacteria at genus-level were identified significant changed, e.g., increasing in Lactobacillus [5.474, (0.949, 9.999)] and Streptococcus [5.095, (0.293, 9.897)] and decreasing in Porphyromonas and Rothia with the same [−8.602, (−11.396, −5.808)]. Sensitivity analysis indicated that the changes of 9 bacterial genus were robust. Subgroup analyses on countries revealed an increasing abundance of Helicobacter and Streptococcus in Koreans with gastric cancer, whereas those with gastric cancer from Portugal had a reduced Neisseria. Regarding the sample sources, the study observed an increase in Lactobacillus and Bacteroides in the gastric mucosa of people with gastric cancer, alongside Helicobacter and Streptococcus. However, the relative abundance of Bacteroides decreased compared to the non-gastric cancer group, which was indicated in fecal samples.ConclusionThis study identified robust changes of 9 bacterial genus in people with gastric cancer, which were country-/sample source-specific. Large-scale studies are needed to explore the mechanisms underlying these changes.Systematic ReviewUnique Identifier: CRD42023437426 https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023437426.
Deep learning model for individualized trajectory prediction of clinical outcomes in mild cognitive impairment
Authors: Jung Wonsik , Kim Si Eun , Kim Jun Pyo , Jang Hyemin , Park Chae Jung , Kim Hee Jin , Na Duk L. , Seo Sang Won , Suk Heung-Il 
Published: May 2024

ObjectivesAccurately predicting when patients with mild cognitive impairment (MCI) will progress to dementia is a formidable challenge. This work aims to develop a predictive deep learning model to accurately predict future cognitive decline and magnetic resonance imaging (MRI) marker changes over time at the individual level for patients with MCI.MethodsWe recruited 657 amnestic patients with MCI from the Samsung Medical Center who underwent cognitive tests, brain MRI scans, and amyloid-β (Aβ) positron emission tomography (PET) scans. We devised a novel deep learning architecture by leveraging an attention mechanism in a recurrent neural network. We trained a predictive model by inputting age, gender, education, apolipoprotein E genotype, neuropsychological test scores, and brain MRI and amyloid PET features. Cognitive outcomes and MRI features of an MCI subject were predicted using the proposed network.ResultsThe proposed predictive model demonstrated good prediction performance (AUC = 0.814 ± 0.035) in five-fold cross-validation, along with reliable prediction in cognitive decline and MRI markers over time. Faster cognitive decline and brain atrophy in larger regions were forecasted in patients with Aβ (+) than with Aβ (−).ConclusionThe proposed method provides effective and accurate means for predicting the progression of individuals within a specific period. This model could assist clinicians in identifying subjects at a higher risk of rapid cognitive decline by predicting future cognitive decline and MRI marker changes over time for patients with MCI. Future studies should validate and refine the proposed predictive model further to improve clinical decision-making.
Temporal dynamics of positive emotion regulation: insights from facial electromyography
Authors: Kreibig Sylvia D. , Gross James J. 
Published: May 2024

IntroductionEmotion regulation (ER) is a complex process that manifests gradually over time. This study investigated the temporal dynamics of ER in modifying positive emotions in terms of both negative affect (NA) and positive affect (PA) dimensions.MethodsAfter participants had been exposed to pleasant pictures for 8,000 ms, they received instructions to either continue viewing the picture (no regulation) or reappraise it with a neutral meaning (neutralize goal) or negative meaning (transform goal) for another 8,000 ms. We obtained corrugator supercilii and zygomaticus major electromyography (EMG) as objective measures of NA and PA.ResultsFor the no-regulation condition, upon instruction onset, we observed maintained low levels of corrugator and high levels of zygomaticus EMG reactivity, indicating sustained PA activation. Compared to the no-regulation condition, for the neutralize goal, we observed no change in corrugator reactivity, which remained at a low level, while zygomaticus reduction started at 1,000 ms after instruction onset, indicating decreased PA and generation of a neutral emotional state. For the transform goal, we observed corrugator increase and zygomaticus decrease both starting at 1,500 ms after instruction onset and co-existing throughout the regulation period. These results indicate increased NA and decreased PA, relating to generation of a negative emotional state. The transform goal differed from the neutralize goal in terms of corrugator increase starting at 2,500 ms after instruction onset. Albeit simultaneous onset of changes on corrugator and zygomaticus reactivity under the transform goal, model-fitting analyses indicated that the best-fitting trajectory was one that first emphasized PA reduction until, at 3,000 ms, it turned into primary NA increase.DiscussionThese distinct temporal patterns highlight the possibility of effecting one-dimensional PA change with the neutralize goal and sequential two-dimensional change (first decreasing PA, then increasing NA) with the transform goal. This research sheds light on the time course of emotional change brought about by different regulatory goals.
Non-linear associations of serum spermidine with type 2 diabetes mellitus and fasting plasma glucose: a cross-sectional study
Authors: Zhang Xiaohong , Zhang Yao , Li Shaojie , Liu Min , Lu Ying , He Mengyao , Sun Zhaoqing , Ma Mingfeng , Zheng Liqiang 
Published: May 2024

BackgroundPrevious animal experiments have demonstrated the potential of spermidine to mitigate glucose intolerance, insulin resistance, and hyperinsulinemia. However, there remains a scarcity of epidemiological evidence supporting these findings. Therefore, we aimed to elucidate the associations of serum spermidine with T2DM and FPG.Materials and methodsThe cross-sectional study was conducted from June to August 2019 in the rural areas of Fuxin County, Liaoning Province, China. A total of 4,437 participants were included in the study. The serum spermidine was detected using high-performance liquid chromatography with a fluorescence detector. FPG was measured using the hexokinase method. T2DM was defined as participants with a FPG level of 7.0 mmol/L or greater, or self-reported diagnosis of diabetes by a doctor. Restricted cubic spline model and piecewise linear regression model were used to explore the associations of serum spermidine with T2DM and FPG, respectively.ResultsThe mean (SD) age of the participants was 59.3 (10.0) years, with 622 out of 4,437 participants being defined as T2DM. The serum spermidine in participants stratified by age and BMI categories was significantly different, with p values of 0.006 and 0.001, respectively. Among all the participants, the association of serum spermidine with T2DM was J-shaped. The log (spermidine) was negatively associated with T2DM (OR = 0.68, 95% CI: 0.52 to 0.92, p = 0.01) below the inflection point, while log (spermidine) was not significantly associated with T2DM (OR = 1.97, 95% CI: 0.93 to 4.15, p = 0.07) above the inflection point. Among the participants without T2DM, the association of serum spermidine with FPG was inverted J-shaped. The log (spermidine) was positively associated with FPG (β = 0.13, 95% CI: 0.05 to 0.21, p = 0.001) below the inflection point, while log (spermidine) was negatively associated with FPG (β = −0.29, 95% CI: −0.42 to −0.16, p &lt; 0.001) above the inflection point.ConclusionIn conclusion, non-linear associations of serum spermidine with T2DM and FPG were found in the cross-sectional study in Chinese rural adults. This provided insights into the use of spermidine for the prevention of T2DM, highlighting the potential role in public health prevention strategies of spermidine.
Lysosomal degradation of PD-L1 is associated with immune-related adverse events during anti-PD-L1 immunotherapy in NSCLC patients
Authors: Kashiwada Takeru , Takano Ryotaro , Ando Fumihiko , Kuroda Shoko , Miyabe Yoshishige , Owada Ryuji , Miyanaga Akihiko , Asatsuma-Okumura Tomoko , Hashiguchi Masaaki , Kanazawa Yoshikazu , Yoshida Hiroshi , Seike Masahiro , Gemma Akihiko , Iwai Yoshiko 
Published: May 2024

Background: Immune checkpoint inhibitors (ICIs) can induce immune-related adverse events (irAEs). Liquid biomarkers to predict irAE occurrence are urgently needed. We previously developed an ELISA system to specifically detect soluble PD-L1 (sPD-L1) with PD-1-binding capacity (bsPD-L1). Here, we investigated the relationship between sPD-L1 and bsPD-L1 in gastric cancer (GC) and non-small cell lung cancer (NSCLC) treated with PD-1/PD-L1 blockade and their association with irAEs.Methods: We examined sPD-L1, bsPD-L1, matrix metalloproteinases (MMPs), and proinflammatory cytokine levels by ELISA in plasma samples from 117 GC patients prior to surgery and 72 NSCLC patients prior to and at 2 months after ICI treatment (anti-PD-1, n = 48; anti-PD-L1, n = 24). In mice treated with anti-PD-1/PD-L1 antibodies (Abs), sPD-L1 levels and localization of Abs were examined by ELISA and immunohistochemistry, respectively.Results:sPD-L1 was detected with higher frequency in GC patients than in NSCLC patients, whereas bsPD-L1 was detected with similar frequencies in GC and NSCLC patients. sPD-L1 levels were correlated with IL-1α, IL-1β, TNF-α, and IL-6 levels, while bsPD-L1 levels were correlated with MMP13, MMP3, and IFN-γ levels. In NSCLC patients, anti-PD-L1, but not anti-PD-1, treatment increased sPD-L1, which was associated with irAE development, but not with clinical outcomes. In mice, trafficking of anti-PD-L1 Abs to lysosomes in F4/80+ macrophages resulted in sPD-L1 production, which was suppressed by treatment with lysosomal degradation inhibitor chloroquine and macrophage depletion.Conclusion: Anti-PD-L1-mediated lysosomal degradation induces sPD-L1 production, which can serve as an indicator to predict irAE development during anti-PD-L1 treatment.
Effects of Artemisia annua supplementation on the performance and gut health of laying hens challenged with mixed Eimeria species
Authors: Sharma Milan Kumar , Liu Guanchen , Choppa Venkata Sesha Reddy , Rafieian-Naeini Hamid Reza , Mahdavi Fatemeh Sadat , Marshall Brett , Gogal Robert M. , Kim Woo Kyun 
Published: May 2024

BackgroundCoccidiosis outbreaks in susceptible laying hens can significantly decrease egg production and cause substantial economic loss to the egg industry. The supplementation of poultry diets with chemotherapeutic agents is limited due to antimicrobial resistance and residue in poultry meat or processed products. Therefore, alternative strategies to control coccidiosis are needed, and Artemisia annua (AA) might have the potential to be a phytogenic feed additive, an alternative to anticoccidial agents. This study aimed to investigate the effect of the dietary supplementation of powdered AA on the performance and gut health of laying hens infected with coccidiosis by Eimeria spp.MethodsA total of 225 Hy-Line W-36 laying hens at 23 weeks of age were allocated into 5 treatment groups: 1) control (NC), 2) pair-fed (PF) control, 3) challenged control (CC), 4) CC with dietary inclusion of 0.5% AA (0.5AA), and v) CC with dietary inclusion of 1% AA (1AA). The hens in the CC, 0.5AA, and 1AA groups were orally inoculated with sporulated oocysts of Eimeria maxima (12,500), Eimeria tenella (12,500), and Eimeria acervulina (62,500) at week 25. The PF hens received the same amount of feed consumed by the CC hens from 0–14 days post-inoculation (dpi) of Eimeria spp. The performance of the laying hens, including body weight (BW), hen–day egg production (HDEP), feed intake (FI), and feed conversion ratio (FCR), was measured weekly. Additionally, markers of intestinal health, including gut permeability, lesion score, intestinal morphometry, and immune responses, were evaluated at 6, 14, and 21 dpi.ResultsAt 6 and 14 dpi, laying hens challenged with Eimeria spp. had a lower BW than PF and NC hens (p &lt; 0.0001). Supplementation of 1% AA improved the HDEP by 8.1% compared to CC hens; however, it was still 15.4% lower than that of PF hens (p &lt; 0.0001). The inclusion of 1% AA did not have any beneficial effect on FI; however, the FCR was improved by 0.61 (2.46) than that of CC hens (3.07; p &lt; 0.0001). The inclusion of 1% AA reduced the severity of the intestinal lesions and increased the recovery of intestinal villi (p &lt; 0.05). Additionally, gut permeability was significantly different between the challenged and non-challenged hens; however, among the challenged hens, the inclusion of AA reduced the gut permeability by 29% compared to CC hens (p &lt; 0.0001). Furthermore, the inclusion of 0.5% AA reduced the inflammatory responses in the infected hens.ConclusionDietary inclusion of AA partially restored the performance and gut health of the laying hens and modulated their inflammatory immune response following Eimeria infection; however, further studies are needed to better understand the mode of action and effective dosages to improve the gut health without negative impacts on the performance.
Changes induced by parental neighboring touch in the clonal plant Glechoma longituba depend on the light environment
Authors: Xing Linya , Quan Jiaxin , Zhang Shuqi , Liu Xiao , Bai Hua , Yue Ming 
Published: May 2024

IntroductionTouch by neighboring plants is a common but overlooked environmental variable for plants, especially in dense vegetation. In addition, shade is inevitable for understory plants. The growth performance of clonal plant to the interaction between thigmomorphogenesis and shade response, and their impact on light adaptability is still unknown.MethodsAt the present study, parental ramets of Glechoma longituba were exposed to two conditions (neighboring touch and shade), and their offspring ramets were in ambient or shaded environment. The phenotype and growth of parental and offspring ramets were analyzed. ResultsThe results showed that neighboring touch of parental ramets regulated the performance of offspring ramets, while the effect depended on the light environment. The parental neighboring touch occurring in ambient environment suppressed the expansion of leaf organ, showed as a shorter petiole and smaller leaf area. Moreover, G. longituba exhibited both shade avoidance and shade tolerance characters to shaded environment, such as increased leaf area ratio and leaf mass ratio, longer specific petiole length and specific stolon length. It was notable that these characters of shade response could be promoted by parental neighboring touch to some extent. Additionally, parental light environment plays an important role in offspring growth, parent with ambient light always had well-grown offspring whatever the light condition of offspring, but the growth of offspring whose parent in shaded environment was inhibited. Finally, for the offspring with shaded environment, the touch between parental ramets in shade environment showed a disadvantage on their growth, but the influence of the touch between parental ramets in ambient environment was slight. DiscussionOverall, the interaction of parental neighboring touch and shade environment complicate the growth of understory plants, the performance of plants is the integrated effect of both. These findings are conducive to an in-depth understanding of the environmental adaptation of plants.