bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the agronomic value of solar-dried sludge and heavy metals bioavailability based on the bioaccumulation factor and translocation index
Authors: An-nori Amal , El Mejahed Khalil , Fels Loubna El , Touhami Driss , Ezzariai Amine , El Gharous Mohamed , Hafidi Mohamed 
Published: April 2023

This study aimed to assess the agronomic value of solar-dried sludge (SDS) and the transfer of Cr, Ni, Pb, and Cu to wheat (Triticum aestivum) and faba bean (Vicia faba). A greenhouse experiment was performed involving two rates of SDS (15 t/ha and 30 t/ha) from an activated sludge-based wastewater treatment plant. In addition to the single use of an SDS amendment, co-application of SDS and mineral fertilizers was also included to determine the best scenario resulting in high yields and less negative implications on the environment. Data for both wheat and faba bean showed that applying SDS at 30 t/ha led to competitive yields compared to the ones obtained previously, while 15 t/ha of SDS and mineral fertilizers were co-applied. The use of SDS increased soil organic matter, slightly decreased the pH value, and increased soil salinity. The contents of Ni, Cu, and Pb were not significantly affected by the application of SDS. Only Cr showed high soil concentrations in proportion to the increasing rates of SDS. The bioaccumulation of heavy metals in roots was more important in 30 t/ha than that in 15 t/ha amended soil. In the case of wheat, the bioconcentration factor (BCF) root values correspond to the following order: Cr (0.89) &gt;Cu (0.85)&gt; Ni (0.28)&gt; Pb (0.22). In the case of faba bean, BCF roots were observed as follows: Cu (1.04 &gt; Ni (0.37)&gt; Cr (0.16)&gt; Pb (0.15). Wheat excluded Cr, Ni, and Pb from the uptake by shoots, and Cu was translocated from roots to shoots with a percentage of 11% at 30 t/ha of applied SDS. Faba beans demonstrated more important values of HM’s translocation by respecting this order (Ni (37.7%) &gt; cu (30.24%)&gt; Cr (17.59%), while Pb was excluded from the translocation. No significant difference was observed regarding the translocation index when the sludge rate has been duplicated from 15 t/ha to 30 t/ha. Based on these outcomes, SDS used at the rate of 30 t/ha is the best scenario to amend the soil and provide nutrients to plants. Wheat is translocating less heavy metal to the edible part; it is, thus, the most suitable crop to be involved in the current context.
Genetic predisposition may not improve prediction of cardiac surgery-associated acute kidney injury
Authors: Douville Nicholas J. , Larach Daniel B. , Lewis Adam , Bastarache Lisa , Pandit Anita , He Jing , Heung Michael , Mathis Michael , Wanderer Jonathan P. , Kheterpal Sachin , Surakka Ida , Kertai Miklos D. 
Published: April 2023

Background: The recent integration of genomic data with electronic health records has enabled large scale genomic studies on a variety of perioperative complications, yet genome-wide association studies on acute kidney injury have been limited in size or confounded by composite outcomes. Genome-wide association studies can be leveraged to create a polygenic risk score which can then be integrated with traditional clinical risk factors to better predict postoperative complications, like acute kidney injury.Methods: Using integrated genetic data from two academic biorepositories, we conduct a genome-wide association study on cardiac surgery-associated acute kidney injury. Next, we develop a polygenic risk score and test the predictive utility within regressions controlling for age, gender, principal components, preoperative serum creatinine, and a range of patient, clinical, and procedural risk factors. Finally, we estimate additive variant heritability using genetic mixed models.Results: Among 1,014 qualifying procedures at Vanderbilt University Medical Center and 478 at Michigan Medicine, 348 (34.3%) and 121 (25.3%) developed AKI, respectively. No variants exceeded genome-wide significance (p &lt; 5 × 10−8) threshold, however, six previously unreported variants exceeded the suggestive threshold (p &lt; 1 × 10−6). Notable variants detected include: 1) rs74637005, located in the exonic region of NFU1 and 2) rs17438465, located between EVX1 and HIBADH. We failed to replicate variants from prior unbiased studies of post-surgical acute kidney injury. Polygenic risk was not significantly associated with post-surgical acute kidney injury in any of the models, however, case duration (aOR = 1.002, 95% CI 1.000–1.003, p = 0.013), diabetes mellitus (aOR = 2.025, 95% CI 1.320–3.103, p = 0.001), and valvular disease (aOR = 0.558, 95% CI 0.372–0.835, p = 0.005) were significant in the full model.Conclusion: Polygenic risk score was not significantly associated with cardiac surgery-associated acute kidney injury and acute kidney injury may have a low heritability in this population. These results suggest that susceptibility is only minimally influenced by baseline genetic predisposition and that clinical risk factors, some of which are modifiable, may play a more influential role in predicting this complication. The overall impact of genetics in overall risk for cardiac surgery-associated acute kidney injury may be small compared to clinical risk factors.
Construction of lncRNA prognostic model related to cuproptosis in esophageal carcinoma
Authors: Zhang Liming , Zong Ling , Li Wenhui , Ning Lu , Zhao Yajun , Wang Shaoqiang , Wang Lina 
Published: April 2023

Background: Esophageal carcinoma (ESCA) is one of the most prevalent malignant tumors in the world. The prognosis of patients has significantly improved with the development of surgery, targeted therapy and immunotherapy. But the 5-year survival rate of ESCA patients is still incredibly low. Cuproptosis is a type of mitochondrial cell death induced by copper. It is unclear how cuproptosis-related lncRNAs (CRLs) affect ESCA prognosis.Methods: In this study, we obtained the clinical data of ESCA patients, the transcriptome data from TCGA and identified CRLs by co-expression analysis, lasso regression, and cox regression analysis, to build a prognostic model. Then we validated the prognostic model using the Kaplan-Meier curve, cox regression analysis, and ROC, to create a nomogram based on risk score to forecast the prognosis of ESCA. Next, the immune escape of the CRLs was examined using the TIDE algorithm to assess its sensitivity to possible ESCA medications.Results: To predict the prognosis of ESCA patients, we created a predictive model using 6 CRLs (AC034199.1, AC125437.1, AC107032.2, CTBP1-DT, AL024508.1, and AC008610.1), validated by the Kaplan-Meier and ROC curves. The model has a higher diagnostic value compared to other clinical features. The 6 CRLs expressed high in TCGA and ESCA specimens. Enrichment analysis revealed CRLs largely contributed to the interaction between cytokines and their receptors as well as complement coagulation cascades. The immunity escape analysis demonstrated that immunotherapy had a worse effect in the low-risk group than in the high-risk group. Additionally, we screened out potential antineoplastic drugs according to the results of the immunoassay and obtained 5 drugs, including CP-466722, crizotinib, MS-275, KIN001-135, and CP-466722.Conclusion: The prognosis of patients with ESCA can be correctly predicted by the 6 CRLs chosen from this investigation. It lays the groundwork for more investigation into the ESCA mechanism and the identification of novel therapeutic targets.
Prevalence estimation of ATTRv in China based on genetic databases
Authors: Yongsheng Zheng , Chong Sun , Bingyou Liu , Jianian Hu , Haofeng Chen , Chongbo Zhao , Zhang Victor Wei , Jie Lin 
Published: April 2023

Introduction: Amyloid transthyretin (ATTR) is divided into either hereditary (ATTRv) or sporadic (ATTRwt) and ATTRv is a rare hereditary disease transmitted as an autosomal dominant manner. Its global prevalence is traditionally estimated as 5,000 to 10,000 persons. However, it may be underestimated and the exact prevalence of ATTRv in China mainland remains unknown.Methods: The Genome Aggregation database (gnomAD) database (containing 125,748 exomes) and two genomic sequencing databases——China Metabolic Analytics Project (ChinaMAP) (containing 10588 individuals) and Amcarelab gene database (containing 45392 exomes), were integrated to estimate the prevalence of ATTRv in the world and mainland Chinese populations. Pathogenic variants allele frequency and the prevalence of ATTRv was calculated.Results: Six variants, counting 470 alleles, were defined as pathogenic variants in gnomAD. The prevalence of ATTRv in the world population was 57.4/100,000. Two variants (2 allele counts) and 15 variants (34 individuals) were defined as pathogenic variants in the ChinaMAP database and the Amcarelab exome database, respectively. Thus, the estimated prevalence interval of ATTRv in mainland China was 18.9/100,000-74,9/100,000.Conclusion: The present study demonstrated that the previous prevalence was greatly underestimated using traditional methods. Therefore, raising awareness of the disease is essential for recognizing ATTRv in its early stage.
The Pseudomonas aeruginosa Secreted Protein PA3611 Promotes Bronchial Epithelial Cell Epithelial-Mesenchymal Transition via Integrin αvβ6-Mediated TGF-β1-Induced p38/NF-κB Pathway Activation
Authors: Shu Lei , Chen Sixia , Lin Shaoqing , Lin Huan , Shao Yan , Yao Jing , Qu Lili , Zhang Yunshi , Liu Xing , Du Xingran , Deng Kaili , Chen Xiaolin , Feng Ganzhu 
Published: April 2023

Graphical AbstractThe role of PA3611 on EMT.
Stem Cell-Derived Exosome as Potential Therapeutics for Microbial Diseases
Authors: Keshtkar Somayeh , Kaviani Maryam , Soleimanian Saeede , Azarpira Negar , Asvar Zahra , Pakbaz Sara 
Published: April 2023

Graphical AbstractSummary of the antimicrobial effect of stem cell-derived exosomes on bacteria, viral, fungal, and parasitic diseases.
Integrating Venom Peptide Libraries Into a Phylogenetic and Broader Biological Framework
Authors: Chase Kevin , Watkins Maren , Safavi-Hemami Helena , Olivera Baldomero M. 
Published: April 2023

The venomous marine snails are conventionally divided into three groups, the cone snails (family Conidae), the auger snails (family Terebridae) and the turrids (formerly all assigned to a single family, Turridae). In this study, a library of venom peptides from species conventionally assigned to the genus Turris was correlated to a phylogenetic analysis. Nucleotide sequences of multiple genes from transcriptomes were used to assess the phylogenetic relationships across a diverse set of species. The resulting tree shows that as conventionally defined, the conoidean genus Turris, is polyphyletic. We describe a new genus, Purpuraturris gen. nov., that comprises the outlier species. In addition to morphological distinctions, molecular data reveal that this group is divergent from Turris sensu stricto. The correlation between phylogenetic information and a family of peptide sequences was used to highlight those peptides mostly likely to be unique and intimately associated with biological diversity. The plethora of peptide sequences available requires two prioritization decisions: which subset of peptides to initially characterize, and after these are characterized, which to comprehensively investigate for potential biomedical applications such as drug developments.Life Science Identifiers: urn:lsid:zoobank.org; pub: 60D46561-28F0-4C39-BAC4-66DC8B4EAEA4
Deep brain stimulation for the treatment of Alzheimer's disease: A systematic review and meta-analysis
Authors: Majdi Alireza , Deng Zhengdao , Sadigh-Eteghad Saeed , De Vloo Philippe , Nuttin Bart , Mc Laughlin Myles 
Published: April 2023

BackgroundOne of the experimental neuromodulation techniques being researched for the treatment of Alzheimer's disease (AD) is deep brain stimulation (DBS). To evaluate the effectiveness of DBS in AD, we performed a systematic review and meta-analysis of the available evidence.MethodsFrom the inception through December 2021, the following databases were searched: Medline via PubMed, Scopus, Embase, Cochrane Library, and Web of Science. The search phrases used were “Alzheimer's disease,” “AD,” “deep brain stimulation,” and “DBS.” The information from the included articles was gathered using a standardized data-collecting form. In the included papers, the Cochrane Collaboration methodology was used to evaluate the risk of bias. A fixed-effects model was used to conduct the meta-analysis.ResultsOnly five distinct publications and 6 different comparisons (one study consisted of two phases) were included out of the initial 524 papers that were recruited. DBS had no impact on the cognitive ability in patients with AD [0.116 SMD, 95% confidence interval (CI), −0.236 to 0.469, p = 0.518]. The studies' overall heterogeneity was not significant (κ2 = 6.23, T2 = 0.053, df = 5, I2 = 19.76%, p = 0.284). According to subgroup analysis, the fornix-DBS did not improve cognitive function in patients with AD (0.145 SMD, 95%CI, −0.246 to 0.537, p = 0.467). Unfavorable neurological and non-neurological outcomes were also reported.ConclusionThe inconsistencies and heterogeneity of the included publications in various target and age groups of a small number of AD patients were brought to light by this meta-analysis. To determine if DBS is useful in the treatment of AD, further studies with larger sample sizes and randomized, double-blinded, sham-controlled designs are required.
Effect of acupuncture in the acute phase of intracerebral hemorrhage on the prognosis and serum BDNF: a randomized controlled trial
Authors: Li Lingcong , Wang Xiujing , Guo Jiaxun , Chen Yilin , Wang Zhenyu 
Published: April 2023

BackgroundIntracerebral hemorrhage (ICH) is a common cerebrovascular disease, with a high rate of disability. In the literature on Chinese traditional medicine, there is increasing evidence that acupuncture can help hematoma absorption and improve neurological deficits after cerebral hemorrhage. Brain-derived neurotrophic factor (BDNF), one of the most studied neurotrophic factors, is involved in a variety of neurological functions and plays an important role in brain injury recovery. We investigated the effect of acupuncture intervention in the acute phase of ICH on the prognosis and serum BDNF levels of several patient groups.ObjectiveTo investigate the influence of acupuncture on the prognosis and brain-derived neurotrophic factor (BDNF) levels in patients in the acute phase of ICH.MethodsFrom November 2021 to May 2022, 109 subjects were consecutively enrolled, including patients with ICH, who were randomized into the acupuncture group (AG) and sham acupuncture group (SAG), and a control group (CG). The CG received the same acupuncture intervention as the AG, and the SAG received sham acupuncture, with 14 interventions in each group. The level of consciousness of patients with ICH was assessed and serum BDNF levels were measured in all three groups before the intervention and at 3 weeks after onset, and the level of consciousness and outcomes were assessed at 12 weeks after onset.ResultsAfter the intervention, the level of consciousness of the AG improved significantly (P &lt; 0.05); the BDNF level of only the AG increased significantly (P &lt; 0.05); the changes in Glasgow Coma Scale (GCS) score and BDNF level were significantly greater in the AG than in the SAG (P &lt; 0.05), especially for locomotion (P &lt; 0.05). At 12 weeks post-onset, the AG showed better outcomes and recovery of consciousness than the SAG (P &lt; 0.05).
Brain region-specific genome-wide deoxyribonucleic acid methylation analysis in patients with Alzheimer’s disease
Authors: Ren Gang , Song Shan , Zhang Sheng-Xiao , Liu Yan , Lv Yan , Wang Yan-Hong , Zhao Rong , Li Xin-Yi 
Published: April 2023

ObjectiveAlzheimer’s disease (AD) is a neurodegenerative disease characterized by neuropathology and cognitive decline and associated with age. The comprehensive deoxyribonucleic acid methylation (DNAm)-transcriptome profile association analysis conducted in this study aimed to establish whole-genome DNAm profiles and explore DNAm-related genes and their potential functions. More appropriate biomarkers were expected to be identified in terms of AD.Materials and methodsIllumina 450KGSE59685 dataset AD (n= 54) and HC (n= 21) and ribonucleic-acid-sequencing data GSE118553 dataset AD patients (n= 21) and HCs (n= 13) were obtained from the gene expression omnibus database before a comprehensive DNAm-transcriptome profile association analysis, and we performed functional enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses (KEGG). Three transgenic mice and three wild-type mice were used to validate the hub genes.ResultsA total of 18,104 DNAm sites in healthy controls (n= 21) and AD patients (n= 54) were surveyed across three brain regions (superior temporal gyrus, entorhinal cortex, and dorsolateral prefrontal cortex). With the addition of the transcriptome analysis, eight hypomethylated-related highly expressed genes and 61 hypermethylated-related lowly expressed genes were identified. Based on 69 shared differentially methylated genes (DMGs), the function enrichment analysis indicated Guanosine triphosphate enzymes (GTPase) regulator activity, a synaptic vesicle cycle, and tight junction functioning. Following this, mice-based models of AD were constructed, and five hub DMGs were verified, which represented a powerful, disease-specific DNAm signature for AD.ConclusionThe results revealed that the cross-brain region DNAm was altered in those with AD. The alterations in DNAm affected the target gene expression and participated in the key biological processes of AD. The study provides a valuable epigenetic resource for identifying DNAm-based diagnostic biomarkers, developing effective drugs, and studying AD pathogenesis.
Habitual low carbohydrate high fat diet compared with omnivorous, vegan, and vegetarian diets
Authors: Bogataj Jontez Nives , Kenig Saša , Šik Novak Karin , Petelin Ana , Jenko Pražnikar Zala , Mohorko Nina 
Published: April 2023

BackgroundDietary patterns which exclude whole food groups, such as vegetarian, vegan and low carbohydrate high fat diet (LCHF), are increasingly popular in general public. When carefully planned, all these diets have some known benefits for health, but concerns are also raised in particular for LCHF. The quality of LCHF diet which individuals follow in real life without supervision is not known.MethodsOne hundred thirty healthy individuals with stable body mass following LCHF, vegan, vegetarian and omnivorous diet for at least six months, were compared in a cross-sectional study. Diet was analyzed through 3-day food records and FFQ, anthropometric measurements were performed and serum metabolic biomarkers determined from fasting blood.ResultsParticipants on LCHF diet had the intakes of micronutrients comparable to other groups, while the intakes of macronutrients differed in line with the definition of each diet. The intakes of saturated fats, cholesterol and animal proteins were significantly higher and the intakes of sugars and dietary fibers were lower compared to other groups. Healthy eating index 2015 in this group was the lowest. There were no differences in the levels of glucose, triacylglycerols and CRP among groups. Total and LDL cholesterol levels were significantly higher in LCHF group, in particular in participants with higher ketogenic ratio. Fatty acids intakes and intakes of cholesterol, dietary fibers and animal proteins explained 40% of variance in total cholesterol level, with saturated fatty acids being the strongest positive predictor and monounsaturated fatty acids a negative predictor.ConclusionNone of the self-advised diets provided all the necessary nutrients in optimal levels. Due to the detected increased levels of serum cholesterols, selection of healthy fat sources, higher intake of dietary fibers and partial replacing of animal sources with plant sources of foods should be recommended to the individuals selecting LCFH dietary pattern.Clinical Trial Registration: ClinicalTrials.gov, identifier NCT04347213.
Synergistic interaction and activation of the opioid receptor-NO–cGMP–K+ channel pathway on peripheral antinociception induced by the α-Bisabolol-diclofenac combination
Authors: Ortiz Mario I. 
Published: April 2023

Introduction: The local peripheral combination of analgesic drugs with herbal derivatives may have beneficial effects. Information on the action mechanism of these interactions between drugs is scarce. Therefore, the main of the present study was to determine the pharmacological interaction and action mechanism of the combination α-Bisabolol and diclofenac.Methods: Rats were injected in the dorsal surface of the right hind paw with 1% formalin. Rats received subcutaneous injections in the dorsal surface of paw of vehicles or increasing doses of α-Bisabolol, diclofenac or their combination before formalin injection into the paw. Antinociception of the α-Bisabolol + diclofenac combination was evaluated with and without the local treatment of naloxone, metformin, NG-nitro-L-arginine methyl ester (L-NAME), 1H- (1,2,4)-oxadiazolo (4,2-a) quinoxalin-1-one (ODQ), glibenclamide, glipizide, 4-aminopyridine, tetraethylammonium, apamin, or charybdotoxin.Results: α-Bisabolol, diclofenac or α-Bisabolol-diclofenac combinations produced significant antinociception in the rat (p &lt; 0.05). The experimental effective dose (ED) value of 109.2 µg/paw was different significantly of the theoretical effective dose (ED) of 245.7 µg/paw (synergism). Blockers significantly reverted the antinociception produced by the synergistic combination of α-Bisabolol and diclofenac.Discussion: Data showed a synergism of the α-Bisabolol-diclofenac combination and the activation of the opioid receptor-Nitric Oxide–cyclic GMP–K+ channels pathway and a biguanide-dependent mechanism in order to produce the potentiation of its peripheral antinociception in the formalin test.
The serum soluble scavenger with 5 domains levels: A novel biomarker for individuals with heart failure
Authors: Ge Yulong , Liu Xiaoqiang , Chen Hangwei , Li Gonghao , Xing Xing , Liu Junyi , Zhang Chunxia , Zhuge Ying , Wang Fang 
Published: April 2023

Background: We aimed to explore the relationship between the serum Soluble Scavenger with 5 Domains (SSC5D) levels and heart failure (HF).Methods and Results: We retrospectively enrolled 276 patients diagnosed with HF or normal during hospitalization in Shanghai General Hospital between September 2020 and December 2021. Previously published RNA sequencing data were re-analyzed to confirm the expression profile of SSC5D in failing and non-failing human and mouse heart tissues. Quantitative real-time polymerase chain reaction assay was used to quantify Ssc5d mRNA levels in murine heart tissue after myocardial infarction and transverse aortic constriction surgery. To understand the HF-induced secreted proteins profile, 1,755 secreted proteins were investigated using human dilated cardiomyopathy RNA-seq data, and the results indicated that SSC5D levels were significantly elevated in failing hearts compared to the non-failing. Using single-cell RNA sequencing data, we demonstrated that Ssc5d is predominantly expressed in cardiac fibroblasts. In a murine model of myocardial infarction or transverse aortic constriction, Ssc5d mRNA levels were markedly increased compared with those in the sham group. Similarly, serum SSC5D levels were considerably elevated in the HF group compared with the control group [15,789.35 (10,745.32–23,110.65) pg/mL, 95% CI (16,263.01–19,655.43) vs. 8,938.72 (6,154.97–12,778.81) pg/mL, 95% CI (9,337.50–11,142.93); p &lt; 0.0001]. Moreover, serum SSC5D levels were positively correlated with N-terminal pro-B-type natriuretic peptide (R = 0.4, p = 7.9e-12) and inversely correlated with left ventricular ejection fraction (R = −0.46, p = 9.8e-16).Conclusion: We concluded that SSC5D was a specific response to HF. Serum SSC5D may function as a novel biomarker and therapeutic target for patients with HF.