bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of bacterial genetic diversity together with the increment of eutrophic and phytotoxic risk, the side effect of using raw poultry waste as soil amendment
Authors: Viso Natalia Pin , Rizzo Pedro , Young Brian , Gabioud Emmanuel , Bres Patricia , Riera Nicolas , Merino Lina , Farber Marisa , Crespo Diana 
Published: April 2022

Abstract
Poultry waste has been used as fertilizer to diminish soil degradation caused by long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter, and to examine the effect of their application to agricultural soils over a period of 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of Total and Extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of waste treatment process in compliance with environmental sustainability guidelines.
The changing landscape of immune cells in the fetal mouse testis
Authors: Hosseini Samira , Moody Sarah C , Fietz Daniela , Indumathy Sivanjah , Schuppe Hans-Christian , Hedger Mark P , Loveland Kate L 
Published: April 2022

Abstract
Fetal testis growth involves cell influx and extensive remodeling. Immediately after sex determination in mouse, macrophages enable normal cord formation and removal of inappropriately positioned cells. This study provides new information about macrophages and other immune cells after cord formation in fetal testes, including their density, distribution, and close cellular contacts. C57BL6J mouse testes from embryonic day (E) 13.5 to birth (PND0), were examined using immunofluorescence, immunohistochemistry and RT-qPCR to identify macrophages (F4/80, CD206, MHCII), T cells (CD3), granulocytes/neutrophils (Ly6G) and germ cells (DDX4). F4/80+ cells were the most abundant, comprising 90% of CD45+ cells at E13.5 and declining to 65% at PND0. Changes in size, shape and markers (CD206 and MHCII) documented during this interval align with the understanding that F4/80+ cells have different origins during embryonic life. CD3+ cells and F4/80−/MHCII+ were absent to rare until PND0. Ly6G+ cells were scarce at E13.5 but increased robustly by PND0 to represent half of the CD45+ cells. These immunofluorescence data were in accord with transcript analysis, which showed immune marker mRNAs increased with testis age. F4/80+ and Ly6G+ cells were frequently inside cords adjacent to germ cells at E13.5 and E15.5. F4/80+ cells were often in clusters next to other immune cells. Macrophages inside cords at E13.5 and E15.5 (F4/80Hi/CD206+) were different than macrophages at PND0 (F4/80Dim/CD206−), indicating they have distinct origins. This histological quantification coupled with transcript information identifies new cellular interactions for immune cells in fetal testis morphogenesis and highlights new avenues for studies of their functional significance.
The targets of aspirin in bladder cancer: Bioinformatics analysis
Authors: Li Xiao , Tai Yanghao , Liu Shuying , Gao Yating , Zhang Kaining , Yin Jierong , Zhang Huijuan , Wang Xia , Li Xiaofei , Zhang Dongfeng 
Published: April 2022

Abstract
Background: The anti-carcinogenic properties of aspirin have been observed in some solid tumors. However, the molecular mechanism of therapeutic effects of aspirin on bladder cancer is still indistinct. We introduced a bioinformatics analysis approach, to explore the targets of aspirin in bladder cancer (BC).Methods: To find out the potential targets of aspirin in BC, we analyzed direct protein targets (DPTs) of aspirin in Drug Bank 5.0. The protein-protein interaction (PPI) network and signaling pathway of aspirin DPTs were then analyzed subsequently. A detailed analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway has shown that aspirin is linked to BC. We identified overexpressed genes in BC comparing with normal samples by Oncomine and genes that interlinked with aspirin target genes in BC by STRING. Results: Firstly, we explored 16 direct protein targets (DPT) of aspirin. We analyzed the protein-protein interaction (PPI) network and signaling pathways of aspirin DPT. We found that aspirin is closely associated with a variety of cancers, including BC. Then, we classified mutations in 3 aspirin DPTs (CCND1, MYC and TP53) in BC using the cBio Portal database. In addition, we extracted the top 50 overexpressed genes in bladder cancer by Oncomine and predicted the genes associated with the 3 aspirin DPTs (CCND1, MYC and TP53) in BC by STRING. Finally, 5 exact genes were identified as potential therapeutic targets of aspirin in bladder cancer.Conclusion: The analysis of relevant databases will improve our mechanistic understanding of the role of aspirin in bladder cancer. This will guide the direction of our next drug-disease interaction studies.
Study on hyperlipidemia mechanism of lotus leaves by Network pharmacology and Molecular docking
Authors: ZHANG yanan 
Published: April 2022

Abstract
ObjectiveBased on network pharmacology and molecular docking, analyzing the mechanism of lotus leaves regulating hyperlipidemia.MethodsThe main active chemical components and targets of lotus leaves were obtained though the TCMSP database and screened by ADME; The main targets of hyperlipidemia were obtained by Genecards, OMIM, TTD and DRUGBANK databases; Protein interactions were analyzed through the STRING database; Finding potential protein functions by constructing a PPI network; Metascape software was used to analyze “drug-component-target” and the biological processes and pathways involved. Build a“lotus leaves component-hyperlipemia target” network though Cytoscape3.7.1 software. Molecular docking verification was performed by Autodocktools software.ResultsThe main active ingredients of lotus leaves regulation of hyperlipidemia are Quercetin, Kaempferol, Isorhamnetin, etc.; The main targets are TNF, IL1B, IFNG, IL-6, CCL2, ICAM1, MAPK14, CXCL8, SELE, VCAM1, AKT1, FOS, IL-10,etc.; The biological pathway of lotus leaves regulating hyperlipidemia mainly acts on HIF-1 signaling pathway, Apelin signaling pathway, PPAR signaling pathway, etc. The functions are mainly to regulate hormone response, cell response to lipid, inflammatory response, smooth muscle cell proliferation response, etc. The binding energy of molecular docking is <-5KJ/mol (-1.2KJ/mol), indicating that the target and the composition are more binding.ConclusionThe preliminary study shows that lotus leaves regulation of hyperlipidemia have a multi-component, multi-target and multi-pathway mechanism, which provides data basis for traditional Chinese medicine to regulate hyperlipidemia.
Transcriptomic analysis of peripheral blood from German Shepherd dogs with osteoarthritis for identification of diagnostic biomarkers
Authors: Garces Gabriela Rudd , Vercellini Rosario , Arias Daniel Osvaldo , García Pilar Peral , Padula Gisel , Giovambattista Guillermo 
Published: April 2022

Abstract
Canine forms of osteoarthritis (OA) are very similar to those in humans and represent a welfare problem in the dog world population. In this study, we investigated the transcriptomic profile of peripheral blood in German Shepherd dogs with OA in order to identify putative diagnosis biomarkers. The bulk RNA-seq experiment was performed in a cohort of 12 adult dogs, 5 OA-affected and 7 unaffected. Radiographs of the affected dogs revealed signs of progressive OA in hip, elbow and stifle joints. The expression analysis showed 171 differentially expressed genes (DEGs), 113 were upregulated and 58 were downregulated compared to control dogs P (< 0.01). This pool of genes was functional annotated for signaling pathways using PANTHER tools. No overrepresented pathways were found. To gain further insights of the functional role of the DEGs in OA, we set a threshold of log2FoldChange value between -1.5 and 1.5. We ended up with 24 top up- and downregulated transcripts. Prioritization of these DEGs according to their known functional knowledge, revealed five possible candidates for OA biomarkers. The downregulated OSCAR gene encodes the osteoclast associated Ig-like receptor, which is involved in osteoclastogenesis regulation and bone homeostasis. In addition, the upregulated microRNA MIR339-1 and ncRNAs: LOC106559235 (downregulated), LOC102156762 (downregulated) and LOC111096460 (upregulated) are regulatory sequences, stable for gene profiling assessment in blood and related to OA pathogenesis regulation. We suggest OSCAR as the more likely candidate biomarker for OA diagnosis in dogs and, provide evidence of new circulating regulatory sequences differentially expressed in canine OA.
Relief Effects of Laoshan Cherry extracts as a Dietary Supplement against the Symptoms of Acute Gouty Arthritis in Rats induced by Urate Crystals
Authors: Guo Jiamin , Sun Daqing , Xu Xiaoxiao , Liu Pei , Sun Haixin 
Published: April 2022

Abstract
We evaluated the effects of Laoshan cherry as a food or dietary supplement on relieving the symptoms of acute gouty arthritis in rats induced by urate crystals. Rats in groups of 10 were given Laoshan cherry functional extracts by oral gavage for 21 days and then injected with a sodium nitrate suspension in the rear leg ankle area as an induced acute gouty arthritis model. The ankle swelling for the model (no treatment) group increased significantly (P＜0.05) compared with blank group and experimental groups receiving 3 different doses of cherry extract; the latter displayed significantly less swelling (P＜0.05). Additionally, inflammation of rat ankles were also significantly less for the rats receiving the cherry extracts. Serum uric acid and xanthine oxidase activity also elevated in the model group and these parameters were significantly less in the rats receiving the cherry extracts. The serum levels of the inflammatory cytokine IL-1β were significantly (P<0.05) increased for the model group and was decreased significantly (P<0.05) according to cherry extract dose. These results demonstrated that the cherries possess a functional substance that possessed a significant alleviating effect on the symptoms of gouty arthritis in rats induced by sodium urate injection.
Effect of Particle Breakage on Strength Characteristics of Limestone Aggregate
Authors: Alhani Israa , Albadri Wael M. , N Mohd Jamaludin Md , LIM Sin Mei , Alwash Adam 
Published: April 2022

Abstract
Particle breakage is one of the issues that significantly affect the strength characteristics of aggregate. In this paper, the strength of pre-crushed limestone aggregate was evaluated through investigating the friction angle, stress-strain behaviour, and single-particle strength. The particle breakage phenomenon was studied for samples prepared at different conditions, including non-soaked samples, water-soaked samples, and acid-soaked samples. The purpose of preparing the samples at different conditions was to simulate the effect of environmental factors on the breakage behaviour of limestone aggregate. The test program of this paper consists of two phases of triaxial tests: the initial shearing and second shearing. The test results showed remarkable variations among the samples since limestone aggregate tended to experience more particle breakage after being soaked in water and acid solution. Also, the volume change results exhibited an increase in dilation as the breakage index increases. The test results of this study presented the importance of considering the role of environmental factors in evaluating the particle breakage of limestone aggregate.
mir-301b-5p regulates the Wnt/β-catenin pathway through TXNIP/NLRP3 to reduce the occurrence of anorectal malformations in rats
Authors: shen miao , Liu Dan , Cao Zhengnong , Ge Wu , Lian Peng , Jia Huimin 
Published: April 2022

Abstract
Background To detect the expression of NOD-like receptor family pyrin domain 3 (NLRP3) inflammasomes and the spatiotemporal changes in mir-301b-5p expression during the anorectal development in normal and ARM fetal rats, and their potential association with anorectal malformations (ARMs).Methods Sixty pregnant Wistar rats were randomly divided into normal (administered normal saline) and ARM groups (administered ethylene thiourea). We used immunohistochemistry, western blotting, real-time quantitative polymerase chain reaction (PCR), and fluorescence in situ hybridization (FISH) to detect the expression of proteins and miRNAs on gestational day (GD)14–GD16. According to the TargetScan, TXNIP is the target of mir-301b-5p and the combination of the two is verified by dual luciferase assay. PCR, western blotting, CCK-8 assay, and ELISA to verify the possible regulatory mechanisms in IEC-6 cells. Results Compared with those in the normal group, the expression of NLRP3 inflammasomes increased on GD15 and GD16 in ARM fetal mice, whereas the expression of mir-301b-5p decreased and was related to the activation of NLRP3 inflammasomes. Overexpression of mir-301b-5p inhibited the expression of NLRP3/caspase-1 and decreased the secretion of IL-1β and IL-18 compared with NC group. The dual luciferase test verified that TXNIP is the target of mir-301b-5p. si-TXNIP inhibits the activation of NLRP3 inflammasomes and reduces the expression of β-catenin.Conclusion mir-301b-5p negatively regulates TXNIP/NLRP3 axis, which regulate the wnt/β-catenin pathway in ARMs.
Pathophysiological crosstalk between migraine aura and epilepsy: Effect of lomerizine hydrochloride
Authors: Fujita Kazuki , Shibata Mamoru , Maruki Yuichi , Sakai Fumihiko 
Published: April 2022

Abstract
Background: Migraine and epilepsy are comorbid diseases. Although they are independent clinical entities, we experienced a case of migraine complicated with epilepsy that exhibited unique temporary changes in clinical manifestation.Case presentation: A 29-year-old woman previously diagnosed with both migraine with aura and epilepsy visited our hospital complaining of unusual headaches. In her 20’s, the prodromal symptoms changed from typical scintillating scotoma lasting 20 minutes to moving lights against deja-vu scenery lasting 1-2 minutes. Then, loss of consciousness and urinary incontinence after headaches began to occur. Even generalized convulsion occurred. Considering the clinical symptoms, her headache was thought to be changed from migraine with typical aura to headache attributed to epileptic seizure. Administration of lomerizine hydrochloride decreased her headache attacks, urinary incontinence and loss of consciousness, and seizure.Conclusions: We report a patient with migraine and epilepsy who was successfully treated with lomerizine hydrochloride, an analog of flunarizine hydrochloride widely used in Japan. There may be mutual crosstalk between migraine and epilepsy. Lomerizine hydrochloride may have the efficacy of alleviating migraine and epilepsy.
Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade
Authors: Suardana Ida Bagus Kade , Mahardika Bayu K. , Pharmawati Made , Sudipa Putu H. , Sari Tri Komala , Mahardika Gusti N. 
Published: April 2022

Abstract
Since its discovery at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into many variants, including subvariant BA.2 and the GKA clade. Genomic clarification is needed for better management of the current pandemic as well as the possible re-emergence of novel variants. The sequence of the original strain Wuhan-Hu-1 and approximately 20 representatives of each variant were downloaded from GenBank and GISAID. Two representatives with no track of un-definitive nucleotides were selected. The sequences were aligned using Muscle. The location of insertion/deletion (indel) in the genome was mapped following the open reading frame (ORF) of Wuhan-Hu-1. Amino acid substitutions in all ORFs were analysed separately. Evolutionary analysis was inferred using maximum likelihood. There are two indel sites in ORF1AB, eight in spike, and one each in ORF3A, Matrix (MA), Nucleoprotein (NP), and the 3’-untranslated regions (3’UTR). Some indel sites are not unique, and some are variant specific. There are 10 residues shared by the Omicron, BA2, and GKA lineages. Three deletions in NP are unique to Omicron and BA.2; two substitutions in ORF1AB, four in spike, three in NP, and two in ORF7A and ORF8 were exclusive to the Delta and GPA clades. Delta, Omicron, and BA.2 share the same single residue spike. Three insertions in spike are unique for Omicron and GKA. Phylogenetic analysis shows that the Omicron, BA.2, and GKA clades share a common cluster that emerged from Delta. In conclusion, whole-genome comparison reveals indels and polymorphic amino acids specific to variants or sub-variants. We propose that the GKA clade is an Omicron subvariant. Finally, the higher transmissibility of BA.2 might be attributed to a 48-nucleotide deletion in the 3’UTR.
Characterisation of pineapple cultivars under different storage conditions using infrared thermal imaging coupled with machine learning algorithms
Authors: Ali Maimunah Mohd , Hashim Norhashila , Aziz Samsuzana Abd , Lasekan Ola 
Published: April 2022

Abstract
The non-invasive ability of infrared thermal imaging has gained interest in various food classification and recognition tasks. In this work, infrared thermal imaging was used to distinguish different pineapple cultivars i.e. MD2, Morris, and Josapine which were subjected at different storage temperatures i.e. 5, 10, and 25 °C and a relative humidity of 85 to 90 %. A total of 14 features from the thermal images were obtained to determine the variation in terms of image parameters among different pineapple cultivars. Principal component analysis was applied for feature reduction in order to prevent any effect of significant difference between the selected features. Several types of machine learning algorithms were compared including linear discriminant analysis, quadratic discriminant analysis, support vector machine, k-nearest neighbour, decision tree, and Naïve Bayes to obtain the best performance for the classification of pineapple cultivars. The results showed that support vector machine achieved the best performance from the combination of optimal image parameters with the highest classification rate of 100 %. The ability of infrared thermal imaging coupled with machine learning approaches can be potentially used to distinguish pineapple cultivars which could enhance the grading and sorting processes of the fruit.
Unsupervised Multi-source Domain Adaptation with Graph Convolution Network and Multi-alignment in Mixed Latent Space
Authors: Zhu Hongqing , Chen Dong , Yang Suyi , Dai Yiwen 
Published: April 2022

Abstract
This paper proposes an unspervised Multi-source Domain Adaptation algorithm with Graph convolution network and Multi-alignment in mixed latent space (MDA-GM), which leverages domain labels, data structure, and category labels in a unified network but improve domain-invariant semantic representation by several innovations. Specifically, a novel data structure alignment is proposed to exploit the inherent properties of different domains while using current domain alignment and classification result alignment. Through this design, category consistency can be considered in both latent space, and domain and structure discrepancy between different source domains and the target domain can be eliminated. Moreover, we also use category alignment based on both CNN and GCN features to optimize category decision boundary. Experiment results show that the proposed method brings sufficient improvement especially for adaptation tasks with large shift in data distribution.
Spatial risk assessment of silver fir and Norway spruce dieback driven by climate warming
Authors: Piedallu Christian , Dallery Donatien , Bresson Célia , Legay Myriam , Gégout Jean-Claude , Pierrat Rodolphe 
Published: April 2022

Abstract
Context: A significant forest decline has been noticed these last years in Europe. Managers need tools to better anticipate these massive events.Objectives: We evaluated the efficiency of easily available data about environmental conditions and stand characteristics to determine stand vulnerability and map different levels of risk.Methods: We combined remote sensing images, photo-interpretation, and digital models describing environmental conditions within a modelling approach to achieve spatial risk assessment of stand vulnerability. We focused on silver fir and Norway spruce stands in the Vosges mountains (8.800 km², north-east of France), where severe symptoms of decline are visible.Results: Easily available factors describing environmental conditions were used to design relevant vulnerability maps: using an independent dataset, we predicted two-times (Norway spruce) and ten-times (silver fir) higher mortality rates in the units with a high level of risk compared to the others. Norway spruce were predicted highly vulnerable on 33% of their area versus 7% for silver fir. Mortality was higher where the soils displayed low water availability and had suffered severe drying events these last years; it was lower when the species belonged to uneven-aged stands, in mixture, and in the absence of forest edges. Furthermore, the stands acclimatised to drought conditions were more resilient. Conclusions: Vulnerability maps based on easily available geographic information describing climate, soil, and topography can efficiently discriminate canopy mortality patterns over broad areas, and can be useful tools for managers to mitigate the effects of climate change on forests.