bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meta-analysis of RNA-Seq datasets highlights novel genes/pathways involved in fat deposition in fat-tail of sheep
Authors: Hosseini Seyedeh Fatemeh , Bakhtiarizadeh Mohammad Reza , Salehi Abdolreza 
Published: May 2023

IntroductionFat-tail in sheep is considered as an important energy reservoir to provide energy as a survival buffer during harsh challenges. However, fat-tail is losing its importance in modern sheep industry systems and thin-tailed breeds are more desirable. Using comparative transcriptome analysis to compare fat-tail tissue between fat- and thin-tailed sheep breeds provides a valuable approach to study the complex genetic factors associated with fat-tail development. However, transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on a meta-analysis.MethodsHence, for the first time, an RNA-Seq meta-analysis on sheep fat-tail transcriptomes was performed using six publicly available datasets.Results and discussionA total of 500 genes (221 up-regulated, 279 down-regulated) were identified as differentially expressed genes (DEGs). A jackknife sensitivity analysis confirmed the robustness of the DEGs. Moreover, QTL and functional enrichment analysis reinforced the importance of the DEGs in the underlying molecular mechanisms of fat deposition. Protein-protein interactions (PPIs) network analysis revealed the functional interactions among the DEGs and the subsequent sub-network analysis led to identify six functional sub-networks. According to the results of the network analysis, down-regulated DEGs in green and pink sub-networks (like collagen subunits IV, V, and VI, integrins 1 and 2, SCD, SCD5, ELOVL6, ACLY, SLC27A2, and LPIN1) may impair lipolysis or fatty acid oxidation and cause fat accumulation in tail. On the other hand, up-regulated DEGs, especially those are presented in green and pink sub-networks (like IL6, RBP4, LEPR, PAI-1, EPHX1, HSD11B1, and FMO2), might contribute to a network controlling fat accumulation in the tail of sheep breed through mediating adipogenesis and fatty acid biosynthesis. Our results highlighted a set of known and novel genes/pathways associated with fat-tail development, which could improve the understanding of molecular mechanisms behind fat deposition in sheep fat-tail.
Application of the “echo-synch protocol” to advance pregnancy onset in ewe lambs at the first reproductive season
Authors: Sotgiu Francesca Daniela , Spezzigu Antonio , Porcu Cristian , Atzori Alberto Stanislao , Sechi Gian Simone , Pasciu Valeria , Molle Giovanni , Berlinguer Fiammetta 
Published: May 2023

IntroductionThis study assessed the efficacy and economic impact of a reproductive protocol based on repeated ultrasound scanning (US) associated with the use of GnRH to advance pregnancy onset in ewe lambs.MethodsPrepubertal ewe lambs (n = 133) were divided into three weight groups (High: HW n = 35; Medium: MW n = 65; Low: LW n = 33). Thereafter, animals were randomly allocated into two subgroups: GnRH, ewe lambs treated with GnRH analog and then exposed to rams; CTR, ewe lambs exposed to rams only. CTR groups were joined with rams as a single flock. GnRH groups were kept separate from rams receiving a single dose of gonadorelin (40 μg/head) and then were evaluated after a week of US. Animals showing corpora lutea received an injection of PGF2α analog (100 μg/head) and then were joined with rams. The remaining ewe lambs received a second dose of gonadorelin and were kept separate from the rams. After another week, animals were checked again and the ones showing corpora lutea were injected with the PGF2α analog, while the others received a third injection of gonadorelin. On the same day, all the animals were joined with rams. Pregnancies were confirmed within 30 days by US. The efficacy of the protocol was determined by assessing differences in the number of days required to achieve pregnancy rates of 25, 50, and 75% and in the total costs and incomes from birth to the end of first lactation within the groups.ResultsThe GnRH-MW group showed the best performances in reaching the threshold pregnancy rates of 25, 50, and 75%, but the effect of treatment was significant only at the 25% threshold (p &lt; 0.01). Both low groups displayed an overall poorer performance at 50 and 75% thresholds than medium and high-weight groups (p = 0.01 and p &lt; 0.01, respectively). The GnRH administration did not advance pregnancy onset in GnRH-HW compared with CTR-HW. In the balance between costs and income, the HW-CTR and MW-GnRH groups showed higher gross margins than the other groups.ConclusionUsing the US/GnRH protocol in ewe lambs appears technically and economically effective in animals that have not reached the optimal weight at the first breeding season, advancing ewe lambs’ pregnncies and increasing farm profitability.
Indolent T-lymphoblastic proliferation with fibrolamellar hepatocellular carcinoma developed after colorectal adenocarcinoma: a case report
Authors: Han Wen , Wang Bei , Yong Xiang , Zhang Yi , Shao Mingyu , Wang Chun 
Published: May 2023

Objective: Indolent T-lymphoblastic proliferation (iT-LBP) is a non-neoplastic disease with an indolent clinical course, manifesting as hyperplasia of immature extrathymic T-lymphoblastic cells. Isolated iT-LBP has been observed, but the majority of iT-LBP cases has been seen in conjunction with other diseases. iT-LBP is easily misdiagnosed as T-lymphoblastic lymphoma/leukemia, and understanding the disease of indolent T-lymphoblastic proliferation may prevent misdiagnosis and missed diagnosis in pathological diagnosis.Case presentation: We report a case morphology, immunophenotypic, and molecular features of iT-LBP combined with fibrolamellar hepatocellular carcinoma developed after colorectal adenocarcinoma and review relevant literature.Conclusion: iT-LBP combined with fibrolamellar hepatocellular carcinoma developed after colorectal adenocarcinoma is relatively rare and should always be considered as a differential diagnosis of T-lymphoblastic lymphoma and scirrhous hepatocellular carcinoma as the two disorders show highly similar clinical features.
Antibacterial Conjugates of Kanamycin A with Vancomycin and Eremomycin: Biological Activity and a New MS-Fragmentation Pattern of Cbz-Protected Amines
Authors: Solyev Pavel N. , Isakova Elena B. , Olsufyeva Evgenia N. 
Published: May 2023

A significant increase of microbial resistance to glycopeptides (especially vancomycin-resistant enterococci and Staphylococcus aureus) prompted researchers to design new semisynthetic glycopeptide derivatives, such as dual-action antibiotics that contain a glycopeptide molecule and an antibacterial agent of a different class. We synthesized novel dimeric conjugates of kanamycin A with glycopeptide antibiotics, vancomycin and eremomycin. Using tandem mass spectrometry fragmentation, UV, IR, and NMR spectral data, it was unequivocally proven that the glycopeptide is attached to the kanamycin A molecule at the position 1 of 2-deoxy-D-streptamine. New MS fragmentation patterns for N-Cbz-protected aminoglycosides were discovered. It was found that the resulting conjugates are active against Gram-positive bacteria, and some are active against vancomycin-resistant strains. Conjugates of two different classes can serve as dual-target antimicrobial candidates for further investigation and improvement.
Characteristics of the Intestine Extracts and Their Effect on the Crude Collagen Fibers of the Body Wall from Sea Cucumber Apostichopus japonicus
Authors: Xu Shi-Qi , Zhang Zheng-Yu , Nie Bin , Du Yi-Nan , Tang Yue , Wu Hai-Tao 
Published: May 2023

Sea cucumbers Apostichopus japonicus will vomit their intestines during certain stimulations, and the collagen of the body wall will then be degraded. To define the effect of the sea cucumber intestine extracts on the body wall, the intestinal extracts and crude collagen fibers (CCF) of sea cucumber A. japonicus were prepared. According to the gelatin zymography, the type of endogenous enzymes in intestinal extracts were mainly serine endopeptidases with optimal activities at pH 9.0 and 40 °C. According to the rheology results, the viscosity of 3% CCF decreased from 32.7 Pa·s to 5.3 Pa·s by adding intestine extracts. The serine protease inhibitor phenylmethanesulfonyl fluoride inhibited the activity of intestinal extracts and increased the viscosity of collagen fibers to 25.7 Pa·s. The results proved that serine protease in the intestinal extracts participated in the process of body wall softening in sea cucumbers.
Bacterial Skin Microbiota of Seabass from Aegean Fish Farms and Antibiotic Susceptibility of Psychrotrophic Pseudomonas
Authors: Aydin Ali , Sudagidan Mert , Mamatova Zhanylbubu , Yurt Mediha Nur Zafer , Ozalp Veli Cengiz , Zornu Jacob , Tavornpanich Saraya , Brun Edgar 
Published: May 2023

Farming seabass (Dicentrarchus labrax) is an essential activity in the Mediterranean basin including the Aegean Sea. The main seabass producer is Turkey accounting for 155,151 tons of production in 2021. In this study, skin swabs of seabass farmed in the Aegean Sea were analysed with regard to the isolation and identification of Pseudomonas. Bacterial microbiota of skin samples (n = 96) from 12 fish farms were investigated using next-generation sequencing (NGS) and metabarcoding analysis. The results demonstrated that Proteobacteria was the dominant bacterial phylum in all samples. At the species level, Pseudomonas lundensis was identified in all samples. Pseudomonas, Shewanella, and Flavobacterium were identified using conventional methods and a total of 46 viable (48% of all NGS+) Pseudomonas were isolated in seabass swab samples. Additionally, antibiotic susceptibility was determined according to standards of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) in psychrotrophic Pseudomonas. Pseudomonas strains were tested for susceptibility to 11 antibiotics (piperacillin-tazobactam, gentamicin, tobramycin, amikacin, doripenem, meropenem, imipenem, levofloxacin, ciprofloxacin, norfloxacin, and tetracycline) from five different groups of antibiotics (penicillins, aminoglycosides, carbapenems, fluoroquinolones, and tetracyclines). The antibiotics chosen were not specifically linked to usage by the aquaculture industry. According to the EUCAST and CLSI, three and two Pseudomonas strains were found to be resistant to doripenem and imipenem (E-test), respectively. All strains were susceptible to piperacillin-tazobactam, amikacin, levofloxacin, and tetracycline. Our data provide insight into different bacteria that are prevalent in the skin microbiota of seabass sampled from the Aegean Sea in Turkey, and into the antibiotic resistance of psychrotrophic Pseudomonas spp.
Transcriptome Analysis of Co-Cultures of THP-1 Human Macrophages with Inactivated Germinated Trichophyton rubrum Conidia
Authors: Cantelli Bruna Aline , Segura Gabriela Gonzalez , Bitencourt Tamires Aparecida , de Abreu Mariana Heinzen , Petrucelli Monise Fazolin , Peronni Kamila , Sanches Pablo Rodrigo , Beleboni Rene Oliveira , da Silva Junior Wilson Araújo , Martinez-Rossi Nilce Maria , Marins Mozart , Fachin Ana Lúcia 
Published: May 2023

Although most mycoses are superficial, the dermatophyte Trichophyton rubrum can cause systemic infections in patients with a weakened immune system, resulting in serious and deep lesions. The aim of this study was to analyze the transcriptome of a human monocyte/macrophage cell line (THP-1) co-cultured with inactivated germinated T. rubrum conidia (IGC) in order to characterize deep infection. Analysis of macrophage viability by lactate dehydrogenase quantification showed the activation of the immune system after 24 h of contact with live germinated T. rubrum conidia (LGC). After standardization of the co-culture conditions, the release of the interleukins TNF-α, IL-8, and IL-12 was quantified. The greater release of IL-12 was observed during co-culturing of THP-1 with IGC, while there was no change in the other cytokines. Next-generation sequencing of the response to T. rubrum IGC identified the modulation of 83 genes; of these, 65 were induced and 18 were repressed. The categorization of the modulated genes showed their involvement in signal transduction, cell communication, and immune response pathways. In total, 16 genes were selected for validation and Pearson’s correlation coefficient was 0.98, indicating a high correlation between RNA-seq and qPCR. Modulation of the expression of all genes was similar for LGC and IGC co-culture; however, the fold-change values were higher for LGC. Due to the high expression of the IL-32 gene in RNA-seq, we quantified this interleukin and observed an increased release in co-culture with T. rubrum. In conclusion, the macrophages-T. rubrum co-culture model revealed the ability of these cells to modulate the immune response, as demonstrated by the release of proinflammatory cytokines and the RNA-seq gene expression profile. The results obtained permit to identify possible molecular targets that are modulated in macrophages and that could be explored in antifungal therapies involving the activation of the immune system.
A Polymorph of Dipeptide Halide Glycyl-L-Alanine Hydroiodide Monohydrate: Crystal Structure, Optical Second Harmonic Generation, Piezoelectricity and Pyroelectricity
Authors: Baptista Rosa M. F. , Gomes Clara S. B. , Silva Bruna , Oliveira João , Almeida Bernardo , Castro Cidália , Rodrigues Pedro V. , Machado Ana , Freitas Ruben B. , Rodrigues Manuel J. L. F. , de Matos Gomes Etelvina , Belsley Michael 
Published: May 2023

A polymorph of glycyl-L-alanine HI.H2O is synthesized from chiral cyclo-glycyl-L-alanine dipeptide. The dipeptide is known to show molecular flexibility in different environments, which leads to polymorphism. The crystal structure of the glycyl-L-alanine HI.H2O polymorph is determined at room temperature and indicates that the space group is polar (P21), with two molecules per unit cell and unit cell parameters a = 7.747 Å, b = 6.435 Å, c = 10.941 Å, α = 90°, β = 107.53(3)°, γ = 90° and V = 520.1(7) Å3. Crystallization in the polar point group 2, with one polar axis parallel to the b axis, allows pyroelectricity and optical second harmonic generation. Thermal melting of the glycyl-L-alanine HI.H2O polymorph starts at 533 K, close to the melting temperature reported for cyclo-glycyl-L-alanine (531 K) and 32 K lower than that reported for linear glycyl-L-alanine dipeptide (563 K), suggesting that although the dipeptide, when crystallized in the polymorphic form, is not anymore in its cyclic form, it keeps a memory of its initial closed chain and therefore shows a thermal memory effect. Here, we report a pyroelectric coefficient as high as 45 µC/m2K occurring at 345 K, one order of magnitude smaller than that of semi-organic ferroelectric triglycine sulphate (TGS) crystal. Moreover, the glycyl-L-alanine HI.H2O polymorph displays a nonlinear optical effective coefficient of 0.14 pm/V, around 14 times smaller than the value from a phase-matched inorganic barium borate (BBO) single crystal. The new polymorph displays an effective piezoelectric coefficient equal to deff=280 pCN−1, when embedded into electrospun polymer fibers, indicating its suitability as an active system for energy harvesting.
In Silico and In Vitro Investigation of the Distribution and Expression of Key Genes in the Fucose Operon of Escherichia coli
Authors: Saif Nehal A. , Hashem Yomna A. , Amin Heba M. , Aziz Ramy K. 
Published: May 2023

Many gut bacteria degrade polysaccharides, providing nutritional advantages to their hosts. Fucose, a mucin degradation product, was suggested as a communication molecule between the resident microbiota and external pathogens. However, the precise role and variants of the fucose utilization pathway remain to be elucidated. Here, we computationally and experimentally investigated the fucose utilization operon of E. coli. While the operon is conserved among E. coli genomes, a variant pathway, in which an ABC transporter system replaces the fucose permease gene (fucP), was computationally identified in 50 out of 1058 genomes. Comparative genomics and subsystems analysis results were confirmed by polymerase chain reaction-based screening of 40 human E. coli isolates, which indicated the conservation of fucP in 92.5% of the isolates (vs. 7.5% of its suggested alternative, yjfF). The in silico predictions were confirmed by in vitro experiments comparing the growth of E. coli strains K12, BL21, and isogenic fucose-utilization K12 mutants. Additionally, fucP and fucI transcripts were quantified in E. coli K12 and BL21, after in silico analysis of their expression in 483 public transcriptomes. In conclusion, E. coli utilizes fucose by two pathway variants, with measurable transcriptional differences. Future studies will explore this variation’s impact on signaling and virulence.
Dynamic Water Quality Changes in the Main Stream of the Yangtze River from Multi-Source Remote Sensing Data
Authors: Zhao Jiarui , Jin Shuanggen , Zhang Yuanyuan 
Published: May 2023

Total nitrogen (TN) and total phosphorus (TP) are important indicators of water quality. Although water quality can be obtained with high accuracy using traditional measurement methods, the cost is high and the area is limited. In the past a single-satellite remote sensing system was normally used to estimate water quality at a large scale, while bands were fewer with limited accuracy. In this paper, inversion models for TN and TP are obtained and validated in the main stream of the Yangtze River using multi-source remote sensing data. The joint inversion models for TN and TP have higher accuracy (R2=0.81 and 0.86, RMSE=0.51 and 0.10 mg L−1) than the single-satellite inversion models (R2=0.61−0.62 and 0.59−0.75, RMSE=0.41−0.61 and 0.07−0.12 mg L−1). Using these models, water quality changes in the Yangtze River are obtained from 2019 to 2021. It is found that TN and TP in the upstream and downstream are high. In spring and autumn, the water quality is poor. The water quality in the Yangtze River is mostly Class III with improvement. Furthermore, it is found that TN and TP are negatively correlated with the water level, temperature and flow in Jiujiang. The p value between water quality and the water level is higher than for other factors, with −0.76 and −0.64 for TN and TP, respectively.
ANALISIS KUALITAS WEBSITE CORONA.JAMBIPROV.GO.ID MENGGUNAKAN METODE WEBQUAL 4.0 DAN IMPORTANCE PERFORMANCE ANALYSIS (IPA)
Authors: Amalia Sintia , Assegaff Setiawan , Sika Xaverius 
Published: May 2023

Abstract

The corona.jambiprov.go.id website is a portal that provides news about Covid 19 in the province of Jambi which was built at the end of March 2020. From the observations made, several problems were found on the corona.jambiprov.go.id website, namely not providing all web sites of all districts that provide information related to the corona virus. The purpose of this study is to determine the level of quality and user ratings of the corona.jambiprov.go.id website based on the results of the analysis using webqual 4.0 and Importance Performance Analysis (IPA). Webqual is divided into 2 variables, namely the independent variable and the dependent variable. The independent variables consist of usability, information quality, service interaction quality. The dependent variable is user satisfaction. Data processing using SPSS IMB 25 software. Based on the results of questionnaire data processing distributed to the special community of Jambi province, it was found that in performance there were variables of service interaction quality that had more influence on the quality of the website and on expectations that the variable of service interactions quality also had more influence on the quality of the Corona.jambiprov.go.id.website.

Keywords: Usability, Information Quality, Service Interaction Quality, User Satisfaction, Webqual

Abstrak

Website corona.jambiprov.go.id merupakan portal yang menyajikan berita seputar covid 19 diwilayah provinsi jambi yang dibangun pada akhir maret 2020. Dari pengamatan yang dilakukan, ditemukan beberapa masalah dalam website corona.jambiprov.go.id yaitu tidak menyediakan semua web dari semua kabupaten yang memberikan informasi terkait corona virus. Tujuan dari penelitian ini yaitu untuk mengetahui tingkat kualitas dan penilaian pengguna terhadap website corona.jambiprov.go.id berdasarkan hasil analisis menggunakan webqual 4.0 dan Importance Performance Analysis (IPA). Webqual terbagi menjadi 2 variabel yaitu variabel bebas dan variabel terikat. Variabel bebas terdiri dari kegunaan, kualitas informasi, kualitas interaksi layanan. Variabel terikat berupa kepuasan pengguna. Pengolahan data menggunakan software SPSS IMB 25. Berdasarkan hasil pengolahan data kuesioner yang disebarkan kepada masyarakat khusus provinsi Jambi didapatkan bahwa pada kinerja terdapat variabel kualitas interaksi layanan lebih berpengaruh terhadap kualitas website dan pada harapan variabel kualitas interaksi layanan juga lebih berpengaruh terhadap kualitas Website corona.jambiprov.go.id.

Kata Kunci: Kegunaan, Kualitas Informasi, Kualitas Interaksi Layanan, Kepuasan Pengguna, Webqual
Eleocharis obtusa (Willd.) Schult. dans la Loire (Région Auvergne-Rhône-Alpes) : une découverte récente ?
Authors: Guillerme Nicolas 
Published: May 2023

Eleocharis obtusa (Willd.) Schult. in the Loire (Auvergne-Rhône-Alpes region of France) : a recent discovery ?
The discovery of Eleocharis obtusa (Willd.) Schult. in the Loire is an interesting discovery. It is a species of North American origin recently observed in Belgium and France. Discreet and very close to Eleocharis ovata (Roth) Roem. & Schult, it could be undervalued in the Auvergne-Rhône-Alpes region and more generally in France. Field surveys confirm that the species is well established in the Forez Plain and in several localities. Apart from a recent part (2001), the consultation of different and ancient parts of herbaria did not confirm the species elsewhere. Finally, the determination criteria derived from the North American keys have been tested on the local populations and are, with some precautions, discriminating.