bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breast cancer cell-derived extracellular vesicles transfer miR-182-5p and promote breast carcinogenesis via the CMTM7/EGFR/AKT axis
Authors: Lu Chong , Zhao Yu , Wang Jing , Shi Wei , Dong Fang , Xin Yue , Zhao Xiangwang , Liu Chunping 
Published: July 2021

Abstract
Background
Extracellular vesicles (EVs) derived from tumor cells are implicated in the progression of malignancies through the transfer of molecular cargo microRNAs (miRNAs or miRs). We aimed to explore the role of EVs derived from breast cancer cells carrying miR-182-5p in the occurrence and development of breast cancer.

Methods
Differentially expressed miRNAs and their downstream target genes related to breast cancer were screened through GEO and TCGA databases. miR-182-5p expression was examined in cancer tissues and adjacent normal tissues from patients with breast cancer. EVs were isolated from breast cancer cell line MDA-MB-231 cells and identified. The gain- and loss-of function approaches of miR-182-5p and CKLF-like MARVEL transmembrane domain-containing 7 (CMTM7) were performed in MDA-MB-231 cells and the isolated EVs. Human umbilical vein endothelial cells (HUVECs) were subjected to co-culture with MDA-MB-231 cell-derived EVs and biological behaviors were detected by CCK-8 assay, flow cytometry, immunohistochemical staining, Transwell assay and vessel-like tube formation in vitro. A xenograft mouse model in nude mice was established to observe the tumorigenesis and metastasis of breast cancer cells in vivo.

Results
miR-182-5p was highly expressed in breast cancer tissues and cells, and this high expression was associated with poor prognosis of breast cancer patients. miR-182-5p overexpression was shown to promote tumor angiogenesis in breast cancer. Moreover, our data indicated that miR-182-5p was highly enriched in EVs from MDA-MD-231 cells and then ultimately enhanced the proliferation, migration, and angiogenesis of HUVECs in vitro and in vivo. Moreover, we found that CMTM7 is a target of miR-182-5p. EVs-miR-182-5p promotes tumorigenesis and metastasis of breast cancer cells by regulating the CMTM7/EGFR/AKT signaling axis.

Conclusions
Taken altogether, our findings demonstrates that EVs secreted by breast cancer cells could carry miR-182-5p to aggravate breast cancer through downregulating CMTM7 expression and activating the EGFR/AKT signaling pathway.
Early alterations of cortical thickness and gyrification in migraine without aura: a retrospective MRI study in pediatric patients
Authors: Guarnera Alessia , Bottino Francesca , Napolitano Antonio , Sforza Giorgia , Cappa Marco , Chioma Laura , Pasquini Luca , Rossi-Espagnet Maria Camilla , Lucignani Giulia , Figà-Talamanca Lorenzo , Carducci Chiara , Ruscitto Claudia , Valeriani Massimiliano , Longo Daniela , Papetti Laura 
Published: July 2021

Abstract
Background
Migraine is the most common neurological disease, with high social-economical burden. Although there is growing evidence of brain structural and functional abnormalities in patients with migraine, few studies have been conducted on children and no studies investigating cortical gyrification have been conducted on pediatric patients affected by migraine without aura.

Methods
Seventy-two pediatric patients affected by migraine without aura and eighty-two controls aged between 6 and 18 were retrospectively recruited with the following inclusion criteria: MRI exam showing no morphological or signal abnormalities, no systemic comorbidities, no abnormal neurological examination. Cortical thickness (CT) and local gyrification index (LGI) were obtained through a dedicated algorithm, consisting of a combination of voxel-based and surface-based morphometric techniques. The statistical analysis was performed separately on CT and LGI between: patients and controls; subgroups of controls and subgroups of patients.

Results
Patients showed a decreased LGI in the left superior parietal lobule and in the supramarginal gyrus, compared to controls. Female patients presented a decreased LGI in the right superior, middle and transverse temporal gyri, right postcentral gyrus and supramarginal gyrus compared to male patients. Compared to migraine patients younger than 12 years, the ≥ 12-year-old subjects showed a decreased CT in the superior and middle frontal gyri, pre- and post-central cortex, paracentral lobule, superior and transverse temporal gyri, supramarginal gyrus and posterior insula. Migraine patients experiencing nausea and/or vomiting during headache attacks presented an increased CT in the pars opercularis of the left inferior frontal gyrus.

Conclusions
Differences in CT and LGI in patients affected by migraine without aura may suggest the presence of congenital and acquired abnormalities in migraine and that migraine might represent a vast spectrum of different entities. In particular, ≥ 12-year-old pediatric patients showed a decreased CT in areas related to the executive function and nociceptive networks compared to younger patients, while female patients compared to males showed a decreased CT of the auditory cortex compared to males. Therefore, early and tailored therapies are paramount to obtain migraine control, prevent cerebral reduction of cortical thickness and preserve executive function and nociception networks to ensure a high quality of life.
Au@Ag Core@Shell Nanoparticles Synthesized with Rumex hymenosepalus as Antimicrobial Agent
Authors: Villalobos-Noriega Jesús Mauro Adolfo , Rodríguez-León Ericka , Rodríguez-Beas César , Larios-Rodríguez Eduardo , Plascencia-Jatomea Maribel , Martínez-Higuera Aarón , Acuña-Campa Heriberto , García-Galaz Alfonso , Mora-Monroy Roberto , Alvarez-Cirerol Francisco Javier , Rodríguez-Vázquez Blanca Esthela , Carillo-Torres Roberto Carlos , Iñiguez-Palomares Ramón A. 
Published: July 2021

AbstractIn this work, we used a sequential method of synthesis for gold–silver bimetallic nanoparticles with core@shell structure (Au@AgNPs).Rumex hymenosepalusroot extract (Rh), which presents high content in catechins and stilbenes, was used as reductor agent in nanoparticles synthesis. Size distribution obtained by Transmission Electron Microscopy (TEM) gives a mean diameter of 36 ± 11 nm for Au@AgNPs, 24 ± 4 nm for gold nanoparticles (AuNPs), and 13 ± 3 nm for silver nanoparticles (AgNPs). The geometrical shapes of NPs were principally quasi-spherical. The thickness of the silver shell over AuNPs is around 6 nm and covered by active biomolecules onto the surface. Nanoparticles characterization included high angle annular dark field images (HAADF) recorded with a scanning transmission electron microscope (STEM), Energy-Dispersive X-ray Spectroscopy (EDS), X-Ray Diffraction (XRD), UV–Vis Spectroscopy, Zeta Potential, and Dynamic Light Scattering (DLS). Fourier Transform Infrared Spectrometer (FTIR), and X-ray Photoelectron Spectroscopy (XPS) show that nanoparticles are stabilized by extract molecules. A growth kinetics study was performed using the Gompertz model for microorganisms exposed to nanomaterials. The results indicate that AgNPs and Au@AgNPs affect the lag phase and growth rate ofEscherichia coliandCandida albicansin a dose-dependent manner, with a better response for Au@AgNPs
Glans–urethral meatus–shaft score and penile parameters as preoperative assessment tools for hypospadias surgery outcome
Authors: Shoukry Ahmed , Abbas Ahmed , Abdelwahab Mohamed , Ghoneima Waleed , Shouman Ahmed , El Ghoneimy Mohamed , Morsi Hani , Badawy Hesham , Eissa Mohamed , Aboulela Waseem 
Published: July 2021

Abstract
Background
Our prospective study aims to assess if penile parameters and GMS score can predict the postoperative outcome of patients with hypospadias repaired with the TIP technique.

Methods
This prospective study included patients (6 months–11 years old) with coronal, distal or mid penile hypospadias who underwent Tubularized incised plate (TIP) urethroplasty technique from 2015 to 2017. All patients were assessed preoperatively using GMS score. GMS score included a scale for each component, with the more unfavorable characteristics assigned higher scores. Penile length, urethral plate length, and penoscrotal length were measured using a ruler. Glans width was measured by using a caliper ruler. Demographics and complications were assessed within 3 months of the procedure.

Results
There was a statistically significant difference between complicated and non-complicated patients regarding GMS score, glans width, penoscrotal length, penile length, and urethral plate length/penile length ratio. According to the ROC curve, the cutoff values for GMS score, glans width and penoscrotal length were 6, 14 mm and 5 cm, respectively. The area under the ROC curve for penile length and for urethral plate/penile length ratio was poor and so we could not get a specific cutoff value for either parameters. According to Stepwise logistic regression, the GMS score was the only significant independent parameter while controlling all the other factors. Any increase in the GMS score by one unit would increase the risk of complications 3 times.

Conclusion
GMS score and penile parameters are good predictors and complete each other in preoperative assessment for hypospadias patients. Patients with a high GMS score (above 6) have a higher risk of complication and patients with a Glans width of 14 mm or more and a penoscrotal length of 5 cm or more are associated with less risk of complication.
Early outcome findings of treatment for transperitoneal laparoscopy-assisted pyeloplasty
Authors: Güler Ahmet Gökhan , Karakaya Ali Erdal , Doğan Ahmet Burak , Kandur Yaşar 
Published: July 2021

Abstract
Background
We retrospectively analyzed the initial results of laparoscopic pyeloplasty, among pediatric patients undergoing the procedure by transperitoneal access.

Methods
We retrospectively reviewed the medical records of patients who were operated with transperitoneal laparoscopy-assisted pyeloplasty at our institution between 2015 and 2020.

Results
The mean age of the 51 patients (M/F = 36/15) was 59 ± 49.8 months. The mean preoperative renal pelvis anterior–posterior diameter was 32.9 ± 13.4 mm, and the relative renal function was 42 ± 12.1% on the operation side. Forty-three (84.3%) patients had no excretion on MAG3 examination preop. The number of patients with no excretion decreased to 10 (19.7%) after surgery. One of them underwent a successful endopyelotomy; eight of them underwent a successful laparoscopic re-pyeloplasty. There was nothing to do in only one patient whose DRF decreased to 11%. The mean anterior posterior diameter decreased significantly to 16.7 ± 11.2 mm after surgery (p < 0.001).

Conclusion
Preoperative increased renal pelvis anterior–posterior diameter detected in our study was found to be a risk factor in the failure of transperitoneal laparoscopy-assisted pyeloplasty procedure.
The effect of short-term use of finasteride versus cyproterone acetate on perioperative blood loss with monopolar transurethral resection of prostate
Authors: Abdelbaki Shabieb A. , Al-Falah Adel , Alhefnawy Mohamed , Abozeid Ahmed , Fathi Abdallah 
Published: July 2021

Abstract
Background
Perioperative bleeding is the most common complication related to transurethral resection of prostate; the aim of the study was to compare the effect of pre-operative use of finasteride versus cyproterone acetate (CPA) on blood loss with monopolar TURP.

Methods
This prospective randomized controlled study was conducted on (60) patients with BPH underwent monopolar TURP between July 2019 and July 2020. Patients were distributed into three equal groups; CPA group: 20 patients received cyproterone acetate 50 mg tab BID for two weeks before TURP, finasteride group: 20 patients received single daily dose of finasteride 5 mg for two weeks before TURP, control group: 20 patients received no treatment before TURP, all patients underwent monopolar TURP, and then histopathological examination of the resected tissues was done with assessment of the microvascular density of the prostate.

Results
Our study showed that there was significant decrease in intraoperative blood loss and operative time in CPA and finasteride groups in comparison with control group (p = 0.0012) (p < 0.0001), respectively, significant decrease in post-operative Hb and HCT value in finasteride and control groups in comparison with CPA group (p < 0.01), significant increase in specimen weight in CPA group compared to other groups (p < 0.01), and there was also significant decrease in microvascular density in CPA group in comparison with other groups (p < 0.01).

Conclusion
Cyproterone acetate is more effective than finasteride in decreasing perioperative bleeding with TURP by decreasing microvascular density of the prostate.
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
Authors: Zhang Zhenmiao , Zhang Lu 
Published: July 2021

AbstractBackgroundDue to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs’ nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters.ResultsWe developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs’ weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities andSharoninfant fecal samples.ConclusionsOur findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.
Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana
Authors: Ueno Daishin , Kawabe Harunori , Yamasaki Shotaro , Demura Taku , Kato Ko 
Published: July 2021

Abstract
Background
RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-dependent RNA degradation has not been studied in detail. Here, we developed truncated RNA end sequencing in Arabidopsis thaliana to identify cleavage sites and evaluate the efficiency of cleavage at each site. Although several features are related to RNA cleavage efficiency, the effect of each feature on cleavage efficiency has not been evaluated by considering multiple putative determinants in A. thaliana.

Results
Cleavage site information was acquired from a previous study, and cleavage efficiency at the site level (CSsite value), which indicates the number of reads at each cleavage site normalized to RNA abundance, was calculated. To identify features related to cleavage efficiency at the site level, multiple putative determinants (features) were used to perform feature selection using the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. The results indicated that whole RNA features were important for the CSsite value, in addition to features around cleavage sites. Whole RNA features related to the translation process and nucleotide frequency around cleavage sites were major determinants of cleavage efficiency. The results were verified in a model constructed using only sequence features, which showed that the prediction accuracy was similar to that determined using all features including the translation process, suggesting that cleavage efficiency can be predicted using only sequence information. The LASSO regression model was validated in exogenous genes, which showed that the model constructed using only sequence information can predict cleavage efficiency in both endogenous and exogenous genes.

Conclusions
Feature selection using the LASSO regression model in A. thaliana identified 155 features. Correlation coefficients revealed that whole RNA features are important for determining cleavage efficiency in addition to features around the cleavage sites. The LASSO regression model can predict cleavage efficiency in endogenous and exogenous genes using only sequence information. The model revealed the significance of the effect of multiple determinants on cleavage efficiency, suggesting that sequence features are important for RNA degradation mechanisms in A. thaliana.
Identification and characterization of amphibian SLC26A5 using RNA-Seq
Authors: Wang Zhongying , Wang Qixuan , Wu Hao , Huang Zhiwu 
Published: July 2021

Abstract
Background
Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domain-swapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs. Frog prestin is the only representative in amphibian lineage and the studies of it were quite rare with only one species identified.

Results
Here we report a new coding sequence of SLC26A5 for a frog species, Rana catesbeiana (the American bullfrog). In our study, the SLC26A5 gene of Rana has been mapped, sequenced and cloned successively using RNA-Seq. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of Rana’s inner ear and HEK293T cells transfected with this new coding gene. HEK293T cells expressing Rana prestin showed electrophysiological features similar to that of hair cells from its inner ear. Comparative studies of zebrafish, chick, Rana and an ancient frog species showed that chick and zebrafish prestin lacked NLC. Ancient frog’s prestin was functionally different from Rana.

Conclusions
We mapped and sequenced the SLC26A5 of the Rana catesbeiana from its inner ear cDNA using RNA-Seq. The Rana SLC26A5 cDNA was 2292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. This new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line. While comparing to its orthologs, the amphibian prestin has been evolutionarily changing its function and becomes more advanced than avian and teleost prestin.
Single nucleotide replacement in the Atlantic salmon genome using CRISPR/Cas9 and asymmetrical oligonucleotide donors
Authors: Straume Anne Hege , Kjærner-Semb Erik , Skaftnesmo Kai Ove , Güralp Hilal , Lillico Simon , Wargelius Anna , Edvardsen Rolf Brudvik 
Published: July 2021

Abstract
Background
New breeding technologies (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) has the potential to expedite genetic improvement in aquaculture. The long generation time in Atlantic salmon makes breeding an unattractive solution to obtain homozygous mutants and improving the rates of perfect HDR in founder (F0) fish is thus required. Genome editing can represent small DNA changes down to single nucleotide replacements (SNR). This enables edits such as premature stop codons or single amino acid changes and may be used to obtain fish with traits favorable to aquaculture, e.g. disease resistance. A method for SNR has not yet been demonstrated in salmon.

Results
Using CRISPR/Cas9 and asymmetrical ODNs, we were able to perform precise SNR and introduce a premature stop codon in dnd in F0 salmon. Deep sequencing demonstrated up to 59.2% efficiency in single embryos. In addition, using the same asymmetrical ODN design, we inserted a FLAG element into slc45a2 and dnd, showing high individual perfect HDR efficiencies (up to 36.7 and 32.7%, respectively).

Conclusions
In this work, we demonstrate that precise SNR and knock-in (KI) can be performed in F0 salmon embryos using asymmetrical oligonucleotide (ODN) donors. We suggest that HDR-induced SNR can be applied as a powerful NBT, allowing efficient introgression of favorable alleles and bypassing challenges associated with traditional selective breeding.
Prevalence of human leukocyte antigen HLA-B*57:01 in individuals with HIV in West and Central Africa
Authors: Kolou Malewe , Poda Armel , Diallo Zelica , Konou Esther , Dokpomiwa Tatiana , Zoungrana Jacques , Salou Mounerou , Mba-Tchounga Lionèle , Bigot André , Ouedraogo Abdoul-Salam , Bouyout-Akoutet Marielle , Ekouevi Didier K. , Eholie Serge P. 
Published: July 2021

AbstractBackgroundThe presence of the human leukocyte antigen HLA-B*57:01 is associated with the development of a hypersensitivity reaction to abacavir (ABC). Limited data exist on HLA-B*57:01 prevalence in individuals with HIV-1 in Africa. This study aimed to estimate HLA-B*57:01 prevalence in individuals with HIV-1 in West and Central Africa.MethodsA cross-sectional study was conducted in four countries in West and central Africa (Burkina-Faso, Côte d’Ivoire, Gabon, and Togo) from January 2016 to February 2020 to determine the status of HLA-B*57:01 in adults with HIV-1. The presence of HLA-B*57:01 was determined by using Single Specific Primer-Polymerase Chain Reaction (SSP-PCR) in blood samples. Prevalence rates were stratified based on country.ResultsA total of 4016 (69.8% women) individuals with HIV were enrolled. Their median age was 45, and the interquartile range was 38–52. We included 500 (12.4%) patients in Burkina-Faso, 1453 (36.2%) in Côte d’Ivoire, 951 (23.7%) in Gabon, and 1112 (27.7%) in Togo. The overall HLA-B*57:01 prevalence was 0.1% [95% CI: 0.0–0.2%]. The prevalence of HLA-B*57:01 was similar according to the four countries. Only one case was reported in each country except Togo, with no cases.ConclusionsHLA-B*57:01 prevalence is low in individuals with HIV in West and central Africa, and there is no difference among countries. This study does not confirm the utility of HLA-B*57:01 allele testing for abacavir use in this region.