Laparoscopic Roux-en-Y gastric bypass (RYGB) is the second most performed bariatric procedure and it is considered the procedure of choice to treat patients with severe obesity and gastroesophageal ...reflux disease (GERD). However, some authors described the new onset or the recurrence of GERD symptoms after RYGB, and data at follow-up were scanty. In our center, we evaluated trend in weight, GERD symptoms and obesity-related comorbidities in 45 patients undergone RYGB at least 60 months before (mean follow-up 99.9 ± 22.9 months). At RYGB 51.1% patients referred preoperative GERD symptoms; among them, 47.8% showed an intraoperative hiatal hernia (HH). At medium-term follow-up mean BMI was significantly lower compared to baseline (p < 0.001). Among patients with preoperative GERD, 69.6% had GERD resolution and 30.4% reported postoperative GERD symptoms. Furthermore, 18.2% without preoperative GERD referred postoperative GERD new onset. We confirmed that RYGB as primary intervention provides satisfactory weight loss and a high percentage of GERD symptoms resolution. However, about 24.4% of patients complained of GERD symptoms at medium-term follow-up. The pathophysiology of GERD after RYGB, de novo or persistence, is not completely understood and several hypotheses could be drawn; however, further studies focusing the pathophysiology of these symptoms are needed.
The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid ...correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women's health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5-V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (
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), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies.
Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In ...such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications.
Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation.
In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame.
Food authentication is a growing concern with rising complexities of the food supply network, with fish being an easy target of food fraud. In this regard, NIR spectroscopy has been used as an ...efficient tool for food authentication. This article reviews the latest research advances on NIR based fish authentication. The process from sampling/sample preparation to data analysis has been covered. Special attention was given to NIR spectra pre-processing and its unsupervised and supervised analysis. Sampling is an important aspect of traceability study and samples chosen ought to be a true representative of the population. NIR spectra acquired is often laden with overlapping bands, scattering and highly multicollinear. It needs adequate pre-processing to remove all undesirable features. The pre-processing technique can make or break a model and thus need a trial-and-error approach to find the best fit. As for spectral analysis and modelling, multicollinear nature of NIR spectra demands unsupervised analysis (PCA) to compact the features before application of supervised multivariate techniques such as LDA, PLS-DA, QDA etc. Machine learning approach of modelling has shown promising result in food authentication modelling and negates the need for unsupervised analysis before modelling.
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•Sampling must encompass all geographical, seasonal and size variability in fish.•NIR spectra acquisition ought to be homogenised for samples to avoid outliers later.•Pre-processing removes undesirable effects from spectra & improve modelling.•Traditional model building with NIR follows data reduction and subsequent modelling.•Machine learning eliminates data reduction and uses all information for modelling.
Background: Recent studies have evaluated the upper esophageal sphincter (UES) with high-resolution manometry (HRM) in some esophageal diseases, but not eosinophilic esophagitis (EoE). The aim of our ...study was to evaluate the function of the UES across EoE, gastroesophageal reflux disease (GERD), functional dysphagia (FD), and the relationship with esophageal symptoms, esophageal body contraction, and esophagogastric junction (EGJ) metrics. Methods: HRM was performed on 30 EoE, 18 GERD, and 29 FD patients according to the Chicago Classification 3.0. The study data were exported to the online analysis platform Swallow Gateway. The UES was assessed in terms of UES Resting Pressure (UES-RP), UES Basal Pressure (UES-BP), UES Integrated Relaxation Pressure (UES-IRP), UES Relaxation Time (UES-RT), Basal UES Contractile Integral (Basal UES-CI), Post-Deglutitive UES Contractile Integral (Post-Deglutitive UES-CI), and Proximal Contractile Integral (PCI). Results: ANOVA analysis showed significantly higher values of Post-Deglutitive UES-CI in EoE patients compared with FD patients (p = 0.001). Basal UES-CI and UES-RP showed significantly higher values in EoE (p = 0.002, p = 0.038) and GERD (p < 0.001, p = 0.001) patients compared with FD patients. Correlations between LES-CI and Post-Deglutitive UES-CI, Basal UES-CI, and UES-RP (p ≤ 0.001, p = 0.027, p = 0.017, respectively), and between LES-BP and Post-Deglutitive UES-CI (p = 0.019), independent of diagnosis, were shown. No correlations have been demonstrated between the UES, EGJ metrics, and esophageal symptoms. Conclusions: Some differences in UES metrics in the three different diseases were found. Further studies are needed to confirm the results of our pilot study and possible applications in clinical practice.
Background: The endometrium remains a difficult tissue for the analysis of microbiota, mainly due to the low bacterial presence and the sampling procedures. Among its pathologies, endometrial cancer ...has not yet been completely investigated for its relationship with microbiota composition. In this work, we report on possible correlations between endometrial microbiota dysbiosis and endometrial cancer. Methods: Women with endometrial cancer at various stages of tumor progression were enrolled together with women with a benign polymyomatous uterus as the control. Analyses were performed using biopsies collected at two specific endometrial sites during the surgery. This study adopted two approaches: the absolute quantification of the bacterial load, using droplet digital PCR (ddPCR), and the analysis of the bacterial composition, using a deep metabarcoding NGS procedure. Results: ddPCR provided the first-ever assessment of the absolute quantification of bacterial DNA in the endometrium, confirming a generally low microbial abundance. Metabarcoding analysis revealed a different microbiota distribution in the two endometrial sites, regardless of pathology, accompanied by an overall higher prevalence of pathogenic bacterial genera in cancerous tissues. Conclusions: These results pave the way for future studies aimed at identifying potential biomarkers and gaining a deeper understanding of the role of bacteria associated with tumors.
•The NIR spectroscopy on intact lemons was able to predict fruits quality properties.•The NIR spectroscopy on intact PGI lemons was able to discriminate cultivars.•The NIR spectroscopy on intact PGI ...lemons discriminated their geographical origins.•The NIR spectra on intact lemon fruit were affected by annual growing variation.•The NIR spectroscopy was an useful tool to avoid fraud of high-quality products.
The reflectance NIR spectroscopy and chemometric data treatment on mature intact lemons, Limone di Sorrento PGI (cv Ovale di Sorrento) and Limone Costa D’Amalfi PGI (cv Sfusato Amalfitano) from Campania region, collected in 2018 and 2019, were used to predict properties, and discriminate cultivar and geographical provenance. By PCA, lemon NIR spectra grouped for production years due to the year variation of lemon properties attributable to annual climatic differences, homogeneous in all sites. This agrees with lemon chemical and physical differences by production year. Consequently, the relationship of NIR spectra with lemon quality properties by MLR and the cultivar and provenances discrimination by LDA were affected by year climatic difference; therefore, better model reliability was for single production year. NIR detectability of lemon properties did not appear beyond lemon thick peels, therefore the measured properties of lemon juices could derive from measurable properties of peel correlating with pulp properties.
The Limone Costa d'Amalfi and Limone di Sorrento lemons from the Sorrento Peninsula have Protected Geographical Indication (PGI) and are subject to origin fraud. The 87Sr/86Sr ratio (SrIR) signature ...of lemons and soils was investigated to verify its reliability to trace the PGI lemons and to highlight environmental factors responsible of the lemon SrIRs. The SrIR ranges of each PGI lemon were not discriminating as they overlapped with each other and some non-PGI lemon SrIRs fell within these ranges. The lemon SrIRs were generally not correlated with bulk and bioavailable soil SrIRs, rather, they were the result of plant Sr uptake with different SrIRs depending on interaction between water supplied to soil and soil with different chemical and physical characteristics. The study of lemon SrIRs and the causes of their origin and variability provides a reliable forecast reference for the other PGI agri-food products in the study area.
•Lemon 87Sr/86Sr ratios were not exhaustive for origin discrimination.•Lemon 87Sr/86Sr ratios were not significantly correlated with those of soils.•Lemon 87Sr/86Sr ratios depended by rainwater, sea spray, irrigation water and soil.•87Sr/86Sr ratio trends in lemons and soils depended on volcanic soil properties.•87Sr/86Sr ratios of Sorrento peninsula, Vesuvius, Sele Plain soils were achieved.
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