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Data Analysis of Multiplex sequencing at sOLiD Platform:A Probabilistic Approach to Characterization and Reliability Increase

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American Journal of Molecular Biology 2018年第1期8卷 26-38页

作者： Fábio Manoel franca Lobato carlos Diego Damasceno Daniela soares Leite Andrea Kelly Ribeiro-dos-santos sylvain Darnet carlos renato francês Nandamudi Lankalapalli Vijaykumar Adamo Lima de santana Engineering and Geoscience Institute Federal University of Western Pará (UFOPa) Santarém Brazil Technological Institute Federal University of Pará (UFPa) Belém Brazil Institute of Mathematical and Computer sciences University of Sao Paulo (USP) Sao Carlos Brazil Department of Morphology and Physiological sciences State University of Pará Marabá Brazil Biological science Institute Federal University of Pará (UFPa) Belém Brazil Laboratory of Computing and Applied Mathematics National Institute for Space Research (INPE) Sao José Dos Campos Brazil

New sequencing technologies such as Illumina/solexa, sOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the sOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on sOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.

关键词： Probabilistic Modeling Health Informatics sOLiD Barcoding system statistical Analysis Multiplex sequencing

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Advancing healthcare through laboratory on a chip technology:Transforming microorganism identification and diagnostics

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World Journal of Clinical Cases 2025年第3期13卷 9-19页

作者： carlos M Ardila Department of Basic sciences Biomedical Stomatology Research GroupUniversidad de Antioquia U de AMedellín 0057Colombia

In a recent case report in the World Journal of Clinical Cases,emphasized the crucial role of rapidly and accurately identifying pathogens to optimize patient treatment ***-on-a-chip(LOC)technology has emerged as a transformative tool in health care,offering rapid,sensitive,and specific identification of *** editorial provides a comprehensive overview of LOC technology,highlighting its principles,advantages,applications,challenges,and future *** studies from the field have demonstrated the practical benefits of LOC devices in clinical diagnostics,epidemiology,and food *** studies have underscored the superiority of LOC technology over traditional methods,showcasing improvements in speed,accuracy,and *** future integration of LOC with biosensors,artificial intelligence,and data analytics promises further innovation and *** call to action emphasizes the importance of continued research,investment,and adoption to realize the full potential of LOC technology in improving healthcare outcomes worldwide.

关键词： Laboratory-on-a-chip Microorganism identification Diagnostics Point-ofcare testing Biosensors

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Natural organic matter quantification in the waters of a semiarid freshwater wetland (Tablas de Daimiel, spain)

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Journal of Environmental sciences 2013年第1期25卷 114-123页

作者： Montserrat Filella Juan carlos Rodríguez-Murillo franc ois Quentel Institute F.-A. Forel University of Geneva10 route de SuisseCH-1290 Versoix Switzerland Museo Nacional de Ciencias Naturales CSICSerrano 115 E-28006 MadridSpain Laboratoire de Chimie Analytique UMR-CNRS 6521 Universit de Bretagne Occidentale6 avenue V.Le GorgeuCS 93837F-29238 Brest Cedex 3France

Dissolved organic matter （DOM） concentrations have been measured in the waters of a semiarid freshwater wetland, the Tablas de Daimiel, spain, when the system-characterised by variable hydroperiodicity conditions, was completely flooded （February 2011）. Fluxes of DOM from the wetland soils to the overlying waters were measured by using a passive diffusion sampler （peeper）. Not only dissolved organic carbon （DOC） concentrations were measured but refractory organic matter （ROM, usually known as humic substances） was also quantified using a novel voltammetric method. Fluorescence spectra were recorded to help in selecting the appropriate standard for ROM quantification, test the homogeneity of DOM in the waters and get an indication of their source. The results obtained show a 7-fold increase in measured ROM concentrations from the Gigtiela River to the outlet, which points to a net exportation of ROM from the wetland and to the existence of an internal source of ROM in the system, probably diffusion from the wetland soils. This hypothesis is confirmed by the flux of ROM from the soils to the water column measured with the peeper and by the common fluorescence characteristics of colunm and interstitial waters. The smaller increase in DOC concentrations along the wetland, in spite of the higher DOC fluxes from soils, suggests that there is significant turnover of organic carbon （OC） in the water column. The system acts as a major carbon sink but, when flooded, exports .OC as DOM.

关键词： organic carbon natural organic matter refractory organic matter DOC ROM humic wetland Daimiel

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Efficacy of antimicrobials in preventing resistance in solid organ transplant recipients:A systematic review of clinical trials

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World Journal of Transplantation 2025年第1期15卷 156-164页

作者： carlos M Ardila Pradeep K Yadalam Jaime Ramírez-Arbelaez Department of Basic sciences Faculty of Dentistry Biomedical Stomatology Research GroupUniversidad de Antioquia U de AMedellín 0057Colombia Department of Postdoctoral Program CIFE University CenterCuernavaca 62330MorelosMexico Department of Periodontics Saveetha Dental CollegeSaveetha Institute of Medical and HealthSIMATSSaveetha UniversityChennai 600077Tamil NaduIndia Department of Transplantation Hospital San Vicente FundaciónRionegro 054047Colombia

BACKGROUND In the absence of effective antimicrobials,transplant surgery is not viable,and antirejection immunosuppressants cannot be administered,as resistant infections compromise the life-saving goal of organ *** To evaluate the efficacy of antimicrobials in preventing resistance in solid organ transplant *** A systematic review was conducted using a search methodology consistent with the preferred reporting items for systematic reviews and *** review included randomized clinical trials that evaluated the efficacy of antimicrobial agents(prophylactic or therapeutic)aimed at preventing antimicrobial *** search strategy involved analyzing multiple databases,including PubMed/MEDLINE,Web of science,Embase,scopus,and sciELO,as well as examining gray literature sources on Google scholar.A comprehensive electronic database search was conducted from the databases’inception until May 2024,with no language *** After the final phase of the eligibility assessment,this systematic review ultimate-ly included 7 articles.A total of 2318 patients were *** most studied microorganisms were cytomegalovirus,although vancomycinresistant enterococci,Clostridioides difficile,and multidrug-resistant Enterobacterales were also *** antimicrobials used in the interventions were mainly maribavir,valganciclovir,gancic-lovir,and *** concern,all clinical trials showed significant proportions of resistant microorga-nisms after the interventions,with no statistically significant differences between the groups(mean resistance 13.47%vs 14.39%),except for two studies that demonstrated greater efficacy of maribavir and valganciclovir(mean resistance 22.2%vs 41.1%in the control group;Ps in three clinical trials were 75,and there were 24 graft rejections in two *** All clinical trials reported significant proportions of antimicrobial-resistant microor

关键词： Antimicrobial resistance Antimicrobials Antivirals solid organ transplant recipients Infections Microorganisms Cytomegalovirus

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No evidence of HPV DNA in esophageal squamous cell carcinoma in a population of southern Brazil

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World Journal of Gastroenterology 2013年第39期19卷 6598-6603页

作者： Luís carlos Moreira Antunes Joo carlos Prolla Antonio de Barros Lopes Marta Pires da Rocha renato Borges Fagundes Programa de Pós-Graduao: Ciências em Gastroenterologia e Hepatologia - Universidade Federal do Rio Grande do sul Porto AlegreRio Grande do Sul 90035-003Brasil Hospital Universitário de santa Maria - Universidade Federal de santa Maria Santa MariaRio Grande do Sul 97119-900Brasil Departamento de Clínica Médica - Universidade Federal de santa Maria Santa MariaRio Grande do Sul 97119-900Brasil

AIM:To investigate the association between human papillomavirus(HPV)and esophageal squamous cell carcinoma(EsCC)in southern ***:We studied 189 esophageal samples from125 patients from three different groups:(1)102 biopsies from 51 patients with EsCC,with one sample from the tumor and another from normal esophageal mucosa distant from the tumor;(2)50 esophageal biopsies from 37 patients with a previous diagnosis of head and neck squamous cell carcinoma(HNsCC);and(3)37 biopsies from esophageal mucosa with normal appearance from 37 dyspeptic patients,not exposed to smoking or alcohol ***-polymerase chain reaction(PCR)with the MY09/11 and GP5/6 L1primers was used to detect HPV L1 in samples fixed in formalin and stored in paraffin *** PCR reactions were performed with a positive control(cervicovaginal samples),with a negative control(Human Genomic DNA)and with a blank reaction containing all reagents except *** took extreme care to prevent DNA contamination in sample collection,processing,and ***:The histological biopsies confirmed the diagnosis of EsCC in 52 samples(51 from EsCC group and 1 from the HNsCC group)and classified as well differentiated(12/52,23.1%),moderately differentiated(27/52,51.9%)or poorly differentiated(7/52,13.5%).One hundred twenty-eight esophageal biopsies were considered normal(51 from the EsCC group,42 from the HNsCC group and 35 from dyspeptic patients).Nine had esophagitis(7 from the HNsCC and 2 from dyspeptic patients).Of a total of 189 samples,only 6 samples had insufficient material for PCR analysis:1 from mucosa distant from the tumor in a patient with EsCC,3from patients with HNsCC and 2 from patients without *** 183 samples(96.8%)GAPDH,G3PDH and/orβ-globin were amplified,thus indicating the adequacy of the DNA in those *** DNA was negative in all the 183 samples tested:52 with EsCC,9 with esophagitis and 122 with normal esophageal ***:There was no evidence of HP

关键词： Esophageal cancer Esophageal squamous cell carcinoma Human papillomavirus Head and neck cancer Polymerase chain reactions Nested-polymerase chain reaction

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Gut microbiota-related complications in cirrhosis

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World Journal of Gastroenterology 2014年第42期20卷 15624-15631页

作者： Isabel Gómez-Hurtado José such Yolanda sanz Rubén francés CIBERehd-Liver Unit Hospital General Universitario Alicante Instituto de Agroquímica y Tecnología de los Alimentos Consejo Superior de Investigaciones Científicas (IATACSIC) Carrer Catedràtic Agustín Escardino Benlloch

Gut microbiota plays an important role in cirrhosis. The liver is constantly challenged with commensal bacteria and their products arriving through the portal vein in the so-called gut-liver axis. Bacterial translocation from the intestinal lumen through the intestinal wall and to mesenteric lymph nodes is facilitated by intestinal bacterial overgrowth, impairment in the permeability of the intestinal mucosal barrier, and deficiencies in local host immune defences. Deranged clearance of endogenous bacteria from portal and systemic circulation turns the gut into the major source of bacterialrelated complications. Liver function may therefore be affected by alterations in the composition of the intestinal microbiota and a role for commensal flora has been evidenced in the pathogenesis of several complications arising in end-stage liver disease such as hepatic encephalopathy, splanchnic arterial vasodilatation and spontaneous bacterial peritonitis. The use of antibioticsis the main therapeutic pipeline in the management of these bacteria-related ***,other strategies aimed at preserving intestinal homeostasis through the use of pre-,pro-or symbiotic formulations are being studied in the last *** this review,the role of intestinal microbiota in the development of the most frequent complications arising in cirrhosis and the different clinical and experimental studies conducted to prevent or improve these complications by modifying the gut microbiota composition are summarized.

关键词： Cirrhosis Encephalopathy Portal hypertension spontaneous bacterial peritonitis Microbiota Bacterial translocation

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Impact of rainfed and irrigated agriculture systems on soil carbon stock under different climate scenarios in the semi-arid region of Brazil

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Journal of Arid Land 2022年第4期14卷 359-373页

作者： André L CARVALHO renato A ARAúJO-NETO Guilherme B LYRA carlos E P CERRI stoécio M F MAIA Center for Agrarian sciences Federal University of AlagoasRio Largo 57072-900Brazil Luiz de Queiroz College of Agriculture The University of Sao PauloPiracicaba 13418-900Brazil Federal Institute of Alagoas Marechal Deodoro 57160-000Brazil

Understanding the dynamics of soil organic carbon(sOC) is of fundamental importance in land use and management, whether in the current researches or in future scenarios of agriculture systems considering climate change. In order to evaluate sOC stock of the three districts(Delmiro Gouveia, Pariconha, and Inhapi districts) in the semi-arid region of Brazil in rainfed and irrigated agriculture systems under different climate scenarios using the Century model, we obtained RCP4.5 and RCP8.5 climate scenarios derived from the Eta Regional Climate Model(Eta-Had GEM2-Es and Eta-MIROC5) from the National Institute for space Research, and then input the data of bulk density, p H, soil texture, maximum temperature, minimum temperature, and rainfall into the soil and climate files of the Century model. The results of this study showed that the Eta-Had GEM2-Es model was effective in estimating air temperature in the future period. In rainfed agriculture system, sOC stock under the baseline scenario was lower than that under RCP4.5 and RCP8.5 climate scenarios, while in irrigated agriculture system, sOC stock in the almost all climate scenarios(RCP4.5 and RCP8.5) and models(Eta-Had GEM2-Es and Eta-MIROC5) will increase by 2100. The results of this study will help producers in the semi-arid region of Brazil adopt specific agriculture systems aimed at mitigating greenhouse gas emissions.

关键词： soil carbon stock agriculture systems climate scenarios Century model semi-arid region

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Immunomodulating effects of antibiotics used in the prophylaxis of bacterial infections in advanced cirrhosis

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World Journal of Gastroenterology 2015年第41期21卷 11493-11501页

作者： Pedro Zapater José Manuel González-Navajas José such Rubén francés CIBERehd Hospital General Universitario de Alicante Digestive Disease Institute Cleveland Clinic Abu Dhabi Departamento Medicina Clínica Universidad Miguel Hernández

The use of norfloxacin either as primary or secondary prophylaxis of bacterial infections in advanced cirrhosis has improved patient's survival. This may be explained not only due to a significant decrease in the number of infections, but also because of a direct immunomodulatory effect. selective intestinal decontamination with norfloxacin reduces translocation of either viable bacteria or bacteria-driven products from the intestinal lumen. In addition, norfloxacin directly modulates the systemic inflammatory response. The proinflammatory cytokine profile secreted by neutrophils from these patients shows a close, significant, and inverse correlation with serum norfloxacin levels. similar effects have been described with other quinolones in different clinical conditions. Although the underlying mechanisms are not well defined for most of the antibiotics, the pathways triggered for norfloxacin to induce such immunomodulatory effects involve the down-regulation of pro-inflammatory inducible nitric oxide synthase, cyclooxygenase-2, and NF-κB and the up-regulation of heme-oxygenase 1 and IL-10 expression. The knowledge of these immunomodulatory effects, additional to their bactericidal role, improves our comprehension of the interaction between antibiotics and the cellular host response and offer new possibilities for the development of new therapeutic strategies to manage and prevent bacterial infections in cirrhosis.

关键词： Cirrhosis Prophylaxis Cytokines Bacterial DNA Norf

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Theranostic of orthotopic gliomas by core-shell structured nanoplatforms

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Light(science & Applications) 2022年第6期11卷 1034-1035页

作者： Luis D.carlos Phantom-G CICECO-Aveiro Institute of MaterialsPhysics DepartmentUniversity of Aveiro3810-193 AveiroPortugal

smart designed core-shell nanostructures formed by a YVO_(4)∶Nd^(3+) nanoparticle as the core,the sonosensitizer hematoporphyrinmonomethyl ether as the carrier,and MnO_(2) nanosheets as the shell demonstrate bimodal ... 详细信息

关键词： modal glioma orthotopic

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A sIMPLE METHOD TO DETERMINE THE DAYLIGHT FACTOR FROM THE VERTICAL DAYLIGHT FACTOR IN DIFFERENT sTREET CANYON GEOMETRY

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Journal of Green Building 2016年第2期11卷 75-92页

作者： Jorge s.carlos C-MADE Centre of Materials and Building TechnologiesUniversity of Beira InteriorCalçada Fonte do Lameiro6200-358 CovilhãPortugal

This paper investigates the main characteristics of daylight on any window in a street *** sky component and the light reflected from the surroundings are described to determine the vertical daylight factor(VDF).several street canyon types are characterized taking into account their different height/width and any level of the window is analysed.A simple calculation method uses trigonometric equations based on the sky and the geometry of the *** results were previ-ously evaluated considering different daylight procedures obtained by other *** study reveals that the reflectance within an urban canyon plays an important role in the amount of daylight onto any window with more relevance in a deep canyon and low sky *** graphical presentation that result from this investiga-tion can rapidly assist building and urban designers in an early stage design where assumptions and the lay out of the main design take place.

关键词： vertical daylight factor urban canyon configuration factor diffuse light isotropic overcast sky

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