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Pulse of the pandemic: Iterative topic filtering for clinical information extraction from social media.

J Biomed Inform 2021 Jun 19;120:103844. Epub 2021 Jun 19.

Dept of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge 02139, MA, USA. Electronic address:

The rapid evolution of the COVID-19 pandemic has underscored the need to quickly disseminate the latest clinical knowledge during a public-health emergency. One surprisingly effective platform for healthcare professionals (HCPs) to share knowledge and experiences from the front lines has been social media (for example, the "#medtwitter" community on Twitter). However, identifying clinically-relevant content in social media without manual labeling is a challenge because of the sheer volume of irrelevant data. Read More

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Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota.

Front Microbiol 2021 4;12:673260. Epub 2021 Jun 4.

Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.

Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in transfer at high rates in the gut microbiota. Read More

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Mitigating Antibiotic Resistance Genes in Wastewater by Sequential Treatment with Novel Nanomaterials.

Polymers (Basel) 2021 May 15;13(10). Epub 2021 May 15.

Advanced Polymer Materials and Polymer Recycling Group, National Institute for Research & Development in Chemistry and Petrochemistry ICECHIM, Splaiul Independentei 202, 060021 Bucharest, Romania.

Wastewater (WW) has been widely recognized as the major sink of a variety of emerging pathogens (EPs), antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which may disseminate and impact wider environments. Improving and maximizing WW treatment efficiency to remove these microbial hazards is fundamentally imperative. Despite a variety of physical, biological and chemical treatment technologies, the efficiency of ARG removal is still far from satisfactory. Read More

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Properties affecting transfer and expression of degradative plasmids for the purpose of bioremediation.

Biodegradation 2021 08 27;32(4):361-375. Epub 2021 May 27.

Department of Civil and Environmental Engineering, Duke University, Box 90287, Durham, NC, 27708, USA.

Plasmids, circular DNA that exist and replicate outside of the host chromosome, have been important in the spread of non-essential genes as well as the rapid evolution of prokaryotes. Recent advances in environmental engineering have aimed to utilize the mobility of plasmids carrying degradative genes to disseminate them into the environment for cost-effective and environmentally friendly remediation of harmful contaminants. Here, we review the knowledge surrounding plasmid transfer and the conditions needed for successful transfer and expression of degradative plasmids. Read More

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Log-based software monitoring: a systematic mapping study.

PeerJ Comput Sci 2021 6;7:e489. Epub 2021 May 6.

Department of Software Technology, Delft University of Technology, Delft, Netherlands.

Modern software development and operations rely on monitoring to understand how systems behave in production. The data provided by application logs and runtime environment are essential to detect and diagnose undesired behavior and improve system reliability. However, despite the rich ecosystem around industry-ready log solutions, monitoring complex systems and getting insights from log data remains a challenge. Read More

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First Report of a Foodborne Serovar Gloucester (4:i:l,w) ST34 Strain Harboring and Genes Located in IS-Mediated Composite Transposon.

Front Microbiol 2021 20;12:646101. Epub 2021 Apr 20.

Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.

Extended-spectrum β-lactamases (ESBLs) production and (fluoro)quinolone (FQ) resistance among pose a public health threat. The objective of this study was the phenotypic and genotypic characterization of an ESBL-producing and nalidixic acid-resistant serovar Gloucester isolate (serotype 4:i:l,w) of sequence type 34 (ST34) from ready-to-eat (RTE) meat products in China. Whole-genome short and long read sequencing (HiSeq and MinION) results showed that it contained , , and genes, with and located in chromosomal IS-mediated composite transposon (IS--IS-Tn-- -IS-IS). Read More

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Evaluation of long-term welfare initiatives on working equid welfare and social transmission of knowledge in Mexico.

PLoS One 2021 4;16(5):e0251002. Epub 2021 May 4.

Department of Psychology, Centre for Comparative and Evolutionary Psychology, University of Portsmouth, Portsmouth, United Kingdom.

Working equids play an essential role in supporting livelihoods, providing resilience and income security to people around the world, yet their welfare is often poor. Consequently, animal welfare focussed NGOs employ a range of initiatives aimed at improving standards of working equid welfare. However, there is debate surrounding the efficacy of welfare initiatives utilised and long term monitoring and evaluation of initiatives is rarely undertaken. Read More

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Chlorine disinfection facilitates natural transformation through ROS-mediated oxidative stress.

ISME J 2021 May 3. Epub 2021 May 3.

Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, Australia.

The bacterial infection that involves antimicrobial resistance is a rising global threat to public health. Chlorine-based water disinfection processes can inactivate antibiotic resistant bacteria. However, at the same time, these processes may cause the release of antibiotic resistance genes into the water as free DNA, and consequently increase the risk to disseminate antibiotic resistance via natural transformation. Read More

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Forecasting the dissemination of antibiotic resistance genes across bacterial genomes.

Nat Commun 2021 04 23;12(1):2435. Epub 2021 Apr 23.

The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.

Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. Read More

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CMV Pancreatitis in an Immunocompromised Patient.

Case Rep Crit Care 2021 19;2021:8811396. Epub 2021 Feb 19.

Nassau University Medical Center-Department of Pulmonary and Critical Care Medicine, USA.

Introduction: Cytomegalovirus (CMV) is a common double-stranded DNA (dsDNA) virus affecting a large majority of the world's population. In immunocompetent patients, CMV infection can range anywhere from an asymptomatic course to mononucleosis. However, in the immunocompromised patient, prognosis can be deadly as CMV can disseminate to the retina, liver, lungs, heart, and GI tract. Read More

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February 2021

High Prevalence of Drug Resistance and Class 1 Integrons in Isolated From River Yamuna, India: A Serious Public Health Risk.

Front Microbiol 2021 9;12:621564. Epub 2021 Feb 9.

Department of Microbiology, University of Delhi South Campus, New Delhi, India.

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of , the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of was also investigated. Read More

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February 2021

Pulse of the Pandemic: Iterative Topic Filtering for Clinical Information Extraction from Social Media.

ArXiv 2021 Feb 13. Epub 2021 Feb 13.

Dept of Electrical Engineering and Computer Science, Massachusetts Institute of Technology.

The rapid evolution of the COVID-19 pandemic has underscored the need to quickly disseminate the latest clinical knowledge during a public-health emergency. One surprisingly effective platform for healthcare professionals (HCPs) to share knowledge and experiences from the front lines has been social media (for example, the "#medtwitter" community on Twitter). However, identifying clinically-relevant content in social media without manual labeling is a challenge because of the sheer volume of irrelevant data. Read More

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February 2021

The proficiency of the original host species determines community-level plasmid dynamics.

FEMS Microbiol Ecol 2021 03;97(4)

Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Read More

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[Pillars for excellence in nutrition units - research].

Nutr Hosp 2021 Apr;38(Spec No1):19-28

U.G.C. de Endocrinología y Nutrición. Hospital Regional Universitario de Málaga. Universidad de Málaga. Instituto de Investigación Biomédica de Málaga. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM).

Introduction: Research in clinical nutrition and dietetics consists of "carrying out intellectual and experimental activities in a systematic way with the purpose of increasing knowledge on this topic." The biomedical research carried out in clinical nutrition and dietetics units (UNCyDs) must be clinical-translational, which is understood as the fastest way to ensure that new scientific knowledge is transferred not only to clinical research but also to clinical practice. When UNCyDs conduct research, regardless of type and extent, they achieve higher quality standards in the health care they provide to their users. Read More

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Metagenomic insights into dissemination of antibiotic resistance across bacterial genera in wastewater treatment.

Chemosphere 2021 May 7;271:129563. Epub 2021 Jan 7.

Civil Engineering Department, New Mexico State University, Las Cruces, NM, 88003, USA. Electronic address:

The aim of this study was to evaluate the impacts of conventional wastewater treatment processes including secondary treatment and chlorination on the removal of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and to assess the association of ARGs with their potential hosts in each treatment process. The results showed chlorination with subinhibitory concentration (<8 mg/L) resulted in an increased ARB number in the disinfection effluent. qPCR analysis indicated secondary treatment increased relative abundance of ARGs in remaining bacteria whereas disinfection reduced the relative abundance of those genes effectively. Read More

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Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance.

Antibiotics (Basel) 2021 Jan 12;10(1). Epub 2021 Jan 12.

Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa.

This paper reviews the occurrence of antimicrobial resistance (AMR) in insects, rodents, and pets. Insects (e.g. Read More

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January 2021

Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum.

J Hazard Mater 2021 04 26;408:124985. Epub 2020 Dec 26.

Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China. Electronic address:

Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Read More

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Tn, a Carrier of Tn Family Transposons, Occurs in the Chromosome and in a Genomic Island of Clinical Strains.

Microorganisms 2020 Dec 15;8(12). Epub 2020 Dec 15.

Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.

Transposons of the accessory gene pool contribute to phenotype and to genome plasticity. We studied local strains to ascertain the encroachment of -type site hunter transposons into clinical settings and their associations with other functional modules. Five different Tn family transposons were detected, all chromosomal. Read More

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December 2020

Feasibility of Rapidly Developing and Widely Disseminating Patient Decision Aids to Respond to Urgent Decisional Needs due to the COVID-19 Pandemic.

Med Decis Making 2021 02 10;41(2):233-239. Epub 2020 Dec 10.

University of Ottawa, Ottawa, ON, Canada.

To meet urgent decisional needs of retirement/nursing home residents and their families, our interdisciplinary stakeholder team rapidly developed and disseminated patient decision aids (PtDAs) regarding leaving one's residence during the COVID-19 pandemic. The development steps were as follows: identify urgent decisional needs, develop PtDAs using the Ottawa Decision Support Framework template and minimal International PtDA Standards, obtain stakeholder feedback, broadly disseminate, and incorporate user feedback. Within 2 wk, we developed 2 PtDAs for retirement and nursing home living environments that were informed by decisional needs (identified from public responses to related media reports), current pandemic regulations/guidance, and recent systematic reviews. Read More

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February 2021

Backpack health reduces data-sharing barriers between the medical community and individuals with rare diseases.

Am J Med Genet C Semin Med Genet 2021 03 5;187(1):7-13. Epub 2020 Dec 5.

Backpack Health, Boston, Massachusetts, USA.

Technology has changed the way we approach medical care: health data is constantly being generated, medical discoveries are progressing more rapidly, and individuals are more connected across the world than ever before. Backpack Health is a global personal health record platform that harnesses the power of technology to connect users to their primary health data sources, the medical community, and researchers. By syncing with existing patient portals, health data can be stored on the Backpack Health platform and easily accessed and controlled by users in one connected interface. Read More

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Transcriptional Silencing by TsrA in the Evolution of Pathogenic Vibrio cholerae Biotypes.

mBio 2020 11 24;11(6). Epub 2020 Nov 24.

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

is a globally important pathogen responsible for the severe epidemic diarrheal disease called cholera. The current and ongoing seventh pandemic of cholera is caused by El Tor strains, which have completely replaced the sixth-pandemic classical strains of To successfully establish infection and disseminate to new victims, relies on key virulence factors encoded on horizontally acquired genetic elements. The expression of these factors relies on the regulatory architecture that coordinates the timely expression of virulence determinants during host infection. Read More

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November 2020

Plasmid-borne colistin resistance gene mcr-1 in a multidrug resistant Salmonella enterica serovar Typhimurium isolate from an infant with acute diarrhea in China.

Int J Infect Dis 2021 Feb 16;103:13-18. Epub 2020 Nov 16.

Chinese PLA Center for Disease Control and Prevention, Beijing, China. Electronic address:

Background: Antimicrobial resistance of Salmonella enterica is a major global concern. Recent findings suggest that colistin as a last resort treatment for multidrug-resistant gram-negative bacteria is seriously threatened by the report of plasmid-mediated colistin resistance gene mcr-1 in China.

Methods: A total of 827 S. Read More

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February 2021

Complete Genomic Analysis of VRE From a Cattle Feedlot: Focus on 2 Antibiotic Resistance.

Front Microbiol 2020 15;11:571958. Epub 2020 Oct 15.

Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa.

Practices in intensive animal farming such as the extensive use of antimicrobials have significant impacts on the genetic make-up of bacterial communities, especially on that of human/animal commensals. In this report, whole genome sequencing of two vancomycin-resistant enterococci (VRE) isolates from a cattle feedlot in the North West Province, South Africa, was used to highlight the threats that extensive antimicrobial usage in intensive animal rearing represents for environmental microbiomes and the food chain. The genomic DNA of the studied strains was extracted using a DNA extraction kit. Read More

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October 2020

Beneficial Chromosomal Integration of the Genes for CTX-M Extended-Spectrum β-Lactamase in for Stable Propagation.

mSystems 2020 Sep 29;5(5). Epub 2020 Sep 29.

Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea

The acquired CTX-M-type extended-spectrum-β-lactamase (ESBL)-producing are of great concern in clinical settings because they limit therapeutic options for patients infected by the pathogens. An intriguing clonality of CTX-M ESBL-producing blood isolates was observed from a national cohort study, and comparative genomics were assessed for the 115 blood isolates carrying the gene. The plasmid preference of particular clones of a sequence type (ST) was assessed by liquid mating. Read More

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September 2020

mTOR Modulates Intercellular Signals for Enlargement and Infiltration in Glioblastoma Multiforme.

Cancers (Basel) 2020 Sep 2;12(9). Epub 2020 Sep 2.

Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Roma 55, 56126 Pisa, Italy.

Recently, exosomal release has been related to the acquisition of a malignant phenotype in glioblastoma cancer stem cells (GSCs). Remarkably, intriguing reports demonstrate that GSC-derived extracellular vesicles (EVs) contribute to glioblastoma multiforme (GBM) tumorigenesis via multiple pathways by regulating tumor growth, infiltration, and immune invasion. In fact, GSCs release tumor-promoting macrovesicles that can disseminate as paracrine factors to induce phenotypic alterations in glioma-associated parenchymal cells. Read More

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September 2020

The 'thanato-resistome' - The funeral industry as a potential reservoir of antibiotic resistance: Early insights and perspectives.

Willis Gwenzi

Sci Total Environ 2020 Dec 25;749:141120. Epub 2020 Jul 25.

Biosystems and Environmental Engineering Research Group, Department of Soil Science and Agricultural Engineering, Faculty of Agriculture, University of Zimbabwe, P.O. Box MP167, Mount Pleasant, Harare, Zimbabwe. Electronic address:

The funeral industry is a potential reservoir of antibiotic resistance. The occurrence, human exposure and health risks of antibiotic resistance in the funeral industry were examined. The funeral industry harbours antibiotic resistance to multiple common and last-resort antibiotics, hence constitutes the 'thanato-resistome'. Read More

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December 2020

Lymphatic Vessels in Tumor Dissemination versus Immunotherapy.

Cancer Res 2020 09 30;80(17):3463-3465. Epub 2020 Jun 30.

Wihuri Research Institute and Translational Cancer Medicine Research Program, University of Helsinki, Biomedicum Helsinki, Helsinki, Finland.

During the growth of various cancers, primary tumors can escape antitumor immune responses of their host and eventually disseminate into distant organs. Peritumoral lymphatic vessels connect the primary tumor to lymph nodes, facilitating tumor entry into lymph nodes, systemic circulation, and metastasis. Lymph node metastases that occur frequently provide sites of tumor cell spread, whereas tumor antigen transfer into and presentation in tumor-draining lymph nodes induce activation of tumor-specific T-lymphocyte responses that can result in cytolytic targeting of the tumor. Read More

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September 2020

How the U.S. Agency for Healthcare Research and Quality Promotes Health Literate Health Care.

Stud Health Technol Inform 2020 Jun;269:313-323

Center for Evidence and Practice Improvement Agency for Healthcare Research and Quality, U.S. Department of Health and Human Services.

This report traces the U.S. Agency for Healthcare Research and Quality's (AHRQ) strategic approach to promote health literate health care delivery systems. Read More

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The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review.

Water Res 2020 Aug 7;180:115880. Epub 2020 May 7.

Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland Galway, Ireland.

The natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. Read More

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Novel Transposon Tn Variants Accelerate the Dissemination of (E) in in an Aerobic Biofilm Reactor under Oxytetracycline Stresses.

Environ Sci Technol 2020 06 21;54(11):6781-6791. Epub 2020 May 21.

State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.

Little is known about the mechanisms that disseminate antibiotic resistance genes (ARGs) in wastewater microbial communities under antibiotic stress. The role of horizontal transfer mechanisms in dissemination of ARGs in an aerobic biofilm reactor under incremental oxytetracycline doses from 0 to 50 mg/L was studied. strains were the most common culturable bacteria in the reactor, with (E) as the most prevalent ARGs (73. Read More

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