Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis

To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplementary material as examples. The use of this compact (∼30 terms) controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.

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SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning

10.1101/2021.05.02.442344 ◽

2021 ◽

Author(s):

Advait Balaji ◽

Bryce Kille ◽

Anthony Kappell ◽

Gene D. Godbold ◽

Madeline Diep ◽

...

Keyword(s):

Dna Sequences ◽

Software Tool ◽

Functional Screening ◽

Microbial Pathogenesis ◽

Emerging Pathogens ◽

Pathogenic Potential ◽

Ensemble Machine Learning ◽

Machine Learning Model ◽

Pathogen Characterization

Modern benchtop DNA synthesis techniques and increased concern of emerging pathogens have elevated the importance of screening oligonucleotides for pathogens of concern. However, accurate and sensitive characterization of oligonucleotides is an open challenge for many of the current techniques and ontology-based tools. To address this gap, we have developed a novel software tool, SeqScreen, that can accurately and sensitively characterize short DNA sequences using a set of curated Functions of Sequences of Concern (FunSoCs), novel functional labels specific to microbial pathogenesis which describe the pathogenic potential of individual proteins. We show that our ensemble machine learning model after training on these curations can label sequences with FunSoCs via an imbalanced multi-class and multi-label classification task with high accuracy. In summary, SeqScreen represents a first step towards a novel paradigm of functionally informed pathogen characterization from genomic and metagenomic datasets. SeqScreen is open-source and freely available for download at: https://www.gitlab.com/treangenlab/seqscreen .

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Catalytic Fluorination of Boron Compounds at a Bismuth Redox Platform

10.26434/chemrxiv.9729143 ◽

2019 ◽

Author(s):

Oriol Planas ◽

Feng Wang ◽

Markus Leutzsch ◽

Josep Cornella

Keyword(s):

Transition Metal ◽

Main Group ◽

Group Element ◽

Oxidation States ◽

Boron Compounds ◽

Main Text ◽

Main Group Element ◽

Rational Ligand Design ◽

Supplementary Material

The ability of bismuth to maneuver between different oxidation states in a catalytic redox cycle, mimicking the canonical organometallic steps associated to a transition metal, is an elusive and unprecedented approach in the field of homogeneous catalysis. Herein we present a catalytic protocol based on bismuth, a benign and sustainable main-group element, capable of performing every organometallic step in the context of oxidative fluorination of boron compounds; a territory reserved to transition metals. A rational ligand design featuring hypervalent coordination together with a mechanistic understanding of the fundamental steps, permitted a catalytic fluorination protocol based on a Bi(III)/Bi(V) redox couple, which represents a unique example where a main-group element is capable of outperforming its transition metal counterparts.<br>A main text and supplementary material have been attached as pdf files containing all the methodology, techniques and characterization of the compounds reported.<br>

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Molecular characterization of SARS-CoV-2

Current Molecular Medicine ◽

10.2174/1566524020999201203213037 ◽

2020 ◽

Vol 20 ◽

Author(s):

Miribane Dërmaku-Sopjani ◽

Mentor Sopjani

Keyword(s):

Public Health ◽

Drug Targets ◽

Virus Genome ◽

Health Crisis ◽

Public Health Crisis ◽

Therapeutic Drugs ◽

New Public Health ◽

New Public ◽

And Function

Abstract:: The coronavirus disease 2019 (COVID-19) is currently a new public health crisis threatening the world. This pandemic disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus has been reported to be originated in bats and by yet unknown intermediary animals were transmitted to humans in China 2019. The SARSCoV- 2 spreads faster than its two ancestors the SARS-CoV and Middle East respiratory syndrome coronavirus (MERSCoV) but has reduced fatality. At present, the SARS-CoV-2 has caused about a 1.16 million of deaths with more than 43.4 million confirmed cases worldwide, resulting in a serious threat to public health globally with yet uncertain impact. The disease is transmitted by inhalation or direct contact with an infected person. The incubation period ranges from 1 to 14 days. COVID-19 is accompanied by various symptoms, including cough, fatigue. In most people the disease is mild, but in some other people, such as in elderly and people with chronic diseases, it may progress from pneumonia to a multi-organ dysfunction. Many people are reported asymptomatic. The virus genome is sequenced, but new variants are reported. Numerous biochemical aspects of its structure and function are revealed. To date, no clinically approved vaccines and/or specific therapeutic drugs are available to prevent or treat the COVID-19. However, there are reported intensive researches on the SARSCoV- 2 to potentially identify vaccines and/or drug targets, which may help to overcome the disease. In this review, we discuss recent advances in understanding the molecular structure of SARS-CoV-2 and its biochemical characteristics.

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Leveraging Local Expertise in Stewardship, Hospital Epidemiology and Public Health to Enrich Postgraduate Training in NYC

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.902 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s311-s312

Author(s):

Kelsie Cowman ◽

Belinda Ostrowsky ◽

Susan Seo ◽

Victor Chen ◽

Rachel Bartash ◽

...

Keyword(s):

Public Health ◽

New York ◽

Case Studies ◽

Postgraduate Training ◽

Medical Center ◽

Effective Means ◽

Emerging Pathogens ◽

Hospital Epidemiology ◽

Full Day ◽

Epidemiology And Public Health

Background: New York City is a gateway for emerging pathogens and global threats. In 2013, faculty from Montefiore Medical Center and Memorial Sloan Kettering developed a free half-day workshop for postgraduate trainees in antimicrobial stewardship (AS), infection prevention (IP), hospital epidemiology, and public health. This annual workshop, sponsored by the Infectious Diseases Society of New York (IDSNY), incorporates case studies and expert panel discussions on timely topics such as Ebola, Candida auris, Clostridiodes difficile, measles, nosocomial influenza, drug shortages, and AS/IP “big data.” Methods: From 2013 through 2017, the workshop involved 10–15 interactive AS/IP cases with audience response questions and panel discussions. In 2018–2019, based on feedback, the format was revised to emphasize breakout sessions in which participants actively practiced AS/IP tools, (eg, medication utilization evaluations, epidemiologic curves, and performance improvement devices). Examples of 2018–2019 cases are shown in Figure 1. A pre- and postseminar paper survey was conducted yearly to understand baseline training in AS/IP, desire for future AS/IP careers, and self-reported effectiveness of the workshop. Results: Initially, the primary audience was NYC ID fellows. From 2018 onward, we opened enrollment to pharmacy residents. Approximately 45 NYC ID fellows were eligible for the course each year. Results from 2013 to 2016 surveys were reported previously (Fig. 2). There were 32 attendees in 2018, 42 in 2019. The survey response rate was 88% in 2018 and 95% in 2019, with 68 (92%) total participants. Most participants had received previous training in IP (82%) and AS (94%) (Fig. 3). Most participants reported that the program was a good supplement to their ID training (98%) and that case studies were an effective means of learning IP (100%) and AS (98%). Furthermore, 92% stated they would like additional AS/IP training, and many since 2013 have requested a full-day course. Self-reported interest in future involvement in AS/IP increased after the workshop: IP, 68%–83% (P =.04) and AS, 88%–91% (P = .61). Conclusions: Most trainees reported satisfaction with the workshop and case-study learning method; interest in future AS/IP careers increased after the seminar. We intend to explore Funding: to expand to a full-day program for all NYC postgraduate trainees and AS/IP junior faculty. As such, we hope to obtain the endorsement of professional societies such as SHEA. This workshop could address a crucial educational gap in AS/IP postgraduate training and help sustain our future workforce.Funding: NoneDisclosures: None

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The Effect of Polymer Waste Addition on the Compressive Strength and Water Absorption of Geopolymer Ceramics

Applied Sciences ◽

10.3390/app11083540 ◽

2021 ◽

Vol 11 (8) ◽

pp. 3540

Author(s):

Numfor Linda Bih ◽

Assia Aboubakar Mahamat ◽

Jechonias Bidossèssi Hounkpè ◽

Peter Azikiwe Onwualu ◽

Emmanuel E. Boakye

Keyword(s):

Public Health ◽

Compressive Strength ◽

Fracture Surface ◽

Water Absorption ◽

Chemical Bonding ◽

Low Density Polyethylene ◽

Low Density ◽

Polymer Waste ◽

Pull Out

The quantity of polymer waste in our communities is increasing significantly. It is therefore necessary to consider reuse or recycling waste to avoid an increase in the risk to public health. This project is aimed at using pulverized low-density polyethylene (LDPE) waste as a source to reinforce and improve compressive strength, and to reduce the water absorption of geopolymer ceramics (GC). Clay:LDPE composition consisting of 5%, 10%, and 15% LDPE was geopolymerized with an NaOH/Na2SiO3 solution and cured at 30 °C and 50 °C. Characterization of the geopolymer samples was carried out using XRF and XRD. The microstructure was analyzed by SEM and chemical bonding by FTIR. The SEM micrographs showed LDPE particle pull-out on the geopolymer ceramics’ fracture surface. The result showed that the compressive strength increases with the addition of pulverized polymer waste compared to the controlled without LDPE addition. Water absorption decreased with an increase in LDPE addition in the geopolymer ceramics composite.

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A Framework Convention on Alcohol Control: Getting Concrete about Its Contents

European Journal of Risk Regulation ◽

10.1017/err.2020.73 ◽

2020 ◽

pp. 1-11

Author(s):

Robin ROOM ◽

Jenny CISNEROS ÖRNBERG

Keyword(s):

Public Health ◽

World Health ◽

Alcohol Industry ◽

Alcohol Control ◽

The World ◽

Draft Convention ◽

History Of ◽

Supplementary Material ◽

Health Organization ◽

Narcotic Drugs

This article proposes and discusses the text of a Framework Convention on Alcohol Control, which would serve public health and welfare interests. The history of alcohol’s omission from current drug treaties is briefly discussed. The paper spells out what should be covered in the treaty, using text adapted primarily from the Framework Convention on Tobacco Control, but for the control of trade from the 1961 narcotic drugs treaty. While the draft provides for the treaty to be negotiated under the auspices of the World Health Organization, other auspices are possible. Excluding alcohol industry interests from the negotiation of the treaty is noted as an important precondition. The articles in the draft treaty and their purposes are briefly described, and the divergences from the tobacco treaty are described and justified. The text of the draft treaty is provided as Supplementary Material. Specification of concrete provisions in a draft convention points the way towards more effective global actions and agreements on alcohol control, whatever form they take.

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Vector-Borne Pathogens with Veterinary and Public Health Significance in Melophagus ovinus (Sheep Ked) from the Qinghai-Tibet Plateau

Pathogens ◽

10.3390/pathogens10020249 ◽

2021 ◽

Vol 10 (2) ◽

pp. 249

Author(s):

Qing-Xun Zhang ◽

Ye Wang ◽

Ying Li ◽

Shu-Yi Han ◽

Bo Wang ◽

...

Keyword(s):

Public Health ◽

Molecular Characterization ◽

Tibet Plateau ◽

Border Disease Virus ◽

Public Health Significance ◽

Melophagus Ovinus ◽

Health Significance ◽

Vector Borne ◽

Qinghai Tibet Plateau

Melophagus ovinus (sheep ked) is a hematophagous ectoparasite that mainly parasitizes sheep. In addition to causing inflammation, wool loss, and skin damage to the animal hosts, M. ovinus also serves as a vector for a variety of pathogens and is highly likely to participate in the life and transmission cycle of pathogenic organisms. Herein, we investigated the presence and molecular characterization of vector-borne pathogens in M. ovinus from Qinghai-Tibet Plateau, China. A total of 92 M. ovinus pools collected from the Qinghai province of China were screened for the presence of selected vector-borne pathogens. The overall positive rate of A. ovis, A. bovis, A. phagocytophilum, and T. ovis in M. ovinus was 39.1%, 17.4%, 9.8%, and 89.1%, respectively. All of the samples were negative for Border disease virus (BDV), other Anaplasma species, Babesia spp., Rickettsia spp., and Borrelia spp. Co-infection of different Anaplasma species and T. ovis occurred in 51.2% of all samples with T. ovis. The positive rates of A. ovis, A. bovis, and A. phagocytophilum in different regions and altitudes of the sampling sites were significantly different. Sequence and phylogenetic analysis of target genes confirmed their identity with corresponding pathogens. Our results elucidate the occurrence and molecular characterization of Anaplasma spp. and Theileria spp. in M. ovinus, which could act as potential zoonotic reservoirs. To the best of our knowledge, this is the first report of the detection of A. bovis and A. phagocytophilum DNA in M. ovinus. This study gives the first extensive molecular survey of vector-borne pathogens with veterinary and public health significance in M. ovinus from the Qinghai-Tibet Plateau, China.

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Study of physiological and enzymatic properties and characterization of pathogenic activity of a fungus isolated from moss Sanionia uncinata (Hedw.) Loeske in Antarctica

Polar Biology ◽

10.1007/s00300-019-02473-9 ◽

2019 ◽

Vol 42 (4) ◽

pp. 783-792 ◽

Cited By ~ 1

Author(s):

Graciéle Cunha Alves de Menezes ◽

Rodrigo Paidano Alves ◽

Filipe de Carvalho Victoria ◽

Jair Putzke ◽

Antonio Batista Pereira ◽

...

Keyword(s):

Enzymatic Properties ◽

Properties And Characterization ◽

Pathogenic Activity ◽

Sanionia Uncinata

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Healing Fukushima: Radiation hazards and disaster medicine in post-3.11 Japan

Social Studies of Science ◽

10.1177/0306312719854540 ◽

2019 ◽

Vol 49 (3) ◽

pp. 333-354 ◽

Cited By ~ 2

Author(s):

Shi Lin Loh ◽

Sulfikar Amir

Keyword(s):

Public Health ◽

Nuclear Power ◽

Radiation Risk ◽

Disaster Medicine ◽

Radiation Hazards ◽

Medical Practitioners ◽

Life And Death ◽

Nuclear Disaster ◽

Fukushima Nuclear Disaster

What happens when expertise is forced to face disasters of unprecedented scales? How is knowledge produced in critical moments when every action and decision is a matter of life and death? And how are local social networks mobilized to cope with unforeseen crisis? This paper addresses these questions by examining the emergence of disaster medicine expertise in the aftermath of Fukushima nuclear disaster that struck Japan in 2011. Studies on Fukushima’s impact have to date revolved around the suffering of Tōhoku citizens and the development of Japan’s nuclear energy industry. Acknowledging the gravity of such work, this paper offers an alternative, but equally crucial angle on the disaster: that of the medical caregiving and public health system built in response to radiation hazards resulting from the triple meltdowns at Fukushima Daiichi nuclear power station. Through detailed interviews conducted with eight medical practitioners in Fukushima Prefecture, this paper analyses the significance and impact of Japan’s most recent radiation disaster on its public health infrastructure. To describe the contingent nature of radiation disaster medicine developed in response to radiation risk in Fukushima, we draw on Jasanoff’s characterization of scientific knowledge as ‘serviceable truths’ with regards to public policy and the law, suggesting that expertise in relation to disasters is usefully understood in analogous terms.

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The use of thesauri in online retrieval

Journal of Information Science ◽

10.1177/016555158400800204 ◽

1984 ◽

Vol 8 (2) ◽

pp. 63-66 ◽

Cited By ~ 8

Author(s):

C.P.R. Dubois

Keyword(s):

Information Retrieval ◽

Data Base ◽

Case Studies ◽

Controlled Vocabulary ◽

Free Text ◽

Data Bases ◽

Online Data ◽

Controlled Vocabularies ◽

Semantic Maps ◽

Actual Use

The controlled vocabulary versus the free text approach to information retrieval is reviewed from the mid 1960s to the early 1980s. The dominance of the free text approach following the Cranfield tests is increasingly coming into question as a result of tests on existing online data bases and case studies. This is supported by two case studies on the Coffeeline data base. The differences and values of the two approaches are explored considering thesauri as semantic maps. It is suggested that the most appropriate evaluatory technique for indexing languages is to study the actual use made of various techniques in a wide variety of search environments. Such research is becoming more urgent. Economic and other reasons for the scarcity of online thesauri are reviewed and suggestions are made for methods to secure revenue from thesaurus display facilities. Finally, the promising outlook for renewed develop ment of controlled vocabularies with more effective online display techniques is mentioned, although such development must be based on firm research of user behaviour and needs.

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