scholarly journals Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

2021 ◽  
Author(s):  
Pilar Gallego-García ◽  
Nair Varela ◽  
Nuria Estévez-Gómez ◽  
Loretta De Chiara ◽  
Iria Fernández-Silva ◽  
...  
Keyword(s):  
Genomic Data ◽  
Genomic Variation ◽  
Contact Tracing ◽  
Prevention Measures ◽  
Genomic Information ◽  
Effective Prevention ◽  
Viral Particles ◽  
Genomic Approach ◽  
Effective Transmission ◽  
Epidemiological Information

A detailed understanding of how and when SARS-CoV-2 transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced 49 SARS-CoV-2 patient samples from ten local clusters for which partial epidemiological information was available, and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be 1-2 viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.

Family-, Media-, and School-Related Risk Factors of Video Game Addiction

2013 ◽  
Vol 25 (3) ◽  
pp. 118-128 ◽  
Author(s):  
Florian Rehbein ◽  
Dirk Baier
Keyword(s):  
Risk Factors ◽  
Video Game ◽  
Age Groups ◽  
Well Being ◽  
Epidemiological Studies ◽  
Prevention Measures ◽  
School Life ◽  
Video Game Addiction ◽  
Effective Prevention ◽  
Game Addiction

In recent years, a variety of epidemiological studies have provided empirical data on the prevalence of video game addiction (GA) in different age groups. However, few studies investigated the causes of GA and could explain why video game playing as a widespread phenomenon leads to a comparatively small percentage of addicted players. Additionally, the existing longitudinal studies mainly consider psychological trait variables and neglect the possible explanatory value of predictors in socialization regarding media availability, media use, and family and everyday school life. In this paper, the results of a two-wave longitudinal study comprising a sample of students from Grades 4 to 9 (N = 406) are presented. The data show that 15-year-old video game addicts had already exhibited a number of specific risk factors at the age of 10. Students from single-parent families seem to be particularly at risk, as are students with low experienced school well-being and with a weaker social integration in class. The data also indicate that problematic use of video games in childhood increases the risk of GA in adolescence. Male students are especially vulnerable for developing GA. The results of this study are an important contribution to understanding risk factors for GA in adolescents, thereby laying the groundwork for effective prevention measures.

scholarly journals Induction of Multiple Prophages from a Marine Bacterium: a Genomic Approach

2006 ◽  
Vol 72 (7) ◽  
pp. 4995-5001 ◽  
Author(s):  
Feng Chen ◽  
Kui Wang ◽  
Jeneen Stewart ◽  
Robert Belas
Keyword(s):  
Mitomycin C ◽  
Marine Bacterium ◽  
Pcr Amplification ◽  
Pulsed Field Gel Electrophoresis ◽  
Bacterial Genomes ◽  
Dominant Type ◽  
Transmission Electron ◽  
Viral Particles ◽  
Genomic Approach ◽  
Primer Sets

ABSTRACT Approximately 70% of sequenced bacterial genomes contain prophage-like structures, yet little effort has been made to use this information to determine the functions of these elements. The recent genomic sequencing of the marine bacterium Silicibacter sp. strain TM1040 revealed five prophage-like elements in its genome. The genomes of these prophages (named prophages 1 to 5) are approximately 74, 30, 39, 36, and 15 kb long, respectively. To understand the function of these prophages, cultures of TM1040 were treated with mitomycin C to induce the production of viral particles. A significant increase in viral counts and a decrease in bacterial counts when treated with mitomycin C suggested that prophages were induced from TM1040. Transmission electron microscopy revealed one dominant type of siphovirus, while pulsed-field gel electrophoresis demonstrated two major DNA bands, equivalent to 35 and 75 kb, in the lysate. PCR amplification with primer sets specific to each prophage detected the presence of prophages 1, 3, and 4 in the viral lysate, suggesting that these prophages are inducible, but not necessarily to the same level, while prophages 2 and 5 are likely defective or non-mitomycin C-inducible phages. The combination of traditional phage assays and modern microbial genomics provides a quick and efficient way to investigate the functions and inducibility of prophages, particularly for a host harboring multiple prophages with similar sizes and morphological features.

scholarly journals Cystamine attenuated behavioral deficiency via increasing the expression of BDNF and activating PI3K/Akt signaling in 2,5-hexanedione intoxicated rats

2017 ◽  
Vol 6 (2) ◽  
pp. 199-204 ◽  
Author(s):  
Shuo Wang ◽  
Xianjie Li ◽  
Ming Li ◽  
Lulu Jiang ◽  
Hua Yuan ◽  
...  
Keyword(s):  
Public Health ◽  
Organic Solvent ◽  
Health Problem ◽  
Public Health Problem ◽  
Akt Signaling ◽  
Prevention Measures ◽  
Effective Prevention

Organic solvent-induced neurodegeneration is a severe public health problem which has no effective prevention measures yet.

The influence of enzyme therapy with adaptogens when candidiasis on blood parameters, increase the livability and meat productivity of geese

2021 ◽  
pp. 41-52
Author(s):  
R. T. Mannapova ◽  
R. R. Shaikhulov ◽  
A. G. Mannapov
Keyword(s):  
Trace Elements ◽  
Therapeutic Effect ◽  
Live Weight ◽  
The Body ◽  
Biologically Active ◽  
Economic Damage ◽  
Meat Production ◽  
Enzyme Therapy ◽  
Prevention Measures ◽  
Effective Prevention

It has been established that in propolis, which is a biologically active product of beekeeping contains several dozen compounds, trace elements and vitamins. It contains most of the compounds of flavonoid and terpenoid nature, phytoncides, unsaturated aromatic acids, trace elements: copper, cobalt, potassium, sodium, manganese, zinc, calcium, barium, titanium, nickel, chromium, vanadium, tin, vitamins (A, B, C, E, PP), glucose, fructose, cinnamon alcohol. This composition provides a favorable complex effect of propolis on the body: bactericidal and virusocidal (kills bacteria and viruses), bacteriostatic (slows their growth), regenerative (restoring tissues, heals wounds) and fungicidal (kills fungi). The main therapeutic effect in this biologically active beekeeping product is provided by ferulic, caffeic and benzoic acids, galantine, chrysin, isalpine, pinocebrin. They are combined with trace elements and vitamins, as well as probiotics and prebiotics, which provide the greatest therapeutic effect. This circumstance is important for fungal diseases of poultry and especially for candidiasis. Geese candidiasis has been causing great economic damage to poultry farming all over the world in recent decades. The search for effective prevention measures and therapies remains an unsolved problem to date. The data on the development of reactions basophils, pseudoeosinophils, eosinophils, lymphocytes, monocytes on the background of candidiasis and their enzyme adaptogens: probiotic and propolis for traditional microbiotheria is not effective and does not contribute to the restoration of cytological reactions and meat production of poultry have been presented in the article. At the same time as shown by our studies in farms affected by candidiasis geese timely application of enzyme therapy on a background of immune propolis and propitiatory not only contributes to the full restoration of all biological indicators, but more intense live weight gain of poultry and improve the livability of their livestock. This underlines the importance of taking measures to prevent candidiasis in goose farms, together with good conditions for feeding and housing poultry.

scholarly journals Risk Perception of COVID−19 Community Transmission among the Spanish Population

2020 ◽  
Vol 17 (23) ◽  
pp. 8967
Author(s):  
José Miguel Mansilla Domínguez ◽  
Isabel Font Jiménez ◽  
Angel Belzunegui Eraso ◽  
David Peña Otero ◽  
David Díaz Pérez ◽  
...  
Keyword(s):  
Risk Perception ◽  
Public Perception ◽  
Online Survey ◽  
Strong Relationship ◽  
Spanish Population ◽  
Prevention Measures ◽  
Perception Of Risk ◽  
Cross Sectional ◽  
Effective Prevention ◽  
Set Up

On 11 March 2020 the SARS-CoV−2 virus was officially declared a pandemic and measures were set up in various countries to avoid its spread among the population. This paper aims to analyse the perception of risk of COVID−19 infection in the Spanish population. A cross-sectional, descriptive observational study was conducted with a total of 16,372 Spanish participants. An online survey was used to gather data for 5 consecutive days over the compulsory lockdown period which was established after the state of emergency was declared. There is an association between socio-demographic variables and risk perception, and a very strong relationship between this perception and contact and direct experience with the virus in a family, social or professional setting. We also found that compared to working from home, working outside the home increased the perception of risk of infection and the perception of worsening health. Understanding the public perception of the risk of COVID−19 infection is fundamental for establishing effective prevention measures.

scholarly journals ImaGene: a convolutional neural network to quantify natural selection from genomic data

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Luis Torada ◽  
Lucrezia Lorenzon ◽  
Alice Beddis ◽  
Ulas Isildak ◽  
Linda Pattini ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Natural Selection ◽  
Convolutional Neural Network ◽  
Positive Selection ◽  
Genomic Data ◽  
Demographic Model ◽  
Genomic Information ◽  
Joint Inference ◽  
Genetic Bases

Abstract Background The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called , to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection. Results enables genomic information from multiple individuals to be represented as abstract images. Each image is created by stacking aligned genomic data and encoding distinct alleles into separate colors. To detect and quantify signatures of positive selection, implements a convolutional neural network which is trained using simulations. We show how the method implemented in can be affected by data manipulation and learning strategies. In particular, we show how sorting images by row and column leads to accurate predictions. We also demonstrate how the misspecification of the correct demographic model for producing training data can influence the quantification of positive selection. We finally illustrate an approach to estimate the selection coefficient, a continuous variable, using multiclass classification techniques. Conclusions While the use of deep learning in evolutionary genomics is in its infancy, here we demonstrated its potential to detect informative patterns from large-scale genomic data. We implemented methods to process genomic data for deep learning in a user-friendly program called . The joint inference of the evolutionary history of mutations and their functional impact will facilitate mapping studies and provide novel insights into the molecular mechanisms associated with human phenotypes.

scholarly journals Prevention Strategies for Sexual Harassment in Academic Medicine: A Qualitative Study

2020 ◽  
pp. 088626052090313
Author(s):  
Sabine C. Jenner ◽  
Pia Djermester ◽  
Sabine Oertelt-Prigione
Keyword(s):  
Sexual Harassment ◽  
Organizational Development ◽  
Preventive Measures ◽  
Qualitative Content Analysis ◽  
Prevention Measures ◽  
Structured Interviews ◽  
Effective Prevention ◽  
Tertiary Referral Center ◽  
Global Issues ◽  
Institutional Strategies

Sexual harassment and gendered discrimination in the workplace are global issues that can affect anyone regardless of their age, gender, job title, or field of employment. The medical field is also relevantly concerned, yet effective prevention measures are scarce. The purpose of this study was to explore preventive options for sexual harassment in an academic medical context from the employees’ perspective and to develop transferable strategies. We conducted semi-structured interviews with 15 female physicians and 15 female nurses working at a tertiary referral center in Berlin, Germany, in the months of April to November 2015. The one-on-one interviews addressed the perception of sexual harassment and available and desirable preventive measures. Data were analyzed by qualitative content analysis. The participants outlined preventive measures at two levels: individual and institutional. Individual options included personal safety measures and individual protection strategies against patients, peers, and superiors. Institutional strategies included guidelines and workplace policies, structured complaint and reporting procedures, formal training options, and organizational development and leadership strategies. The current study highlights how the prevention of sexual harassment hinges on a combination of individualized and system-wide measures to capture the personal as well as the organizational dimension of sexual harassment. Only a concerted effort addressing both aspects will sensitize the workforce, support the victims, and prevent sexual harassment in medical institutions.

scholarly journals Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1028
Author(s):  
Bruna Pinheiro-Lima ◽  
Rita C. Pereira-Carvalho ◽  
Dione M. T. Alves-Freitas ◽  
Elliot W. Kitajima ◽  
Andreza H. Vidal ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Control Strategies ◽  
Genomic Data ◽  
Plant Viruses ◽  
Asia Minor ◽  
Plant Interactions ◽  
Experimental Conditions ◽  
Lower Efficiency ◽  
Viral Particles ◽  
Pathogenicity Tests

The knowledge of genomic data of new plant viruses is increasing exponentially; however, some aspects of their biology, such as vectors and host range, remain mostly unknown. This information is crucial for the understanding of virus–plant interactions, control strategies, and mechanisms to prevent outbreaks. Typically, rhabdoviruses infect monocot and dicot plants and are vectored in nature by hemipteran sap-sucking insects, including aphids, leafhoppers, and planthoppers. However, several strains of a potentially whitefly-transmitted virus, papaya cytorhabdovirus, were recently described: (i) bean-associated cytorhabdovirus (BaCV) in Brazil, (ii) papaya virus E (PpVE) in Ecuador, and (iii) citrus-associated rhabdovirus (CiaRV) in China. Here, we examine the potential of the Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) to transmit BaCV, its morphological and cytopathological characteristics, and assess the incidence of BaCV across bean producing areas in Brazil. Our results show that BaCV is efficiently transmitted, in experimental conditions, by B. tabaci MEAM1 to bean cultivars, and with lower efficiency to cowpea and soybean. Moreover, we detected BaCV RNA in viruliferous whiteflies but we were unable to visualize viral particles or viroplasm in the whitefly tissues. BaCV could not be singly isolated for pathogenicity tests, identification of the induced symptoms, and the transmission assay. BaCV was detected in five out of the seven states in Brazil included in our study, suggesting that it is widely distributed throughout bean producing areas in the country. This is the first report of a whitefly-transmitted rhabdovirus.

scholarly journals Prediction of the Long-Term Potential Distribution of Cryptorhynchus lapathi (L.) under Climate Change

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 5 ◽  
Author(s):  
Ya Zou ◽  
Linjing Zhang ◽  
Xuezhen Ge ◽  
Siwei Guo ◽  
Xue Li ◽  
...  
Keyword(s):  
Climate Change ◽  
North America ◽  
Potential Distribution ◽  
Climate Models ◽  
Global Climate ◽  
Global Climate Models ◽  
Prevention Measures ◽  
Climate Data ◽  
Effective Prevention ◽  
Future Global Warming

The poplar and willow borer, Cryptorhynchus lapathi (L.), is a severe worldwide quarantine pest that causes great economic, social, and ecological damage in Europe, North America, and Asia. CLIMEX4.0.0 was used to study the likely impact of climate change on the potential global distribution of C. lapathi based on existing (1987–2016) and predicted (2021–2040, 2041–2080, and 2081–2100) climate data. Future climate data were simulated based on global climate models from Coupled Model Inter-comparison Project Phase 5 (CMIP5) under the RCP4.5 projection. The potential distribution of C. lapathi under historical climate conditions mainly includes North America, Africa, Europe, and Asia. Future global warming may cause a northward shift in the northern boundary of potential distribution. The total suitable area would increase by 2080–2100. Additionally, climatic suitability would change in large regions of the northern hemisphere and decrease in a small region of the southern hemisphere. The projected potential distribution will help determine the impacts of climate change and identify areas at risk of pest invasion in the future. In turn, this will help design and implement effective prevention measures for expanding pest populations, using natural enemies, microorganisms, and physical barriers in very favorable regions to impede the movement and oviposition of C. lapathi.

scholarly journals 333 Animal –GRIN a platform for animal genetic information

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 49-49
Author(s):  
Harvey D Blackburn ◽  
Ted Manahan ◽  
Carrie S Wilson ◽  
Wenkai Fu ◽  
Eduardo Cajueiro ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Genomic Data ◽  
Gene Bank ◽  
Genomic Information ◽  
Landscape Genomics ◽  
Bank Managers ◽  
On Line ◽  
The U.S ◽  
Ruby On Rails

Abstract An information system, Animal-GRIN, has been constructed as part of the U.S., Brazilian, and Canadian livestock genetic resource programs. It is designed to provide information to gene bank managers, the research community, and livestock producers about livestock breeds and subpopulations acquired in gene bank collections. The system was developed using a range of free software tools, including: MySQL, Ruby on Rails, Java Script, etc. The system is dynamic and publically accessible (https://nrrc.ars.usda.gov/A-GRIN). Exemplary information in Animal-GRIN consists of: animal identifiers, number and type of samples in the collection, pedigrees, coefficients of genetic relationships between animals within a breed, breeding values, phenotypes, and geographic source. To meet the national need for the long term archiving of genomic information developed with public funds, Animal-GRIN was expanded to store and make publically available genomic information (SNP) from any SNP chip, including custom products. Researchers are encouraged to submit their data upon completion of their publically funded projects. With the drill down concept, users can search the database for genomic information, physical samples associated with the genomic information, and phenotypic information on specific animals. Once animals of interest are found, on-line tools enable users to request either germplasm samples or genomic data. Progress in meeting genetic security for a breed’s collection can also be viewed. To date the U.S. collection has 52,639 animals with almost a million samples representing 36 species, 167 breeds, and 331 subpopulations and these have been entered into Animal-GRIN. Genomic data has been acquired on 1,899 animals representing 36 breeds. The next phase of Animal-GRIN development will be development of landscape genomics components. Acquisition of germplasm samples and associated genomic information are a continuing effort.

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