scholarly journals Genetic diversity of Leptospira isolates in Lao PDR and genome analysis of an outbreak strain

2021 ◽  
Vol 15 (12) ◽  
pp. e0010076
Author(s):  
Linda Grillová ◽  
Matthew T. Robinson ◽  
Anisone Chanthongthip ◽  
Antony T. Vincent ◽  
Cecilia Nieves ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Genome Analysis ◽  
Current Knowledge ◽  
Lao Pdr ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Clonal Group ◽  
Niche Adaptation ◽  
Large Outbreak ◽  
Causative Agents

Background Although Southeast Asia is one of the most leptospirosis afflicted regions, little is known about the diversity and molecular epidemiology of the causative agents of this widespread and emerging zoonotic disease. Methodology/Principal findings We used whole genome sequencing to examine genetic variation in 75 Leptospira strains isolated from patients in the Lao PDR (Laos) between 2006 and 2017. Eleven serogroups from 4 Leptospira species and 43 cgMLST-defined clonal groups (CGs) were identified. The most prevalent CG was CG272 (n = 18, 26.8%), composed of L. interrogans serogroup Autumnalis isolates. This genotype was recovered throughout the 12-year period and was associated with deaths, and with a large outbreak in neighbouring Thailand. Genome analysis reveals that the CG272 strains form a highly clonal group of strains that have, for yet unknown reasons, recently spread in Laos and Thailand. Additionally, accessory genes clearly discriminate CG272 strains from the other Leptospira strains. Conclusions/Significance The present study reveals a high diversity of Leptospira genotypes in Laos, thus extending our current knowledge of the pan- and core-genomes of these life-threatening pathogens. Our results demonstrate that the CG272 strains belong to a unique clonal group, which probably evolved through clonal expansion following niche adaptation. Additional epidemiological studies are required to better evaluate the spread of this genotype in Southeast Asia. To further investigate the key factors driving the virulence and spread of these pathogens, more intense genomic surveillance is needed, combining detailed clinical and epidemiological data.

scholarly journals Methods for epidemiological studies in competitive cycling: an extension of the IOC consensus statement on methods for recording and reporting of epidemiological data on injury and illness in sport 2020

2021 ◽  
pp. bjsports-2020-103906
Author(s):  
Benjamin Clarsen ◽  
Babette M Pluim ◽  
Víctor Moreno-Pérez ◽  
Xavier Bigard ◽  
Cheri Blauwet ◽  
...  
Keyword(s):  
Consensus Statement ◽  
Expert Panel ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Population Characteristics ◽  
Exposure Study ◽  
Injury Mechanisms ◽  
Study Population ◽  
Final Manuscript ◽  
Collection Methods

In 2020, the IOC released a consensus statement that provides overall guidelines for the recording and reporting of epidemiological data on injury and illness in sport. Some aspects of this statement need to be further specified on a sport-by-sport basis. To extend the IOC consensus statement on methods for recording and reporting of epidemiological data on injury and illness in sports and to meet the sport-specific requirements of all cycling disciplines regulated by the Union Cycliste Internationale (UCI). A panel of 20 experts, all with experience in cycling or cycling medicine, participated in the drafting of this cycling-specific extension of the IOC consensus statement. In preparation, panel members were sent the IOC consensus statement, the first draft of this manuscript and a list of topics to be discussed. The expert panel met in July 2020 for a 1-day video conference to discuss the manuscript and specific topics. The final manuscript was developed in an iterative process involving all panel members. This paper extends the IOC consensus statement to provide cycling-specific recommendations on health problem definitions, mode of onset, injury mechanisms and circumstances, diagnosis classifications, exposure, study population characteristics and data collection methods. Recommendations apply to all UCI cycling disciplines, for both able-bodied cyclists and para-cyclists. The recommendations presented in this consensus statement will improve the consistency and accuracy of future epidemiological studies of injury and illness in cycling.

scholarly journals Genetic Contribution of Endometriosis to the Risk of Developing Hormone-Related Cancers

2021 ◽  
Vol 22 (11) ◽  
pp. 6083
Author(s):  
Aintzane Rueda-Martínez ◽  
Aiara Garitazelaia ◽  
Ariadna Cilleros-Portet ◽  
Sergi Marí ◽  
Rebeca Arauzo ◽  
...  
Keyword(s):  
Mendelian Randomization ◽  
Clear Cell ◽  
Association Studies ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Gynecological Disorder ◽  
Robust Evidence

Endometriosis is a common gynecological disorder that has been associated with endometrial, breast and epithelial ovarian cancers in epidemiological studies. Since complex diseases are a result of multiple environmental and genetic factors, we hypothesized that the biological mechanism underlying their comorbidity might be explained, at least in part, by shared genetics. To assess their potential genetic relationship, we performed a two-sample mendelian randomization (2SMR) analysis on results from public genome-wide association studies (GWAS). This analysis confirmed previously reported genetic pleiotropy between endometriosis and endometrial cancer. We present robust evidence supporting a causal genetic association between endometriosis and ovarian cancer, particularly with the clear cell and endometrioid subtypes. Our study also identified genetic variants that could explain those associations, opening the door to further functional experiments. Overall, this work demonstrates the value of genomic analyses to support epidemiological data, and to identify targets of relevance in multiple disorders.

scholarly journals Molecular Subtyping of Blastocystis sp. Isolated from Farmed Animals in Southern Italy

2021 ◽  
Vol 9 (8) ◽  
pp. 1656
Author(s):  
Simona Gabrielli ◽  
Marialetizia Palomba ◽  
Federica Furzi ◽  
Emanuele Brianti ◽  
Gabriella Gaglio ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Pcr Amplification ◽  
Epidemiological Studies ◽  
Fallow Deer ◽  
Small Subunit ◽  
Zoonotic Transmission ◽  
Ssu Rrna ◽  
Molecular Approaches ◽  
Wide Range ◽  
Blastocystis Sp

Blastocystis is a common intestinal protist distributed worldwide, infecting humans and a wide range of domestic and wild animals. It exhibits an extensive genetic diversity and, so far, 25 distinct small subunit ribosomal RNA (SSU rRNA) lineages termed subtypes (STs)) have been characterized; among them, 12 have thus far been reported in humans. The aims of the present study were to detect and genetically characterize Blastocystis sp. in synantropic animals to improve our current knowledge on the distribution and zoonotic transmission of Blastocystis STs in Italy. Samples were collected from N = 193 farmed animals and submitted to DNA extraction and PCR amplification of the SSU rRNA. Blastocystis was detected in 60 samples (31.08%) and successfully subtyped. Phylogenetic analysis evidenced that the isolates from fallow deer, goats, and pigs (N = 9) clustered within the ST5; those from pheasants (N = 2) in the ST6; those from chickens (N = 8) in the ST7; those from sheep (N = 6) in the ST10; and those from water buffaloes (N = 9) in the ST14 clade. The comparison between the present isolates from animals and those previously detected in humans in Italy suggested the animal-to-human spillover for ST6 and ST7. The present study represents the widest Blastocystis survey performed thus far in farmed animals in Italy. Further epidemiological studies using molecular approaches are required to determine the occurrence and distribution of Blastocystis STs in other potential animal reservoirs in Italy and to define the pathways of zoonotic transmission.

scholarly journals A deep cascaded segmentation of obstructive sleep apnea-relevant organs from sagittal spine MRI

2021 ◽  
Vol 16 (4) ◽  
pp. 579-588
Author(s):  
Tatyana Ivanovska ◽  
Amro Daboul ◽  
Oleksandr Kalentev ◽  
Norbert Hosten ◽  
Reiner Biffar ◽  
...  
Keyword(s):  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Soft Palate ◽  
High Speed ◽  
Sleep Apnea Syndrome ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Obstructive Sleep ◽  
Validation Set ◽  
Spine Mri

Abstract Purpose The main purpose of this work was to develop an efficient approach for segmentation of structures that are relevant for diagnosis and treatment of obstructive sleep apnea syndrome (OSAS), namely pharynx, tongue, and soft palate, from mid-sagittal magnetic resonance imaging (MR) data. This framework will be applied to big data acquired within an on-going epidemiological study from a general population. Methods A deep cascaded framework for subsequent segmentation of pharynx, tongue, and soft palate is presented. The pharyngeal structure was segmented first, since the airway was clearly visible in the T1-weighted sequence. Thereafter, it was used as an anatomical landmark for tongue location. Finally, the soft palate region was extracted using segmented tongue and pharynx structures and used as input for a deep network. In each segmentation step, a UNet-like architecture was applied. Results The result assessment was performed qualitatively by comparing the region boundaries obtained from the expert to the framework results and quantitatively using the standard Dice coefficient metric. Additionally, cross-validation was applied to ensure that the framework performance did not depend on the specific selection of the validation set. The average Dice coefficients on the test set were $$0.89\pm 0.03$$ 0.89 ± 0.03 , $$0.87\pm 0.02$$ 0.87 ± 0.02 , and $$0.79\pm 0.08$$ 0.79 ± 0.08 for tongue, pharynx, and soft palate tissues, respectively. The results were similar to other approaches and consistent with expert readings. Conclusion Due to high speed and efficiency, the framework will be applied for big epidemiological data with thousands of participants acquired within the Study of Health in Pomerania as well as other epidemiological studies to provide information on the anatomical structures and aspects that constitute important risk factors to the OSAS development.

scholarly journals A New Multiplex Real-Time RT-PCR for Simultaneous Detection and Differentiation of Avian Bornaviruses

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1358
Author(s):  
Brigitte Sigrist ◽  
Jessica Geers ◽  
Sarah Albini ◽  
Dennis Rubbenstroth ◽  
Nina Wolfrum
Keyword(s):  
Real Time ◽  
Simultaneous Detection ◽  
Epidemiological Studies ◽  
Virus Species ◽  
Rt Pcr ◽  
P Gene ◽  
Field Samples ◽  
Causative Agents ◽  
Species Specific ◽  
Proventricular Dilatation Disease

Avian bornaviruses were first described in 2008 as the causative agents of proventricular dilatation disease (PDD) in parrots and their relatives (Psittaciformes). To date, 15 genetically highly diverse avian bornaviruses covering at least five viral species have been discovered in different bird orders. Currently, the primary diagnostic tool is the detection of viral RNA by conventional or real-time RT-PCR (rRT-PCR). One of the drawbacks of this is the usage of either specific assays, allowing the detection of one particular virus, or of assays with a broad detection spectrum, which, however, do not allow for the simultaneous specification of the detected virus. To facilitate the simultaneous detection and specification of avian bornaviruses, a multiplex real-time RT-PCR assay was developed. Whole-genome sequences of various bornaviruses were aligned. Primers were designed to recognize conserved regions within the overlapping X/P gene and probes were selected to detect virus species-specific regions within the target region. The optimization of the assay resulted in the sensitive and specific detection of bornaviruses of Psittaciformes, Passeriformes, and aquatic birds. Finally, the new rRT-PCR was successfully employed to detect avian bornaviruses in field samples from various avian species. This assay will serve as powerful tool in epidemiological studies and will improve avian bornavirus detection.

Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

2007 ◽  
Vol 9 (12) ◽  
pp. 2993-3007 ◽  
Author(s):  
Lisa Y. Stein ◽  
Daniel J. Arp ◽  
Paul M. Berube ◽  
Patrick S. G. Chain ◽  
Loren Hauser ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Niche Adaptation ◽  
Ammonia Oxidizing Bacterium

Incest: What do we Really Know about It?

1987 ◽  
Vol 21 (4) ◽  
pp. 430-440 ◽  
Author(s):  
R. Kosky
Keyword(s):  
Adverse Effects ◽  
Sexual Activity ◽  
Sexual Intercourse ◽  
Current Knowledge ◽  
Epidemiological Studies ◽  
Scientific Basis ◽  
Long Term Effects ◽  
Clinical Series ◽  
General Populations

The literature on incest is reviewed. Current knowledge rests on a very insecure scientific basis and has been mainly derived from small, highly selected clinical series. Recently, some important epidemiological studies of general populations have been reported, but the results of prevalence are inconsistent. Overall, however, it appears that incest, when defined in terms of sexual intercourse, occurs in less than 1% of the population, but other forms of intrafamilial sexual activity may affect 10% of females before they are 16 years of age. Some children are more at risk than others. Because information has generally been derived from court or treatment samples, we are unclear about the long-term effects of incest experiences but, overall, the impression is that incest has markedly adverse effects, especially if it is accompanied by violence and threats and is directed, as it usually is, at the young pre-pubescent child.

scholarly journals The Effect of Random Error in Exposure Measurement upon the Shape of the Exposure Response

Dose-Response ◽  
2005 ◽  
Vol 3 (4) ◽  
pp. dose-response.0 ◽  
Author(s):  
Kenny S. Crump
Keyword(s):  
Measurement Error ◽  
Measurement Errors ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Random Errors ◽  
Exposure Measurement ◽  
Considerable Uncertainty ◽  
Exposure Response ◽  
Log Normal ◽  
Normally Distributed

Although statistical analyses of epidemiological data usually treat the exposure variable as being known without error, estimated exposures in epidemiological studies often involve considerable uncertainty. This paper investigates the theoretical effect of random errors in exposure measurement upon the observed shape of the exposure response. The model utilized assumes that true exposures are log-normally distributed, and multiplicative measurement errors are also log-normally distributed and independent of the true exposures. Under these conditions it is shown that whenever the true exposure response is proportional to exposure to a power r, the observed exposure response is proportional to exposure to a power K, where K < r. This implies that the observed exposure response exaggerates risk, and by arbitrarily large amounts, at sufficiently small exposures. It also follows that a truly linear exposure response will appear to be supra-linear—i.e., a linear function of exposure raised to the K-th power, where K is less than 1.0. These conclusions hold generally under the stated log-normal assumptions whenever there is any amount of measurement error, including, in particular, when the measurement error is unbiased either in the natural or log scales. Equations are provided that express the observed exposure response in terms of the parameters of the underlying log-normal distribution. A limited investigation suggests that these conclusions do not depend upon the log-normal assumptions, but hold more widely. Because of this problem, in addition to other problems in exposure measurement, shapes of exposure responses derived empirically from epidemiological data should be treated very cautiously. In particular, one should be cautious in concluding that the true exposure response is supra-linear on the basis of an observed supra-linear form.

scholarly journals Environment, arbovirus transmission and control of epidemics

1992 ◽  
Vol 8 (3) ◽  
pp. 249-253 ◽  
Author(s):  
Roger Cordellier ◽  
Nicolas Degallier
Keyword(s):  
Yellow Fever Virus ◽  
Current Knowledge ◽  
Ground Level ◽  
Epidemiological Studies ◽  
Transmission Cycle ◽  
The People ◽  
Natural Foci ◽  
Effective Role ◽  
Control Of Epidemics ◽  
And Control

In order to illustrate the relationships between the biotopes (or phytogeographical zones), arbovirus vectors and vertebrate hosts (including man), and epidemiology, current knowledge on the transmission of Yellow Fever virus in West Africa is reported. A dynamic scheme has been devised to integrate the observed geographical distribution of cases and the timing of their occurrence. Two principal areas, endemicity and epidetnicity, were defined according to the presence or absence of sylvatic monkey-mosquito transmission. The intensity and potential of contacts between humans and vectors depends on the degree of man-made changes in the environment, often increasing the extension of ecotone areas where the mosquitoes are easily biting at the ground level. Prevention and/or control of arbovirus diseases require detailed eco-epidemiological studies to determine: (1) the effective role of each potential vector in each phytogeographical region; (2) the risk factors for the people living in or near areas with a sylvatic transmission cycle; (3) the priorities - vaccination and/or control - for preventing the expansion of natural foci.

scholarly journals Epidemiological trends in digestive cancers compared to trends in alcohol consumption. Facts from Romania: correlation or coincidence?

2018 ◽  
Vol 91 (4) ◽  
pp. 376-386
Author(s):  
Simona Valean ◽  
Romeo Chira ◽  
Dan Dumitrascu
Keyword(s):  
Alcohol Consumption ◽  
Population Level ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Incidence Rates ◽  
Human Populations ◽  
Causative Relationship ◽  
Consumption Data ◽  
Digestive Cancers ◽  
Epidemiological Trends

Cancer has emerged as the leading cause of death in human populations, according to recent estimations. Epidemiological studies emphasized the role of life style and of environmental factors in promoting the risk for digestive cancers. The contribution of alcohol was highly suspected. Even for digestive cancers with dominant infection etiology, like liver cancer and gastric cancer, the contribution of alcohol should be assessed. At population level there is therefore a need to compare trends in epidemiological data of gastrointestinal cancers and data on alcohol consumption, in order to extrapolate any causative relationship. The purpose of this review was to analyze the time trend of digestive cancers in Romania, in terms of mortality rates (between 1955-2012), and incidence rates (between 2008-2012), in males and females, and to analyze the alcohol consumption data, aiming to find out if there is any association.

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