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Article ; Online: Mature Rotavirus Particles Contain Equivalent Amounts of

Moreno-Contreras, Joaquin / Sánchez-Tacuba, Liliana / Arias, Carlos F / López, Susana

2022 Volume 96, Issue 17, Page(s) e0115122

Abstract: Viruses have evolved different strategies to overcome their recognition by the host innate immune system. The addition of caps at their 5' RNA ends is an efficient mechanism not only to ensure escape from detection by the innate immune system but also to ...

Abstract	Viruses have evolved different strategies to overcome their recognition by the host innate immune system. The addition of caps at their 5' RNA ends is an efficient mechanism not only to ensure escape from detection by the innate immune system but also to ensure the efficient synthesis of viral proteins. Rotavirus mRNAs contain a type 1 cap structure at their 5' end that is added by the viral capping enzyme VP3, which is a multifunctional protein with all the enzymatic activities necessary to add the cap and also functions as an antagonist of the 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway. Here, the relative abundances of capped and noncapped viral RNAs during the replication cycle of rotavirus were determined. We found that both classes of rotaviral plus-sense RNAs (+RNAs) were encapsidated and that they were present in a 1:1 ratio in the mature infectious particles. The capping of viral +RNAs was dynamic, since different ratios of capped and noncapped RNAs were detected at different times postinfection. Similarly, when the relative amounts of capped and uncapped viral +RNAs produced in an
MeSH term(s)	2',5'-Oligoadenylate Synthetase ; Capsid Proteins/metabolism ; Endoribonucleases/metabolism ; RNA Caps/analysis ; RNA Caps/chemistry ; RNA Caps/metabolism ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Rotavirus/genetics ; Rotavirus/metabolism ; Virion/genetics ; Virion/metabolism ; Virus Replication
Chemical Substances	Capsid Proteins ; RNA Caps ; RNA, Double-Stranded ; RNA, Viral ; VP3 protein, Rotavirus ; 2',5'-Oligoadenylate Synthetase (EC 2.7.7.84) ; Endoribonucleases (EC 3.1.-) ; 2-5A-dependent ribonuclease (EC 3.1.26.-)
Language	English
Publishing date	2022-08-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01151-22
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Article ; Online: Saliva sampling and its direct lysis is an excellent option for SARS-CoV-2 diagnosis in paediatric patients: comparison with the PanBio COVID-19 antigen rapid test in symptomatic and asymptomatic children.

Moreno-Contreras, Joaquín / Espinoza, Marco A / Cantú-Cuevas, Marco A / Madrid-González, Daniel A / Barón-Olivares, Héctor / Ortiz-Orozco, Oscar D / Guzmán-Rodríguez, Cecilia / Arias, Carlos F / Lopez, Susana

Journal of medical microbiology

2023 Volume 72, Issue 11

Abstract: Introduction. ...

Abstract	Introduction.
MeSH term(s)	Humans ; Child ; SARS-CoV-2/genetics ; COVID-19 Testing ; Saliva ; COVID-19/diagnosis ; Polymerase Chain Reaction ; Sensitivity and Specificity
Language	English
Publishing date	2023-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001779
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Article ; Online: Increasing the Capping Efficiency of the Sindbis Virus nsP1 Protein Negatively Affects Viral Infection.

LaPointe, Autumn T / Moreno-Contreras, Joaquín / Sokoloski, Kevin J

mBio

2018 Volume 9, Issue 6

Abstract: Alphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs (ncgRNAs), which are ... ...

Abstract	Alphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs (ncgRNAs), which are packaged into virions during infections of vertebrate and invertebrate cells. However, the roles that the ncgRNAs play during alphaviral infection have yet to be exhaustively characterized. Here, the importance of the ncgRNAs to alphaviral infection was assessed by using mutations of the nsP1 protein of Sindbis virus (SINV), which altered the synthesis of the ncgRNAs during infection by modulating the protein's capping efficiency. Specifically, point mutations at residues Y286A and N376A decreased capping efficiency whereas a point mutation at D355A increased the capping efficiency of the SINV genomic RNA during genuine viral infection. Viral growth kinetics levels were significantly reduced for the D355A mutant relative to wild-type infection, whereas the Y286A and N376A mutants showed modest decreases in growth kinetics. Overall genomic translation and nonstructural protein accumulation were found to correlate with increases and decreases in capping efficiency. However, genomic, minus-strand, and subgenomic viral RNA synthesis were largely unaffected by the modulation of alphaviral capping activity. In addition, translation of the subgenomic alphaviral RNA (vRNA) was found not to be impacted by changes in capping efficiency. The mechanism by which the decreased presence of ncgRNAs reduced viral growth kinetics levels operated through the impaired production of viral particles. Collectively, these data illustrate the importance of ncgRNAs to viral infection and suggest that they play an integral role in the production of viral progeny.
MeSH term(s)	Amino Acid Substitution ; Animals ; Cell Line ; Cricetinae ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Point Mutation ; Protein Biosynthesis ; RNA, Viral/metabolism ; Sindbis Virus/enzymology ; Sindbis Virus/genetics ; Sindbis Virus/growth & development ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Mutant Proteins ; RNA, Viral ; Viral Nonstructural Proteins ; nsP1 protein, Sindbis virus
Language	English
Publishing date	2018-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02342-18
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Article: Automated Reverse Transcription Polymerase Chain Reaction Data Analysis for Sars-CoV-2 Detection.

Gómez-Romero, Laura / Tovar, Hugo / Moreno-Contreras, Joaquín / Espinoza, Marco A / de-Anda-Jáuregui, Guillermo

Revista de investigacion clinica; organo del Hospital de Enfermedades de la Nutricion

2021 Volume 73, Issue 6, Page(s) 339–346

Abstract: Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a current public health concern. Rapid diagnosis is crucial, and reverse transcription polymerase chain reaction (RT-PCR) is presently the reference standard for ... ...

Abstract	Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a current public health concern. Rapid diagnosis is crucial, and reverse transcription polymerase chain reaction (RT-PCR) is presently the reference standard for SARS-CoV-2 detection. Objective: Automated RT-PCR analysis (ARPA) is a software designed to analyze RT-PCR data for SARSCoV-2 detection. ARPA loads the RT-PCR data, classifies each sample by assessing its amplification curve behavior, evaluates the experiment's quality, and generates reports. Methods: ARPA was implemented in the R language and deployed as a Shiny application. We evaluated the performance of ARPA in 140 samples. The samples were manually classified and automatically analyzed using ARPA. Results: ARPA had a true-positive rate = 1, true-negative rate = 0.98, positive-predictive value = 0.95, and negative-predictive value = 1, with 36 samples correctly classified as positive, 100 samples correctly classified as negative, and two samples classified as positive even when labeled as negative by manual inspection. Two samples were labeled as invalid by ARPA and were not considered in the performance metrics calculation. Conclusions: ARPA is a sensitive and specific software that facilitates the analysis of RT-PCR data, and its implementation can reduce the time required in the diagnostic pipeline.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Diagnosis, Computer-Assisted ; Humans ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Saliva/virology ; Software
Language	English
Publishing date	2021-11-05
Publishing country	Mexico
Document type	Journal Article
ZDB-ID	138348-6
ISSN	0034-8376
ISSN	0034-8376
DOI	10.24875/RIC.21000189
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Article ; Online: Increasing the Capping Efficiency of the Sindbis Virus nsP1 Protein Negatively Affects Viral Infection

Autumn T. LaPointe / Joaquín Moreno-Contreras / Kevin J. Sokoloski

mBio, Vol 9, Iss

2018 Volume 6

Abstract: ABSTRACT Alphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs (ncgRNAs), ... ...

Abstract	ABSTRACT Alphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs (ncgRNAs), which are packaged into virions during infections of vertebrate and invertebrate cells. However, the roles that the ncgRNAs play during alphaviral infection have yet to be exhaustively characterized. Here, the importance of the ncgRNAs to alphaviral infection was assessed by using mutations of the nsP1 protein of Sindbis virus (SINV), which altered the synthesis of the ncgRNAs during infection by modulating the protein’s capping efficiency. Specifically, point mutations at residues Y286A and N376A decreased capping efficiency whereas a point mutation at D355A increased the capping efficiency of the SINV genomic RNA during genuine viral infection. Viral growth kinetics levels were significantly reduced for the D355A mutant relative to wild-type infection, whereas the Y286A and N376A mutants showed modest decreases in growth kinetics. Overall genomic translation and nonstructural protein accumulation were found to correlate with increases and decreases in capping efficiency. However, genomic, minus-strand, and subgenomic viral RNA synthesis were largely unaffected by the modulation of alphaviral capping activity. In addition, translation of the subgenomic alphaviral RNA (vRNA) was found not to be impacted by changes in capping efficiency. The mechanism by which the decreased presence of ncgRNAs reduced viral growth kinetics levels operated through the impaired production of viral particles. Collectively, these data illustrate the importance of ncgRNAs to viral infection and suggest that they play an integral role in the production of viral progeny. IMPORTANCE Alphaviruses have been the cause of both localized outbreaks and large epidemics of severe disease. Currently, there are no strategies or vaccines which are either safe or effective for preventing alphaviral ...
Keywords	RNA processing ; RNA virus ; alphavirus ; molecular biology ; Microbiology ; QR1-502
Subject code	570
Language	English
Publishing date	2018-12-01T00:00:00Z
Publisher	American Society for Microbiology
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Increasing the Capping Efficiency of the Sindbis Virus nsP1 Protein Negatively Affects Viral Infection

Autumn T. LaPointe / Joaquín Moreno-Contreras / Kevin J. Sokoloski

mBio, Vol 9, Iss 6, p e02342-

2018 Volume 18

Abstract: Alphaviruses have been the cause of both localized outbreaks and large epidemics of severe disease. Currently, there are no strategies or vaccines which are either safe or effective for preventing alphaviral infection or treating alphaviral disease. This ...

Abstract	Alphaviruses have been the cause of both localized outbreaks and large epidemics of severe disease. Currently, there are no strategies or vaccines which are either safe or effective for preventing alphaviral infection or treating alphaviral disease. This deficit of viable therapeutics highlights the need to better understand the mechanisms behind alphaviral infection in order to develop novel antiviral strategies for treatment of alphaviral disease. In particular, this report details a previously uncharacterized aspect of the alphaviral life cycle: the importance of noncapped genomic viral RNAs for alphaviral infection. This offers new insights into the mechanisms of alphaviral replication and the impact of the noncapped genomic RNAs on viral packaging.Alphaviruses are arthropod-borne RNA viruses that are capable of causing severe disease and are a significant burden to public health. Alphaviral replication results in the production of both capped and noncapped viral genomic RNAs (ncgRNAs), which are packaged into virions during infections of vertebrate and invertebrate cells. However, the roles that the ncgRNAs play during alphaviral infection have yet to be exhaustively characterized. Here, the importance of the ncgRNAs to alphaviral infection was assessed by using mutations of the nsP1 protein of Sindbis virus (SINV), which altered the synthesis of the ncgRNAs during infection by modulating the protein’s capping efficiency. Specifically, point mutations at residues Y286A and N376A decreased capping efficiency whereas a point mutation at D355A increased the capping efficiency of the SINV genomic RNA during genuine viral infection. Viral growth kinetics levels were significantly reduced for the D355A mutant relative to wild-type infection, whereas the Y286A and N376A mutants showed modest decreases in growth kinetics. Overall genomic translation and nonstructural protein accumulation were found to correlate with increases and decreases in capping efficiency. However, genomic, minus-strand, and subgenomic viral RNA synthesis were largely unaffected by the modulation of alphaviral capping activity. In addition, translation of the subgenomic alphaviral RNA (vRNA) was found not to be impacted by changes in capping efficiency. The mechanism by which the decreased presence of ncgRNAs reduced viral growth kinetics levels operated through the impaired production of viral particles. Collectively, these data illustrate the importance of ncgRNAs to viral infection and suggest that they play an integral role in the production of viral progeny.
Keywords	RNA processing ; RNA virus ; alphavirus ; molecular biology ; Microbiology ; QR1-502
Subject code	570
Language	English
Publishing date	2018-12-01T00:00:00Z
Publisher	American Society for Microbiology
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Automated Reverse Transcription Polymerase Chain Reaction Data Analysis for Sars-CoV-2 Detection

Laura Gómez-Romero / Hugo Tovar / Joaquín Moreno-Contreras / Marco A. Espinoza / Guillermo de-Anda-Jáuregui

Revista de Investigación Clínica, Vol 73, Iss

2021 Volume 6

Abstract	Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a current public health concern. Rapid diagnosis is crucial, and reverse transcription polymerase chain reaction (RT-PCR) is presently the reference standard for SARS-CoV-2 detection. Objective: Automated RT-PCR analysis (ARPA) is a software designed to analyze RT-PCR data for SARSCoV-2 detection. ARPA loads the RT-PCR data, classifies each sample by assessing its amplification curve behavior, evaluates the experiment’s quality, and generates reports. Methods: ARPA was implemented in the R language and deployed as a Shiny application. We evaluated the performance of ARPA in 140 samples. The samples were manually classified and automatically analyzed using ARPA. Results: ARPA had a true-positive rate = 1, true-negative rate = 0.98, positive-predictive value = 0.95, and negative-predictive value = 1, with 36 samples correctly classified as positive, 100 samples correctly classified as negative, and two samples classified as positive even when labeled as negative by manual inspection. Two samples were labeled as invalid by ARPA and were not considered in the performance metrics calculation. Conclusions: ARPA is a sensitive and specific software that facilitates the analysis of RT-PCR data, and its implementation can reduce the time required in the diagnostic pipeline.
Keywords	Severe acute respiratory syndrome coronavirus-2 detection. Reverse transcription polymerase chain reaction. Automatic analysis. Amplification curves ; Internal medicine ; RC31-1245
Subject code	572
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Permanyer
Document type	Article ; Online
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Article: Development of films based on chitosan, gelatin and collagen extracted from bocachico scales (

Moreno-Ricardo, María A / Gómez-Contreras, Paula / González-Delgado, Ángel Darío / Hernández-Fernández, Joaquín / Ortega-Toro, Rodrigo

Heliyon

2024 Volume 10, Issue 3, Page(s) e25194

Abstract: Biodegradable biopolymers from species of the animal kingdom or their byproducts are sustainable as ecological materials due to their abundant supply and compatibility with the environment. The research aims to obtain a biodegradable active material from ...

Abstract	Biodegradable biopolymers from species of the animal kingdom or their byproducts are sustainable as ecological materials due to their abundant supply and compatibility with the environment. The research aims to obtain a biodegradable active material from chitosan, gelatin, and collagen from bocachico scales (Prochilodus magdalenae). Regarding the methodology, films were developed from gelatin, chitosan, and collagen from bocachico scales (Prochilodus magdalenae) at different concentrations using glycerol as a plasticizer and citric acid as a cross-linker. The films were obtained with the hydrated mass processed by compression molding and characterized according to humidity, water solubility, contact angle, mechanical properties, and structural properties. The results of the films showed a hydrophobic characteristic. First, the chitosan-collagen (CS/CO) films showed a yellowish color, while the gelatin-collagen (Gel/CO) films were transparent and less soluble than the gelatin-collagen (Gel/CO) films. Concerning mechanical properties, gelatin films showed higher stiffness and tensile strength than chitosan films. Furthermore, in the morphological analysis, more homogeneous chitosan films were obtained by increasing the concentration of citric acid. In general, chitosan, gelatin, and collagen extracted from the scales of the bocachico (Prochilodus magdalenae) are an alternative in the application of films in the food industry.
Language	English
Publishing date	2024-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e25194
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Article ; Online: Pooling saliva samples as an excellent option to increase the surveillance for SARS-CoV-2 when re-opening community settings.

Moreno-Contreras, Joaquín / Espinoza, Marco A / Sandoval-Jaime, Carlos / Cantú-Cuevas, Marco A / Madrid-González, Daniel A / Barón-Olivares, Héctor / Ortiz-Orozco, Oscar D / Muñoz-Rangel, Asunción V / Guzmán-Rodríguez, Cecilia / Hernández-de la Cruz, Manuel / Eroza-Osorio, César M / Arias, Carlos F / López, Susana

PloS one

2022 Volume 17, Issue 1, Page(s) e0263114

Abstract: In many countries a second wave of infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has occurred, triggering a shortage of reagents needed for diagnosis and compromising the capacity of laboratory testing. There is an ...

Abstract	In many countries a second wave of infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has occurred, triggering a shortage of reagents needed for diagnosis and compromising the capacity of laboratory testing. There is an urgent need to develop methods to accelerate the diagnostic procedures. Pooling samples represents a strategy to overcome the shortage of reagents, since several samples can be tested using one reaction, significantly increasing the number and speed with which tests can be carried out. We have reported the feasibility to use a direct lysis procedure of saliva as source for RNA to SARS-CoV-2 genome detection by reverse transcription quantitative-PCR (RT-qPCR). Here, we show that the direct lysis of saliva pools, of either five or ten samples, does not compromise the detection of viral RNA. In addition, it is a sensitive, fast, and inexpensive method that can be used for massive screening, especially considering the proximity of the reincorporation of activities in universities, offices, and schools.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Nucleic Acid Testing/methods ; COVID-19 Nucleic Acid Testing/standards ; Humans ; Mass Screening/methods ; Mass Screening/standards ; Quarantine/standards ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/pathogenicity ; Saliva/virology ; Sensitivity and Specificity
Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0263114
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Article ; Online: Occupational exposure to pesticides and symptoms of depression in agricultural workers. A systematic review.

Cancino, Javier / Soto, Karly / Tapia, Joaquín / Muñoz-Quezada, María Teresa / Lucero, Boris / Contreras, Caterina / Moreno, Jaime

Environmental research

2023 Volume 231, Issue Pt 2, Page(s) 116190

Abstract: Background: The use of pesticides can result in harm to both the environment and human health. There is a growing concern in the field of occupational health about the impact on the mental health of agricultural workers.: Objectives: The objective of ...

Abstract	Background: The use of pesticides can result in harm to both the environment and human health. There is a growing concern in the field of occupational health about the impact on the mental health of agricultural workers. Objectives: The objective of this review was to systematize scientific evidence from the last ten years on the impact of occupational exposure to pesticides on the development of depression symptoms in agricultural workers. Methods: We conducted a comprehensive search in the PubMed and Scopus databases from 2011 to September 2022. Our search included studies in English, Spanish, and Portuguese that examined the association between occupational exposure to pesticides and symptoms of depression in agricultural workers, following the guidelines recommended by the PRISMA statement and the PECO strategy (Population, Exposure, Comparison, and Outcomes). Results: Among the 27 articles reviewed, 78% of them indicated a link between exposure to pesticides and the incidence of depression symptoms. The pesticides most frequently reported in the studies were organophosphates (17 studies), herbicides (12 studies), and pyrethroids (11 studies). The majority of the studies were rated as having intermediate to intermediate-high quality, with the use of standardized measures to assess both exposure and effect. Conclusion: The updated evidence presented in our review indicates a clear association between pesticide exposure and the development of depressive symptoms. However, more high-quality longitudinal studies are necessary to control for sociocultural variables and utilize pesticide-specific biomarkers and biomarkers of depression. Given the increased use of these chemicals and the health risks associated with depression, it is crucial to implement more stringent measures to monitor the mental health of agricultural workers regularly exposed to pesticides and to enhance surveillance of companies that apply these chemicals.
MeSH term(s)	Humans ; Pesticides/toxicity ; Farmers ; Depression/chemically induced ; Depression/epidemiology ; Occupational Exposure/adverse effects ; Biomarkers ; Agricultural Workers' Diseases/epidemiology
Chemical Substances	Pesticides ; Biomarkers
Language	English
Publishing date	2023-05-20
Publishing country	Netherlands
Document type	Systematic Review ; Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2023.116190
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