The largest database of trusted experimental protocols
> Phenomena > Phenomenon or Process > Disease Outbreaks

Disease Outbreaks

Disease Outbreaks: Unexpected and rapid spread of infectious diseases across populations, often posing significant public health challenges.
Closely monitor emerging and re-emerging infectious diseases, analyze transmission patterns, and implement effective prevention and control strategies.
Leverage data-driven insights to optimize research protocols and enhance disease outbreak preparedness.
Explore the latest advancements in outbreak management and discover how AI-powered platforms like PubCompare.ai can support your disease outbreak reseach and response efforts.

Most cited protocols related to «Disease Outbreaks»

The epidemic curve was constructed by date of illness onset, and key dates relating to epidemic identification and control measures were overlaid to aid interpretation. Case characteristics were described, including demographic characteristics, exposures, and health care worker status. The incubation period distribution (i.e., the time delay from infection to illness onset) was estimated by fitting a log-normal distribution to data on exposure histories and onset dates in a subset of cases with detailed information available. Onset-to-first-medical-visit and onset-to-admission distributions were estimated by fitting a Weibull distribution on the dates of illness onset, first medical visit, and hospital admission in a subset of cases with detailed information available. We fitted a gamma distribution to data from cluster investigations to estimate the serial interval distribution, defined as the delay between illness onset dates in successive cases in chains of transmission.
We estimated the epidemic growth rate by analyzing data on the cases with illness onset between December 10 and January 4, because we expected the proportion of infections identified would increase soon after the formal announcement of the outbreak in Wuhan on December 31. We fitted a transmission model (formulated with the use of renewal equations) with zoonotic infections to onset dates that were not linked to the Huanan Seafood Wholesale Market, and we used this model to derive the epidemic growth rate, the epidemic doubling time, and the basic reproductive number (R0), which is defined as the expected number of additional cases that one case will generate, on average, over the course of its infectious period in an otherwise uninfected population. We used an informative prior distribution for the serial interval based on the serial interval of SARS with a mean of 8.4 and a standard deviation of 3.8.11 (link)Analyses of the incubation period, serial interval, growth rate, and R0 were performed with the use of MATLAB software (MathWorks). Other analyses were performed with the use of SAS software (SAS Institute) and R software (R Foundation for Statistical Computing).
Publication 2020
Epidemics Gamma Rays Infection Seafood Severe Acute Respiratory Syndrome Transmission, Communicable Disease Workers Zoonoses
The complete genome of E. coli K-12 W3110 [112 (link)], was downloaded from RefSeq (AC_000091). This genome was used as the ancestral genome and evolution was simulated along a balanced tree for three evolutionary rates using the Seq-Gen package [113 (link)] with parameters mHKY -t4.0 -l4646332 -n1 -k1 and providing the corresponding binary tree evolved at three evolutionary rates: 0.00001, 0.0001, and 0.001 SNPs per site, per branch. This corresponds to a minimum percent identity of approximately 99%, 99.9%, and 99.99% between the two most divergent genomes, respectively, reflecting the variation seen in typical outbreak analyses. No small (<5 bp) or large Indels were introduced, but an average of 10 1 Kbp rearrangements (inversions and translocations) were added, per genome, using a custom script [114 ]. Paired reads were simulated to model current MiSeq lengths (2 × 150 bp) and error rates (1%). Moderate coverage, two million PE reads (64X coverage), was simulated for each of the 32 samples using wgsim (default parameters, no Indels), from samtools package version 0.1.17 [55 (link)].
Two of the simulated read sets were independently run through iMetAMOS [93 (link)] to automatically determine the best assembler. The consensus pick across both datasets was SPAdes version 3.0 [81 (link)], which was subsequently run on the remaining 30 simulated read sets using default parameters. The final contigs and scaffolds files were used as input to the genome alignment methods. For mapping methods, the raw simulated reads were used. For accuracy comparisons, Indels were ignored and called SNPs were required to be unambiguously aligned across all 32 genomes (that is, not part of a subset relationship; SNPs present but part of a subset relationship were ignored).
Publication 2014
Biological Evolution Escherichia coli Gene Rearrangement Genome INDEL Mutation Inversion, Chromosome Single Nucleotide Polymorphism Translocation, Chromosomal Trees Vision
Three different datasets were used for evaluation in the present study, comprising selected Salmonella Montevideo [17] (link), Staphylococcus aureus CC398 [5] , and Salmonella Typhimurium DT104 [18] (link) from previous studies.
For S. Montevideo 12 closely related outbreak strains where sequenced once by US Food and Drug Administration using Roche Genome sequencer FLX system, Illumina MiSeq and Life Technologies Ion Torrent and made publicly available (Table S1), although only the MiSeq data was used in the original study [16] (link). The raw data were downloaded from the Sequence Read Archive (SRA). For Staphylococcus aureus CC398, the completely sequenced and annotated strain SO385 (AM990992.1) as well as four additional strains were selected from a previously published study [5] and sequenced twice using both MiSeq and Ion Torrent. HiSeq was used in the original study for sequencing. All the strains except for the reference strain were chosen from the same clade, named IIa1i in the original study. The strains are not epidemiologically related but have all been isolated from Danish Pigs and are shown to be closely related in the original study. For S. Typhimurium DT104 the reference strain NCTC 13348 (HF937208.1) and an additional three isolates from the same outbreak [18] (link) were sequenced twice on both MiSeq and Ion Torrent.
Genomic DNA (gDNA) was purified from the isolates using the Easy-DNA extraction kit (Invitrogen) and DNA concentrations determined using the Qubit dsDNA BR Assay Kit (Invitrogen). The isolates were sequenced twice on the MiSeq platform (Illumina) and Ion Torrent PGM (Life Technologies).
For Ion Torrent the isolates were sequenced following the manufacturer’s protocols for 200 bp gDNA fragment library preparation (Ion Xpress Plus gDNA and Amplicon Library 96 Preparation), template preparation (Ion OneTouch System), and sequencing (Ion PGM 200 Sequencing kit) using the 316 chip. For MiSeq the isolates chromosomal DNA of the isolates was used to create genomic libraries using the Nextera XT DNA sample preparation kit (Illumina, cat. No. FC-131-1024) and sequenced using v2, 2×250 bp chemistry on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA).
Publication 2014
Biological Assay BP protocol Chromosomes cyclo(D-tyrosyl-arginyl-arginyl-3-(2-naphthyl)alanyl-glycyl) DNA, Double-Stranded DNA Chips DNA Library Genome Genomic Library Salmonella Salmonella typhimurium Staphylococcus aureus Strains Sus scrofa

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2020
Adult COVID 19 Inpatient Lung Patients SARS-CoV-2

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2020
COVID 19 Epidemics Gamma Rays Human Body Transmission, Communicable Disease

Most recents protocols related to «Disease Outbreaks»

Example 5

To investigate whether a Canine/FL/04-like influenza virus had circulated among greyhound populations in Florida prior to the January 2004 outbreak, archival sera from 65 racing greyhounds were tested for the presence of antibodies to Canine/FL/04 using the HI and MN assays. There were no detectable antibodies in 33 dogs sampled from 1996 to 1999. Of 32 dogs sampled between 2000 and 2003, 9 were seropositive in both assays—1 in 2000, 2 in 2002, and 6 in 2003 (Table 5). The seropositive dogs were located at Florida tracks involved in outbreaks of respiratory disease of unknown etiology from 1999 to 2003, suggesting that a Canine/FL/04-like virus may have been the causative agent of those outbreaks. To investigate this possibility further, we examined archival tissues from greyhounds that died from hemorrhagic bronchopneumonia in March 2003. Lung homogenates inoculated into MDCK cells and chicken embryos from one dog yielded H3N8 influenza virus, termed A/Canine/Florida/242/2003 (Canine/FL/03). Sequence analysis of the complete genome of Canine/FL/03 revealed >99% identity to Canine/FL/04 (Table 4), indicating that Canine/FL/04-like viruses had infected greyhounds prior to 2004.

Patent 2024
Antibodies Biological Assay Bronchopneumonia Canis familiaris Chickens Disease Outbreaks Embryo Genome Hemorrhage Influenza Influenza A Virus, H3N8 Subtype Lung Madin Darby Canine Kidney Cells Orthomyxoviridae Population Group Respiration Disorders Respiratory Rate Sequence Analysis Serum Tissues Virus
Followed by in silico screening of resistance genes using ABRicate [30 ] and the National Center for Biotechnology Information (NCBI) Antimicrobial Resistance Gene Finder Plus database [31 (link)], assemblies passing quality controls were uploaded to the SeqSphere+ software version 7.7.5 (Ridom, Muenster, Germany), which was used for multilocus sequence typing (MLST) following the Achtman scheme and core genome (cg)MLST based on the Enterobase E. coli scheme (2,513 loci). Pairwise allelic differences between isolates were used to construct a neighbour-joining tree with metadata annotated using Interactive Tree Of Life (iTOL) version 6.5.7 [32 (link)]. We further conducted single-nucleotide polymorphism (SNP)-based analyses of the core genome for isolates of specific sequence types (ST). Using the CSI Phylogeny 1.4 server (Call SNPs & Infer Phylogeny; https://cge.cbs.dtu.dk/services/CSIPhylogeny) with default settings, which includes the pruning of SNP within 10 bp, a separate phylogenetic analysis was performed on assemblies of isolates of each ST to construct an SNP distance matrix that was visualised in a heatmap using iTOL. Clusters within the phylogenetic tree corresponding to clonal dissemination were defined based on a pairwise SNP distance of ≤ 100 between isolates, as has recently been suggested for OXA-244-producing E. coli in France [33 (link)]. In this context, it has to be noted that, in the absence of a clear consensus on the maximum cut-off to define clonality, the SNP distance chosen here may appear high compared with thresholds typically used to elucidate local outbreaks. However, to account for our long-term surveillance data, we used this liberal threshold as we expect that identified clusters may reflect patterns on a broader genetic scale, such as clonal lineages. Moreover, we did not correct for recombination which is known to increase genetic diversity. Therefore, we are confident that the SNP distances obtained represent a reliable measure of genetic relatedness between isolates. To illustrate distribution patterns, cluster isolates were mapped based on the first three digits of the postal code.
Publication 2023
Alleles Clone Cells Disease Outbreaks Escherichia coli Genes, vif Genetic Diversity Genome Microbicides Nucleotides Recombination, Genetic Reproduction Self Confidence Single Nucleotide Polymorphism Thumb Trees
Based on the relevant literature—as described in the Literature Review section—we identified a few teacher characteristics that could be related to Self-Efficacy for Integrating Technology in Teaching and to Success in Teaching in ERT. Hence, we measured variables in a few categories, as described below. Descriptive statistics for these variables are reported in the Research Population section.
Demographic variables. Participants were asked to report on their Gender [Men, Women], Age (by reporting on birth year), and Mother Tongue [Hebrew, Arabic, Other]. Our participants included 599 females and 136 males (81% and 19%, accordingly), ranging in age between 21 and 69 years of age (M = 44, SD = 8.7, N = 735). These characteristics are largely aligned with the demographics of the Israeli teaching staff (Central Bureau of Statistics, 2020 ). Note that we assume normality for the age variable, as tests for skewness and kurtosis resulted with satisfyingly low values of 0.10 and − 0.31, respectively. Of the participants, 59% (437 of 735) reported that their Mother Tongue was Hebrew, 33% reported on Arabic (246 of 735), other languages were reported to relatively low degrees, hence we grouped them as “Other” (52 of 735, 7%); these ratios are slightly biased towards the Arab-speaking population, as teachers in the Arabic sector in Israel are about 22% of the overall teaching force at secondary education (Central Bureau of Statistics, 2021 ).
Teaching-related variables. We measured a few variables that helped us distinguish between teachers based on their professional characteristics. Specifically, we measured the following: Teaching Experience [years]; Experience in Teaching with Technology [5-point Likert scale]; Leading Role at School [yes/no for each of the following: grade coordinator, domain coordinator, ICT coordinator, counselor, vice principal, principal] – while processing the data, we aggregated this into a binary variable of managing position [yes/no]; Teaching Domain [Mathematics; Science; Technology; Language (mother tongue or second language); Humanities; Social Sciences; Arts; Physical Education; Other] – these values were chosen based on the way the Israeli curriculum is built, however while processing the data, and based on the responses, we defined only three categories: STEM (Science, Technology, Engineering, and Mathematics), Humanities and Social Sciences, and Language (either mother tongue of second language).
Our participants had an average Teaching Experience of 14.7 years (SD = 8.9, N = 735), with an average index of Experience of Teaching with Technology of 3.4 of 5 (SD = 1.1, N = 735). Note that we assume normality for these two variables; tests for skewness and kurtosis for Teaching Experience resulted with satisfyingly low values of 0.67 and − 0.34, respectively, and for Experience of Teaching with Technology they were − 0.10 and − 0.61, respectively. Of the participants, 32% (238 of 735) had a leading role at school, being part of the management team. Regarding their Teaching Domains, we had similar ratios of teachers teaching STEM (33%, 241 of 735), Language (either mother tongue or second language, 30%, 224 of 735), and Social Sciences or Humanities (37%, 270 of 735).
COVID-19-related variables. Finally, we measured a few variables that were unique to the COVID-19 pandemic outbreak. The variable Risk Group [Yes/No] indicates whether the participant or one of their household members were defined as being in a risk group for a severe illness from COVID-19; this group includes, among others, pregnant women, people over 60 years old, those who have a background of critical medical condition, and people who live in nursing homes. Additionally, we surveyed for four factors that were perceived as challenging working from home during the COVID-19 pandemic, each of which was ranked on a 3-point Likert scale: Physical Space Difficulties, Technology Difficulties (infrastructure-wise), Familial Difficulties, and Emotional Difficulties.
Of our participants, 24% (177 of 735) were in a Risk Group for COVID-19. Regarding the factors that influenced their working from home, Familial Difficulties where the most common (M = 1.96, SD = 0.75, N = 714), followed by Emotional Difficulties (M = 1.73, SD = 0.68, N = 708), Physical Space Difficulties (M = 1.633, SD = 0.73, N = 728), and finally Technology Difficulties (M = 1.627, SD = 0.73, N = 724).
Publication 2023
Arabs Childbirth Counselors COVID 19 Emotions Females Gender Households Males Mothers Physical Education Physical Examination Population at Risk Pregnant Women Stem, Plant Tongue Woman
This study was conducted in Israel, where the education system is mostly public, centralized and is typically divided into three school levels: elementary schools (1st -6th grades), middle schools (7th -9th grades), and high schools (10th -12th grades). The school year in Israel begins on September 1st, and ends at the end of June. As in most of the world, the COVID-19 pandemic outbreak has dramatically impacted the education system in Israel, with most schools operating remotely for a period of a few months; middle schools were the ones in which remote teaching was held for the longest time, which is our reason for focusing on them. Our data collection was held a few weeks after most of middle schools had re-opened and teachers and students returned to the physical buildings. Notably, during our data collection, schools across the country had to close again for a few days to a regional military conflict.
The current study included N = 735 teachers from 68 middle schools across Israel. As it is common in Israel to teach in both middle- and high-schools, our inclusion criteria included that at least 50% of the teaching hours were done in middle school grades. In order to survey teachers who had experienced the transition from traditional teaching to emergency remote teaching, another inclusion criteria was teaching during both the 2020/21 school year (when data was collected) and the prior year (i.e., before COVID-19 days).
Publication 2023
ARID1A protein, human COVID 19 Emergencies Middle School Teachers Military Personnel Physical Examination Student Teaching
Partner frame-of-reference instructions were used, with reference to the coronavirus pandemic, which put stress on relationships (i.e., “Since the coronavirus outbreak, I do the following things to MAKE MY ROMANTIC PARTNER FEEL BETTER”). Eight subscales were assessed with four items each (expressive suppression, downward social comparison, distraction, humor, direct action, reappraisal, receptive listening, and valuing). Sample items include “I ask them to put a brave face on” (expressive suppression) or “I do what I can to find an answer for them” (direct action). Participants rated each item on a 6-point scale, from 1 (Strongly Disagree) to 6 (Strongly Agree).
Publication 2023
Coronavirus Face Feelings Pandemics Reading Frames Social Comparison

Top products related to «Disease Outbreaks»

Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
Sourced in United States, Austria, Japan, Belgium, United Kingdom, Cameroon, China, Denmark, Canada, Israel, New Caledonia, Germany, Poland, India, France, Ireland, Australia
SAS 9.4 is an integrated software suite for advanced analytics, data management, and business intelligence. It provides a comprehensive platform for data analysis, modeling, and reporting. SAS 9.4 offers a wide range of capabilities, including data manipulation, statistical analysis, predictive modeling, and visual data exploration.
Sourced in United States, Austria, Japan, Cameroon, Germany, United Kingdom, Canada, Belgium, Israel, Denmark, Australia, New Caledonia, France, Argentina, Sweden, Ireland, India
SAS version 9.4 is a statistical software package. It provides tools for data management, analysis, and reporting. The software is designed to help users extract insights from data and make informed decisions.
Sourced in Germany, United States, United Kingdom, France, Spain, Japan, China, Netherlands, Italy, Australia, Canada, Switzerland, Belgium
The QIAamp Viral RNA Mini Kit is a laboratory equipment designed for the extraction and purification of viral RNA from various sample types. It utilizes a silica-based membrane technology to efficiently capture and isolate viral RNA, which can then be used for downstream applications such as RT-PCR analysis.
Sourced in United States, China, United Kingdom, Germany, France, Australia, Canada, Japan, Italy, Switzerland, Belgium, Austria, Spain, Israel, New Zealand, Ireland, Denmark, India, Poland, Sweden, Argentina, Netherlands, Brazil, Macao, Singapore, Sao Tome and Principe, Cameroon, Hong Kong, Portugal, Morocco, Hungary, Finland, Puerto Rico, Holy See (Vatican City State), Gabon, Bulgaria, Norway, Jamaica
DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
Sourced in United States, China, Germany, United Kingdom, Spain, Australia, Italy, Canada, Switzerland, France, Cameroon, India, Japan, Belgium, Ireland, Israel, Norway, Finland, Netherlands, Sweden, Singapore, Portugal, Poland, Czechia, Hong Kong, Brazil
The MiSeq platform is a benchtop sequencing system designed for targeted, amplicon-based sequencing applications. The system uses Illumina's proprietary sequencing-by-synthesis technology to generate sequencing data. The MiSeq platform is capable of generating up to 15 gigabases of sequencing data per run.
Sourced in Germany, United States, United Kingdom, Spain, Canada, Netherlands, Japan, China, France, Australia, Denmark, Switzerland, Italy, Sweden, Belgium, Austria, Hungary
The DNeasy Blood and Tissue Kit is a DNA extraction and purification product designed for the isolation of genomic DNA from a variety of sample types, including blood, tissues, and cultured cells. The kit utilizes a silica-based membrane technology to efficiently capture and purify DNA, providing high-quality samples suitable for use in various downstream applications.
Sourced in Germany, United States, France, United Kingdom, Netherlands, Spain, Japan, China, Italy, Canada, Switzerland, Australia, Sweden, India, Belgium, Brazil, Denmark
The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
Sourced in United States, United Kingdom, China, Germany, Japan, France, Italy, Belgium, Australia, Canada, Spain, Austria, Netherlands, Ireland, Argentina, Switzerland, Denmark, Morocco, Brazil, New Zealand, Moldova, Republic of, Poland
MEM is a cell culture medium designed for the growth and maintenance of a variety of cell types in vitro. It provides a balanced salt solution, amino acids, vitamins, and other essential nutrients required for cell proliferation and survival.
Sourced in United States, United Kingdom, Denmark, Belgium, Spain, Canada, Austria
Stata 12.0 is a comprehensive statistical software package designed for data analysis, management, and visualization. It provides a wide range of statistical tools and techniques to assist researchers, analysts, and professionals in various fields. Stata 12.0 offers capabilities for tasks such as data manipulation, regression analysis, time-series analysis, and more. The software is available for multiple operating systems.

More about "Disease Outbreaks"

Disease outbreaks are unexpected and rapid spreads of infectious diseases across populations, often posing significant public health challenges.
These outbreaks require close monitoring of emerging and re-emerging infectious diseases, analyzing transmission patterns, and implementing effective prevention and control strategies.
Leveraging data-driven insights can help optimize research protocols and enhance disease outbreak preparedness.
Advanced AI-powered platforms like PubCompare.ai can support disease outbreak research and response efforts by allowing users to locate and compare protocols from literature, pre-prints, and patents using sophisticated comparison tools.
This enables the identification of the most effective protocols and products to enhance disease outbreak readiness.
Experinence the power of data-driven decision making with PubCompare.ai, which can assist in discovering the latest advancements in outbreak management.
Researchers can utilize this platform to explore a wide range of resources, including information from FBS, SAS 9.4, SAS version 9.4, QIAamp Viral RNA Mini Kit, DMEM, MiSeq platform, DNeasy Blood and Tissue Kit, QIAamp DNA Mini Kit, MEM, and Stata 12.0, to optimize their disease outbreak preparedness and response strategies.