Crowd cluster data in the USA for analysis of human response to COVID-19 events and policies.

We provide data on daily social contact intensity of clusters of people at different types of Points of Interest (POI) by zip code in Florida and California. This data is obtained by aggregating fine-scaled details of interactions of people at the spatial resolution of 10 m, which is then normalized as a social contact index. We also provide the distribution of cluster sizes and average time spent in a cluster by POI type. This data will help researchers perform fine-scaled, privacy-preserving analysis of human interaction patterns to understand the drivers of the COVID-19 epidemic spread and mitigation. Current mobility datasets either provide coarse-level metrics of social distancing, such as radius of gyration at the county or province level, or traffic at a finer scale, neither of which is a direct measure of contacts between people. We use anonymized, de-identified, and privacy-enhanced location-based services (LBS) data from opted-in cell phone apps, suitably reweighted to correct for geographic heterogeneities, and identify clusters of people at non-sensitive public areas to estimate fine-scaled contacts.

A cytokine gene screen uncovers SOCS1 as genetic risk factor for multiple sclerosis.

Cytokine and cytokine receptor genes, including IL2RA, IL7R and IL12A, are known risk factors for multiple sclerosis (MS). Excitotoxic oligodendroglial death mediated by glutamate receptors contributes to demyelinating reactions. In the present study, we screened 368 single-nucleotide polymorphisms (SNPs) in 55 genes or gene clusters coding for cytokines, cytokine receptors, suppressors of cytokine signaling (SOCS), complement factors and glutamate receptors for association with MS in a Spanish-Basque resident population. Top-scoring SNPs were found within or nearby the genes coding for SOCS-1 (P=0.0005), interleukin-28 receptor, alpha chain (P=0.0008), oncostatin M receptor (P=0.002) and interleukin-22 receptor, alpha 2 (IL22RA2; P=0.003). The SOCS1 rs243324 variant was validated as risk factor for MS in a separate cohort of 3919 MS patients and 4003 controls (combined Cochran-Mantel-Haenszel P=0.00006; odds ratio (OR)=1.13; 95% confidence interval (CI)=1.07-1.20). In addition, the T allele of rs243324 was consistently increased in relapsing-remitting/secondary progressive versus primary-progressive MS patients, in each of the six data sets used in this study (P(CMH)=0.0096; OR=1.24; 95% CI 1.05-1.46). The association with SOCS1 appears independent from the chr16MS risk locus CLEC16A.

IOTEML: An Internet of Things (IoT)-Based Enhanced Machine Learning Model for Tumour Investigation.

In the current age of technology, various diseases in the body are also on the rise. Tumours that cause more discomfort in the body are set to increase the discomfort of most patients. Patients experience different effects depending on the tumour size and type. Future developments in the medical field are moving towards the development of tools based on IoT devices. These advances will in the future follow special features designed based on multiple machine learning developed by artificial intelligence. In that order, an improved algorithm named Internet of Things-based enhanced machine learning is proposed in this paper. What makes it special is that it involves separate functions to diagnose each type of tumour. It analyzes and calculates things like the size, shape, and location of the tumour. Cure from cancer is determined by the stage at which we find cancer. Early detection of cancer has the potential to cure quickly. At a saturation point, the proposed Internet of Things-based enhanced machine learning model achieved 94.56% of accuracy, 94.12% of precision, 94.98% of recall, 95.12% of F1-score, and 1856 ms of execution time. The simulation is conducted to test the efficacy of the model, and the results of the simulation show that the proposed Internet of Things-based enhanced machine learning obtains a higher rate of intelligence than other methods.

Validation of IRF5 as multiple sclerosis risk gene: putative role in interferon beta therapy and human herpes virus-6 infection.

In recent reports, IRF5 polymorphisms showed significant association with multiple sclerosis (MS) susceptibility in three studied populations and Irf5-deficient mice exhibited an increased susceptibility to viral infection, linked to a significant decrease in the induction of serum type I interferon (IFN). In the present study, we evaluated the association of two IRF5 polymorphisms with MS predisposition and we also addressed whether these polymorphisms were associated with active replication of human herpes virus-6 (HHV-6) observed in a subgroup of MS patients, and/or with response to IFN-ß therapy. A total of 1494 MS patients and 1506 ethnically matched controls were genotyped for rs4728142 and rs3807306 with TaqMan pre-designed assays. One hundred and six patients were classified as responders to IFN-ß therapy (no relapses/increases in EDSS over the 2-year follow-up) and 112 as non-responders (at least two relapses or an increase in expanded disability status scale (EDSS) of at least one point during the same period). The combined analysis of available datasets yielded an effect size on MS with odds ratio (OR)(Mantel-Haenszel)=1.14 (P<0.002) for the IRF5 polymorphisms rs4728142 and rs3807306. Additionally, trends for association were observed between rs3807306T and infection with HHV-6 [p=0.05, OR (95% CI)=1.56 (1.00-2.44)] and response to IFN-ß therapy [P=0.09, OR (95% CI)=1.39 (0.95-2.05)].

Restriction fragment length polymorphism in four virulence-associated genes of Listeria monocytogenes.

We observed restriction fragment length polymorphism in 4 genes of Listeria monocytogenes associated with virulence. Using the polymerase chain reaction (PCR) and primers derived from published sequences, we amplified the following genes: hlyA coding for listeriolysin O, iap coding for a putative invasion-associated factor, mpl coding for a metalloprotease, and the prfA gene that positively regulates the hylA gene. PCR-amplified DNA were cut with several restriction endonucleases, and the restriction profiles from 29 strains, representing 6 serovars (serovars 1/2a, 1/2b, 1/2c, 3a, 3b and 4b) were compared. Based on these restriction profiles, the strains were categorized into 2 subgroups: one group contained all 10 strains of serovars 1/2a, 1/2c and 3a, the other group contained all 19 strains of serovars 1/2b, 3b and 4b. This division is in complete agreement with multilocus enzyme electrophoretic analysis data which divide the species into the same 2 subgroups. Whether the differences observed in the nucleotide sequences of the 4 virulence-associated genes for the 2 subgroups of L. monocytogenes represent salient variations in pathogenic mechanisms is not known.

Immunogold labelling of Listeria monocytogenes virulence-related factors within Caco-2 cells.

We demonstrated by immunoelectron microscopy that listeriolysin O (LLO), phospholipases and other putative virulence-related proteins produced by Listeria monocytogenes were primarily cell-wall-associated when the bacterium infected Caco-2 tissue culture cell monolayers. Antibodies made to LLO, serogroup 1/2a reacted poorly with serogroup 4b cells and vice-versa, indicating fundamental structural differences in the two proteins. Finally, comet-tail pseudopod structures shown to be involved in cell-to-cell passage of Listeria in Caco-2 cells did not possess detectable Listeria antigens on their anterior surface or within their structure, suggesting that the phagocytic process is primarily host-cell-dependent once it is initiated by the bacterial cell.

Immunoaffinity purification, stabilization and comparative characterization of listeriolysin O from Listeria monocytogenes serotypes 1/2a and 4b.

We developed a simple and highly effective procedure for stabilizing the haemolytic activity of listeriolysin O (LLO) from Listeria monocytogenes after immunoaffinity purification. The haemolytic activity of LLO was stabilized by eluting it directly into tubes containing an alkaline buffer (5 mM lysine, 140 mM KCl, 50% ethylene glycol, pH 11.5). The purified LLO retained 100% of its haemolytic activity after 6 weeks of storage at -20 degrees C. LLO purified from a strain of L. monocytogenes serotype 1/2a (ATCC 43249) and LLO purified from a strain of L. monocytogenes serotype 4b (F 2365) isolated from a Mexican-style cheese, showed no significant differences in pH and temperature stability. When incubated in buffers at pH values from 4 to 12 at 4 degrees C and 25 degrees C, LLO from serotypes 1/2a and 4b retained maximal haemolytic activity at pH 8 after 4 h of incubation. LLO from both serotypes lost their haemolytic activity after incubation at 50 degrees C for 25 min.

Evaluation of a chemiluminescent DNA probe assay for the rapid confirmation of Listeria monocytogenes.

A Listeria monocytogenes-specific, acridinium-ester-labelled DNA probe was evaluated in a chemiluminescent homogeneous protection assay (HPA) for the rapid confirmation of suspect L. monocytogenes colonies from blood agar plates. The HPA uses an acridinium-ester-labelled chemiluminescent DNA probe in a free-solution hybridization format. After the DNA probe hybridized with the target ribosomal RNA, the acridinium label on the unhybridized probe was inactivated by a chemical differential hydrolysis step. Formation of a hybrid between probe and target was detected in a luminometer after the addition of a detection reagent. The assay can be completed in 30 to 45 min and allows for simultaneous processing of several (50-100) samples. The probe showed 100% sensitivity and 100% specificity for L. monocytogenes when evaluated in the HPA against L. monocytogenes, other Listeria species and other Gram-positive bacteria. The lower detection limit of the HPA was between 10(4) and 10(5) cells. In an evaluation with 296 bacterial colonies isolated from food, the HPA colony confirmation showed 100% agreement with conventional biochemical characterization. HPA will be useful for the rapid confirmation of L. monocytogenes isolated from food and clinical specimens.

Outbreak of neonatal listeriosis associated with mineral oil.

In June, 1989, an outbreak of nosocomial listeriosis occurred in Costa Rica. Listeria monocytogenes was isolated from 9 ill infants 4 to 8 days old who were born after the delivery of an infant with early onset listeriosis. One nosocomial infection was fatal, 2 required mechanical ventilation and 1 resulted in hemiparesis. A higher proportion of cases than other infants born during the outbreak were delivered by cesarean section (55% vs. 24%, P = 0.04). Compared with the mothers of 36 random controls, case mothers were more often primiparous (odds ratio, 6.2, P = 0.03) or received general anesthesia before delivery (odds ratio, 4.4, P = 0.09). All infants were bathed with mineral oil from a multidose container. Culture of the oil by cold enrichment grew L. monocytogenes 4b with the same electrophoretic enzyme type as the outbreak strain. We hypothesize that aspiration of contaminated oil may have resulted in systemic listeriosis. General anesthesia may have increased the risk of aspiration. Lung tissue from the infant who died showed lipid-laden macrophages consistent with oil aspiration and had evidence of L. monocytogenes DNA detected by polymerase chain reaction. This is the first nosocomial outbreak of listeriosis in which a common source suggested epidemiologically was microbiologically confirmed. The high attack rate (greater than 200 times the United States rate of perinatal listeriosis) emphasizes the susceptibility of healthy neonates to L. monocytogenes. The results of our study led to the discontinuation of the use of mineral oil for bathing neonates in Costa Rica.

Characterization of gyrA mutations associated with fluoroquinolone resistance in Campylobacter coli by DNA sequence analysis and MAMA PCR.

Increasing numbers of fluoroquinolone-resistant Campylobacter coli isolates received at the Minnesota State Public Health Laboratory and at the Centers for Disease Control and Prevention have been a cause for concern. The gyrA quinolone resistance-determining regions of several fluoroquinolone-resistant isolates were sequenced to examine the mechanism of resistance. Ciprofloxacin-resistant C. coli isolates examined by DNA sequencing had a Thr-86 to Ile (ACT-->ATT) gyrA mutation, leading to resistance to fluoroquinolone antibiotics. A mismatch amplification mutation assay polymerase chain reaction protocol was developed to detect this gyrA mutation.

PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis.

PulseNet is a national network of pubic health and food regulatory laboratories established in the US to detect clusters of foodborne disease and respond quickly to foodborne outbreak investigations. PulseNet laboratories currently subtype Escherichia coli O157:H7, non-typhoidal Salmonella, and Shigella isolates by a highly standardized 1-day pulsed-field gel electrophoresis (PFGE), and exchange normalized DNA "fingerprint" patterns via the Internet. We describe a standardized molecular subtyping protocol for subtyping Listeria monocytogenes that was recently added to PulseNet. The subtyping can be completed within 30 h from the time a pure culture of the bacteria is obtained.

Factors influencing the detection and enumeration of Escherichia coli O157:H7 on alfalfa seeds.

Isolating Escherichia coli O157:H7 from batches of alfalfa seeds used to produce sprouts implicated in human illness has been difficult, perhaps due to nonhomogenous and very low-level contamination and inaccessibility of the pathogen entrapped in protected areas of the seed coat. We evaluated the effectiveness of various treatments in releasing E. coli O157:H7 from seeds. The influence of homogenization (blending or stomaching for 1 or 2 min), rinsing method (shaking for 5 min), soaking time (0. 1, 3, 6, or 15 h), soaking temperature (4 or 21 degrees C), and the addition of surfactants (0.1%, 0.5%, or 1.0% Tween 80 or Span 20) to rinse water was determined. Blending or stomaching for 1 or 2 min, and soaking for 1 h or longer at 4 or 21 degrees C, respectively, resulted in maximum release of E. coli O157:H7 from seeds. Soaking seeds at 37 degrees C for 15 h increased cell populations of E. coli O157:H7 by approximately 3.6 log10 CFU/g, likely due to bacterial growth. The maximum number of cells released from seeds by rinse water containing 1.0% Span 20 was at 21 degrees C, whereas at 37 degrees C, 0.1% or 0.5% Tween 80 was more effective. Detection of E. coli O157:H7 on seeds stored at 37 degrees C for up to 13 weeks and on sprouts derived from these seeds was compared. E. coli O157:H7 inoculated on seeds at 2.0 log10 CFU/g was detected after storage of seeds for up to 8 weeks at 37 degrees C and in sprouts produced from the seeds. The pathogen was not detected on seeds stored for 13 weeks at 37 degrees C and was not isolated from sprouts produced from these seeds. Identifying seed treatment methods that enhance removal of E. coli O157:H7 from alfalfa seeds can aid the isolation and enumeration of the pathogen on seeds. With a combination of optimal conditions for detecting the pathogen, i.e. soaking seeds for 1 h and pummeling seeds for 1 min, an enrichment step in modified tryptic soy broth (TSB), and the use of immunomagnetic beads for separation of E. coli O157:H7 cells, E. coli O157:H7 was detected in alfalfa seeds incubated at 37 degrees C for up to 8 weeks as effectively as in sprouts produced from the seeds.

WHO-sponsored international collaborative study to evaluate methods for subtyping Listeria monocytogenes: restriction fragment length polymorphism (RFLP) analysis using ribotyping and Southern hybridization with two probes derived from L. monocytogenes chromosome.

Seven laboratories participated in a WHO-sponsored international collaborative study, to evaluate methods for subtyping Listeria monocytogenes, by performing restriction fragment length polymorph sm (RFLP) analysis-based subtyping of an international study set of 80 strains of L. monocytogenes that included 22 epidemiologically related groups. The RFLP analysis was done by Southern hybridization with one of two types of probes found in multiple copies on the chromosome of L. monocytogenes. Six laboratories performed ribotyping. These laboratories used EcoRI enzyme to restrict the L. monocytogenes DNA and ribosomal RNA or DNA as the probe for Southern hybridizations. The seventh laboratory used Ncil to restrict the DNA, and two probes, one randomly cloned and the other containing repeat sequences cloned from L. monocytogenes DNA. The overall discriminating power of ribotyping, as estimated by calculation of Simpson's index of diversity, ranged from 0.83 to 0.88 for the six laboratories. The discriminating power of the combination of two probes used by Laboratory 7 was 0.91. Ribotyping and the cloned probes used by Laboratory 7 discriminated poorly between serotype 4b strains. Neither method identified three atypical strains (identified by other subtyping methods) included in three apparently epidemiologically related groups. Ribotyping did not discriminate between strains of serotypes 4b and 4b(X) in one epidemiologically related group of strains; one cloned probe used by Laboratory 7 discriminated between these strains. Intra-laboratory reproducibilities for the seven laboratories ranged from 80.0 to 100%. as determined by their abilities to correctly identify 11 pairs of duplicate strains included in the study set. Inter-laboratory reproducibilities were generally very good considering that no attempt was made to standardize protocols used by the participants.

Isolation and identification of rutin as the major mutagen of red wine.

The polyphenolics of a red wine were concentrated by salt-induced phase separation into acetone-alcohol and fractionated by Sephadex LH-20 and multi-layer counter-current chromatography. The mutagenicity of each fraction was evaluated by the Salmonella mutagenesis assay. The mutagen of red wine required activation by both rat-liver microsomal enzymes and human-fecal enzymes (fecalase). The mutagenic component of red wine was purified to homogeneity by reverse-phase high-performance liquid chromatography (RPHPLC) on Lichrosorb C18 and was identified as rutin by UV spectrometry, co-chromatography with authentic standard on RPHPLC and gas-liquid chromatography/mass spectrometry.

Mutagenicity of proanthocyanidins.

Several procyanidins with different degrees of polymerization (dimers, a trimer and a polymer) and extracted from different natural sources were found to be non-mutagenic in the Salmonella mutagenesis assay system. A mutagenic impurity in procyanidin B-4 was isolated by means of reversed-phase high-performance liquid chromatography (HPLC) and identified as rutin with UV spectrometry, co-chromatography on reversed-phase HPLC and gas chromatography-mass spectrometry.

Evaluation of the genotoxicity of lac dye.

Red lac dye, a by-product of the shellac industry, has the potential for use in foods, drugs and cosmetics as a colouring agent. As part of a series of tests of the suitability of lac dye for this purpose an evaluation of its genotoxicity was carried out. Lac dye was non-mutagenic in Ames tests using five strains of Salmonella typhimurium with or without metabolic activation. No cytotoxicity or mutagenicity was observed in Chinese hamster lung (V79) cells exposed to lac dye in vitro. A clastogenic effect was observed in the bone-marrow cells of mice that had been treated with lac dye ip or orally.

Fate of Escherichia coli O157:H7 in coleslaw during storage.

An outbreak of Escherichia coli O157:H7 infection associated with the consumption of coleslaw in several units of a restaurant chain prompted a study to determine the fate of the pathogen in two commercial coleslaw preparations (pH 4.3 and 4.5) held at 4, 11, and 21 degrees C for 3 days. At an initial population of 5.3 log10 CFU/g of coleslaw, E. coli O157:H7 did not grow in either coleslaw stored at the three temperatures. Rather, the population of E. coli O157:H7 decreased by 0.1 to 0.5 log10 CFU/g within 3 days. The greatest reduction (0.4 and 0.5 log10 CFU/g) in population occurred at 21 degrees C, whereas only slight decreases (0.1 to 0.2 log10 CFU/g) occurred at 4 and 11 degrees C. A pH of 4.3 to 4.5 of coleslaw had little effect on reducing E. coli O157:H7 populations. Results suggest that the tolerance of E. coli O157:H7 to acid pH, not temperature abuse, is a major factor influencing the pathogen's fate in restaurant-prepared coleslaw.

Fate of Shigella sonnei on parsley and methods of disinfection.

Outbreaks of shigellosis associated with chopped parsley used as a garnish for foods occurred in four states in the United States and in two Canadian provinces in 1998. This prompted a study to determine survival and growth characteristics of Shigella sonnei inoculated onto raw parsley. Two inoculum levels (approximately 10(3) and 10(6) CFU/g) were applied to parsley leaves, portions of which were then chopped. Inoculated whole and chopped parsley leaves were held at 4 degrees C or 21 degrees C for up to 14 days. Initial populations of the organism on chopped parsley receiving high or low levels of inoculum increased by approximately 3 log10 CFU/g, within 1 day at 21 degrees C. Populations of S. sonnei on inoculated chopped or whole parsley leaves held at 4 degrees C decreased by 2.5 to 3.0 log10 CFU/g during a 14-day storage period. The pathogen multiplied, without a lag phase, on inoculated (2.72 log10 CFU/g) chopped parsley held at 21 degrees C, exceeding 6 log10 CFU/g within 24 h. Treatment of inoculated whole parsley leaves with vinegar containing 5.2% (vol/vol) acetic acid or 200 ppm free chlorine for 5 min at 21 degrees C reduced the population of S. sonnei by more than 6 log10 CFU/g, whereas treatment with vinegar containing 7.6% acetic acid or 250 ppm free chlorine reduced initial populations of 7.07 and 7.26 log10 CFU/g, respectively, to undetectable levels (<0.6 log10 CFU/g). These studies revealed that S. sonnei can grow rapidly on chopped parsley held at ambient temperature and remain viable for at least 14 days at 4 degrees C. Treatment of contaminated parsley with vinegar or chlorinated water offers a simple method to reduce markedly or eliminate the pathogen in food-service or home settings.

Rapid detection of salmonellae in mechanically deboned poultry meat.

Samples of frozen mechanically deboned poultry (chicken and turkey) meat were examined for the presence of salmonellae by the conventional cultural method and by a modified membrane filter - disc immunoimmobilization (MFD1) procedure. The modified MFD1 procedure consisted of the following steps: pre-enrichment for 18 hr at 35 C; selective enrichment for 6 hr at 35 C; filtration of 1 ml of selective enrichment culture through a .45 micrometer membrane filter; and incubation for 18 to 24 hr at 35 C of the membrane filter on a semi-solid selective medium in the presence of a disc impregnated with Salmonella polyvalent flagellar antiserum. Presence of Salmonella in a sample was indicated by the immobilization of Salmonella on contact with the antiserum in the semi-solid medium. The modified MFDI procedure was found to be more sensitive than the conventional cultural method for the isolation of salmonella from mechanically deboned poultry meat. Of 100 samples analyzed, only 22 were positive for Salmonella by the conventional cultural procedure while 61 were positive by the modified MFDI procedure. The modified MFDI procedure yielded 1 false negative while the conventional procedure yielded 38 false negatives.

Effect of five cycle rapid freeze-thaw treatment in conjunction with various chemicals for the reduction of Salmonella typhimurium.

A five cycle rapid freeze-rapid thaw process was used in conjunction with chemicals to reduce numbers of Salmonella typhimurium cells on poultry meat. The second portion of chicken wings consisting of ulna and radius with attached skin and muscle was inoculated with 400 to 900 colony forming units (CFU/g) of a nalidixic acid resistant strain of S. typhimurium. Chemicals used were 20 ppm chlorine, 5% potassium sorbate, 5% lactic acid, and 5% calcium propionate. The wings were either sprayed with or dipped into all chemicals before the freeze-thaw process. Wings were also chemically treated and not subjected to the freeze-thaw process. Numbers of S. typhimurium were determined by the most probable number procedure. The relative effectiveness of combinations of chemicals and the freeze-thaw process was compared to a control with the following percentage reductions of numbers of S. typhimurium cells: lactic acid, 98%; calcium propionate, 96%; potassium sorbate, 96%; chlorine, 95%; and freeze-thaw process without chemicals, 95%. There were no statistically significant differences among the treatments. In pilot plant study simulating commercial conditions, a carbon dioxide freezer was used for the rapid freeze and a microwave oven was used for the rapid thaw. Treatment of wings with 5% lactic acid plus freeze-thaw process resulted in statistically significant fewer numbers of S. typhimurium cells when compared to the freeze-thaw process without chemical treatment or to wings chemically treated without the freeze-thaw process.