Tag: statistics

Foodborne Pathog Dis. 2023 Sep 19. doi: 10.1089/fpd.2023.0050. Online ahead of print.

ABSTRACT

Milk is an important source of food, and it is also a nutrient-rich medium, which can harbor multiple microorganisms. Staphylococcus aureus is an important foodborne pathogen in food-producing animals, and there have been many reports on its infection and antimicrobial resistance (AMR), which has significant global public health concerns. This study was designed to isolate, characterize, and analyze the AMR pattern of S. aureus from milk samples collected in Chennai, India. A total of 259 raw milk samples from 3 groups: dairy farms, local vendors, and retail outlets were analyzed, and it was found that 34% (89/259) were positive for S. aureus. Positive isolates were further characterized by pulsed-field gel electrophoresis and isolates recovered from different sources, study areas, and locations showed high genetic diversity with no similarity. The presence of AMR has been further assessed by phenotypic methods as per CLSI-M100 performance standards, and all the isolates were susceptible to ampicillin/sulbactam, mupirocin, and tylosin. Additionally, all of the isolates were resistant to ampicillin. There were 28 isolates categorized as multidrug-resistant, which showed resistance to more than 2-3 classes of antimicrobials. This is the first report of inducible clindamycin resistance and mupirocin sensitivity pattern from S. aureus isolates recovered from milk. This study established the occurrence varied with genetic diversity in the isolates prevalent in the study area and divergence pattern of AMR S. aureus. The AMR in these isolates and with methicillin-resistant S. aureus could pose a serious threat to food safety and economic implications.

PMID:37722022 | DOI:10.1089/fpd.2023.0050

Cannabis Cannabinoid Res. 2023 Sep;8(S1):S71-S82. doi: 10.1089/can.2023.0038.

ABSTRACT

Introduction: Tetrahydrocannabivarin (THCV) is an understudied cannabinoid that appears to have effects that vary as a function of dose. No human study has evaluated the safety and nature of effects in a wide range of THCV doses. Methods: This was a two-phase, dose-ranging, placebo-controlled trial of the Δ⁸ isomer of oral THCV in healthy adults. Phase 1 utilized an unblinded, single-ascending dose design (n=3). Phase 2 used a double-blind, randomized, within-participant crossover design (n=18). Participants received single acute doses of placebo and 12.5, 25, 50, 100, and 200 mg of THCV. Safety measures and subjective and cognitive effects were assessed predose and up to 8 h postdose. Results: Most adverse events (AEs; 55/60) were mild. Euphoric mood was the most common AE. The 12.5, 25, and 200 mg doses produced significantly lower minimum times to complete the digit vigilance test (ps=0.01). The 25 mg dose showed elevations on mean ratings of “energetic” at 1-, 2-, and 4-h postdose, but the maximum postdose rating for this dose did not achieve statistical significance relative to placebo ([95% confidence interval]=3.2 [-0.5 to 6.9], p=0.116). The 100 and 200 mg doses showed elevations on ratings of “feel a drug effect” and “like the drug effect.” Almost all urine drug screens (78/79) at 8 h postdose in the active THCV conditions tested positive for tetrahydrocannabinol (THC). Conclusion: All THCV doses displayed a favorable safety profile. Several THCV doses showed a preliminary signal for improved sustained attention, but the effect was not dose dependent. Though mild and not associated with impairment, THC-like effects were observed at higher THCV doses. Oral THCV-containing products could lead to positive urine drug screens for THC. ClinicalTrials.gov ID: NCT05210634.

PMID:37721990 | DOI:10.1089/can.2023.0038

PLoS Negl Trop Dis. 2023 Sep 18;17(9):e0011604. doi: 10.1371/journal.pntd.0011604. Online ahead of print.

ABSTRACT

Synthetic insecticides are the primary vector control method used globally. However, the widespread use of insecticides is a major cause of insecticide-resistance in mosquitoes. Hence, this study aimed at elucidating permethrin and temephos-resistant protein expression profiles in Ae. aegypti using quantitative proteomics. In this study, we evaluated the susceptibility of Ae. aegypti from Penang Island dengue hotspot and non-hotspot against 0.75% permethrin and 31.25 mg/l temephos using WHO bioassay method. Protein extracts from the mosquitoes were then analysed using LC-ESI-MS/MS for protein identification and quantification via label-free quantitative proteomics (LFQ). Next, Perseus 1.6.14.0 statistical software was used to perform differential protein expression analysis using ANOVA and Student’s t-test. The t-test selected proteins with≥2.0-fold change (FC) and ≥2 unique peptides for gene expression validation via qPCR. Finally, STRING software was used for functional ontology enrichment and protein-protein interactions (PPI). The WHO bioassay showed resistance with 28% and 53% mortalities in adult mosquitoes exposed to permethrin from the hotspot and non-hotspot areas. Meanwhile, the susceptibility of Ae. aegypti larvae revealed high resistance to temephos in hotspot and non-hotspot regions with 80% and 91% mortalities. The LFQ analyses revealed 501 and 557 (q-value <0.05) differentially expressed proteins in adults and larvae Ae. aegypti. The t-test showed 114 upregulated and 74 downregulated proteins in adult resistant versus laboratory strains exposed to permethrin. Meanwhile, 13 upregulated and 105 downregulated proteins were observed in larvae resistant versus laboratory strains exposed to temephos. The t-test revealed the upregulation of sodium/potassium-dependent ATPase β2 in adult permethrin resistant strain, H15 domain-containing protein, 60S ribosomal protein, and PB protein in larvae temephos resistant strain. The downregulation of troponin I, enolase phosphatase E1, glucosidase 2β was observed in adult permethrin resistant strain and tubulin β chain in larvae temephos resistant strain. Furthermore, the gene expression by qPCR revealed similar gene expression patterns in the above eight differentially expressed proteins. The PPI of differentially expressed proteins showed a p-value at <1.0 x 10-16 in permethrin and temephos resistant Ae. aegypti. Significantly enriched pathways in differentially expressed proteins revealed metabolic pathways, oxidative phosphorylation, carbon metabolism, biosynthesis of amino acids, glycolysis, and citrate cycle. In conclusion, this study has shown differentially expressed proteins and highlighted upregulated and downregulated proteins associated with insecticide resistance in Ae. aegypti. The validated differentially expressed proteins merit further investigation as a potential protein marker to monitor and predict insecticide resistance in field Ae. aegypti. The LC-MS/MS data were submitted into the MASSIVE database with identifier no: MSV000089259.

PMID:37721966 | DOI:10.1371/journal.pntd.0011604

PLoS One. 2023 Sep 18;18(9):e0291428. doi: 10.1371/journal.pone.0291428. eCollection 2023.

ABSTRACT

BACKGROUND: The fast-changing labor market highlights the need for an in-depth understanding of occupational mobility impacted by technological change. However, we lack a multidimensional classification scheme that considers similarities of occupations comprehensively, which prevents us from predicting employment trends and mobility across occupations. This study fills the gap by examining employment trends based on similarities between occupations.

METHOD: We first demonstrated a new method that clusters 756 occupation titles based on knowledge, skills, abilities, education, experience, training, activities, values, and interests. We used the Principal Component Analysis to categorize occupations in the Standard Occupational Classification, which is grouped into a four-level hierarchy. Then, we paired the occupation clusters with the occupational employment projections provided by the U.S. Bureau of Labor Statistics. We analyzed how employment would change and what factors affect the employment changes within occupation groups. Particularly, we specified factors related to technological changes.

RESULTS: The results reveal that technological change accounts for significant job losses in some clusters. This poses occupational mobility challenges for workers in these jobs at present. Job losses for nearly 60% of current employment will occur in low-skill, low-wage occupational groups. Meanwhile, many mid-skilled and highly skilled jobs are projected to grow in the next ten years.

CONCLUSION: Our results demonstrate the utility of our occupational classification scheme. Furthermore, it suggests a critical need for skills upgrading and workforce development for workers in declining jobs. Special attention should be paid to vulnerable workers, such as older individuals and minorities.

PMID:37721950 | DOI:10.1371/journal.pone.0291428

PLoS Genet. 2023 Sep 18;19(9):e1010546. doi: 10.1371/journal.pgen.1010546. Online ahead of print.

ABSTRACT

Genome-wide association studies (GWAS) are commonly used to identify genomic variants that are associated with complex traits, and estimate the magnitude of this association for each variant. However, it has been widely observed that the association estimates of variants tend to be lower in a replication study than in the study that discovered those associations. A phenomenon known as Winner’s Curse is responsible for this upward bias present in association estimates of significant variants in the discovery study. We review existing Winner’s Curse correction methods which require only GWAS summary statistics in order to make adjustments. In addition, we propose modifications to improve existing methods and propose a novel approach which uses the parametric bootstrap. We evaluate and compare methods, first using a wide variety of simulated data sets and then, using real data sets for three different traits. The metric, estimated mean squared error (MSE) over significant SNPs, was primarily used for method assessment. Our results indicate that widely used conditional likelihood based methods tend to perform poorly. The other considered methods behave much more similarly, with our proposed bootstrap method demonstrating very competitive performance. To complement this review, we have developed an R package, ‘winnerscurse’ which can be used to implement these various Winner’s Curse adjustment methods to GWAS summary statistics.

PMID:37721937 | DOI:10.1371/journal.pgen.1010546

Med Sci Monit. 2023 Sep 18;29:e940948. doi: 10.12659/MSM.940948.

ABSTRACT

BACKGROUND The aim of this study was to analyze the correlation and the accuracy of lower-extremity torsion deformities measured by physical examination, CT scan, and three-dimensional gait analysis in children with CP. MATERIAL AND METHODS The study group included 72 children with CP with lower-extremity torsion deformities. All subjects were assessed by: 1. physical examination: maximum internal rotation (MIR), maximum external rotation (MER) for hip joint torsion, and transmalleolar axis (TMA) for tibial torsion; 2. CT scanning: femoral anteversion (FAV) and tibial torsion (TT); 3. three-dimensional gait analysis kinematic parameters: single-support phase of femoral rotation, double-support phase of femoral rotation, swing phase of femoral rotation and single-support phase of tibial rotation, double-support phase of tibial rotation, and swing phase of tibial rotation. Statistical analysis was performed using the Pearson correlation test. A significance level of P<0.05 was set. RESULTS In femurs, MIR and MER were correlated with FAV, and the correlation of MER was higher, while physical examination and FAV were not correlated with any kinematic data in gait analysis. In tibias, there was no correlation between TMA and TT, but both TMA and TT were correlated with the gait analysis kinematic data, and the correlation of TT was higher. TMA was more correlated with tibial rotation during swing phase, while TT was more correlated with tibial rotation in single-support phase. CONCLUSIONS Three-dimensional gait analysis can analyze the tibial rotation of children with cerebral palsy, which is highly correlated with CT and physical examination. However, femoral rotation was not associated with CT and physical examination.

PMID:37721931 | DOI:10.12659/MSM.940948

PLOS Glob Public Health. 2023 Sep 18;3(9):e0002326. doi: 10.1371/journal.pgph.0002326. eCollection 2023.

ABSTRACT

Voluntary medical male circumcision (VMMC) has primarily been promoted for HIV prevention. Evidence also supports that male circumcision offers protection against other sexually transmitted infections. This analysis assessed the effect of circumcision on syphilis, hepatitis B virus (HBV) infection and HIV. Data from the 2015 to 2019 Population-based HIV Impact Assessments (PHIAs) surveys from Rwanda, Tanzania, Uganda, Zambia, and Zimbabwe were used for the analysis. The PHIA surveys are cross-sectional, nationally representative household surveys that include biomarking testing for HIV, syphilis and HBV infection. This is a secondary data analysis using publicly available PHIA data. Univariate and multivariable logistic regression models were created using pooled PHIA data across the five countries to assess the effect of male circumcision on HIV, active and ever syphilis, and HBV infection among sexually active males aged 15-59 years. Circumcised men had lower odds of syphilis infection, ever or active infection, and HIV, compared to uncircumcised men, after adjusting for covariates (active syphilis infection = 0.67 adjusted odds ratio (aOR), 95% confidence interval (CI), 0.52-0.87, ever having had a syphilis infection = 0.85 aOR, 95% CI, 0.73-0.98, and HIV = 0.53 aOR, 95% CI, 0.47-0.61). No difference between circumcised and uncircumcised men was identified for HBV infection (P = 0.75). Circumcised men have a reduced likelihood for syphilis and HIV compared to uncircumcised men. However, we found no statistically significant difference between circumcised and uncircumcised men for HBV infection.

PMID:37721926 | DOI:10.1371/journal.pgph.0002326

Biomedica. 2023 Aug 31;43(Sp. 1):144-155. doi: 10.7705/biomedica.6852.

ABSTRACT

INTRODUCTION: Drug resistance to azoles is a growing problem in the Candida genus.

OBJECTIVE: To analyze molecularly the genes responsible for fluconazole resistance in Candida tropicalis strains.

MATERIALS AND METHODS: Nineteen strains, with and without exposure to fluconazole, were selected for this study. The expression of MDR1, CDR1, ERG11, and ERG3 genes was analyzed in sensitive, dose-dependent sensitive, and resistant strains exposed to different concentrations of the antifungal drug.

RESULTS: MDR1, ERG11 and ERG3 genes were significantly overexpressed in the different sensitivity groups. CDR1 gene expression was not statistically significant among the studied groups. Seven of the eight fluconazole-resistant strains showed overexpression of one or more of the analyzed genes. In some dose-dependent sensitive strains, we found overexpression of CDR1, ERG11, and ERG3.

CONCLUSION: The frequency of overexpression of ERG11 and ERG3 genes indicates that they are related to resistance. However, the finding of dose-dependent resistant/sensitive strains without overexpression of these genes suggests that they are not exclusive to this phenomenon. More basic research is needed to study other potentially involved genes in the resistance mechanism to fluconazole.

PMID:37721916 | DOI:10.7705/biomedica.6852

Biomedica. 2023 Aug 31;43(Sp. 1):206-216. doi: 10.7705/biomedica.6872.

ABSTRACT

INTRODUCTION: Fungal infections in patients with COVID-19 was one of the most debated topics during the pandemic.

OBJECTIVES: To analyze the clinical characteristics and evolution of people living with HIV/AIDS and coinfection with cryptococcus and COVID-19 (group A) or without it (group B).

MATERIALS AND METHODS: This is an analytical and retrospective study. We reviewed medical records of patients with meningeal cryptococcosis between April 2020 and May 2021.

RESULTS: We studied 65 people living with HIV/AIDS and with cryptococcosis infection diagnosed from April 2020 to May 2021. Fifteen patients with HIV/AIDS suffered from cryptococcosis and COVID-19, and out of these, 14 presented meningitis (group A), while 28 suffered from meningeal cryptococcosis, but did not have COVID-19 (group B).

CONCLUSIONS: No statistically significant differences were observed between the two groups (A and B) considering: intracranial hypertension, presence of Cryptococcus antigens in cerebrospinal fluid, sensorium deterioration or mortality. The detection of Cryptococcus antigens in serum by lateral flow assay was highly effective to rapidly diagnose cryptococcosis in patients with HIV/AIDS who also developed COVID-19. Patients of both groups consulted for cryptoccocosis sometime after, in comparison with the pre-pandemic cases related to this infection.

PMID:37721913 | DOI:10.7705/biomedica.6872

Biomedica. 2023 Aug 31;43(Sp. 1):255-266. doi: 10.7705/biomedica.7020.

ABSTRACT

INTRODUCTION: Pneumocystis jirovecii is an opportunistic fungus that affects mainly people living with HIV (CD4 cell count lower than 200 cells/ml) and other immunosuppressed patients. Since P. jirovecii does not grow on routine mycological media, diagnosis of P. jirovecii pneumonia relies on indirect evidence of its presence in respiratory samples.

OBJECTIVES: To associate the results of direct immunofluorescence and two molecular methods with a score to predict P. jirovecii pneumonia in patients with AIDS.

MATERIALS AND METHODS: A prospective study was conducted with 40 patients. A respiratory sample collected before treatment was subjected to direct immunofluorescence using the Merifluor kit, to nested PCR targeting the mitochondrial large subunit ribosomal RNA, and to the VIASURE real-time PCR kit.

RESULTS: These three techniques revealed P. jirovecii in 6, 12, and 15 samples, respectively. All positive samples by direct immunofluorescence were positive by nested PCR, and all positive samples by nested PCR amplified by real-time PCR. There was a statistically significant association between the P. jirovecii pneumonia score and the molecular methods. Two patients were early diagnosed and responded well to treatment.

CONCLUSION: Molecular methods, especially real-time PCR, are recommended for early diagnosis of P. jirovecii pneumonia in AIDS patients.

PMID:37721900 | DOI:10.7705/biomedica.7020