Reproducible image-based profiling with Pycytominer.

Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process thousands of image-based features from microscopy images. These features represent valuable single-cell phenotypes that contain information about cell state and biological processes. The use of these features for biological discovery is known as image-based or morphological profiling. However, these raw features need processing before use and image-based profiling lacks scalable and reproducible open-source software. Inconsistent processing across studies makes it difficult to compare datasets and processing steps, further delaying the development of optimal pipelines, methods, and analyses. To address these issues, we present Pycytominer, an open-source software package with a vibrant community that establishes an image-based profiling standard. Pycytominer has a simple, user-friendly Application Programming Interface (API) that implements image-based profiling functions for processing high-dimensional morphological features extracted from microscopy images of cells. Establishing Pycytominer as a standard image-based profiling toolkit ensures consistent data processing pipelines with data provenance, therefore minimizing potential inconsistencies and enabling researchers to confidently derive accurate conclusions and discover novel insights from their data, thus driving progress in our field.

Morphology and gene expression profiling provide complementary information for mapping cell state.

Morphological and gene expression profiling can cost-effectively capture thousands of features in thousands of samples across perturbations by disease, mutation, or drug treatments, but it is unclear to what extent the two modalities capture overlapping versus complementary information. Here, using both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, we perturb human A549 lung cancer cells with 1,327 small molecules from the Drug Repurposing Hub across six doses, providing a data resource including dose-response data from both assays. The two assays capture both shared and complementary information for mapping cell state. Cell Painting profiles from compound perturbations are more reproducible and show more diversity but measure fewer distinct groups of features. Applying unsupervised and supervised methods to predict compound mechanisms of action (MOAs) and gene targets, we find that the two assays not only provide a partially shared but also a complementary view of drug mechanisms. Given the numerous applications of profiling in biology, our analyses provide guidance for planning experiments that profile cells for detecting distinct cell types, disease phenotypes, and response to chemical or genetic perturbations.

Association between Cholera Outbreak and Traditional Gold Mining in Northern State, Sudan 2017.

INTRODUCTION: Cholera is one of the health problems causing considerable morbidity and mortality. The Northern State of Sudan experienced a recent cholera outbreak, however, there are limited data on the outbreak. METHODS: The objective of this study was to assess the magnitude and risk factors associated with the cholera outbreak in the Northern State of Sudan. A retrospective case series study was conducted in the Northern State of Sudan, which involved tracing cases of cholera outbreak of 2017. Data were collected through reports and interviews. A geographical information system was used to map all cases during the outbreak. Chi-square test and logistic regression were used to identify associated factors. RESULTS: There were 957 cholera cases reported in the state with an attack rate of 14.2/10,000 persons. Dalgo locality had the highest number (415) of cases reported with an attack rate of 167.2/10,000 persons. About 78% of cases were adult males, while 56.2% of cases were immigrants from other states. Immigrants in Halfa and Dalgo localities were four times (odds ratio [OR] = 4.031, 95% confidence interval [CI]: 2.482-6.547) and eight times (OR = 8.318, 95% CI: 5.674-12.193), respectively, at risk of cholera infection compared to immigrants in Dongola locality. The overall case-fatality rate was 1.9%. This was significantly higher in younger (5.8%) and older (22.7%) age groups (P < 0.05). CONCLUSIONS: The study revealed that the cholera outbreak spread highly along with traditional gold mining areas due to poor sanitation. Therefore, improving sanitation services and establishing an effective surveillance system in these areas are essential to prevent future occurrence of outbreaks.

The Prospect of Lactoferrin Use as Adjunctive Agent in Management of SARS-CoV-2 Patients: A Randomized Pilot Study.

Background and Objectives: Preventive, adjunctive and curative properties of lactoferrin have been evaluated since the first wave of severe acute respiratory syndrome coronavirus (SARS-CoV), a viral respiratory disease, emerged 18 years ago. Despite the discovery of new vaccine candidates, there is currently no widely approved treatment for SARS-CoV-2 (COVID-19). Strict adherence to infection prevention and control procedures, as well as vaccines, can, however, prevent the spread of SARS-CoV-2. This study aimed to evaluate the efficacy of lactoferrin treatment in improving clinical symptoms and laboratory indices among individuals with mild to moderate coronavirus disease-19 (COVID-19). Materials and Method: A randomized, prospective, interventional pilot study conducted between 8 July and 18 September 2020 used a hospital-based sample of 54 laboratory-confirmed participants with mild to moderate symptoms of COVID-19. Randomization into a control and two treatment groups ensured all groups received the approved Egyptian COVID-19 management protocol; only treatment group participants received lactoferrin at different doses for seven days. Clinical symptoms and laboratory indices were assessed on Days 0, 2 and 7 after starting treatments. Mean values with standard deviation and one-way analysis of variance with least significant difference of demographic and laboratory data between control and treatment groups were calculated. Results: Our study showed no statistically significant difference among studied groups regarding recovery of symptoms or laboratory improvement. Conclusions: Further research into therapeutic properties particularly related to dosage, duration and follow-up after treatment with lactoferrin in individuals with COVID-19 is required.

MALDI-TOF MS Based Typing for Rapid Screening of Multiple Antibiotic Resistance E. coli and Virulent Non-O157 Shiga Toxin-Producing E. coli Isolated from the Slaughterhouse Settings and Beef Carcasses.

BACKGROUND: The emergence of multiple antibiotic resistance (MAR) Escherichia coli (E. coli) and virulent non-O157 Shiga toxin-producing Escherichia coli (STEC) poses a growing concern to the meat industry. Non-O157 STEC strains including O26, O45, O103, O111, O121, and O145 have been implicated in the occurrence of bloody diarrhea and hemolytic uremic syndrome in humans. This research assessed prevalence, matrix-assisted laser desorption/ionization-time of flight mass-spectrometry (MALDI-TOF MS) protein mass-spectra profiles, multidrug-resistance traits, polymerase chain reaction detection of virulence, and antibiotic-resistance genes of E. coli isolated from beef carcasses and slaughterhouse environments. METHODS: A total of 180 convenience sponge samples were collected from two different sources-specific parts of beef carcasses and surfaces of the processing environment at the slaughterhouse of Ha'il, Saudi Arabia between September and November 2020. MALDI BioTyper and phylotype-based identification methods accurately identified and classified the samples as belonging to the genus belonging to the Escherichia coli domain of bacteria (NCBI txid: 562). RESULTS: Expected changes were seen in the mass peak spectrum defining nine closely related isolates and four unrelated E. coli isolates. Serological typing of E. coli revealed enterotoxigenic E. coli O166 (19.10%); enteropathogenic E. coli O146 (16.36%) and O44 (18.18%); enterohemorrhagic E. coli O111 (31.18%) and O26 (14.54%). Forty-five percent of examined E. coli were resistant to seven antimicrobials; 75% of 20 selected isolates were resistant to three or more antimicrobials. phoA and blaTEM genes were detected in all selected E. coli isolates. CONCLUSION: This study confirmed the efficiency and validity of Matrix-assisted laser desorption/ionization time of flight mass-spectrometry in screening for multi-drug resistant E. coli isolated from slaughterhouse derived beef carcasses in Ha'il, Saudi Arabia. We contributed by revealing the distinction between related and non-related strains of E.coli in livestock. The findings in this study can inform improved policy development decision making and resource allocation related to livestock processing regarding antimicrobial use in food animals and rapid screening for effective multiple antibiotic resistance E. coli and virulent non-O157 STEC control in the slaughterhouses.

Engaging vulnerable populations in parent-led support groups: Testing a recruitment strategy.

Despite the proven benefits of parenting interventions, parent engagement in such interventions remains low and is particularly challenging among vulnerable populations. This theoretically grounded study tested the effectiveness of a recruitment strategy - a simulated parent-led support group (PSG) - to increase intentions to attend a PSG in a predominantly low income, minority sample. The study also examined sociodemographic characteristics that may influence the effectiveness of the recruitment strategy and engagement in PSGs. Surveys assessing intentions to attend a PSG were administered before and after the simulation, and a 2-month follow-up survey assessed subsequent PSG attendance. A total of 95 participants were included in this study. Results indicate that participants' intentions to attend a PSG significantly increased following the PSG simulation (Cohen's d = 1.15), especially among Hispanics. However, PSG attendance in the 2 months following the PSG simulation was relatively low, with only 13% of parents attending a PSG or a planning meeting to start a new PSG. Nevertheless, this recruitment strategy may serve as an important component of a larger engagement effort, especially given the substantial challenges of engaging vulnerable populations in PSGs and other parenting interventions to reduce educational and health disparities.

Depression and HIV risk among men who have sex with men in Tanzania.

Studies have shown high rates of depression among men who have sex with men (MSM) in developed countries. Studies have also shown association between depression and HIV risk among MSM. However, very little research has been done on depression among African MSM. We assessed depression and HIV risk among a sample of MSM in Tanzania. We reviewed data on 205 MSM who were recruited from two Tanzanian cities using the respondent driven sampling method. Demographic and behavioral data were collected using a structured questionnaire. HIV and sexually transmitted infections data were determined from biological tests. Depression scores were assessed using the Patient Health Questionnaire (PHQ-9). For the analysis, depression scores were dichotomized as depressed (PHQ > 4) and not depressed (PHQ ≤ 4). Bivariate and multivariable Poisson regression analyses were conducted to assess factors associated with depression. The prevalence of depression in the sample was 46.3%. The mean (±SD) age of the sample was 25 (±5) years. In bivariate analysis, depression was associated with self-identifying as gay (p = .001), being HIV positive (p < .001: <8% of MSM knew they were HIV infected) and having a high number of sexual partners in the last 6 months (p = .001). Depression was also associated with sexual (p = .007), physical (p = .003) and verbal (p < .001) abuse. In the Poisson regression analysis, depression was associated with verbal abuse (APR = 1.91, CI = 1.30-2.81). Depression rates were high among MSM in Tanzania. It is also associated with abuse, HIV and HIV risk behaviors. Thus, reducing the risk of depression may be helpful in reducing the risk of HIV among MSM in Africa. We recommend the colocation of mental health and HIV preventive services as a cost-effective means of addressing both depression and HIV risk among MSM in Africa.

Substance-use and sexual harm reduction strategies of methamphetamine-using men who have sex with men and inject drugs.

Research indicates that men who have sex with men (MSM), use methamphetamine, and inject drugs are at high risk of HIV infection and they employ multiple harm reduction strategies simultaneously to reduce that risk. In this study, we identified substances most commonly injected and harm reduction strategies most often employed by methamphetamine-using MSM, used latent class analysis (LCA) to identify patterns of harm reduction strategies, and differentiated MSM within each class by individual characteristics. We analyzed data from 284 participants who completed an online cross-sectional survey. Commonly injected substances were methamphetamine (93.70%), gamma-hydroxybutyrate/gamma-butyrolactone (41.55%), flunitrazepam (40.49%), and cocaine (35.56%). The substance-use strategies most often used were avoidance of sharing needles (85.92%) and use of bleach to clean drug paraphernalia (64.08%). The sexual strategy most often used was avoidance of condomless anal intercourse (CAS) while using drugs (77.11%). Using an LCA approach, we identified three classes distinguishable by age, race/ethnicity, and outness. One class (19%) employed lay strategies to reduce harm: they avoided sharing drug preparation equipment, serosorted when sharing needles and equipment or having CAS, and practiced withdrawal when having CAS. The largest class (53%) combined sexual and substance-use strategies: they avoided sharing needles, used bleach to clean needles and equipment, avoided CAS when using drugs, and used extra lubricant when having CAS. The remaining class (28%) employed only substance-use rather than sexual strategies. More MSM of color were in the substance-use class, and more young, non-Hispanic White men were in the lay class. The low utilization of sexual strategies by younger, non-Hispanic White men in the lay class is concerning as they are just as likely as older, non-Hispanic White men in the combined class to have CAS with multiple male partners. Interventionists should consider these differences when developing interventions tailored to methamphetamine-using MSM.