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.Comment: 13 pages, 4 figure

Aerobic fitness is a potential crucial factor in protecting paralympic athletes with locomotor impairments from atherosclerotic cardiovascular risk

PurposeTo test the hypothesis that aerobic fitness is inversely related to the risk of atherosclerotic cardiovascular disease (ACVD) in athletes with locomotor impairments deriving from health conditions, such as spinal cord injury (SCI), lower limb amputation, cerebral palsy, poliomyelitis, and other health conditions different from the previous ones.MethodsA total of 68 male athletes who competed in either summer or winter Paralympic games were divided in two health conditions groups (35 with SCI, mean age 37.28.0 years, and 33 with different health conditions, mean age 37.89.9 years) and in four sport type groups (skill, power, intermittent-mixed metabolism-and endurance). They were evaluated through anthropometric and blood pressure measurements, laboratory blood tests, and graded cardiopulmonary maximal arm cranking exercise test, with oxygen uptake peak (VO2peak) measurement. Cardiovascular risk profile was assessed in each athlete.ResultsThe prevalence of ACVD-risk factors in the overall population was 20.6% for hypertension; 47% and 55.9% for high values of total and LDL cholesterol, respectively; 22.1% for reduce glucose tolerance; and 8.8% for obesity. No difference was found between athletes with and without SCI, while the prevalence of obesity was significantly higher in those practicing skill sports (22.7%, p=0.035), which was the sport type group with Paralympic athletes with the lowest VO2peak (22.5 +/- 5.70 ml kg(-1) min(-1)). VO2peak was lower in athletes with SCI than those with different health conditions (28.6 +/- 10.0 vs 33.6 +/- 8.9 ml kg(-1) min(-1)p=0.03), and in those with 3-4 risk factors (19.09 +/- 5.34 ml kg(-1) min(-1)) than those with 2 risk factors (27.1 +/- 5.50 ml kg(-1) min(-1)), 1 risk factor (31.6 +/- 8.55 ml kg(-1) min(-1)), or none (36.4 +/- 8.76 ml kg(-1) min(-1)) (p<0.001).ConclusionsThe present study suggests that having higher VO2peak seems to offer greater protection against ACVD in individuals with a locomotor impairment. Prescribing physical exercise at an intensity similar to that of endurance and intermittent sports should become a fundamental tool to promote health among people with a locomotor impairment.Open access funding provided by Universita degli Studi dell'Aquila within the CRUI-CARE Agreement

Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response

Although the efficacy of methadone maintenance treatment (MMT) in opioid dependence disorder has been well established, the influence of methadone pharmacokinetics in dose requirement and clinical outcome remains controversial. The aim of this study is to analyze methadone dosage in responder and nonresponder patients considering pharmacogenetic and pharmacokinetic factors that may contribute to dosage adequacy. Opioid dependence patients (meeting Diagnostic and Statistical Manual of Mental Disorders, [4th Edition] criteria) from a MMT community program were recruited. Patients were clinically assessed and blood samples were obtained to determine plasma concentrations of (R,S)-, (R) and (S)- methadone and to study allelic variants of genes encoding CYP3A5, CYP2D6, CYP2B6, CYP2C9, CYP2C19, and P-glycoprotein. Responders and nonresponders were defined by illicit opioid consumption detected in random urinalysis. The final sample consisted in 105 opioid dependent patients of Caucasian origin. Responder patients received higher doses of methadone and have been included into treatment for a longer period. No differences were found in terms of genotype frequencies between groups. Only CYP2D6 metabolizing phenotype differences were found in outcome status, methadone dose requirements, and plasma concentrations, being higher in the ultrarapid metabolizers. No other differences were found between phenotype and responder status, methadone dose requirements, neither in methadone plasma concentrations. Pharmacokinetic factors could explain some but not all differences in MMT outcome and methadone dose requirements

How much information about antibiotics do people recall after consulting in primary care?

Funding: Public Health England