ABSTRACT
Segmenting autophagic bodies in yeast TEM images is a key technique for measuring changes in autophagosome size and number in order to better understand macroautophagy/autophagy. Manual segmentation of these images can be very time consuming, particularly because hundreds of images are needed for accurate measurements. Here we describe a validated Cellpose 2.0 model that can segment these images with accuracy comparable to that of human experts. This model can be used for fully automated segmentation, eliminating the need for manual body outlining, or for model-assisted segmentation, which allows human oversight but is still five times as fast as the current manual method. The model is specific to segmentation of autophagic bodies in yeast TEM images, but researchers working in other systems can use a similar process to generate their own Cellpose 2.0 models to attempt automated segmentations. Our model and instructions for its use are presented here for the autophagy community.Abbreviations: AB, autophagic body; AvP, average precision; GUI, graphical user interface; IoU, intersection over union; MVB, multivesicular body; ROI, region of interest; TEM, transmission electron microscopy; WT,wild type.
ABSTRACT
The reef-building coral Acropora cervicornis was a dominant ecosystem element on the Caribbean reef until the 1980s, when it declined by some 97% due primarily to anthropogenic ecosystem changes and disease. This branching species expanded its colony footprint and achieved local dominance largely through fragmentation and regrowth, thus is suited to nursery culture towards restoration. In this experiment, fragments of Acropora cervicornis of four lineages or genets were followed and measured for growth and health over 12 months in 2006 and 2007 on buoyant drop-loop line nurseries at one shallow and one deep fore-reef site in Montego Bay, Jamaica. Sixty-five of these corals were then out-planted to wild reef sites of similar depth and condition to their respective nurseries and monitored photographically for 11 months through 2007 and 2008. A period of rapid death was seen in the out-planted material at both sites over the first four months, followed by a period of relative stability or recuperation. Hermodice carunculata predation was the primary problem in the shallow fore-reef, and was combined with a banding syndrome at the deeper site. This syndrome was noted in the samples prior to planting, during a one week storage period on the seafloor. Continued slow decline occurred in the subsequent seven months in the shallow fore-reef site; however, regrowth was noted in the deeper site in the remaining material. Including these losses, final total live coral length was more than fourfold greater than the initial wild harvest: a net increase through multi-stage propagative restoration or coral gardening. Returns were noted particularly in the faster-growing genets of the nursery and larger planted corals tended to retain more material at eleven months, suggesting that propagative restoration programmes invest in stronger genets and larger corals. Adaptive management and maintenance gardening of the planted material and reef would likely have greatly improved outcomes.
La especie constructora de arrecifes de coral Acropora cervicornis era un elemento dominante del ecosistema en el arrecife caribeño hasta la década de 1980, cuando disminuyó en un 97% a nivel regional principalmente debido a cambios antropogénicos y por enfermedad. Esta especie de ramificación amplió su huella de colonia para lograr un dominio local a través de la fragmentación y el rebrote, así se adapta al cultivo de vivero para la restauración. En este experimento, fragmentos de Acropora cervicornis de cuatro linajes fueron seguidos y medidos para el crecimiento y la salud durante 12 meses en 2006 y 2007 en viveros en línea tipo “buoyant drop-loop“ en un sitio somero y otro profundo en el arrecife frontal de Bahía Montego, Jamaica. Sesenta y cinco de estos corales fueron plantados en sitios de arrecife silvestre con condiciones y profundidad similar a sus respectivos viveros y monitoreados mediante fotográfias por 11 meses durante el 2007 y 2008. Se observó un período de muerte rápida en el material plantado en ambos sitios durante los primeros cuatro meses, seguidos por un período de relativa estabilidad o recuperación. La depredación de Hermodice carunculata fue el principal problema en el arrecife frontal poco profundo y se combinó con un síndrome de bandas en el sitio más profundo. Este síndrome se observó en las muestras antes de la siembra, durante un período de almacenamiento de una semana en el suelo marino. A continuación ocurrió un lento descenso en los posteriores siete meses en el sitio de arrecife frontal poco profundo; sin embargo, se observó un rebrote en el sitio más profundo con el material restante. Aún incluyendo estas pérdidas, al final la longitud de coral vivo total fue más de cuatro veces que la inicial: un aumento neto a través de varias etapas de restauración propagativa o de jardinería de coral. Los rechazos fueron observados especialmente en el linaje de crecimiento más rápido del vivero y corales plantados más grandes que tienden a retener más material en once meses, lo que sugiere que los programas de restauración propagativo deben invertir en linajes de coral más fuertes y más grandes. Probablemente se obtengan mayores resultados con un manejo adaptativo y mantenimiento de jardinería del material plantado y de arrecife.
Subject(s)
Lice Infestations/epidemiology , Adolescent , Animals , Child , Child, Preschool , England/epidemiology , Humans , Incidence , Prevalence , Wales/epidemiologyABSTRACT
BACKGROUND: There is good evidence of reduced prescribing of antibiotics in recent years, but the reason for this has not been established. AIM: To study the incidence of respiratory tract infections presenting to general practitioners (GPs) in England and Wales in relation to the incidence of other infections and to the prescription of antibiotics. SETTING: Sentinel practices in England and Wales who contribute to the Weekly Returns Service (WRS) of the Royal College of General Practitioners. DESIGN: Time-series analysis of disease incidence data reported by the practices and of antibiotic prescription data from the Prescription Pricing Authority (PPA) during the years 1994-2000. METHOD: Incidence data reported weekly from 73 practices in England and Wales, serving a population of 600,000, for acute respiratory tract infections, otitis media, infectious mononucleosis, shingles, urinary tract infections, and skin infections, were consolidated into quarterly datasets and examined graphically for evidence of secular and seasonal trends. Trends in antibiotic prescription items (data for England only were supplied by the PPA) were examined for association after adjustment for seasonal variation. RESULTS: The incidence of respiratory tract infections and antibiotic prescribing showed virtually identical seasonal variation, with both declining from 1995: respiratory tract infections by 48% in winter and 38% in summer, and antibiotic prescriptions by 34% and 21%, respectively. Trends in both were very highly correlated. The incidence of shingles and skin infections was constant. The incidence of urinary tract infections declined by 10%. The incidence of otitis media in children and acute bronchitis in the elderly followed the all-age trend in the reduction of respiratory tract infections. CONCLUSION: The considerable reduction in the incidence of respiratory tract infections between 1995 and 2000 is the main reason for the decline in antibiotic prescribing rather than changing prescribing thresholds for antibiotics.
Subject(s)
Anti-Bacterial Agents/therapeutic use , Respiratory Tract Infections/prevention & control , Data Collection , England/epidemiology , Female , Humans , Incidence , Male , Practice Patterns, Physicians' , Respiratory Tract Infections/epidemiology , Wales/epidemiologyABSTRACT
The efficacy and safety of atorvastatin 10 mg versus simvastatin 20 mg and atorvastatin 80 mg versus simvastatin 80 mg was determined in a 6-week, prospective, randomized, open-label, blinded end-point trial of dyslipidemic patients with and without coronary heart disease. A total of 1,732 patients with hypercholesterolemia and triglycerides < or =600 mg/dl (6.8 mmol/L) were randomized to receive either atorvastatin 10 mg (n = 650), simvastatin 20 mg (n = 650), atorvastatin 80 mg (n = 216), or simvastatin 80 mg (n = 216). The primary efficacy parameter was the change in low-density lipoprotein (LDL) cholesterol from baseline to week 6. Secondary efficacy parameters included the percent change from baseline to week 6 in total cholesterol, triglyceride, high-density lipoprotein (HDL) cholesterol, very-low-density lipoprotein cholesterol, apolipoprotein B, and the percent of patients achieving their National Cholesterol Education Program (NCEP) LDL cholesterol goal at study end. Atorvastatin had significantly greater reductions from baseline in LDL cholesterol than simvastatin in both comparator groups: atorvastatin 10 mg (37.1%) versus simvastatin 20 mg (35.4%) (p = 0.0097), and atorvastatin 80 mg (53.4%) versus simvastatin 80 mg (46.7%) (p <0.0001). Atorvastatin 10 and 80 mg also provided significantly greater reductions in total cholesterol, triglycerides, very-low-density lipoprotein cholesterol, and apolipoprotein B than simvastatin 20 and 80 mg, respectively (all p <0.05). All treatment groups had a significantly decreased LDL cholesterol/HDL cholesterol ratio from baseline (all p <0.0001). In both comparator groups a higher proportion of atorvastatin-treated patients reached their NCEP LDL cholesterol goal compared with simvastatin. All 4 study treatments were well tolerated.
