Benchmarking database systems for Genomic Selection implementation

Motivation: With high-throughput genotyping systems now available, it has become feasible to fully integrate genotyping information into breeding programs. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able to collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize it in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs, one would need an efficient genotyping data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems. Results: We found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix

When the Wandering Boy Comes Home / words by Jack Little Little, Dave Oppenheimer, and Ira Schuster

Cover: a photo of a man; Publisher: Robbins Music Corporation (New York)https://egrove.olemiss.edu/sharris_e/1027/thumbnail.jp

PhD Annual Yearbook New Series Volume 1 October 2009

An edited volume with contributions from six PhD researchers in the school of Humanities and Social Sciences at the University of East London. Each contributor details their research work in progress. Topics in this volume include: Gypsy/Traveller children in England, refugee experiences in Education, Atget at Bercy, The textile self re/collected and a virtual conceptualization of the digital. This edition also includes two book reviews: Pitcher, B., (2009), The Politics Of Multiculturalism: Race and Racism in Contemporary Britain, Hampshire, Palgrave Macmillan and Back, L., (2007), The Art of Listening, Oxford, Berg

Alcoholic vs. Nonalcoholic Steatohepatitis: Vascular Branching Heterogeneity on Magnetic Resonance Imaging as a Diagnostic Marker

Background and aims: Distinguishing alcoholic steatohepatitis (ASH) and nonalcoholic steatohepatitis (NASH) with biopsy alone is often difficult without a reliable clinical context. A novel finding on liver imaging, perivascular branching heterogeneity, has shown promise in distinguishing between these chronic liver diseases. Our study investigated the role of this finding on imaging to differentiate between ASH and NASH. The aim of this study was to determine the utility and reproducibility of this novel radiographic marker to help distinguish ASH from NASH. Methods: This was a retrospective cohort study conducted between 2016 and 2020 in patients with both liver biopsy-confirmed steatohepatitis/chronic hepatitis and abdominal magnetic resonance imaging within 13 months of each other. Two radiologists, blinded to patient clinical history and diagnosis, categorized the appearance of the liver as: 1- homogeneity, 2- mild heterogeneity, 3- moderate heterogeneity, 4- possible perivascular branching, 5- definite perivascular branching. Results: Of the 90 patients in the study, 60 were identified as NASH and 30 as ASH. The area under the curve (AUC) for both reader 1 and 2 when using the 5-point scale was 0.69 (CI: 0.56-0.82, p=0.006) and 0.72 (CI: 0.60-0.85, p=0.001), respectively. The positive predictive value (PPV) for identification of ASH when scoring 5 was 64.7% and 66.7% for reader 1 and 2, respectively. Interclass correlation coefficient was 0.74 in patients with ASH, indicating moderate reliability among both readers. Conclusions: Identification of this perivascular branching pattern on imaging is a promising novel diagnostic marker that can be used with other methods to help distinguish between ASH and NASH

Nomogram to Predict Insignificant Prostate Cancer at Radical Prostatectomy in Korean Men: A Multi-Center Study

PURPOSE: Due to the availability of serum prostate specific antigen (PSA) testing, the detection rate of insignificant prostate cancer (IPC) is increasing. To ensure better treatment decisions, we developed a nomogram to predict the probability of IPC. MATERIALS AND METHODS: The study population consisted of 1,471 patients who were treated at multiple institutions by radical prostatectomy without neoadjuvant therapy from 1995 to 2008. We obtained nonrandom samples of n = 1,031 for nomogram development, leaving n = 440 for nomogram validation. IPC was defined as pathologic organ-confined disease and a tumor volume of 0.5 cc or less without Gleason grade 4 or 5. Multivariate logistic regression model (MLRM) coefficients were used to construct a nomogram to predict IPC from five variables, including serum prostate specific antigen, clinical stage, biopsy Gleason score, positive cores ratio and maximum % of tumor in any core. The performance characteristics were internally validated from 200 bootstrap resamples to reduce overfit bias. External validation was also performed in another cohort. RESULTS: Overall, 67 (6.5%) patients had a so-called "insignificant" tumor in nomogram development cohort. PSA, clinical stage, biopsy Gleason score, positive core ratio and maximum % of biopsy tumor represented significant predictors of the presence of IPC. The resulting nomogram had excellent discrimination accuracy, with a bootstrapped concordance index of 0.827. CONCLUSION: Our current nomogram provides sufficiently accurate information in clinical practice that may be useful to patients and clinicians when various treatment options for screen-detected prostate cancer are consideredope

BrAPI-an application programming interface for plant breeding applications

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases

Growth kinetics and modelling of S. cerevisiae (NCYC 431) during de-lignified waste banana fermentation and chemical characterization

S. cerevisiae (NCYC 431) growth kinetics was studied using mathematical models in order to ascertain the optimum operational parameters for banana waste fermentation. Chapman-Richards model was used to describe yeast growth kinetics under varying pH and temperatures and the results were compared to Bergter and Andrew models. Alkaline-delignification of the wastes was done to solubilize lignin prior fermentation. This is because lignin is a complex organic plant compound that has been reported not to be degraded easily by many microorganisms. From the results temperatures 22–28 °C and pH 4.5–5.6 were noted as optimum for yeast growth on delignified waste bananas (DWB). Chapman model results were close to Bergter and Andrew models with very low RMSE. Delignification was noted to aid yeast growth with higher microbial populations (log10 cfu/g) registered with DWB samples as compared to non-delignified waste bananas (NDWB). Also, chemical characterization of the DWB and NDWB indicated higher proteins and lipids in the former than the latter by 3 and 4% respectively. This suggested the possible use of the upgraded wastes as chicken feed supplements. Higher minerals in DWB of 8.6% also suggested the possible use of the waste as a nutrient-rich fertilizer

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700