Determination of optimum raw product sampling procedures with special reference to green beans for processing

Most raw product received at processing plants in Oregon is sampled to determine quality characteristics as a basis of grower payment. Raw product sampling procedures must provide the processor with a means of sampling which will be sufficiently precise to satisfy himself as well, as his growers, and thus avoid misunderstandings relative to the true grade of product delivered. How well a given sampling scheme will accurately provide this information depends upon the amount and nature of variability among characteristics of the product within a given load and the size and type of sample being drawn, Through the use of probability sampling theory it is possible to judge the precision of a sampling procedure by examining the frequency distribution generated for the estimate if the procedure is applied repeatedly. Based upon the knowledge of the frequency distribution of the estimate, it is possible to determine the range within which, as an example, 95 per cent of all possible samples would fall. The processor not only is interested in the precision and accuracy of his sampling procedures, but he also is concerned with costs of sampling. This study considers costs of sampling as well as precision in determining optimum sampling procedures which will minimize cost in achieving a given level of precision or maximize precision for a given cost. Green beans for processing were used in the application of sampling theory. Green beans are delivered to the processing plants in tote bins loaded on trucks. Two-stage sampling procedures are used where a sample of totes is drawn from the truck and a sample of beans is drawn from each tote selected. Repeated sampling was used to estimate the variation existing among primary and secondary sampling units. Three sampling schemes were employed to estimate components of variation: In Sampling Scheme A two 1O pound secondary units were drawn from each of two primary units. Sample Scheme B consisted of drawing two 3O-pound secondary units from each of two primary units. Sample Scheme C consisted of drawing a single continuous sample drawn from each of two primary units. The study was designed so that a comparison might be made of (1) the precision achieved by various numbers of primary and secondary sample units, (2) the effect of the size of the secondary units on among primary and among secondary unit variation, (3) the completely random and the random systematic (continuous) method of obtaining the secondary unit. Costs involved in sampling raw product were estimated by economic-engineering techniques. Costs were divided into two components - - costs associated with the drawing of the primary unit, and costs incurred in drawing and grading the secondary unit. Grading costs were a major portion of total estimated costs of sampling. Variance and cost estimates were brought together for use in the final analysis as follows: (1) optimum sampling plans were determined for each of the three sampling schemes for selected levels of precision; (2) comparisons were made of the optimum for each of the three schemes to determine the scheme which provides selected levels of precision at the lowest costs; (3) generalizations were made with regard to other sampling schemes involving sub-samples of sizes other than those included in the study and (4) a comparison was made of the simple random and the continuous method of selecting the sub-sample. Based on the range of precision and confidence considered in the study, sampling Scheme A appears to provide a least cost method of achieving given levels of precision and confidence

flowCore: a Bioconductor package for high throughput flow cytometry

<p>Abstract</p> <p>Background</p> <p>Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates.</p> <p>Results</p> <p>We developed a set of flexible open source computational tools in the R package flowCore to facilitate the analysis of these complex data. A key component of which is having suitable data structures that support the application of similar operations to a collection of samples or a clinical cohort. In addition, our software constitutes a shared and extensible research platform that enables collaboration between bioinformaticians, computer scientists, statisticians, biologists and clinicians. This platform will foster the development of novel analytic methods for flow cytometry.</p> <p>Conclusion</p> <p>The software has been applied in the analysis of various data sets and its data structures have proven to be highly efficient in capturing and organizing the analytic work flow. Finally, a number of additional Bioconductor packages successfully build on the infrastructure provided by flowCore, open new avenues for flow data analysis.</p

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

SH2- and SH3-mediated Interactions between Focal Adhesion Kinase and Src

Intramolecular SH2 and SH3 interactions mediate enzymatic repression of the Src kinases. One mechanism of activation is disruption of these interactions by the formation of higher affinity SH2 and SH3 interactions with specific ligands. We show that a consensus Src SH3-binding site residing upstream of the Src SH2-binding site in FAK can function as a ligand for the Src SH3 domain. Surface plasmon resonance experiments indicate that a FAK peptide containing both the Src SH2- and SH3-binding sites exhibits increased affinity for Src. Furthermore, the presence of both sites in vitro more potently activates c-Src. A FAK mutant (FAKPro-2) with substitutions destroying the SH3-binding site shows reduced binding to Src in vivo. This mutation also reduces Src-dependent tyrosine phosphorylation on the mutant itself and downstream substrates, such as paxillin. These observations suggest that an SH3-mediated interaction between Src-like kinases and FAK may be important for complex formation and downstream signaling in vivo

A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies

A promising direction in drug development is to exploit the ability of natural killer cells to kill antibody-labeled target cells. Monoclonal antibodies and drugs designed to elicit this effect typically bind cell-surface epitopes that are overexpressed on target cells but also present on other cells. Thus it is important to understand adhesion of cells by antibodies and similar molecules. We present an equilibrium model of such adhesion, incorporating heterogeneity in target cell epitope density and epitope immobility. We compare with experiments on the adhesion of Jurkat T cells to bilayers containing the relevant natural killer cell receptor, with adhesion mediated by the drug alefacept. We show that a model in which all target cell epitopes are mobile and available is inconsistent with the data, suggesting that more complex mechanisms are at work. We hypothesize that the immobile epitope fraction may change with cell adhesion, and we find that such a model is more consistent with the data. We also quantitatively describe the parameter space in which binding occurs. Our results point toward mechanisms relating epitope immobility to cell adhesion and offer insight into the activity of an important class of drugs.Comment: 13 pages, 5 figure

Experimental Granulomatous Pulmonary Nocardiosis in BALB/C Mice

Pulmonary nocardiosis is a granulomatous disease with high mortality that affects both immunosuppressed and immunocompetent patients. The mechanisms leading to the establishment and progression of the infection are currently unknown. An animal model to study these mechanisms is sorely needed. We report the first in vivo model of granulomatous pulmonary nocardiosis that closely resembles human pathology. BALB/c mice infected intranasally with two different doses of GFP-expressing Nocardia brasiliensis ATCC700358 (NbGFP), develop weight loss and pulmonary granulomas. Mice infected with 109 CFUs progressed towards death within a week while mice infected with 108 CFUs died after five to six months. Histological examination of the lungs revealed that both the higher and lower doses of NbGFP induced granulomas with NbGFP clearly identifiable at the center of the lesions. Mice exposed to 108 CFUs and subsequently to 109 CFUs were not protected against disease severity but had less granulomas suggesting some degree of protection. Attempts to identify a cellular target for the infection were unsuccessful but we found that bacterial microcolonies in the suspension used to infect mice were responsible for the establishment of the disease. Small microcolonies of NbGFP, incompatible with nocardial doubling times starting from unicellular organisms, were identified in the lung as early as six hours after infection. Mice infected with highly purified unicellular preparations of NbGFP did not develop granulomas despite showing weight loss. Finally, intranasal delivery of nocardial microcolonies was enough for mice to develop granulomas with minimal weight loss. Taken together these results show that Nocardia brasiliensis microcolonies are both necessary and sufficient for the development of granulomatous pulmonary nocardiosis in mice

Is there a divide between local medicinal knowledge and Western medicine? a case study among native Amazonians in Bolivia

Background: Interest in ethnomedicine has grown in the last decades, with much research focusing on how local medicinal knowledge can contribute to Western medicine. Researchers have emphasized the divide between practices used by local medical practitioners and Western doctors. However, researchers have also suggested that merging concepts and practices from local medicinal knowledge and Western science have the potential to improve public health and support medical independence of local people. In this article we study the relations between local and Western medicinal knowledge within a native Amazonian population, the Tsimane'. Methods: We used the following methods: 1) participant observation and semi-structured interviews to gather background information, 2) free-listing and pile-sorting to assess whether Tsimane' integrate local medicinal knowledge and Western medicine at the conceptual level, 3) surveys to assess to what extent Tsimane' combine local medicinal knowledge with Western medicine in actual treatments, and 4) a participatory workshop to assess the willingness of Tsimane' and Western medical specialists to cooperate with each other. Results: We found that when asked about medical treatments, Tsimane' do not include Western treatments in their lists, however on their daily practices, Tsimane' do use Western treatments in combination with ethnomedical treatments. We also found that Tsimane' healers and Western doctors express willingness to cooperate with each other and to promote synergy between local and Western medical systems. Conclusion: Our findings contrast with previous research emphasizing the divide between local medical practitioners and Western doctors and suggests that cooperation between both health systems might be possible

The Perceived Benefits of Height: Strength, Dominance, Social Concern, and Knowledge among Bolivian Native Amazonians

Research in industrial countries suggests that, with no other knowledge about a person, positive traits are attributed to taller people and correspondingly, that taller people have slightly better socioeconomic status (SES). However, research in some non-industrialized contexts has shown no correlation or even negative correlations between height and socioeconomic outcomes. It remains unclear whether positive traits remain attributed to taller people in such contexts. To address this question, here we report the results of a study in a foraging-farming society of native Amazonians in Bolivia (Tsimane’)–a group in which we have previously shown little association between height and socioeconomic outcomes. We showed 24 photographs of pairs of Tsimane’ women, men, boys, and girls to 40 women and 40 men >16 years of age. We presented four behavioral scenarios to each participant and asked them to point to the person in the photograph with greater strength, dominance, social concern, or knowledge. The pairs in the photographs were of the same sex and age, but one person was shorter. Tsimane’ women and men attributed greater strength, dominance, and knowledge to taller girls and boys, but they did not attribute most positive traits to taller adults, except for strength, and more social concern only when women assessed other women in the photographs. These results raise a puzzle: why would Tsimane’ attribute positive traits to tall children, but not tall adults? We propose three potential explanations: adults’ expectations about the more market integrated society in which their children will grow up, height as a signal of good child health, and children’s greater variation in the traits assessed corresponding to maturational stages