Agricultural Information Needs and Food Access in the Stann Creek District of Belize

The purpose of this study was to describe agricultural information sources available to farmers and to describe food access and availability for the people of Dangriga, Stann Creek, Belize. This study used descriptive survey research methods with convenience sampling of the general public (n=22) and of farmers (n = 38) in the summer of 2017. Farmers use a variety of agricultural information sources with the extension service cited most often, followed by friends and fellow farmers. Weather, lack of information, pests, and inadequate access to capital were of primary concern for farmers. Face-to-face meetings were used most often by extension officers for disseminating agricultural information. Smallholder farmers and the general public have very similar levels of food access and availability. No significant difference was foundbetween the smallholder farmers and the general public on food insecurity with both groups reporting mild to severe food insecurity. Recommendations focused on practical operational strategies for the local Department of Agriculture, as well as the Belize Ministry of Agriculture to eradicate hungerand increase overall food access and availability throughout Belize

Designing in context : a new building for Boston's Beacon Hill

Thesis (M. Arch.)--Massachusetts Institute of Technology, Dept. of Architecture, 1982.MICROFICHE COPY AVAILABLE IN ARCHIVES AND ROTCH.Includes bibliographical references.The importance of contextually sensitive design is once again becoming recognized by the architectural profession. A contextual design is based upon an understanding of historical and social factors as well as the physical context of the project. This thesis is an exploration of the relationship between an existing environment and the design for a contemporary building. The design will be set on Boston's Beacon Hill, an architecturally rich area that has been designated as a National Historical Landmark by the National Parks Service. The site itself is a relatively large parcel of land located on the Hill's North Slope, an area of somewhat dilapidated houses, now undergoing considerable rehabilitation. The program chosen, that of a residential community for the area's older residents, will take advantage of the site's relatively large size to develop collective facilities as well as approximately 70-80 apartments. While the overall size and collective nature of this project distinguish it from the prevailing pattern of house size and organization on Beacon Hill, they serve to emphasize the need for traditional patterns to be modified and adapted to serve contemporary needs and lifestyles. The design exploration will be preceded by an examination of the historical, social, and physical features of Beacon Hill. Ways in which these aspects of the environment have been used to create contextually successful buildings will be briefly explored. Then the programmatic principles of congregate living environments for older people will be considered. Contextual decisions will be traced from site planning to building organization, focusing on the development of a formal vocabulary for the building exterior. The goal will be to create a new building, modern in execution, but compatible with the traditional forms of Beacon Hill.by Donna L. Harris.M.Arch

Evaluation of an IUL Flash & Go Automated Colony Counter

An IUL Flash & Go automated colony counter was used to enumerate E. coli (ATCC 700728) colonies and its performance was compared with manual counting on spiral plates. A total of 85 plates were analyzed. Linear regression analysis and the log differences between the manual and automated counts were determined. The results were analyzed to evaluate the reliability and accuracy of the colony counter.  A correlation coefficient of 0.969, a slope of 0.932 and intercept of 0.25 all indicate a strong, linear relationship. The mean log value difference between the manual and Flash & Go count methods was -0.035. Of the 85 plates counted, 95% of the plates were within 0.15 log10 difference between the manual and Flash & Go automated counts. These results demonstrate that the Flash & Go automated colony counter is an effective, accurate and time saving alternative to the standard method of manual counting.      

Seismic and drilling constraints on velocity structure and reflectivity near IODP Hole U1309D on the central dome of Atlantis Massif, Mid-Atlantic Ridge 30°N

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 10 (2009): Q01010, doi:10.1029/2008GC002121.The seismic structure of the upper ∼1 km of the central dome of Atlantis Massif is investigated in the context of lithologies known from seafloor drilling and physical property measurements obtained within the borehole and on core samples. A new analysis of seafloor refraction data and multichannel reflection data acquired in the immediate vicinity of Integrated Ocean Drilling Program (IODP) Site U1309 was motivated by a discrepancy between initial seismic interpretations, which indicated mantle velocities at shallow depth, and the gabbroic sequence recovered by drilling. A new seismic velocity model is derived that is consistent with the full suite of geological and geophysical data in the central dome area; all of these data show that mafic intrusive rocks dominate the upper portion of the footwall of this oceanic core complex and that laterally extensive zones of ultramafic rocks are not required by the data. The origin of subseafloor reflectivity beneath the central dome was also considered. We find that seafloor scattering complicates the interpretation of multichannel seismic data acquired near Site U1309 but that detectable subsurface impedance contrasts do occur. Downhole variations in alteration may generate reflections observed from the upper kilometer of the central dome.Support for this study was provided by JOI to JAC, DKB, and AH (grants T304B22, T305A22, and T305A1 respectively)

The Interaction between AID and CIB1 Is Nonessential for Antibody Gene Diversification by Gene Conversion or Class Switch Recombination

Activation-induced deaminase (AID) initiates somatic hypermutation, gene conversion and class switch recombination by deaminating variable and switch region DNA cytidines to uridines. AID is predominantly cytoplasmic and must enter the nuclear compartment to initiate these distinct antibody gene diversification reactions. Nuclear AID is relatively short-lived, as it is efficiently exported by a CRM1-dependent mechanism and it is susceptible to proteasome-dependent degradation. To help shed light on mechanisms of post-translational regulation, a yeast-based screen was performed to identify AID-interacting proteins. The calcium and integrin binding protein CIB1 was identified by sequencing and the interaction was confirmed by immunoprecipitation experiments. The AID/CIB1 resisted DNase and RNase treatment, and it is therefore unlikely to be mediated by nucleic acid. The requirement for CIB1 in AID-mediated antibody gene diversification reactions was assessed in CIB1-deficient DT40 cells and in knockout mice, but immunoglobulin gene conversion and class switch recombination appeared normal. The DT40 system was also used to show that CIB1 over-expression has no effect on gene conversion and that AID-EGFP subcellular localization is normal. These combined data demonstrate that CIB1 is not required for AID to mediate antibody gene diversification processes. It remains possible that CIB1 has an alternative, a redundant or a subtle non-limiting regulatory role in AID biology

VarSight: prioritizing clinically reported variants with binary classification algorithms.

BackgroundWhen applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.MethodsWe tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.ResultsWe treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.ConclusionsWe demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets

Mutations in epigenetic regulators including SETD2 are gained during relapse in pediatric acute lymphoblastic leukemia

Relapsed pediatric acute lymphoblastic leukemia (ALL) has high rates of treatment failure. Epigenetic regulators have been proposed as modulators of chemoresistance, here we sequence genes encoding epigenetic regulators in matched diagnosis-remission-relapse ALL samples. We find significant enrichment of mutations in epigenetic regulators at relapse with recurrent somatic mutations in SETD2, CREBBP, MSH6, KDM6A and MLL2, mutations in signaling factors are not enriched. Somatic alterations in SETD2, including frameshift and nonsense mutations, are present at 12% in a large de novo ALL patient cohort. We conclude that the enrichment of mutations in epigenetic regulators at relapse is consistent with a role in mediating therapy resistance

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

<p>Abstract</p> <p>Background</p> <p>Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies.</p> <p>Results</p> <p>We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiD™ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease.</p> <p>Conclusions</p> <p>Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.</p

The lady vanishes: what's missing from the stem cell debate

Most opponents of somatic cell nuclear transfer and embryonic stem cell technologies base their arguments on the twin assertions that the embryo is either a human being or a potential human being, and that it is wrong to destroy a human being or potential human being in order to produce stem cell lines. Proponents’ justifications of stem cell research are more varied, but not enough to escape the charge of obsession with the status of the embryo. What unites the two warring sides in ‘the stem cell wars’ is that women are equally invisible to both: ‘the lady vanishes’. Yet the only legitimate property in the body is that which women possess in their reproductive tissue and the products of their reproductive labour. By drawing on the accepted characterisation in law of property as a bundle of rights, and on a Hegelian model of contract as mutual recognition, we can lessen the impact of the tendency to regard women and their eggs as merely receptacles and women’s reproductive labour as unimportant

Drug-gene interactions of antihypertensive medications and risk of incident cardiovascular disease: a pharmacogenomics study from the CHARGE consortium

Background Hypertension is a major risk factor for a spectrum of cardiovascular diseases (CVD), including myocardial infarction, sudden death, and stroke. In the US, over 65 million people have high blood pressure and a large proportion of these individuals are prescribed antihypertensive medications. Although large long-term clinical trials conducted in the last several decades have identified a number of effective antihypertensive treatments that reduce the risk of future clinical complications, responses to therapy and protection from cardiovascular events vary among individuals. Methods Using a genome-wide association study among 21,267 participants with pharmaceutically treated hypertension, we explored the hypothesis that genetic variants might influence or modify the effectiveness of common antihypertensive therapies on the risk of major cardiovascular outcomes. The classes of drug treatments included angiotensin-converting enzyme inhibitors, beta-blockers, calcium channel blockers, and diuretics. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, each study performed array-based genome-wide genotyping, imputed to HapMap Phase II reference panels, and used additive genetic models in proportional hazards or logistic regression models to evaluate drug-gene interactions for each of four therapeutic drug classes. We used meta-analysis to combine study-specific interaction estimates for approximately 2 million single nucleotide polymorphisms (SNPs) in a discovery analysis among 15,375 European Ancestry participants (3,527 CVD cases) with targeted follow-up in a case-only study of 1,751 European Ancestry GenHAT participants as well as among 4,141 African-Americans (1,267 CVD cases). Results Although drug-SNP interactions were biologically plausible, exposures and outcomes were well measured, and power was sufficient to detect modest interactions, we did not identify any statistically significant interactions from the four antihypertensive therapy meta-analyses (Pinteraction &gt; 5.0×10−8). Similarly, findings were null for meta-analyses restricted to 66 SNPs with significant main effects on coronary artery disease or blood pressure from large published genome-wide association studies (Pinteraction ≥ 0.01). Our results suggest that there are no major pharmacogenetic influences of common SNPs on the relationship between blood pressure medications and the risk of incident CVD