A global perspective on decadal challenges and priorities in biodiversity informatics

Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent ‘decadal view’ of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid ‘siloing’ and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic

Motivation for Change in Heroin and Opiate Users

Opioid and heroin abuse is a continuing problem in the United States that has been increasing dramatically since 2000. Common treatment programs tend to use methadone and behavioral therapies that do not focus on motivational factors despite the research suggesting it is an important element to treatment retention and sustained abstinence. Motivation for the purposes of this study is defined as an individual’s inner reasons for change. The current study focused on differences in motivation for change among different substance abusers. We found that opiate and heroin abusers had higher motivational scores in comparison to other substance abusers. These results imply that treatment programs should focus on increasing motivation and explore the circumstances and factors that may hinder it

2002-2003 Boca Trombone Festival

https://spiral.lynn.edu/conservatory_otherseasonalconcerts/1075/thumbnail.jp

Generation of orthotopic patient-derived xenografts from gastrointestinal stromal tumor.

BackgroundGastrointestinal stromal tumor (GIST) is the most common sarcoma and its treatment with imatinib has served as the paradigm for developing targeted anti-cancer therapies. Despite this success, imatinib-resistance has emerged as a major problem and therefore, the clinical efficacy of other drugs has been investigated. Unfortunately, most clinical trials have failed to identify efficacious drugs despite promising in vitro data and pathological responses in subcutaneous xenografts. We hypothesized that it was feasible to develop orthotopic patient-derived xenografts (PDXs) from resected GIST that could recapitulate the genetic heterogeneity and biology of the human disease.MethodsFresh tumor tissue from three patients with pathologically confirmed GISTs was obtained immediately following tumor resection. Tumor fragments (4.2-mm3) were surgically xenografted into the liver, gastric wall, renal capsule, and pancreas of immunodeficient mice. Tumor growth was serially assessed with ultrasonography (US) every 3-4 weeks. Tumors were also evaluated with positron emission tomography (PET). Animals were sacrificed when they became moribund or their tumors reached a threshold size of 2500-mm3. Tumors were subsequently passaged, as well as immunohistochemically and histologically analyzed.ResultsHerein, we describe the first model for generating orthotopic GIST PDXs. We have successfully xenografted three unique KIT-mutated tumors into a total of 25 mice with an overall success rate of 84% (21/25). We serially followed tumor growth with US to describe the natural history of PDX growth. Successful PDXs resulted in 12 primary xenografts in NOD-scid gamma or NOD-scid mice while subsequent successful passages resulted in 9 tumors. At a median of 7.9 weeks (range 2.9-33.1 weeks), tumor size averaged 473 ± 695-mm³ (median 199-mm3, range 12.6-2682.5-mm³) by US. Furthermore, tumor size on US within 14 days of death correlated with gross tumor size on necropsy. We also demonstrated that these tumors are FDG-avid on PET imaging, while immunohistochemically and histologically the PDXs resembled the primary tumors.ConclusionsWe report the first orthotopic model of human GIST using patient-derived tumor tissue. This novel, reproducible in vivo model of human GIST may enhance the study of GIST biology, biomarkers, personalized cancer treatments, and provide a preclinical platform to evaluate new therapeutic agents for GIST

Spatial heterogeneity of habitat suitability for Rift Valley fever occurrence in Tanzania: an ecological niche modelling approach

Despite the long history of Rift Valley fever (RVF) in Tanzania, extent of its suitable habitat in the country remains unclear. In this study we investigated potential effects of temperature, precipitation, elevation, soil type, livestock density, rainfall pattern, proximity to wild animals, protected areas and forest on the habitat suitability for RVF occurrence in Tanzania. Presence-only records of 193 RVF outbreak locations from 1930 to 2007 together with potential predictor variables were used to model and map the suitable habitats for RVF occurrence using ecological niche modelling. Ground-truthing of the model outputs was conducted by comparing the levels of RVF virus specific antibodies in cattle, sheep and goats sampled from locations in Tanzania that presented different predicted habitat suitability values. Habitat suitability values for RVF occurrence were higher in the northern and central-eastern regions of Tanzania than the rest of the regions in the country. Soil type and precipitation of the wettest quarter contributed equally to habitat suitability (32.4% each), followed by livestock density (25.9%) and rainfall pattern (9.3%). Ground-truthing of model outputs revealed that the odds of an animal being seropositive for RVFV when sampled from areas predicted to be most suitable for RVF occurrence were twice the odds of an animal sampled from areas least suitable for RVF occurrence (95% CI: 1.43, 2.76, p < 0.001). The regions in the northern and central-eastern Tanzania were more suitable for RVF occurrence than the rest of the regions in the country. The modelled suitable habitat is characterised by impermeable soils, moderate precipitation in the wettest quarter, high livestock density and a bimodal rainfall pattern. The findings of this study should provide guidance for the design of appropriate RVF surveillance, prevention and control strategies which target areas with these characteristics

Registration of the OS9XQ36 Mapping Population of Wheat (Triticum aestivum L.)

The OS9XQ36 wheat (Triticum aestivum L.) mapping population (Reg. No. MP-2, NSL 465170) is a set of 164 F6–derived recombinant inbred lines (USDA–ARS Germplasm Resources Information Network [GRIN] accession no. GSTR 11903 through GSTR 12066) from the cross between OS9A (PI 658243), a single plant selection from the cultivar Stephens (CI 17596), and QCB36 (PI 658244), a single plant selection from the elite breeding line OR9900553. This population was developed to investigate the consistently lower grain hardness and superior end-use quality of OR9900553 compared with Stephens. This population has also been genotyped with diversity array technology (DArT) and simple sequence repeat (SSR) markers resulting in the construction of a 270-marker linkage map covering 1785 cM at a density of one marker per 7 cM. This F6–derived population is one of 20 mapping populations being used by the WheatCAP consortium (http://maswheat.ucdavis.edu/) for extensive quantitative trait locus analysis and forms part of a publicly available long-term genetic resource to map complex traits in wheat

Creation of a multiple-use recombinant inbred line population for the development of molecular markers in soft white winter wheat

Tese de doutoramento em Física (Pré-Bolonha), especialidade de Física Experimental, apresentada à Faculdade de Ciências e Tecnologia da Universidade de CoimbraPositron emission tomography based on resistive plate chambers (RPC-PET) has been proposed for both preclinical and clinical applications. We firstly present imaging results of needle-like and planar 22Na sources obtained with a prototype of a high-acceptance small-animal RPC-PET. The two detector modules utilized in this experiment had an effective front face of 6.4 x 6.4 cm^2 and consisted of 5 gas gaps and 6 glass electrodes with a total thickness of 5 mm. The data included lines of response (LORs) inclined up to 58º, and the depth of interaction (DOI) was accurately measured, demonstrating the parallax-free property inherent to RPC-PET. The maximum likelihood expectation-maximization (MLEM) reconstruction of the acquired data yielded an excellent and stable resolution of 0.4 mm full width at half maximum (FWHM). Concurrently, we pursued studies of a suggested whole-body single-bed RPC-PET. It has been shown by simulation that RPC-PET with an axial field-of-view (AFOV) of 2.4 m is feasible and yields an absolute sensitivity at least one order of magnitude superior to that of typical crystal-based PET scanners. In addition, RPC-PET offers an important time-of-flight (TOF) advantage and provides a potentially very-high spatial resolution at the detector level. In the second part of this work, a fully three-dimensional reconstruction algorithm capable of processing the very inclined LORs from large AFOV systems such as RPC-PET is demonstrated. It relies on the application of a TOF-based-kernel into the MLEM algorithm. With the 300 ps FWHM time resolution, already experimentally demonstrated, a rejection of 63% of the body-scattered events is obtained. We present reconstructed results from blind simulations corresponding to the anthropomorphic phantom, NCAT, with oncological lesions introduced into different locations within the human body. A comparison between 300 and 600 ps FWHM TOF reconstructed images is performed, with an increasing detectability being observed for a better TOF resolution. We finally compare issues related to image convergence speed. An alternative new approach, which consists in dividing the full-body data into nine different image regions that are reconstructed independently with graphical processing unit (GPU) assistance, provides a six times faster reconstruction compared with a GPU-based whole-body reconstruction. For a 300 ps FWHM RPC-PET scanner, this allows reaching a reconstructed image, that results from 1.6 x 10^10 annihilations within 7 minutes and upon injection of 2 mCi, just 4 minutes after the end of data acquisition. We conclude that RPC-PET is well oriented to compete with other commercial PET scanners in the global market.A tomografia por emissão de positrões baseada em detectores do tipo câmaras de placas resistivas (RPC-PET) foi proposta para aplicação em ensaios com pequenos animais e na prática clínica. Neste trabalho, apresentamos primeiramente resultados experimentais obtidos a partir de um protótipo RPC-PET de alta aceitação para pequenos animais. Foram obtidas imagens de fontes do radioisótopo 22Na, uma quase pontual e outra planar. Usámos dois módulos de detectores RPC com uma área activa de 6.4 x 6.4 cm^2 e uma espessura de 5 mm, constituída por 6 vidros empilhados e 5 espaços gasosos definidos entre eles. Os dados adquiridos incluíram linhas de coincidência (LORs) inclinadas até um ângulo de 58º, tornando essencial a medida precisa da profundidade de interacção. A identificação dos espaços gasosos onde ocorreram as avalanches permitiu demonstrar a ausência de erro de paralaxe nas medidas realizadas com o RPC-PET para pequenos animais. A partir da reconstrução dos dados processados com o algoritmo maximum likelihood expectation-maximization (MLEM), obtivemos uma resolução espacial com largura a meia altura (FWHM) de 0.4 mm, excelente e estável. Em paralelo, continuámos a estudar as potencialidades de um protótipo RPC-PET de corpo inteiro e cama única, orientado para pessoas. Já foi anteriormente demonstrado por simulação que um scanner RPC-PET com 2.4 m de campo de visão axial (AFOV) é viável e permitirá o aumento de sensibilidade de pelo menos uma ordem de grandeza em relação aos scanners PET com cristais. Duas outras virtudes do RPC-PET são a sua capacidade de medição do tempo de voo (TOF) dos fotões e a elevada resolução espacial ao nível do detector. Na segunda parte deste trabalho apresentamos um algoritmo de reconstrução, totalmente tridimensional, capaz de processar LORs muito inclinadas em sistemas com um AFOV longo, como é o caso do RPC-PET. Este algoritmo acrescenta um kernel ao algoritmo MLEM, baseado na informação de TOF. Com uma resolução temporal de 300 ps FWHM, já experimentalmente comprovada, é possível rejeitar 63% dos eventos dispersados no corpo humano. Exibimos imagens reconstruídas obtidas a partir de simulações do fantoma antropomórfico, NCAT, com lesões oncológicas situadas em diferentes locais do corpo humano. A comparação entre imagens conseguidas com resoluções temporais de 300 ps e 600 ps FWHM, permite observar uma detectabilidade acrescida associada à melhor resolução de TOF. Por último, são estudados os tempos de convergência da reconstrução. Um método inovador e alternativo, que consiste na divisão dos dados do corpo humano em nove regiões e na reconstrução independente desses dados com recurso a unidades de processamento gráfico (GPUs), permite uma reconstrução seis vezes mais rápida do que a reconstrução de corpo inteiro também com o auxílio de GPUs. A partir de dados de 1.6 x 10^10 aniquilações ocorridas durante uma aquisição de 7 minutos e para uma actividade injectada de 2 mCi, um scanner RPC-PET com uma resolução temporal de 300 ps FWHM permitirá obter uma imagem reconstruída apenas 4 minutos após o fim da aquisição. Podemos assim concluir que o RPC-PET está bem colocado para competir no mercado dos scanners PET comerciais