Migrating relational data to an OODB: strategies and lessions from a molecular biology experience

Journal ArticleThe growing maturity of OODB technology is causing many enterprises to consider migrating relational databases to OODBs. While data remapping is relatively straightforward, greater challenges lie in economically and non-invasively adapting legacy application software. We report on a genetics laboratory database migration experiment, which was facilitated by both organization of the relational data in object-like form and a C++ framework designed to insulate application code from relational artifacts. To our surprise, the framework failed to encapsulate three subtle aspects of the relational implementation, thereby "contaminating" application code. We describe the underlying issues, and offer cautionary guidance to future migrators

Differential behavioral state-dependence in the burst properties of CA3 and CA1 neurons

Brief bursts of fast high-frequency action potentials are a signature characteristic of CA3 and CA1 pyramidal neurons. Understanding the factors determining burst and single spiking is potentially significant for sensory representation, synaptic plasticity and epileptogenesis. A variety of models suggest distinct functional roles for burst discharge, and for specific characteristics of the burst in neural coding. However, little in vivo data demonstrate how often and under what conditions CA3 and CA1 actually exhibit burst and single spike discharges. The present study examined burst discharge and single spiking of CA3 and CA1 neurons across distinct behavioral states (awake-immobility and maze-running) in rats. In both CA3 and CA1 spike bursts accounted for less than 20% of all spike events. CA3 neurons exhibited more spikes per burst, greater spike frequency, larger amplitude spikes and more spike amplitude attenuation than CA1 neurons. A major finding of the present study is that the propensity of CA1 neurons to burst was affected by behavioral state, while the propensity of CA3 to burst was not. CA1 neurons exhibited fewer bursts during maze running compared with awake-immobility. In contrast, there were no differences in burst discharge of CA3 neurons. Neurons in both subregions exhibited smaller spike amplitude, fewer spikes per burst, longer inter-spike intervals and greater spike amplitude attenuation within a burst during awake-immobility compared with maze running. These findings demonstrate that the CA1 network is under greater behavioral state-dependent regulation than CA3. The present findings should inform both theoretic and computational models of CA3 and CA1 function. © 2006 IBRO

Etnobotânica e divergência genética de variedades de mandioca, Poconé, Mato Grosso.

A região denominada Baixada Cuiabana fica ao norte do Pantanal Mato-Grossense. É uma das poucas regiões do Mato Grosso que preserva as antigas características de comunidades de agricultores de subsistência que mantêm expressiva diversidade de mandioca (Manihot esculenta Crantz) e outros cultivos, visto a região ser centro de diversidade do gênero. Este estudo teve por objetivo caracterizar a diversidade genética de mandiocas mediante o conhecimento etnobotânico das variedades e marcadores microssatélites para compreender a dinâmica de conservação e manejo do acervo usado pelos agricultores da Comunidade São Benedito, Poconé, Mato Grosso. O presente trabalho foi autorizado pelo Conselho de Gestão do Patrimônio Genético (processo n. 02000.003025/2013-13-MMA deliberado em 28 de abril de 2015 e publicado no D.O.U em 13 de julho de 2015). Para o inventário etnobotânico foram aplicadas entrevistas semiestruturadas em 10 unidades domésticas para obter informações sobre as mandiocas cultivadas. Das 11 variedades locais cultivadas foi realizada análise por microssatélites (12 locus). Apesar da baixa diversidade etnobotânica encontrada (H?=2,05), foi encontrada alta heterozigosidade observada (Ho = 0,92) e diversidade gênica (He = 0,75). Os agricultores que sobrevivem basicamente do cultivo da mandioca e produção de farinha para comercialização, direcionam suas escolhas de variedades para as mais produtivas e menos suscetíveis ao ataque de pragas. A variedade brava foi a mais frequente (80% das roças) e é apontada como a mais rentável para a produção de farinha, sendo uma importante fonte de recurso genético para programas de melhoramento. Através da análise de rede pode-se observar que a rede de circulação de propágulos e informações ocorre entre os moradores e também com outras comunidades da região, importantes fontes de novas variedades. Dois agricultores foram identificados como os mais atuantes nas trocas. De acordo com o agrupamento e análise de coordenadas principais feitos utilizando os dados genéticos, as variedades introduzidas mais recentemente separam-se das introduzidas há mais tempo. As variedades apontadas como com alto teor de ácido cianídrico pelos agricultores também ficaram agrupadas. Notou-se que as variedades locais apresentam genes úteis para características importantes como, resistência a estresses bióticos e abióticos.Edição Especial dos Anais do 3 Simpósio da Rede de Recursos Genéticos Vegetais do Nordeste, Aracaju, out. 2017

Influence of the use of manioc on its genetic diversity conservation in a quilombo community in Mato Grosso, Brazil.

Local cassava varieties play an important role in food security and the autonomy of subsistence farmers. They can be important resources for breeding and conservation programs. We examined the genetic diversity of cassava through ethnobotanical knowledge and microsatellite markers to understand the dynamics of conservation and management of the varieties used local small-scale farmers of a rural quilombo (a slave-descendant community) in Mato Grosso, Brazil. To obtain ethnobotanical information, semi-structured interviews were applied to 10 family units who cultivated cassava. Each family cultivated from one to five varieties, with 2.3 ± 1.16 varieties/farmer, on average. Genetic analysis was was made of the 11 local varieties with microsatellite markers (12 loci). Despite low ethnobotanical diversity (H' = 2.05), high genetic diversity was found (Na = 6.75, HO = 0.92, HE = 0.75, on average) in these local varieties. These farmers, who derive their income mainly from cassava cultivation and flour production for the market, direct their variety choices to those that are most productive. Brava variety was the most frequent (found in eight family units) and was considered the most profitable for the production of flour Network analysis showed that propagule circulation and information occurs between the residents and also with other communities of the region, which are important sources of new varieties. Two farmers were identified as the most active in this network, showing potential as key elements for the circulation of propagating material. According to the cluster analysis using the genetic data, the most recently introduced varieties (Baixinha, Liberatona, Broto roxo, Mansa, Ramo branco, Carneiro and Cuiabana) are separated from those introduced a long time ago. The varieties pointed out as bitter by the farmers were also grouped together. The results showed the importance of traditional farmers in maintaining a high genetic diversity of manioc varieties, despite the directing of the choice of varieties to meet market needs

Ultrasound prediction of Zika virus-associated congenital injury using the profile of fetal growth.

Zika virus (ZIKV) is a mosquito-transmitted flavivirus, recently linked to microcephaly and central nervous system anomalies following infection in pregnancy. Striking findings of disproportionate growth with a smaller than expected head relative to body length have been observed more commonly among fetuses with exposure to ZIKV in utero compared to pregnancies without ZIKV infection regardless of other signs of congenital infection including microcephaly. This study's objective was to determine the diagnostic accuracy of femur-sparing profile of intrauterine growth restriction for the identification of ZIKV-associated congenital injuries on postnatal testing. A retrospective cohort study of pregnant women with possible or confirmed ZIKV infection between January 1, 2016 and December 31, 2017 were included. Subjects were excluded if no prenatal ultrasound was available. A femur-sparing profile of growth restriction determined using INTERGROWTH-21st sonographic standard for head circumference to femur length (HC: FL). Congenital injuries were determined postnatally by imaging, comprehensive eye exam and standard newborn hearing screen. A total of 111 pregnant women diagnosed with ZIKV infection underwent fetal ultrasound and 95 neonates had complete postnatal evaluation. Prenatal microcephaly was detected in 5% of fetuses (6/111). Postnatal testing detected ZIKV-associated congenital injuries in 25% of neonates (24/95). A HC: FL Z-score ≤ -1.3 had a 52% specificity (95% CI 41-63%), 82% negative predictive value (NPV, 95% CI 73-88%) for the detection of ZIKV-associated congenital injuries in the neonatal period. A more stringent threshold with a Z-score ≤ -2 was associated with a 90% specificity (95% CI 81-95%), 81% NPV (95% CI 77-85%). Excluding cases of fetal microcephaly, HC: FL (Z-score ≤ -2) demonstrated a similar specificity (89%, 95% CI 81-95%) with superior NPV (87%, 95% CI 84-90%). The sonographic recognition of a normally proportioned fetus may be useful prenatally to exclude a wider spectrum of ZIKV-associated congenital injuries detected postnatally

I/O Impedance Matching Algorithm for HighPerformance ASICs

Abstract This paper discusses a design style that utilizes an area array of flip-chip solder bump connections, I/O circuit designs that implement a programmable impedance matching algorithm, and a design system that must utilize these features during chip layout, chip checking, and release to manufacturing. Results from a recent test chip will also be given

Global selective sweep of a highly inbred genome of the cattle parasite Neospora caninum

Neospora caninum, a cyst-forming apicomplexan parasite, is a leading cause of neuromuscular diseases in dogs as well as fetal abortion in cattle worldwide. The importance of the domestic and sylvatic life cycles of Neospora, and the role of vertical transmission in the expansion and transmission of infection in cattle, is not sufficiently understood. To elucidate the population genomics of Neospora, we genotyped 50 isolates collected worldwide from a wide range of hosts using 19 linked and unlinked genetic markers. Phylogenetic analysis and genetic distance indices resolved a single genotype of N. caninum. Whole-genome sequencing of 7 isolates from 2 different continents identified high linkage disequilibrium, significant structural variation, but only limited polymorphism genome-wide, with only 5,766 biallelic single nucleotide polymorphisms (SNPs) total. Greater than half of these SNPs (∼3,000) clustered into 6 distinct haploblocks and each block possessed limited allelic diversity (with only 4 to 6 haplotypes resolved at each cluster). Importantly, the alleles at each haploblock had independently segregated across the strains sequenced, supporting a unisexual expansion model that is mosaic at 6 genomic blocks. Integrating seroprevalence data from African cattle, our data support a global selective sweep of a highly inbred livestock pathogen that originated within European dairy stock and expanded transcontinentally via unisexual mating and vertical transmission very recently, likely the result of human activities, including recurrent migration, domestication, and breed development of bovid and canid hosts within similar proximities

Serotonergic, brain volume and attentional correlates of trait anxiety in primates.

Trait anxiety is a risk factor for the development and maintenance of affective disorders, and insights into the underlying brain mechanisms are vital for improving treatment and prevention strategies. Translational studies in non-human primates, where targeted neurochemical and genetic manipulations can be made, are critical in view of their close neuroanatomical similarity to humans in brain regions implicated in trait anxiety. Thus, we characterised the serotonergic and regional brain volume correlates of trait-like anxiety in the marmoset monkey. Low- and high-anxious animals were identified by behavioral responses to a human intruder (HI) that are known to be sensitive to anxiolytic drug treatment. Extracellular serotonin levels within the amygdala were measured with in vivo microdialysis, at baseline and in response to challenge with the selective serotonin reuptake inhibitor, citalopram. Regional brain volume was assessed by structural magnetic resonance imaging. Anxious individuals showed persistent, long-term fearful responses to both a HI and a model snake, alongside sustained attention (vigilance) to novel cues in a context associated with unpredictable threat. Neurally, high-anxious marmosets showed reduced amygdala serotonin levels, and smaller volumes in a closely connected prefrontal region, the dorsal anterior cingulate cortex. These findings highlight behavioral and neural similarities between trait-like anxiety in marmosets and humans, and set the stage for further investigation of the processes contributing to vulnerability and resilience to affective disorders.This research was supported by a Medical Research Programme Grant (G0901884) from the Medical Research Council UK (MRC) to Angela Roberts, and a PhD studentship from MRC and final-term funding from Trinity College, Cambridge, UK to Yevheniia Mikheenko.This is the author accepted manuscript. The final version is available from NPG at http://www.nature.com/npp/journal/v40/n6/full/npp2014324a.htm