GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments

BACKGROUND: The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. RESULTS: GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. CONCLUSION: GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets

Development of a “Universal” Phantom for Standardization of Chemical Exchange Saturation Transfer (CEST) MRI

https://openworks.mdanderson.org/sumexp22/1039/thumbnail.jp

Involvement of Noradrenergic Neurotransmission in the Stress- but not Cocaine-Induced Reinstatement of Extinguished Cocaine-Induced Conditioned Place Preference in Mice: Role for β-2 Adrenergic Receptors

The responsiveness of central noradrenergic systems to stressors and cocaine poses norepinephrine as a potential common mechanism through which drug re-exposure and stressful stimuli promote relapse. This study investigated the role of noradrenergic systems in the reinstatement of extinguished cocaine-induced conditioned place preference by cocaine and stress in male C57BL/6 mice. Cocaine- (15 mg/kg, i.p.) induced conditioned place preference was extinguished by repeated exposure to the apparatus in the absence of drug and reestablished by a cocaine challenge (15 mg/kg), exposure to a stressor (6-min forced swim (FS); 20–25°C water), or administration of the α-2 adrenergic receptor (AR) antagonists yohimbine (2 mg/kg, i.p.) or BRL44408 (5, 10 mg/kg, i.p.). To investigate the role of ARs, mice were administered the nonselective β-AR antagonist, propranolol (5, 10 mg/kg, i.p.), the α-1 AR antagonist, prazosin (1, 2 mg/kg, i.p.), or the α-2 AR agonist, clonidine (0.03, 0.3 mg/kg, i.p.) before reinstatement testing. Clonidine, prazosin, and propranolol failed to block cocaine-induced reinstatement. The low (0.03 mg/kg) but not high (0.3 mg/kg) clonidine dose fully blocked FS-induced reinstatement but not reinstatement by yohimbine. Propranolol, but not prazosin, blocked reinstatement by both yohimbine and FS, suggesting the involvement of β-ARs. The β-2 AR antagonist ICI-118551 (1 mg/kg, i.p.), but not the β-1 AR antagonist betaxolol (10 mg/kg, i.p.), also blocked FS-induced reinstatement. These findings suggest that stress-induced reinstatement requires noradrenergic signaling through β-2 ARs and that cocaine-induced reinstatement does not require AR activation, even though stimulation of central noradrenergic neurotransmission is sufficient to reinstate

TOI-954 B And K2-329 B: Short-Period Saturn-Mass Planets That Test Whether Irradiation Leads To Inflation

We report the discovery of two short-period Saturn-mass planets, one transiting the G subgiant TOI-954 (TIC 44792534, V = 10.343, T = 9.78) observed in TESS sectors 4 and 5 and one transiting the G dwarf K2-329 (EPIC 246193072, V = 12.70, K = 10.67) observed in K2 campaigns 12 and 19. We confirm and characterize these two planets with a variety of ground-based archival and follow-up observations, including photometry, reconnaissance spectroscopy, precise radial velocity, and high-resolution imaging. Combining all available data, we find that TOI-954 b has a radius of ${0.852}_{-0.062}^{+0.053}\,{R}_{{\rm{J}}}$and a mass of ${0.174}_{-0.017}^{+0.018}$MJ and is in a 3.68 day orbit, while K2-329 b has a radius of ${0.774}_{-0.024}^{+0.026}\,{R}_{{\rm{J}}}$and a mass of ${0.260}_{-0.022}^{+0.020}$MJ and is in a 12.46 day orbit. As TOI-954 b is 30 times more irradiated than K2-329 b but more or less the same size, these two planets provide an opportunity to test whether irradiation leads to inflation of Saturn-mass planets and contribute to future comparative studies that explore Saturn-mass planets at contrasting points in their lifetimes

Cause of Death and Predictors of All-Cause Mortality in Anticoagulated Patients With Nonvalvular Atrial Fibrillation : Data From ROCKET AF

M. Kaste on työryhmän ROCKET AF Steering Comm jäsen.Background-Atrial fibrillation is associated with higher mortality. Identification of causes of death and contemporary risk factors for all-cause mortality may guide interventions. Methods and Results-In the Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF) study, patients with nonvalvular atrial fibrillation were randomized to rivaroxaban or dose-adjusted warfarin. Cox proportional hazards regression with backward elimination identified factors at randomization that were independently associated with all-cause mortality in the 14 171 participants in the intention-to-treat population. The median age was 73 years, and the mean CHADS(2) score was 3.5. Over 1.9 years of median follow-up, 1214 (8.6%) patients died. Kaplan-Meier mortality rates were 4.2% at 1 year and 8.9% at 2 years. The majority of classified deaths (1081) were cardiovascular (72%), whereas only 6% were nonhemorrhagic stroke or systemic embolism. No significant difference in all-cause mortality was observed between the rivaroxaban and warfarin arms (P=0.15). Heart failure (hazard ratio 1.51, 95% CI 1.33-1.70, P= 75 years (hazard ratio 1.69, 95% CI 1.51-1.90, P Conclusions-In a large population of patients anticoagulated for nonvalvular atrial fibrillation, approximate to 7 in 10 deaths were cardiovascular, whereasPeer reviewe

Like mother, like child : investigating perinatal and maternal health stress in post-medieval London.

Post-Medieval London (sixteenth-nineteenth centuries) was a stressful environment for the poor. Overcrowded and squalid housing, physically demanding and risky working conditions, air and water pollution, inadequate diet and exposure to infectious diseases created high levels of morbidity and low life expectancy. All of these factors pressed with particular severity on the lowest members of the social strata, with burgeoning disparities in health between the richest and poorest. Foetal, perinatal and infant skeletal remains provide the most sensitive source of bioarchaeological information regarding past population health and in particular maternal well-being. This chapter examined the evidence for chronic growth and health disruption in 136 foetal, perinatal and infant skeletons from four low-status cemetery samples in post-medieval London. The aim of this study was to consider the impact of poverty on the maternal-infant nexus, through an analysis of evidence of growth disruption and pathological lesions. The results highlight the dire consequences of poverty in London during this period from the very earliest moments of life

Development of the J-2X Engine for the Ares I Crew Launch Vehicle and the Ares V Cargo Launch Vehicle: Building on the Apollo Program for Lunar Return Missions

The United States (U.S.) Vision for Space Exploration has directed NASA to develop two new launch vehicles for sending humans to the Moon, Mars, and beyond. In January 2006, NASA streamlined its hardware development approach for replacing the Space Shuttle after it is retired in 2010. Benefits of this approach include reduced programmatic and technical risks and the potential to return to the Moon by 2020, by developing the Ares I Crew Launch Vehicle (CLV) propulsion elements now, with full extensibility to future Ares V Cargo Launch Vehicle (CaLV) lunar systems. The Constellation Program selected the Pratt & Whitney Rocketdyne J-2X engine to power the Ares I Upper Stage Element and the Ares V Earth Departure Stage. This decision was reached during the Exploration Systems Architecture Study and confirmed after the Exploration Launch Projects Office performed a variety of risk analyses, commonality assessments, and trade studies. This paper narrates the evolution of that decision; describes the performance capabilities expected of the J-2X design, including potential commonality challenges and opportunities between the Ares I and Ares V launch vehicles; and provides a current status of J-2X design, development, and hardware testing activities. This paper also explains how the J-2X engine effort mitigates risk by testing existing engine hardware and designs; building on the Apollo Program (1961 to 1975), the Space Shuttle Program (1972 to 2010); and consulting with Apollo-era experts to derive other lessons lived to deliver a human-rated engine that is on an aggressive development schedule, with its first demonstration flight in 2012

Family Resemblance in Unsupervised Categorization: A Dissociation Between Production and Evaluation

A plurality of the categories we hold exhibit family resemblance (FR; i.e., many characteristic but few defining features), suggesting FR may occupy a central role in human category formation. However, research in unsupervised learning has shown that when people are asked to sort an array of novel items into categories, they ubiquitously use a unidimensional (UNI) rule – despite the availability of a FR solution. This work suggests that, perhaps, FR similarity is not a core tendency in category formation. Here, we question whether the UNI bias is a result of the sorting paradigm. Specifically, we speculate the paradigm conflates two components vital for category formation: production and evaluation. Across three experiments we show that when evaluation is separated from generation – by using a novel forced-choice task that pits different category organizational schemes against one another – people exhibit a FR over UNI preference. The implications of these results are discussed