Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.

Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats.

Sexually-dimorphic alterations in cannabinoid receptor density depend upon prenatal/early postnatal history.

Recent research has demonstrated that the endogenous cannabinoid system is central to the brain's response to stress. As part of an ongoing collaboration, we sought to examine the effects of prenatal and early postnatal rearing and housing conditions on developing endocannabinoid systems. We compare brain cannabinoid receptors (CBR) in offspring of either prenatal vehicle intubated or non-treated dams (Experiment 1) or in rats derived from a vendor and shipped at weaning to a collaborating lab (Experiment 2).

Perceptual Assessment of Velopharyngeal Dysfunction by Otolaryngology Residents.

Objective: To assess the ability of otolaryngology residents to rate the hypernasal resonance of patients with velopharyngeal dysfunction. We hypothesize that experience (postgraduate year [PGY] level) and training will result in improved ratings of speech samples.

Study Design: Prospective cohort study.

Eating Behavior, Low-Frequency Functional Mutations in the Melanocortin-4 Receptor (MC4R) Gene, and Outcomes of Bariatric Operations: A 6-Year Prospective Study.

Objective: Data on the effects of eating behavior and genetics on outcomes of gastrointestinal surgery for diabesity have been sparse, often flawed, and controversial. We aimed to assess long-term outcomes of bariatric operations in patients characterized for eating behavior and rare mutations in the melanocortin-4 receptor (MC4R) gene, which is strongly implicated in energy balance.

Research Design And Methods: Between 1996 and 2005, 1,264 severely obese Swiss patients underwent current laparoscopic adjustable gastric banding, gastroduodenal bypass, or a hybrid operation.

GW100: Benchmarking G0W0 for Molecular Systems.

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW.

Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases.

Even with the widespread use of liquid chromatography mass spectrometry (LC/MS) based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges.

Rapidly improving stroke symptoms: a pilot, prospective study.

Background: Rapidly improving stroke symptoms (RISSs) are a controversial exclusion for intravenous recombinant tissue plasminogen activator (rt-PA) for acute ischemic stroke (AIS). We estimated the frequency of 4 prespecified RISS definitions and explored their relationship to clinical outcome.

Methods: Pilot, prospective study of AIS patients admitted within 4.

Spatial memory in nonhuman primates implanted with the subdural pharmacotherapy device.

This study investigated the possible influence of the Subdural Pharmacotherapy Device (SPD) on spatial memory in 3 adult, male bonnet macaques (Macaca radiata). The device was implanted in and above the subdural/subarachnoid space and cranium overlaying the right parietal/frontal cortex: a circuitry involved in spatial memory processing. A large test chamber, equipped with four baited and four non-baited food-ports at different locations, was used: reaches into empty food ports were counted as spatial memory errors.

Comparison of Lidocaine Gel-Assisted Transconjunctival and Transcutaneous Local Anesthesia for Outpatient Eyelid Surgery.

Purpose: Determine whether transconjunctival local anesthesia using 2% lidocaine gel decreases pain perception in comparison with transcutaneous anesthesia in patients undergoing outpatient eyelid surgery.

Methods: This is a randomized controlled clinical trial. This study approved by an institutional review board and adhered to the Declaration of Helsinki and the Health Insurance Portability and Accountability Act.

Complement factor B activation in patients with preeclampsia.

Preeclampsia is a leading cause of maternal and fetal morbidity and mortality. Bb, the active fragment of complement factor B (fB), has been reported to be a predictor of preeclampsia. However, conflicting results have been found by some investigators.

The prevalence of sleep-disordered breathing in children with asthma and its behavioral effects.

Objectives: To determine the prevalence of sleep-disordered breathing (SDB) in children with asthma compared to non-asthmatic children and to determine if behavior problems are associated with asthma and SDB.

Study Design: Cross-Sectional.

Methods: Parents of 263 children with asthma and 266 controls ages 2 to 15 years attending routine pediatric office visits completed the Pediatric Sleep Questionnaire (PSQ) and the Child Behavior Checklist.

Influence of surgeon behavior on trainee willingness to speak up: a randomized controlled trial.

Background: Our aim was to determine if a surgeon's behaviors can encourage or discourage trainees from speaking up when they witness a surgical mistake.

Study Design: A randomized clinical trial in which medical students (n = 55) were randomly assigned to an "encouraged" (n = 28) or "discouraged" (n = 27) group. Participants underwent personality tests to assess decision-making styles, and were then trained on basic tasks ("burn" then "cut") on a laparoscopic surgery simulator.

Helium superfluidity. Shapes and vorticities of superfluid helium nanodroplets.

Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~10(8) to 10(11) atoms.

From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data.

Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.

Single trial nicotine conditioned place preference in pre-adolescent male and female rats.

The mean age of first voluntary tobacco inhalation is 12.3 years (DiFranza et al., 2004).

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser.

Cost-benefit analysis of polysomnography versus Clinical Assessment Score-15 (CAS-15) for treatment of pediatric sleep-disordered breathing.

Objective: To determine the cost of medical care using the Clinical Assessment Score-15 (CAS-15) scale versus polysomnography (PSG) for children with sleep-disordered breathing in terms of benefit.

Study Design: Cost-benefit analysis.

Setting: Hospital-based pediatric otolaryngology practice.

Diagnostic accuracy of microEEG: a miniature, wireless EEG device.

Measuring the diagnostic accuracy (DA) of an EEG device is unconventional and complicated by imperfect interrater reliability. We sought to compare the DA of a miniature, wireless, battery-powered EEG device ("microEEG") to a reference EEG machine in emergency department (ED) patients with altered mental status (AMS). Two hundred twenty-five ED patients with AMS underwent 3 EEGs.

EEG interpretation reliability and interpreter confidence: a large single-center study.

The intrarater and interrater reliability (I&IR) of EEG interpretation has significant implications for the value of EEG as a diagnostic tool. We measured both the intrarater reliability and the interrater reliability of EEG interpretation based on the interpretation of complete EEGs into standard diagnostic categories and rater confidence in their interpretations and investigated sources of variance in EEG interpretations. During two distinct time intervals, six board-certified clinical neurophysiologists classified 300 EEGs into one or more of seven diagnostic categories and assigned a subjective confidence to their interpretations.

The effect of positional changes on intraocular pressure during sleep in patients with and without glaucoma.

Purpose: To determine whether sleeping at a 20-degree head-up position decreases nocturnal intraocular pressure (IOP) compared with lying supine (flat) in patients with and without glaucoma.

Design: Prospective, nonrandomized comparative case series.

Materials And Methods: Thirty patients were recruited based on self-reported disease status with 15 glaucoma and 15 nonglaucoma patients; a total of 60 eyes were tested.

Moderated path analysis of the relationships between masculinity and men's attitudes toward seeking psychological help.

This study tested a theoretical model of one mediator and 4 moderators of the relationships between 2 masculinity variables (Traditional Masculinity Ideology and Gender Role Conflict) and Attitudes Toward Seeking Professional Psychological Services (Attitudes). Self-stigma was the hypothesized mediator, and the hypothesized moderators were (a) Depression, (b) General Self-efficacy, (c) Precontemplation, and (d) Barriers to Help-seeking. A sample of 654 men responded to an online survey of 9 questionnaires.

Shape dependence of band-edge exciton fine structure in CdSe nanocrystals.

The band-edge exciton fine structure of wurtzite CdSe nanocrystals is investigated by a plane-wave pseudopotential method that includes spin-orbit coupling, screened electron-hole Coulomb interactions, and exchange interactions. Large-scale, systematic simulations have been carried out on quantum dots, nanorods, nanowires, and nanodisks. The size and shape dependence of the exciton fine structure is explored over the whole diameter-length configuration space and is explained by the interplay of quantum confinement, intrinsic crystal-field splitting, and electron-hole exchange interactions.

Further evaluation of plasma sphingomyelin levels as a risk factor for coronary artery disease.

Background: Sphingomyelin (SM) is the major phospholipid in cell membranes and in lipoproteins. In human plasma, SM is mainly found in atherogenic lipoproteins; thus, high levels of SM may promote atherogenesis.

Methods: We investigated in a median follow up of 6.

Serum sphingomyelin levels are related to the clearance of postprandial remnant-like particles.

It is known that sphingomyelin (SM) content is higher in apolipoprotein B-containing particles (BLps) than in high density lipoproteins and that BLp levels, including chylomicrons and their remnant particles, are positively related to atherosclerosis. To evaluate the relationship between serum SM and postprandial remnant particle levels, we determined SM, triglyceride (TG), and cholesterol levels in serum and in remnant-like particles (RLPs) before and 3, 5, 7, and 10 h after a high-fat meal in 31 healthy subjects. We found that serum SM, like serum TG, was increased to its maximum 3 h after fat loading and then gradually decreased to basal levels after 10 h.

The computational challenges of applying comparative-based computational methods to whole genomes.

The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tools will play a fundamental role in analysing the enormous amount of new data that is currently being generated. The synthesis of computationally intensive comparative computational approaches with the requirement for whole genome analysis represents both an unprecedented challenge and opportunity for computational scientists.