Computer aided manual validation of mass spectrometry-based proteomic data.

Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design.

The persistent impact of incidental experience.

As we perform daily activities--driving to work, unlocking the office door, or grabbing a coffee cup--our actions seem automatic and preprogrammed. Nonetheless, routine, well-practiced behavior is continually modulated by incidental experience: In repetitive experimental tasks, recent (~4) trials reliably influence performance and action choice. Psychological theories downplay the significance of sequential effects, explaining them as rapidly decaying perturbations of behavior, with no long-term consequences.

A conditional process model of children's behavioral engagement and behavioral disaffection in sport based on self-determination theory.

The potential benefits of children's engagement in sport for their psychological, social, and physical health are well established. Yet children may also experience psychological and social impairments due, in part, to a variety of detrimental coach behaviors. In the current study, we proposed and tested a conditional process model of children's self-reported behavioral engagement and behavioral disaffection in sport based on self-determination theory.

The effect of protease and nonstarch polysaccharide enzymes on manure odor and ammonia emissions from finisher pigs.

A 2 × 2 factorial experiment was conducted to investigate the effect of dietary protease (0 and 200 mg/kg) and xylanase (0 and 200mg/kg) in reducing manure odor and NH(3) from finisher pigs. Sixteen pigs were assigned to 1 of 4 dietary treatments, (i) basal diet, (ii) basal diet + xylanase, (iii) basal diet + protease, or (iv) basal diet + xylanase + protease, for 24 d. The manure samples from pigs offered diets containing protease showed increased (P < 0.

The smoothing artifact of spatially constrained canonical correlation analysis in functional MRI.

A wide range of studies show the capacity of multivariate statistical methods for fMRI to improve mapping of brain activations in a noisy environment. An advanced method uses local canonical correlation analysis (CCA) to encompass a group of neighboring voxels instead of looking at the single voxel time course. The value of a suitable test statistic is used as a measure of activation.

The mediating role of psychological need satisfaction in relationships between types of passion for sport and athlete burnout.

Research indicates that obsessive and harmonious passion can explain variability in burnout through various mediating processes (e.g., Vallerand, Paquet, Phillippe, & Charest, 2010).

Optimizing the performance of local canonical correlation analysis in fMRI using spatial constraints.

The benefits of locally adaptive statistical methods for fMRI research have been shown in recent years, as these methods are more proficient in detecting brain activations in a noisy environment. One such method is local canonical correlation analysis (CCA), which investigates a group of neighboring voxels instead of looking at the single voxel time course. The value of a suitable test statistic is used as a measure of activation.

A within-subject ERP and fMRI investigation of orientation-specific recognition memory for pictures.

Despite a large body of recognition memory research, its temporal, measured with ERPs, and spatial, measured with fMRI, substrates have never been investigated in the same subjects. In the present study, we obtained this information in parallel sessions, in which subjects studied and recognized images of visual objects and their orientation. The results showed that ERP-familiarity processes between 240 and 440 ms temporally preceded recollection processes and were structurally associated with prefrontal brain regions.

Evidence of a role for fibrocyte and keratinocyte-like cells in the formation of hypertrophic scars.

Burn injuries affect millions of people every year, and dermal fibrosis is a common complication for the victims. This disfigurement has functional and cosmetic consequences and many research groups have made it the focus of their work to understand the mechanisms that underlie its development. Although significant progress has been made in wound-healing processes, the complexity of events involved makes it very difficult to come up with a single strategy to prevent this devastating fibrotic condition.

Glucocorticoid compounds modify smoothened localization and hedgehog pathway activity.

The Hedgehog signaling pathway is linked to a variety of diseases, notably a range of cancers. The first generation of drug screens identified Smoothened (Smo), a membrane protein essential for signaling, as an attractive drug target. Smo localizes to the primary cilium upon pathway activation, and this transition is critical for the response to Hedgehog ligands.

The limits of feedforward vision: recurrent processing promotes robust object recognition when objects are degraded.

Everyday vision requires robustness to a myriad of environmental factors that degrade stimuli. Foreground clutter can occlude objects of interest, and complex lighting and shadows can decrease the contrast of items. How does the brain recognize visual objects despite these low-quality inputs? On the basis of predictions from a model of object recognition that contains excitatory feedback, we hypothesized that recurrent processing would promote robust recognition when objects were degraded by strengthening bottom-up signals that were weakened because of occlusion and contrast reduction.

Familiarity in source memory.

Familiarity and recollection are thought to be separate processes underlying recognition memory. Event-related potentials (ERPs) dissociate these processes, with an early (approximately 300-500ms) frontal effect relating to familiarity (the FN400) and a later (500-800ms) parietal old/new effect relating to recollection. It has been debated whether source information for a studied item (i.

Stereoselective synthesis of (S)-3-(methylamino)-3-((R)-pyrrolidin-3-yl)propanenitrile.

(S)-3-(methylamino)-3-((R)-pyrrolidin-3-yl)propanenitrile (1) is a key intermediate in the preparation of PF-00951966, (1) a fluoroquinolone antibiotic for use against key pathogens causing community-acquired respiratory tract infections including multidrug resistant (MDR) organisms. The current work describes the development of a highly efficient and stereoselective synthesis of 1 in 10 steps with an overall yield of 24% from readily available benzyloxyacetyl chloride. Two key transformations in the synthetic sequence involve (a) catalytic asymmetric hydrogenation with chiral DM-SEGPHOS-Ru(II) complex to afford β-hydroxy amide 11b in good yield (73%) and high stereoselectivity (de 98%, ee >99%) after recrystallization and (b) S(N)2 substitution reaction with methylamine to provide diamine 14 with inversion of configuration at the 1'-position in high yield (80%), after efficient purification using a simple acid/base extraction protocol.

Rising incidence of Pneumocystis jirovecii pneumonia suggests iatrogenic exposure of immune-compromised patients may be becoming a significant problem.

Against a background of point-source outbreaks of Pneumocystis pneumonia (PCP) in renal transplant units in Europe, we undertook a retrospective 3 year observational review of PCP in Northern Ireland. This showed an unexpected increase in incidence, with a mortality rate of 30 %. Fifty-one cases were confirmed compared to 10 cases confirmed in the preceding 7 years.

Extending local canonical correlation analysis to handle general linear contrasts for FMRI data.

Local canonical correlation analysis (CCA) is a multivariate method that has been proposed to more accurately determine activation patterns in fMRI data. In its conventional formulation, CCA has several drawbacks that limit its usefulness in fMRI. A major drawback is that, unlike the general linear model (GLM), a test of general linear contrasts of the temporal regressors has not been incorporated into the CCA formalism.

Oxytocin can impair memory for social and non-social visual objects: a within-subject investigation of oxytocin's effects on human memory.

Oxytocin is important to social behavior and emotion regulation in humans. Oxytocin's role derives in part from its effect on memory performance. More specifically, previous research suggests that oxytocin facilitates recognition of social (e.

A preliminary study of functional abnormalities in aMCI subjects during different episodic memory tasks.

Functional magnetic resonance imaging (fMRI) is an important imaging modality to understand the neurodegenerative course of mild cognitive impairment (MCI) and early Alzheimer's disease (AD), because the memory dysfunction may occur before structural degeneration is obvious. In this research, we investigated the functional abnormalities of subjects with amnestic MCI (aMCI) using three episodic memory paradigms that are relevant to different memory domains in both encoding and recognition phases. Both whole-brain analysis and region-of-interest (ROI) analysis of the medial temporal lobes (MTL), which are central to the memory formation and retrieval, were used to compare the efficiency of the different memory paradigms and the functional difference between aMCI subjects and normal control subjects.

Cognitive control reflects context monitoring, not motoric stopping, in response inhibition.

The inhibition of unwanted behaviors is considered an effortful and controlled ability. However, inhibition also requires the detection of contexts indicating that old behaviors may be inappropriate--in other words, inhibition requires the ability to monitor context in the service of goals, which we refer to as context-monitoring. Using behavioral, neuroimaging, electrophysiological and computational approaches, we tested whether motoric stopping per se is the cognitively-controlled process supporting response inhibition, or whether context-monitoring may fill this role.

Optimization of contrast detection power with probabilistic behavioral information.

Recent progress in the experimental design for event-related fMRI experiments made it possible to find the optimal stimulus sequence for maximum contrast detection power using a genetic algorithm. In this study, a novel algorithm is proposed for optimization of contrast detection power by including probabilistic behavioral information, based on pilot data, in the genetic algorithm. As a particular application, a recognition memory task is studied and the design matrix optimized for contrasts involving the familiarity of individual items (pictures of objects) and the recollection of qualitative information associated with the items (left/right orientation).

Crk1/2-dependent signaling is necessary for podocyte foot process spreading in mouse models of glomerular disease.

The morphology of healthy podocyte foot processes is necessary for maintaining the characteristics of the kidney filtration barrier. In most forms of glomerular disease, abnormal filter barrier function results when podocytes undergo foot process spreading and retraction by remodeling their cytoskeletal architecture and intercellular junctions during a process known as effacement. The cell adhesion protein nephrin is necessary for establishing the morphology of the kidney podocyte in development by transducing from the specialized podocyte intercellular junction phosphorylation-mediated signals that regulate cytoskeletal dynamics.

Acute respiratory distress syndrome caused by Mycoplasma pneumoniae diagnosed by polymerase chain reaction.

Mycoplasma pneumoniae (M. pneumoniae) is a common pathogen in cases of atypical pneumonia. Most individuals with Mycoplasma pneumonia run a benign course, with non-specific symptoms of malaise, fever and non-productive cough that usually resolve with no long-term sequelae.

Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data.

We present MINEMO (Minimal Information for Neural ElectroMagnetic Ontologies), a checklist for the description of event-related potentials (ERP) studies. MINEMO extends MINI (Minimal Information for Neuroscience Investigations)to the ERP domain. Checklist terms are explicated in NEMO, a formal ontology that is designed to support ERP data sharing and integration.

The adaptor protein CRK is a pro-apoptotic transducer of endoplasmic reticulum stress.

Excessive demands on the protein-folding capacity of the endoplasmic reticulum (ER) cause irremediable ER stress and contribute to cell loss in a number of cell degenerative diseases, including type 2 diabetes and neurodegeneration. The signals communicating catastrophic ER damage to the mitochondrial apoptotic machinery remain poorly understood. We used a biochemical approach to purify a cytosolic activity induced by ER stress that causes release of cytochrome c from isolated mitochondria.