The association between implicit and explicit affective inhibitory control, rumination and depressive symptoms

Inhibitory control underlies one’s ability to maintain goal-directed behavior by inhibiting prepotent responses or ignoring irrelevant information. Recent models suggest that impaired inhibition of negative information may contribute to depressive symptoms, and that this association is mediated by rumination. However, the exact nature of this association, particularly in non-clinical samples, is unclear. The current study assessed the relationship between inhibitory control over emotional vs. non-emotional information, rumination and depressive symptoms. A non-clinical sample of 119 participants (mean age: 36.44 ± 11.74) with various levels of depressive symptoms completed three variations of a Go/No-Go task online; two of the task variations required either explicit or implicit processing of emotional expressions, and a third variation contained no emotional expressions (i.e., neutral condition). We found reductions in inhibitory control for participants reporting elevated symptoms of depression on all three task variations, relative to less depressed participants. However, for the task variation that required implicit emotion processing, depressive symptoms were associated with inhibitory deficits for sad and neutral, but not for happy expressions. An exploratory analysis showed that the relationship between inhibition and depressive symptoms occurs in part through trait rumination for all three tasks, regardless of emotional content. Collectively, these results indicate that elevated depressive symptoms are associated with both a general inhibitory control deficit, as well as affective interference from negative emotions, with implications for the assessment and treatment of mood disorders

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

A combination of structural approaches yields a complete atomic model of the highly biochemically characterized Escherichia coli RNA polymerase, enabling fuller exploitation of E. coli as a model for understanding transcription

Enhancing Evolution: When Spatial Structure and Environmental Change Improve Adaptation

Thesis (Ph.D.)--University of Washington, 2013Evolution by natural selection is the primary creative force in biology. In order for populations to thrive, or even survive, requires a continual generative process. An understand of the process of natural selection, its strengths and weaknesses, is necessary for both predictions about the future course of life, as well as its history. Evolution by natural selection requires the combination of three elements: variation, heredity, and selection. In natural populations, variation can be introduced by random mutation, recombination (such as by sex), and migration from differing populations. Heredity, or the correlation between traits of the parents with that of their offspring, is mediated by genetic material. Selection is the process whereby the traits of some members of the population are more successful (fit) and hence contribute more offspring to future generations. When these three factors are present, populations can (over the course of many generations) increase in fitness to become better adapted to their environment. The ability to adapt is not restricted to populations in natural environments, as artificial populations such as microbes grown in laboratory settings can also evolve. In fact, simulated, digital populations that possess the three features needed for evolution by natural selection can also adapt. In this dissertation, I utilize both microbes evolving in artificial settings and digital organisms, which exist only in a computer's memory, to make general statements about the process of evolution. Of course, such generalizations must be taken with a grain of salt, as the specifics of any system may interfere with assumptions made in the follow models. But, I present the following work as forays into the possible; I demonstrate that certain processes can affect the course of evolution, and such processes should be taken into account when seeking an understand of evolution in other (perhaps more natural) situations. In Chapter 1, I investigate how a non-transitive system of microbial competitors evolves, and demonstrate that the phenomenon of "survival of the weakest" requires the presence of population structure. In Chapter 2, I explore the effect of structure on evolving populations, and I find that structure can enhance the rate of adaptation in certain circumstances. Lastly in Chapter 3, I describe and demonstrate circumstances where environmental change can enhance the rate of adaption

Polarimetric interferometry for assessment of corneal stromal lamellae orientation

Purpose: To analyze corneal stromal lamellae orientation in normal subjects and patients with various corneal conditions using a polarimetric interferometer. Methods: Thirty-two healthy control subjects (59 eyes) and 16 patients (22 eyes) with corneal conditions or postkeratoplasty were included in the study. All patients were imaged using the interferometer and slit lamp photography. The interferometer produces an orthogonal cross-like image of stromal lamellae by illuminating the cornea in phaselight polarization angle. Corneal haze was graded on a scale from 0 to 4. Interferometer cross-like images were graded on a scale from 0 to 5 by a masked observer. Keratometry, corneal central pachymetry, and optical densitometry were obtained with Scheimpflug corneal tomography. Results: The cross-like image was observed in 31 of 32 healthy control subjects (58 of 59 eyes) and in 13 of 16 patients (19 of 22 eyes). The image was not detectable in 3 patients, 1 with total corneal neovascularization and scarring, 1 with central leukoma, and 1 with failed deep lamellar keratoplasty. Corneal haze was the main factor obscuring the cross-like image (P 0.05). Conclusions: Corneal stromal lamellae orientation can be efficiently assessed and displayed as a cross-like image by the polarimetric interferometer. Stromal lamellae orientation imaging may have potential implications in corneal diagnostics and surgery

Supplementing intensive targeted computerized cognitive training with social cognitive exercises for people with schizophrenia: An interim report.

OBJECTIVE: Individuals with schizophrenia demonstrate cognitive, social cognitive and motivational deficits that contribute to impairment in real-world functioning. In the current study, we investigated the effects of supplementing computerized neurocognitive training with social cognitive exercises, as compared to neurocognitive training alone. METHODS: In this ongoing, double-blind, randomized controlled trial of 111 participants with psychosis, we compare the effects of supplementing intensive targeted cognitive training with social cognitive training exercises (TCT+SCT), to the effects of targeted cognitive training alone (TCT-only). Participants were assessed on cognition, symptoms, functional capacity and functional outcomes, as well as social cognition and measures related to reward processing. RESULTS: Both treatment groups showed significant improvement in multiple cognitive domains and improvement in functional capacity. However, as predicted, TCT+SCT group participants showed significant improvement in prosody identification and reward processing relative to TCT-only participants. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE: Our findings indicate that supplementing intensive computerized cognitive training with social cognitive exercises in people with psychosis confers greater benefits in prosody identification and reward processing relative to cognitive training alone, even though both approaches drive significant improvements in cognition and functional capacity. Impairments in both prosody identification and reward processing have been associated with greater negative symptoms and poorer functional outcomes in schizophrenia, raising the possibility that this form of treatment may lead to better long-term outcomes than traditional cognitive training approaches. Follow-up assessments will determine if results are durable and generalize over time to improvements in symptoms and functioning. CLINICALTRIALS.GOV IDENTIFIER: NCT0210577

Supplementing Intensive Targeted Computerized Cognitive Training With Social Cognitive Exercises for People With Schizophrenia: An Interim Report

ObjectiveIndividuals with schizophrenia demonstrate cognitive, social cognitive, and motivational deficits that contribute to impairment in real-world functioning. In the current study, we investigated the effects of supplementing computerized neurocognitive training with social cognitive exercises, as compared with neurocognitive training alone.MethodIn this ongoing, double-blind, randomized controlled trial of 111 participants with psychosis, we compare the effects of supplementing intensive targeted cognitive training with social cognitive training exercises (TCT + SCT) with the effects of targeted cognitive training alone (TCT-only). Participants were assessed on cognition, symptoms, functional capacity, and functional outcomes, as well as social cognition and measures related to reward processing.ResultsBoth treatment groups showed significant improvement in multiple cognitive domains and improvement in functional capacity. However, as predicted, TCT + SCT group participants showed significant improvement in prosody identification and reward processing relative to TCT-only participants.Conclusions and implications for practiceOur findings indicate that supplementing intensive computerized cognitive training with social cognitive exercises in people with psychosis confers greater benefits in prosody identification and reward processing relative to cognitive training alone, even though both approaches drive significant improvements in cognition and functional capacity. Impairments in both prosody identification and reward processing have been associated with greater negative symptoms and poorer functional outcomes in schizophrenia, raising the possibility that this form of treatment may lead to better long-term outcomes than traditional cognitive training approaches. Follow-up assessments will determine whether results are durable and generalize over time to improvements in symptoms and functioning. (PsycINFO Database Recor