Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of acute antidepressant administration on negative affective bias in depressed patients.

OBJECTIVE Acute administration of an antidepressant increases positive affective processing in healthy volunteers, an effect that may be relevant to the therapeutic actions of these medications. The authors investigated whether this effect is apparent in depressed patients early in treatment, prior to changes in mood and symptoms. METHOD In a double-blind, placebo-controlled, between-groups randomized design, the authors examined the effect of a single 4-mg dose of the norepinephrine reuptake inhibitor reboxetine on emotional processing. Thirty-three depressed patients were recruited through primary care clinics and the community and matched to 31 healthy comparison subjects. Three hours after dosing, participants were given a battery of emotional processing tasks comprising facial expression recognition, emotional categorization, and memory. Ratings of mood, anxiety, and side effects were also obtained before and after treatment. RESULTS Depressed patients who received placebo showed reduced recognition of positive facial expressions, decreased speed in responding to positive self-relevant personality adjectives, and reduced memory for this positive information compared to healthy volunteers receiving placebo. However, this effect was reversed in patients who received a single dose of reboxetine, despite the absence of changes in subjective ratings of mood or anxiety. CONCLUSIONS Antidepressant drug administration modulates emotional processing in depressed patients very early in treatment, before changes occur in mood and symptoms. This effect may ameliorate the negative biases in information processing that characterize mood and anxiety disorders. It also suggests a mechanism of action compatible with cognitive theories of depression.
Design and performance evaluation of temporal motion and color energy features for objectionable video classification

With the increasing demand for access of mobile Internet via smartphones, the needs of adult images and videos filtering is escalating. In this paper, we propose a simple and fast objectionable video classification scheme using temporal motion and color energy features (TMCEF) and evaluate the performance on accuracy and processing time. The video segments extracted from a video clip have similar color and motion characteristics. System framework for TMCEF consists of key frame extraction, motion energy calculation, skin color energy calculation, and feature extraction based on statistical distribution metric using mean, standard deviation, and frequency analysis using discrete cosine transform (DCT). The motion energy is extracted based on foreground motion detection scheme and the color energy based on skin color detection method. In order to verify the performance of these video-based temporal features, support vector machine (SVM) classifier is used. In experiments, 64F-TMCEF (36) (the case of extracting 64 key frames and using 36 temporal motion and color energy features) yields the best performance on accuracy. However, due to excessive processing time of 64F-TMCEF, 36F-TMCEF (36) (the case of extracting 36 key frames and using 36 temporal motion and color energy features) is more practical. For smartphone applications, 16F-TCEF (18) (the case of extracting 16 key frames and using 18 temporal color energy features) is adequate enough to use.
Improvement of Small-write Performance Using the ECL-based Technique

Though erasure codes are widely adopted in high fault tolerance storage systems, there exists a serious small-write problem. Many algorithms are proposed to improve the small-write performance in RAID systems, but not considering the network bandwidth usage. However, the network bandwidth is expensive in cloud distributed storage systems. In this paper, we proposed an ECL-based (E-MBR codes, Caching and Logging-based) technique to improve the small-write performance without using extra network bandwidth. Experimental results show that the proposed algorithm outperforms the competing algorithm.
A molecular dynamics study of the ion selectivity and conductanace of Neisserial PorB March 2012

A new atomic structure of the PorB porin in Neisseria meningitidis, the causative agent of meningitis, has recently been resolved. The aim of the project was to simulate the porin’s ionic selectivity and conductance using various Molecular Dynamics approaches including: electrophysiology to measure the ionic flux through the channel by maintaining a transmembrane electric potential, due to an ionic imbalance; as well as equilibrium simulations to determine the potential-of-mean-force (PMF) landscapes for ceasium cations and evaluate suggested locations of binding sites.
Research with, by, for and about Children: Lessons from Disaster Contexts

There is a need for critically informed studies that include children's perspectives on the role of children in disaster contexts, given the increased incidence of disasters resulting from the global forces of climate change. Three case studies are presented from two different disaster contexts in Australia and New Zealand, where the notion of child empowerment fits within the broader political culture of liberal democracy. Each of these case studies promotes children's right to participate, consistent with the UN Convention on the Rights of the Child (UNCRC). In attempting to provide opportunities for children to articulate their perspective on disaster, this study recognizes the manner in which the increased prevalence and scale of disasters may further complicate and distort possibilities for the actualization of children's participation rights. In doing so the authors recommend a theory-informed approach, including recognizing the complementarity of competing theories of childhood, and advocate for children's capacity and right to participate in decision-making which affects their lives. This article promotes these concepts while still recognizing their right to safety. It also demonstrates how the use of distancing and framing provides a safe space for child involvement within disaster-related research, and provides examples of appropriate methodologies to engage children and provide opportunities for meaningful contributions. Finally, implementation partnerships are discussed as a means of embedding the research within existing supported environments.
Direct and Quantitative Single-Cell Analysis of Human Immunodeficiency Virus Type 1 Reactivation from Latency

ABSTRACT The ability of human immunodeficiency virus type 1 (HIV-1) to establish latent infections in cells has received renewed attention owing to the failure of highly active antiretroviral therapy to eradicate HIV-1 in vivo. Despite much study, the molecular bases of HIV-1 latency and reactivation are incompletely understood. Research on HIV-1 latency would benefit from a model system that is amenable to rapid and efficient analysis and through which compounds capable of regulating HIV-1 reactivation may be conveniently screened. We describe a novel reporter system that has several advantages over existing in vitro systems, which require elaborate, expensive, and time-consuming techniques to measure virus production. Two HIV-1 molecular clones (NL4-3 and 89.6) were engineered to express enhanced green fluorescent protein (EGFP) under the control of the viral long terminal repeat without removing any viral sequences. By using these replication-competent viruses, latently infected T-cell (Jurkat) and monocyte/macrophage (THP-1) lines in which EGFP fluorescence and virus expression are tightly coupled were generated. Following reactivation with agents such as tumor necrosis factor alpha, virus expression and EGFP fluorescence peaked after 4 days and over the next 3 weeks each declined in a synchronized manner, recapitulating the establishment of latency. Using fluorescence microscopy, flow cytometry, or plate-based fluorometry, this system allows immediate, direct, and quantitative real-time analysis of these processes within single cells or in bulk populations of cells. Exploiting the single-cell analysis abilities of this system, we demonstrate that cellular activation and virus reactivation following stimulation with proinflammatory cytokines can be uncoupled.
The Irrationality Illusion: A New Paradigm for Economics and Behavioral Economics

A new conceptual and formal framework for analyzing economic decisions, the homo communitatis paradigm, is introduced. The framework is in the form of seven principles, which collectively articulate the entire range of factors that affect choice, including all aspects of individual behavior and of the social context—the communities—the actor is a member of. Traditional economic analysis is shown to be a special case of homo communitatis analysis in which key variables are omitted. Using the principles, we show that experimental results such as loss aversion, framing effects, mental accounting, and judgment biases are not irrational and that the apparent irrationality is in every case an illusion arising from incomplete specification and control of independent variables elucidated in the principles. Several implications for future work are discussed, including high-fidelity models of socioeconomic systems, significantly more powerful and detailed economics simulations, and adoption of significantly different approach to design of economic experiments, one that takes into account all the variables involved in human choice.
Selecting optimum DNA oligos for microarrays

High-density DNA oligonucleotide microarrays are widely used in biomedical research. In this paper, we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. Having optimized probes for each gene is valuable for two reasons: (1) by minimizing background hybridization, they provide more accurate determinations of true expression levels, and (2) having optimum probes eliminates the need for multiple probes per gene, as is usually done now, thereby decreasing the cost of each microarray and increasing their usage. The criteria for truly optimum probes is easily stated, but they are not computable at present. We have developed a heuristic approach that is efficiently computable and should provide a good approximation to the true optimum set. We have run the program on the complete genomes for several model organisms and deposited the results in a database that is available online ().
Conceptualizing and Measuring How Employees and Organizations Manage Uncertainty

The study of uncertainty is central to an understanding of organizational communication. This research investigates the organizational work climates that emerge from the way employees manage uncertainty as well as the way they perceive their organization manages uncertainty. The uncertainty management matrix (UMM) is presented as a conceptual framework, followed by three scale development studies. The article concludes with a variety of research questions to direct future communication research.
Clustering user queries of a search engine

In order to increase retrieval precision, some new search engines provide manually verified answers to Frequently Asked Queries (FAQs). An underlying task is the identification of FAQs. This paper describes our attempt to cluster similar queries according to their contents as well as user logs. Our preliminary results show that the resulting clusters provide useful information for FAQ identification.
The body in clinical cognitive theory: from beck to mindfulness

Working with the body in Mindfulness-Based Cognitive Therapy (MBCT) is often seen as a ‘means to an end’; that is, a vehicle for diverting attention from negative thought patterns, thereby fostering a detached metacognitive awareness of problematic thinking. The MBCT literature, however, accords the body a more central role. The literature expresses both the idea that the body is integral to a basic level of meaning creation experienced as a ‘bodily felt sense of something’ and that direct sensory or bodily awareness can contribute to a critical change in the felt sense of emotional difficulties. Tracing the development of the concept of the body in clinical cognitive theory, the paper concludes that these ideas of the body are anticipated in earlier revisions to Beck's schema theory. The paper concludes that research into the psychological mechanisms behind bodily awareness would be a fruitful supplement to the current research focus on metacognitive awareness.
Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911T

ABSTRACT Here, we report the draft genome sequence of Acetobacterium wieringae DSM 1911T, an anaerobic, autotrophic, acetogenic, d,l-lactate-utilizing bacterium. The genome consists of a chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes.
Mediator and moderator effects of demands on self-control in the relationship between work load and indicators of job strain

Abstract Employees are increasingly facing concentration requirements (qualitative work load) and high work pressure (quantitative work load) combined with demands on self-control (impulse control, resisting distractions, and overcoming inner resistances). This study focuses on self-control processes through which high work load increases job strain, thus having a debilitating effect on the employee. It is one of only a few investigations into these mechanisms. In line with theoretical notions of Hacker's (2005) Action Regulation Theory and empirical findings on self-control, it was assumed that demands on self-control mediate the adverse impact of high work load on indicators of job strain. Furthermore, since increased work load and self-control demands elicit similar control processes drawing on the same limited regulatory resources, both stressors were also expected to interact in the prediction of high strain at work. Using data from 574 employees of a large administrative organization in Germany, Structural Equation Modelling revealed that overcoming inner resistance partly functioned as a mediator in the prediction of job strain by qualitative work load. In addition, significant interaction effects between qualitative work load and impulse control as well as between both of the work load variables and resisting distractions were found. Emotional exhaustion as a job-related dimension of psychological well-being, and anxiety representing a general aspect of well-being, were considered as indicators of job strain.
Development of cortical asymmetry in typically developing children and its disruption in attention-deficit/hyperactivity disorder.

CONTEXT Just as typical development of anatomical asymmetries in the human brain has been linked with normal lateralization of motor and cognitive functions, disruption of asymmetry has been implicated in the pathogenesis of neurodevelopmental disorders such as attention-deficit/hyperactivity disorder (ADHD). No study has examined the development of cortical asymmetry using longitudinal neuroanatomical data. OBJECTIVE To delineate the development of cortical asymmetry in children with and without ADHD. DESIGN Longitudinal study. SETTING Government Clinical Research Institute. PARTICIPANTS A total of 218 children with ADHD and 358 typically developing children, from whom 1133 neuroanatomical magnetic resonance images were acquired prospectively. MAIN OUTCOME MEASURES Cortical thickness was estimated at 40 962 homologous points in the left and right hemispheres, and the trajectory of change in asymmetry was defined using mixed-model regression. RESULTS In right-handed typically developing individuals, a mean (SE) increase in the relative thickness of the right orbitofrontal and inferior frontal cortex with age of 0.011 (0.0018) mm per year (t(337) = 6.2, P < . 001) was balanced against a relative left-hemispheric increase in the occipital cortical regions of 0.013 (0.0015) mm per year (t(337) = 8.1, P < . 001). Age-related change in asymmetry in non-right-handed typically developing individuals was less extensive and was localized to different cortical regions. In ADHD, the posterior component of this evolving asymmetry was intact, but the prefrontal component was lost. CONCLUSIONS These findings explain the way that, in typical development, the increased dimensions of the right frontal and left occipital cortical regions emerge in adulthood from the reversed pattern of childhood cortical asymmetries. Loss of the prefrontal component of this evolving asymmetry in ADHD is compatible with disruption of prefrontal function in the disorder and demonstrates the way that disruption of typical processes of asymmetry can inform our understanding of neurodevelopmental disorders.
Knowledge-based approach for functional MRI analysis by SOM neural network using prior labels from Talairach stereotaxic space

Among the methods proposed for the analysis of functional MR we have previously introduced a model-independent analysis based on the self-organizing map (SOM) neural network technique. The SOM neural network can be trained to identify the temporal patterns in voxel time-series of individual functional MRI (fMRI) experiments. The separated classes consist of activation, deactivation and baseline patterns corresponding to the task-paradigm. While the classification capability of the SOM is not only based on the distinctness of the patterns themselves but also on their frequency of occurrence in the training set, a weighting or selection of voxels of interest should be considered prior to the training of the neural network to improve pattern learning. Weighting of interesting voxels by means of autocorrelation or F-test significance levels has been used successfully, but still a large number of baseline voxels is included in the training. The purpose of this approach is to avoid the inclusion of these voxels by using three different levels of segmentation and mapping from Talairach space: (1) voxel partitions at the lobe level, (2) voxel partitions at the gyrus level and (3) voxel partitions at the cell level (Brodmann areas). The results of the SOM classification based on these mapping levels in comparison to training with all brain voxels are presented in this paper.
A High Performance Computing Framework for Data Mining

Mining large data sets is no longer the prerogative of computer scientists - specialists in a wide variety of domains are performing analytics as a day-to-day activity. Often such analyses are specific to the domain and analysts are required to devise new algorithms or techniques. For such scenarios, providing a high-level programming environment that delivers high performance on clusters is a challenge. We propose a framework that supports high-level programming using domain abstractions in data mining while delivering scalable performance on commodity clusters i.e. clusters of multi-core workstations. This framework includes a domain specific programming language, DWARF, to enable data mining specialists to rapidly prototype algorithms. DWARF is supported by a compiler that automatically parallelizes code by identifying domain specific patterns and translating them to parallel code that exploits data parallelism and task parallelism. The compiler generates code for a hybrid virtual machine supporting distributed memory model at the top level and shared memory model nested within. The code generated by the compiler can be scheduled on commodity clusters. We compare the proposed framework with other frameworks commonly used for data mining on distributed platforms.
On the ( Ir ) relevance of Psycholinguistics for Anaphora Resolution

Psycholinguistic experiments show that pronouns tend to be resolved differently depending on whether they occur in main or subordinate clauses. If a pronoun in a subordinate clause has more than one potential antecedent in the main clause, then the pronoun tends to refer to the antecedent which has a certain thematic role (depending on the verb and on the subordinating conjunction). In contrast, pronouns in main clauses tend to refer back to the subject of the previous main clause, and this tendency is not affected by any verbs or conjunctions. In natural language processing, these findings have recently led to a proposal that pronoun resolution systems should have a split architecture, i.e. that they should use different mechanisms for pronoun resolution in the two cases. With the help of two parsed and coreference-annotated corpora, this paper estimates the impact of the split-architecture proposal. The findings of this work are as follows: (1) Subject pronouns in authentic texts behave the same way in main and subordinate clauses. (2) The number of sentences in which a split architecture would behave differently than a system that treats both cases the same way is close to zero. Therefore, a separate treatment of resolution within and across units is unlikely to improve the performance of any system. This result casts a doubt on the split-architecture proposal, and more generally on approaches that directly incorporate psycholinguistic results into performance-oriented algorithms for anaphora resolution without assessing the relative importance of the phenomena that underlie them.
Predicting the likelihood of an isocitrate dehydrogenase 1 or 2 mutation in diagnoses of infiltrative glioma.

BACKGROUND Several variables are associated with the likelihood of isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation in gliomas, though no guidelines yet exist for when testing is warranted, especially when an R132H IDH1 immunostain is negative. METHODS A cohort of 89 patients was used to build IDH1/2 mutation prediction models in World Health Organization grades II-IV gliomas, and an external cohort of 100 patients was used for validation. Logistic regression and backward model selection with the Akaike information criterion were used to develop prediction models. RESULTS A multivariable model, incorporating patient age, glioblastoma multiforme diagnosis, and prior history of grade II or III glioma, was developed to predict IDH1/2 mutation probability. This model generated an area under the curve (AUC) of 0.934 (95% CI: 0.878, 0.978) in the external validation cohort and 0.941 (95% CI: 0.918, 0.962) in the cohort of The Cancer Genome Atlas. When R132H IDH1 immunostain information was added, AUC increased to 0.986 (95% CI: 0.967, 0.998). This model had an AUC of 0.947 (95% CI: 0.891, 0.995) in predicting whether an R132H IDH1 immunonegative case harbored a less common IDH1 or IDH2 mutation. The models were also 94% accurate in predicting IDH1/2 mutation status in gliomas from The Cancer Genome Atlas. An interactive web-based application for calculating the probability of an IDH1/2 mutation is now available using these models. CONCLUSIONS We have integrated multiple variables to generate a probability of an IDH1/2 mutation. The associated web-based application can help triage diffuse gliomas that would benefit from mutation testing in both clinical and research settings.