Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-trial ERPs elicited by visual stimuli at two contrast levels: Analysis of ongoing EEG and latency/amplitude jitters

To analyze the trial-to-trial variability in brain dynamics in response to visual stimuli at high- and low-contrast levels, three factors (i.e. ongoing EEG, latency jitter and amplitude jitter of ERP components) were analyzed in this preliminary study. Eight subjects were recruited to perform a visual discriminate task when electrical activity was recorded. Results derived from PO4 showed that: 1) P1 and N1 latency deviated from normal distribution under either stimulus condition; 2) the peak latency of P1 and N1 was shortened distinctly in response to high-contrast stimulus; 3) high-contrast stimulus consistently elicited larger P1-N1 amplitude, which implied the relative amplitude was likely a more reliable measurement of visual stimulus intensity.
Gene duplication and the evolution of ribosomal protein gene regulation in yeast

Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in Saccharomyces cerevisiae, but the cis and trans factors associated with them are surprisingly diverged across Ascomycota fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them. Here, we address this question in the context of the evolution of the regulation of RP gene expression by using a comparative genomics approach together with cross-species functional assays. We show that an activator (Ifh1) and a repressor (Crf1) that control RP gene regulation in normal and stress conditions in S. cerevisiae are derived from the duplication and subsequent specialization of a single ancestral protein. We provide evidence that this regulatory innovation coincides with the duplication of RP genes in a whole-genome duplication (WGD) event and may have been important for tighter control of higher levels of RP transcripts. We find that subsequent loss of the derived repressor led to the loss of a stress-dependent repression of RPs in the fungal pathogen Candida glabrata. Our comparative computational and experimental approach shows how gene duplication can constrain and drive regulatory evolution and provides a general strategy for reconstructing the evolutionary trajectory of gene regulation across species.
Draft Genome Sequence of the Deep-Sea Basidiomycetous Yeast Cryptococcus sp. Strain Mo29 Reveals Its Biotechnological Potential

ABSTRACT Cryptococcus sp. strain Mo29 was isolated from the Rainbow hydrothermal site on the Mid-Atlantic Ridge. Here, we present the draft genome sequence of this basidiomycetous yeast strain, which has highlighted its biotechnological potential as revealed by the presence of genes involved in the synthesis of secondary metabolites and biotechnologically important enzymes.
Memory Consolidation and the Hippocampal Complex

The hippocampal complex, is widely accepted as the structure supporting the acquisition of declarative memories. Another less unanimously shared position is that the same structures, which are necessary for the acquisition of declarative memories, are involved in the maintenance of them in the period after the initial learning occurred. Evidence from amnesic patients that suffered damage to the hippocampal complex suggests, that the retrievability of memories acquired prior to the trauma causing amnesia is similarly affected as the capability to form new memories. As remote memories are frequently found preserved, a process of consolidation is assumed, which makes declarative memories gain independence from the hippocampal complex with time. Two theories currently are in the centre of the debate about consolidation. The “Standard Model of Memory Consolidation” (SM) assumes the temporally-limited dependency of all kinds of declarative memories on the hippocampal complex until the consolidation process is complete. The “Multiple Trace Model” (MTT), on the other hand, assumes a similar process of consolidation for semantic memories, but the lifelong dependency of episodic memories on the hippocampal complex. The aim of this paper is to reflect the consolidation debate and to evaluate the capability of the theories to explain the available evidence from amnesic patient studies. In the end of this paper two conclusions will be drawn from the patterns of anterograde and retrograde memory impairment. Firstly, the impairment of remote episodic memories can extend at least over 4 decades, which is indicating an extremely long-lasting consolidation process. Secondly, the complexity of a memory trace and the frequency of re-activation are factors determining the time course of consolidation, leading to differences in the extents of impairment between semantic and episodic memories. Both theories are exhibiting shortcomings in their capability to explain these patterns. The SM is assuming a consolidation period of a few years, and is, in its original version, not able to account for a difference in the extents of the retrograde impairment between semantic and episodic memories. However, it can be reconciled with the data by the integration of quantitative differences in complexity and re-activation frequency between semantic and episodic memories, and by abandoning the interpretation of consolidation as a mechanism of adaptation lasting a few years. The MTT, on the other hand, is assuming the dependency of episodic memories on the hippocampal complex, as long as they exist. Though there are several studies indicating a susceptibility of remote episodic memories to damage in this region, a lifelong dependency of episodic memories could not be established reliably. However, there are uncertainties about the quality of remote episodic memories in normal subjects, and future studies might show that memories exhibiting a rich and multifaceted episodic quality are dependent on the hippocampal complex, as the MTT claims. Christian Mühl Memory Consolidation 4
Dynamic programming algorithm for stereo correspondence of contour

Stereo correspondence is one of the most promising research areas in stereo vision. In order to solve the problem that there are large areas of similar gray-scale region and the time-consuming of the dense reconstruction, the contour of stereo pairs was extracted to reconstruct the scene. To reduce the noise which may lead to incorrect results during the stereo matching, a stereo matching algorithm based on the dynamic programming is proposed in the paper. Based on the reasonable and commonly assumption that the disparity of the scene is always smooth, the stereo matching algorithm puts a restraint on the disparity map and applies the dynamic algorithm on the disparity space image (DSI) to obtain the optimal disparity of the contour. Since the sum of points needed to be computed is greatly reduced, the algorithm could implement the stereo correspondence with high speed and matching rate than dense reconstruction could.
Give me a reason to dig Minecraft and psychology of motivation

Recently both game industry professionals and academic researchers have started focusing on player-generated behavioral data as a mean to gather insights on player psychology through datamining. Although some research has already proven solid correlations between in-game behavior and personality, most techniques focus on extracting knowledge from in-game behavior data alone. This paper posits that triangulating exclusively behavioral datasets with established theoretical frameworks serving as hermeneutic grids, may help extracting additional meaning and information. The hermeneutic grid selected for this study is the Reiss Motivation Profiler and it is applied to behavioral data gathered from Minecraft players.
Temporally Nonadjacent Nonlinguistic Sounds Affect Speech Categorization

Speech perception is an ecologically important example of the highly context-dependent nature of perception; adjacent speech, and even nonspeech, sounds influence how listeners categorize speech. Some theories emphasize linguistic or articulation-based processes in speech-elicited context effects and peripheral (cochlear) auditory perceptual interactions in non-speech-elicited context effects. The present studies challenge this division. Results of three experiments indicate that acoustic histories composed of sine-wave tones drawn from spectral distributions with different mean frequencies robustly affect speech categorization. These context effects were observed even when the acoustic context temporally adjacent to the speech stimulus was held constant and when more than a second of silence or multiple intervening sounds separated the nonlinguistic acoustic context and speech targets. These experiments indicate that speech categorization is sensitive to statistical distributions of spectral information, even if the distributions are composed of nonlinguistic elements. Acoustic context need be neither linguistic nor local to influence speech perception.
The Activity-Regulated Cytoskeletal-Associated Protein (Arc/Arg3.1) Is Required for Memory Consolidation of Pavlovian Fear Conditioning in the Lateral Amygdala

The activity-regulated cytoskeletal-associated protein (Arc/Arg3.1) is an immediate early gene that has been widely implicated in hippocampal-dependent learning and memory and is believed to play an integral role in synapse-specific plasticity. Here, we examined the role of Arc/Arg3.1 in amygdala-dependent Pavlovian fear conditioning. We first examined the regulation of Arc/Arg3.1 mRNA and protein after fear conditioning and LTP-inducing stimulation of thalamic inputs to the lateral amygdala (LA). Quantitative real-time PCR, in situ hybridization, Western blotting and immunohistochemistry revealed a significant upregulation of Arc/Arg3.1 mRNA and protein in the LA relative to controls. In behavioral experiments, intra-LA infusion of an Arc/Arg3.1 antisense oligodeoxynucleotide (ODN) was observed to be anatomically restricted to the LA, taken up by LA cells, and to promote significant knockdown of Arc/Arg3.1 protein. Rats given intra-LA infusions of multiple doses of the Arc/Arg3.1 ODN showed an impairment of LTM (tested ∼24 later), but no deficit in STM (tested 3 h later) relative to controls infused with scrambled ODN. Finally, to determine whether upregulation of Arc/Arg3.1 occurs downstream of ERK/MAPK activation, we examined Arc/Arg3.1 expression in rats given intra-LA infusion of the MEK inhibitor U0126. Relative to vehicle controls, infusion of U0126 impaired training-induced increases in Arc/Arg3.1 expression. These findings suggest that Arc/Arg3.1 expression in the amygdala is required for fear memory consolidation, and further suggest that Arc/Arg3.1 regulation in the LA is downstream of the ERK/MAPK signaling pathway.
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers

UNLABELLED Aptamers are 'synthetic antibodies' that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict the BIND: ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis. AVAILABILITY AND IMPLEMENTATION MPBind software and documents are available at http://www.morgridge. net/MPBind.html. The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge. net/Aptamer/.
Mechanisms Underlying Plk1 Polo-Box Domain-Mediated Biological Processes and Their Physiological Significance

Mammalian polo-like kinase 1 (Plk1) has been studied intensively as a key regulator of various cell cycle events that are critical for proper M-phase progression. The polo-box domain (PBD) present in Plk1’s C-terminal non-catalytic region has been shown to play a central role in targeting the N-terminal kinase domain of Plk1 to specific subcellular locations. Subsequent studies reveal that PBD binds to a phosphorylated motif generated by one of the two mechanisms - self-priming by Plk1 itself or non-self-priming by a Pro-directed kinase, such as Cdc2. Here, we comparatively review the differences in the biochemical steps of these mechanisms and discuss their physiological significance. Considering the diverse functions of Plk1 during the cell cycle, a better understanding of how the catalytic activity of Plk1 functions in concert with its cis-acting PBD and how this coordinated process is intricately regulated to promote Plk1 functions will be important for providing new insights into different mechanisms underlying various Plk1-mediated biological events that occur at the multiple stages of the cell cycle.
Textual representations for corpus-based bilingual retrieval

The traditional approach to information retrieval is based on using words as the indexing and search terms for documents. However, word-based representations have difficulty addressing morphological processes that confound retrieval, such as inflection, derivation, and compounding. One part of this research investigates alternative methods for representing text, including a method based on overlapping sequences of characters called n-gram tokenization. N-grams are studied in depth and one notable finding is that they achieve a 20% improvement in retrieval effectiveness over words in certain situations. The other focus of this research is improving retrieval performance when foreign language documents must be searched and translation is required. In this scenario bilingual dictionaries are often used to translate user queries; however even among the most commonly spoken languages, for which large bilingual lexicons exist, dictionary-based translation suffers from several significant problems. These include: difficulty handling proper names, which are often missing; issues related to morphological variation since entries, or query terms, may not be lemmatized; and, an inability to robustly handle multiword phrases, especially non-compositional expressions. These problems can be addressed when translation is accomplished using parallel collections, sets of documents available in more than one language. Using parallel texts enables statistical translation of character n-grams rather than words or stemmed words, and with this technique highly effective bilingual retrieval performance is obtained. In this dissertation I present an overview of the field of cross-language information retrieval and then introduce the foundational concepts in n-gram tokenization and corpus-based translation. Then monolingual and bilingual experiments on test sets in 13 languages are described. Analysis of these experiments gives insight into: the relative efficacy of various tokenization methods; reasons for the effectiveness of n-grams; the utility of automated relevance feedback, in both monolingual and bilingual contexts; the interplay between tokenization and translation; and, how translation resource selection and size influence bilingual retrieval.
Software Quality model Analysis Program

It is vital that data is obtained so that actions can be taken to improve the performance. Such improvement can be measured in terms of improved quality, increased customer satisfaction and decreased cost of quality. Different researchers have proposed software quality models to help measure the quality of software products. These models often include metrics for this purpose. Some of the classical and recent models are discussed and analyzed in this paper showing the points of strength and weakness of each model type. A new comprehensive model is proposed and analyzed. A complete solution is discussed through the paper to enable an effective and efficient use of the proposed model to help the development team in prioritizing the important metrics while developing the software products according to some inputs from the user and the objectives of the software being developed. The solution developed is called the quality model analysis program (QAP) and is a fuzzy system that weights the proposed model attributes according to certain rules. The solution enables software project managers to better utilize their resources and take specific actions to better improve the quality of the software produced.
Magnetic resonance imaging of hippocampal subfields in posttraumatic stress disorder.

CONTEXT Most neuroimaging studies of posttraumatic stress disorder (PTSD) have focused on potential abnormalities in the whole hippocampus, but the subfields of this structure, which have distinctive histological characteristics and specialized functions, have not been investigated. Studies of individual subfields may clarify the role of the hippocampus in PTSD. OBJECTIVE To determine if PTSD is associated with structural alterations in specific subfields of the hippocampus. DESIGN Case-control study. PARTICIPANTS A total of 17 male veterans with combat trauma and PTSD (mean [SD] age, 41 [12] years) and 19 age-matched male veterans without PTSD who were recruited from the outpatient mental health clinic of the San Francisco Veterans Affairs Medical Center and by advertising in the community. INTERVENTIONS High-resolution magnetic resonance imaging at 4 T. MAIN OUTCOME MEASURE Volumes of hippocampal subfields. RESULTS Posttraumatic stress disorder was associated with 11.4% (1.5%) (P = .02) smaller mean (SD) cornu ammonis 3 (CA3)/dentate gyrus subfield volumes, irrespective of age-related alterations, whereas other subfields were spared. Age was associated with reduced volume of the CA1 subfield (P = .03). Total hippocampal volume was also reduced in PTSD by a mean (SD) of 6.5% (0.6%) but, related to both PTSD (P = .05) and age (P = .01), was consistent with the measurements in the subfields. CONCLUSIONS The findings indicate for the first time in humans that PTSD is associated with selective volume loss of the CA3/dentate gyrus subfields, consistent with animal studies, implying that chronic stress suppresses neurogenesis and dendritic branching in these structures.
MRPC: A high performance RPC system for MPMD parallel computing

MRPC is an RPC system that is designed and optimized for MPMD parallel computing. Existing systems based on standard RPC incur an unnecessarily high cost when used on high‐performance multi‐computers, limiting the appeal of RPC‐based languages in the parallel computing community. MRPC combines the efficient control and data transfer provided by Active Messages (AM) with a minimal multithreaded runtime system that extends AM with the features required to support MPMD. This approach introduces only the necessary RPC overheads for an MPMD environment. MRPC has been integrated into Compositional C++ (CC++), a parallel extension of C++ that offers an MPMD programming model. Basic performance in MRPC is within a factor of two from those of Split‐C, a highly tuned SPMD language, and other messaging layers. CC++ applications perform within a factor of two to six from comparable Split‐C versions, which represent an order of magnitude improvement over previous CC++ implementations. Copyright © 1999 John Wiley & Sons, Ltd.
European Conference on Information Systems ( ECIS ) 5-15-2012 EXPLORING THE SHADOWS : IT GOVERNANCE APPROACHES TO USER-DRIVEN INNOVATION

Information Systems (IS) researchers traditionally have the assumption that Information Technology (IT) innovations are conceived within the IT department. Developments like ubiquitous computing, web services and the emerging culture of digital natives (DN) challenge this foundational assumption as they enable individuals to implement their own IT innovations quickly. Placing such empowered individuals into a strictly regulated IT environment will drive them away from the IT department and towards their own IT solutions and inevitably to non-compliance. Such useror business-driven solutions are not necessarily the result of strict policies or limited user rights but may be caused by the inability of the IT department to fulfil business needs. The phenomenon of user-driven fulfilment of requirements is called Shadow IT (SIT). While receiving very limited scholarly attention, SIT is a widespread challenge amongst IT departments. We employ a triangulation approach using three independent data sources to address this phenomenon within the three domains of IS research, IS Security (ISsec), IT Governance (ITG) and Business IT Alignment (BITA). Our findings suggest that practitioners follow three different ITG approaches to SIT based on their business or IT strategy: IT-control, user-oriented and user-driven.
SHAPE directed RNA folding

Summary Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the viennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. Availability and implementation The capability for SHAPE directed RNA folding is part of the upcoming release of the viennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi. univie.ac. at/RNA. Contact michael.wolfinger@univie.ac. at Supplementary information Supplementary data is attached.
Enabling the discovery of computational characteristics of enzyme dynamics

Biology demonstrates powerful information processing capabilities. Of particular interest are enzymes, which process information in highly complex dynamic environments. Exploring the information processing characteristics of an enzyme by selectively altering its environment may lead to the discovery of new modes of computation. The physical experiments required to perform such exploration are combinatorial in nature. Thus resource consumption, both time and money, poses major limiting factors on any exploratory work. New tools are required to mitigate these factors. One such tool is lab-on-chip based autonomous experimentation system, where a microfluidic experimentation platform is driven by machine learning algorithms. The lab-on-chip approach provides an automated platform that can perform complex protocols, which is also capable of reducing the resource cost of experimentation. The machine learning algorithms provide intelligent experiment selection that reduces the number of experiments required for discovery. Here we discuss development of the experimentation platform and machine learning software that will lead to fully autonomous characterisation of enzymes.