Miracle-dz/UniFAR-FTUs huggingface dataset:
Pantothenate kinase-associated neurodegeneration: altered mitochondria membrane potential and defective respiration in Pank2 knock-out mouse model

Neurodegeneration with brain iron accumulation (NBIA) comprises a group of neurodegenerative disorders characterized by high brain content of iron and presence of axonal spheroids. Mutations in the PANK2 gene, which encodes pantothenate kinase 2, underlie an autosomal recessive inborn error of coenzyme A metabolism, called pantothenate kinase-associated neurodegeneration (PKAN). PKAN is characterized by dystonia, dysarthria, rigidity and pigmentary retinal degeneration. The pathogenesis of this disorder is poorly understood and, although PANK2 is a mitochondrial protein, perturbations in mitochondrial bioenergetics have not been reported. A knock-out (KO) mouse model of PKAN exhibits retinal degeneration and azoospermia, but lacks any neurological phenotype. The absence of a clinical phenotype has partially been explained by the different cellular localization of the human and murine PANK2 proteins. Here we demonstrate that the mouse Pank2 protein localizes to mitochondria, similar to its human orthologue. Moreover, we show that Pank2-defective neurons derived from KO mice have an altered mitochondrial membrane potential, a defect further corroborated by the observations of swollen mitochondria at the ultra-structural level and by the presence of defective respiration.
Enhancing the Serviceability and the Availability of IMS-Based Multimedia Services: Avoiding Core Service Failures

The delivery of a highly available and robust service offering is one of the critical objectives of service providers. Reaching this objective depends on the level of control service providers have on underlying transport infrastructure. Despite current deployment of IMS-based architectures assumes a vertical integration, IMS-based services can be offered without having a control on the underlying IP network. This paper introduces a solution to enhance the robustness of IMS-based architectures without assuming a vertically integrated system. The paper focuses on failures experienced by core service nodes and describes an autonomic solution to allow customers to access to the service during failures. This paper introduces a novel entity called SBC_PROXY which relays messages from peer SBCs (session border controller) to core service platform. An autonomous mode in which all SBCs are involved in the lookup and routing processes is also described. This paper does not make any assumption on the nature of the service which is offered through IMS. Nevertheless, a focus is put on session-based services such as audio/video telephony.
Plasmid-Encoded Diacetyl (Acetoin) Reductase in Leuconostoc pseudomesenteroides

ABSTRACT A plasmid-borne diacetyl (acetoin) reductase (butA) from Leuconostoc pseudomesenteroides CHCC2114 was sequenced and cloned. Nucleotide sequence analysis revealed an open reading frame encoding a protein of 257 amino acids which had high identity at the amino acid level to diacetyl (acetoin) reductases reported previously. Downstream of the butA gene of L. pseudomesenteroides, but coding in the opposite orientation, a putative DNA recombinase was identified. A two-step PCR approach was used to construct FPR02, a butA mutant of the wild-type strain, CHCC2114. FPR02 had significantly reduced diacetyl (acetoin) reductase activity with NADH as coenzyme, but not with NADPH as coenzyme, suggesting the presence of another diacetyl (acetoin)-reducing activity in L. pseudomesenteroides. Plasmid-curing experiments demonstrated that the butA gene is carried on a 20-kb plasmid in L. pseudomesenteroides.
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

In many cases of protein structure determination by NMR a high‐quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of α‐helical and β‐sheet proteins using homology models and/or X‐ray structures. The program produced no erroneus stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good‐quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root‐mean‐square‐deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 791–797, 2006
An exploration of illness representations in older age

The Common Sense Model of illness representations (CSMIR) (Leventhal et al., 1994) has been extensively investigated in relation to chronic health conditions in the general population. However the literature on the role of illness representations in older age has not been investigated to the same extent despite the high prevalence of health conditions in older people. The present study aimedto examine what has been studied to date in relation to illness representations and older people living with health conditions in this population. A systematic review of three databases (PsycINFO, MEDLINE and CINAHL plus with Full Text) was conducted in February 2013. Inclusion and exclusion criteria were applied and ten studies were identified. The findings of the studies were analysed using qualitative methods. Three main themes were identified in the literature: ‘associations between the constructs of the CSMIR’, ‘coping and health outcomes’ and ‘variables associated with illness representations’. The findings revealed a number of areas that may be of clinical importance and provide some support for the clinical relevance of Leventhal’s model of illness representations in relation to this population, defined by the relationship of the model with clinical outcomes. However the literature is limited and further research is required to examine the role of the model in clinical settings and multidisciplinary health interventions.
An Orientation-Adaptive Extension to Scale-Adaptive Local Binary Patterns

Methods based on Local Binary Patterns have been used successfully in a wide range of texture classification tasks. A restriction shared by all methods based on Local Binary Patterns is the high sensitivity to signal scale. In recent work we presented a general framework for scale-adaptive computation of Local Binary Patterns, improving the accuracy in texture classification scenarios involving varying texture-scales highly. In this work, the scale-adaptive methodology is extended by an orientation-adaptive computation of patterns, leading to a scale- and rotation invariant classification. The results suggest that estimating a global orientation to build orientation-adaptive LBPs is superior to the previously introduced rotation-invariant encodings. The proposed framework allows the use of the highly-discriminative LBPs in less-constrained situations, where both orientation, as well as scale variations, are to be expected.
Regularly visited patches in human mobility

In this paper, we propose a new analytic unit for human mobility analysis -- the patch. We developed a process to identify Regularly Visited Patches (RVP) and a set of metrics to characterize and measure their spatial patterns. Using a large dataset of Foursquare check-ins as a test bed, we show that RVP analysis reveals fundamental patterns of human mobility and will lead to promising research with strong implications for businesses.
Aryl Hydrocarbon Receptor–Dependent Stanniocalcin 2 Induction by Cinnabarinic Acid Provides Cytoprotection against Endoplasmic Reticulum and Oxidative Stress

The aryl hydrocarbon receptor (AhR) is a cytosolic ligand-activated transcription factor historically known for its role in xenobiotic metabolism. Although AhR activity has previously been shown to play a cytoprotective role against intrinsic apoptotic stimuli, the underlying mechanism by which AhR confers cytoprotection against apoptosis is largely unknown. Here, we demonstrate that activation of AhR by the tryptophan catabolite cinnabarinic acid (CA) directly upregulates expression of stanniocalcin 2 (Stc2) to elicit cytoprotection against apoptosis induced by endoplasmic reticulum stress and oxidative stress. Chromatin immunoprecipitation studies demonstrated that CA treatment induces direct AhR binding to a region of the Stc2 promoter containing multiple xenobiotic response elements. Using isolated primary hepatocytes from AhR wild-type (AhR floxed) and liver-specific AhR conditional knockout mice, we showed that pretreatment with CA conferred cytoprotection against hydrogen peroxide (H2O2)-, thapsigargin-, and ethanol-induced apoptosis in an AhR-dependent manner. Furthermore, suppressing Stc2 expression using RNA interference confirmed that the cytoprotective properties of CA against H2O2, thapsigargin, and ethanol injury were absolutely dependent on Stc2. Immunochemistry revealed the presence of Stc2 in the endoplasmic reticulum and on the cell surface, consistent with Stc2 secretion and autocrine and/or paracrine signaling. Finally, in vivo data using a mouse model of acute alcohol hepatotoxicity demonstrated that CA provided cytoprotection against ethanol-induced apoptosis, hepatic microvesicular steatosis, and liver injury. Collectively, our data uncovered a novel mechanism for AhR-mediated cytoprotection in the liver that is dependent on CA-induced Stc2 activity.
Small-world network organization of functional connectivity of EEG gamma oscillation during emotion-related processing

In this study we investigated whether functional brain networks are variously organized during different emotional processing. Electroencephalography (EEG) activities were recorded in 27 healthy subjects when they performed a spatial search task for facial expressions. Correlations between all possible pairs of electrodes placed over the scalp were determined by coherence and the coherence matrices were calculated within gamma frequency bands, i.e. low gamma for 30-50Hz and high gamma for 50-80Hz, respectively. Graph theoretical analysis was applied to these matrices using two measures: the clustering coefficient and the characteristic path length. We found the network organization of the EEG gamma oscillation during emotion processing showed characteristic of small-world networks; this type of organization is slightly but significantly more evident during negative emotional processing. We concluded that negative emotion processing showed more effective and optimal network organization for information processing than positive.
Screen of MicroRNA Targets in Zebrafish Using Heterogeneous Data Sources: A Case Study for Dre-miR-10 and Dre-miR-196

It has been established that microRNAs (miRNAs) play an important role in gene expression by post-transcriptional regulation of messengerRNAs (mRNAs). However, the precise relationships between microRNAs and their target genes in sense of numbers, types and biological relevance remain largely unclear. Dissecting the miRNA-target relationships will render more insights for miRNA targets identification and validation therefore promote the understanding of miRNA function. In miRBase, miRanda is the key algorithm used for target prediction for Zebrafish. This algorithm is high-throughput but brings lots of false positives (noise). Since validation of a large scale of targets through laboratory experiments is very time consuming, several computational methods for miRNA targets validation should be developed. In this paper, we present an integrative method to investigate several aspects of the relationships between miRNAs and their targets with the final purpose of extracting high confident targets from miRanda predicted targets pool. This is achieved by using the techniques ranging from statistical tests to clustering and association rules. Our research focuses on Zebrafish. It was found that validated targets do not necessarily associate with the highest sequence matching. Besides, for some miRNA families, the frequency of their predicted targets is significantly higher in the genomic region nearby their own physical location. Finally, in a case study of dre-miR-10 and dre-miR-196, it was found that the predicted target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar characteristics as validated target genes and therefore represent high confidence target candidates. Keywords—MicroRNA targets validation, microRNA-target relationships, dre-miR-10, dre-miR-196.
Viewpoints and flashpoints in the study of video game violence and aggression

Researchers from different backgrounds have approached the topic of violent video games and aggression with varying assumptions, methods, and goals. Researchers from an experimental psychology orientation seek to test theories under controlled conditions, and assume that all children are at risk of harm from acting out violence during gameplay. They champion policies to reduce youth exposure to violent game content. Researchers from applied fields such as public health, clinical psychology and criminology assume that video game effects (negative or positive) will vary by child, circumstance and content, and seek to identify high-risk patterns via studies in real-world settings. These different lenses illuminate ongoing disagreements about the relationship, if any, between violent video games and harmful aggressive behaviors. Some disagreements could be mitigated through greater clarity in definitions and methods. For example, confusion arises when researchers fail to clearly define “aggression”; treat aggressive thoughts, feelings, and behaviors as part of a continuum; or view aggression as equivalent to harmful intent or violence. Studies suggest that media violence researchers, like all humans, tend to disproportionately seek out and value evidence that supports their point of view. Actively searching for common ground, and welcoming new researchers from a variety of disciplines, may help move the field forward.
PENGARUH DISIPLIN KERJA DAN MOTIVASI KERJA TERHADAP KINERJA KARYAWAN

Abstract : Human resources is one of the key actors in the success of a company. Where the good management of tablespoons can improve the quality of a company. However, the quality obtained often vary it due to the factor of labor discipline and motivation of each individual is different. This study used quantitative research. Where labor discipline and motivation to work as an independent variable and the performance of the employee as the dependent variable. The technique of sampling using the Proportionate stratified random sampling with a sample of 67 full-time employees executing. The analytical method used is multiple linear regression analysis with SPSS software version 18.0. The results showed that 1) working Discipline significant positive effect on employee performance 2) work motivation and a significant positive effect on employee performance 3) work discipline and motivation to work simultaneously affect the performance of employees. Keywords: work discipline, work motivation and employee performance.
Nine cytological segregates in the Simulium damnosum complex (Diptera: Simuliidae).

A preliminary examination of salivary gland chromosomes of Simulium damnosum sent from Uganda revealed 4 distinct cytological categories. Because of the relative closeness of the 3 localities from which the material came and the sympatry of 2 of the forms it was considered in a previous paper a that these categories represent sibling species, and that S. damnosum is a sibling species complex. Reported here are the results of a more detailed reexamination of the material on which the previous paper was based, and a similar examination of about two-thirds of the material received by the present author since 1964. Nine categories are recognized so far; the original 4 (with 2 minor name changes)-namely, Sebwe (formerly Sebwe B), Sanje (formerly Sebwe A), Nile, and Kagera-and additionally, Bandama, Nkusi, Ketaketa, Kulfo, and Kibwezi. It should be recognized that these are not legitimate species names but convenient designations lifted from accompanying collection labels.
Domain Adaptation from User-level Facebook Models to County-level Twitter Predictions

Several studies have demonstrated how language models of user attributes, such as personality, can be built by using the Facebook language of social media users in conjunction with their responses to psychology questionnaires. It is challenging to apply these models to make general predictions about attributes of communities, such as personality distributions across US counties, because it requires 1. the potentially inavailability of the original training data because of privacy and ethical regulations, 2. adapting Facebook language models to Twitter language without retraining the model, and 3. adapting from users to county-level collections of tweets. We propose a two-step algorithm, Target Side Domain Adaptation (TSDA) for such domain adaptation when no labeled Twitter/county data is available. TSDA corrects for the different word distributions between Facebook and Twitter and for the varying word distributions across counties by adjusting target side word frequencies; no changes to the trained model are made. In the case of predicting the Big Five county-level personality traits, TSDA outperforms a state-of-the-art domain adaptation method, gives county-level predictions that have fewer extreme outliers, higher year-to-year stability, and higher correlation with county-level outcomes.
Reliability constrained unit commitment with electric vehicle to grid using Hybrid Particle Swarm Optimization and Ant Colony Optimization

Vehicle-to-grid (V2G) technology as a new generation of Energy Storage Units (ESUs) is receiving an increasing research attention. Because of the capability of reducing dependencies on small expensive units and optimizing the fluctuation of load curve, they can play an important role in power system. This paper proposes a novel approach for considering Gridable Vehicles (GVs) of V2G in a short-term unit commitment problem. Inclusion of V2G in the problem could result some reliability challenges. Some contributed reliability indices are taken into account in order to maintain the reliability in an acceptable level. The unit commitment problem is solved by a Hybrid Particle Swarm Optimization and Ant Colony Optimization. The results show that the total operation cost of the system increases as the allowed reliability limits decrease. The efficiency of the proposed method in near-optimal unit commitment solution can also be concluded.
Timing detection for realtime dialog systems using prosodic and linguistic information

If a dialog system can respond to the user as reasonable as a human, the interaction will become smoother. Timing of response such as backchannels and turn-taking plays important role in such a smooth dialog as in human-human interaction. We are now developing a dialog system which can generate response timing in real time. In this paper, we introduce a response timing generator for such a dialog system. First, we analyzed conversations between two persons and extracted prosodic and linguistic information which had effects on the timing. Then we constructed a decision tree to detect the timing based on the features coming from the information and examined the decision rules. We also applied the decision tree to a timing generator. The timing generator decides the action of the system at every 100ms in user’s pause. We evaluated the timing generator by subjective and objective evaluation.
Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors

The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal carcinoids. In contrast to the relatively conserved karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. In SCLC tumors, as well as bronchial carcinoids and carcinoids of gastrointestinal origin, recurrent CN alterations were observed in 203 genes, including the RB1 gene and 59 microRNAs of which 51 locate in the DLK1-DIO3 domain. These findings suggest the existence of partially shared CN alterations in these tumor types. In contrast, CN alterations of the TP53 gene and the MYC family members were predominantly observed in SCLC. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resembles that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics-based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.
On the Origins of Eccentric Close-In Planets

Strong tidal interaction with the central star can circularize the orbits of close-in planets. With the standard tidal quality factor Q of our solar system, estimated circularization times for close-in extrasolar planets are typically shorter than the ages of the host stars. While most extrasolar planets with orbital radii a≲ 0.1 AU indeed have circular orbits, some close-in planets with substantial orbital eccentricities have recently been discovered. This new class of eccentric close-in planets implies that either their tidal Q factor is considerably higher, or circularization is prevented by an external perturbation. Here we constrain the tidal Q factor for transiting extrasolar planets by comparing their circularization times with accurately determined stellar ages. Using estimated secular perturbation timescales, we also provide constraints on the properties of hypothetical second planets exterior to the known ones.
D-branes in Melvin background

In this paper we discuss D-branes in the Melvin background and its supersymmetric generalizations. In particular we determine the D-brane spectra in these backgrounds by constructing their boundary states explicitly, where some of the D-branes are supersymmetric. The results sensitively depend on whether the value of magnetic flux in the Melvin background is rational or irrational. For the rational case the D-branes are regarded as the generalizations of fractional D-branes in abelian orbifolds n/N of type-II or type-0 string theory. For the irrational case we found a very limited spectrum. Since the background includes the non-trivial H-flux, the D-branes will provide interesting examples from the viewpoint of the non-commutative geometry.