Miracle-dz/UniFAR-FTUs huggingface dataset:
9 Role of FKBPs in Parkinson ’ s Disease

Parkinson’s disease (PD) is the second most common neurodegenerative disease among the elderly. While sporadic PD constitutes 99% of the cases, the remaining 1% is of genetic origin. The neuropathological hallmarks of PD are progressive degeneration of dopaminergic (DA) neurons and presence of Lewy neurites and Lewy bodies (LBs) intracytoplasmic proteinaceous inclusions that contain -synuclein (SYN), synphilin-1, components of the ubiquitin proteasomal pathway and parkin (Dawson, 2006). The loss of DA neurons in substantia nigra pars compacta (SNpc) results in decreased signalling in the striatum thereby giving rise to motor defects like resting tremor, bradykinesia, rigidity and posture instability. Besides DA neuronal loss, microglial activation and increased astroglial and lymphocyte infiltration also occur in PD. A role for inflammation in PD has been inferred from the identification of human leukocyte antigen (HLA)-DR positive reactive microglia in the brains of PD patients (McGeer et al., 1988). Additionally, levels of proinflammatory cytokines like IL-6, IL-1, TNF have been found to be elevated in the blood and cerebrospinal fluid (CSF) of PD patients (Nagatsu & Sawada, 2005; Dawson, 2006) Although these inflammatory components might serve as useful biomarkers, the aetiology of striatal DA degeneration still remains enigmatic. In the last decade, identification of mutations in several distinct genes (LRRK2, parkin, PINK1, DJ-1, -synuclein, MAPT, UCHL1 etc) linked to different forms of familial Parkinsonism has imparted a new direction to understanding PD pathogenesis (Tong & Shen, 2009). The question as to how seemingly divergent genes cause PD still remains unanswered, as there is no common molecular pathway involving these gene products. While parkin, -synuclein (SYN) and ubiquitin C-terminal hydrolase L1 (UCHL1) are functionally associated with the cellular ubiquitin proteasomal system (UPS), DJ-1 and PINK1 protect against oxidative stress and mitochondrial dysfunction. More recently, microarray analysis of SNpc from parkinsonian brain (Mandel et al., 2005) has shown that 68 genes related to protein degradation, signal transduction, dopaminergic transmission, iron transport and glycolysis are downregulated. Prominent among these are the protein chaperone HSC-70, subunits of the UPS and SKP1A, a member of the E3 ubiquitin ligase complex. Therefore, it is most likely that impairment in energy metabolism and/or alterations in UPS are the underlying mechanisms for PD pathogenesis (Eriksen et al., 2005; Mandel et al., 2005). Current PD treatment regimes can be divided into three categories: symptomatic, protective and restorative. Only symptomatic treatment via the administration of L-dopa and other
Eurographics/ Ieee-vgtc Symposium on Visualization 2008 Illustrative Parallel Coordinates

Illustrative parallel coordinates (IPC) is a suite of artistic rendering techniques for augmenting and improving parallel coordinate (PC) visualizations. IPC techniques can be used to convey a large amount of information about a multidimensional dataset in a small area of the screen through the following approaches: (a) edge-bundling through splines; (b) visualization of " branched " clusters to reveal the distribution of the data; (c) opacity-based hints to show cluster density; (d) opacity and shading effects to illustrate local line density on the parallel axes; and (e) silhouettes, shadows and halos to help the eye distinguish between overlapping clusters. Thus, the primary goal of this work is to convey as much information as possible in a manner that is aesthetically pleasing and easy to understand for non-experts.
Isolation and Identification of Ferulic Acid From Aerial Parts of Kelussia odoratissima Mozaff.

Background Kelussia odoratissima Mozaff. is one of the newest genera of Umbelliferae which is represented by only one species. This sweet-smelling, self-growing monotypic medicinal plant is endemic to a restricted area in west of Iran and is locally called Karafse-koohi. The aerial parts of the plant are commonly used as a popular garnish and a sedative medicinal plant. There are several reports concerning antioxidant, anti-inflammatory, anxiolytic and hypolipidemic activities of aerial parts of K. odoratissima. Objectives The current research aimed to evaluate some phenolic contents of the plant for the first time . It is confirmed that secondary metabolites and especially phenolic compounds have important role in the biological activities of the plant. Available information indicates that phenolic contents of K. odoratissima have not been the subject of any investigation Material and Methods Aerial parts of K. odoratissima were extracted with acetone by maceration method. Normal and reversed phase vacuum liquid chromatography used to fractionate the extract. 1H-NMR, 13CNMR, EI-Mass and IR spectra were used to elucidate isolated compound. Results The phenolic acid isolated compound was identified as 4-hydroxy-3-methoxycinnamic acid (ferulic acid). Conclusions Compared with previous reported antioxidant and anti-inflammatory properties of ferulic acid, a chemical-biological relation can be postulated.
HI deficiency in the galaxy cluster ACO 3627. ATCA observations in the Great Attractor region

ATCA 21 cm HI observations of the rich galaxy cluster ACO 3627 in the Great Attractor region are presented. Three fields of 30' diameter located within one Abell radius of ACO 3627 were observed with a resolution of 15'' and an rms noise of \sim 1 mJy/beam. Only two galaxies were detected in these fields. We compare their HI distribution to new optical R-band images and discuss their velocity fields. The first galaxy is a gas-rich unperturbed spiral whereas the second shows a peculiar HI distribution. The estimated 3-sigma HI mass limit of our observations is \sim 7 x 10^8 M_{\odot} for a line width of 150 km s^{-1}. The non-detection of a considerable number of luminous spiral galaxies indicates that the spiral galaxies are HI deficient. The low detection rate is comparable to the HI deficient Coma cluster (Bravo-Alfaro et al. 2000). ACO 3627 is a bright X-ray cluster. We therefore suspect that ram pressure stripping is responsible for the HI deficiency of the bright cluster spirals.
A Potential Galaxy Threshing System in the COSMOS Field

We report on the discovery of a new potential galaxy threshing system in the COSMOS 2 square degree field using the prime-focus camera, Suprime-Cam, on the 8.2 m Subaru Telescope. This system consists of a giant elliptical galaxy with MV ≈ -21.6 and a tidally disrupted satellite galaxy with MV ≈ -17.7 at a photometric redshift of z ≈ 0.08. This redshift is consistent with the spectroscopic redshift of 0.079 for the giant elliptical galaxy obtained from the Sloan Digital Sky Survey (SDSS) archive. The luminosity masses of the two galaxies are 3.7 × 1012 and 3.1 × 109 ℳ☉, respectively. The distance between the two galaxies is greater than 100 kpc. The two tidal tails emanating from the satellite galaxy extend over 150 kpc. This system would be the second well-defined galaxy threshing system found so far.
Tomographic Image of the Southern California Mantle

P wave teleseismic travel time delays recorded by the Southern California Array are inverted by the method of backprojection tomography to obtain images of variations in the P wave velocity structure to a depth of 750 km. Two major upper mantle features arc resolved: one beneath the Transverse Ranges region and another beneath the Salton Trough region. The Transverse Ranges feature appears as a curtainlike, east trending, high-velocity anomaly. This feature is ∼60 km thick, extends most deeply on its eastern end (to ∼250 km), and attains a maximum velocity −3% greater than average southern California mantle of the same depth. The Salton Trough feature, which is not as well resolved as the Transverse Ranges feature, is composed of low velocities in the upper 70–100 km. These P wave velocities arc depressed 3–4% compared to average southern California mantle. Tests of the inversion indicate the major aspects of the imaged structure are authentic.
Addressing the Problem of Negative Lexical Transfer Errors in Chilean University Students

Studies of second language learning have revealed a connection between first language transfer and errors in second language production. This paper describes an action research study carried out among Chilean university students studying English as part of their degree programmes. The study focuses on common lexical errors made by Chilean Spanish-speakers due to negative first language transfer and aims to analyse the effects of systematic instruction and practice of this problematic lexis. It is suggested that raising awareness of lexical transfer through focused attention on common transfer errors is valued by students and seems essential for learners to achieve productive mastery.
Sources of individual differences in depressive symptoms: analysis of two samples of twins and their families.

OBJECTIVE Self-reported symptoms of depression are commonly used in mental health research to assess current psychiatric state, yet wide variation in these symptoms among individuals has been found in both clinical and epidemiologic populations. The authors sought to understand, from a genetic-epidemiologic perspective, the sources of individual differences in depressive symptoms. METHODS Self-reported symptoms of depression were assessed in two samples of twins and their spouses, parents, siblings, and offspring: one sample contained volunteer twins recruited through the American Association of Retired Persons and their relatives (N = 19,203 individuals) and the other contained twins from a population-based twin registry in Virginia and their relatives (N = 11,242 individuals). Model fitting by an iterative, diagonal, weighted least squares method was applied to the 80 different family relationships in the extended twin-family design. RESULTS Independent analyses of the two samples revealed that the level of depressive symptoms was modestly familial, and familial resemblance could be explained solely by genetic factors and spousal resemblance. The estimated heritability of depressive symptoms was between 30% and 37%. There was no evidence that the liability to depressive symptoms was environmentally transmitted from parents to offspring or was influenced by environmental factors shared either generally among siblings or specifically between twins. With correction for unreliability of measurement, genetic factors accounted for half of the stable variance in depressive symptoms. CONCLUSIONS Depressive symptoms in adulthood partly reflect enduring characteristics of temperament that are substantially influenced by hereditary factors but little, or not at all, by shared environmental experiences in the family of origin.
Nondeterministic Finite Automata in Hardware-the Case of the Levenshtein Automaton

The Levenshtein Nondeterministic Finite state Automaton (NFA) recognizes input strings within a set edit distance of a configured pattern in linear time. This automaton can be pipelined to recognize all substrings of an input text in linear time with the use of additional nondeterministic branches. In general, von Neumann hardware cannot directly simulate NFAs without significant time or space overhead. A von Neumann simulation of the Levenshtein automaton incurs substantial overhead in the general case, even with a large number of cores because of the von Neumann Bottleneck. A common technique to avoid the simulation overhead is to convert the pipelined NFA to a DFA, but at the expense of heavy pre-computation and high space overhead. In this paper, we introduce a novel technique for executing a pipelined Levenshtein NFA using Micron’s Automata Processor (AP), avoiding the run time and space overheads associated with CPU and GPU implementations. We show that run time remains asymptotically linear with the input while the space requirement of the automaton becomes linear in the product of the configured pattern length and edit distance. These properties allow the AP to execute large instances of the Levenshtein NFA or many small instances in parallel thus making the automaton a viable building block for future approximate string applications on the AP.
Development Of An Adaptive Soft Sensor Based On FCMILSSVR

Facing with dynamic environment of industrial plants involves us design soft sensors capable of online learning. To response this requirement, an adaptive soft sensor based on a combination of Least Square Support Vector Regression (LSSVR) with Fuzzy C-Means (FCM) clustering is proposed in this paper. In this approach, first the samples are divided into several partitions. Consequently, for each partition we develop a local model using a new formulation of LSSVR which enables incremental learning. The proposed method is implemented on a chemical plant and compared with the online Support Vector Regression (SVR) algorithm. Simulation results indicate that the proposed method improves the generalization ability of soft sensor and the computation time decreases to a large extent in comparison to the online SVR.
Radically Data-driven Methods of Speech Analysis

We present two simple statistical methods for analyzing spoken language as represented in transcription corpora. The methods are strictly data-driven, in the sense that no preset grammatical category system and no lexical knowledge are assumed. The first method (called Siblings) is used for word type clustering within one language; the second method (called Cousins) is used for word-to-word translation between two cognate languages. Examples are given using Danish and Swedish transcription data. We conclude with a discussion of how the methods could be applied to languages that do not have a writing system at all – and no record of linguistic description.
Role of BmDredd during Apoptosis of Silk Gland in Silkworm, Bombyx mori

Silk glands (SGs) undergo massive apoptosis driven degeneration during the larval-pupal transformation. To better understand this event on molecular level, we investigated the expression of apoptosis-related genes across the developmental transition period that spans day 4 in the fifth instar Bombyx mori larvae to day 2 pupae. Increases in the expression of BmDredd (an initiator caspase homolog) closely followed the highest BmEcR expression and resembled the expression trend of BmIcE. Simultaneously, we found that BmDredd expression was significantly higher in SG compared to other tissues at 18 h post-spinning, but reduced following injection of the apoptosis inhibitor (Z-DEVD-fmk). Furthermore, BmDredd expression correlated with changes of caspase3-like activities in SG and RNAi-mediated knockdown of BmDredd delayed SG apoptosis. Moreover, caspase3-like activity was increased in SG by overexpression of BmDredd. Taken together, the results suggest that BmDredd plays a critical role in SG apoptosis.
T-junction: Experiments, trajectory collection, and analysis

For the proper understanding and modelling of pedestrian dynamics, reliable empirical data is necessary for analysis and verification. This paper discusses laboratory experiments at T-junctions: the setup, the extraction of the trajectories of the pedestrians and the analysis of the resulting data. Such experiments give us the opportunity to selectively analyse parameters independent of undesired influences and adjust them to high densities seldom seen in field studies. For the T-junction the density inside the junction has been varied and analysed. Two strategies for the time-efficient automatic extraction of accurate pedestrian trajectories from stereo recordings are presented. One strategy uses marker for detection and the other one based on a perspective depth field. From these trajectories the fundamental diagram of T-junction flow is analysed, the density, velocity and specific flow profiles are obtained using the Voronoi method.
Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs

MOTIVATION There is a very large and growing level of effort toward improving the platforms, experiment designs, and data analysis methods for microarray expression profiling. Along with a growing richness in the approaches there is a growing confusion among most scientists as to how to make objective comparisons and choices between them for different applications. There is a need for a standard framework for the microarray community to compare and improve analytical and statistical methods. RESULTS We report on a microarray data set comprising 204 in-situ synthesized oligonucleotide arrays, each hybridized with two-color cDNA samples derived from 20 different human tissues and cell lines. Design of the approximately 24 000 60mer oligonucleotides that report approximately 2500 known genes on the arrays, and design of the hybridization experiments, were carried out in a way that supports the performance assessment of alternative data processing approaches and of alternative experiment and array designs. We also propose standard figures of merit for success in detecting individual differential expression changes or expression levels, and for detecting similarities and differences in expression patterns across genes and experiments. We expect this data set and the proposed figures of merit will provide a standard framework for much of the microarray community to compare and improve many analytical and statistical methods relevant to microarray data analysis, including image processing, normalization, error modeling, combining of multiple reporters per gene, use of replicate experiments, and sample referencing schemes in measurements based on expression change. AVAILABILITY/SUPPLEMENTARY INFORMATION Expression data and supplementary information are available at http://www.rii. com/publications/2003/HE_SDS. htm
Dirichlet forms and symmetric Markovian semigroups on CCR algebras with respect to quasi-free states

Employing the construction method of Dirichlet forms on standard forms of von Neumann algebras developed in Infinite Dimensional Analysis, Quantum Probability and Related Topics, 2000, Vol. 3, No. 1, pp. 1–14 (Ref. 1), we construct Dirichlet forms and associated symmetric Markovian semigroups on CCR algebras with respect to quasi-free states. More precisely, let A(h0) be the CCR algebra over a complex separable pre-Hilbert space h0 and let ω be a quasi-free state on A(h0). For any normalized admissible function f and complete orthonormal system (CONS) {gn}⊂h0, we construct a Dirichlet form and corresponding symmetric Markovian semigroup on the natural standard form associated to the GNS representation of (A(h0),ω). It turns out that the form is independent of admissible function f and CONS {gn} chosen. By analyzing the spectrum of the generator (Dirichlet operator) of the semigroup, we show that the semigroup is ergodic and tends to the equilibrium exponentially fast.
Translational read-through of the RP2 Arg120stop mutation in patient iPSC-derived retinal pigment epithelium cells

Mutations in the RP2 gene lead to a severe form of X-linked retinitis pigmentosa. RP2 patients frequently present with nonsense mutations and no treatments are currently available to restore RP2 function. In this study, we reprogrammed fibroblasts from an RP2 patient carrying the nonsense mutation c.519C>T (p.R120X) into induced pluripotent stem cells (iPSC), and differentiated these cells into retinal pigment epithelial cells (RPE) to study the mechanisms of disease and test potential therapies. RP2 protein was undetectable in the RP2 R120X patient cells, suggesting a disease mechanism caused by complete lack of RP2 protein. The RP2 patient fibroblasts and iPSC-derived RPE cells showed phenotypic defects in IFT20 localization, Golgi cohesion and Gβ1 trafficking. These phenotypes were corrected by over-expressing GFP-tagged RP2. Using the translational read-through inducing drugs (TRIDs) G418 and PTC124 (Ataluren), we were able to restore up to 20% of endogenous, full-length RP2 protein in R120X cells. This level of restored RP2 was sufficient to reverse the cellular phenotypic defects observed in both the R120X patient fibroblasts and iPSC-RPE cells. This is the first proof-of-concept study to demonstrate successful read-through and restoration of RP2 function for the R120X nonsense mutation. The ability of the restored RP2 protein level to reverse the observed cellular phenotypes in cells lacking RP2 indicates that translational read-through could be clinically beneficial for patients.
The Dynamics of Organizational Identity

Although many organizational researchers make reference to Mead’s theory of social identity, none have explored how Mead’s ideas about the relationship between the ‘I’ and the ‘me’ might be extended to identity processes at the organizational level of analysis. In this article we define organizational analogs for Mead’s ‘I’ and ‘me’ and explain how these two phases of organizational identity are related. In doing so, we bring together existing theory concerning the links between organizational identities and images, with new theory concerning how reflection embeds identity in organizational culture and how identity expresses cultural understandings through symbols. We offer a model of organizational identity dynamics built on four processes linking organizational identity to culture and image. Whereas the processes linking identity and image (mirroring and impressing) have been described in the literature before, the contribution of this article lies in articulation of the processes linking identity and culture (reflecting and expressing), and of the interaction of all four processes working dynamically together to create, maintain and change organizational identity. We discuss the implications of our model in terms of two dysfunctions of organizational identity dynamics: narcissism and loss of culture.
An exploratory study of code smells in evolving aspect-oriented systems

Although aspect-oriented programming (AOP) aims to improve software maintainability, developers can unwittingly introduce code smells in their programs. A code smell is any symptom in the source code that possibly indicates a deeper maintainability problem. Even though a few code smells for AOP have been reported in the literature, there is no evidence if and how they occur in evolving software projects. There is also little knowledge on their actual impact on maintenance effort, such as required refactorings or corrective changes in later software releases. This paper presents an exploratory analysis of code smells recurrently observed in a set of evolving aspect-oriented systems. We analyzed instances of code smells previously reported in the literature and newly-revealed ones. Our study involved in total 18 releases of 3 evolving aspect-oriented systems from different domains. The outcome of our evaluation suggests that previously-documented AOP smells might not occur as often as claimed. Our analysis also revealed that: (1) newly-discovered code smells might occur more often than well-known ones, and (2) the former ones seemed to be consistently associated with non-trivial refactorings and corrective changes.
Timoshenko Beam Theory based Dynamic Modeling of Lightweight Flexible Link Robotic Manipulators

The purpose of this volume is to encourage and inspire the continual invention of robot manipulators for science and the good of humanity. The concepts of artificial intelligence combined with the engineering and technology of feedback control, have great potential for new, useful and exciting machines. The concept of eclecticism for the design, development, simulation and implementation of a real time controller for an intelligent, vision guided robots is now being explored. The dream of an eclectic perceptual, creative controller that can select its own tasks and perform autonomous operations with reliability and dependability is starting to evolve. We have not yet reached this stage but a careful study of the contents will start one on the exciting journey that could lead to many inventions and successful solutions.