Miracle-dz/UniFAR-FTUs huggingface dataset:
The deubiquitinase USP15 antagonizes Parkin-mediated mitochondrial ubiquitination and mitophagy

Loss-of-function mutations in PARK2, the gene encoding the E3 ubiquitin ligase Parkin, are the most frequent cause of recessive Parkinson's disease (PD). Parkin translocates from the cytosol to depolarized mitochondria, ubiquitinates outer mitochondrial membrane proteins and induces selective autophagy of the damaged mitochondria (mitophagy). Here, we show that ubiquitin-specific protease 15 (USP15), a deubiquitinating enzyme (DUB) widely expressed in brain and other organs, opposes Parkin-mediated mitophagy, while a panel of other DUBs and a catalytically inactive version of USP15 do not. Moreover, knockdown of USP15 rescues the mitophagy defect of PD patient fibroblasts with PARK2 mutations and decreased Parkin levels. USP15 does not affect the ubiquitination status of Parkin or Parkin translocation to mitochondria, but counteracts Parkin-mediated mitochondrial ubiquitination. Knockdown of the DUB CG8334, the closest homolog of USP15 in Drosophila, largely rescues the mitochondrial and behavioral defects of parkin RNAi flies. These data identify USP15 as an antagonist of Parkin and suggest that USP15 inhibition could be a therapeutic strategy for PD cases caused by reduced Parkin levels.
Backward-Forward Combined Convolutive Blind Source Separation

Many blind source separation algorithms only try to find the estimation of original signals and the de-mixing system. However, finding the mixing system is also an important task, which is a representation for the recording environment. Direct inversing the mixing system will introduce many noises. We proposed a correlation based backward-forward combined algorithm to do blind source separation. In the proposed algorithm, an alternative optimization strategy is applied. The estimation of mixing/de-mixing system is used as an initial guess to optimize the de-mixing/mixing system iteratively. This alternative optimization algorithm can obtain better estimation for mixing and de-mixing system at the same time. In addition, it can reduce the chance to be tracked into a local minimal. As a result, we can get a better estimation for the sources. Good experimental results were obtained on both simulated and real signals.
A new measure of tipover stability margin for mobile manipulators

Mobile manipulators operating in field environments will be required to perform tasks on uneven terrain which may cause the system to approach, or achieve, a dangerous tipover instability. To avoid tipover in an automatic system, or to provide a human operator with an indication of proximity to tipover, it is necessary to define a measure of stability margin. This work presents a new tipover stability measure (the force-angle stability measure) which is easily computed and sensitive to topheaviness. The proposed metric is applicable to systems subject to inertial and external forces, operating over even or uneven terrains. Performance of the measure is demonstrated using a forestry vehicle simulation.
Induction and Determination of Apoptotic and Necrotic Cell Death by Cadmium Chloride in Testis Tissue of Mouse

Background Cadmium chloride which is potentially toxic is currently used in industry. The toxic effects of cadmium on testes have been reported to range from apoptosis to necrosis, with different effects on fertility. This research aimed to study the effect of different doses of cadmium on testicular tissues at acute stage by light and electron microscopy. Methods Cadmium chloride was injected into mature Balb/c mice intraperitoneally in 7 doses. Five mice were studied in each group. After 48 hr, the testes were extracted and prepared for light microscopy. Then two concentrations (15 and 25 µM/kg) of them were selected for electron microscopic study based on histological changes. The cellular changes of luminal epithelium of seminiferous tubules were studied under an electron microscope. Histological and ultrastructural changes were reported. Results The absence of sperm in the tubules was observed at 20 µM/kg concentration. At 25 µM/kg, histological destruction and epithelial damages were observed. Histological changes were not remarkable at 5 and 10 µM/kg. However, ultrastructural changes of seminiferous tubules at 20 µM/kg included spermatogonial cell death. At 25 µM/kg, vacuolation of Sertoli cells and death of spermatids as well as spermatocytes were observed. Cell death in the tubules was limited to germ cells. However, Sertoli cells exhibited architectural alterations without any cell death. Conclusion Both apoptosis and necrosis occurred in testicular tissue by exposure to cadmium in a concentration-dependent manner. Gonadal cells were sensitive to cadmium administration. Supportive cells such as Sertoli cells in seminiferous tubules did not exhibit sensitivity to cadmium.
Analyzing the accuracy of the binocular stereo locating system for meridian visualization

In this paper, we investigate a structural parameters model with the trigonometric method in order to improve the measurement precision of the binocular stereo vision measuring system. We find the relationship between the accuracy of the optical locating and structural parameters through analyzing the baseline(X direction), the angle of view ω, and the convergence angle α which is formed by the baseline and optical axes. Finally, we will represent some simulation results under different structural parameters where the optimal range of the structural parameters can be obtained with a small error. Also, the correctness of the theoretical analysis is verified by experimental results.
Biasing the structure of scheduling problems through classical planners

Since Planning and Scheduling address complementary aspects of Problem Solving, much attention is recently being paid to the possibility of mutually exchanging the information yielded during the planning and the scheduling search procedures. In this context, we investigate a loosely coupled approach, which consists of cascading a planner and a scheduler. While other implementations of this framework have already been reported, our work aims at analyzing the structural properties of the scheduling problem which results from the planning component, focusing on the bias produced by different planning approaches in the light of makespan-optimizing scheduling.
Majority Voting: Material Classification by Tactile Sensing Using Surface Texture

In this paper, we present an application of machine learning to distinguish between different materials based on their surface texture. Such a system can be used for the estimation of surface friction during manipulation tasks; quality assurance in the textile, cosmetics, and harvesting industries; and other applications requiring tactile sensing. Several machine learning algorithms, such as naive Bayes, decision trees, and naive Bayes trees, have been trained to distinguish textures sensed by a biologically inspired artificial finger. The finger has randomly distributed strain gauges and polyvinylidene fluoride (PVDF) films embedded in silicone. Different textures induce different intensities of vibrations in the silicone. Consequently, textures can be distinguished by the presence of different frequencies in the signal. The data from the finger are preprocessed, and the Fourier coefficients of the sensor outputs are used to train classifiers. We show that the classifiers generalize well for unseen datasets with performance exceeding previously reported algorithms. Our classifiers can distinguish between different materials, such as carpet, flooring vinyls, tiles, sponge, wood, and polyvinyl-chloride (PVC) woven mesh with an accuracy of on unseen test data.
Continuous On-line Evolution of Agent Behaviours with Cartesian Genetic Programming

Evolutionary Computation has been successfully used to synthesise controllers for embodied agents and multi-agent systems in general. Notwithstanding this, continuous on-line adaptation by the means of evolutionary algorithms is still under-explored, especially outside the evolutionary robotics domain. In this paper, we present an on-line evolutionary programming algorithm that searches in the agent design space for the appropriate behavioural policies to cope with the underlying environment. We discuss the current problems of continuous agent adaptation, present our on-line evolution testbed for evolutionary simulation.
ROUTINE VERSUS INNOVATIVE ORGANIZATIONAL LEARNING : TOWARDS A RESOLUTION ?

The work presented in this paper is based on the MILK project. MILK (IST Project 2001-33165) is the acronym of Multimedia Interaction for Learning and Knowing. Partners of the MILK project are Irso Global Services. This paper is focused on the dynamic idea of knowledge management as a way to enable learning, communication and networking processes between and within communities of practice made up by knowledge workers. As knowledge workers become more and more mobile, often changing working environments between being in the office and being out e.g. by a client or working from home a knowledge system based on the " the right knowledge at the right time " is introduced and related to different working situations in which mobile knowledge workers need different information and knowledge and different communication channels.
C A ] 3 0 M ay 2 00 3 Wavelets on Fractals ∗ †

We show that there are Hilbert spaces constructed from the Hausdorff measures H on the real line R with 0 < s < 1 which admit multiresolution wavelets. For the case of the middle-third Cantor set C ⊂ [0, 1], the Hilbert space is a separate subspace of L(R, (dx)) where s = log 3 (2). While we develop the general theory of multi-resolutions in fractal Hilbert spaces, the emphasis is on the case of scale 3 which covers the traditional Cantor set C. Introducing ψ 1 (x) = √ 2χ C (3x− 1) and ψ 2 (x) = χ C (3x) − χ C (3x− 2) we first describe the subspace in L(R, (dx)) which has the following family as an orthonormal basis (ONB): ψi,j,k(x) = 2 j ψi(3 j x− k), where i = 1, 2, j, k ∈ Z.
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa

Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103 215 tentative unique sequences (TUSs) have been produced from 435 018 Roche/454 reads and 21 491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49 437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20 634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42 141 aligned TUSs with putative gene structures (including 39 281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44 639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.
Metric-Free Natural Gradient for Joint-Training of Boltzmann Machines

This paper introduces the Metric-Free Natural Gradient (MFNG) algorithm for training Boltzmann Machines. Similar in spirit to the Hessian-Free method of Martens [8], our algorithm belongs to the family of truncated Newton methods and exploits an efficient matrix-vector product to avoid explicitely storing the natural gradient metric $L$. This metric is shown to be the expected second derivative of the log-partition function (under the model distribution), or equivalently, the variance of the vector of partial derivatives of the energy function. We evaluate our method on the task of joint-training a 3-layer Deep Boltzmann Machine and show that MFNG does indeed have faster per-epoch convergence compared to Stochastic Maximum Likelihood with centering, though wall-clock performance is currently not competitive.
Automatic and independent Domain Name Service Configuration Management

In this paper we propose an Automated and Distributed Network Service Configuration Management subsystem that, using independent network service configurations, abstracts the heterogeneous service implementation details and enables the development of high-level independent management applications. This overcomes the need for intermediary static configuration translation schemes, while providing an efficient way to deal with heterogeneous service management. To prove the usefulness of our architecture, an automated and independent Domain Name Service (DNS) configuration management prototype tool was built. Implementing an independent server-centric management approach, the prototype provides a group of advanced features to simplify DNS management. Automatic configuration replication procedures were performed to demonstrate the framework's management independence to the service implementation details.
Six Year Refractive Change among White Children and Young Adults: Evidence for Significant Increase in Myopia among White UK Children

Objective To determine six-year spherical refractive error change among white children and young adults in the UK and evaluate differences in refractive profiles between contemporary Australian children and historical UK data. Design Population-based prospective study. Participants The Northern Ireland Childhood Errors of Refraction (NICER) study Phase 1 examined 1068 children in two cohorts aged 6–7 years and 12–13 years. Prospective data for six-year follow-up (Phase 3) are available for 212 12–13 year olds and 226 18–20 year olds in each cohort respectively. Methods Cycloplegic refractive error was determined using binocular open-field autorefraction (Shin-Nippon NVision-K 5001, cyclopentolate 1%). Participants were defined by spherical equivalent refraction (SER) as myopic SER ≤-0.50D, emmetropic -0.50D<SER<+2.00 or hyperopic SER≥+2.00D. Main Outcome Measures Proportion and incidence of myopia. Results The proportion of myopes significantly increased between 6–7 years (1.9%) and 12–13 years (14.6%) (p<0.001) but not between 12–13 and 18–20 years (16.4% to 18.6%, p = 0.51). The estimated annual incidence of myopia was 2.2% and 0.7% for the younger and older cohorts respectively. There were significantly more myopic children in the UK at age 12–13 years in the NICER study (16.4%) than reported in Australia (4.4%) (p<0.001). However by 17 years the proportion of myopia neared equivalence in the two populations (NICER 18.6%, Australia 17.7%, p = 0.75). The proportion of myopic children aged 12–13 years in the present study (2006–2008) was 16.4%, significantly greater than that reported for children aged 10–16 years in the 1960’s (7.2%, p = 0.01). The proportion of hyperopes in the younger NICER cohort decreased significantly over the six year period (from 21.7% to 14.2%, p = 0.04). Hyperopes with SER ≥+3.50D in both NICER age cohorts demonstrated persistent hyperopia. Conclusions The incidence and proportion of myopia are relatively low in this contemporary white UK population in comparison to other worldwide studies. The proportion of myopes in the UK has more than doubled over the last 50 years in children aged between 10–16 years and children are becoming myopic at a younger age. Differences between the proportion of myopes in the UK and in Australia apparent at 12–13 years were eliminated by 17 years of age.
How Large are Search Frictions?

This paper shows that we can normalize job and worker characteristics such that without frictions there exists a linear relationship between wages on the one hand and worker and job type indices on the other. However, for five European countries and the US we find strong evidence for a systematic concave relation. An assignment model with search frictions provides a parsimonious explanation for our findings. This model yields two restrictions on the coefficients that fit the data well. Allowing for unobserved heterogeneity and measurement error we find that reservation wages are 25% lower than they would be in a frictionless world. Our results relate to the literature on industry wage differentials and on structural identification in hedonic models.
Drug Design on the Cell BroadBand Engine

We evaluate a well known protein docking application in the bioinformatic field, Fourier Transform Docking (FTDock) (Gabb et al., 1997), on a Blade with two 3.2GHz cell broadband engine (BE) processor (Kahle et al., 2005). FTDock is a geometry complementary approximation of the protein docking problem, and uses 3D FFTs to reduce the complexity of the algorithm. FTDock achieves a significant speedup when most time consuming functions are offloaded to SPEs, and vectorized. We show the performance impact evolution of of-loading and vectorizing two functions of FTDock (CM and SC) on 1 SPU. We show total execution time of FTDock when CM and SC run in the PPU (bar 1), CM is off loaded (bar 2), CM is also vectorized (bar 3), SC is offloaded (bar 4) and SC is also vectorized (bar 5). Parallelizing functions that are not offloaded, using OpenMP for instance, on the dual-thread PPE helps to increase the PPEpipeline use and system throughput, and the scalability of the application.
Risk aversion in the present and the future : An experimental study

We design an experiment to study the consistency of risk preferences between lotteries that are resolved and paid in the present versus in the future. The results show that a substantial fraction of subjects (38.6%) exhibits a greater level of risk aversion for lotteries resolved and paid in the present than in the future. Additional treatments suggest that the effect is not specific to gambles that are realized immediately, nor is due to steep discounting of future payoffs. Our experiment suggests that risk tolerance increases the farther in the future the gamble is realized.
Optimizing Large Join Queries Using A Graph-Based Approach

Although many query tree optimization strategies have been proposed in the literature, there still is a lack of a formal and complete representation of all possible permutations of query operations (i.e., execution plans) in a uniform manner. A graph-theoretic approach presented in the paper provides a sound mathematical basis for representing a query and searching for an execution plan. In this graph model, a node represents an operation and a directed edge between two nodes indicates the older of executing these two operations in an execution plan. Each node is associated with a weight and so is an edge. The weight is an expression containing optimization required parameters, such as relation size, tuple size, join selectivity factors. All possible execution plans are representable in this graph and each spanning tree of the graph becomes an execution plan. It is a general model which can be used in the optimizer of a DBMS for internal query representation. On the basis of this model, we devise an algorithm that finds a near optimal execution plan using only polynomial time. The algorithm is compared with a few other popular optimization methods. Experiments show that the proposed algorithm is superior to the others under most circumstances.
Is disposition related to momentum in Chinese market

Purpose - – The purpose of this paper is to examine whether the framework of Prospect Theory and Mental Accounting proposed by Grinblatt and Han (2005) can be applied to analyzing the relationship between the disposition effect and momentum in the Chinese stock market. Design/methodology/approach - – The paper applies the methodology proposed by Grinblatt and Han (2005). Findings - – Using firm-level data, with a sample period from January 1998 to June 2013, the authors find evidence that the momentum effect in the Chinese stock market is not driven by the disposition effect, contradicting the findings of Grinblatt and Han (2005) concerning the US stock market. The discrepancies in the findings between the Chinese and US stock markets are robust and independent of sample periods. Research limitations/implications - – The findings suggest that Grinblatt and Han’s model may not be applicable to the Chinese stock market. This is possibly because of the regulatory differences between the two stock markets and cross-national variation in investor behavior; in particular, the short-selling prohibition in the Chinese stock market and greater reference point adaptation to unrealized gains/losses among Chinese compared to Americans. Originality/value - – This study provides evidence of the inapplicability of Grinblatt and Han’s model for the Chinese stock market, and shows the differences in the relationship between disposition effect and momentum between the Chinese and US stock markets.
Data Mining for Autonomic System Management: A Case Study at FIU-SCIS

Over the years, the advancements in science and technology have led to the increased complexity in computing systems. The systems are thus becoming increasingly more complex with growing number of heterogeneous software and hardware components, increasingly more difficult to monitor, manage and maintain. As a result, it is not a trivial task to provide high performance, high dependability, and high manageability for such computing systems. In this paper, we first present an integrated data-driven architecture for computing system management and then present a case study on Autonomic System Manager: a software system we developed that is currently being used by the system and network administrators of School of Computing and Information Sciences (SCIS) at Florida International University (FIU).
Weighted Association Rule Mining and Clustering in Non-binary Search Space

Association Rule Induction and Clustering are some of the most useful data mining techniques. The former focuses on finding regularities in data trends, while the latter on discovering groups and identifying interesting distributions and patterns in the underlying data. Several research attempts have been made for the purpose of clustering transactions based on the binary data space. In this paper, an algorithm has been proposed for the same purpose but based on the non-binary data space. We also propose a novel mechanism to yield weighted association rules in non-binary search space. It is capable of clustering and mining weighted association rules more close to the real life situations as it considers the Strength of Presence of each item implicitly. Also they can be directly applied to the real time data repository.