Miracle-dz/UniFAR-FTUs huggingface dataset:
The pRb/E2F cell-cycle pathway mediates cell death in Parkinson's disease

The mechanisms leading to degeneration of dopaminergic neurons (DNs) in the substantia nigra of patients with Parkinson's disease (PD) are not completely understood. Here, we show, in the postmortem human tissue, that these neurons aberrantly express mitosis-associated proteins, including the E2F-1 transcription factor, and appear to duplicate their nuclear DNA. We further demonstrate that the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine injected into mice and application of its active metabolite 1-methyl-4-phenylpyridinium to mesencephalic cultures activate the retinoblastoma–E2F pathway in postmitotic DNs. We also find that cell death rather than mitotic division followed the toxin-induced replication of DNA, as determined by BrdU incorporation in DNs. In addition, blocking E2F-1 transcription protected cultured DNs against 1-methyl-4-phenylpyridinium toxicity. Finally, E2F-1-deficient mice were significantly more resistant to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced dopaminergic cell death than their wild-type littermates. Altogether, BrdU incorporation in mature neurons and lack of evidence for newborn neurons argue against neuronal turnover in normal conditions or during pathological states in the substantia nigra. Instead, our results demonstrate that mitosis-like signals are activated in mature DNs in patients with PD and mediate neuronal death in experimental models of the disease. Inhibition of mitosis-like signals may therefore provide strategies for neuroprotection in PD.
Improving soft skills and communication in response to youth unemployment

ABSTRACT Several studies have been conducted into the high rates of graduate youth unemployment in South Africa. Results from these investigations have isolated some determinants which can be categorised under three broad headings – government, business practices and graduate attributes. the article focuses on graduates’ attributes that negatively impact on their employability. One attribute that was identified was their soft skills, particularly, their communication ability or their levels of pragmatic language usage. Pragmatic competence is an ability which is not always consequential to ordinary language development; there needs to be explicit instruction for such development. This is a reflective article with the objective of examining the nature of communication in the workplace and what strategies can enhance graduates’ communication ability, and in turn improve their employability. this article concludes that enhancing graduates’ communication skills should be a cooperative venture involving all the stakeholders in education – students, parents, higher education institutions, business and government.
On Training Deep Boltzmann Machines

The deep Boltzmann machine (DBM) has been an important development in the quest for powerful "deep" probabilistic models. To date, simultaneous or joint training of all layers of the DBM has been largely unsuccessful with existing training methods. We introduce a simple regularization scheme that encourages the weight vectors associated with each hidden unit to have similar norms. We demonstrate that this regularization can be easily combined with standard stochastic maximum likelihood to yield an effective training strategy for the simultaneous training of all layers of the deep Boltzmann machine.
Histone H3K56 Acetylation, Rad52, and Non-DNA Repair Factors Control Double-Strand Break Repair Choice with the Sister Chromatid

DNA double-strand breaks (DSBs) are harmful lesions that arise mainly during replication. The choice of the sister chromatid as the preferential repair template is critical for genome integrity, but the mechanisms that guarantee this choice are unknown. Here we identify new genes with a specific role in assuring the sister chromatid as the preferred repair template. Physical analyses of sister chromatid recombination (SCR) in 28 selected mutants that increase Rad52 foci and inter-homolog recombination uncovered 8 new genes required for SCR. These include the SUMO/Ub-SUMO protease Wss1, the stress-response proteins Bud27 and Pdr10, the ADA histone acetyl-transferase complex proteins Ahc1 and Ada2, as well as the Hst3 and Hst4 histone deacetylase and the Rtt109 histone acetyl-transferase genes, whose target is histone H3 Lysine 56 (H3K56). Importantly, we use mutations in H3K56 residue to A, R, and Q to reveal that H3K56 acetylation/deacetylation is critical to promote SCR as the major repair mechanism for replication-born DSBs. The same phenotype is observed for a particular class of rad52 alleles, represented by rad52-C180A, with a DSB repair defect but a spontaneous hyper-recombination phenotype. We propose that specific Rad52 residues, as well as the histone H3 acetylation/deacetylation state of chromatin and other specific factors, play an important role in identifying the sister as the choice template for the repair of replication-born DSBs. Our work demonstrates the existence of specific functions to guarantee SCR as the main repair event for replication-born DSBs that can occur by two pathways, one Rad51-dependent and the other Pol32-dependent. A dysfunction can lead to genome instability as manifested by high levels of homolog recombination and DSB accumulation.
Statistical image segmentation using triplet Markov fields

Hidden Markov fields (HMF) are widely used in image processing. In such models, the hidden random field of interest X=(Xs) is a Markov field, and the distribution p(y/x) of the observed random field Y=(Ys) conditional on X is given by the product of p(ys/xs), with s in the set of pixels. The posterior distribution p(x/y) is then a Markov distribution, which affords different Bayesian processing. However, when dealing with the segmentation of images containing numerous classes with different textures, the simple form of the distribution p(y/x) above is insufficient and has to be replaced by a Markov field distribution. This poses problems, because taking p(y/x) Markovian implies that the posterior distribution p(x/y), whose Markovianity is needed to use Bayesian techniques, may no longer be a Markov distribution, and so different model approximations must be made to remedy this. This drawback disappears when considering directly the Markovianity of (X, Y); in these recent 'Pairwise Markov Fields (PMF) models, both p(y/x) and p(x/y) are then Markovian, the first one allowing us to model textures, and the second one allowing us to use Bayesian restoration without model approximations. In this paper we generalize the PMF to Triplet Markov Fields (TMF) by adding a third random field U=(Us) and considering the Markovianity of (X, U, Y). We show that in TMF X is still estimable from Y by Bayesian methods. The parameter estimation with Iterative Conditional Estimation (ICE) is specified and we give some numerical results showing how the use of TMF can improve the classical HMF based segmentation.
Web-based biometric mouse decision support system for user's emotional and labour productivity analysis

In order to increase the efficiency of employees’ activities, a Web-based Biometric Mouse Decision Support System for User’s Emotional and Labour Productivity Analysis (MDSS-UELPA) was developed by the authors. MDSS-UELPA consists of seven subsystems: Data Capture and Collection Subsystem, Feature Extraction Subsystem, Database Management Subsystem, Model-base Management Subsystem, Equipment Subsystem, e-Self-Reports Subsystem and Graphical Interface. MDSS-UELPA is an online system and allows for more physiological, psychological and behavioural data to be generated from a larger pool of users for further analysis and research. Data is accumulated in individual user modules based on the user’s mouse movements, palm state and e-self-reports. The basic assumption was that MDSS-UELPA could successfully model user behaviours on the basis of the above-mentioned physiological, psychological and behavioural data. MDSSUELPA is briefly analysed in this paper.
Real-Time System Design Based on Logic OR Constrained Optimization

The logic relationship among the equality and inequality constraints in a standard constrained optimization problem (SCOP) is the logical AND. Various efficient, convergent and robust algorithms have been developed for such a SCOP. However, a more general constrained optimization problem (GCOP) with not only logic AND but also OR relationships exists in many practical applications. In order to solve such a generalized problem, a new mathematical transformations which can transfer a set of inequalities with logic OR into inequalities with logic AND relationships is developed. This transformation provides a necessary and sufficient condition which enables us to formulate real-time system design as a mixed Boolean-integer programming problem. A Branch and Bound Algorithm is applied to find the optimal solution. Experimental results have been presented to show its
Morphogenesis of the Caenorhabditis elegans vulva

Understanding how cells move, change shape, and alter cellular behaviors to form organs, a process termed morphogenesis, is one of the great challenges of developmental biology. Formation of the Caenorhabditis elegans vulva is a powerful, simple, and experimentally accessible model for elucidating how morphogenetic processes produce an organ. In the first step of vulval development, three epithelial precursor cells divide and differentiate to generate 22 cells of 7 different vulval subtypes. The 22 vulval cells then rearrange from a linear array into a tube, with each of the seven cell types undergoing characteristic morphogenetic behaviors that construct the vulva. Vulval morphogenesis entails many of the same cellular activities that underlie organogenesis and tissue formation across species, including invagination, lumen formation, oriented cell divisions, cell–cell adhesion, cell migration, cell fusion, extracellular matrix remodeling, and cell invasion. Studies of vulval development have led to pioneering discoveries in a number of these processes and are beginning to bridge the gap between the pathways that specify cells and their connections to morphogenetic behaviors. The simplicity of the vulva and the experimental tools available in C. elegans will continue to make vulval morphogenesis a powerful paradigm to further our understanding of the largely mysterious mechanisms that build tissues and organs. WIREs Dev Biol 2013, 2:75–95. doi: 10.1002/wdev.87
An Algorithm for Permuting Variables of Recursively Represented Polynomials

A straightforward way to represent multivariate polynomial in software is to implement them recursively as univariate polynomials over a polynomial ring. This is especially common in an object oriented context. We present a short algorithm which maps polynomials from one polynomial ring to another polynomial ring where the order of variables is permuted. This algorithm uses the recursive representation and does not change to another representation.
Cytomegalovirus Misleads Its Host by Priming of CD8 T Cells Specific for an Epitope Not Presented in Infected Tissues

Cytomegaloviruses (CMVs) code for several proteins that inhibit the presentation of antigenic peptides to CD8 T cells. Although the molecular mechanisms of CMV interference with the major histocompatibility complex class I pathway are long understood, surprisingly little evidence exists to support a role in vivo. Here we document the first example of the presentation of an antigenic peptide being blocked by a CMV immune evasion protein in organs relevant to CMV disease. Although this Db-restricted peptide, which is derived from the antiapoptotic protein M45 of murine CMV (mCMV), is classified as an immunodominant peptide based on response magnitude and long-term memory, adoptive transfer of M45 epitope-specific CD8 T cells did not protect against infection with wild-type mCMV. Notably, the same cells protected C57BL/6 mice infected with an mCMV mutant in which immune evasion protein m152/gp40 is deleted. These data indicate that direct presentation or cross-presentation of an antigenic peptide by professional antigen-presenting cells can efficiently prime CD8 T cells that fail in protection against CMV organ disease because m152/gp40 prevents presentation of this peptide in pathogenetically relevant tissue cells.
MOGAT: a cloud-based mobile game system with auditory training for children with cochlear implants

Musical auditory habilitation is an essential process in adapting cochlear implant recipients to the musical hearing context provided by cochlear implants. However, due to the cost and time limitation, it is impossible for hearing healthcare professionals to provide intensive and extensive musical auditory habilitation for every cochlear implant recipient. In order to provide an efficient and cost-effective musical auditory training for children with cochlear implants, we designed and developed MObile Games with Auditory Training (MOGAT) on off-the-shelf mobile devices. MOGAT includes three intuitive and interesting mobile games for training pitch perception and production, and a cloud-based web service for music therapists to support and evaluate individual habilitation. We demonstrate MOGAT for enhancing musical habilitation for children with cochlear implants.
Adaptive modulation for cooperative wireless communication systems

Cooperative wireless communication network provides diversity by emulating multi-input and multi-output (MIMO) system for devices that are spatially too small to harbor multiple antennas. Since mobility and easy handling require terminal miniaturization, cooperative communication is required to fill the gap for MIMO. Conventional cooperative protocols such as amplify-and-forward (AF) and decode-and-forward (DF) attain diversity gain at the cost of reduced spectral efficiency which as a result brings about reduced throughput. In this paper, adaptive modulation is applied to improve the throughput performance of AF wireless cooperative strategy. The source and relay respond to the channel state information (CSI) obtained from the destination as a feedback to change M-QAM types. Simulation results show that modulation adaptive cooperation performs better than the non adaptive counterpart in overall throughput.
Kinematics analysis of a transformable wheel-track robot with self-adaptive mobile mechanism

Performing the dangerous mission such as planetary exploration, reconnaissance, anti-terrorism, and rescue, the mobile robot should be capable of moving in the complex and unpredictable environment where the ground may be soft and hard, even and uneven. To access to such terrain features, a novel robot with the self-adaptive mobile mechanism, named as Amoeba-III, has been proposed and developed. It consists of a control system unit and two symmetric transformable wheel-track (TWT) units. Driven only by one servo motor, each TWT unit can efficiently drive over rough terrain by changing the locomotion mode and transforming the track configuration. It means that the mobile mechanism of the robot has self-adaptability to the irregular environment. This paper briefly introduces the mobile mechanism of Amoeba-III, analyses its locomotion modes and postures when the robot runs on the different terrain. Kinematics analysis is presented to verify the movement of Amoeba-III. Finally, experimental results show the validity of this platform.
3D catheter path reconstruction from biplane angiograms

The 3D coronary vessels can be reconstructed by means of different cardiac imaging modalities. Two of the most widely used modalities for the purpose of coronary tree reconstruction are intravascular ultrasounds (IVUS) and biplane angiography. Current 3D vessel reconstruction based on IVUS pullback imaging is limited by the lack of information about the real vessel curvature, because the path of the catheter is assumed to be a straight line. This limitation can be overcome if information from an IVUS sequence is fused with a biplane X-ray image of the catheter acquired at the start of the pullback procedure. This work focuses on the reconstruction of the catheter path from biplane angiograms. This reconstruction represents the 3D path followed by the catheter inside the vessel of interest. While other approaches reconstruct the vessel after it has been segmented in both images independently, our approach, based on the snakes technique, allows us to segment and reconstruct the catheter trajectory merging information from both images simultaneously. The result is a more robust reconstruction since 3D constraints can be used and no correspondence of points between the projections is required. This reconstruction will allow a posterior more exact combination of IVUS and biplane angiography image modalities.
Multicategory Classification using Extended SVM-RFE and Markov Blanket on SELDI-TOF Mass Spectrometry Data

Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry data has been increasingly analyzed for identifying biomarkers for disease to help early detection of the disease. Recently, support vector machine (SVM) algorithm based on recursive feature elimination (RFE) was proposed to find a set of genes for cancer classification. In our study, we extend the SVM-RFE such that it can be used in the multicategory classification work using SELDI-TOF mass spectrometry data and propose a new feature selection algorithm (SVM-MB/RFE : SVM-Markov Blanket/Recursive Feature Elimination). In the preprocessing task of SVM-MB/RFE, ANOVA (Analysis of Variance) and binning methods are used for feature filtering. We demonstrate that the performance is improved through the preprocessing work. Compared with other methods such as not only SVM-RFE and Markov blanket but also PCA (Principle Components Analysis)+LDA (Linear Discriminant Analysis) and other feature selection algorithms, SVM-MB/RFE performs better than them.
Proposing a fast circular HOG descriptor for detecting rotated objects

Object detection is one of the most interesting branches in computer vision. Accurate detection systems can be utilized to various areas. There are two steps in detection, feature extraction and classification. In this paper, new feature extraction method is proposed. Histogram Oriented Gradient (HOG) is famous, fast and accurate feature, but it is not rotation invariant. This paper proposes a new shape of HOG for fast detection of rotated objects. The proposed method is faster than conventional method in rotational object detection.
Pulsed magnetization transfer spin‐echo MR imaging

Cross relaxation between macromolecular protons and water protons is known to be important in biologic tissue. In magnetic resonance (MR) imaging sequences, selective saturation of the characteristically short T2 macromolecular proton pool can produce contrast called magnetization transfer contrast, based on the cross‐relaxation process. Selective saturation can be achieved with continuous wave irradiation several kilohertz off resonance or short, intense 0° pulses on resonance. The authors analyze 0° binomial pulses for T2 selective saturation, present design guidelines, and demonstrate the use of these pulses in spin‐echo imaging sequences in healthy volunteers and patients. Using the phenomenologic Bloch equations modified for two‐site exchange, the authors derive the analytic expressions for water proton relaxation under periodic pulsed saturation of the macromolecular protons. This relaxation is shown to be monoexpo‐nential, with a rate constant dependent on the saturation pulse repetition rate and the individual and cross‐relaxation rates.
Validation of the Korean Version of the DN4 Diagnostic Questionnaire for Neuropathic Pain in Patients with Lumbar or Lumbar-Radicular Pain

Purpose To evaluate the diagnostic value of the Korean version of the Douleur Neuropathique 4 (DN4) questionnaire and to validate this questionnaire in terms of psychometric properties in patients with chronic pain due to degenerative spinal disease. Materials and Methods The Korean version of the DN4 questionnaire, which was translated and linguistically validated by the MAPI Research Group, was tested on 83 patients with lumbar or lumbar-radicular pain. Test-retest reliability was evaluated in a subsample of 40 patients who completed two assessments with an interval of 2 weeks. Nociceptive pain and neuropathic component pain were diagnosed in 40 and 43 patients, respectively. Results The Cronbach's α coefficient of internal consistency was 0.819, and the test-retest intraclass correlation coefficient (3, 1) (95% confidence interval) was 0.813 (0.776–0.847) (n=40). The area under the receiver-operator characteristics curve was 0.953 (p<0.001), with 95% confidence interval between 0.869 and 0.990. The Korean version of the DN4 questionnaire showed a sensitivity of 100% and 87.1%, and a specificity of 88.2% and 94.1% at the cutoff value of 3/10 and 4/10, respectively, for discriminating neuropathic component pain. Conclusion The present study demonstrated the good discriminatory power of DN4 between nociceptive pain and neuropathic component pain in patients with lumbar or lumbar-radicular pain.
Elements of Dynamic Programming in Sorting

Dynamic programming is an effective algorithm design method. Sorting is believed to be an unusual area for dynamic programming. Our finding is contrary to this conventional belief. Though it appears that classical sorting algorithms were designed using bottom up design approach, but we have found the evidence which suggests that some classical sorting algorithms can also be designed using Dynamic programming design method. Even the development of classical Merge algorithm shows elements of dynamic programming. This paper finds that development of sorting algorithms can be looked from an entirely different point of view. This work will reveal some new facts about the design or development of some key sorting algorithms. It was discovered that this new interpretation gives a deep insight about the design of some fundamental sorting algorithms.
Economic and energy analysis of a Thermal Energy Storage power system

The continuous use of fossil fuels has resulted in reserve depletion and environmental problems. It is felt that renewable energy sources (RES), such as wind and solar, are quite capable to actively contribute to meeting the today's energy demand. However, RES have a time dependent nature that constitutes their major disadvantage. To overcome this drawback, an energy storage system needs to be set up. In this manner, the stored energy can be utilized in the absence of RES or under peak load conditions. High-temperature pumped thermal energy storage (PTES) using packed bed constitutes an attractive solution. For this reason, in the present paper, the state of the art of high temperature energy storage for power generation is briefly reviewed. Subsequently, a modified plant scheme has been developed and built in Matlab environment. In order to predict the packed bed behaviour, a detailed model of the hot and cold storage has been included. Energy and economic evaluations have been performed to understand the feasibility of the proposed system. The modified PTES architecture shows better energy and economic performance than previous developed schemes.