Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Learning Procedure in Loopy Belief Propagation for Probabilistic Image Processing

We give a fast and practical algorithm for statistical learning hyperparameters from observable data in probabilistic image processing, which is based on Gaussian graphical model and maximum likelihood estimation. Although hyperparameters in the probabilistic model are determined so as to maximize a marginal likelihood, a practical algorithm is described for the EM algorithm with the loopy belief propagation which is one of approximate inference algorithms in artificial intelligence
The Prohibitins: emerging roles in diverse functions

The prohibitins, Phb1 and Phb2 are highly conserved proteins in eukaryotic cells that are present in multiple cellular compartments. Initial investigations focused on the role of Phb1 as an inhibitor of cell proliferation hence the original name prohibitin. However both proteins appear to have a diverse range of functions and recent evidence suggests that the prohibitins have very similar but as yet only partially understood functions. In addition to their role as chaperone proteins in the mitochondria, and their ability to target to lipid rafts, their is now compelling evidence that both prohibitins are localized in the nucleus and can modulate transcriptional activity by interacting with various transcription factors, including the steroid hormone receptors, either directly or indirectly. In addition Phb1 and Phb2 are present in the circulation and can be internalized when added to cultured cells suggesting that the circulating prohibitins may have some regulatory role. This review presents some of the recent developments in prohibitin research and focuses on the similarities in the structure and function of these interesting proteins.
Speech enhancement: new approaches to soft decision

In this paper, we propose new approaches to speech enhancement based on soft decision. In order to enhance the statistical reliability in estimating speech activity, we introduce the concept of a global speech absence probability (GSAP). First, we compute the conventionalspeech absence probability (SAP) and then modify it according to the newly proposed GSAP. Moreover, for improving the performance of the SAP’s at voice tails (transition periods from speech to silence), we revise the SAP’s using a hang-over scheme based on hidden Markov model (HMM). In addition, we suggest a robust noise update algorithm in which the noise power is estimated not only in the periods of speech absence but also during speech activity by noise and speech spectrum estimation based on soft decision. Also, for improving the SAP determination and noise update routine we present a new signal to noise ratio (SNR) concept which is called the predicted SNR in this paper. The prediced SNR is deﬁned by the ratio between estimated speech and noise spectrum makes a further improvement the discrete cosine transform (DCT). Results from the test show that the proposed algorithm which is called the speech enhancement based on soft decision (SESD) yields better performance than the conventional methods.
Inhibition of Heme Oxygenase-1 Interferes with the Transforming Activity of the Kaposi Sarcoma Herpesvirusencoded G Protein-coupled Receptor*♦

Heme oxygenase-1 (HO-1), the inducible enzyme responsible for the rate-limiting step in the heme catabolism, is expressed in AIDS-Kaposi sarcoma (KS) lesions. Its expression is up-regulated by the Kaposi sarcoma-associated herpesvirus (KSHV) in endothelial cells, but the mechanisms underlying KSHV-induced HO-1 expression are still unknown. In this study we investigated whether the oncogenic G protein-coupled receptor (KSHV-GPCR or vGPCR), one of the key KSHV genes involved in KS development, activated HO-1 expression. Here we show that vGPCR induces HO-1 mRNA and protein levels in fibroblasts and endothelial cells. Moreover, targeted knock-down gene expression of HO-1 by small hairpin RNA and chemical inhibition of HO-1 enzymatic activity by tin protoporphyrin IX (SnPP), impaired vGPCR-induced survival, proliferation, transformation, and vascular endothelial growth factor (VEGF)-A expression. vGPCR-expressing cells implanted in the dorsal flank of nude mice developed tumors with elevated HO-1 expression and activity. Chronic administration of SnPP to the implanted mice, under conditions that effectively blocked HO-1 activity and VEGF-A expression in the transplanted cells, strikingly reduced tumor growth, without apparent side effects. On the contrary, administration of the HO-1 inducer cobalt protoporphyrin (CoPP) further enhanced vGPCR-induced tumor growth. These data postulate HO-1 as an important mediator of vGPCR-induced tumor growth and suggest that inhibition of intratumoral HO-1 activity by SnPP may be a potential therapeutic strategy.
Leprosy and the Adaptation of Human Toll-Like Receptor 1

Leprosy is an infectious disease caused by the obligate intracellular pathogen Mycobacterium leprae and remains endemic in many parts of the world. Despite several major studies on susceptibility to leprosy, few genomic loci have been replicated independently. We have conducted an association analysis of more than 1,500 individuals from different case-control and family studies, and observed consistent associations between genetic variants in both TLR1 and the HLA-DRB1/DQA1 regions with susceptibility to leprosy (TLR1 I602S, case-control P = 5.7×10−8, OR = 0.31, 95% CI = 0.20–0.48, and HLA-DQA1 rs1071630, case-control P = 4.9×10−14, OR = 0.43, 95% CI = 0.35–0.54). The effect sizes of these associations suggest that TLR1 and HLA-DRB1/DQA1 are major susceptibility genes in susceptibility to leprosy. Further population differentiation analysis shows that the TLR1 locus is extremely differentiated. The protective dysfunctional 602S allele is rare in Africa but expands to become the dominant allele among individuals of European descent. This supports the hypothesis that this locus may be under selection from mycobacteria or other pathogens that are recognized by TLR1 and its co-receptors. These observations provide insight into the long standing host-pathogen relationship between human and mycobacteria and highlight the key role of the TLR pathway in infectious diseases.
Formalizing Causality as a Desideratum for Memory Models and Transformations of Parallel Programs

It has been observed in previous work that it is desirable to avoid causal violations in any execution or transformation of a parallel program. In this paper, we formalize the notion of causality in memory consistency models and code transformations. For memory models, we introduce a framework of causality graph that can be used to analyze if a particular memory model violates causality. We show that a popular memory model as the Java memory model (JMM) [16], can lead to program executions that exhibit causality violations with respect to our definition of causality. The same analysis appears to also apply to a recent proposal of C++ specification [7] where the underline memory model may also lead to similar problems. For code transformations, we identify transformations that are causality-preserving and those that are potentially causality-violating. We found that 10 of the 13 code transformation examples that were identified as causality-preserving with respect to the Java Memory Model fail our causality graph test and thus represent causality violations in our framework. Likewise, we also present examples to illustrate how the recently proposed C++ Memory Model can lead to potential causality violations. Using our formalization, we establish causality as a desideratum for memory models and code transformations of parallel programs and define a Causal Memory Model (CMM) as the weakest memory model that preserves causality. We identify specific code transformations that are guaranteed to be causality-preserving. Finally, we present preliminary experimental results for a load elimination optimization to motivate the performance benefit of using the CMM model relative to the Sequential Consistency (SC) model. For the benchmark program studied, the number of getfield operations performed was reduced by 37.9% by using the CMM model instead of the SC model, and the execution time on a 16-core processor was reduced by 46.2%.
Non-Linear Stability Analysis of a Reduced Scale Model Pump-Turbine at Off-Design Operation

Nowadays, the pump-storage power plants are a proven solution for storing electricity at large scale and offering flexibility to the power management. Therefore, the hydraulic machines are increasingly subject to off-design operation, start-up and shutdown sequences. However, the fast and frequent switching between pumping mode and generating mode presents technical challenges. In the present study, the reduced scale model of a low specific speed pump-turbine is investigated in generating mode at off-design conditions. The operation in the typical “S-shaped” curve of pump-turbine may become unstable and the machine may switch back and forth from generating mode to reverse pumping mode preventing the correct experimental survey of this part during the model testing. The instability has been solved by a testing procedure imposing a restriction of section and a control valve for being able to increase the energy losses. This procedure, commonly used in model testing of pump-turbines, significantly improves the stability of the machine and allows for the survey of the entire “S-curve”. The aim of the present investigation is to understand and explain the origin of the switch to reverse pumping mode. Thus, a hydro-acoustic test rig model was developed with the In-house EPFL SIMSEN software and a comparison between the systems with and without a restriction of section was studied. A numerical analysis indicates that the operating points of a pump-turbine system are defined by the solution of the equation relating the test rig characteristic and the energy-discharge characteristic of the hydraulic machine for a given rotational speed and a constant guide vanes opening. Furthermore, the addition of a restriction alters the curvature of the test rig characteristic and creates a new degree of freedom to achieve stable operating points in the “S-curve”. Finally, to ensure the stability of each operating points described by the numerical model, an eigenvalue study of the non-linear hydraulic system is necessary.
Functional electrical stimulation increases neural stem/progenitor cell proliferation and neurogenesis in the subventricular zone of rats with stroke

Background Functional electrical stimulation (FES) is known to promote the recovery of motor function in rats with ischemia and to upregulate the expression of growth factors which support brain neurogenesis. In this study, we investigated whether postischemic FES could improve functional outcomes and modulate neurogenesis in the subventricular zone (SVZ) after focal cerebral ischemia. Methods Adult male Sprague‐Dawley rats with permanent middle cerebral artery occlusion (MCAO) were randomly assigned to the control group, the placebo stimulation group, and the FES group. The rats in each group were further assigned to one of four therapeutic periods (1, 3, 7, or 14 days). FES was delivered 48 hours after the MCAO procedure and divided into two 10‐minute sessions on each day of treatment with a 10‐minute rest between them. Two intraperitoneal injections of bromodeoxyuridine (BrdU) were given 4 hours apart every day beginning 48 hours after the MCAO. Neurogenesis was evaluated by immunofluorescence staining. Wnt‐3 which is strongly implicated in the proliferation and differentiation of neural stem cells (NSCs) was investigated by Western blotting analysis. The data were subjected to one‐way analysis of variance (ANOVA), followed by a Tukey/Kramer or Dunnett post hoc test. Results FES significantly increased the number of BrdU‐positive cells and BrdU/glial fibrillary acidic protein double‐positive neural progenitor cells in the SVZ on days 7 and 14 of the treatment (P <0.05). The number of BrdU/doublecortin (DCX) double‐positive migrating neuroblast cells in the ipsilateral SVZ on day 14 of the FES treatment group ((522.77±33.32) cells/mm2) was significantly increased compared with the control group ((262.58±35.11) cells/mm2, P <0.05) and the placebo group ((266.17±47.98) cells/mm2, P <0.05). However, only a few BrdU/neuron‐specific nuclear protein‐positive cells were observed by day 14 of the treatment. At day 7, Wnt‐3 was upregulated in the ipsilateral SVZs of the rats receiving FES ((0.44±0.05)%) compared with those of the control group rats ((0.31±0.02)%, P <0.05) or the placebo group rats ((0.31±0.04)%, P <0.05). At day 14, the corresponding values were (0.56±0.05)% in the FES group compared with those of the control group rats ((0.50±0.06)%, P <0.05) or the placebo group rats ((0.48±0.06)%, P <0.05). Conclusion FES augments the proliferation, differentiation, and migration of NSCs and thus promotes neurogenesis, which may be related to the improvement of neurological outcomes.
Whey Protein Supplementation Improves Rehabilitation Outcomes in Hospitalized Geriatric Patients: A Double Blinded, Randomized Controlled Trial

ABSTRACT Whey protein supplementation (WPS) has been shown to improve functional outcomes in populations that are able to participate in high-intensity resistance training. The purpose of the study was to evaluate the efficacy of WPS on rehabilitation outcomes in a frail, hospitalized elderly population. Men and women (n = 47) were randomly assigned to either a control group or WPS group for the length of their hospital stay. Several functional and serum measures were determined pre- and post-intervention. WPS significantly increased average daily protein intake and was well tolerated. The WPS group exhibited significant improvements in grip strength and knee extensor force over the control group, and a significant positive correlation was found between change in prealbumin and percent-increase knee extensor force. These findings support the use of WPS to improve protein nutritional status and rehabilitation outcomes in a clinical setting involving a frail, elderly population.
Do Asian Stock Markets Follow a Random Walk? Evidence from LM Unit Root Tests with One and Two Structural Breaks

This paper applies univariate and panel Lagrange Multiplier (LM) unit root tests with one and two structural breaks to examine the random walk hypothesis for stock prices in eight Asian countries. The results from the univariate LM unit root tests and panel LM unit root test with one structural break suggest that stock prices in each country is characterized by a random walk, but the findings from the panel LM unit root test with two structural breaks suggest that stock prices in the eight countries are mean reverting.
Instability of the Mitofusin Fzo1 Regulates Mitochondrial Morphology during the Mating Response of the Yeast Saccharomyces cerevisiae*

Mitochondria form a highly dynamic network that is shaped by continuous fission and fusion of these organelles. In the yeast Saccharomyces cerevisiae two machineries are involved in this process, one of which includes the mitochondrial fusion promoting GTPase Fzo1. Although a role for the F-box protein Mdm30 in regulating the stability of Fzo1 has been proposed, the molecular basis for the regulation of the fission to fusion ratio of mitochondria remains unknown. To discern the mechanism of the regulation of mitochondrial morphology, we arrested cells at different stages of the cell cycle and examined mitochondrial morphology as well as the stability of mitochondrial fission and fusion proteins. In response to a G1 arrest evoked by the mating pheromone α factor the mitochondrial network fragmented into small pieces, which was accompanied by dramatic down-regulation of Fzo1. Mating pheromone also triggered the degradation of Fzo1 produced under the control of a constitutive promoter, and Fzo1 was stabilized upon proteasome inhibition, indicating a role for the proteasome system in the degradation of Fzo1. However, deletion of MDM30 did not stabilize Fzo1 after mating pheromone treatment, showing a different mechanism from the previously reported process of steady state Fzo1 regulation. We show an example for a regulated change of the mitochondrial fission to fusion ratio during the life cycle of budding yeast. Proteasomal degradation of Fzo1 in response to the mating pheromone is proposed to mediate the remodeling of the mitochondrial network during the process of mating.
Communication architecture for monitoring and control of power distribution grids over heterogeneous ICT networks

In order to provide a comprehensive monitoring and controll infrastructure capable of fulfilling the requirements for security, control-ability and reliability of a modern Smart Grid, several factors for the adaptation of ICT technologies and architectures need to be considered. In this context Smart Grid systems operate on two time scales: first requiring delays in the order of μs for reporting events, e.g. short-circuits or component failures, and second data collection of the operational grid state from a huge number of sources, e.g. smart meters, sensors, etc., on the order of seconds to minutes. In this paper we focus on how network technologies can support this communication requirement of Smart Grid operation. Therefore, the focus is on reliability and control-ability of the network by providing the appropriate quality of service. For this purpose an overall heterogeneous communication architecture is presented, mapping the logical components and interfaces of multi-domain use cases to particular physical components and interfaces, which are implemented in testbeds and simulation models for assessment. Hereby, the major objective of the presented reference architecture is an unique definition of technical interfaces, components and information flows. It furthermore provides a framework for the specification of different technological options, information management and data aggregation. This work results in a novel approach for monitoring and controlling of energy distribution grids over heterogeneous communication networks is presented, which is based on two inter-related inner and outer control-loops for energy grid and communication network control. Furthermore, an application scenario is presented based on the integration of advanced meter reading and customer energy management systems into the overall architecture.
Reversible Oxidative Modification as a Mechanism for Regulating Retroviral Protease Dimerization and Activation

ABSTRACT Human immunodeficiency virus protease activity can be regulated by reversible oxidation of a sulfur-containing amino acid at the dimer interface. We show here that oxidation of this amino acid in human immunodeficiency virus type 1 protease prevents dimer formation. Moreover, we show that human T-cell leukemia virus type 1 protease can be similarly regulated through reversible glutathionylation of its two conserved cysteine residues. Based on the known three-dimensional structures and multiple sequence alignments of retroviral proteases, it is predicted that the majority of retroviral proteases have sulfur-containing amino acids at the dimer interface. The regulation of protease activity by the modification of a sulfur-containing amino acid at the dimer interface may be a conserved mechanism among the majority of retroviruses.
A Study on Feature Selection for Trend Prediction of Stock Trading Price

The movement of price is influenced by many factors or features in stock market. It is a challenging work how to select these features and provide the relation between them and the movement of price. This paper applies two recursive feature elimination (RFE) methods SVM-RFE and RF-RFE to feature selection in the trend prediction of stock price, where SVM-RFE and RF-RFE are based on the famous support vector machine (SVM) and random forest (RF) techniques, respectively. Both the stability and classification performance for the subset of features selected are investigated. The experimental results on nine shares from Shanghai Stock Exchange in China show that both SVM and RF are effective for the trend prediction, and SVM performs better than RF. In addition, SVM seems to be unaffected by the correlation and redundant features and it turns better for the most shares when more features are used for modeling. Therefore, a suggestion for RFE in the trend prediction of stock price is that it may be unnecessary for SVM while it is needed for RF.
The non-commutative brane world

We propose a new higher-dimensional mechanism to localize scalar fields as well as fermionic and gauge fields. The underlying theory is a six-dimensional non-commutative field theory where non-commutativity is allowed along two extra infinite spatial dimensions and the four-dimensional brane is provided by a scalar soliton living in the non-commutative space. Making use of the powerful correspondence between non-commutative coordinates and operators on a single particle Hilbert space, we show that the non-commutative brane world admits localized chiral fermions and it ensures the localization of massless gauge fields. It may also give rise to a variety of different low-energy spectra since the localized zero mode may come along either with a discrete tower of degenerate heavy states or with a tower of Kaluza-Klein heavy states, or it may even be the only state in the low-energy spectrum.
A 16Gb/s 1st-Tap FFE and 3-Tap DFE in 90nm CMOS

Much effort has been made toward producing a high-speed multi-tap decision feedback equalizer (DFE), which would be a key component in removing inter-symbol interference (ISI) in high-speed chip-to-chip communication. A loop-unrolled approach is widely used in work toward the design of high-speed multi-tap DFEs. It eliminates the feedback operation in first post-cursor equalization [1–3], an operation that limits operational speed in conventional multi-tap DFEs. There are two problems, however, to its application to equalization of 16Gb/s signals. The first is that additional components in the feedback path, used for speculation on the basis of sampled data, increase 2nd-tap feedback delay, preventing high-speed operations. The second problem is that jitter increase in equalized waveforms prevents accurate clock timing recovery because the 1st tap ISI of the waveform is left un-equalized. In response to this situation, we have developed three techniques for achieving 16Gb/s communication: (1) an analog feedforward technique for high-speed 1st-tap ISI equalization, (2) an analog feedforward technique for jitter reduction in equalized edges, and (3) technique for employing bypass feedback and a voltage swing limiter in order to speed-up both 2ndtap and 3rd-tap equalization. We have applied these techniques to a 16Gb/s equalizer fabricated in a 90nm CMOS process, and their use helps achieve a 33% increase in operating speed over that with conventional multi-tap DFEs[3].