Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Depletion Causes Neonatal-Onset Leigh Syndrome, Myopathy, and Renal Tubulopathy

The authors describe a newborn with postnatal myopathy who subsequently developed feeding difficulties, ophthalmoplegia, ptosis, encephalopathy, and seizures. She became ventilator dependent after sudden apnea. The myopathy was without ragged red fibers in the muscle biopsy. An electron transport chain study showed a markedly generalized low level of enzyme activity, particularly in complexes I, I + III, and IV. An initial electroencephalogram finding was normal; subsequent electroencephalograms showed suppression bursts. The mitochondrial copy number in skeletal muscle was 2% of normal.
Morbimortality indicators in severe acute pancreatitis.

OBJECTIVE The aim of this study was to determine the factors related to the development of systemic complications, mortality and pancreatic necrosis in patients with severe acute pancreatitis. PATIENTS Thirty-nine patients (22.3%) out of 175 patients with acute pancreatitis who were admitted to our center, had an APACHE II score greater than 8; they were classified as having severe acute pancreatitis and were evaluated in the study. MAIN OUTCOME MEASURES Sepsis-related Organ Failure Assessment (SOFA) and Marshall scores were obtained. The variables analyzed were age, sex, etiology, hematocrit, leukocyte count, CRP level, CT findings and length of hospital stay. These variables were related to the development of systemic complications, mortality and necrotizing pancreatitis. RESULTS The mean APACHE II value of the patients included was 11.6+/-3.1, the mean SOFA score was 3.2+/-2.0 and the Marshall score was 1.5+/-1.9. Eleven patients developed necrotizing pancreatitis. The mortality rate among severe acute pancreatitis patients was 3 out of 39 (7.7%). Variables found to be related to systemic complications were the APACHE II score as well as SOFA and Marshall scores greater than 3. The variables related to mortality were SOFA score greater than 3 and leukocytosis greater than 19,000 mm(-3). CRP greater than 19.5 mg/dL and length of hospital stay were related to necrotizing pancreatitis. CONCLUSIONS The scoring systems, especially the SOFA score, were related to the development of systemic complications and mortality. CRP showed a relationship to necrotizing pancreatitis. There was no relationship between the evaluated scoring systems and necrotizing pancreatitis in patients with severe acute pancreatitis.
Delay-Dependent Doppler Probability Density Functions for Vehicle-to-Vehicle Scatter Channels

Novel joint delay Doppler probability density functions for vehicle-to-vehicle communications channels are introduced. Prior measurements of vehicle-to-vehicle channels have unveiled their nonstationarity; thus, the wide-sense stationary and also the uncorrelated scattering assumption for such channels is often violated, which makes their modeling challenging. In this work it is proposed to exploit geometry-based stochastic modeling to cope with the nonstationarity of vehicle-to-vehicle channels. To this end, delay-dependent Doppler pdfs are derived for arbitrary times. It is assumed that scatterers are randomly distributed on an ellipse with two moving vehicles being in its foci. The proposed approach allows reducing the dimensionality of the resulting problem. This in turn leads to a significantly simplified derivation of the delay-dependent Doppler pdfs for general vehicle-to-vehicle propagation environments; moreover, the resulting computations can be performed almost fully analytically. By combining the calculated Doppler pdf with a delay pdf, the joint pdf of delay and Doppler is obtained. The joint pdf then can be put into relation with the generalized local scattering function. The presented modeling approach is simple yet very scalable and accurate, which allows its application in different vehicular scenarios. The obtained modeling results correspond very well with measurement data reported in prior works.
Efficient Cellular Transformation by the Met Oncoprotein Requires a Functional Grb2 Binding Site and Correlates with Phosphorylation of the Grb2-associated Proteins, Cbl and Gab1*

The Tpr-Met oncoprotein consists of the catalytic kinase domain of the hepatocyte growth factor/scatter factor receptor tyrosine kinase (Met) fused downstream from sequences encoded by thetpr gene. Tpr-Met is a member of a family of tyrosine kinase oncoproteins generated following genomic rearrangement and has constitutive kinase activity. We have previously demonstrated that a single carboxyl-terminal tyrosine residue, Tyr489, is essential for efficient transformation of Fr3T3 fibroblasts by Tpr-Met and forms a multisubstrate binding site for Grb2, phosphatidylinositol 3′ kinase, phospholipase Cγ, SHP2, and an unknown protein of 110 kDa. A mutant Tpr-Met protein that selectively fails to bind Grb2 has reduced transforming activity, implicating pathways downstream of Grb2 in Tpr-Met mediated cell transformation. We show here that the 110-kDa Tpr-Met substrate corresponds to the recently identified Grb2-associated protein, Gab1. Moreover, we show that tyrosine phosphorylation of the Cbl protooncogene product as well as Gab1 required Tyr489 and correlated with the ability of Tpr-Met to associate with Grb2 and to transform cells, providing evidence that pathways downstream of Gab1 and/or Cbl may play a role in Tpr-Met-mediated cell transformation.
OptiTuner: On Performance Composition and Server Farm Energy Minimization Application

This paper develops a software service for dynamic performance optimization and control in performance-sensitive systems. The next generation of performance-sensitive systems is expected to be more distributed and dynamic. They will have multiple "knobs” that affect performance and resource allocation. However, relying on the conglomeration of independent knob controls can become increasingly suboptimal. The problem lies in performance composability or lack thereof; a challenge that arises because individual optimizations in performance-sensitive systems generally do not compose well when combined. Performance adaptation in such systems needs to be carefully designed and implemented by holistically considering performance composability in order to achieve desired system performance. A flexible supporting software layer is therefore needed to easily apply different holistic performance management techniques. In this paper, we develop a software service, called OptiTuner, that monitors the current performance and the resource availability in performance-sensitive systems and allows easy implementation of different performance management schemes based on theoretical concepts of constrained optimization and feedback control. In order to show the efficacy of OptiTuner, we apply it to implement three holistic energy minimization techniques in a real-time web server farm comprising 18 machines. Using an industry standard e-Business benchmark, TPC-W, we demonstrate that the three approaches save up to 40 percent of total energy cost compared to the baseline approaches that do not holistically optimize the cost.
Exploring Active Video Games (AVGS) as an Intervention Promoting Wellbeing as It Relates to Depression

Depression and anxiety are the two most common forms of mental illness that affect people in the U.S. Great strides have been made over the years in improving the mental health of persons with these and other forms of mental illness. Although newer medications such as SSRls can greatly enhance one's quality of life, there are lifestyle behaviors such as exercise and meaningful engagement in activities that have also purported similar positive outcomes. A challenge for health care providers is how to motivate mental health patients to change their behaviors, especially considering the apathy and passivity, typically associated with the illness, may have affected one's ability to initiate such activities. A novel approach to encourage physical activity could be the use of active video games (AVGs) such as the Xbox Kinect. The advantages of applying video game technology are that it allows active participation on an inpatient unit, and allows portability once a patient is discharged to the community. In addition; if the movement were also associated with a meaningful activity that provides intrinsic satisfaction, then there would be a greater motivation to continue the behavior beyond the institutional setting. This paper is a summary of related research to the use of active video games in the treatment of people with depression and anxiety. Suggestions for the future application of active video games are also provided. Degree Type Open Access Senior Honors Thesis Department Health Sciences First Advisor David Thomas
String-Wise Information Flow Tracking against Script Injection Attacks

Nowadays, security of web applications faces a threat of script injection attacks. DTP (Dynamic Taint Propagation) and DIFT (Dynamic Information Flow Tracking) have been established as powerful techniques to detect script injection attacks. However current DTP/DIFT systems still suffer from tradeoff between false positives and negatives.This paper proposes String-Wise Information Flow Tracking, SWIFT. SWIFT traces memory access of program execution, detects string access and distinguishes string operations from other memory access. Current DTP/DIFT systems propagate taint from source to destination operands. Instead of that, SWIFT propagates taint information under string operations. This makes SWIFT provide a better accuracy on detection of script injection attacks than current DTP/DIFT systems.We implemented SWIFT on an IA-32 emulator Bochs, executed typical string operations and made injection attacks to some real-world web applications with known vulnerabilities. As a result, SWIFT shows a high precision in our security experiments.
Optimal Tradeoff between Energy Consumption and Response Time in Large-Scale MapReduce Clusters

The increasing growth of the size of the digital databases has given rise to the need for the development of infrastructures, such as large scale data centers and computational clusters, which are capable of storing and processing very large volumes of data. To date, most clusters have been designed for performance. Due to non-linear speed-ups that are common to typical applications, performance maximization involves the decision of the number of the nodes to process a specific (intensive) task, as opposed to the utilization of the full cluster. In addition, energy consumption has recently attracted significant attention, given that the cost to operate a cluster may well exceed its acquisition cost. This issue calls for judicious use of resources as well. The aim of this study is to present a method that achieves the optimal tradeoff between energy consumption and response time in distributed clusters, such as Map Reduce clusters. To this end, we propose an algorithm that derives the fraction of the nodes that minimizes the energy consumption without sacrificing performance (in terms of response time) more than a user-defined threshold. Moreover, we present a generic and configurable framework to describe performance and energy consumption as a function of the nodes used, our framework can accommodate the widely spread Map Reduce-like parallel executions in a straightforward manner. The evaluation results show that our methodology can lead to significant energy savings with acceptable performance penalty in many realistic situations.
Modèles de RI fondés sur l'information

Nous presentons dans cet article une vue analytique des contraintes heuristiques recemment proposees pour les fonctions d’ordonnancement (retrieval function). Ces caracterisations permettent ainsi de tester simplement si un modele de recherche d’information (RI) respecte ces contraintes ou non. De plus, nous examinons un certain nombre de resultats empiriques sur les distributions de frequences de mots et le role central joue par le phenomene de rafale, pour lequel nous proposons une definition formelle. Nous introduisons ensuite une nouvelle famille de modeles probabilistes pour la RI, fondee sur la notion d’information. Lorsque la loi de probabilite sous-jacente est capable de modeliser le phenomene de rafale, alors le modele devient naturellement valide au sens des contraintes heuristiques. Les distributions log-logistique et SPL sont presentees dans ce contexte et les experiences, menees sur trois collections differentes, illustrent le comportement adequat de ces modeles ; ils surpassent Okapi BM25 et les modeles de langues, avec lissage de Jelinek-Mercer ou de Dirichlet, a la fois pour la precision moyenne et la precision en tete de liste, et fournissent des resultats similaires aux modeles DFR (Divergence from Randomness) tout en les simplifiant.
Cold denaturation of ubiquitin at high pressure

Cold‐induced conformational transition of ubiquitin was studied at pH 4.5 under a constant pressure of 2 kbar using variable pressure one‐dimensional 1H and two‐dimensional 15N/1H NMR spectroscopy as well as IR spectroscopy. Although a tendency for preferential stabilization of a peculiar locally disordered and partially hydrated conformer I, identical with that previously found with variable‐pressure NMR at 0 °C, is recognized, the transition of the folded conformer N to the unfolded conformer U occurs largely cooperatively with decreasing temperature, reaching near completion at − 21 °C. NMR spectral features as well as the analysis of NMR relaxation parameters indicate that the polypeptide chain is almost fully unfolded, fairly well‐hydrated and floppy at − 21 °C, whereas the IR spectrum shows a substantial decrease of the β‐sheet. The Gibbs energy change from the folded state (a mixture of N and I) to the unfolded state at 2 kbar obtained from the 1H NMR data is fitted well with a single ΔCp value of 2.43 ± 0.13 (kJ/K mol) for the entire temperature range between − 21 and 90 °C, covering both the cold denaturation and heat denaturation, showing that the two denatured states actually belong to a single thermodynamic phase of the protein. The ΔCp value determined at 2 kbar is substantially smaller than the ΔCp determined at 1 bar (3.8–5.8 (kJ/K mol)), which is consistent with the fact that the denaturation takes place from a mixture of N and I at 2 kbar rather than from pure N at 1 bar. Copyright © 2006 John Wiley & Sons, Ltd.
Towards Arbitrary-View Face Alignment by Recommendation Trees

Learning to simultaneously handle face alignment of arbitrary views, e.g. frontal and profile views, appears to be more challenging than we thought. The difficulties lay in i) accommodating the complex appearance-shape relations exhibited in different views, and ii) encompassing the varying landmark point sets due to self-occlusion and different landmark protocols. Most existing studies approach this problem via training multiple viewpoint-specific models, and conduct head pose estimation for model selection. This solution is intuitive but the performance is highly susceptible to inaccurate head pose estimation. In this study, we address this shortcoming through learning an Ensemble of Model Recommendation Trees (EMRT), which is capable of selecting optimal model configuration without prior head pose estimation. The unified framework seamlessly handles different viewpoints and landmark protocols, and it is trained by optimising directly on landmark locations, thus yielding superior results on arbitrary-view face alignment. This is the first study that performs face alignment on the full AFLWdataset with faces of different views including profile view. State-of-the-art performances are also reported on MultiPIE and AFW datasets containing both frontaland profile-view faces.
Generation and Characterization of a Defined Mutant of Streptococcus suis Lacking Suilysin

ABSTRACT A defined allelic-replacement mutant of the sly gene, encoding a thiol-activated cytolysin, from a European isolate ofStreptococcus suis serotype 2 was generated and characterized. Unlike the parental strain, it is nonhemolytic, noncytotoxic for cultured macrophage-like cells, avirulent in a mouse infection model, yet only slightly attenuated in a porcine model of systemic infection.
Effects of stroke localization on cardiac autonomic balance and sudden death.

BACKGROUND AND PURPOSE Stroke has been shown to alter autonomic function. The purpose of this study was to show the differential effects of stroke localization on autonomic function parameters assessed by heart rate variability (HRV). METHODS To determine the differential effect of ischemic stroke localization on autonomic cardiac innervation, we evaluated 62 patients with ischemic stroke and 62 age- and sex-matched controls. The localization of the infarct was determined by CT and MRI. Power spectrum analysis of HRV was performed. Myocardial necrosis was ruled out by echocardiography and creatine kinase myocardial isoenzymes measurements. RESULTS All stroke patients had significantly decreased low frequency, high frequency, and standard deviation of all relative risk intervals values (P<0.001). However, patients with right-middle cerebral artery (R-MCA) and insula lesions had significantly lower power spectrum analysis values compared with all other localizations (P<0.001). In addition, 5 patients with R-MCA insular lesions died suddenly compared with 2 patients with left-middle cerebral artery insular lesions during hospitalization. Both sympathetic- and parasympathetic-controlled HRV were decreased in patients with ischemic stroke. The most pronounced decrease was found in the territory of R-MCA insular cortex, which suggests that cardiac autonomic tone may be regulated by insula and that these patients are more prone to cardiac complications such as arrhythmias and sudden death due to autonomic imbalance. CONCLUSION We conclude that stroke in the region of insula (especially the right) leads to decreased HRV and to increased incidence of sudden death.
USER AUTHENTICATION SCHEMES FOR MOBILE AND HANDHELD DEVICES

User authentication is a difficulty for every system providing safe access to precious, private information, or personalized services. It is a continual problem, particularly with mobile and handheld devices such as Personal Digital Assistants (PDAs). User authentication is the primary line of defence for a handheld device that comes into the hands of an unauthorized individual. Password or Personal Identification Number (PIN) based authentication is the leading mechanism for verifying the identity of actual device users but this method has been shown to have considerable drawbacks. For example, users tend to pick PIN or passwords that can be easily guessed. On the other hand, if a password is hard to guess, then it is often hard to remember. To address this problem in handheld devices, some researchers have developed comparatively more secure, affordable and memorable authentication schemes based on graphical assistance, images and audio. In this paper, we conduct a comprehensive survey and analysis of such existing user authentication schemes for mobile and handheld devices. The complete analysis of these schemes in term of usability and security are also discussed in this paper. This paper will be useful for information security researchers and practitioners who are interested in finding an alternative to password based authentication schemes.
On seamless connectivity over multi-radio and multi-channel wireless mesh networks

In IEEE802.11 wireless mesh networks (WMN), we had suffered from performance degradation caused by contention and interference. To avoid the issue with a reasonable cost, we have been working on the configuration where nodes are equipped with multiple commodity IEEE802.11 interfaces and antennas. Although the WMNs of the configuration were segmented by multi-channelized links, traditional applications needed it to be a single-tier and easy-to-use network. In this paper, we present a scheme introducing a virtual link layer that allows mobile nodes to move around without changing its identifier and losing its connectivity to such kind of WMNs. We have implemented a prototype system of our scheme using the click modular router framework [2]. We have confirmed that existing applications, such as DHCP and mDNS, run on the multi-radio and multichannel WMN without any modification.
On-line references reshaping and control reconfiguration for non-minimum phase nonlinear fault tolerant control

Abstract In this paper we consider the problem of graceful performance degradation , for affine non-minimum phase nonlinear systems. The method is an optimization based scheme, that gives a constructive way to re-shape on-line the output reference for the post-fault system, and explicitly take into account the actuators and states saturations. The on-line output reference reshaping is associated with an on-line, MPC-based, controller reconfiguration, that forces the post-fault system to track the new output reference. The effect of FDD uncertainties on the online controller reconfiguration stability are studied, to ensure at least boundeness of the closed-loop system's states. The reshaping and reconfiguration schemes are applied to the Caltech ducted fan numerical example, which is described by a non-minimum phase nonlinear model.
Visualizing the Engram: Learning Stabilizes Odor Representations in the Olfactory Network

The nature of memory is a central issue in neuroscience. How does our representation of the world change with learning and experience? Here we use the transcription of Arc mRNA, which permits probing the neural representations of temporally separated events, to address this in a well characterized odor learning model. Rat pups readily associate odor with maternal care. In pups, the lateralized olfactory networks are independent, permitting separate training and within-subject control. We use multiday training to create an enduring memory of peppermint odor. Training stabilized rewarded, but not nonrewarded, odor representations in both mitral cells and associated granule cells of the olfactory bulb and in the pyramidal cells of the anterior piriform cortex. An enlarged core of stable, likely highly active neurons represent rewarded odor at both stages of the olfactory network. Odor representations in anterior piriform cortex were sparser than typical in adult rat and did not enlarge with learning. This sparser representation of odor is congruent with the maturation of lateral olfactory tract input in rat pups. Cortical representations elsewhere have been shown to be highly variable in electrophysiological experiments, suggesting brains operate normally using dynamic and network-modulated representations. The olfactory cortical representations here are consistent with the generalized associative model of sparse variable cortical representation, as normal responses to repeated odors were highly variable (∼70% of the cells change as indexed by Arc). Learning and memory modified rewarded odor ensembles to increase stability in a core representational component.
Metric-Based Scan Matching Algorithms for Mobile Robot Displacement Estimation

This paper presents a metric-based matching algorithm to estimate the robot planar displacement by matching dense two-dimensional range scans. The contribution is a geometric distance that takes into account the translation and orientation of the sensor at the same time. This result is used in the two steps of the matching - estimation process. The correspondences between scans are established with this measure and the minimization of the error is also carried out in terms of this distance. As a result, the translation and rotation are compensated in this framework simultaneously. In fact, this is the contribution with respect to previous work that addressed only translation or translation and rotation but separately. The new technique has been implemented and tested on a real vehicle. The experiments illustrate how it is more robust and accurate than prior techniques. At the end of the paper, we give an extension of our distance measure to 3D range-data matching problems.