Miracle-dz/UniFAR-FTUs huggingface dataset:
Combinatorial auction-based virtual machine provisioning and allocation in clouds

COMBINATORIAL AUCTION-BASED VIRTUAL MACHINE PROVISIONING AND ALLOCATION IN CLOUDS by SHARRUKH ZAMAN May 2013 Advisor: Dr. Daniel Grosu Major: Computer Science Degree: Doctor of Philosophy Current cloud providers use fixed-price based mechanisms to allocate Virtual Machine (VM) instances to their users. But economic theory states that when there are large amount of resources to be allocated to large number of users, auctions are the most efficient alloca- tion mechanisms. Auctions achieve efficiency of allocation and also maximize the providers’ revenue, which a fixed-price based mechanism is unable to do. We argue that combinato- rial auctions are best suited for the problem of VM provisioning and allocation in clouds, since they provide the users with the most flexible way to express their requirements. In combinatorial auctions, users bid for bundles of items rather than individual ones, there- fore they are able to express whether the items they require are complementary to each other. The objective of this Ph.D. dissertation is to design, study, and implement combina- torial auction-based mechanisms for efficient provisioning and allocation of VM instances in clouds. The central hypothesis is that allocation efficiency and revenue maximization can be obtained by inducing users to fully express and truthfully report their preferences to the system. The rationale for our research is that, once efficient resource provision- ing and allocation mechanisms that take into account the incentives of the users and cloud providers are developed and implemented, it will become more efficient to utilize cloud com- puting environments for solving challenging problems in business, science and engineering.
Multi-Robot Exploration and Mapping with a Rotating 3D Scanner

Abstract This paper investigates the field of exploration and map-building with multiple cooperating mobile robots. New and efficient exploration and mapping technique is proposed by employing laser scanners. The paper also aims to extend existing exploration and mapping techniques of single robot to multi-robot to increase the exploration efficiency (i.e. to reduce the environment exploration time required). The goal of the proposed method is to have multiple mobile robots exploring a given unknown environment as fast as possible, while coordinating their actions and sharing their local maps in certain time instances. In the suggested technique, each robot is equipped with a laser scanner that is continuously rotating to scan the environment, and is employing a frontier-based exploration algorithm which is important to guide the robots during the exploration. A new factor is introduced to enhance the performance of the frontier-based exploration. This factor aims at spreading robots in the environment to reduce overlap.
Brain lateralization and neural plasticity for musical and cognitive abilities in an epileptic musician

The use of intracarotid propofol procedure (IPP) when assessing musical lateralization has not been reported in literature up to now. This procedure (similar to Wada Test) has provided the opportunity to investigate not only lateralization of language and memory functions on epileptic patients but also offers a functional mapping approach with superior spatial and temporal resolution to analyze the lateralization of musical abilities. Findings in literature suggest that musical training modifies functional and structural brain organization. We studied hemispheric lateralization in a professional musician, a 33 years old woman with refractory left medial temporal lobe (MTL) epilepsy (TLE). A longitudinal neuropsychological study was performed over a period of 21 months. Before epilepsy surgery, musical abilities, language and memory were tested during IPP by means of a novel and exhaustive neuropsychological battery focusing on the processing of music. We used a selection of stimuli to analyze listening, score reading, and tempo discrimination. Our results suggested that IPP is an excellent method to determine not only language, semantic, and episodic memory, but also musical dominance in a professional musician who may be candidate for epilepsy surgery. Neuropsychological testing revealed that right hemisphere's patient is involved in semantic and episodic musical memory processes, whereas her score reading and tempo processing require contribution from both hemispheres. At one-year follow-up, outcome was excellent with respect to seizures and professional skills, meanwhile cognitive abilities improved. These findings indicate that IPP helps to predict who might be at risk for postoperative musical, language, and memory deficits after epilepsy surgery. Our research suggests that musical expertise and epilepsy critically modifies long-term memory processes and induces brain structural and functional plasticity.
On packet loss rates in modern 802.11 networks

The knowledge of link packet loss rates (PLRs) at different PHY layer configurations is vital for a number of wireless network optimization schemes. However, the very large number of PHY layer configurations offered by modern 802.11 n/ac networks has made probing-based PLR estimation at each available configuration extremely challenging. In this paper, we seek to answer the question “How to estimate the PLRs at each available PHY layer configuration with minimal overhead? ” Our analysis of the PLR datasets collected from three 802.11 n/ac testbeds reveals that, for any given link, there are several configurations with similar PLR. However, capturing this similarity using well-known link quality indicators like RSSI, or PHY layer features such as MCS or number of MIMO streams is hard. Consequently, we explore the approach of clustering the available PHY layer configurations into a small number of clusters with similar PLR, independent of any other parameter, and only probe one representative configuration in each cluster. Using two real-world case studies — rate adaptation and multihop routing, we show that the proposed clustering-based PLR estimation helps network optimization schemes to reach optimal configurations faster leading to significant performance improvements.
Quantum Ordered Binary Decision Diagrams with Repeated Tests

Quantum branching programs (quantum binary decision diagrams, respectively) are a convenient tool for examining quantum computations using only a logarithmic amount of space. Recently several types of restricted quantum branching programs have been considered, e. g. read--once quantum branching programs. This paper considers quantum ordered binary decision diagrams (QOBDDs) and answers the question: How does the computational power of QOBDDs increase, if we allow repeated tests. Additionally it is described how to synthesize QOBDDs according to Boolean operations.
Gene Deletion of Protein Tyrosine Phosphatase 1B Protects Against Sepsis-Induced Cardiovascular Dysfunction and Mortality

Objective—Cardiovascular dysfunction is a major cause of mortality in patients with sepsis. Recently, we showed that gene deletion or pharmacological inhibition of protein tyrosine phosphatase 1B (PTP1B) improves endothelial dysfunction and reduces the severity of experimental heart failure. However, the cardiovascular effect of PTP1B invalidation in sepsis is unknown. Thus, we explored the beneficial therapeutic effect of PTP1B gene deletion on lipopolysaccharide (LPS)-induced cardiovascular dysfunction, inflammation, and mortality. Approach and Results—PTP1B−/− or wild-type mice received LPS (15 mg/kg) or vehicle followed by subcutaneous fluid resuscitation (saline, 30 mL/kg). &agr;-1–dependent constriction and endothelium-dependent dilatation, assessed on isolated perfused mesenteric arteries, were impaired 8 hours after LPS and significantly improved in PTP1B−/− mice. This was associated with reduced vascular expression of interleukin1-&bgr;, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, cyclooxygenase-2, and inducible nitric oxide synthase mRNA. PTP1B gene deletion also limited LPS-induced cardiac dysfunction assessed by echocardiography, left ventricular pressure–volume curves, and in isolated perfused hearts. PTP1B−/− mice also displayed reduced LPS-induced cardiac expression of tumor necrosis factor-&agr;, interleukin1-&bgr;, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and Gp91phox, as well as of several markers of cellular infiltration. PTP1B deficiency also reduced cardiac P38 and extracellular signal–regulated protein kinase 1 and 2 phosphorylation and increased phospholamban phosphorylation. Finally, PTP1B−/− mice displayed a markedly reduced LPS-induced mortality, an effect also observed using a pharmacological PTP1B inhibitor. PTP1B deletion also improved survival in a cecal ligation puncture model of sepsis. Conclusions—PTP1B gene deletion protects against septic shock-induced cardiovascular dysfunction and mortality, and this may be the result of the profound reduction of cardiovascular inflammation. PTP1B is an attractive target for the treatment of sepsis.
Molecular cytogenetic analysis of medulloblastomas and supratentorial primitive neuroectodermal tumors by using conventional banding, comparative genomic hybridization, and spectral karyotyping.

OBJECT Medulloblastomas and related primitive neuroectodermal tumors (PNETs) of the central nervous system are malignant, invasive embryonal tumors with predominantly neuronal differentiation that comprise 20% of pediatric brain tumors. Cytogenetic analysis has shown that alterations in chromosome 17, particularly the loss of 17p and the formation of isochromosome 17q, as well as the gain of chromosome 7 are the most common changes among this group of tumors. Comparative genomic hybridization (CGH) studies have largely confirmed these cytogenetic findings and have also identified novel regions of gain, loss, and amplification. The advent of more sophisticated multicolored fluorescence in situ hybridization (FISH) procedures such as spectral karyotyping (SKY) now permits complete recognition of all aberrations including extremely complex rearrangements. The authors report a retrospective analysis of 19 medulloblastoma and five PNET cases studied using combinations of classic banding analysis, FISH, CGH, and SKY to examine comprehensively the chromosomal aberrations present in this tumor group and to attempt to identify common structural rearrangement(s). METHODS The CGH data demonstrate gains of chromosomes 17q and 7 in 60% of the tumors studied, which confirms data reported in the current literature. However, the authors have also combined the results of all three molecular cytogenetic assays (Giemsa banding, CGH, and SKY) to reveal the frequency of chromosomal rearrangement (gained, lost, or involved in structural rearrangement). CONCLUSIONS The combined results indicate that chromosomes 7 and 17 are the most frequently rearranged chromosomes (10.1% and 8.9%, respectively, in all rearrangements detected). Furthermore, chromosomes 3 (7.8%), 14 (7%), 10 (6.7%), and 22 (6.5%) were also found to be frequently rearranged, followed by chromosomes 6 (6.5%), 13 (6.2%), and 18 (6.2%). Eight (33%) of 24 tumors exhibited high-level gains or gene amplification. Amplification of MYCN was identified in four tumors, whereas amplification of MYCC was identified in one tumor. One tumor exhibited a high-level gain of chromosome 9p. Additionally, desmoplastic medulloblastomas and large-cell medulloblastomas exhibited higher karyotype heterogeneity, amplification, and aneusomy than classic medulloblastomas.
Constitutive Aberrant Endogenous Interleukin-1 Facilitates Inflammation and Growth in Human Melanoma

Interleukin (IL)-1–mediated inflammation is proposed to contribute to the development and progression of some cancers. IL-1 family member proteins are known to be expressed constitutively in many melanoma tumor cells, and we hypothesize that these support molecular pathways of inflammation and facilitate tumor growth. To investigate the expression of IL-1α and IL-1β in melanoma patients, and their association with disease progression, immunohistochemical staining was carried out on tissues from 170 patients including benign nevi, primary melanomas, and metastatic melanomas. IL-1β levels were low (or zero) in benign nevi and higher in primary and metastatic melanomas (P < 0.0001). IL-1α was expressed in about 73% of nevi and 55% of metastatic melanomas, with levels significantly higher in primary tumors (P < 0.0001); most (98%) primary melanoma samples were positive for IL-1α. In vitro studies with seven human melanoma cell lines showed that five cell lines expressed IL-1α and IL-1β proteins and mRNA. We identified for the first time several important downstream signaling pathways affected by endogenous IL-1, including reactive oxygen and nitrogen species, COX-2, and phosphorylated NF-κB inhibitor (IκB) and stress-activated protein kinase/c-jun-NH2-kinase; all of which were decreased by siRNA to IL-1s. Downregulation of IL-1α, IL-1β, or MyD88 substantially increased p21 and p53 levels. Treatment with IL-1 receptor type I neutralizing antibody or IL-1 pathway–specific siRNAs led to growth arrest in IL-1–positive melanoma cells. Furthermore, blocking the IL-1 pathway increased autophagy in IL-1–positive melanoma cells. These results indicate that the endogenous IL-1 system is functional in most human melanoma and interrupting its signaling inhibits the growth of IL-1–positive melanoma cells. Mol Cancer Res; 9(11); 1537–50. ©2011 AACR.
Leveraging users' likes in a video streaming P2P platform

This paper investigates how a p2p television platform can take advantage of the presence of frequent channel viewers to grant them a more satisfying service than to less regular spectators. The idea we explore is to learn beforehand about the users' interests, in order to cluster them in groups that display different behaviors; then, the neighborhood creation strategy and video chunk scheduling algorithm of the overlay is altered, with the aim of serving frequent spectators in a privileged manner, providing them with a faster access to the selected channel without overly penalizing less habitual customers. An analytical model is developed, to capture the difference in startup delay that the proposed modifications introduce; several additional performance metrics are numerically determined, in order to thoroughly size up the performance of both groups of viewers. The obtained results show that a clear service differentiation is achieved and also quantify the effects that alternative neighborhood creation algorithms have on the amount of such gap.
Three-Dimensional Identification of Microorganisms Using a Digital Holographic Microscope

This paper reports a method for three-dimensional (3D) analysis of shift-invariant pattern recognition and applies to holographic images digitally reconstructed from holographic microscopes. It is shown that the sequential application of a 2D filter to the plane-by-plane reconstruction of an optical field is exactly equivalent to the application of a more general filter with a 3D impulse response. We show that any 3D filters with arbitrary impulse response can be implemented in this way. This type of processing is applied to the two-class problem of distinguishing different types of bacteria. It is shown that the proposed technique can be easily implemented using a modified microscope to develop a powerful and cost-effective system with great potential for biological screening.
Terahertz spectroscopy for the assessment of burn injuries in vivo

Abstract. A diagnosis criterion is proposed for noninvasive grading of burn injuries using terahertz radiation. Experimental results are presented from in vivo terahertz time-domain spectroscopy of second- and third-degree wounds, which are obtained in a 72-hour animal study. During this period, the change in the spectroscopic response of the burned tissue is studied. It is shown that terahertz waves are sensitive not only to the postburn formation of interstitial edema, but also to the density of skin structures derived from image processing analysis of histological sections. Based on these preliminary results, it is suggested that the combination of these two effects, as probed by terahertz spectroscopy of the tissue, may ultimately be used to differentiate partial-thickness burns that will naturally heal from those that will require surgical intervention.
Myocardial Fibrosis in DOCA-Salt Hypertensive Rats: Effect of Endothelin ETA Receptor Antagonism

BackgroundTo test the hypothesis that endothelin-1 contributes to cardiac fibrosis, cardiac collagen deposition was studied in deoxycorticosterone acetate–salt (DOCA-salt) hypertensive rats, in which the endothelin system is activated. The effects of the ETA-selective endothelin receptor antagonist A-127722 were evaluated. Methods and ResultsA-127722 (30 mg/kg per day) was administered for 4 weeks. Myocardial fibrosis was evaluated after Sirius red F3BA staining. Systolic blood pressure was 103±1.6 mm Hg in unilaterally nephrectomized rats (Uni-Nx), 202±3.2 mm Hg in DOCA-salt rats (P <0.01 versus Uni-Nx), and 182±3.1 mm Hg in ETA antagonist–treated DOCA-salt rats (P <0.01 versus DOCA-salt or Uni-Nx). In DOCA-salt rats, interstitial and perivascular collagen density was increased in the subendocardial and midmyocardial regions of the left ventricle (3- to 4-fold, P <0.05), whereas in subepicardial myocardium, the increase was predominantly perivascular. The ETA antagonist prevented cardiac fibrosis in DOCA-salt rats. Procollagen I and III mRNA, which were increased in hearts of DOCA-salt rats, were normalized by ETA antagonist treatment. TGF-&bgr;1 mRNA and TGF-&bgr;1 protein increased at 1 week in DOCA-salt rats and were lowered in ETA antagonist–treated rats. ConclusionsETA receptor–mediated collagen deposition in hearts of DOCA-salt rats results from increased procollagen synthesis associated with an initial increment in expression of TGF-&bgr;1. These results support the hypothesis of a role for endothelin-1 in cardiac collagen deposition in mineralocorticoid hypertension, which may have pathophysiological and pharmacological implications in hypertensive heart disease.
Cubic to hexagonal structural transformation in Gd2O3 at high pressure

High-pressure X-ray diffraction studies on gadolinium sesquioxide (Gd2O3) have been carried out up to a pressure of ∼25 GPa in a diamond-anvil cell at room temperature. Gadolinium oxide, which has a cubic or bixbyite structure under ambient conditions, undergoes an irreversible structural phase at around 12 GPa. The high-pressure phase has been identified as a hexagonal La2O3-type structure. The bulk modulus and its pressure derivative of this phase have been calculated.
Runtime Data Layout Scheduling for Machine Learning Dataset

Machine Learning (ML) approaches are widelyused classification/regression methods for data mining applications. However, the time-consuming training process greatly limits the efficiency of ML approaches. We use the example of SVM (traditional ML algorithm) and DNN (state-of-the-art ML algorithm) to illustrate the idea in this paper. For SVM, a major performance bottleneck of current tools is that they use a unified data storage format because the data formats can have a significant influence on the complexity of storage and computation, memory bandwidth, and the efficiency of parallel processing. To address the problem above, we study the factors influencing the algorithm’s performance and conduct auto-tuning to speed up SVM training. DNN training is even slower than SVM. For example, using a 8-core CPUs to train AlexNet model by CIFAR-10 dataset costs 8.2 hours. CIFAR-10 is only 170 MB, which is not efficient for distributed processing. Moreover, due to the algorithm limitation, only a small batch of data can be processed at each iteration. We focus on finding the right algorithmic parameters and using auto-tuning techniques to make the algorithm run faster. For SVM training, our implementation achieves 1:7.16:3 speedup (6:8 on average) against the non-adaptive case (using the worst data format) for various datasets. For DNN training on CIFAR-10 dataset, we reduce the time from 8.2 hours to only roughly 1 minute. We use the benchmark of dollars per speedup to help the users to select the right deep learning hardware.
Prediction of primary somatosensory neuron activity during active tactile exploration

Primary sensory neurons form the interface between world and brain. Their function is well-understood during passive stimulation but, under natural behaving conditions, sense organs are under active, motor control. In an attempt to predict primary neuron firing under natural conditions of sensorimotor integration, we recorded from primary mechanosensory neuronsof awake, head-fixed mice as they explored a pole with their whiskers, and simultaneously measured both whisker motion and forces with high-speed videography. Using Generalised Linear Models, we found that primary neuron responses were poorly predicted by kinematics but well-predicted by rotational forces acting on the whisker: both during touch and free-air whisker motion. These results are discrepant with previous studies of passive stimulation, but could be reconciled by differences in the kinematics-force relationship between active and passive conditions. Thus, simple statistical models can predict rich neural activity elicited by natural, exploratory behaviour involving active movement of the sense organs.
HBNG: Graph theory based visualization of hydrogen bond networks in protein structures

HBNG is a graph theory based tool for visualization of hydrogen bond network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains and rings in protein structures. HBNG takes hydrogen bonds list files (output from HBAT, HBEXPLORE, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT and T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures. Availability Program is available from the authors for non-commercial purposes.
Linear-Programming Decoding of Nonbinary Linear Codes

A framework for linear-programming (LP) decoding of nonbinary linear codes over rings is developed. This framework facilitates LP-based reception for coded modulation systems which use direct modulation mapping of coded symbols. It is proved that the resulting LP decoder has the ldquomaximum-likelihood (ML) certificaterdquo property. It is also shown that the decoder output is the lowest cost pseudocodeword. Equivalence between pseudocodewords of the linear program and pseudocodewords of graph covers is proved. It is also proved that if the modulator-channel combination satisfies a particular symmetry condition, the codeword error rate performance is independent of the transmitted codeword. Two alternative polytopes for use with LP decoding are studied, and it is shown that for many classes of codes these polytopes yield a complexity advantage for decoding. These polytope representations lead to polynomial-time decoders for a wide variety of classical nonbinary linear codes. LP decoding performance is illustrated for ternary Golay code with ternary phase-shift keying (PSK) modulation over additive white Gaussian noise (AWGN), and in this case it is shown that the performance of the LP decoder is comparable to codeword-error-rate-optimum hard-decision-based decoding. LP decoding is also simulated for medium-length ternary and quaternary low-density parity-check (LDPC) codes with corresponding PSK modulations over AWGN.