Miracle-dz/UniFAR-FTUs huggingface dataset:
The Price of Safety : Evaluating IOMMU Performance

IOMMUs, IO Memory Management Units, are hardware devices that translate device DMA addresses to machine addresses. An isolation capable IOMMU restricts a device so that it can only access parts of memory it has been explicitly granted access to. Isolation capable IOMMUs perform a valuable system service by preventing rogue devices from performing errant or malicious DMAs, thereby substantially increasing the system’s reliability and availability. Without an IOMMU a peripheral device could be programmed to overwrite any part of the system’s memory. Operating systems utilize IOMMUs to isolate device drivers; hypervisors utilize IOMMUs to grant secure direct hardware access to virtual machines. With the imminent publication of the PCI-SIG’s IO Virtualization standard, as well as Intel and AMD’s introduction of isolation capable IOMMUs in all new servers, IOMMUs will become ubiquitous. Although they provide valuable services, IOMMUs can impose a performance penalty due to the extra memory accesses required to perform DMA operations. The exact performance degradation depends on the IOMMU design, its caching architecture, the way it is programmed and the workload. This paper presents the performance characteristics of the Calgary and DART IOMMUs in Linux, both on bare metal and in a hypervisor environment. The throughput and CPU utilization of several IO workloads, with and without an IOMMU, are measured and the results are analyzed. The potential strategies for mitigating the IOMMU’s costs are then discussed. In conclusion a set of optimizations and resulting performance improvements are presented.
On the Cross-Correlation of a Ternary $m$-sequence of Period $3^{4k}-1$ and Its Decimated Sequence by $\frac{(3^{2k}+1)^{2}}{20}$

Let $d=\frac{(3^{2k}+1)^{2}}{20}$, where $k$ is an odd integer. We show that the magnitude of the cross-correlation values of a ternary $m$-sequence $\{s_{t}\}$ of period $3^{4k}-1$ and its decimated sequence $\{s_{dt}\}$ is upper bounded by $5\sqrt{3^{n}}+1$, where $n=4k$.
Oligodendroglial p130Cas Is a Target of Fyn Kinase Involved in Process Formation, Cell Migration and Survival

Oligodendrocytes are the myelinating glial cells of the central nervous system. In the course of brain development, oligodendrocyte precursor cells migrate, scan the environment and differentiate into mature oligodendrocytes with multiple cellular processes which recognize and ensheath neuronal axons. During differentiation, oligodendrocytes undergo dramatic morphological changes requiring cytoskeletal rearrangements which need to be tightly regulated. The non-receptor tyrosine kinase Fyn plays a central role in oligodendrocyte differentiation and myelination. In order to improve our understanding of the role of oligodendroglial Fyn kinase, we have identified Fyn targets in these cells. Purification and mass-spectrometric analysis of tyrosine-phosphorylated proteins in response to overexpressed active Fyn in the oligodendrocyte precursor cell line Oli-neu, yielded the adaptor molecule p130Cas. We analyzed the function of this Fyn target in oligodendroglial cells and observed that reduction of p130Cas levels by siRNA affects process outgrowth, the thickness of cellular processes and migration behavior of Oli-neu cells. Furthermore, long term p130Cas reduction results in decreased cell numbers as a result of increased apoptosis in cultured primary oligodendrocytes. Our data contribute to understanding the molecular events taking place during oligodendrocyte migration and morphological differentiation and have implications for myelin formation.
A new multi agent based PSO approaches for optimal power flows with security constraints using different cost functions

This paper proposes new evolutionary multi agent based particle swarm optimization algorithms for solving optimal power flows with security constraints(line flows and bus voltages). These methods combines the multi agents in two dimensional and cubic lattice structures with particle swarm optimization (PSO) to form two new algorithms. In Cubic lattice structured multi agent based PSO(CLSMAPSO), an agent represents a particle in cubic lattice structure to PSO, and a candidate solution to the OPF problem. In Two dimensional lattice structured multi agent based PSO(TDLSMAPSO), an agent represents a particle in square lattice structure to PSO, and a candidate solution to the OPF problem. All agents live in a cubic and square lattice like environments, with agents fixed on a lattice point in the ascending order of their fitness value. In order to obtain the optimal solution, each agent in cubic and square lattice competes and cooperates with its neighbor. Making use of these agent-agent interactions, CLSMAPSO and TDLSMAPSO realizes the purpose of minimizing the objective function value. In this paper, Variable constriction factor has been considered for TDLSMAPSO and CLSMAPSO. The OPF problem has been considered with three different cost functions to realize Optimal Power Flow using CLSMAPSO and TDLSMAPSO applied to IEEE 30 bus system. Simulation results show that proposed approaches gives better solution than earlier reported approaches in very quick time.
Affibody for Detection of HER 2 Expression and Pharmacodynamic Response to HER 2-Modulating Therapies

Purpose: Expression of HER2 has profound implications on treatment strategies in various types of cancer. We investigated the specificity of radiolabeled HER2-targeting ZHER2:2891 Affibody, [F]GE-226, for positron emission tomography (PET) imaging. Experimental design: Intrinsic cellular [F]GE-226 uptake and tumor-specific tracer binding were assessed in cells and xenografts with and without drug treatment. Specificity was further determined by comparing tumor localization of a fluorescently labeled analogue with DAKO HercepTest. Results: [F]GE-226 uptake was 11 to 67-fold higher in ten HER2 positive versus negative cell lines in vitro independent of lineage. Uptake in HER2 positive xenografts was rapid with net irreversible binding kinetics making possible the distinction of HER2 negative (MCF7 and MCF7-p95HER2: NUV60 (%ID/mL) 6.1 ± 0.7; Ki (mL/cm /min) 0.0069 ± 0.0014) from HER2 positive tumors (NUV60 and Ki: MCF7-HER2, 10.9 ± 1.5 and 0.015 ± 0.0035; MDA-MB-361, 18.2 ± 3.4 and 0.025 ± 0.0052; SKOV-3, 18.7 ± 2.4 and 0.036 ± 0.0065) within 1h. Tumor uptake correlated with HER2 expression determined by ELISA (r = 0.78), and a fluorophore-labled tracer analogue co-localized with HER2 expression. Tracer uptake was not influenced by shortterm or continuous treatment with trastuzumab in keeping with differential epitope binding, but reflected HER2 degradation by short-term NVP-AUY922 treatment in SKOV-3 xenografts (NUV60: 13.5 ± 2.1 versus 9.0 ± 0.9 %ID/mL for vehicle or drug, respectively). Conclusions: [F]GE-226 binds with high specificity to HER2 independent of cell lineage. The tracer has potential utility for HER2 detection, irrespective of prior trastuzumab treatment, and to discern HSP90 inhibitor-mediated HER2 degradation. Research. on April 13, 2017. © 2014 American Association for Cancer clincancerres.aacrjournals. org Downloaded from Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Author Manuscript Published OnlineFirst on February 3, 2014; DOI: 10.1158/1078-0432.CCR-13-2421
Routing and Wavelength Assignment in Single Hop All Optical Networks with Minimum Blocking

wdm networks oer a technology that can transferred several optical signals into a single optical fiber. This allows for more ecient use of the huge capacity of optical fibers but it also poses new network design and management problems such as routing and wavelength planning. This paper discusses the rwa problem, i.e., the routing and wavelength assignment problem in wdm networks. Given a set of requests and the number of available wavelengths the fibers support, we are to find, through the network, a route for each connection and assign wavelengths to them. In this paper, we consider the objective of minimizing the number of connections that have to be denied. We propose a multi-phase heuristic algorithm called rwabou. It begins with an initialization step in which we compute for each connection, rshortest paths from each source to their destination. It is followed by an algorithm with two interactive phases. The first phase integrates a Tabu Search heuristic for the wavelength assignment followed by and interacting with a partial rerouting heuristic phase for the blocked connections. Computational experience shows that the rwabou heuristic outperforms some recently published work on trac instances run on the nsf and the eon networks. Moreover, comparing the lower bound of the rwabou heuristic with the best known upper bound allows to conclude to the optimality of the rwa solution for several benchmark problems and to the very high quality of several others.
Kardiovaskularni sustav i infekcija virusom humane imunodeficijencije

Klju~ne rije~iAIDSdilatacijska kardiomiopatijaendokarditisHAARTHIVmiokarditisperikardni izljevplu}na hipertenzijaKey wordsAIDSdilated cardiomyopathypericardial effusionendocarditisHAARTHIVpulmonary hypertensionmyocarditisPrimljeno: 2005–04–13Received: 2005–04–13Prihva}eno: 2005–05–25Accepted: 2005–05–25
Infection Exposure is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility.

UNLABELLED Earlier in the past century, infections were regarded as the most likely cause of childhood B-cell precursor acute lymphoblastic leukemia (pB-ALL). However, there is a lack of relevant biologic evidence supporting this hypothesis. We present in vivo genetic evidence mechanistically connecting inherited susceptibility to pB-ALL and postnatal infections by showing that pB-ALL was initiated in Pax5 heterozygous mice only when they were exposed to common pathogens. Strikingly, these murine pB-ALLs closely resemble the human disease. Tumor exome sequencing revealed activating somatic, nonsynonymous mutations of Jak3 as a second hit. Transplantation experiments and deep sequencing suggest that inactivating mutations in Pax5 promote leukemogenesis by creating an aberrant progenitor compartment that is susceptible to malignant transformation through accumulation of secondary Jak3 mutations. Thus, treatment of Pax5(+/-) leukemic cells with specific JAK1/3 inhibitors resulted in increased apoptosis. These results uncover the causal role of infection in pB-ALL development. SIGNIFICANCE These results demonstrate that delayed infection exposure is a causal factor in pB-ALL. Therefore, these findings have critical implications for the understanding of the pathogenesis of leukemia and for the development of novel therapies for this disease.
Analysis and Design of Multi Agent Knowledge Development Process

Within multi agent systems (MAS), knowledge plays an important role in agent communication, reasoning and supporting interoperability. It is often considered as an ontology which contains explicit domain knowledge to be used by agents. Although there are many ontology development or engineering methodologies, current efforts to incorporate knowledge into MAS are too focused on computational aspects or ad hoc. Working at the computational model is too low level, and many processes are left implicit to the developer. This paper focuses on engineering the agent knowledge development process. A set of activities is proposed to externalize processes involved in managing agent domain knowledge, preferring software engineering approaches to ad hoc processes. The activities are classified into analysis and design steps together forming a development model suite (e.g. user model, motivation model, task model and design model). With guidance, we have successfully developed agents' knowledge based on a real life application in finding a potential advisor for a graduate student. Finally, it enables the agent developer to use, reuse and maintain the agent knowledge.
The Flash Crash: The Impact of High Frequency Trading on an Electronic Market

We use E-mini S&P 500 futures market audit-trail data to compare the trading of High Frequency Traders and other traders during the Flash Crash of May 6, 2010 with the three prior trading days. On all 4 days, High Frequency Trader’s inventories rarely exceeded 3000 contracts, mean-reverted to 0 with a half-life of approximately two minutes, and had similar correlations with price changes over one second intervals. The Flash Crash was triggered by a 75,000 contract sell program. We conclude that the inventories of High Frequency Traders were too small to have caused or prevented the Flash Crash.
Attention Deficit Hyperactivity Disorder and Academics

Attention deficit hyperactivity disorder (ADHD) is the most commonly diagnosed psychological disorder of childhood. Prevalence of ADHD currently is estimated at 5% among school-age children making it a serious concern for educators. One aspect of ADHD, however, that has received comparatively little attention is the academic difficulties that are commonly associated with ADHD. This chapter provides an overview of the extent and nature of academic problems of students with ADHD. First, a theoretical perspective on academic deficits of students with ADHD drawn from Barkley's (2006) theoretical work is presented. Second, the academic status of students with ADHD is discussed. Third, drawing on longitudinal studies, the academic trajectory of students with ADHD is examined. Fourth, possible causal factors for academic problems and core deficit areas of working memory and executive functions are discussed. Next, progress in academic interventions for ADHD is assessed and promising interventions are noted. Finally, some possible directions for future intervention research are provided.
Inhibition of angiogenesis and metastasis in two murine models by the matrix metalloproteinase inhibitor, BMS-275291.

BMS-275291 is an p.o. bioavailable, sulfhydryl-based matrix metalloproteinase (MMP) inhibitor currently in clinical development for the treatment of cancer. This inhibitor was designed to potently inhibit MMP activities while minimally affecting those of other metalloproteases (e.g., sheddases) involved in the release of cell-associated molecules such as tumor necrosis factor-alpha, tumor necrosis factor-alpha receptor, interleukin-6 receptor, or L-selectin. In vitro, BMS-275291 is a potent inhibitor (nM) of the activities of MMP-1, MMP-2, MMP-7, MMP-9, and MMP-14. BMS-275291 inhibits tumor growth in a B16BL6 model of experimental metastasis, and in this model, BMS-275291 treatment results in a dose-dependent reduction in the number of lung metastases compared with vehicle controls. BMS-275291 also inhibits angiogenesis in a murine angiogenesis model, where once daily treatment with BMS-275291 results in a dose-dependent inhibition of endothelial cell migration into s.c. implanted Matrigel plugs. Pharmacokinetic studies demonstrated that the plasma concentrations of parent BMS-275291 in mice exceeds the in vitro IC(50) values for MMP-1, MMP-2, MMP-7, MMP-9, and MMP-14 for at least 4 h after the administration of a therapeutic dose of BMS-275291. Taken together, these data demonstrate that BMS-275291 inhibits MMP activities that contribute to tumor metastasis and angiogenesis.
Analysis of Mycobacterium tuberculosis-Specific CD8 T-Cells in Patients with Active Tuberculosis and in Individuals with Latent Infection

CD8 T-cells contribute to control of Mycobacterium tuberculosis infection, but little is known about the quality of the CD8 T-cell response in subjects with latent infection and in patients with active tuberculosis disease. CD8 T-cells recognizing epitopes from 6 different proteins of Mycobacterium tuberculosis were detected by tetramer staining. Intracellular cytokines staining for specific production of IFN-γ and IL-2 was performed, complemented by phenotyping of memory markers on antigen-specific CD8 T-cells. The ex-vivo frequencies of tetramer-specific CD8 T-cells in tuberculous patients before therapy were lower than in subjects with latent infection, but increased at four months after therapy to comparable percentages detected in subjects with latent infection. The majority of CD8 T-cells from subjects with latent infection expressed a terminally-differentiated phenotype (CD45RA+CCR7−). In contrast, tuberculous patients had only 35% of antigen-specific CD8 T-cells expressing this phenotype, while containing higher proportions of cells with an effector memory- and a central memory-like phenotype, and which did not change significantly after therapy. CD8 T-cells from subjects with latent infection showed a codominance of IL-2+/IFN-γ+ and IL-2−/IFN-γ+ T-cell populations; interestingly, only the IL-2+/IFN-γ+ population was reduced or absent in tuberculous patients, highly suggestive of a restricted functional profile of Mycobacterium tuberculosis-specific CD8 T-cells during active disease. These results suggest distinct Mycobacterium tuberculosis specific CD8 T-cell phenotypic and functional signatures between subjects which control infection (subjects with latent infection) and those who do not (patients with active disease).
Solving a resource allocation problem in wireless mesh networks: A comparison between a CP‐based and a classical column generation

This article presents a column generation approach to a resource allocation problem arising in managing Wireless Mesh Networks. The problem consists in routing the given demands over the network and to allocate time resource to pairs of nodes. Half‐duplex constraints are taken into account together with the aggregate interference due to simultaneous transmissions, which affects the signal quality. Different problems are considered, according to the assumptions on the transmission power and rate. The resource allocation problem can be formulated as a Mixed Integer Linear Programming (MILP) problem and dealt with a column generation‐based approach. The pricing problem, due to signal quality constraints, turns out to be computationally demanding. To tackle these difficulties, besides a classical mathematical programming approach, we have applied a hybrid column generation approach where the pricing subproblem is solved using Constraint Programming. Numerical results show that the two methods are comparable. The results of the column generation are then used to solve heuristically the problem. The obtained results provide very small gaps (between lower bounds and Heuristic solutions) for two of the three considered problems and reasonable gaps for the third problem. © 2009 Wiley Periodicals, Inc. NETWORKS, 2010
Improving secondary education for orphans and vulnerable children in Malawi: One non-governmental organization's perspective

ABSTRACT Education is critical to individual and national well-being. Yet, orphans and vulnerable children (OVC) are challenged to obtain it. Based on a literature review and a non-governmental organizations (NGO) case description, this article aims to describe the status of secondary education for OVC in Malawi. Aims include describing (a) one NGO's efforts to support students, (b) facilitators and barriers, and (c) steps to increase opportunity. Findings show that the poorest students, and girls especially, experience disparity. An inability to pay fees, a complex school system of varying quality, and other barriers impede achievement. Nevertheless OVC are motivated and have some support. One NGO has supported secondary education since 2006, resulting in students' matriculation to tertiary institutions. The authors recommend increasing opportunities for the poorest, especially girls; improving access and quality; better allocating resources; and leveraging supports. OVC may then reach their potential, contributing to family and national health and wealth.
Computerized Medical Imaging and Graphics Assessment of 3d Dce-mri of the Kidneys Using Non-rigid Image Registration and Segmentation of Voxel Time Courses

Keywords: DCE-MRI Kidney Multi-modality non-rigid image registration k-means clustering Time series analysis Renal function a b s t r a c t We have applied automated image analysis methods in the assessment of human kidney perfusion based on 3D dynamic contrast-enhanced MRI data. This approach consists of non-rigid 3D image registration of the moving kidney followed by k-means clustering of the voxel time courses with split between left and right kidney. This method was applied to four data sets acquired from healthy volunteers, using 1.5 T (2 exams) and 3 T scanners (2 exams). The proposed registration method reduced motion artifacts in the image time series and improved further analysis of the DCE-MRI data. The subsequent clustering to segment the kidney compartments was in agreement with manually delineations (similarity score of 0.96) in the same motion corrected images. The resulting mean intensity time curves clearly show the successive transition of contrast agent through kidney compartments (cortex, medulla, and pelvis). The proposed method for motion correction and kidney compartment segmentation might improve the validity and usefulness of further model-based pharmacokinetic analysis of kidney function in patients.
Turbo Factor Analysis

A few years ago, Pearl’s probability propagation algorithm in graphs with cycles was shown to produce excellent results for error-correcting “turbodecoding”. Ever since, we have wondered whether iterative probability propagation could be used successfully for machine learning. As a first step in this direction, we study iterative inference and learning in the simple factor analyzer network – a two-layer densely connected network that models bottom layer sensory inputs as a linear combination of top layer factors plus independent Gaussian sensor noise. The number of bottom-up/top-down iterations needed to exactly infer the factors given a network and an input scales with the number of factors in the top layer. In online learning, this iterative procedure must be reinitialized upon each pattern presentation and so learning becomes prohibitively slow in big networks, such as those used for face recognition and for large-scale models of the cortex. We show that probability propagation in a factor analyzer usually takes just a few iterations to achieve a low inference error, even in networks with 320 sensors and 80 factors. We derive an expression for the algorithm’s fixed point and provide an eigenvalue condition for global convergence. We also show how iterative inference can be used to do online learning and give results on using this method to do online dimensionality reduction for the purpose of recognizing 560-pixel images of faces using a 40-dimensional subspace. This work suggests that iterative probability propagation in densely connected networks may lead to a broad class of useful algorithms for machine learning. UW/CS Adaptive Computation TR-99-1, Apr 10, 1999. Submitted to Neural Computation, May 25, 1999.