Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategic directions in research in theory of computing

This report focuses oll two core areas of theory of computing: discrete algorithms and computational complexity theory. The report reviews the purposes and goals of theoretical research, summarizes selected past and recent achievements, explains the importance of sustaining core research, and identifies promising opportunities for filture research. Some research opportunities build bridges between theory of computing and other areas of computer science, and other science and engineering disciplines.
Error Exponents for Joint Source-Channel Coding With Side Information

In this paper, we study upper and lower bounds on the error exponents for joint source-channel coding with decoder side-information. The results in the paper are nontrivial extensions of Csiszár's classical paper “Joint Source-Channel Error Exponent”, Problems of Control and Information Theory, 1980. Unlike the joint source-channel coding result in Csiszár's paper, it is not obvious whether the lower bound and the upper bound are equivalent even if the channel coding error exponent is known. For a class of channels, including symmetric channels, we apply a game-theoretic result to establish the existence of a saddle point and, hence, prove that the lower and upper bounds are the same if the channel coding error exponent is known. More interestingly, we show that encoder side-information does not increase the error exponents in this case.
Performance study of TCP Veno in wireless/asymmetric links

TCP Veno was recently proposed to eliminate TCP performance suffering from wireless links. Real network measurements and live Internet results have validated Veno's significant throughput improvement in wireless networks and its harmonious coexistent behavior with TCP Reno connections in wired networks. In this paper, we study Veno's performance in asymmetric networks such as ADSL, HFC, where network congestion occurs on the reverse path of acks rather than on the forward path of data sending. Our real experiments demonstrate that Veno continues to reach higher throughput in these asymmetric networks, regardless of wireless or wire links being embedded. Throughput improvement up to 88% over Reno is reached.
The Use of Activity-based Costing with Competitive Strategies: Impact on Firm Performance

Abstract Purpose To empirically test for an impact on profit performance when activity-based costing (ABC) is used in companies with customer service and low-price strategies. We also investigate whether the profit impact of ABC usage is affected by higher-quality information systems. Methodology/approach Survey. Findings We find a positive impact on profit performance when ABC is used by companies with customer service as a strategic priority but not when ABC is used by companies with lower emphasis on customer service. For companies emphasizing low-price strategies, we find a positive impact on profit performance, especially when ABC is used together with high-quality information systems. Research limitations/implications This study develops a method of measuring strategic priorities of a firm. It divides firms into strategy groups based on their degree of emphasis on three strategic priorities: low price, flexibility, and customer service. Practical implications Identifies certain contexts when ABC is especially beneficial. Originality/value of paper If the use of ABC information leads to better strategic and operational decisions, firm performance should improve. However, prior research on the impact of ABC on firm performance has found little to no connection and usually only when it is used with other practices. This is the first study to find an impact on profit performance for firms with customer service and low-price strategies and high-quality information systems.
The Many Faces of Mitochondrial Autophagy: Making Sense of Contrasting Observations in Recent Research

Research into the selective autophagic degradation of mitochondria—mitophagy—has intensified in recent years, yielding significant insights into the function, mechanism, and regulation of this process in the eukaryotic cell. However, while some molecular players in budding yeast, such as Atg32p, Uth1p, and Aup1p, have been identified, studies further interrogating the mechanistic and regulatory features of mitophagy have yielded inconsistent and sometimes conflicting results. In this review, we focus on the current understanding of mitophagy mechanism, induction, and regulation in yeast, and suggest that differences in experimental conditions used in the various studies of mitophagy may contribute to the observed discrepancies. Consideration and understanding of these differences may help place the mechanism and regulation of mitophagy in context, and further indicate the intricate role that this essential process plays in the life and death of eukaryotic cells.
The Inapproximability of Side-Chain Positioning

Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optimized. In [5], we showed that it is NP-complete to find even a reasonable approximate solution to this problem. Here, we explain, for non-computer scientists, the result in more detail.
Molecular characterization of an attenuated human immunodeficiency virus type 2 isolate

Naturally occurring strains of human immunodeficiency virus (HIV) can vary considerably in their in vitro biological properties, and such differences may also be reflected in their in vivo pathogenesis. In an attempt to define genetic determinants of viral pathogenicity, we have molecularly cloned, sequenced, and characterized an attenuated isolate of HIV type 2 (HIV-2/ST) that differs from prototype HIV-2 strains in its inability to fuse with and kill susceptible CD4-bearing target cells. A proviral clone, termed JSP4-27, was identified to be transfection competent and to fully exhibit the noncytopathic and nonfusogenic properties of its parental isolate. Nucleotide sequence analysis of this clone revealed a genomic organization very similar to that of cytopathic HIV-2 strains and an overall nucleotide sequence homology of 88 to 90%. Amino acid sequence comparison confirmed the integrity of all major viral gene products in JSP4-27 but identified two amino acid sequence substitutions in its envelope fusion region. To investigate whether these mutations were responsible for the nonfusogenic phenotype of JSP4-27, we amplified, cloned, and sequenced the envelope fusion regions of four additional HIV-2/ST strains, two of which represented in vitro-generated, fusogenic and cytopathic variants of HIV-2/ST. The analysis showed that all HIV-2/ST strains examined, including the fusogenic variants, contained the same amino acid sequence changes. On the basis of these findings, we conclude that the attenuated phenotype of JSP4-27, and that of its parental virus, is not due to a direct alteration of the envelope fusion domain. Our results also show, for the first time, that individual replication-competent proviral clones can be representative of attenuated strains of HIV.
Learner Models as Drivers for Metacognitive Processes

Maintaining a model of the learner’s understanding as they interact with an e-learning environment allows adaptation to the learner’s educational needs. An Open Learner Model makes this machine's representation of the learner available to them. Typically, the state of the learner's knowledge is presented in some form, ranging from a simple overall mastery score, to a detailed display of how much and what the learner appears to know, their misconceptions and their progress through a course. This means that an Open Learner Model provides a suitable interface onto the learner model for use by the learner, and in some cases for others who support their learning, including peers, parents and teachers. This chapter considers some of the similarities between the goals of supporting and encouraging metacognition in intelligent tutoring systems and learning in general, and the benefits of opening the learner model to the user. We provide examples of two important classes of open learner models: those within a particular teaching system and those that are first-class citizens with value independently of a teaching system. The chapter provides a foundation for understanding the range of ways that Open Learner Models have already been used to support learning as well as directions yet to be explored, with reference to encouraging metacognitive activity and self-directed learning.
Establishment of Infection Models in Zebrafish Larvae (Danio rerio) to Study the Pathogenesis of Aeromonas hydrophila

Aeromonas hydrophila is a Gram-negative opportunistic pathogen of fish and terrestrial animals. In humans, A. hydrophila mainly causes gastroenteritis, septicaemia, and tissue infections. The mechanisms of infection, the main virulence factors and the host immune response triggered by A. hydrophila have been studied in detail using murine models and adult fish. However, the great limitation of studying adult animals is that the animal must be sacrificed and its tissues/organs extracted, which prevents the study of the infectious processes in the whole living animal. Zebrafish larvae are being used for the analysis of several infectious diseases, but their use for studying the pathogenesis of A. hydrophila has never been explored. The great advantage of zebrafish larvae is their transparency during the first week after fertilization, which allows detailed descriptions of the infectious processes using in vivo imaging techniques such as differential interferential contrast (DIC) and fluorescence microscopy. Moreover, the availability of fluorescent pathogens and transgenic reporter zebrafish lines expressing fluorescent immune cells, immune marker genes or cytokines/chemokines allows the host–pathogen interactions to be characterized. The present study explores the suitability of zebrafish larvae to study the pathogenesis of A. hydrophila and the interaction mechanisms between the bacterium and the innate immune responses through an infection model using different routes for infection. We used an early-embryo infection model at 3 days post-fertilization (dpf) through the microinjection of A. hydrophila into the duct of Cuvier, caudal vein, notochord, or muscle and two bath infection models using 4 dpf healthy and injured larvae. The latter resembled the natural conditions under which A. hydrophila produces infectious diseases in animals. We compared the cellular processes after infection in each anatomical site by confocal fluorescence imaging and determined the implication of inflammatory immune genes by measuring gene expression by qPCR.
Cohort Decomposition for Markov Cost-Effectiveness Models

Cohort analysis is a widespread tool for computing expected costs and quality-adjusted life years (QALYs) in Markov models for medical cost-effectiveness analyses. Although not always explicitly identified, such models commonly have multiple simple factors, or components. In these, a health state consists of a multiple component vector, one component for each factor, and arbitrary combinations of components are possible. The authors show here that when the model does not assume any probabilistic dependence among these factors, then a standard cohort analysis may be decomposed into several independent cohort analyses, one for each factor, and the results may be combined to produce desired expected costs and QALYs. These single-factor cohort analyses are not only simpler but also computationally more efficient. The authors derive the appropriate formulas for this cohort decomposition in discrete time and give several examples of their use based on published cost-effectiveness analyses. Explicitly identifying the simple factors of which a model is composed allows these factors to be portrayed graphically. Graphical depiction of the simple factors that comprise a model reduces model complexity, makes model formulation easier and more transparent, and thereby facilitates peer inspection and critique.
Aging & older adulthood

Contents ix Credits and Sources xix Integrated Themes in Aging and Older Adulthood xxiii Preface and Acknowledgments xxxiii 1 Introduction to Aging and Older Adulthood 1 2 Theory and Method in Studying Aging and Older Adulthood 33 3 Biological Aging and Health 61 4 Sensation, Perception, and Attention 100 5 Memory 132 6 Intellectual Functioning 165 7 Cognition and Problem Solving in the Everyday World 199 8 Personality and Coping 234 9 Social Interaction and Social Ties 265 10 Employment, Retirement, and Living Arrangements 298 11 Mental Health, Psychopathology, and Therapy 329 12 Coping with Death, Dying, and Bereavement 361 13 Looking Ahead: Aging in the Future 383 Glossary 394 References 408 Index 442
False-positive (1,3) β-D-glucan assay in a patient with intracranial germinoma.

676 | www.pidj. com © 2015 Wolters Kluwer Health, Inc. All rights reserved. exposure to elemental iron or nail hardeners and other systemic disorders. Red transverse chromonychia in Kawasaki disease was first described in 4 patients by Lindsley in 1992. This was followed by a report of transverse orange-brown chromonychia in 2 patients with Kawasaki disease by Thapa and Pal. Pal and Giri were the first to do a large case series studying the nail beds of 40 pediatric patients with Kawasaki disease diagnosed over a 2-year period in India, finding that 29 of the patients, 75% of the total, had orangebrown chromonychia that appeared between the 5th and 8th day after the onset of fever. Presumably, chromonychia is related to the vasculitis that is the hallmark of Kawasaki disease. Since it has been reported only twice in a total of 7 patients in the US, perhaps, there are genetic or other factors that may predispose some individuals to this manifestation.
Dectin-1 and DC-SIGN Polymorphisms Associated with Invasive Pulmonary Aspergillosis Infection

The recognition of pathogen-derived structures by C-type lectins and the chemotactic activity mediated by the CCL2/CCR2 axis are critical steps in determining the host immune response to fungi. The present study was designed to investigate whether the presence of single nucleotide polymorphisms (SNPs) within DC-SIGN, Dectin-1, Dectin-2, CCL2 and CCR2 genes influence the risk of developing Invasive Pulmonary Aspergillosis (IPA). Twenty-seven SNPs were selected using a hybrid functional/tagging approach and genotyped in 182 haematological patients, fifty-seven of them diagnosed with proven or probable IPA according to the 2008 EORTC/MSG criteria. Association analysis revealed that carriers of the Dectin-1 rs3901533 T/T and Dectin-1 rs7309123 G/G genotypes and DC-SIGN rs4804800 G, DC-SIGN rs11465384 T, DC-SIGN 7248637 A and DC-SIGN 7252229 C alleles had a significantly increased risk of IPA infection (OR = 5.59 95%CI 1.37–22.77; OR = 4.91 95%CI 1.52–15.89; OR = 2.75 95%CI 1.27–5.95; OR = 2.70 95%CI 1.24–5.90; OR = 2.39 95%CI 1.09–5.22 and OR = 2.05 95%CI 1.00–4.22, respectively). There was also a significantly increased frequency of galactomannan positivity among patients carrying the Dectin-1 rs3901533_T allele and Dectin-1 rs7309123_G/G genotype. In addition, healthy individuals with this latter genotype showed a significantly decreased level of Dectin-1 mRNA expression compared to C-allele carriers, suggesting a role of the Dectin-1 rs7309123 polymorphism in determining the levels of Dectin-1 and, consequently, the level of susceptibility to IPA infection. SNP-SNP interaction (epistasis) analysis revealed significant interactions models including SNPs in Dectin-1, Dectin-2, CCL2 and CCR2 genes, with synergistic genetic effects. Although these results need to be further validated in larger cohorts, they suggest that Dectin-1, DC-SIGN, Dectin-2, CCL2 and CCR2 genetic variants influence the risk of IPA infection and might be useful in developing a risk-adapted prophylaxis.
Analysis of DoS Attacks in Delay Tolerant Networks for Emergency Evacuation

In the event of a disaster, there is a severe damage/destruction to physical infrastructures such as telecommunication and power lines which result in the disruption of communication in this areas. For such scenarios, Delay Tolerant Network (DTN) provides an alternative means of communication. In Delay Tolerant Networks (DTNs), a message from a source node may be delivered to the destination node despite the non-existence of an infrastructure and an end-to-end connectivity. However DTNs are susceptible to security threats such as DoS attacks targeted at disrupting relayed packets or dropping critical packets during a disaster rescue operation. DoS attacks consist of blackhole, grayhole, wormhole, packet flooding attacks etc. The scope of this paper is to study the impacts of blackhole and packet flooding attacks in a post disaster communication network using DTN. Various performance metrics in DTN have been used to study the impacts of different DoS attacks in DTN and a comprehensive analysis is presented.
Stereo‐selectivity of HIV‐1 reverse transcriptase toward isomers of thymidine‐5′‐O‐1‐thiotriphosphate

The first pre‐steady‐state kinetic analysis of the stereo‐selective incorporation of Rp‐ and Sp‐isomers of thymidine‐5′‐O‐1‐thiotriphosphate (TTPαS) by HIV‐1 reverse transcriptase (RT) is reported. Rates of polymerization (kpol), apparent dissociation constants (Kd), and substrate specificities (kpol/Kd) were measured for TTP, Rp‐TTPαS, and Sp‐TTPαS in the presence of Mg2+, Mn2+, and Co2+. HIV‐1 RT exhibits a strong preference to incorporate Sp‐TTPαS over Rp‐TTPαS in the presence of Mg2+; however, this stereo‐selective preference was decreased when Mg2+ was replaced with Mn2+ and Co2+. Furthermore, HIV‐1 RT exhibited no phosphorothioate elemental effects for the incorporation of Sp‐TTPαS, but large elemental effects were calculated for Rp‐TTPαS for each of the metals tested. These results are discussed in relation to our current understanding of the RT active‐site structure and the mechanism of DNA synthesis.
Selection of a sublibrary enriched for a chromosome from total human bacterial artificial chromosome library using DNA from flow sorted chromosomes as hybridization probes.

The division of total genomic libraies into chromosome-specific sublibraries is critical for efficient analysis and mapping of the genome. A new colony hybridization-based approach to rapidly identify chromosome-specific clones from a human genomic bacterial artificial chromosome (BAC) library (1,2) is described. The most ideal hybridization probe for identifying all of the chromosome-specific clones from a genomic library in a single hybridization would be the chromosome itself. Using flow sorted chromosome 22 DNA as a probe, which was obtained as previously described (3,4), we screened a 4x human genomic BAC library gridded onto 42 hybridization filters at 5 x 5 density using a Biomekl,000 'gndding tool (2). 100 ng of sorted DNA was labeled with [a-2P]dCTP and [a-32P]dATP by random priming and hybridized to the filters under suppressive condition (2). Chromosomes 21 and 22 are similar in size, and they both are acrocentric chromosomes carrying ribosomal repeats. Therefore we also hybridized the library filters with sorted chromosome 21 DNA probe as a control. Comparison of hybridization results from both chromosomal DNA allowed us to identify many of the non-chromosome-specific false positives that arose from cross hybridization between highly repetitive elements present in different chromosomes. The hybridization images were digitized via PhosphorImager (Molecular Dynamics) and processed using a computer program (5) that extracts the coordinate and intensity information for each colony on the filters. Due to the highly complex nature of the chromosomal probes, the hybridization suffered from background noise as well as low hybridization signal intensity. Quantitation and analysis of numerous weak signals with varying intensities necessitated the use of a detection method more sensitive than exposing to X-ray films and a computer based approach to read the hybridization images. Colonies belonging approximately to the top 5% intensity group from each filter were selected from each chromosomal hybridization. Most of the clones with strong signals in both chromosomal hybridizations tumed out to contain ribosomal and other repeats (Fig. 1). After excluding these common hits, -3300 and 3000 A
Contemporary Cryptology Provable Security for Public Key Schemes

Since the appearance of public-key cryptography in the Die-Hellman seminal paper, many schemes have been proposed, but many have been broken. Indeed, for a long time, the simple fact that a cryptographic algorithm had withstood cryptanalytic attacks for several years was considered as a kind of validation. But some schemes took a long time before being widely studied, and maybe thereafter being broken. A much more convincing line of research has tried to provide \provable" security for cryptographic proto- cols, in a complexity theory sense: if one can break the cryptographic protocol, one can ecien tly solve the underlying problem. Unfortunately, this initially was a purely theoretical work: very few practical schemes could be proven in this so-called \standard model" because such a security level rarely meets with eciency . Ten years ago, Bellare and Rogaway proposed a trade-o to achieve some kind of validation of ecien t schemes, by identifying some concrete cryptographic objects with ideal random ones. The most famous identication appeared in the so-called \random-oracle model". More recently, another direction has been taken to prove the security of ecien t schemes in the standard model (without any ideal assumption) by using stronger computational assumptions. In these lectures, we focus on practical asymmetric protocols together with their \reductionist" security proofs, mainly in the random-oracle model. We cover the two main goals that public-key cryptography is devoted to solve: authentication with digital signatures, and conden tiality with public-key encryption schemes.
Towards Learning Error-Driven Transformations for Information Extraction

Transformation-based and error-driven induction of rules has proven to be a successful and applicable technique for Part-of-Speech tagging and other natural language processing tasks. This paper presents the ongoing work to create a universal algorithm for learning transformations in the domain of information extraction and semantic annotation. Such a method can be applied to different and useful tasks in real world problems, e.g., correcting systematic labeling errors of statistical models or improving data sets annotated by humans. We show the applicability of the current prototype in the domain of reference segmentation, where our method is able to reduce the labeling errors of conditional random fields.
Optimizing Classifier Performance Via the Wilcoxon-Mann-Whitney Statistic

Cross entropy and mean squared error are typical cost functions used to optimize classi er performance. The goal of the optimization is usually to achieve the best correct classi cation rate. However, for many two-class real-world problems, the ROC curve is a more meaningful performance measure. We demonstrate that minimizing cross entropy or mean squared error does not necessarily maximize the area under the ROC curve (AUC). We then consider alternative objective functions for training a classi er to maximize the AUC directly. We propose an objective function that is an approximation to the Wilcoxon-Mann-Whitney statistic, which is equivalent to AUC. The proposed objective function is di erentiable, so gradient-based methods can be used to train the classi er. After discussing the improved results of the new objective function over several UCI data sets, we apply the new objective function to real-world customer behavior prediction problems for a wireless service provider and a cable service provider, and achieve reliable and signi cant improvements in the ROC curve.