Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.
Intelligent System to Measure the Strength of Authentication

This paper presents an investigation into the development of an intelligent system to measure the strength of authentication. Many computer users do not have enough security knowledge to be able to select strong password. The term strong password is not well defined; usually considers the computational complexity of cracking by unwanted user or hacker. In other words, the quicker the crack can be achieved the weaker the password is. Many measurement tools exist to help users to measure their password strength before using it. It is noticed that available techniques have not taken into consideration all critical complexity issues that can affect the password strength. In this paper a new methodology and tool (PTool) using Fuzzy rules is presented to measures the password strength based on the three defined attacks together rather one of them at a time; dictionary attack, time crack and shoulder surfing attacks (social engineering). The paper is also presents a quantitative approach to the password strength to demonstrates the merits and capabilities of the proposed intelligent tool. To achieve a maximum level of security during the process of changing the password, an API functions is deployed to assess the password securely and to limit the effect of spywares and hacking scripts.
A Survey on Feature Selection Techniques for Internet Traffic Classification

Feature selection technique has a great importance in Internet traffic classification. Machine learning (ML) algorithms have been generally applied in novel traffic classification. In this paper we provide an overview of three major approaches to classify different categories of Internet traffic: Port based approach, Payload based approach, Statistical-based approach. This paper also explain feature selection algorithms, which are classified into 3 methods: Filter method, Wrapper method, Embedded Method along with their benefits and limitations and also provides an overview of some of the feature selection technique present in literature. The aim of the survey gives a brief idea about feature selection techniques which can be applied to many machine learning algorithms to avoid problems like class imbalance, concept drift, low efficiency, and low classification rate etc.
Application of Deterministic Annealing EM Algorithm to Markovian Arrival Process Parameter Estimation

This paper proposes a variant of EM (expectation-maximization) algorithm for Markovian arrival process (MAP) parameter estimation. Especially, we derive the deterministic annealing EM (DAEM) algorithm for MAP parameter estimation. The DAEM algorithm is one of the methods to overcome a local maxima problem associated with the conventional EM algorithm. This paper derives concrete E- and M-step formulas for MAP parameter estimation from inter-arrival time data in the framework of DAEM algorithm. Numerical examples demonstrate the DAEM algorithm for Markov-modulated Poisson process (MMPP), and we show that the DAEM algorithm is superior to the conventional EM algorithm in terms of avoiding the convergence to local maxima.
Diversity: A Design Goal for Heterogeneous Processors

A growing number of processors have CPU cores that implement the same instruction set architecture (ISA) using different microarchitectures. The underlying motivation for single-ISA heterogeneity is that a diverse set of cores can enable runtime flexibility. Modern processors are subject to strict power budgets, and heterogeneity provides the runtime scheduler with more latitude to decide the level of performance a program should have based on the amount of power that can be spent. We argue that selecting a diverse set of heterogeneous cores to enable flexible operation at runtime is a non-trivial problem due to diversity in program behavior. We further show that common evaluation methods lead to false conclusions about diversity. Finally, we suggest the KS statistical test as an evaluation metric. The KS test is the first step toward a heterogeneous design methodology that optimizes for runtime flexibility.
Technological Adoption with Imperfect Markets in the Italian Economy

The last twenty years have seen a marked slowdown of the Italian productivity growth rate. The literature has underlined the role of international factors, such as globalization and adoption of the euro. In this paper we emphasize the role and dynamics of capital accumulation investigating the impact of the introduction of information technology on capital and production in the Italian economy and the extent to which that is being affected by skills in the labour force.The model is specified and estimated as continuous-time general disequilibrium framework. It presents original features: it analyzes the effects of the introduction of the ICT technology on the Italian economy not in a partial equilibrium context of a single market but from a macro point of view where input markets interact; it does not assume that these markets instantaneously clear but rather that there are imperfections and frictions; it does not impose the condition that the economy necessarily converges to a steady state. The model behaves quite well in replicating the dynamics of the Italian economy. It also shows however that there remains some structural inefficiency that worsened in recent years. In fact, our main finding shows that there exists a permanent gap between “optimal” and actual output which increased in the latter part of the sample period. While a fraction of this gap can be attributed to unavoidable (market and non market) adjustment costs some is associated to efficiency losses.
A Homolog of the Vaccinia Virus D13L Rifampicin Resistance Gene is in the Entomopoxvirus of the Parasitic wasp, Diachasmimorpha longicaudata

Abstract The parasitic wasp, Diachasmimorpha longicaudata (Ashmead) (Hymenoptera: Braconidae), introduces an entomopoxvirus (DlEPV) into its Caribbean fruit fly host, Anastrepha suspensa. (Loew) (Diptera: Tephritidae), during oviposition. DlEPV has a 250–300 kb unipartite dsDNA genome, that replicates in the cytoplasm of the host's hemocytes, and inhibits the host's encapsulation response. The putative proteins encoded by several DlEPV genes are highly homologous with those of poxviruses, while others appear to be DlEPV specific. Here, a 2.34 kb sequence containing a 1.64 kb DlEPV open reading frame within a cloned 4.5 kb EcoR1 fragment (designated R1–1) is described from a DlEPV EcoRI genomic library. This open reading frame is a homolog of the vaccinia virus rifampicin resistance (rif) gene, D13L, and encodes a putative 546 amino acid protein. The DlEPV rif contains two EcoRV, two HindIII, one XbaI, and one DraII restriction sites, and upstream of the open reading frame the fragment also contains EcoRV, HindII, SpEI, and BsP106 sites. Early poxvirus transcription termination signals (TTTTTnT) occur 236 and 315 nucleotides upstream of the consensus poxvirus late translational start codon (TAAATG) and at 169 nucleotides downstream of the translational stop codon of the rif open reading frame. Southern blot hybridization of HindIII-, EcoRI-, and BamH1-restricted DlEPV genomic DNA probed with the labeled 4.5 kb insert confirmed the fidelity of the DNA and the expected number of fragments appropriate to the restriction endonucleases used. Pairwise comparisons between DlEPV amino acids and those of the Amsacta moorei, Heliothis armigera, and Melanoplus sanguinipes entomopoxviruses, revealed 46, 46, and 45 % similarity (identity + substitutions), respectively. Similar values (41–45%) were observed in comparisons with the chordopoxviruses. The mid portion of the DlEPV sequence contained two regions of highest conserved residues similar to those reported for H. armigera entomopoxvirus rifampicin resistance protein. Phylogenetic analysis of the amino acid sequences suggested that DlEPV arose from the same ancestral node as other entomopoxviruses but belongs to a separate clade from those of the grasshopper- infecting M. sanguinipes entomopoxvirus and from the Lepidoptera-infecting (Genus B or Betaentomopoxvirus) A. moorei entomopoxvirus and H. armigera entomopoxvirus. Interestingly, the DlEPV putative protein had only 3–26.4 % similarity with RIF-like homologs/orthologs found in other large DNA non-poxviruses, demonstrating its closer relationship to the Poxviridae. DlEPV remains an unassigned member of the Entomopoxvirinae (http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/index.htm) until its relationship to other diptera-infecting (Gammaentomopoxvirus or Genus C) entomopoxviruses can be verified. The GenBank accession number for the nucleotide sequence data reported in this paper is EF541029.
Dynamic Software Product Lines

The Software Engineering Institute (SEI) defines an SPL as a set of software-intensive systems that share a common, managed set of features satisfying the specific needs of a particular market segment or mission. A fundamental principle of SPLs is variability management, which involves separating the product line into three parts - common components, parts common to some but not all products, and individual products with their own specific requirements - and managing these throughout development. Using SPLs seeks to maximize reusable variation and eliminate wasteful generic development of components used only once. Although traditional SPL engineering recognizes that variation points are bound at different stages of development, and possibly also at runtime, it typically binds variation points before delivery of the software. In contrast, DSPL engineers typically aren't concerned with pre-runtime variation points. However, they recognize that in practice mixed approaches might be viable, where some variation points related to the environment's static properties are bound before runtime and others related to the dynamic properties are bound at runtime.
A Novel Hybrid system for Large-Scale Chinese Text Classification Problem

Most of the Chinese text classification systems are all based on the technology of bag of words (BW) which is a valid probability tool for text representation and can provide a better semantic architecture. But the weakness in classification accuracy is still unconquerable. Support vector machine (SVM) has become a popular classification tool and can be applied in the scheme, but the main disadvantages of SVM algorithms are their large memory requirement and computation time to deal with very large datasets. In this paper, we propose a hybrid system based on BW and a novel cascade SVM with feedback that can be splitting the problem into smaller subsets and training a network to assign samples of different subsets. The proposed parallel training algorithm on large-scale classification problems where multiple SVM classifiers are applied speeds up the process of training SVM and increase the classification accuracy.
ER-associated retrograde SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic ER fusion pathway

SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic endoplasmic reticulum (ER) fusion pathway in yeast. When both pathways and the reticulons are simultaneously disrupted, cells are inviable. This demonstrates that homotypic ER fusion is an essential process in yeast and that the Dsl1 complex has vesicle trafficking-independent functions.
International Journal of Copd Dovepress Interleukin-6 and Interleukin-8 Blood Levels' Poor Association with the Severity and Clinical Profile of Ex-smokers with Copd

Background: The role of interleukins in the severity and clinical profile of chronic obstructive pulmonary disease (COPD) is not known, but evidence supports the contribution of systemic inflammation to disease pathophysiology. This study evaluated the relationship of serum biomarkers to the severity and clinical parameters of COPD. Methods and findings: Serum levels of high-sensitivity C-reactive protein, interleukin-6 (IL-6), and interleukin-8 (IL-8) were measured in 50 patients with stable COPD and in 16 controls. The levels of these biomarkers were compared with parameters of severity, such as the grading of flow obstruction using the recommendations of the Global initiative for chronic Obstructive Lung Disease, the BMI (body mass index), obstruction, dyspnea, exercise capacity (health index) index, the number of exacerbations within the last year, and peripheral oxygen saturation after the six-minute walk test, and with clinical parameters, such as bronchitis and non-bronchitis phenotypes, the number of associated comorbidities, and the smoking burden. COPD patients exhibited higher levels of IL-6 and IL-8 compared to the control group. Higher levels of IL-6 occurred in COPD groups with body mass index ,21 kg/m 2 , with more than two exacerbations in the past year, with a higher smoking burden, and with bronchitis. The increase in serum IL-8 was found only in the group with the highest number of exacerbations within the previous year. Conclusion: Increased IL-6 was mainly associated with smoking burden, in patients who had smoked for more than 30 pack-years and exhibited a bronchitis phenotype. No direct association was observed for both IL-6 and IL-8 blood levels with the severity of COPD in ex-smokers.
Cannabinoid Agonists Inhibit Neuropathic Pain Induced by Brachial Plexus Avulsion in Mice by Affecting Glial Cells and MAP Kinases

Background Many studies have shown the antinociceptive effects of cannabinoid (CB) agonists in different models of pain. Herein, we have investigated their relevance in neuropathic pain induced by brachial plexus avulsion (BPA) in mice. Methodology/Principal Findings Mice underwent BPA or sham surgery. The mRNA levels and protein expression of CB1 and CB2 receptors were assessed by RT-PCR and immunohistochemistry, respectively. The activation of glial cells, MAP kinases and transcription factors were evaluated by immunohistochemistry. The antinociceptive properties induced by cannabinoid agonists were assessed on the 5th and 30th days after surgery. We observed a marked increase in CB1 and CB2 receptor mRNA and protein expression in the spinal cord and dorsal root ganglion, either at the 5th or 30th day after surgery. BPA also induced a marked activation of p38 and JNK MAP kinases (on the 30th day), glial cells, such as microglia and astrocytes, and the transcription factors CREB and NF-κB (at the 5th and 30th days) in the spinal cord. Systemic treatment with cannabinoid agonists reduced mechanical allodynia on both the 5th and 30th days after surgery, but the greatest results were observed by using central routes of administration, especially at the 30th day. Treatment with WIN 55,212-2 prevented the activation of both glial cells and MAP kinases, associated with an enhancement of CREB and NF-κB activation. Conclusions/Significance Our results indicate a relevant role for cannabinoid agonists in BPA, reinforcing their potential therapeutic relevance for the management of chronic pain states.
Design of a multi GBPS Single Carrier digital baseband for 60GHz applications and its FPGA implementation

This paper describes the system architecture, design methodology and subsequent FPGA mapping of a millimeter wave digital baseband for wireless communication in the 60GHz spectral band. The baseband is designed to be compliant with the 802.11ad Single Carrier and Control PHY draft specifications and supports a data rate of 2.5Gbps at the physical layer. The demanding throughput and latency requirements are achieved with a parallel implementation. However, due to limited capacity of the FPGAs present in our prototype platform and complex partitioning requirements, only a scaled down version of the full single carrier baseband that operates at 1/10th the throughput of the specification could be mapped. A minimal real-time hardware MAC was also incorporated and coupled with a 60GHz RF beam-forming front-end to demonstrate file transfer between two independent FPGA prototyping systems. A system throughput of 59Mbps was achieved at the application layer using π/2 QPSK modulation with a 13/16 LDPC code rate.
Two Pricing Mechanisms in Sponsored Search Advertising

Sponsored search advertising has grown rapidly since the last decade and is now a significant revenue source for search engines. To ameliorate revenues, search engines often set fixed or variable reserve price to in influence advertisers’ bidding. This paper studies and compares two pricing mechanisms: the generalized second-price auction (GSP) where the winner at the last ad position pays the larger value between the highest losing bid and reserve price, and the GSP with a posted reserve price (APR) where the winner at the last position pays the reserve price. We show that if advertisers’ per-click value has an increasing generalized failure rate, the search engine’s revenue rate is quasi-concave and hence there exists an optimal reserve price under both mechanisms. While the number of advertisers and the number of ad positions have no effect on the selection of reserve price in GSP, the optimal reserve price is affected by both factors in APR and it should be set higher than GSP.
Multiple Zeta-Functions Associated with Linear Recurrence Sequences and the Vectorial Sum Formula

Abstract We prove the holomorphic continuation of certain multi-variable multiple zeta-functions whose coefficients satisfy a suitable recurrence condition. In fact, we introduce more general vectorial zeta-functions and prove their holomorphic continuation. Moreover, we show a vectorial sum formula among those vectorial zeta-functions from which some generalizations of the classical sum formula can be deduced.
Heuristics for designing enjoyable user interfaces: Lessons from computer games

In this paper, I will discuss two questions: (1) Why are computer games so captivating? and (2) How can the features that make computer games captivating be used to make other user interfaces interesting and enjoyable to use? After briefly summarizing several studies of what makes computer games fun, I will discuss some guidelines for designing enjoyable user interfaces. Even though I will focus primarily on what makes systems enjoyable, I will suggest how some of the same features that make systems enjoyable can also make them easier to learn and to use.
The E92K Melanocortin 1 Receptor Mutant Induces cAMP Production and Arrestin Recruitment but Not ERK Activity Indicating Biased Constitutive Signaling

Background The melanocortin 1 receptor (MC1R) constitutes a key regulator of melanism. Consequently, many naturally-occurring MC1R mutations are associated with a change in color. An example is the Glu-to-Lys substitution found at position II:20/2.60 in the top of transmembrane helix II which has been identified in melanic mice and several other species. This mutation induces a pronounced increase in MC1R constitutive activity suggesting a link between constitutive activity and melanism which is corroborated by the attenuation of α-melanocyte stimulating hormone (αMSH) induced activation. However, the mechanism by which the mutation induces constitutive activity is currently not known. Methodology/Principal Findings Here we characterize the constitutive activity, cell surface expression and internalization of the mouse mutant, Mc1r E92K. As previously reported, only positively charged residues at position II:20/2.60 induced an increase in constitutive activity as measured by cAMP accumulation and CREB activation. Furthermore, the mutation induced a constitutive recruitment of β-arrestin. This phenomenon is only observed in MC1R, however, as the equivalent mutations in MC2-5R had no effect on receptor signaling. Interestingly, the mutation did not induce constitutive ERK1/2 phosphorylation or increase the internalization rate indicating the constitutive activity to be biased. Finally, to identify regions of importance for the increased constitutive activity of Mc1r E92K, we employed a chimeric approach and identified G102 and L110 in the extracellular loop 1 to be selectively important for the constitutive activity as this, but not αMSH-mediated activation, was abolished upon Ala substitution. Conclusions/Significance It is concluded that the E92K mutation induces an active conformation distinct from that induced by αMSH and that the extracellular loop 1 is involved in maintaining this conformational state. In turn, the results suggest that in MC1R, which lacks an extracellular loop 2, the first extracellular loop may play a more prominent role during receptor activation than in general.
Suggesting ( More ) Friends Using the Implicit Social Graph ∗

Although users of online communication tools rarely categorize their contacts into groups such as ”family”, ”co-workers”, or ”jogging buddies”, they nonetheless implicitly cluster contacts, by virtue of their interactions with them, forming implicit groups. In this paper, we describe the implicit social graph which is formed by users’ interactions with contacts and groups of contacts, and which is distinct from explicit social graphs in which users explicitly add other individuals as their ”friends”. We introduce an interaction-based metric for estimating a user’s affinity to his contacts and groups. We then describe a novel friend suggestion algorithm that uses a user’s implicit social graph to generate a friend group, given a small seed set of contacts which the user has already labeled as friends. We show experimental results that demonstrate the importance of both implicit group relationships and interaction-based affinity ranking in suggesting friends. Finally, we discuss two applications of the Friend Suggest algorithm that have been released as Gmail Labs features. ∗ This is an updated version of Roth et al. ”Suggesting Friends Using the Implicit Social Graph” that appeared in SIGKDD, 2010. Please see that paper for all references. Appearing in Proceedings of the 28 th International Conference on Machine Learning, Bellevue, WA, USA, 2011. Copyright 2011 by the author(s)/owner(s).