Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Analysis of Major Tick and Mite Vectors of Human Pathogens Table 1. Summary of Proposed Tick and Mite Vectors Genome Projects Classification Genome Sequencing (no. Species at 100x Genome Coverage) Transcriptome Sequencing (no. Rnaseq Reads in Millions)*

Executive Summary Ticks and mites (subphylum Chelicerata: class Acari) transmit a greater variety of human and animal pathogens than any other arthropod vector. Tickand mite-borne diseases are global health problems caused by a variety of bacterial, viral and protozoan pathogens, which are responsible for significant morbidity and thousands of human deaths annually. The incidence of many tick-borne diseases is increasing worldwide many are emerging zoonoses or exotic diseases that could be introduced to the U.S. The Acari are a diverse and basal group within the phylum Arthropoda, comprised of two lineages; the Acariformes or chigger mites and the Parasitiformes which includes the ticks (suborder Ixodida) and other medically important mites. Despite their impact on human health, little is known about the biology and genetic basis of vector competence in the Acari. The NIH funded Ixodes scapularis (Lyme disease tick) assembly represents the only available genome sequence of a medically important species within this entire diverse lineage. Unfortunately, application of this resource is limited by low sequence coverage and fragmentation of the assembly. Here we propose immediate sequencing of the mite vector of scrub typhus, Leptotrombidium deliense, and additional sequencing of I. scapularis to expand genomic resources for this group (summarized in Table 1). These projects will provide the anchor for additional sampling of species at increasing evolutionary distance. We also identify six members of the Ixodida (Dermacentor variabilis, Amblyomma americanum, I. pacificus, I. ricinus, I. persulcatus and Ornithodorus turicata) that are considered high priority sequencing targets by the tick and mite research communities. The haploid genome size of these ticks is expected to exceed 1 Gbp. Recognizing the inherent challenges associated with de novo sequencing and assembly of such genomes and the likely rapid advances anticipated in genome sequencing and assembly technology, we propose extensive transcriptome sequencing of these species to position them for anticipated genome sequencing efforts. Should sequencing of L. deliense and I. scapularis prove successful, we identify two additional species of Ixodida (D. variabilis and O. turicata) as candidates for genome sequencing efforts.
Avaliação de métodos de inferência de redes de regulação gênica.

The representation of the gene regulation system by means of a Gene Regulatory Network (GRN) can help the understanding of biological processes at the molecular level, elucidating the behavior of genes and leading to the discovery of disease causes and the development of new drugs. GRNs allow to evaluate which genes are active and how they influence the system. In recent years, many computational methods have been developed for networks inference from gene expression data. This study presents a comparative analysis of GRN inference methods, reviewing the experimental modeling present in the state-of-art scientific publications applied to datasets with small data samples. The use of ensembles was proposed to improve the quality of the network inference. As results, we show that the use of small data samples (less than 50 samples) do not show a good result in the network inference problem. We also show that the use of ensemble improve the network inference.
Virtual Reality and Prototyping

Prototype design and testing is an indispensable stage of any project development in many fields of activity, such as aeronautical, spatial, automotive industries or architecture. Scientists and engineers rely on prototyping for a visual confirmation and validation of both their ideas and concepts. Using computers for designing digital prototypes is not a new idea since CAD applications are nowadays widely used. In this paper we present how new advances in 3D interaction and real time visualisation research domains lead to the development of a collaborative and really interactive system for virtual prototyping. This work is supported by the European Community through the ESPRIT programme 4. "
A Hybrid Real-Time Vision-Based Person Detection Method

In this paper, we introduce a hybrid real-time method for vision-based pedestrian detection made up by the sequential combination of two basic methods applied in a coarse to fine fashion. The proposed method aims to achieve an improved balance between detection accuracy and computational load by taking advantage of the strengths of these basic techniques. Haar-like features combined with Boosting techniques, which have been demonstrated to provide rapid but not accurate enough results in human detection, are used in the first stage to provide a preliminary candidate selection in the scene. Then, feature extraction and classification methods, which present high accuracy rates at expenses of a higher computational cost, are applied over boosting candidates providing the final prediction. Experimental results show that the proposed method performs effectively and efficiently, which supports its suitability for real applications.
Electron Muon Ranger (EMR) Hardware Characterization

The Electron Muon Ranger (EMR) is a totally active scintillator which purpose is the electron background rejection downstream the cooling channel at the international Muon Ionization Cooling Experiment. It consists in 2832 plastic scintillator bars divided in 48 planes in an X-Y arrangement and uses particle range reconstruction as its main variable to tag muons and discriminate electrons. In the context of a Master Thesis, several short analyses were conducted to characterize the hardware of the EMR and determine if everything is working as designed. All the results were beyond satisfactory as, even though 4 channels (0.15 % of the detector) are dead, the entirety of the electronics work perfectly and every last one of the 5664 clear fibres coming from the bars gives out a good amount of light. Two channels were found mismatched and the DAQ channel map was subsequently corrected. The level of crosstalk was within range for the type of Multi Anode PMT used with less than 0.5 % likelihood of crosstalk in most of the channels and an average of 4.5 $\pm$ 1.5 % of the initial channel intensity measured upon occurrence. The efficiency of the signal acquisition, defined as the probability of recording a signal in a plane when a particle goes through it in beam conditions, reaches 99.73 $\pm$ 0.02 %.
Improving Quality of Service for Radio Station Hosting: An Online Recommender System Based on Information Fusion

We present a new recommender system developed for the Russian interactive radio network FMhost. The system aims to improve the quality of this service; it is designed specifically to deal with small datasets, overcoming the shortage of data on observed user behavior. The underlying model combines a collaborative user-based approach with information from tags of listened tracks in order to match user and radio station profiles. It follows an adaptive online learning strategy based on both user history and implicit feedback. We compare the proposed algorithms with industry standard methods based on Singular Value Decomposition (SVD) in terms of precision, recall, and Normalized Discounted Cumulative Gain (NDCG) measures; experiments show that in our case the fusion-based approach produces the best results.
Application of Classical Encryption Techniques for Securing Data-a Threaded Approach

The process of protecting information by transforming (encrypting) it into an unreadable format is called cryptography. Only those who possess secret key can decipher (decrypt) the message into plain text. Encrypted messages can sometimes be broken by cryptanalysis, also called code breaking, so there is a need for strong and fast cryptographic methods for securing the data from attackers. Although modern cryptography techniques are virtually unbreakable, sometimes they also tend to attack. As the Internet, big data, cloud data storage and other forms of electronic communication become more prevalent, electronic security is becoming increasingly important. Cryptography is used to protect e-mail messages, credit card information, corporate data, cloud data and big data so on. So there is a need for best and fast cryptographic methods for protecting the data. In this paper a method is proposed to protect the data in faster way by using classical cryptography. The encryption and decryption are done in parallel using threads with the help of underlying hardware. The time taken by sequential and parallel method is analysed.
RISK EVALUATION AFTER HEART VALVE REPLACEMENT BY SAS PROC PHREG

Identification of long-term risk factors after heart valve replacement can be quite challenging due to the nature of the covariates. Two specific factors need to be considered : (1) time-dependent covariates, and (2) the validity of the proportional hazard model. PHREG in SAS® is a very convenient procedure for solving these problems. In addition to those commonly encountered problems such as variable selection and influence assessment, we will use a data set from our St. Jude Medical valve prothesis database to illustrate how to use DATA step statement to incorporate time-dependent covariates into the proportional hazard model and how to plot martingale residuals to check model validity. Results from our analysis indicated that cardiopulmonary bypass time during surgery should be treated as time-dependent because its adverse effect faded away after six months. The proportional hazard model fitted this data set reasonably well once the effect of timedependence was taken into consideration.
An Empirical Test of the Mg II λ1240 Doublet Branching Ratio and Oscillator Strength

We empirically confirm the theoretical branching ratio and oscillator strength for the weak Mg II 3s-4p doublet at 1240 Å as determined by Theodosiou & Federman. We use the independent methods of apparent optical depth analysis for the sight lines toward μ Col, γ Ara, and ρ Leo and profile component fitting for the sight line toward μ Col in order to determine the branching ratio. We find f1239/f1240 = 1.74 ± 0.06, in agreement with the theoretical value of 1.78 ± 0.03. Profile fitting for the line of sight toward μ Col gives an f-value for the doublet of 9.71 ± 0.32 × 10-4, which agrees with both the theoretical value of Theodosiou & Federman and the empirical value of Fitzpatrick.
Correcting for Miniature Eye Movements in High Resolution Scanning Laser Ophthalmoscopy

The newest generation of confocal scanning laser ophthalmoscopes with adaptive optics correction of ocular aberrations provides retinal images of unprecedented resolution, allowing for real-time imaging of photoreceptors in the living human eye. Natural fixational eye movements made by the subject/patient during recording produce distortions that are unique in each frame. Correction for these distortions is necessary before multiple frames can be added together to achieve noise reduction or to build a mosaic image from different retinal areas. Here we describe the characteristics of fixational eye movements and the distortions they produce during retinal imaging, we show examples of images with particular distortions, and show eye movement records obtained during the correction of these distortions
Discriminant function method of selection in Vegetable Cowpea [Vigna unguiculata (L.) Walp.]

Sixty diverse genotypes of vegetable cowpea were evaluated for twelve characters in order to construct selection indices. The characters, which had desirable correlation as well as moderate to high direct effect on green pod yield per plant were considered as selection index criterion. The green pod yield per plant (X 1 ) along with its three components viz . , number of pods per plant (X 2 ), pod length (X 3 ) and ten pod weight (X 4 ) were utilized for the construction of selection indices. The discriminant function had higher genetic gain and relative efficiency over straight selection for green pod yield per plant alone. The relative efficiencies of selection indices constructed in combinations of two or more characters were ranged from 3.99 to 136.46%, while genetic advance ranged from 3.99 to 136.28g. There was an increase in genetic gain and relative efficiency with inclusion of an additional trait in the character combination. A selection index involving green pod yield per plant, number of pods per plant, pod length and ten pod weight (X 1 .X 2 .X 3 .X 4 ) followed by green pod yield per plant, number of pods per plant and ten pod weight (X 1 .X 2 .X 4 ) or green pod yield per plant, pod length and ten pod weight (X 1 .X 3 .X 4 ) could be advantageously exploited in the vegetable cowpea breeding programmes.
WIRELESS SENSOR NETWORKS LOCLAIZATION ALGORITHMS: A COMPARATIVE STUDY

Wireless Sensor Networks (WSNs) are the type of networks that are currently used in many applications. Some of these applications are critical and their information is very sensitive e.g. battle field and health care monitoring. Any transferred data has to be known from where it comes. In other words, most of the WSNs applications depend mainly on the location of each node in the network. In fact, the location may affect the decision to be made. The importance of localization is not only due to location identification but also it provides the base for routing, density control, tracking, and number many of other communication network aspects. Therefore, it is very important that each node reports its location accurately. Unfortunately, GPS is not suitable for WSNs due to its cost in terms of nodes consumed energy as well as its availability. Many localization algorithms are proposed for WSNs; however, their accuracy is the main concern. This paper is designated to help the WSNs designers in selecting suitable localization algorithm for their applications. The paper presents as well as implements different localization algorithms and evaluate them.
Cal Poly Csc 466: Knowledge Discovery from Data Alexander Dekhtyar Information Retrieval

Definitions Information Retrieval (IR). The process of finding documents from a given document collection that are relevant to the user's query. Document collections. The key assumption of IR is that document collections are large. Note: This is not always the case. There are some specialized uses of IR techniques, where the document collections are on the order of tens or hunderds of documents, not hundreds of thousands/millions as is usual for traditional IR settings. Queries. A user query is a formal representation of an information need. The two are not the same. An information need is an articulated desire to obtain certain information (or to find documents that contain certain information). A query is a representation of an information need that can be processed by the specific Information Retrieval system. Example. The user information need is to find all information about the University of Alabama's 1992 football season, in particular, to find the list of all games. The user query to a search engine (google) can be: "University of Alabama Crimson Tide football 1992 season games schedule". (Given this query, Google returns the wikipedia page on the 1992 Alabama football season, with the list of games as the top page).
Motivation, Empowerment, and Innovation: Teachers' Beliefs About How Participating in the Edmodo Math Subject Community Shapes Teaching and Learning

Abstract Educators around the world participate in virtual communities, social media sites, and online networks in order to gain support and ideas for improving their practice. Many researchers have explored how and why teachers participate in these online spaces; however, there is limited research on how participation might impact teaching and learning. This study was designed to examine how K–12 teachers' participation in the Edmodo math subject community, an informal online space for educators, shaped their learning and practice. Data were collected through an online survey of 150 participants and in-depth, follow-up interviews with 10 participants. Three themes emerged from the participants' responses: motivation, empowerment, and innovation. The participants were motivated to spend time learning how to improve their practice, they felt empowered to make changes to their practice, and they believed they were able to adopt innovative, student-centered practices. Implications and ideas for further research are discussed.
Assessing School Readiness in Cyprus

School readiness is a concept used to describe a set of necessary prerequisites for a child’s satisfactory transition to the schooling experience. It undoubtedly involves the complex, interdisciplinary and inter-depending relations between the child, school and family and leads to a dynamic perspective of this system, whose parts are inter-subsidized with the final aim to achieve the integration of the child into the Primary school system. This multidimensional view of school readiness sets the context for this paper, which reports on a study with an aim to establish a reliable diagnostic test for school readiness for Cypriot kindergarten children entering the primary school. We start with an overview of how school readiness has been measured internationally so far, and a review of the main findings in regards to such measures, like the association with children’s background characteristics and their future performance. We then present our instrument and report on the results of our pilot investigations with a sample of 128 children aged 5.5 to 6.5 years old. Our methods and analysis include both the use of the Rasch model for the validation of our constructed school readiness measures, as well as further statistical models for the for the comparison of children of various backgrounds on these measures. We conclude with a discussion of our main findings and the implications from the use of the constructed measures for potential language disorders, and identification of possible weaknesses at the four measurable aspects of school readiness (cognitive, language, motor and emotional).
'They made it a living thing didn't they...': the growth of things and the fossilisation of heritage

Christine: [. ] I think everything has feelings. Even a piece of stone that was carved all those years ago. I feel that it's, well they made it a living thing didn't they? Siân: Mmmm Christine: When they did that. Siân: Yes, when they created it? Christine: Yes. They made a living thing. So I feel, yes, I think when it goes back into the ground it will be home. Siân: Yes, that's really interesting. Christine laughs. Christine: I do, I feel it's waiting to go back. We've taken it out, disturbed it, we've looked at it and it, I mean I know it has to have lots of things done to it to preserve it erm, but I think once it goes back I feel it'll shine in its own . Siân: In its place? Christine: Yes. And I hope it goes back where it was found. Because I feel that that's right.
REGIONALIZATION AND CONVERGENCE IN THE EUROPEAN UNION*

The construction of a European political economy through regional integration is a dramatic social change that raises critical challenges for the study of markets. Does regionalization drive convergence among integrating national economies, or does regionalization deepen existing macroeconomic inequalities? The dominant theoretical approaches are at odds: orthodox economic theory and the political-institutionalist approach to markets predict convergence, whereas world systems theory and its interpretation of integration as exploitation suggest divergence. Economic theory highlights market mechanisms, whereas the political-institutional approach privileges rules and scripts of the new regional social order. Existing evidence on the convergence debate is marked by contradictory findings and a general failure to measure regional integration. This paper reports results from a time series analysis of income dispersion among the 15 countries of the European Union for the 1950-2000 period. The central finding is that regional integration is associated with convergence. The effects of political integration are especially powerful, lending support to the political-institutional approach to regionalization.
ML ESTIMATION OF THE t DISTRIBUTION USING EM AND ITS EXTENSIONS, ECM AND ECME

The multivariate t distribution has many potential applications in applied statistics. Current computational advances will make it routinely available in practice in the near future. Here we focus on maximum likelihood estimation of the parameters of the multivariate t, with known and unknown degrees of freedom, with and without missing data, and with and without covariates. We describe EM, ECM and ECME algorithms and indicate their relative computational e ciencies. All three algorithms are analytically quite simple, and all have stable monotone convergence to a local maximum likelihood estimate. ECME, however, can have a dramatically faster rate of convergence.
Research Statement Hossam Sharara Doctoral Research Network Evolution Bi-modal Interaction Dynamics

My research interests span the areas of data mining, machine learning, and social network analysis. A common thread in my research is understanding the different types of interactions that occur within social networks, and their effects on the users’ behavior. In particular, my research focuses on reasoning in dynamic, multi-modal, multi-relational network settings, where there exist multiple entity types (such as people, social groups, organizations, locations, etc.), and different types of relationships (such as friendship, membership, affiliation, etc.). For example, in social network settings, in addition to friendship relationships, users can have family ties with other users, join multiple social groups, be affiliated with various organizations, or belong to different geographical sub-networks. By considering the complex structure of these networks rather than limiting the analysis to a single entity or relationship type, we can build richer models that provide better understanding of the dynamics in these settings, and thus help in providing highly accurate predictions about future events. My long-term research goals are to analyze a number of aspects related to information networks (such as group formation, network clustering, information diffusion, etc.), create explanatory and predictive models of the interactions that occur in complex network settings, and investigate the implications of these studies on applications in different domains. Based on my doctoral research, I believe that capturing different types of dependencies that exist in networked systems is a propitious approach for understanding the dynamics of the corresponding domains, particularly human behavior and actions in social context.
Effect of wind barrier on the steady aerodynamic characteristic of trains by numerical simulation *

To investigate the relationship of aerodynamic characteristic between presence and absence of wind barrier, a simplified CRH3 model on the ground subjected to crosswinds is simulated using Computational Fluid Dynamics (CFD). Firstly, the independence of mesh generation is tested, the streamlines on the surfaces of train and the wake structures are compared with the results presented in the previous studies. Then, the aerodynamic coefficients for yaw angles 0<β≤45° are calculated, and a “transformation” is proposed based on Baker hypothesis. Lastly, the aerodynamic coefficients after installing wind barriers are obtained by the “transformation”, and compared with the results of numerical simulation. The results show that the “transformation” is applicable for calculating the lateral drag and lift coefficients of head nose, but is not adequate for those of end nose. After installing wind barriers, the lift-drag ratios of the end nose are significantly changed, and the flow separation lines at the bottom of the end nose move from leeward to windward.