Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Wide Adaptations of Plasmodium falciparum in Response to Lumefantrine Selective Drug Pressure

The combination therapy of the Artemisinin-derivative Artemether (ART) with Lumefantrine (LM) (Coartem®) is an important malaria treatment regimen in many endemic countries. Resistance to Artemisinin has already been reported, and it is feared that LM resistance (LMR) could also evolve quickly. Therefore molecular markers which can be used to track Coartem® efficacy are urgently needed. Often, stable resistance arises from initial, unstable phenotypes that can be identified in vitro. Here we have used the Plasmodium falciparum multidrug resistant reference strain V1S to induce LMR in vitro by culturing the parasite under continuous drug pressure for 16 months. The initial IC50 (inhibitory concentration that kills 50% of the parasite population) was 24 nM. The resulting resistant strain V1SLM, obtained after culture for an estimated 166 cycles under LM pressure, grew steadily in 378 nM of LM, corresponding to 15 times the IC50 of the parental strain. However, after two weeks of culturing V1SLM in drug-free medium, the IC50 returned to that of the initial, parental strain V1S. This transient drug tolerance was associated with major changes in gene expression profiles: using the PFSANGER Affymetrix custom array, we identified 184 differentially expressed genes in V1SLM. Among those are 18 known and putative transporters including the multidrug resistance gene 1 (pfmdr1), the multidrug resistance associated protein and the V-type H+ pumping pyrophosphatase 2 (pfvp2) as well as genes associated with fatty acid metabolism. In addition we detected a clear selective advantage provided by two genomic loci in parasites grown under LM drug pressure, suggesting that all, or some of those genes contribute to development of LM tolerance – they may prove useful as molecular markers to monitor P. falciparum LM susceptibility.
Developmental analysis of the eye lens obsolescence (Elo) gene in the mouse: cell proliferation and Elo gene expression in the aggregation chimera.

This study investigates the primary effect of the eye lens obsolescence (Elo) gene of the mouse. Morphological features of the Elo lens were defined as follows: (1) deficient elongation of lens fiber cells, (2) morphological abnormality of nuclei of lens fiber cells, (3) lack of eosinophilic granules in the central fiber cells and (4) rupture of lens capsule in the posterior region. We have immunohistologically examined, by means of an in vivo BrdU incorporation system, whether or not the Elo gene regulates cell proliferation during lens development. The lens fiber cells were morphologically abnormal in day 13 embryonic Elo lens. However, there were no significant differences in morphology or cell proliferation between normal and Elo lens epithelium until day 14 of gestation. After day 15, the total cell number in the Elo lens epithelium was significantly less than that in the normal, but the total numbers of S-phase cells in the two genotypes were not significantly different. The ratio of the total S-phase cell number to the total number of lens epithelial cells may be affected by the developmental stage, but not directly by the genotype. The genotype, however, may be having a direct influence at later ages because malformation of Elo lens fiber cells must cause reduction of the total number of lens epithelial cells in older embryos. Although, at 30 days old, Elo lens cells were externally extruded through the ruptured capsule into the vitreous cavity, BrdU-labelled lens epithelial cells were detectable. To investigate whether the Elo lens phenotype is determined by its own genotype or by its cellular environment, we produced aggregation chimeras between C3H-Elo/+(C/C) and BALB/c(c/c). Most lenses of BALB/c dominant chimeras were oval in shape without the ruptured lens capsule. However, they were opaque in the center and slightly smaller in size than normal. The lenses of C3H-Elo/+ dominant chimeras were morphologically similar to the Elo lens. Although normal nuclei were regularly arranged in the anterior region, Elo-type nuclei were located in the posterior region. Immunohistological staining by using anti-C3H strain-specific antibody demonstrated that the lens fiber cells with abnormal nuclei were derived only from C3H-Elo/+, not from BALB/c. These observations suggest that the primary effect of the Elo gene in the developing lens may be specific to the fiber cell differentiation rather than to the cell proliferation. (ABSTRACT TRUNCATED AT 400 WORDS)
Detecting Network Intrusions

The purpose of this project is to create a predictive model for detecting network intrusions. It makes use of a dataset, which consists of nine weeks of raw TCP dump data for a local area network (LAN) that was designed to simulate a typical U.S. Air Force LAN. We implemented a variety of different classification algorithms based on Logistic Regression and the Naïve Bayesian model to determine if individual connections were malicious. False positive and negative error rates were used as criteria to evaluate the relative performance of these approaches. We determined that a multi-dimensional Naïve Bayesian model is an effective approach for filtering network connections that minimizes impedance of normal network activity.
User grouping based on large scale channel information in multi-cell downlink cooperative multi-antenna systems

In this paper, we study low feedback user grouping in downlink cooperative transmission multi-antenna systems. Users in the same group are served on the same frequency and time resource by multiple cooperative BSs using the zero-forcing precoder. We first derive the user's average received signal to interference and noise ratio (SINR). It shows that each user's SINR is an increasing function of the large scale signal to interference ratio (SIR) of users in neighbor cells, which can be obtained using the large scale channel information. We then propose a novel fair user grouping algorithm based on the large scale SIR. Simulation results show that our algorithm achieves better cell edge throughput compared with existing methods with minor reduction of cell throughput.
HOTTest: A model-based test design technique for enhanced testing of domain-specific applications

Model-based testing is an effective black-box test generation technique for applications. Existing model-based testing techniques, however, fail to capture implicit domain-specific properties, as they overtly rely on software artifacts such as design documents, requirement specifications, etc., for completeness of the test model. This article presents a technique, HOTTest, which uses a strongly typed domain-specific language to model the system under test. This allows extraction of type-related system invariants, which can be related to various domain-specific properties of the application. Thus, using HOTTest, it is possible to automatically extract and embed domain-specific requirements into the test models. In this article we describe HOTTest, its principles and methodology, and how it is possible to relate domain-specific properties to specific type constraints. HOTTest is described using the example of HaskellDB, which is a Haskell-based embedded domain-specific language for relational databases. We present an example application of the technique and compare the results to some other commonly used Model-based test automation techniques like ASML-based testing, UML-based testing, and EFSM-based testing.
Semantic tagging and classification of blogs

User generated content is one of the main exciting portion of the web. Blogs constitutes an important part of this portion, which is growing rapidly. It is fast becoming a tool for information sharing and social networking. A blog is a website maintained by an individual that contains commentary, descriptions of events, graphics or video. Entries in blogs are always displayed in reverse chronological order. In the recent years the uses of blogs have drastically increased. Because of its diversified use and its rapid increase, it has widely attracted researcher's attention. Blog classification is required for the relevant blog searches, grouping blogs at a higher conceptual level, and its use for blog post recommendations.
Prolaci in Release-inhibitory Effects of Progesterone , Megestrol Acetate , and Mifepristone ( RU 38486 ) by Cultured Rat Pituitary Tumor Cells 1

The prolactin (PRL) release-inhibitory effects of progesterone, dexamethasone, megestrol acetate, and mifepristone (RU 38486) were studied in cultured pituitary tumor cells prepared from the 7315a and 7315b tumor. Both tumors contain similar numbers of estrogen and progesterone receptors, while only the 731Sa tumor also has glucocorticoid receptors. PRL release by the 731Sa tumor was stimulated by low concentrations of dexamethasone ( ill '" ill '' M) and was inhibited in a dose-dependent manner by higher concentrations (â€”86%by III M). In contrast only Ml"" and in ' M dexamethasone inhibited PRL release by the 7315b cells by 14 and 24%, respectively. Progesterone caused a dose-dependent inhibition of PRL release, which was similar in the 731Sa and b tumor cells. Progesterone ( in"' M) inhibited PRL release by 62% and this inhibition was completely prevented by 100 n\i estradici, which was stimulatory by itself (+48%). Mifepristone inhibited PRL release by both tumors in a dose-dependent manner, but more powerfully in the 7315a tumor. Id " M concentrations of the compound inhibited PRL release by S2% in the 7315a and by 26% in the 731Sb tumor cells. Megestrol acetate inhibited PRL release in both tumors in a dosedependent manner, but more powerfully in the 731Sb tumor; a 10 * M concentration of the compound inhibited PRL release by S4% in the 731Sb tumor and by 14% in the 731Sa tumor. In the 731Sa tumor 10 ' M megestrol acetate even stimulated PRL release, suggesting a dexamethasone-like glucocorticoid effect of the drug on this tumor. Thereafter the interaction of mifepristone and megestrol acetate on PRL release was investigated. In the 731Sa tumor cells different combinations of both drugs neutralized each other's inhibitory effects on PRL release, while both drugs had additional inhibitory effects on PRL release by 731Sb tumor cells. Changes in PRL release by the cultured pituitary tumor cells were in all instances closely correlated with changes in the PRL content, the protein content, and the DNA content of the tumor cells. This suggests that the inhibitory effect of the compounds studied on PRL release is paralleled by an inhibitory effect on the number of pituitary tumor cells. These studies show the importance of the presence of glucocorticoid receptors in the effectiveness and mechanism of action of the antitumor effects of megestrol acetate and mifepristone. In the presence of gluco corticoid receptors (731Sa tumor) the effects of a combination of both compounds are neutralized, while in the absence of these receptors (731Sb tumor) the antitumor effects of both drugs are additive, presumably via an effect on the progesterone receptor. These observations might be of importance in clinical studies involving combinations and/or sequential use of megestrol acetate, mifepristone. and dexamethasone in the treat ment of endocrine-dependent cancer in humans.
Self-Declaration of Diabetes and Factors Associated with Having Regular Eye Examinations among Patients with Type 2 Diabetes in Turkey

Purpose To assess the awareness of diabetic retinopathy (DR), decided by self-declaration of diabetes, and the factors associated with having regular eye examinations among patients with type 2 diabetes in Turkey. Methods Between January and June 2014, 3322 adult patients attending an outpatient ophthalmology clinic were screened and 160 patients with type 2 diabetes with a known duration of at least 5 years were included. All patients were asked for their complaints and self-declaration of diabetes was noted. A questionnaire including questions about demographic characteristics, disease process, and follow-up was applied to responders, and all patients underwent a detailed ophthalmologic examination with dilation. Results A total of 31.9% of the patients self-declared that they had diabetes and/or requested examination for DR. A total of 29.4% reported that they had regular eye examinations. In regression analyses, factors associated with having regular eye examination were longer duration of diabetes (odds ratio [OR] 2.42; 95% confidence interval [CI] 1.01-5.8; p = 0.049), insulin use (OR 4.45; 95% CI 1.7-10.7; p = 0.001), and self-declaration of diabetes (OR 8.16; 95% CI 3.5-19.2; p<0.001). Conclusions The rates of self-declaration of diabetes and having regular eye examinations among patients with type 2 diabetes are low in Turkey. All adults undergoing an eye examination should be questioned for diabetes. Education of both patients with diabetes and the health care stuff dealing with them could improve the rates of patients having regular eye examinations and enhance the early detection of DR.
Research of the Design and Application of the Negotiation Service Management Agent

The Negotiation Service Management Agent (NSMA) is the directorial proxy of negotiation service in the E-Commerce negotiation platform based on Service-Oriented Architecture, and takes the tasks of acceptance the registration of the negotiation web services, startup the negotiation services and the message communication management among the negotiators in the negotiation procedure. This paper presented a SOA Negotiation platform with the kernel part of NSMA, designed and implemented the main algorithm of the negotiation request response, the negotiation ontology similarity computation and the negotiation services invoker in the NSMA. The results validated the efficiency of the NSMA in the negotiation procedure.
On the Mechanism of Human Red Blood Cell Longevity: Roles of Calcium, the Sodium Pump, PIEZO1, and Gardos Channels

In a healthy adult, the transport of O2 and CO2 between lungs and tissues is performed by about 2 · 1013 red blood cells, of which around 1.7 · 1011 are renewed every day, a turnover resulting from an average circulatory lifespan of about 120 days. Cellular lifespan is the result of an evolutionary balance between the energy costs of maintaining cells in a fit functional state versus cell renewal. In this Review we examine how the set of passive and active membrane transporters of the mature red blood cells interact to maximize their circulatory longevity thus minimizing costs on expensive cell turnover. Red blood cell deformability is critical for optimal rheology and gas exchange functionality during capillary flow, best fulfilled when the volume of each human red blood cell is kept at a fraction of about 0.55–0.60 of the maximal spherical volume allowed by its membrane area, the optimal-volume-ratio range. The extent to which red blood cell volumes can be preserved within or near these narrow optimal-volume-ratio margins determines the potential for circulatory longevity. We show that the low cation permeability of red blood cells allows volume stability to be achieved with extraordinary cost-efficiency, favouring cell longevity over cell turnover. We suggest a mechanism by which the interplay of a declining sodium pump and two passive membrane transporters, the mechanosensitive PIEZO1 channel, a candidate mediator of Psickle in sickle cells, and the Ca2+-sensitive, K+-selective Gardos channel, can implement red blood cell volume stability around the optimal-volume-ratio range, as required for extended circulatory longevity.
A Comparative Study of Piezoelectric Materials Using Smart Angular Accelerometers

In this work we present a comparative study of piezoelectric materials using an angular accelerometer to test them. The piezoelectric materials used in this work were either a pre-polarised PVDF film, a pre-polarised PTCa plate, a pre-polarised PZT plate or a polymer/ceramic piezoelectric composite of PTCa:P(VDF/TrFE) (50:50vol%). The angular accelerometer used to study the several materials consists of a circular plate with two masses connected together mechanically and electrically. The experimental results are in good agreement with the theoretical ones, however the best results were obtained when the piezoelectric ceramic PZT was used. This is due to the higher piezoelectric activity of this material.
The Psychology of Abilities, Competencies, and Expertise: Frontmatter

The goal of this book is to characterize the nature of abilities, competencies, and expertise and to understand the relations among them. The book therefore seeks to integrate into a coherent discipline what formerly have been, to a large extent, three separate disciplines. Such integration makes both theoretical and practical sense because abilities represent potentials to achieve competencies and, ultimately, expertise. Chapter authors (a) present their views on the nature of abilities, competencies, and expertise; (b) present their views on the interrelationships among these three constructs; (c) state their views on how these three constructs can be assessed and developed; (d) present empirical data supporting their positions; (e) compare and contrast their positions to alternative positions, showing why they believe their positions to be preferred; and (f) speculate on the implications of their viewpoints for science, education, and society.
An efficient process for enhancing genotype imputation in Genome-wide association studies using high performance computing

Genotype imputation based analysis usually consumes computational and data intensive. This paper presents a practical and efficient process for enhancing the genotype imputation based analysis on Single Nucleotide Polymorphism (SNP) using High Performance Computing (HPC). Our process is split into data quality control, haplotype estimation, and imputation. We validate and measure the process on a standard workstation and a server for pilot dataset of chromosome 22 from Genetic Analysis Workshop 16 (GAW16) provided by the North American Rheumatoid Arthritis Consortium (NARAC). The NARAC dataset consists of 2,062 individuals and 545,080 SNP variants. We use 1000 Genomes database as reference panels. Our process correctly and rapidly produces results more than ordinary steps of the genotype imputation based analysis.
Preparation of a Bioactive Poly(methyl methacrylate)/Silica Nanocomposite

The nanocomposite of a poly(methyl methacrylate)/silica containing calcium salt was synthesized through the sol–gel method. Methyl methacrylate was co-polymerized with 3-(trimethoxysilyl)propyl methacrylate and then co-condensed with tetraethyl orthosilicate and calcium nitrate tetrahydrate. Low crystalline hydroxycarbonate apatite was successfully formed on the surface after soaking in simulated body fluid for 1 week at 36.5°C. This study demonstrates that this nanocomposite may be used as a bioactive bone substitute or filler for poly(methyl methacrylate) bone cement.
Biomechanics of C. elegans as probed by micropipette deflection

In this PhD thesis, a novel experimental technique has been implemented to study the variables controlling the undulatory locomotion of a tiny worm. Well known for its elegant slithering motion and simple biology, the millimetre-sized nematode Caenorhabditis elegans was chosen to serve as a model organism for our work. The emphasis of this thesis, as embodied by three separate research projects, has been to study the passive and active biomechanical properties of C. elegans, as well as to investigate inter-worm interactions. Micropipette deflection has been used to directly probe forces in a time-resolved manner and with high dynamic resolution. The viscoelastic material properties of C. elegans were explored on a biologically and structurally relevant length scale, and the elastic properties of the body were quantified. Furthermore, the soft tissue was found to behave as a shear-thinning fluid: a non-Newtonian property that has interesting implications on the undulatory locomotion strategy of the nematode. Micropipette deflection furthermore allowed for measurements of the active swimming dynamics of C. elegans. Our experiments quantified the drag coefficients of the tiny worm as well as the viscous forces present in its swimming motion. Swimming experiments were performed in a normal buffer solution, in the confinement of solid boundaries, as well as in fluids with increased viscosities, and the dynamics of the gait modulating worm was investigated. Finally, the binary interactions between two swimming nematodes were studied, utilizing the high micromechanical control provided by the micropipette-based technique. Our findings provide new insight into the physics of undulatory locomotion and active materials in general.
Query Interaction Based Approach for Horizontal Data Partitioning

With the explosion of data, several applications are designed around analytical aspects, with data warehousing technology at the heart of the construction chain. The exploitation of this data warehouse is usually performed by the use of complex queries involving selections, joins and aggregations. These queries bring the following characteristics: (1) their routinely aspects, (2) their large number, and (3) the high operation sharing between queries. This interaction has been largely identified in the context of multi-query optimization, where graph data structures were proposed to capture it. Also during the physical design, the structures have been used to select redundant optimization structures such as materialized views and indexes. Horizontal data partitioning (HDP) is another non-redundant optimization structure that can be selected in the physical design phase. It is a pre-condition for designing extremely large databases in several environments: centralized, distributed, parallel and cloud. It aims to reduce the cost of the above operations. In HDP, the optimization space of potential candidates for partitioning grows exponentially with the problem size making the problem NP-hard. This paper proposes a new approach based on query interactions to select a partitioning schema of a data warehouse in a divide and conquer manner to achieve an improved trade-off between the optimization algorithm's speed and the quality of the solution. The effectiveness of our approach is proven through a validation using the Star Schema Benchmark (100 GB) on Oracle11g.
The implications of male human papilloma virus infection in couples seeking assisted reproduction technologies

Human papilloma virus (HPV) is one of the most common viral sexually-transmitted diseases worldwide. The prevalence of HPV is higher in infertile males when compared with fertile men and ranges between 10 and 35.7% in men affected by unexplained infertility. HPV can bind to spermatozoa and can potentially be transferred to fertilized oocytes. Viral detection in blastocysts and trophoblastic cells is associated with impaired embryo development and poor pregnancy outcomes. Nevertheless, attempts to eliminate HPV-DNA from sperm samples through routine washing techniques have failed. In assisted reproduction technologies (ART), intracytoplasmic sperm injection involves no natural selection of the sperm cell, which means that these procedures have a plausible risk of injecting sperm containing HPV. The possible detrimental effects of HPV on ART in couples with infected male partners are summarized in this review.