Miracle-dz/UniFAR-FTUs huggingface dataset:
Fasciola hepatica cathepsin L1 from a Turkish isolate is related to Asiatic isolates

Cathepsin L1 (CatL1) is one of the major molecules in the excretory-secretory products of Fasciola hepatica and is secreted by all stages of the developing parasite; it is involved in tissue penetration, immune evasion, feeding and pathogenesis. Our aim in this study was to clone and characterise the F. hepatica CatL1 gene from a Turkish isolate. This is the first report of cDNA encoding CatL1 protein of F. hepatica from a Turkish isolate. Phylogenetic analysis based on the CatL1 showed that the Turkish isolate is genetically related to Asiatic isolates. The cathepsin L1 gene may be used for DNA vaccination and recombinant protein derived from the gene can be used for serological diagnosis against F. hepatica in Turkey.
Compounds Activity Prediction in Large Imbalanced Datasets with Substructural Relations Fingerprint and EEM

Modern drug design procedures involve the process of virtual screening, a highly efficient filtering step used for maximizing the efficiency of the preselection of compounds which are valuable drug candidates. Recent advances in introduction of machine learning models to this process can lead to significant increase in the overall quality of the drug designing pipeline. Unfortunately, for many proteins it is still extremely hard to come up with a valid statistical model. It is a consequence of huge classes disproportion (even 1000:1), large datasets (over 100,000 of samples) and restricted data representation (mostly high-dimensional, sparse, binary vectors). In this paper, we try to tackle this problem through three important innovations. First we represent compounds with 2-dimensional, graph representation. Second, we show how one can provide extremely fast method for measuring similarity of such data. Finally, we use the Extreme Entropy Machine which shows increase in balanced accuracy over Extreme Learning Machines, Support Vector Machines, one-class Support Vector Machines as well as Random Forest. Proposed pipeline brings significantly better results than all considered alternative, state-of-the-art approaches. We introduce some important novel elements and show why they lead to better model. Despite this, it should still be considered as a proof of concept and further investigations in the field are needed.
On Adaptive Function Estimation

General results on adaptive function estimation are obtained with respect to a collection of estimation strategies for both density estimation and nonparametric regression under square L 2 loss. It is shown that without knowing which strategy in a given countable collection works best for the underlying function, a single strategy can be constructed by mixing the proposed ones so that it is adaptive in terms of an average cumulative risk. An implication is that under some mild conditions, a minimax-rate adaptive estimator exists for a given countable collection of function classes, i.e., a single estimator can be constructed to be simultaneously minimax optimal in terms of rates of convergence for all the function classes being considered. Examples for high-dimensional function estimation are provided.
Comprehensive Genotyping in Two Homogeneous Graves' Disease Samples Reveals Major and Novel HLA Association Alleles

Background Graves' disease (GD) is the leading cause of hyperthyroidism and thyroid eye disease inherited as a complex trait. Although geoepidemiology studies showed relatively higher prevalence of GD in Asians than in Caucasians, previous genetic studies were contradictory concerning whether and/or which human leukocyte antigen (HLA) alleles are associated with GD in Asians. Methodology/Principal Findings We conducted a case-control association study (499 unrelated GD cases and 504 controls) and a replication in an independent family sample (419 GD individuals and their 282 relatives in 165 families). To minimize genetic and phenotypic heterogeneity, we included only ethnic Chinese Han population in Taiwan and excluded subjects with hypothyroidism. We performed direct and comprehensive genotyping of six classical HLA loci (HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1) to 4-digit resolution. Combining the data of two sample populations, we found that B*46:01 (odds ratio under dominant model [OR] = 1.33, Bonferroni corrected combined P [PBc] = 1.17×10−2), DPB1*05:01 (OR = 2.34, PBc = 2.58×10−10), DQB1*03:02 (OR = 0.62, PBc = 1.97×10−2), DRB1*15:01 (OR = 1.68, PBc = 1.22×10−2) and DRB1*16:02 (OR = 2.63, PBc = 1.46×10−5) were associated with GD. HLA-DPB1*05:01 is the major gene of GD in our population and singly accounts for 48.4% of population-attributable risk. Conclusions/Significance These GD-associated alleles we identified in ethnic Chinese Hans, and those identified in other Asian studies, are totally distinct from the known associated alleles in Caucasians. Identification of population-specific association alleles is the critical first step for individualized medicine. Furthermore, comparison between different susceptibility/protective alleles across populations could facilitate generation of novel hypothesis about GD pathophysiology and indicate a new direction for future investigation.
Jointly Optimized Multiuser Beamforming for the MIMO Broadcast Channel with Limited Feedback

This paper considers the joint optimization of the transmitter beamforming filters and receiver combining filters for the multiple-input multiple-output (MIMO) broadcast channel. A low-complexity iterative algorithm to compute the filters is proposed and then a closed-form expression of the filters for the downlink with two transmit antennas is derived, avoiding the need for iterative computation in this case. To enable practical implementation, a new limited feedback algorithm is proposed that exploits the channel structure in the closed form solution, and is independent of the number of receive antennas. Performance is evaluated by Monte Carlo simulations as a function of the amount of feedback. With two receive antennas, the proposed method performs close to the sum capacity of the MIMO broadcast channel, without the need for multiuser diversity and with only limited feedback.
A Unified Relational Approach to Grid Information Services

We propose an approach to Grid information services (GIS) that is based on the relational data model instead of the hierarchical data model that is currently prevalent, especially in U.S.-based Grid efforts. Furthermore, the approach integrates static and dynamic information into one information framework. Our core observation is that many highly desirable queries involve constraints on compositions of information. Such queries map naturally into joins within the relational model. In addition, we expect that updates will be a common feature in GIS systems, and relational databases are more likely to achieve high update rates. Herein we lay out an argument for the relational model, describe our plans and the research questions we see, and show early performance results.
Internet Usage and Its Addiction Level among Students in a Selected College in Ras Al Khaimah Emirate: A Cross-Sectional Study

Background and aim: The internet is a worldwide area network that connects computer system throughout the world providing a variety of information and communication. Internet addiction is defined as any online-related, compulsive behavior which interferes with normal living and causes severe stress on family, friends, loved ones, and one's work environment. Aim: This study assessed the internet usage and its addiction level among university students in a selected university in Ras Al Khaimah, United Arab Emirate. University students are highly predisposed to internet addiction which can affect their personal, family, educational, interactive and societal life. Study design: A cross-sectional design . The sample of the study consisted of 110 nursing students who were selected using convenient sample. Internet addiction test, internet usage questionnaire and student attitude scale were used as data collection instruments.Results: The findings showed that more than half (50.9%) of students were aged 21-<25 years, with more than two- fifth (45.5% of them being average online internet user. Less than two-third (62.7%) of students had favorable attitude towards internet usage. There is a positive correlation between internet addiction score and age of the study group with no statistically significant differenceConclusions: the study concluded that nursing students are average internet users, they have favorable attitude to internet use, with positive correlation between internet addiction score and age, though experiencing occasional problems. The use of social networking sites, especially by the young people, should be done sparingly so as not to provoke extreme behaviors and negative impact to their education performance and social life that can lead to destruction of the life of youths globally as revealed in this study Internet addiction is a serious problem among university students generally which indicates the need for more public attention and resources to develop effective prevention/intervention strategies.
Cost-Aware Result Caching for Meta-Search Engines

Our goal in this paper is to design cost-aware result caching approaches for meta-search engines. We introduce different levels of eviction, namely, query-, resource- and entry-level, based on the granularity of the entries to be evicted from the cache when it is full. We also propose a novel entry-level caching approach that is tailored for the meta-search scenario and superior to alternative approaches.
Disordered eating: Influence of body image, sociocultural attitudes, appearance anxiety and depression - a focus on college males and a gender comparison

Abstract This study is the continuation of a broader eating disorder study with a focus on males, which examines the influence of body image, sociocultural attitudes, appearance anxiety, and depression on disordered eating behaviors among college students. Based on EAT-26 scores, 10.5% of males were at risk of an eating disorder. Body image dissatisfaction was almost as common among males (65.2%) as females (68.6%) and BMI was not a significant predictor of dissatisfaction. Among participants who reported dissatisfaction with their bodies, eating disorder risk was higher among females than males. While there were differences between men and women in general, at-risk men and women showed quite similar self-report ratings on most measures of the SATAQ scale. The main gender difference was that Social Appearance Anxiety and Depression were significant predictors of eating disorder risk among females, but not males. This study indicates that risk of an eating disorder is more prevalent among males than previously reported. The risk is significant for college students as a whole and it is important to have preventative measures before disordered eating behaviors turn into an eating disorder.
Enhancing Writing Skills of EFL Learners through Blogging.

In such a rapidly developing world, it has been inevitable to integrate some modern assessment approaches and tools into English teaching. Hence, several up to date Formative Assessment Tools have been used by teachers during the learning process to modify teaching and learning activities by means of acquiring qualitative feedback. Blogs or Blogging is one of these formative assessment tools which are on focus. The aim of this exploratory case study is to find out whether or not writing blogs does have an effect on high school students’ writing skills. The findings suggest that the blog is an effective tool for students to improve their English writing skills. Besides it was observed that blogging enhanced the students’ eagerness to write and fostered the autonomous writing. This study also implies that writing blogs is of a great value for English learners, language instructors, material developers and curriculum designers as well as having the potential for further research.
γ-synuclein is a novel player in the control of body lipid metabolism

Synucleins are a family of homologous, predominantly neuronal proteins known for their involvement in synaptic transmission and neurodegeneration. γ-synuclein is predominantly localized in axons and presynaptic terminals of selected populations of peripheral and central neurons but is also highly expressed in human white adipose tissue (WAT) and increased in obesity. We have recently shown that γ-synuclein is nutritionally regulated in murine adipocytes while its loss protects mice from high fat diet (HFD)-induced obesity and associated metabolic complications. This protection was coupled with increased adipocyte lipolysis, lipid oxidation, and energy expenditure in HFD-fed γ-synuclein-null mutant compared with wild-type mice. Cellular studies suggest that relocalization of ATGL to the lipid droplet in γ-synuclein-deficient adipocytes may contribute to increased lipolysis in these cells. Loss of γ-synuclein in adipocytes also attenuates the assembly of SNARE complexes, an important component of lipid droplet fusion machinery, possibly due to reduced chaperoning of SNAP-23 to the assembling SNARE complex by γ-synuclein. Together our data suggests that not only is γ-synuclein a novel regulator of lipid handling in adipocytes but also that the deficiency of this protein has a significant effect on whole body energy expenditure.
Productivity , and Market Value

Measuring the private returns to R&D requires knowledge of its private depreciation or obsolescence rate, which is inherently variable and responds to competitive pressure. Nevertheless, most of the previous literature has used a constant depreciation rate to construct R&D capital stocks and measure the returns to R&D, a rate usually equal to 15 per cent. In this paper I review the implications of this assumption for the measurement of returns using two different methodologies: one based on the production function and another that uses firm market value to infer returns. Under the assumption that firms choose their R&D investment optimally, that is, marginal expected benefit equals marginal cost, I show that both estimates of returns can be inverted to derive an implied depreciation rate for R&D capital. I then test these ideas on a large unbalanced panel of U.S. manufacturing firms for the years 1974 to 2003. The two methods do not agree, in that the production function approach suggests depreciation rates near zero (or even appreciation) whereas the market value approach implies depreciation rates ranging from 20 to 50 per cent, depending on the period. The concluding section discusses the possible reasons why this is true. 1 University of California at Berkeley, University of Maastricht, NBER, and IFS London. email: bhhall@econ.berkeley. edu. This is a revision of a paper presented at the International Conference in memory of Zvi Griliches, Paris, August 2003 and the Conference in memory of Tor Jakob Klette, Oslo, Norway, in August 2004. The paper has benefited from comments by participants in those conferences and especially from the editors of this special issue, Jacques Mairesse and Manuel Trajtenberg. B. H. Hall/Annales November 2006 2 R&D, Productivity, and Market Value Bronwyn H. Hall
Nonlinear Growth and the Productivity Slowdown

In this paper we study the productivity slowdown taking as a starting point the nonlinear shape of the growth path. We relate the slowdown to the evolution of the world income distribution in the periods before and after the oil shock of 1973 and show that: i) in both periods growth is nonlinear; ii) the productivity slowdown consists in a downward shift of the nonlinear growth path; iii) in both periods we observe a medium-run tendency to polarization, but the long-run distribution features convergence in the first period and polarization in the second. We provide theoretical and empirical arguments suggesting that the interaction between nonlinear growth and international technology spillovers can explain how a temporary shock may have permanent effects on world growth.
Molecular Cloning and Ovarian Expression Profiles of Thrombospondin,a Major Component of Cortical Rods in Mature Oocytes of Penaeid Shrimp, Marsupenaeus japonicus1

Abstract In penaeid shrimp, cortical rods (CRs) are formed in peripheral crypts of the oocyte after completion of yolk accumulation; subsequently the CRs are utilized as a source of jelly materials that surround fertilized eggs. In our previous study, of five major components, three CR proteins displayed quite similar immunological characteristics. In this study, cDNA sequences and developmental expression profiles at both transcriptional and protein levels were examined to elucidate the molecular characteristics of CR proteins and the process of CR formation. Sequencing cDNAs exhibited the presence of three related forms that have identical sequences except for the loss of 246 and 369 bp in medium and short forms, respectively, suggesting that a single gene generates three transcriptional variants corresponding to the three CR proteins. Their deduced amino acid sequences revealed similarities to those of extracellular matrix proteins in a thrombospondin (TSP) 3,4/cartilage oligomeric protein family, and thereby the CR proteins were designated mjTSP. Semiquantitative analysis by real-time polymerase chain reaction revealed the presence of mjTSP transcripts, at similar levels, in immature, vitellogenic, and mature ovaries. Furthermore, in situ hybridization localized the majority of transcripts in previtellogenic oocytes in ovaries at all developmental stages. By the Western blot, on the other hand, mjTSP proteins were undetectable in immature ovaries but became obvious at the early vitellogenic stage. The immunosignals were enhanced during vitellogenic stages and maintained a high intensity in mature ovaries. Thus, transcription, translation of mjTSP, and formation of the CR structure occurred at different stages of ovarian development.
On Feedback Effects from Hedging Derivatives

This paper proposes a new explanation for the smile and skewness effects in implied volatilities. Starting from a microeconomic equilibrium approach, we develop a diffusion model for stock prices explicitly incorporating the technical demand induced by hedging strategies. This leads to a stochastic volatility endogenously determined by agents’ trading behavior. By using numerical methods for stochastic differential equations, we quantitatively substantiate the idea that option price distortions can be induced by feedback effects from hedging strategies.
Behavioral Neuroscience

Among efforts to establish an appropriate animal model to test this novel hypothesis, two most recent studies reported promising results, using an established animal model featured with selective damage in the white matter of the central nervous system (CNS) caused by cuprizone (CPZ) (Matsushima and Morell, 2001; Yang et al., 2009), a copper chelator. In the fi rst study by our lab, C57BL/6 mice given CPZ showed schizophrenia-like behaviors including defi cits in prepulse inhibition (PPI) of acoustic startle refl ex, less social interaction, and impaired spatial working memory. These animals also showed evident myelin sheath loss and decrease in the number of OLs in the brain (Xu et al., 2009). In the second study adolescent rats exposed to CPZ showed decreased expression of mRNA transcripts encoding oligodendroglial proteins within the medial prefrontal cortex (PFC); these rats also displayed a specifi c defi cit in the ability to shift between perceptual dimensions in the attention set-shifting task (Gregg et al., 2009), a PFC-mediated behavioral paradigm modeled after the Wisconsin Card Sorting Test (Franke et al., 1992). These studies suggest that the CPZ-exposed mice/rats are potential animal models of schizophrenia to test the OL hypothesis. For the fi rst time, this study examined effects of some antip-sychotics on the behavioral abnormalities and neurobiological changes seen in C57BL/6 mice exposed to cuprizone. Our results provided experimental evidence supporting a role for altered OLs in the pathophysiology and treatment of schizophrenia. The drugs
The causal pathways linking health literacy to health outcomes.

OBJECTIVE To provide an evidence-based review of plausible causal pathways that could best explain well-established associations between limited health literacy and health outcomes. METHODS Through analysis of current findings in medical and public health literature on health literacy we derived a conceptual causal model. RESULTS Health literacy should be viewed as both a patient and a system phenomenon. Three distinct points along a continuum of health care are suggested to be influenced by health literacy: (1) access and utilization of health care, (2) patient-provider relationship, and (3) self-care. CONCLUSIONS The conceptual model organizes what has been learned to date and underscores promising areas of future inquiry and intervention.
Pulmonary Inflammation Induced by Pseudomonas aeruginosa Lipopolysaccharide, Phospholipase C, and Exotoxin A: Role of Interferon Regulatory Factor 1

ABSTRACT Chronic pulmonary infection with Pseudomonas aeruginosa is common in cystic fibrosis (CF) patients. P. aeruginosa lipopolysaccharide (LPS), phosholipase C (PLC), and exotoxin A (ETA) were evaluated for their ability to induce pulmonary inflammation in mice following intranasal inoculation. Both LPS and PLC induced high levels of tumor necrosis factor alpha (TNF-α), interleukin 1β (IL-1β), IL-6, gamma interferon (IFN-γ), MIP-1α and MIP-2 in the lungs but did not affect IL-18 levels. ETA did not induce TNF-α and was a weak inducer of IL-1β, IL-6, macrophage inflammatory protein 1α (MIP-1α), and MIP-2. Remarkably, ETA reduced constitutive lung IL-18 levels. LPS was the only factor inducing IFN-γ. LPS, PLC, and ETA all induced cell infiltration in the lungs. The role of interferon regulatory factor-1 (IRF-1) in pulmonary inflammation induced by LPS, PLC, and ETA was evaluated. When inoculated with LPS, IRF-1 gene knockout (IRF-1 KO) mice produced lower levels of TNF-α, IL-1β, and IFN-γ than did wild-type (WT) mice. Similarly, a milder effect of ETA on IL-1β and IL-18 was observed for IRF-1 KO than for WT mice. In contrast, the cytokine response to PLC did not differ between WT and IRF-1 KO mice. Accordingly, LPS and ETA, but not PLC, induced expression of IRF-1 mRNA. IRF-1 deficiency had no effect on MIP-1α and MIP-2 levels and on cell infiltration induced by LPS, PLC, or ETA. Flow cytometric evaluation of lung mononuclear cells revealed strongly reduced percentages of CD8+ and NK cells in IRF-1 KO mice compared to percentages observed for WT mice. These data indicate that different virulence factors from P. aeruginosa induce pulmonary inflammation in vivo and that IRF-1 is involved in some of the cytokine responses to LPS and ETA.
‘Keen as fuck’: youth participation in qualitative research as ‘parallel projects’

Youth researchers continue to pursue the ideals of youth participation in research. This pursuit reflects a broader concern for the problems of participant-researcher power dynamics in qualitative research. Youth researchers develop and adopt a variety of techniques and ethical principles that attempt to position young people as active research participants. However, these methods and principles have not solved the challenges of participation. In this article, I argue that there is a need to accept that some of the power asymmetries of participation might be unsolvable, and to reposition the power relationship between young people and researchers. A central concern in this article is the paradoxically unethical outcomes produced by adult-centric ethics review processes. I argue that youth participation in qualitative research can be understood as parallel projects and that in doing so researchers can value young people’s reasons for participation. In fact, young people might be ‘keen as fuck’ (participant quote) to participate.