Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational analysis of vaccinia virus nucleoside triphosphate phosphohydrolase II, a DExH box RNA helicase

Vaccinia virus nucleoside triphosphate phosphohydrolase II (NPH-II), a 3'-to-5' RNA helicase, displays sequence similarity to members of the DExH family of nucleic acid-dependent nucleoside triphosphatases (NTPases). The contributions of the conserved GxGKT and DExH motifs to enzyme activity were assessed by alanine scanning mutagenesis. Histidine-tagged versions of NPH-II were expressed in vaccinia virus-infected BSC40 cells and purified by nickel affinity and conventional fractionation steps. Wild-type His-NPH-II was indistinguishable from native NPH-II with respect to RNA helicase, RNA binding, and nucleic acid-stimulated NTPase activities. The K-191-->A (K191A), D296A, and E297A mutant proteins bound RNA as well as wild-type His-NPH-II did, but they were severely defective in NTPase and helicase functions. The H299A mutant was active in RNA binding and NTP hydrolysis but was defective in duplex unwinding. Whereas the NTPase of wild-type NPH-II was stimulated > 10-fold by polynucleotide cofactors, the NTPase of the H299A mutant was nucleic acid independent. Because the specific NTPase activity of the H299A mutant in the absence of nucleic acid was near that of wild-type enzyme in the presence of DNA or RNA and because the Km for ATP was unaltered by the H299A substitution, we regard this mutation as a "gain-of-function" mutation and suggest that the histidine residue in the DExH box is required to couple the NTPase and helicase activities.
A sliding controller for bipedal balancing using integrated movement of contact and non-contact limbs

We present an algorithm that provides enhanced flexibility and robustness in the control of single-leg humanoid standing through the coordination of stance leg ankle torques and stabilizing movements of non-contact limbs. Current control approaches generally assume the presence of explicitly specified joint reference trajectories or desired virtual force calculations that ignore system dynamics. Here we describe a practical controller that 1) simplifies control of abstract variables such as the center of mass location using a two-stage model-based plant linearization; 2) determines motion of non-contact limbs useful for achieving control targets while satisfying dynamic balance constraints; and 3) provides robustness to modeling error using a sliding controller. The controller is tested with a morphologically realistic, 3-dimensional, 18 degree-of-freedom humanoid model serving as the plant. It is demonstrated that the controller can use less detailed control targets, and reject stronger disturbances, than previously implemented controllers that employ desired virtual forces and static body calculations.
Expression of Serine/Threonine Protein-Kinases and Related Factors in Normal Monkey and Human Retinas: The Mechanistic Understanding of a CDK2 Inhibitor Induced Retinal Toxicity

Protein-kinase inhibitors are among the most advanced compounds in development using the new drug discovery paradigm of developing small-molecule drugs against specific molecular targets in cancer. After treatment with a cyclin dependent kinase CDK2 inhibitor in monkey, histopathological analysis of the eye showed specific cellular damage in the photoreceptor layer. Since this CDK2 inhibitor showed activity also on other CDKs, in order to investigate the mechanism of toxicity of this compound, we isolated cones and rods from the retina of normal monkey and humans by Laser Capture Microdissection. Using Real-Time PCR we first measured the expression of cyclin dependent protein-kinases (CDK)1, 2, 4, 5, Glycogen synthase kinase 3β (GSK3β) and microtubule associated protein TAU. We additionally verified the presence of these proteins in monkey eye sections by immunohistochemistry and immunofluorescence analysis and afterwards quantified GSK3β, phospho-GSK3β and TAU by Reverse Phase Protein Microarrays. With this work we demonstrate how complementary gene expression and protein-based technologies constitute a powerful tool for the understanding of the molecular mechanism of a CDK2 inhibitor induced toxicity. Moreover, this investigative approach is helpful to better understand and characterize the mechanism of species-specific toxicities and further support a rational, molecular mechanism-based safety assessment in humans.
Identification of a human cDNA encoding a functional high affinity lipoxin A4 receptor

Lipoxin A4 (LXA4) triggers selective responses with human neutrophils that are pertussis toxin sensitive and binds to high affinity receptors (Kd = 0.5 +/- 0.3 nM) that are modulated by stable analogues of guanosine 5'-triphosphate (GTP). Here, we characterized [11,12-(3)]LXA4 specific binding with neutrophil granule and plasma membranes, which each display high affinity binding sites (Kd = 0.7 +/- 0.1 nM) that were regulated by GTP gamma S. Since functional LXA4 receptors are inducible in HL-60 cells, we tested orphan cDNAs encoding 7- transmembrane region receptors cloned from these cells for their ability to bind and signal with LXA4. Chinese hamster ovary (CHO) cells transfected with the orphan receptor cDNA (pINF114) displayed specific 3H-LXA4 high affinity binding (1.7 nM). When displacement of LXA4 binding with pINF114-transfected CHO cells was tested with other eicosanoids, including LXB4, leukotriene D4 (LTD4), LTB4, or prostaglandin E2, only LTD4 competed with LXA4, giving a Ki of 80 nM. In transfected CHO cells, LXA4 also stimulated GTPase activity and provoked the release of esterified arachidonate, which proved to be pertussis toxin sensitive. These results indicate that pINF114 cDNA encodes a 7-transmembrane region-containing protein that displays high affinity for 3H-LXA4 and transmits LXA4-induced signals. Together, they suggest that the encoded protein is a candidate for a LXA4 receptor in myeloid cells.
Constructing Efficient Attribute-Based Broadcast Encryption

Attribute Based Broadcast Encryption (ABBE) is a novel Broadcast Encryption (BE) approach. Compared to existing BE approaches that requires an explicitly specified decrypters list, ABBE encrypter enforces an expressive access policy composed of one or more attributes. Although ABBE is more flexible and efficient with reduced storage overhead, ciphertext size of current ABBE schemes is linearly proportional to the numbers of attributes. In this paper, we investigate the solution on how to reduce the ABBE's ciphertext size to a constant value. Moreover, we explore the capability of using ABBE in secure many-to-many communication environments.
Positive selection of FLP-mediated unequal sister chromatid exchange products in mammalian cells

Site-specific recombination provides a powerful tool for studying gene function at predetermined chromosomal sites. Here we describe the use of a blasticidin resistance system to select for recombination in mammalian cells using the yeast enzyme FLP. The vector is designed so that site-specific recombination reconstructs the antibiotic resistance marker within the sequences flanked by the FLP target sites. This approach allows the detection of DNA excised by FLP-mediated recombination and facilitates the recovery of recombination products that would not be detected by available screening strategies. We used this system to show that the molecules excised by intrachromosomal recombination between tandem FLP recombinase target sites do not reintegrate into the host genome at detectable frequencies. We further applied the direct selection approach to recover a rare FLP-mediated recombination event displaying the characteristics of an unequal sister chromatid exchange between FLP target sites. Implications of this approach for the generation of duplications to assess their effect on gene dosage and chromosome stability are discussed.
How preferred ear for listening moderates emotional cognitions in the prediction of personality

Two studies investigate how cognitions of aurally presented information interact with aural preference (self-reported preferred ear for listening) in the prediction of personality. In Study 1, participants provided attractiveness cognitions of various statements after listening to aurally presented material. Aural preference × attractiveness interactions significantly predicted Extraversion and Neuroticism. In Study 2, participants provided cognitions of pleasantness from various scenarios. An aural preference × pleasantness interaction significantly predicted Neuroticism. Although other interpretations are possible, I conclude that these findings support the idea of aural preference as a useful measure of hemispheric asymmetry, such that the right hemisphere (left aural preference) provides facilitation of emotional expression, whereas the left hemisphere (right aural preference) provides suppression. My findings support a more historical view of emotional asymmetry than the more modern approach–avoidance perspective and suggest that moderating effects of hemispheric asymmetry are important to include in studies investigating emotions associated with personality.
Fast L1-based sparse representation of EEG for motor imagery signal classification

Improvement of classification performance is one of the key challenges in electroencephalogram (EEG) based motor imagery brain-computer interface (BCI). Recently, sparse representation based classification (SRC) method has been shown to provide satisfactory classification accuracy in motor imagery classification. In this paper, we aim to evaluate the performance of the SRC method in terms of not only its classification accuracy but also of its computation time. For this purpose, we investigate the performance of recently developed fast L1 minimization methods for their use in SRC, such as homotopy and fast iterative soft-thresholding algorithm (FISTA). From experimental analysis, we note that the SRC method with the fast L1 minimization algorithms is shown to provide robust classification performance, compared to support vector machine (SVM), both in time and accuracy.
Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations

Lynch syndrome, the most frequent hereditary colorectal cancer syndrome, is caused by defects in mismatch repair genes. Genetic testing is important in order to identify mutation carriers who can benefit from intensive surveillance programs. One of the challenges with genetic testing is the interpretation of pathogenicity of detected DNA variants. The aim of this study was to investigate all putative pathogenic variants tested for at the Division of Molecular Medicine, Pathology North, in Newcastle, Australia, to establish whether previous variant classification is in accordance with that recently performed in the InSiGHT collaboration.
Simple cellular automaton-based simulation of ink behaviour and its application to Suibokuga-like 3D rendering of trees

Suibokuga is a style of monochrome painting characterized by the use of Chinese black ink (sumi), a complex interaction between brush, ink and paper, and such visual features as Noutan (shade), Kasure (scratchiness), and Nijimi (blur). In this paper we present a simple behavioural model of water and ink particles based on a 2D cellular automaton computational model, and its application to a Suibokuga-like rendering of 3D trees. Copyright © 1999 John Wiley & Sons, Ltd.
Australian Study on Public Knowledge of Human Genetics and Health

Aims: This study was designed to obtain data on public understanding of genetic concepts in the adult population of Western Australia. It explored knowledge of genetic risk of disease, inheritance, biology, determinism, and factors that predict relatively higher genetic knowledge within the general population. Method: A cross-sectional telephone survey of 1,009 respondents. Results: Most members of the Western Australian community are aware of basic genetic concepts and the link between genes, inheritance, and risk of disease. Significantly fewer understand the biological mechanisms underlying these concepts and there was some misconception around the meaning of ‘increased genetic risk’. The odds of higher genetic knowledge (>19 out of 24 questions correct) were greater among those with 12 years or more education (OR = 3.0), those aged 18–44 years (OR = 2.3), women (OR = 2.0), those with annual household income of AUD 80,000 or more (OR = 1.8), and those who had talked with someone (OR = 1.7) or searched the internet (OR = 1.6) for information on genes and health. Conclusions: This study provides evidence of an association between social location and public knowledge of human genetic concepts related to health and disease. This is consistent with previous findings and raises questions about the acquisition of textbook genetics knowledge within socio-cultural contexts. The impact of misconceptions about genetic concepts on the uptake of preventive health behaviors requires further investigation, as does the level of genetics knowledge that is required to empower informed participation in individual and societal decisions about genetics and health.
A Simple Method to Estimate the Time-dependent ROC Curve Under Right Censoring

The time-dependent Receiver Operating Characteristic (ROC) curve is often used to study the diagnostic accuracy of a single continuous biomarker, measured at baseline, on the onset of a disease condition when the disease onset may occur at different times during the follow-up and hence may be right censored. Due to censoring, the true disease onset status prior to the pre-specified time horizon may be unknown on some patients, which causes difficulty in calculating the time-dependent sensitivity and specificity. We study a simple method that adjusts for censoring by weighting the censored data by the conditional probability of disease onset prior to the time horizon given the biomarker and the observed censoring time. Our numerical study shows that the proposed method produces unbiased and efficient estimators of time-dependent sensitivity and specificity as well as area under the ROC curve, and outperforms several other published methods currently implemented in R packages. A Simple Method to Estimate the Time-dependent ROC Curve Under Right Censoring Liang Li, Tom Greene, Bo Hu Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, U.S.A. E-mail: LLi15@mdanderson.org Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, U.S.A. Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, U.S.A.
Modelling effects of diquat under realistic exposure patterns in genetically differentiated populations of the gastropod Lymnaea stagnalis

Pesticide use leads to complex exposure and response patterns in non-target aquatic species, so that the analysis of data from standard toxicity tests may result in unrealistic risk forecasts. Developing models that are able to capture such complexity from toxicity test data is thus a crucial issue for pesticide risk assessment. In this study, freshwater snails from two genetically differentiated populations of Lymnaea stagnalis were exposed to repeated acute applications of environmentally realistic concentrations of the herbicide diquat, from the embryo to the adult stage. Hatching rate, embryonic development duration, juvenile mortality, feeding rate and age at first spawning were investigated during both exposure and recovery periods. Effects of diquat on mortality were analysed using a threshold hazard model accounting for time-varying herbicide concentrations. All endpoints were significantly impaired at diquat environmental concentrations in both populations. Snail evolutionary history had no significant impact on their sensitivity and responsiveness to diquat, whereas food acted as a modulating factor of toxicant-induced mortality. The time course of effects was adequately described by the model, which thus appears suitable to analyse long-term effects of complex exposure patterns based upon full life cycle experiment data. Obtained model outputs (e.g. no-effect concentrations) could be directly used for chemical risk assessment.
Information Technology and Product Variety: Evidence from Panel Data

This paper examines the relationship between information technology and product variety. Consistent with prior theoretical work, we argue that IT and product variety are complements. IT innovations such as computer-aided design and flexible manufacturing technology have enabled firms to offer greater product variety at a reasonable cost. Similarly, firms seeking to offer greater variety can facilitate this strategy through IT investment. Using a novel approach to measuring product variety at the firm level through trademark counts we examine the relationship between IT and variety in four ways: direct correlations, IT and variety demand estimation, productivity analyses, and market value analyses. We utilize an 11-year panel data set of information technology capital stock, trademark holdings, and other measures for 512 Fortune 1000 firms to test our hypotheses. Overall, we find that IT is found to be associated with increased product variety, and that increased product variety increases demand for IT investment. Complementarities between IT and product variety are not significant in the productivity analysis but appear strongly when we consider their influence on firm valuation.
PENGEMBANGAN MODUL BIOLOGI BERBASIS ISLAM-SAINS SEBAGAI BAHAN AJAR MANDIRI PADA SUB MATERI POKOK KOMPONEN EKOSISTEM UNTUK SISWA KELAS X MADRASAH ALIYAH (MA)

Penelitian ini bertujuan: 1) mengembangkan modul Biologiberbasis Islam-Sains sebagai bahan ajar mandiri pada sub materi pokok komponen ekosistem untuk siswa kelas X Madrasah Aliyah; 2) mengetahui kualitas modul Biologi berbasis Islam-Sains yang akan dikembangkan melalui penilaian produk yang dihasilkan oleh ahli keterpaduan, ahli konten materi, ahli media, peer reviewer, dan guru Biologi; 3) mengetahui respon siswa kelas X Madrasah Aliyah terhadap modul Biologi berbasis Islam-Sains sebagai bahan ajar mandiri pada sub materi pokok Komponen Ekosistem untuk siswa kelas X Madrasah Aliyah. Penelitian ini merupakan penelitian pengembangan dengan menggunakan model ADDIE yang dibatasi sampai pada tahap pengembangan (Development). Prosedur penelitian terdiri dari tahap Analisis (Analysis), tahap Perancangan (Design), serta tahap Pengembangan (Development). Subjek penilai berjumlah 8 orang yang terdiri dari 2 ahli materi, 1 ahli media, 3 peer reviewer, 2 guru MAN Yogyakarta III untuk mengetahui kualitas modul Biologi. Instrumen penelitian berupa angket penilaian kualitas modul untuk ahli materi, ahli media, peer reviewer, guru Biologi dengan menggunakan skala Likert yang dibuat dalam bentuk checklist. Instrumen untuk siswa berupa angket respon siswa untuk 10 siswa kelas X MAN Yogyakarta III. Data dianalisis secara kualitatif untuk mengetahui tingkat kelayakan produk sesuai dengan kriteria kategori penilaian ideal dan kategori persentase keidealan. Hasil penelitian ini adalah tersusunnya modul Biologi berbasis Islam-Sains pada sub materi pokok komponen ekosistem untuk siswa kelas X Madrasah Aliyah (MA) yang dikembangkan dengan model ADDIE. Berdasarkan hasil penilaian kualitas modul dengan kategori Sangat Baik (SB) diperoleh dari ahli keterpaduan, ahli konten materi, peer reviewer, dan guru Biologi dan kategori Baik (B) diperoleh dari ahli media. Kategori Sangat Setuju (SS) diperoleh dari hasil respon siswa kelas X MAN Yogyakarta III. Hasil penelitian ini dapat disimpulkan bahwa modul Biologi berbasis Islam-Sains pada sub materi pokok komponen ekosistem yang dikembangkan layak digunakan sebagai bahan ajar mandiri untuk siswa kelas X Madrasah Aliyah (MA).
RelaxDHT: A churn-resilient replication strategy for peer-to-peer distributed hash-tables

DHT-based P2P systems provide a fault-tolerant and scalable means to store data blocks in a fully distributed way. Unfortunately, recent studies have shown that if connection/disconnection frequency is too high, data blocks may be lost. This is true for most of the current DHT-based systems' implementations. To deal with this problem, it is necessary to build more efficient replication and maintenance mechanisms. In this article, we study the effect of churn on PAST, an existing DHT-based P2P system. We then propose solutions to enhance churn tolerance and evaluate them through discrete event simulation.
Determining user expertise for improving recommendation performance

Recommender systems are designed to predict user preference for items using his/her past activities. Predominant studies have focused on modeling and developing recommendation algorithm to predict the user preference accurately. In this paper, we assume there are some more reliable and important users for recommendation process, who have deep and broad knowledge of specific domains. Instead of developing a new recommendation model, we propose a method for quantifying user's expertise and exploiting tem to improve performance of existing recommendation algorithms. More specifically, we suggest three general expert factors called early adoption (EA), heavy access (HA) and niche-item access (NA), and we explain how to determine the expertise of each user using a latent variable model. Additionally, we show how our method can be applied to existing recommendation models. On the real-world data from last.fm, our approach shows not only accurate but novel and serendipitous recommendation.
Cloning and sequencing of the gene for a lactococcal endopeptidase, an enzyme with sequence similarity to mammalian enkephalinase

The gene specifying an endopeptidase of Lactococcus lactis, named pepO, was cloned from a genomic library of L. lactis subsp. cremoris P8-2-47 in lambda EMBL3 and was subsequently sequenced. pepO is probably the last gene of an operon encoding the binding-protein-dependent oligopeptide transport system of L. lactis. The inferred amino acid sequence of PepO showed that the lactococcal endopeptidase has a marked similarity to the mammalian neutral endopeptidase EC 3.4. 24.11 (enkephalinase), whereas no obvious sequence similarity with any bacterial enzyme was found. By means of gene disruption, a pepO-negative mutant was constructed. Growth and acid production of the mutant strain in milk were not affected, indicating that the endopeptidase is not essential for growth of L. lactis in milk.
Fast simulation and rendering techniques for fluid objects

Movies with actions and light effects of fluid objects are aesthetically pleasing and interesting. Until now, the calculation costs of simulation and rendering of fluid objects have been very high. Using a modern PC system and appropriate methods, we achieved a time of 10‐20 seconds per frame for this application. Our system uses a full Navier‐Stokes equation solver with uniform Eulerian mesh, marching cube isosurface techniques, Catmull‐Clark subdivision surface techniques, ray tracing techniques on each vertex and conventional polygon base rendering by HW accelerator. In this paper, we describe the components of our system and the reasons for choosing them. By measuring CPU times of each process for some movie scenes of fluid objects, we evaluate this system. We consider what factors are important for creating movies of fluid objects with short TAT.
From Exploring and Constructing to Understanding: Mediating Intermediate-Level Knowledge

My dissertation work is inspired by Löwgren's intermediate-level knowledge (ILK). Drawing on encouraging creative multi-explorations and epistemic differences in HCI, we construct archetype-based stimuli as "communicated artifacts" to open multidimensional possibilities and as a means to probe how ILK works within cross-disciplinary ideation.