Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and Structure

Pim-1 kinase, a serine/threonine protein kinase encoded by the pim proto-oncogene, is involved in several signalling pathways such as the regulation of cell cycle progression and apoptosis. Many cancer types show high expression levels of Pim kinases and particularly Pim-1 has been linked to the initiation and progression of the malignant phenotype. In several cancer tissues somatic Pim-1 mutants have been identified. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of Pim-1 kinase. We expressed and purified some of the mutants of Pim-1 kinase that are expressed in cancer tissues and reported in the single nucleotide polymorphisms database. The point mutations in the variants significantly affect the conformation of the native state of Pim-1. All the mutants, expressed as soluble recombinant proteins, show a decreased thermal and thermodynamic stability and a lower activation energy values for kinase activity. The decreased stability accompanied by an increased flexibility suggests that Pim-1 variants may be involved in a wider network of protein interactions. All mutants bound ATP and ATP mimetic inhibitors with comparable IC50 values suggesting that the studied Pim-1 kinase mutants can be efficiently targeted with inhibitors developed for the wild type protein.
A Critical Function of Mad2l2 in Primordial Germ Cell Development of Mice

The development of primordial germ cells (PGCs) involves several waves of epigenetic reprogramming. A major step is following specification and involves the transition from the stably suppressive histone modification H3K9me2 to the more flexible, still repressive H3K27me3, while PGCs are arrested in G2 phase of their cycle. The significance and underlying molecular mechanism of this transition were so far unknown. Here, we generated mutant mice for the Mad2l2 (Mad2B, Rev7) gene product, and found that they are infertile in both males and females. We demonstrated that Mad2l2 is essential for PGC, but not somatic development. PGCs were specified normally in Mad2l2−/− embryos, but became eliminated by apoptosis during the subsequent phase of epigenetic reprogramming. A majority of knockout PGCs failed to arrest in the G2 phase, and did not switch from a H3K9me2 to a H3K27me3 configuration. By the analysis of transfected fibroblasts we found that the interaction of Mad2l2 with the histone methyltransferases G9a and GLP lead to a downregulation of H3K9me2. The inhibitory binding of Mad2l2 to Cyclin dependent kinase 1 (Cdk1) could arrest the cell cycle in the G2 phase, and also allowed another histone methyltransferase, Ezh2, to upregulate H3K27me3. Together, these results demonstrate the potential of Mad2l2 in the regulation of both cell cycle and the epigenetic status. The function of Mad2l2 is essential in PGCs, and thus of high relevance for fertility.
User-centered concept development process for emerging technologies

This paper describes a user-centered concept development process especially suitable for emerging technologies. The process consists of four phases: 1) Definition of development goals, 2) User and technology research, 3) Iterative concept development and 4) Process wrap-up. Our variation of concept development process differs from prior ones by having a stronger emphasis on technology framework surrounding the concept development. The findings are gathered from 16 cases during the last three years in research projects and post-graduate courses.
Monocular 3 D Scene Reconstruction

Structure from motion is the most widely used principle for obtaining 3D scene information with a standard monocular camera. In this report we present an explorative project into a simple structure from motion processing system using two-view geometry and keypoint matching. The resulting system shows some promise, but remains quite unstable. We show some preliminary results and make a few suggestions on useful improvements.
QoS Performance Improvement for WLAN Using Priority Random Early Detection

In this article, we pay attention to the qualities of service (QoS) on wireless LAN. We proposed a Priority Random Early Detection (PRED) algorithm, which integrated random early detection (RED) with IEEE 802.11e EDCF so that QoS performance can be improved for WLAN. Under heavy traffic load condition, the performance of channel accessing will be inefficient due to collisions. PRED provides good differentiation among different access categories (AC). Compared with the usage of the traditional first-in-first-out (FIFO) queuing strategy with different priorities in a node, PRED supports higher throughput for high priority packets.
Cusp-Free, Time-Invariant, 3D Feedback Control Law for a Nonholonomic Floating Robot

In this paper, the feedback control of a nonholonomic 3D vehicle is considered; namely, the problem of steering an underactuated rigid body to a target position along a desired direction is addressed. A simple time-invariant strategy is determined on the basis of standard vector kinematics and a Lyapunov-like stability analysis. The resulting control law guarantees almost global exponential convergence of the configuration error to zero with paths that do not exhibit any cusps, thus satisfying a major requirement for the application of such results on real systems that are not allowed or desired to move in both the forward and backward directions.
Receipt of Life-Sustaining Treatments for Taiwanese Pediatric Patients Who Died of Cancer in 2001 to 2010

AbstractAggressive life-sustaining treatments have the potential to be continued beyond benefit, but have seldom been systematically/nationally explored in pediatric cancer patients. Furthermore, factors predisposing children dying of cancer to receive life-sustaining treatments at end of life (EOL) have never been investigated in a population-based study. This population-based study explored determinants of receiving life-sustaining treatments in pediatric cancer patients’ last month of life.For this retrospective cohort study, we used administrative data on 1603 Taiwanese pediatric cancer patients who died in 2001 to 2010. Individual patient-level data were linked with encrypted identification numbers from the National Register of Deaths Database, Cancer Registration System database, National Health Insurance claims datasets, and Database of Medical Care Institutions Status. Life-sustaining treatments included intensive care unit (ICU) care, cardiopulmonary resuscitation (CPR), and mechanical ventilation. Associations of patient, physician, hospital, and regional factors with receiving ICU care, CPR, and mechanical ventilation in the last month of life were evaluated by multilevel generalized linear mixed models.In their last month of life, 22.89%, 46.48%, and 61.45% of pediatric cancer patients received CPR, mechanical ventilation, and ICU care, respectively, with no significant decreasing trends from 2001 to 2010. Patients were more likely to receive all three identified life-sustaining treatments at EOL if they were diagnosed with a hematologic malignancy or a localized disease, died within 1 year of diagnosis, and received care from a pediatrician. Receipt of ICU care or mechanical ventilation increased with increasing EOL-care intensity of patients’ primary hospital, whereas use of mechanical ventilation decreased with increasing quartile of hospice beds in the patients’ primary hospital region.Taiwanese pediatric cancer patients received aggressive life-sustaining treatments in the month before death. Healthcare policies and interventions should aim to help pediatricians treating at-risk pediatric cancer patients and hospitals with a tendency to provide aggressive EOL treatments to avoid the expense of life-sustaining treatments when chance of recovery is remote and to devote resources to care that produces the greatest benefits for children, parents, and society.
A Framework to Classify Distributed Shared Memory Systems

Software Distributed Shared Memory (DSM) systems combine the ease of shared memory programming with the efficiency of message passing architectures. However, there is several design and implementation issues related to DSM software that strongly affect their overall performance. Unfortunately there is still no clear understanding of these issues and their performance tradeoffs. This paper is a survey of the most recent years of DSM research and places the various design and implementation issues in a comprehensive framework while discussing their tradeoffs explicitly. The paper also classifies the prominent DSM research projects obtained so far according to this framework.
Communication-oriented cooperative spectrum sensing in cognitive radio

Cooperative spectrum sensing improves detection performance over fading and shadowing channels by using multiple cognitive radio (CR) users. Compared with local spectrum sensing with individual CR user, it can either reduce sensitivity requirements for each CR user or shorten the overall sensing duration. These advantages are from spatial diversity when all cooperative users sense a common primary user. However, in practice, CR users at different locations may receive signals from different primary users, which may confuse the fusion user and result in the loss of communication opportunities. In this paper, we propose a cooperative sensing approach by taking the reliability of each partner user into account. Simulation results illustrate significant performance improvement of the proposed approach.
A key component extraction method based on HMM and dependency parsing

Increasing attention has been paid for POI (Point of Interest) data query for travel information service. The correct extraction of key components in question is crucial for improving the accuracy of query results. The paper proposes a key component extraction method based on HMM (Hidden Markov Model) and dependency parsing. Firstly, the sentence pattern classifier is established by HMM. And then, questions are classified by classifier. Finally, combination of sentence pattern's structure, the four key components are extracted by dependency parsing. The results show that the F1-Measure is 0.83, which well proves the effectiveness of the method.
ChickVD: a sequence variation database for the chicken genome

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the ‘Chicken Variation Database’ (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics. org.cn.
CrowdReply: A Crowdsourced Multiple Choice Question Answering System

Crowdsourcing has applications where machine learning falls short. We describe the design, implementation, and deployment of CrowdReply, a crowdsourced multiple choice question answering (MCQA) system. We deployed an Android app to enable the audience watching “Who wants to be millionaire? ” quiz-show on TV to play along on their smartphones simultaneously. The app enabled us to collect data from 1000s of users about MCQA dynamics. Our ﬁndings indicate that it is possible to aggregate the crowd’s answers to build a super-player
Swift Observations of the X-Ray-Bright GRB 050315

This paper discusses Swift observations of the γ-ray burst GRB 050315 (z = 1.949) from 80 s to 10 days after the onset of the burst. The X-ray light curve displayed a steep early decay (t-5) for ~200 s and several breaks. However, both the prompt hard X-ray/γ-ray emission (observed by the BAT) and the first ~300 s of X-ray emission (observed by the XRT) can be explained by exponential decays, with similar decay constants. Extrapolating the BAT light curve into the XRT band suggests that the rapidly decaying, early X-ray emission was simply a continuation of the fading prompt emission; this strong similarity between the prompt γ-ray and early X-ray emission may be related to the simple temporal and spectral character of this X-ray-rich GRB. The prompt (BAT) spectrum was steep down to ~15 keV and appeared to continue through the XRT bandpass, implying a low peak energy, inconsistent with the Amati relation. Following the initial steep decline, the X-ray afterglow did not fade for ~1.2 × 104 s, after which time it decayed with a temporal index of α ≈ 0.7, followed by a second break at ~2.5 × 105 s to a slope of α ~ 2. The apparent "plateau" in the X-ray light curve, after the early rapid decay, makes this one of the most extreme examples of the steep-flat-steep X-ray light curves revealed by Swift. If the second afterglow break is identified with a jet break, then the jet opening angle was θ0 ~ 5°, implying Eγ ≳ 1050 ergs.
Chinese Coreference Resolution via Ordered Filtering

We in this paper present the model for our participation (BCMI) in the CoNLL-2012 Shared Task. This paper describes a pure rule-based method, which assembles different filters in a proper order. Different filters handle different situations and the filtering strategies are designed manually. These filters are assigned to different ordered tiers from general to special cases. We participated in the Chinese and English closed tracks, scored 51.83 and 59.24 respectively.
Synthesis of Mixed Software-Hardware Implementations from CFSM Specifications

Embedded controller for reactive real-time applications are implemented as mixed software- hardware systems. In [CGH+ 93], a formal specification model called Co-design Finite State Machine (CFSM) is introduced. In this paper we present a methodology for partitioning and automatic synthesis of software-hardware systems specified with CFSMs, CFSM networks are partitioned into software ad hardware domains. Interfaces between hardware and/or software partitions are defined. An implementation of the entire system is automatically generated and optimization techniques are applied to both software and hardware. To reduce the complexity of the design and the representation, library modules can be predefined and reused. An example from the automotive industry is used to demonstrate the method.
A Closer Look at ADC Multivariate GARCH

In the past thirty years, academia and the marketplace have devoted significant effort and resources toward gaining a better understanding of how volatility changes over time in the financial markets and how changes in one market affect changes in another. All of these attempts involve modeling the covariance matrix of two or more asset returns using the period-earlier covariance matrix. In this paper, we outline the volatility modeling process for an Antisymmetric Dynamic Covariance (ADC) multivariate Generalized Autoregressive Conditional Heteroskedacity (GARCH) model, explain the math involved, and attempt to estimate the parameters of the model using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) optimization algorithm. We find several barriers to estimating parameters using BFGS and suggest using alternative algorithms to estimate the ADC multivariate GARCH in the future.
PENGARUH PERSON-JOB FIT TERHADAP JOB INVOLVEMENT DENGAN INTRINSIC MOTIVATION SEBAGAI VARIABEL INTERVENING PADA KARYAWAN KANTOR PUSAT PT BANK PEMBANGUNAN DAERAH JAWA TIMUR TBK, SURABAYA

Indonesia merupakan salah satu Negara yang tergabung dalam MEA. Dampak terciptanya MEA menuntut perusahaan dapat bersaing secara kompetitif untuk mempertahankan eksistensinya diantara para pesaing. Dalam hal ini perusahaan membutuhkan karyawan yang memiliki tingkat job involvement yang tinggi untuk dapat bekerja secara efektif dan efisien. Job involvement merupakan sikap positif karyawan yang mendorong untuk berkontribusi secara positif terhadap pekerjaan. Tujuan dari penelitian ini adalah untuk emnganalisis pengaruh person-job fit terhadap job involvement dengan intrinsic motivation sebagai variabel intervening. Data dalam penelitian ini dikumpulkan melalui observasi dan penyebaran kuesioner yang melibatkan 131 karyawan kantor pusat PT. Bank Pembangunan Daerah Jawa Timur Tbk, Surabaya. Pengambilan sampel dilakukan dengan metode simple random sampling. Teknis pengujian data yang digunakan dalam penelitian ini adalah SEM-PLS dan uji sobel untuk menguji efek mediasi. Hasil penelitian ini menunjukkan bahwa person-job fit berpengaruh secara positif signifikan terhadap job involvement dan intrinsic motivation. Intrinsic motivation terbukti memediasi hubungan antara person-job fit terhadap job involvement. Kata kunci: person-job fit , intrinsic motivation, job involvement.
Design on Lattice Wave Digital Filters in SPW Environment

Lattice Wave Digital Filters (LWDFs) are known to be insensitive to finite precision arithmetic effects and can readily be designed for standard filtering applications using a set of explicit formulas elaborated by Gazsi. This paper presents the necessary elements to develop an LWDF design package within the Signal Processing Workstation (SPW) design framework. This package, based on Gazsi's formulas and additional frequency transformations, supports the realisation of lowpass, highpass, bandpass and band-reject filters using either Butterworth, Chebyshev, or Elliptic approximations. Ideal and finite precision arithmetic models of the basic LWDF components are also provided to perform detailed simulations.
Stated Preference valuation methods: an evolving tool for understanding choices and informing policy

We examine the value of Stated Preference (SP) valuation methods as part of the environmental economist’s toolbox. We review a number of policy design issues where we believe SP methods have advantages over alternative approaches. We also discuss the role of SP methods in exploring a few aspects of peoples’ preferences and values which have wider implications for economics and behavioral sciences: (a) the effects of information, learning and knowledge; (b) testing the standard model of compensatory, rational choice; (c) the influence of behavioural levers such as social norms; and (d) the role of “deep” drivers of preference heterogeneity, such as personality and emotions. We also review what is known about the extent to which hypothetical choices reveal something about people’s true preferences. Finally, we speculate on some areas where SP methods may be useful in the future.
D-instantons and matrix models

We discuss the matrix model aspect of configurations saturating a fixed number of fermionic zero-modes. This number is independent of the rank of the gauge group and the instanton number. This will allow us to define a large-Nc limit of the embedding of K D-instantons in the matrix model and make contact with the leading term (the measure factor) of the supergravity computations of D-instanton effects. We show that the connection between these two approaches is made through the Abelian modes of the matrix variables.
The Associations between Immunity-Related Genes and Breast Cancer Prognosis in Korean Women

We investigated the role of common genetic variation in immune-related genes on breast cancer disease-free survival (DFS) in Korean women. 107 breast cancer patients of the Seoul Breast Cancer Study (SEBCS) were selected for this study. A total of 2,432 tag single nucleotide polymorphisms (SNPs) in 283 immune-related genes were genotyped with the GoldenGate Oligonucleotide pool assay (OPA). A multivariate Cox-proportional hazard model and polygenic risk score model were used to estimate the effects of SNPs on breast cancer prognosis. Harrell’s C index was calculated to estimate the predictive accuracy of polygenic risk score model. Subsequently, an extended gene set enrichment analysis (GSEA-SNP) was conducted to approximate the biological pathway. In addition, to confirm our results with current evidence, previous studies were systematically reviewed. Sixty-two SNPs were statistically significant at p-value less than 0.05. The most significant SNPs were rs1952438 in SOCS4 gene (hazard ratio (HR) = 11.99, 95% CI = 3.62–39.72, P = 4.84E-05), rs2289278 in TSLP gene (HR = 4.25, 95% CI = 2.10–8.62, P = 5.99E-05) and rs2074724 in HGF gene (HR = 4.63, 95% CI = 2.18–9.87, P = 7.04E-05). In the polygenic risk score model, the HR of women in the 3rd tertile was 6.78 (95% CI = 1.48–31.06) compared to patients in the 1st tertile of polygenic risk score. Harrell’s C index was 0.813 with total patients and 0.924 in 4-fold cross validation. In the pathway analysis, 18 pathways were significantly associated with breast cancer prognosis (P<0.1). The IL-6R, IL-8, IL-10RB, IL-12A, and IL-12B was associated with the prognosis of cancer in data of both our study and a previous study. Therefore, our results suggest that genetic polymorphisms in immune-related genes have relevance to breast cancer prognosis among Korean women.
Prognosis of High-Grade Carcinoid Tumor Patients using Dynamic Limited-Memory Influence Diagrams

Dynamic limited-memory influence diagrams (DLIMIDs) have been developed as a framework for decision-making under uncertainty over time. We show that DLIMIDs constructed from twostage temporal LIMIDs can represent infinitehorizon decision processes. Given a treatment strategy supplied by the physician, DLIMIDs may be used as prognostic models. The theory is applied to determine the prognosis of patients that suffer from an aggressive type of neuroendocrine tumor.
A Superfast Algorithm for Determining the Discrete-time Stability for Matrix Polynomials

The classical Schur-Cohn criterion for checking the discrete-time stability of a given scalar polynomial f(z) requires O(n) arithmetic operations where n = deg f(z). Recall that the discrete-time stability means that all the roots of f(z) lie in the interior of the unit circle. Though the importance of the Schur-Cohn test is difficult to overestimate, it applies only to scalar polynomials, i.e., its area of applications is limited to SISO (singleinput-single-output) systems. In this paper we study the stability for the more general matrix polynomials of the form L(z) = zI + zn−1An−1 + . + zA1 + A0 that occur in MIMO (multi-input-multi-output) systems. Here the coefficients Ak are m × m matrices. In this case instead of the roots one usually considers the eigenvalues of L(z) which are defined as complex numbers {zk} for which the m × m matrix L(zk) is not invertible. Unfortunately, there are no known efficient (fast or superfast) procedures to check if L(z) is stable. In this extended abstract we present a first superfast O(mn log n) algorithm to check the discrete-type stability for a given matrix polynomial. Thus, even in the simplest scalar case our algorithm outperforms the classical Schur-Cohn procedure. The derivation of our method is based on a nontrivial reduction of computations on matrix polynomials to computations with dense block-structured matrices, and then using the concept of blockdisplacement structure to design a superfast procedure. Recently the method of dispacement was used to design a fast method for list decoding of algebraic geometric codes. Here we apply it to solve an important problem in control. We expect that our method will be useful in several application in digital filtering.