Miracle-dz/UniFAR-FTUs huggingface dataset:
Querying Large Similar Sequences in a Compressed Format Efficiently

With the advances in next-generation sequencing technologies, the amount of genomic sequence data being produced continues to grow at an exponential rate. A unique characteristic of these sequences is that they are over 99% similar, and therefore highly compressible using their differences with respect to a reference sequence. Still, an increasingly pressing challenge is how to efficiently query these massive amounts of sequence data in their compressed format. In this paper we study the problem of answering subsequence-search queries on a compressed set of long sequences. We develop novel index structures for the differences and algorithms for answering queries. We present various optimization techniques to further reduce the space requirement and query response time. We demonstrate the efficiency of these techniques using a thorough experimental study on real genomic data.
During the last ten years four chlamydia species have been isolated from humans and from different domestic and wild animals : Chlamydia psittaci

In order to diagnose chlamydiosis caused by bacteria Chlamydophila sp. , the humoral immunity response in domestic bovines was examined. A possible difference in titre of specific antibodies between latently, acutely and chronically infected animals was also studied. At the same time we confirmed the applicability and reliability of complement-fixation tests (CFT) and enzyme–linked immunosorbent assay (ELISA) on the basis of their specificity, sensitivity and comparativeness. Of 276 bovines examined, originating from 10 herds on Croatian territory, CFT revealed Chlamydophila sp. specific antibodies in 14.2% of sera samples, ELISA in 35.8%, and indirect immunofluorescent test (IIF) in 27.1% sera samples. These results suggest that CFT, ELISA and IIF can be used as reliable serological methods for diagnostics of chlamydiosis, being in accordance with Office International des Epizooties (OIE) recommendations.
Efficient Retrieval of Aggregate Data in Uncertain and Probabilistic Databases

— Aggregation is handled in the Trio system for uncertain and probabilistic data. Because of “exact” aggregation in uncertain database can produce exponentially sized results. It provides three alternatives such as, (1) Low bound on the aggregate value (2) High bound on the value and (3) Expected value. Above variants return a single result efficient to compute for aggregation queries. The current system provides efficient way of handling uncertain and probabilistic database. It identifies uncertain and certain data. It shows the way of handling distinct queries on uncertain database. It provides efficient way for getting better performance in the case of handling multiple aggregation variants, multiple queries and sub queries. We show how system provides efficient way and get better performance through some result analysis. It provides formal definitions, semantics to implement aggregation on non correlated data.
KEBIJAKAN UNTUK KEBERLANJUTAN EKOLOGI, SOSIAL, EKONOMI WADUK DAN BUDIDAYA KERAMBA JARING APUNG DI WADUK CIRATA

Cirata merupakan nama waduk terbesar di Jawa Barat yang memiliki fungsi utama sebagai pembangkit listrik tenaga air (PLTA) untuk pasokan listrik wilayah pulau Jawa dan Bali. Selain menyediakan pasokan listrik, waduk ini dimanfaatkan untuk kegiatan perikanan tangkap, perikanan budidaya keramba jaring apung (KJA), transportasi dan pariwisata. Aktivitas di perairan waduk yang melebihi daya dukung lingkungan menimbulkan permasalahan tersendiri yang dapat mengancam status keberlanjutan waduk sebagai PLTA maupun sebagai perairan umum daratan. Oleh karena itu, diperlukan pengelolaan waduk yang berkelanjutan. Penelitian ini bertujuan untuk menganalisis status keberlanjutan waduk dan keberlanjutan budidaya KJA dalam multidimensi keberlanjutan (ekologi, ekonomi dan sosial) dengan menggunakan analisis multidimentional scaling dengan alat analisis Rapid Appraisal for Fisheries Status (Rapfish), kemudian dilakukan analisis sensitivitas dan ketidakpastian menggunakan analisis Monte Carlo dan Leverage. Berdasarkan hasil penelitian status keberlanjutan waduk dan budidaya KJA termasuk dalam status kurang berkelanjutan. Status keberlanjutan Waduk Cirata lebih baik dari status keberlanjutan budidaya KJA yang terdapat di perairan waduk, hal ini dapat dilihat dari nilai indeks keberlanjutan budidaya KJA yang cenderung lebih besar. Atribut-atribut yang sensitif memerlukan respon kebijakan yang tepat demi terwujudnya pengelolaan waduk yang berkelanjutan. Kondisi keberlanjutan waduk dan budidaya KJA sangat mempengaruhi satu sama lain, yang artinya kondisi buruk salah satu elemen keberlanjutan akan menghambat terwujudnya keberlanjutan yang lainnya.
Modeling and simulation of concurrent workload processing in cloud-distributed enterprise information systems

Cloud Computing enables provisioning and distribution of highly scalable services in a reliable, on-demand and sustainable manner. Distributed Enterprise Information Systems (dEIS) are a class of applications with important economic value and with strong requirements in terms of performance and reliability. In order to validate dEIS architectures, stability, scaling and SLA compliance, large testing deployments are necessary, adding complexity to the design and testing of such systems. To fill this gap, we present and validate a methodology for modeling and simulating such complex distributed systems using the CloudSim cloud computing simulator, based on measurement data from an actual distributed system. We present an approach for creating a performance-based model of a distributed cloud application using recorded service performance traces. We then show how to integrate the created model into CloudSim. We validate the CloudSim simulation model by comparing performance traces gathered during distributed concurrent experiments with simulation results using different VM configurations. We demonstrate the usefulness of using a cloud simulator for modeling properties of real cloud-distributed applications.
Paclitaxel-carboplatin alone or with bevacizumab for non-small-cell lung cancer.

BACKGROUND Bevacizumab, a monoclonal antibody against vascular endothelial growth factor, has been shown to benefit patients with a variety of cancers. METHODS Between July 2001 and April 2004, the Eastern Cooperative Oncology Group (ECOG) conducted a randomized study in which 878 patients with recurrent or advanced non-small-cell lung cancer (stage IIIB or IV) were assigned to chemotherapy with paclitaxel and carboplatin alone (444) or paclitaxel and carboplatin plus bevacizumab (434). Chemotherapy was administered every 3 weeks for six cycles, and bevacizumab was administered every 3 weeks until disease progression was evident or toxic effects were intolerable. Patients with squamous-cell tumors, brain metastases, clinically significant hemoptysis, or inadequate organ function or performance status (ECOG performance status, >1) were excluded. The primary end point was overall survival. RESULTS The median survival was 12.3 months in the group assigned to chemotherapy plus bevacizumab, as compared with 10.3 months in the chemotherapy-alone group (hazard ratio for death, 0.79; P=0.003). The median progression-free survival in the two groups was 6.2 and 4.5 months, respectively (hazard ratio for disease progression, 0.66; P<0.001), with corresponding response rates of 35% and 15% (P<0.001). Rates of clinically significant bleeding were 4.4% and 0.7%, respectively (P<0.001). There were 15 treatment-related deaths in the chemotherapy-plus-bevacizumab group, including 5 from pulmonary hemorrhage. CONCLUSIONS The addition of bevacizumab to paclitaxel plus carboplatin in the treatment of selected patients with non-small-cell lung cancer has a significant survival benefit with the risk of increased treatment-related deaths. (ClinicalTrials.gov number, NCT00021060.)
A Task Analysis of Therapeutic Engagement in a Professionally Facilitated Online Intervention for Young Couples Affected By Breast Cancer

Engagement in online intervention, defined as the extent to which participants are involved in and attentive to the contents of the intervention, has been shown to predict treatment outcome. However, research has found that participants’ engagement and completion rates in online interventions are often quite low. Because professional facilitation has been shown to increase intervention participation and effectiveness, the therapeutic alliance that develops between facilitators and participants might be one factor that influences engagement. Thus, in this study a modified task analysis was conducted in order to examine how facilitators develop a therapeutic alliance with participants to increase engagement in an online intervention for couples affected by breast cancer, called Couplelinks. Task analysis involves a process of combining rational investigation and empirical observation to create a model of successful task performance, which in the present study is the promotion and maintenance of intervention engagement. In the present analysis, a rational model based on facilitators’ experience was first created. Next, an empirical model was created by observing facilitators’ communications with three engaged couples and three unengaged couples. The resulting synthesised model suggests that engagement promotion involves three meta-processes, designated as ‘friendly and positive yet firm approach,’ ‘inclusive empathic attitude,’ and ‘humanizing the technology’ (initially identified in the rational model), as well as various behavioural facilitator interventions, or ‘techniques. ’ The latter facilitator techniques were observed in the empirical model, and fall into the following three broad categories, which represent the different interacting relationships in the intervention: 1) fostering the couple-facilitator bond; 2) fostering program adherence (i.e., fostering the couple-program bond); and 3) fostering the within-couple bond. Through the process of creating a composite measure of engagement, we also found that couples could be separated into couple ‘engagement-
THE USE OF GRAPH THEORY IN A PARALLEL MULTIFRONTAL METHOD FOR SEQUENCES OF UNSYMMETRIC PATTERN SPARSE MATRICES

Multifrontal matrix factorization methods used for solving large, sparse systems of linear equations decompose sparse matrices into overlapping dense submatrices which can be represented by vertices with relationships between submatrices shown via various types of edges. This paper describes the use of graph theory in a new parallel, distributed memory multifrontal method for the LU factorization of sequences of matrices with an identical, unsymmetric pattern. The directed acyclic graphs formed by these vertices and the various edge sets are used to structure the computations, schedule the parallel factorization, and provide a robust capability to dynamically change the pivot ordering to maintain numerical stability. Pivot reordering determines necessary permutations based on a path analysis of two component edge sets. The path properties represented by these edge sets deene the impacts of these permutations on the structures of the submatrices and the number of nonzeros in the matrix factors. Transitive reductions of these edge sets provide the communications paths needed for parallel implementation.
Empirical Analysis of the Market Risk of Chinese Open-Ended Funds Based on GARCH-VaR Models

Traditional study has some limitation on GARCH models to describe VAR in a market of great volatility, so the purpose of this paper is to look for an effective GARCH model for measuring VAR value of the market risk of open-ended funds. This paper adopted variance-covariance method and introduced the GARCH series models to calculate the conditional variance for VaR value. The authors used the GARCH models to conduct the empirical research under three different distributions. The result shows that GARCH models under Student T distribution perform best in evaluating VAR value and simulating the market risk in a fluctuate market. The authors suggest that the funds management companies in China should enhance the efficiency of risk control with the help of suitable GARCH models and distribution
Attachment Theory and Simulating Secure Base Behaviour : Dr . Bowlby meet the Reverend Bayes

In this paper we describe how information processing constructs originating in AI have become part of the Attachment Theory tool kit. We survey the early influence of AI within the theoretical framework that John Bowlby formed as the foundation of Attachment Theory between the 1950s and 1980s. We then review recent work which has built upon Bowlby’s framework and is concerned with modelling and simulating attachment phenomena. We conclude by discussing some possible advantages that might arise from incorporating recent work on Bayesian arbitration into attachment control system models.
Recognition of distance cues from a virtual spatialization model

Emerging issues in the auditory display aim at increasing the usability of interfaces. In this paper we present a virtual resonating environment, which synthesizes distance cues by means of rever-beration. We realize a model that recreates the acoustics inside a tube, applying a numerical scheme called Waveguide Mesh, and we present the psychophysical experiments we have conducted for validating the information about distance conveyed by the virtual environment
AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination

RNA Polymerase II (Pol II) termination is dependent on RNA processing signals as well as specific terminator elements located downstream of the poly(A) site. One of the two major terminator classes described so far is the Co-Transcriptional Cleavage (CoTC) element. We show that homopolymer A/T tracts within the human β-globin CoTC-mediated terminator element play a critical role in Pol II termination. These short A/T tracts, dispersed within seemingly random sequences, are strong terminator elements, and bioinformatics analysis confirms the presence of such sequences in 70% of the putative terminator regions (PTRs) genome-wide.
Cell Coupling and Uncoupling in the Ventricular Zone of Developing Neocortex

Cells within the ventricular zone (VZ) of developing neocortex are coupled together into clusters by gap junction channels. The specific role of clustering in cortical neurogenesis is unknown; however, clustering provides a means for spatially restricted local interactions between subsets of precursors and other cells within the VZ. In the present study, we have used a combination of 5-bromo-2′-deoxyuridine (BrDU) pulse labeling, intracellular biocytin labeling, and immunocytochemistry to determine when in the cell cycle VZ cells couple and uncouple from clusters and to determine what cell types within the VZ are coupled to clusters. Our results indicate that clusters contain radial glia and neural precursors but do not contain differentiating or migrating neurons. In early neurogenesis, all precursors in S and G2 phases of the cell cycle are coupled, and approximately half of the cells in G1 are coupled. In late neurogenesis, however, over half of the cells in both G1 and S phases are not coupled to VZ clusters, whereas all cells in G2 are coupled to clusters. Increased uncoupling in S phase during late neurogenesis may contribute to the greater percentage of VZ cells exiting the cell cycle at this time. Consistent with this hypothesis, we found that pharmacologically uncoupling VZ cells with octanol decreases the percentage of VZ cells that enter S phase. These results demonstrate that cell clustering in the VZ is restricted to neural precursors and radial glia, is dynamic through the cell cycle, and may play a role in regulating neurogenesis.
How to Successfully Establishing Online Stores?

In internet era, online stores and its discussions is dramatically growing. However, how to operate online stores well is confusing enterprise and scholars. The main reason is the processes to establish online store aren't enough and sufficient. Once the process is well built, which can assist companies to successfully set up online stores, then save many efforts and resources. Therefore, this research builds "implementation map to establishing online store" through reviewing literature and implementing qualitative method, then sets up the framework of establishment process and department authority. This result can assist enterprises (1) raise management efficiency through blending academic and practical opinions, (2) improve project performance, (3) make the business decision more accurate.
Full Solid Angle Panoramic Viewing by Depth Image Warping on Field Programmable Gate Array

To construct 3D virtual scenes from two-dimensional images with depth information, image warping techniques could be used. In this paper, a novel approach of cylindrical depth image warping is presented and implemented on a field programmable gate array hardware platform, which can implement a full solid angle panoramic viewing. By the approach, we use a virtual projective cylindrical camera model. The scene to render is firstly projected onto the surface of a cylinder with perspective projection for the top and bottom view and parallel projection for the side view respectively. Both color and depth images are captured after projection. Using the projective cylindrical reference images as the source, we employ a two-pass rendering process to generate new views of the 3D scene through a horizontal and vertical pre-warping followed by standard texture mapping. By taking the parallelism and reconfigurability of hardware, the algorithm is optimized for the architecture of circuit and well designed for memory management. Experimental results show that an improved rendering speed with generation of good quality images could be achieved on the hardware platform.
Experience-based adaptation of locomotion behaviors for kinematically complex robots in unstructured terrain

Kinematically complex robots such as legged robots provide a large degree of mobility and flexibility, but demand a sophisticated motion control, which has more tunable parameters than a general planning and decision layer should take into consideration. A lot of parameterizations exist which produce locomotion behaviors that fulfill the desired action but with varying performance, e.g., stability or efficiency. In addition, the performance of a locomotion behavior at any given time is highly depending on the current environmental context. Consequently, a complex mapping is required that closes the gap between robot-independent actions and robot-specific control parameters considering the environmental context and a given prioritization of performance indices.
Annotating Question Types for Consumer Health Questions

This paper presents a question classification scheme and a corresponding annotated corpus of consumer health questions. While most medical question classification methods have targeted medical professionals, the 13 question types we present are targeted toward disease questions posed by consumers. The corpus consists of 1,467 consumer-generated requests for disease information, containing a total of 2,937 questions. The goal of question type classification is to indicate the best strategy for selecting answers from publicly available health information resources, such as medical encyclopedias and medical research websites. The annotated question corpus, along with detailed annotation guidelines, are publicly available.
Characterization of PVD Oxides

The state-of-the-art tools for machining metals are primarily based on a metal-ceramic composite (WC-Co) coated with different combinations of carbide, nitride and oxide coatings. Combinations of these coating materials are optimized to withstand specific wear conditions. Oxide coatings are especially desired because of their possible high hot hardness, chemical inertness with respect to the workpiece, and their low friction. This thesis deals with process and coating characterization of new oxide coatings deposited by physical vapor deposition (PVD) techniques, focusing on the Cr-Zr-O and Al-Cr-Si-O systems. The thermal stability of α-Cr0.28Zr0. 10O0.61 deposited by reactive radio frequency (RF)-magnetron sputtering at 500 °C was investigated after annealing up to 870 °C. The annealed samples showed transformation of α-(Cr,Zr)2O3 and amorphous ZrOx-rich areas into tetragonal ZrO2 and bcc Cr. The instability of the α-(Cr,Zr)2O3 is surprising and possibly related to the annealing being done under vacuum, facilitating the loss of oxygen. The stabilization of the room temperature metastable tetragonal ZrO2 phase, due to surface energy effects, may prove to be useful for metal cutting applications. The observed phase segregation of α-(Cr,Zr)2O3 and formation of tetragonal ZrO2 with corresponding increase in hardness for this pseudo-binary oxide system also opens up design routes for pseudo-binary oxides with tunable microstructural and mechanical properties. The inherent difficulties of depositing insulating oxide films with PVD, demanding a closed circuit, makes the investigation of process stability an important part of this research. In this context, we investigated the influence of adding small amount of Si in Al-Cr cathode on plasma characteristics, process parameters, and coating properties. Si was chosen here due to a previous study showing improved erosion behavior of Al-Cr-Si over pure Al-Cr cathode without Si incorporation in the coating. This work shows small improvements in cathode erosion and process stability (lower pressure and cathode voltage) when introducing 5 at % Si in the Al70Cr30-cathode. This also led to fewer droplets at low cathode current and intermediate O2 flow. A larger positive effect on cathode erosion was observed with respect to cleaning the cathode from oxide contamination by increasing cathode current with 50%. However, higher cathode current also resulted in increased amount of droplets in the coating which is undesirable. Through plasma analysis the presence of volatile SiO species could be confirmed but the loss of Si through volatile SiO species was negligible, since the coating composition matched the cathode composition. The positive effect of added Si on the …
Identification of genes associated with tumor suppression in Syrian hamster embryo cells.

Loss of a tumor-suppressor gene function appears to play a critical role in the multistep process of neoplastic transformation of Syrian hamster embryo (SHE) cells in vitro. Clonal variants of two independent, preneoplastic cell lines have been isolated that have either retained (termed supB+) or lost (termed supB-) the ability to suppress the tumorigenicity of a highly malignant benzo[alpha]pyrene-transformed SHE cell line (BP6T) in cell hybrids. We have pursued several approaches in an attempt to identify genes that are responsible for tumor suppression in these cells. The only consistent differences detected in two-dimensional gel analyses of supB+ and supB- cellular proteins were decreases in the levels of two high molecular weight isoforms of tropomyosin in supB- cells. Differential screening of a supB+ cDNA library for genes that are preferentially expressed in supB+ cells yielded cDNA clones for four genes, i.e., collagen type II, collagen type IX, H19, and a previously unidentified gene (clone 5). Nuclear run-on assays suggested that higher transcription rates were responsible for the increased steady-state levels of some of these transcripts in supB+ cells. DNA sequence comparisons showed that two copies of a 9 bp element, previously identified in each of the mouse H19 enhancers, were also present in the 5' flanking region of the rat type II collagen gene. A transcription factor that controls expression of the collagen and H19 genes through binding to this conserved motif would be an attractive candidate for the supB+ gene or at least a mediator of the supB+ phenotype.