Miracle-dz/UniFAR-FTUs huggingface dataset:
Enrichment of regulatory signals in conserved non-coding genomic sequence

MOTIVATION Whole genome shotgun sequencing strategies generate sequence data prior to the application of assembly methodologies that result in contiguous sequence. Sequence reads can be employed to indicate regions of conservation between closely related species for which only one genome has been assembled. Consequently, by using pairwise sequence alignments methods it is possible to identify novel, non-repetitive, conserved segments in non-coding sequence that exist between the assembled human genome and mouse whole genome shotgun sequencing fragments. Conserved non-coding regions identify potentially functional DNA that could be involved in transcriptional regulation. RESULTS Local sequence alignment methods were applied employing mouse fragments and the assembled human genome. In addition, transcription factor binding sites were detected by aligning their corresponding positional weight matrices to the sequence regions. These methods were applied to a set of transcripts corresponding to 502 genes associated with a variety of different human diseases taken from the Online Mendelian Inheritance in Man database. Using statistical arguments we have shown that conserved non-coding segments contain an enrichment of transcription factor binding sites when compared to the sequence background in which the conserved segments are located. This enrichment of binding sites was not observed in coding sequence. Conserved non-coding segments are not extensively repeated in the genome and therefore their identification provides a rapid means of finding genes with related conserved regions, and consequently potentially related regulatory mechanism. Conserved segments in upstream regions are found to contain binding sites that are co-localized in a manner consistent with experimentally known transcription factor pairwise co-occurrences and afford the identification of novel co-occurring Transcription Factor (TF) pairs. This study provides a methodology and more evidence to suggest that conserved non-coding regions are biologically significant since they contain a statistical enrichment of regulatory signals and pairs of signals that enable the construction of regulatory models for human genes. CONTACT samuel.levy@celera.com.
Detection of Candida albicans mRNA in Archival Histopathology Samples by Reverse Transcription-PCR

ABSTRACT The feasibility of detecting Candida albicans mRNA in formalin-fixed paraffin-embedded archival human histopathology specimens by reverse transcription-PCR (RT-PCR) was investigated. RT with gene-specific primers was used to detect five single-copy C. albicans gene transcripts, including those of two housekeeping genes, in oral candidiasis samples up to 8 years of age.
Understanding Information Seeking Behaviour in Financial Advisory

In light of the financial crisis, it has become even more critical for financial service providers to remain competitive. This paper discusses new perspec- tives on the problems of today’s advisory services, including the customer's dissatisfaction with personalization and individualization. Thereby we draw on research in human information behavior, particularly Wilson's model, which provides a promising framework to better understand the information behavior of clients and in turn helps us understand some of the IT-enablers of individualized financial services. Our findings are supported by data col- lected from mystery shopping episodes and focus group discussions.
Analysis of Metal–Insulator–Metal Structure and Its Application to Sensor

In this paper, analysis and design method of a metal-insulator-metal (MIM) structure is introduced. When an electromagnetic wave enters an MIM structure, a surface plasmon is excited on both metals. In this case, an electromagnetic-field standing wave by the surface plasmon used as a wave source is generated in the insulator. This electromagnetic-field standing wave has various modes depending on the thickness of the insulator. In this paper, we establish by calculation, 3-D simulation, and measurement that a plasmon resonant wave can be controlled by changing the thickness of the insulator. We propose a sensor with an MIM structure that exploits this phenomenon. If the insulator of the MIM structure comprises air, the target solution can be injected into the insulator by capillary action, and the MIM structure is thus used as a sensor. This is because the wavelength of the electromagnetic-field standing wave in the insulator is made shorter in proportion to the refractive index of the target solution. We have confirmed this fact by calculation, 3-D simulations, and measurement. Our measurements show good agreement with the calculations and 3-D simulations, indicating that our MIM sensor is able to detect differences in refractive index of the order of 0.7%.
Spatio-Temporal Tensor Decomposition of a Polyaffine Motion Model for a Better Analysis of Pathological Left Ventricular Dynamics

Given that heart disease can cause abnormal motion dynamics over the cardiac cycle, understanding and quantifying cardiac motion can provide insight for clinicians to aid with diagnosis, therapy planning, and determining prognosis. The goal of this paper is to extract population-specific motion patterns from 3D displacements in order to identify the mean motion in a population, and to describe pathology-specific motion patterns in terms of the spatial and temporal components. Since there are common motion patterns observed in patients with the same condition, extracting these can lead towards a better understanding of the disease. Quantifying cardiac motion at a population level is not a simple task since images can vary widely in terms of image quality, size, resolution, and pose. To overcome this, we analyze the parameters obtained from a cardiac-specific Polyaffine motion-tracking algorithm, which are aligned both spatially and temporally to a common reference space. Once all parameters are aligned, different subjects can be compared and analyzed in the space of Polyaffine transformations by projecting the transformations to a reduced order subspace in which dominant motion patterns in each population can be extracted. Using tensor decomposition, the spatial and temporal aspects can be decoupled in order to study the components individually. The proposed method was validated on healthy volunteers and Tetralogy of Fallot patients according to known spatial and temporal behavior for each population. A key advantage of this method is the ability to regenerate motion sequences from the models, which can be visualized in terms of the full motion.
Specification and Verification of Interaction Protocols : a Computational Logic Approach Based on Abduction

In this paper we propose a logic-based approach for the specification and verification of interaction protocols. We give the syntax of the proposed language, declarative and operational semantics of an abductive proof procedure for compliance verification. The proof procedure uses constraints for efficiently dealing with large-scale problems, and is implemented in Constraint Handling Rules. We give an example of specification and on-the-fly verification of compliance in a negotiation protocol.
AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions

Genome annotation, assisted by computer programs, is one of the great advances in modern biology. Nevertheless, the in silico identification of small and complex coding sequences is still challenging. We observed that amino acid sequences inferred from coding—but rarely from non-coding—DNA sequences accumulated alignments in low-stringency BLAST searches, suggesting that this alignments accumulation could be used to highlight coding regions in sequenced DNA. To investigate this possibility, we developed a computer program (AnABlast) that generates profiles of accumulated alignments in query amino acid sequences using a low-stringency BLAST strategy. To validate this approach, all six-frame translations of DNA sequences between every two annotated exons of the fission yeast genome were analysed with AnABlast. AnABlast-generated profiles identified three new copies of known genes, and four new genes supported by experimental evidence. New pseudogenes, ancestral carboxyl- and amino-terminal subtractions, complex gene rearrangements, and ancient fragments of mitDNA and of bacterial origin, were also inferred. Thus, this novel in silico approach provides a powerful tool to uncover new genes, as well as fossil-coding sequences, thus providing insight into the evolutionary history of annotated genomes.
Planning of Pushing Manipulation by a Mobile Robot Considering Cost of Recovery Motion

This paper presents a planning method of pushing manipulation by a mobile robot. It is sometimes very useful if the robot can take recovery action, namely, re-approaching and re-pushing, when it turns out to be ineffective to keep current pushing motion. The proposed planning framework is based on the idea of mode switching, where three modes; approaching, pushing and re-pushing, are considered. The pushing motion is first built with dynamic programming, which provides value function of the state. Based on the value, planning of re-approaching to the object and re-pushing is conducted using a value iteration algorithm extended to state space with uncertainty. The proposed planning framework was evaluated in simulation, and it was shown that it provides more effective behaviour of the robot by recovery motion at an appropriate timing.
GPU-Based Techniques for Global Illumination Effects

Abstract This book presents techniques to render photo-realistic images by programming the Graphics Processing Unit (GPU). We discuss effects such as mirror reflections, refractions, caustics, diffuse or glossy indirect illumination, radiosity, single or multiple scattering in participating media, tone reproduction, glow, and depth of field. The book targets game developers, graphics programmers, and also students with some basic understanding of computer graphics algorithms, rendering APIs like Direct3D or OpenGL, and shader programming. In order to make the book self-contained, the most important concepts of local illumination and global illumination rendering, graphics hardware, and Direct3D/HLSL programming are reviewed in the first chapters. After these introductory chapters we warm up with simple methods including shadow and environment mapping, then we move on toward advanced concepts aiming at global illumination rendering. Since it would have been impossible to give a rigorous review of all appro.
A programming model for GPU-based parallel computing with scalability and abstraction

In this paper, we present a multi-level programming model for recent GPU-based high performance computing systems. Involving cooperative stream threads and symmetric multiprocessing threads our model gives a computational framework that scales through multi-GPU environments to GPU-cluster systems. Instead of hiding the execution environment from the programmer using compiler extensions or metaprogramming techniques we aim a solution that both enables optimizations and provides abstract problem space mapping with code reusability and virtualization of hardware resources in order to decrease the programming effort. We evaluate an implementation of our model based on CUDA, OpenMP, and MPI2 technologies on a complex practical application scenario and discuss its performance scaling behavior.
Video Covariance Matrix Logarithm for Human Action Recognition in Videos

In this paper, we propose a new local spatio-temporal descriptor for videos and we propose a new approach for action recognition in videos based on the introduced descriptor. The new descriptor is called the Video Covariance Matrix Logarithm (VCML). The VCML descriptor is based on a covariance matrix representation, and it models relationships between different low-level features, such as intensity and gradient. We apply the VCML descriptor to encode appearance information of local spatio-temporal video volumes, which are extracted by the Dense Trajectories. Then, we present an extensive evaluation of the proposed VCML descriptor with the Fisher vector encoding and the Support Vector Machines on four challenging action recognition datasets. We show that the VCML descriptor achieves better results than the state-of-the-art appearance descriptors. Moreover, we present that the VCML descriptor carries complementary information to the HOG descriptor and their fusion gives a significant improvement in action recognition accuracy. Finally, we show that the VCML descriptor improves action recognition accuracy in comparison to the state-of-the-art Dense Trajectories, and that the proposed approach achieves superior performance to the state-of-theart methods.
Stock Trend Prediction by Using K-Means and AprioriAll Algorithm for Sequential Chart Pattern Mining

In this paper we present a model to predict the stock trend based on a combination of sequential chart pattern, K-means and AprioriAll algorithm. The stock price sequence is truncated to charts by sliding window, then the charts are clustered by K-means algorithm to form chart patterns. Therefore, the chart sequences are converted to chart pattern sequences, and frequent patterns in the sequences can be extracted by AprioriAll algorithm. The existence of frequent patterns implies that some specific market behaviors often appear accompanied, thus the corresponding trend can be predicted. Experiment results show that the proposed system can produce better index return with fewer trades. Its annualized return is also better than award winning mutual funds. Therefore, the proposed method makes profits on the real market, even in a long-term usage.
Ubiquitin-specific protease 12 interacting partners Uaf-1 and WDR20 are potential therapeutic targets in prostate cancer

The androgen receptor (AR) is a key transcription factor in the initiation and progression of prostate cancer (PC) and is a major therapeutic target for the treatment of advanced disease. Unfortunately, current therapies are not curative for castration resistant PC and a better understanding of AR regulation could identify novel therapeutic targets and biomarkers to aid treatment of this disease. The AR is known to be regulated by a number of post-translational modifications and we have recently identified the deubiquitinating enzyme Usp12 as a positive regulator of AR. We determined that Usp12 deubiquitinates the AR resulting in elevated receptor stability and activity. Furthermore, Usp12 silencing was shown to reduce proliferation of PC cells. Usp12 is known to require the co-factors Uaf-1 and WDR20 for catalytic activity. In this report we focus further on the role of Uaf-1 and WDR20 in Usp12 regulation and investigate if these co-factors are also required for controlling AR activity. Firstly, we confirm the presence of the Usp12/Uaf-1/WDR20 complex in PC cells and demonstrate the importance of Uaf-1 and WDR20 for Usp12 stabilisation. Consequently, we show that individual silencing of either Uaf-1 or WDR20 is sufficient to abrogate the activity of the Usp12 complex and down-regulate AR-mediated transcription via receptor destabilisation resulting in increased apoptosis and decreased colony forming ability of PC cells. Moreover, expression of both Uaf-1 and WDR20 is higher in PC tissue compared to benign controls. Overall these results highlight the potential importance of the Usp12/Uaf-1/WDR20 complex in AR regulation and PC progression. Highlights: Androgen receptor is a key transcriptional regulator in prostate cancer Usp12/Uaf-1/WDR20 complex plays a crucial role in androgen receptor stability and activity Destabilising an individual Usp12/Uaf-1/WDR20 complex member reduces the protein levels of the whole complex and diminishes androgen receptor activity Protein levels of all members of the Usp12/Uaf-1/WDR20 complex are significantly increased in PC
Evaluating Byzantine Quorum Systems

Replication is a mechanism extensively used to guarantee the availability and good performance of data storage services. Byzantine Quorum Systems (BQS) have been proposed as a solution to guarantee the consistency of that kind of services, even if some of the replicas fail arbitrarily. Many BQS have been proposed recently, but comparing their performance is not simple. In fact, it has been shown that theoretical metrics like the number of steps or communication rounds say as much about the practical performance of distributed algorithms as they hide. This paper presents a comparative evaluation of several BQS algorithms in the literature. The evaluation is based both on experiments and simulations. For that purpose, a framework for evaluating BQS called BQSNeko was developed. The results of the evaluation allow a better understanding of the algorithms and the tradeoffs involved.
Verification of Temporal Properties

The paper presents a relatively complete deductive system for proving branching time temporal properties of reactive programs. No deductive system for verifying branching time temporal properties has been presented before. Our deductive system enjoys the following advantages. First, given a well-formed specification there is no need to translate it into a normal-form specification since the system can handle any well-formed specification. Second, given a specification to be verified, the proof rule to be applied is easily determined according to the top level operator of the specification. Third, the system reduces temporal verification to assertional reasoning rather than to temporal reasoning.
Big science, internationalisation, professionnalisation et fonction sociale de la science à travers l’analyse diachronique des recensions d’ouvrage.

The aim of this paper is to analyze the evolution of some ecdotical variables in an academic genre that has so far received little attention, viz, book reviews (BR). Toward that end, we analyzed 100 BR written in French and published in 2 different time periods: between 1890 and 1900 (Block A) and between 1990 and 2000 (Block B). The variable we studied were: 1) the book reviewed (its length, genre and original language), 2) the book author (a single author, an editor or a co-editor and the way his credentials are presented), 3) the BR itself (its length, the frequency of courtesy markers and of bibliographical references) and 4) the BR author (anonymat vs. identification). Quantitative results were analyzed by means of the Chi square. Our most salient results show that in both Blocks the most frequent book type is the monographie, followed by the traite and the manuel in Bloc A, and by congress proceedings in Bloc B (a genre non-extant in Bloc A). In Block A, BR are 4 times longer than those of Block B (p = .0001). The great majority of the books reviewed in this Bloc are single-authored books (p = .0001 when comparing their frequency to that of multi-authored books) written in French (p = .0001 when comparing their frequency to that of books written in other languages). The BR author very frequently remains “almost-anonymous” (his initials only are mentioned), and courtesy markers are a rhetorical hallmark of these end-of-19th century BR. Conversely, in Block B most books reviewed are multi-authored/edited books (p = .0001 and p = .0047 when comparing their frequency to that registered in Bloc A) written in English (p= .0001 when comparing their frequency with that recorded in Block A). Contrary to what was observed in Block A, most books reviewed in Block B are then collaborative works. Finally, the name of the publishing company is a routine feature of BR in Bloc B, whereas it not so in Bloc A. These quantitative results are explained from a socioconstructivist standpoint. We conclude that they underline the hyper specialization, professionalization and internationalization of today’s science and reflect the increasing social … and commercial concern of today’s scientific enterprise.
Effect of different anesthetic agents on left ventricular systolic function assessed by echocardiography in hamsters

Determination of left ventricular ejection fraction (LVEF) using in vivo imaging is the cardiac functional parameter most frequently employed in preclinical research. However, there is considerable conflict regarding the effects of anesthetic agents on LVEF. This study aimed at assessing the effects of various anesthetic agents on LVEF in hamsters using transthoracic echocardiography. Twelve female hamsters were submitted to echocardiography imaging separated by 1-week intervals under the following conditions: 1) conscious animals, 2) animals anesthetized with isoflurane (inhaled ISO, 3 L/min), 3) animals anesthetized with thiopental (TP, 50 mg/kg, intraperitoneal), and 4) animals anesthetized with 100 mg/kg ketamine plus 10 mg/kg xylazine injected intramuscularly (K/X). LVEF obtained under the effect of anesthetics (ISO=62.2±3.1%, TP=66.2±2.7% and K/X=75.8±1.6%) was significantly lower than that obtained in conscious animals (87.5±1.7%, P<0.0001). The K/X combination elicited significantly higher LVEF values compared to ISO (P<0.001) and TP (P<0.05). K/X was associated with a lower dispersion of individual LVEF values compared to the other anesthetics. Under K/X, the left ventricular end diastolic diameter (LVdD) was increased (0.60±0.01 cm) compared to conscious animals (0.41±0.02 cm), ISO (0.51±0.02 cm), and TP (0.55±0.01 cm), P<0.0001. The heart rate observed with K/X was significantly lower than in the remaining conditions. These results indicate that the K/X combination may be the best anesthetic option for the in vivo assessment of cardiac systolic function in hamsters, being associated with a lower LVEF reduction compared to the other agents and showing values closer to those of conscious animals with a lower dispersion of results.
Emergent Vulnerability in Integrated Operations: A Proactive Simulation Study of Risk and Organizational Learning

The implementation of integrated operations (IO) for oil and gas recovery - a real-time linkage among platform-based facilities, on-shore control centers and suppliers - is anticipated to reduce operating costs by 30%, extend the lifetime of current production fields by five years or longer and maintain Norwegian continental shelf production for 50-100 years. The changes in operating procedures require extensive training to ensure continued personal and environmental safety. Vulnerabilities may emerge during the rollout of updated techniques and integration of IO technology with existing work practices. We focus on user knowledge as key to successful change. A system dynamics simulation is presented that defines work process and knowledge transition. Interviews and historical records assisted in parameterizing the model. The simulation suggests that great care should be taken to facilitate and monitor the rate of knowledge maturation, even in the face of expensive implementation delays, to reduce the risk of catastrophic failure from endemic incidents