Miracle-dz/UniFAR-FTUs huggingface dataset:
On-line haemodiafiltration with and without acetate.

BACKGROUND In patients on on-line convective treatments, given the considerable quantity of dialysis fluid re-infused, the small amount of acetate present in bicarbonate dialysis fluid as a pH stabilizing factor may allow a significant transfer of that anion to the patient, possibly inducing cytokine activation. METHODS To verify this hypothesis, we performed on-line haemodiafiltration (OL-HDF) with (3 mmol/l) and without acetate in dialysis fluid in a cross-over randomized order on 12 prevalent patients. RESULTS In comparison with the pre-treatment values, plasma acetate levels were unchanged during and after acetate-free OL-HDF, while they were 5-6 times higher in the course of OL-HDF containing acetate in dialysis fluid; plasma acetate levels returned to basal values 2 h after the end of the procedure. The total increase of bases in the patient attributable to acetate was 36%. Plasma bicarbonate values at the end of treatment were significantly lower in treatments without acetate, as compared to those with acetate. Interleukin-6 plasma levels were super-imposable at the beginning and in the course of the two methods compared, but there was a tendency towards a greater increase at an interval of 2 h following OL-HDF with acetate. CONCLUSIONS Our preliminary results confirm the assumption that body gain of acetate is particularly high in convective treatments, while acetate-free OL-HDF slows down acetate burden. Clinical advantages due to these effects should be evaluated in properly designed prospective studies.
TRedD—A database for tandem repeats over the edit distance

A ‘tandem repeat’ in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon the concept of ‘evolutive tandem repeats’. In addition, we have developed a tool, called TandemGraph, to graphically depict the repeats occurring in a sequence. This tool can be coupled with any repeat finding software, and it should greatly facilitate analysis of results. Database URL: http://tandem.sci.brooklyn.cuny. edu/
A Family of Insertion Sequences That Impacts Integrons by Specific Targeting of Gene Cassette Recombination Sites, the IS1111-attC Group

ABSTRACT Integrons facilitate the evolution of complex phenotypes by physical and transcriptional linkage of genes. They can be categorized as chromosomal integrons (CIs) or mobile resistance integrons (MRIs). The significance of MRIs for the problem of multiple antibiotic resistance is well established. CIs are more widespread, but their only demonstrated significance is as a reservoir of gene cassettes for MRIs. In characterizing CIs associated with Pseudomonas, we discovered a subfamily of insertion sequences, termed the IS1111-attC group, that insert into the recombination sites of gene cassettes (attC site) by site-specific recombination. IS1111-attC elements appear to have recently spread from Pseudomonas species to clinical class 1 integrons. Such elements are expected to significantly impact integrons. To explore this further, we examined CIs in 24 strains representing multiple levels of evolutionary divergence within the genus Pseudomonas. Cassette arrays frequently had a degenerated “footprint” of an IS1111-attC group element at their terminus and in three cases were occupied by multiple functional IS1111-attC elements. Within Pseudomonas spp. the IS-integron interaction appears to follow an evolutionarily rapid cycle of infection, expansion, and extinction. The final outcome is extinction of the IS element and modification of the right-hand boundary of the integron. This system represents an unusual example of convergent evolution whereby heterologous families of site-specific recombinases of distinct genetic elements have adopted the same target site. The interactions described here represent a model for evolutionary processes that offer insights to a number of aspects of the biology of integrons and other mosaic genetic elements.
Screening for Prostate Cancer by Digital Rectal Examination and PSA Determination in Senegal

Objectives. The goal of our study was to investigate the prevalence of prostate cancer in an unselected population of Senegalese men. Patients and Methods. We conducted the study over two years (2008 and 2009) on an unselected population of 572 Senegalese men, aged 35 and older. The following parameters have been investigated: the subject's age, the presence or absence of urination disorders, the family's history of prostate cancer or prostate surgery, the aspects of the prostate on digital rectal examination (DRE), the total PSA level, and the outcomes of the prostate biopsies. Data entry was performed with Epi Info 6 software and was analyzed and recorded using Excel software. We performed mean and frequency calculations. Results. The mean age of our patients was 65.5 years, with extremes of 38 and 93 years. Age groups from 50 to 59 and from 60 to 69 were the most represented. DRE was normal in the age group from 35 to 39, and only one patient in the age group from 40 to 49 had a prostate nodule. PSA level was greater than or equal to 4 ng/mL in 66 cases. A total of 5.4% patients had a PSA level greater than or equal to 10 ng/mL. Only two patients in the age group from 40 to 49 had a PSA level greater than 4 ng/mL. Of the 72 biopsies we performed, prostatic adenocarcinoma was found in 30.6% of the cases. It is the only type of prostate cancer we found in our series. The cases of prostate cancer were mostly observed in the age groups from 60 to 69 and from 70 to 79. No cases were detected for ages younger than 50. DRE gave indications of possible adenocarcinoma in 27.30% cases. Its sensitivity was 27%, while its positive predictive value was estimated at 35%. Of all positive biopsies, 4.5% had a PSA level between 0 and 3.9 ng/mL. In this case, the sensitivity of PSA was 95.5%, and the positive predictive value was 31.8%. High-grade intraepithelial neoplasiae were observed in 21 cases. Conclusion. Prostate cancer is frequent in Senegal, and screening remains the best way for early diagnosis.
The X-ray nuclei of intermediate-redshift radio sources

We present a Chandra and XMM-Newtonspectral analysis of the nuclei of the radio galaxies and radio-loud quasars from the 3CRR sample in the redshift range 0.1 < z < 0.5. In the range of radio luminosity sampled by these objects, mostly FRIIs, it has been clear for some time that a population of radio galaxies (‘low-excitation radio galaxies’) cannot easily participate in models that unify narrow-line radio galaxie s and broad-line objects. We show that low-excitation and narrow-line radio galaxies have systematically different nuclear Xray properties: while narrow-line radio galaxies universa lly show a heavily absorbed nuclear X-ray component, such a heavily absorbed component is rarely found in sources classed as low-excitation objects. Combining our data with the results of our earlier work on the z < 0.1 3CRR sources, we discuss the implications of this result for unified models, for the origins of mid-infrared emission from radio sources, and for the nature of the apparent FRI/FRII dichotomy in the X-ray. The lack of direct evidence for accretion-related X-ray emission in FRII LERGs leads us to argue that there is a strong possibility that some, or most, FRII LERGs accrete in a radiatively inefficient mode. However, our result s are also consistent with a model in which the accretion mode is the same for low- and high-excitation FRIIs, with the lower accretion luminosities in FRII LERGs attributed instead to more efficient radio luminosity production in those objects.
Characterizing Large Dataset GPU Compute Workloads Targeting Systems with Die-Stacked Memory

The increasing adoption of GPUs as mainstream computing devices, coupled with the imminent availability of large high-bandwidth caches based on die-stacked memory makes it important to analyze and understand modern GPU compute applications from the perspective of their memory access and data reuse characteristics. This paper presents detailed workload characterization studies on four GPU compute applications that process large data sets. The applications studied include tree traversal and search algorithms, a partial differential equation (PDE) solver, and a synthetic array processing application. Our studies indicate that while the memory footprint consumed by these applications can be very large, the effectiveness of several GB worth of cache may vary significantly across workloads. This suggests that provisioning cache resources in a die-stacked memory based system needs to be done very carefully, through detailed characterization of target workloads. An added benefit of our work was the discovery that accurate memory characterization data can lead to a significantly more optimized strategy for scheduling GPU threads by taking advantage of a workload's access characteristics. In particular, for the PDE solver, our analysis led to an optimization that achieved 30% measured gain in application performance. This paper also describes our analysis methodology for conducting these types of studies. The methodology is based on trace analysis, where the traces capture memory traffic and calls to the GPU compute API. For each application we highlight the characterization metrics and analysis techniques that were most useful in generating insights about their memory access patterns.
Correlated industries mining for Chinese financial news based on LDA trained with research reports

Application of latent Dirichlet allocation (LDA) in text analysis has received much attention because it is capable of characterizing the hidden topics of the documents within the Bayesian framework. In this paper, we train the LDA model with financial research reports to predict the most correlated industries of the financial news among the 24 first-level industries of Chinese market. Since the topics of the tagged research reports are more concentrated than that of news, we calculate the optimal industry topic distributions with least loss of information to overcome the mismatch. Then the Jensen-Shannon divergence is introduced for mining the correlated industries. The promising performance of this method provides a solid foundation for financial information retrieval and the event-driven research.
SCPD: a promoter database of the yeast Saccharomyces cerevisiae

MOTIVATION In order to facilitate a systematic study of the promoters and transcriptionally regulatory cis-elements of the yeast Saccharomyces cerevisiae on a genomic scale, we have developed a comprehensive yeast-specific promoter database, SCPD. RESULTS Currently SCPD contains 580 experimentally mapped transcription factor (TF) binding sites and 425 transcriptional start sites (TSS) as its primary data entries. It also contains relevant binding affinity and expression data where available. In addition to mechanisms for promoter information (including sequence) retrieval and a data submission form, SCPD also provides some simple but useful tools for promoter sequence analysis. AVAILABILITY SCPD can be accessed from the URL http://cgsigma.cshl. org/jian. The database is continually updated.
An Approach to Synchronize UML-Based Design Components for Model-Driven Protocol Development

Applying UML diagrams for the design of dependable systems like communication protocols helps to visualize the protocol behavior in multiple representations. In principle, protocols are comprehensible by modeling its behaviors through sequence diagrams. However, the sequence diagrams encapsulate local protocol functions, such as protocol data unit coding/decoding, correctness checks, etc. To model the local actions of the protocol entities activity diagrams may be used as a balancing model. By using two different models, one should ensure that the described behaviors are consistent. To prove this we present an approach in this paper to synchronize the UML sequence and activity diagrams through mapping rules. The rules are predefined according to the UML specification by a stereotype. Later they are used for validating the two diagrams. We show the approach for an example protocol function.
The Fosfomycin Resistance Gene fosB3 Is Located on a Transferable, Extrachromosomal Circular Intermediate in Clinical Enterococcus faecium Isolates

Some VanM-type vancomycin-resistant Enterococcus faecium isolates from China are also resistant to fosfomycin. To investigate the mechanism of fosfomycin resistance in these clinical isolates, antimicrobial susceptibility testing, filter-mating, Illumina/Solexa sequencing, inverse PCR and fosfomycin resistance gene cloning were performed. Three E. faecium clinical isolates were highly resistant to fosfomycin and vancomycin with minimal inhibitory concentrations (MICs) >1024 µg/ml and >256 µg/ml, respectively. The fosfomycin and vancomycin resistance of these strains could be co-transferred by conjugation. They carried a fosfomycin resistance gene fosB encoding a protein differing by one or two amino acids from FosB, which is encoded on staphylococcal plasmids. Accordingly, the gene was designated fosB3. The fosB3 gene was cloned into pMD19-T, and transformed into E. coli DH5α. The fosfomycin MIC for transformants with fosB3 was 750-fold higher than transformants without fosB3. The fosB3 gene could be transferred by an extrachromosomal circular intermediate. The results indicate that the fosB3 gene is transferable, can mediate high level fosfomycin resistance in both Gram-positive and Gram-negative bacteria, and can be located on a circular intermediate.
Initiative in work teams: adaptation and validation of the Personal Initiative at Group Level Scale / Iniciativa en los equipos de trabajo: adaptación y validación de la Escala de Iniciativa Personal a nivel Grupal

Abstract In this study, we conceptualize personal initiative as a collective construct and adapt and validate a scale to evaluate it with a sample of 308 Spanish participants belonging to 91 work teams. Personal initiative at group level is a behavioural syndrome in which the team shows an approach to work that is self-initiated, proactive, persistent, capable of modifying the atmosphere and pro organization. As a predictive variable, we analysed the climate for initiative as well as personal initiative at group level. The resulting variables that were analysed referred to organization and team performance, with the team productivity and innovation as the criteria, analysing radical innovation. The scale has suitable psychometric properties. The results show that there is a relationship between the two predictive variables. Furthermore, personal initiative at group level is related to team productivity, while the climate for initiative is related to innovation.
A COMPARATIVE STUDY OF THE EFFECTS OF MOTIVATIONAL AND ATTITUDINAL FACTORS ON STUDYING STATISTICS

This study focuses on the differential effects of motivations and attitudes on Critical Thinking and Self-Regulation. Two different samples of Psychology students of Open Universiteit Nederland have been studied. The first sample is composed of students, confronted with an integrated, research-based teaching and learning design; the second sample is composed of students, exposed to classic service courses in statistics and research methods. Results reveal that motivations significantly affect Critical Thinking and Self-Regulation and that motivations and attitudes affect learning processes and achievement in their own characteristic way. Moreover the crucial role of an integrated teaching and learning design as a significant contributor to optimal motivations, more favourable attitudes and more adequate learning strategies for studying statistics and research methods has been endorsed. BACKGROUND Most studies concerning statistics (service) courses in the social sciences focus on attitudes and achievement. However, in the domain of educational psychology particularly motivations are regarded as crucial contributors to the learning process (Pintrich and Schunk, 2002). In the domain of statistics education studies generally focus on attitudes, based on empirically proven relations with achievement, disregarding or neglecting motives and learning strategies. Nevertheless, Critical Thinking and Meta-Cognition are recognized as essential learning strategies for the construction of statistical literacy and statistical reasoning (Pfannkuch, 1999; Reading, 1996; Watson and Callingham, 2003). Based on an extensive literature study in the domain of education, psychology and statistics we decided to study motivations and attitudes simultaneously to clarify their relations with Critical Thinking, Meta-Cognitive Strategies and achievement in statistics and research methods. Our comprehensive study comprises four studies, and our research findings go far beyond the space at our disposal in this paper, so we will emphasize our findings concerning motivations, attitudes, Critical Thinking, Meta-Cognitive Strategies and achievement in two different learning contexts in this paper, the latter because of the endorsement of the impact and role of instructional design in educational literature.
Estimating Elasticity for Residential Electricity Demand in China

Residential demand for electricity is estimated for China using a unique household level dataset. Household electricity demand is specified as a function of local electricity price, household income, and a number of social-economic variables at household level. We find that the residential demand for electricity responds rather sensitively to its own price in China, which implies that there is significant potential to use the price instrument to conserve electricity consumption. Electricity elasticities across different heterogeneous household groups (e.g., rich versus poor and rural versus urban) are also estimated. The results show that the high income group is more price elastic than the low income group, while rural families are more price elastic than urban families. These results have important policy implications for designing an increasing block tariff.
Approximating Ricci solitons and quasi-Einstein metrics on toric surfaces

We present a general numerical method for investigating prescribed Ricci curvature problems on toric K\"ahler manifolds. This method is applied to two generalisations of Einstein metrics, namely Ricci solitons and quasi-Einstein metrics. We begin by recovering the Koiso--Cao soliton and the L\"u--Page--Pope quasi-Einstein metrics on $\mathbb{CP}^{2}\sharp\overline{\mathbb{CP}}^{2}$ (in both cases the metrics are known explicitly). We also find numerical approximations to the Wang--Zhu soliton on $\mathbb{CP}^{2}\sharp 2\overline{\mathbb{CP}}^{2}$ (here the metric is not known explicitly). Finally, a substantial numerical investigation of the quasi-Einstein equation on $\mathbb{CP}^{2}\sharp 2\overline{\mathbb{CP}}^{2}$ is conducted. In this case it is an open problem as to whether such metrics exist on this manifold. We find metrics that solve the quasi-Einstein equation to the same degree of accuracy as the approximations to the Wang--Zhu soliton solve the Ricci soliton equation.
Optimization and learning for rough terrain legged locomotion

We present a novel approach to legged locomotion over rough terrain that is thoroughly rooted in optimization. This approach relies on a hierarchy of fast, anytime algorithms to plan a set of footholds, along with the dynamic body motions required to execute them. Components within the planning framework coordinate to exchange plans, cost-to-go estimates, and ‘certificates’ that ensure the output of an abstract high-level planner can be realized by lower layers of the hierarchy. The burden of careful engineering of cost functions to achieve desired performance is substantially mitigated by a simple inverse optimal control technique. Robustness is achieved by real-time re-planning of the full trajectory, augmented by reflexes and feedback control. We demonstrate the successful application of our approach in guiding the LittleDog quadruped robot over a variety of types of rough terrain. Other novel aspects of our past research efforts include a variety of pioneering inverse optimal control techniques as well as a system for planning using arbitrary pre-recorded robot behavior.
Agent oriented requirements engineering for a data warehouse

In recent years, a number of requirements engineering (RE) proposals for a data warehouse (DW) systems have been made. In the traditional/operational systems, requirements engineering has been divided into two phases: early & late requirements engineering phase. Most of the data warehouse requirements engineering (DWRE) approaches have not distinguished early requirements engineering phase from late requirements engineering phase. A very few approaches are seen in the literature that explicitly model early & late requirements for a DW. In this paper, we propose an AGDI (Agent-Goal-Decision-Information) model to support early requirements engineering issues for a data warehouse. Here, early requirements have been modeled through organization modeling and goal modeling activities as an illustration of proposed AGDI model to support decisional goals of the organization for which DW is to be built.
Study on 3D scene reconstruction in robot navigation using stereo vision

In this paper, a 3D scene reconstruction by using stereo vision is presented. Stereo camera parameters from the camera calibration process and disparity map are two important parameters to obtain an accurate result for the 3D reconstruction. 3D reconstruction process generates the coordinates of world points (point cloud). From the information of the point cloud, the interested object is segmented out. Additionally, the noises left in the image is eliminated. The experimental result obtained shows that only the background and the interested object from the overall scene appeared in the processed image. The center of gravity is also determined as the reference value for the robot navigation. An estimation error model is also introduced in this study to increase the accuracy of the distance measurement by using the developed stereo vision system from the mobile robot. This experiment provides a foundation for navigation and object tracking for a mobile robot.
Quasirandomness, Counting and Regularity for 3-Uniform Hypergraphs

The main results of this paper are regularity and counting lemmas for 3-uniform hypergraphs. A combination of these two results gives a new proof of a theorem of Frankl and Rödl, of which Szemerédi's theorem for arithmetic progressions of length 4 is a notable consequence. Frankl and Rödl also prove regularity and counting lemmas, but the proofs here, and even the statements, are significantly different. Also included in this paper is a proof of Szemerédi's regularity lemma, some basic facts about quasirandomness for graphs and hypergraphs, and detailed explanations of the motivation for the definitions used.