Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive High-Performance Processor Understanding via the Web

 High-performance computer processors have become much more complex in recent years, especially in the research community. We describe a Web-based interactive simulation and graphics tool under development at URI for the new Levo research processor. The tool mimics Levo operation and structure, aiding in broad understanding by researchers, students and engineers. Index Terms Microarchitecture, high-performance computing, online simulation, user-defined content.
RNA Interference (RNAi)-Dependent and RNAi-Independent Association of the Chp1 Chromodomain Protein with Distinct Heterochromatic Loci in Fission Yeast

ABSTRACT The establishment of centromeric heterochromatin in the fission yeast Schizosaccharomyces pombe is dependent on the RNA interference (RNAi) pathway. Dicer cleaves centromeric transcripts to produce short interfering RNAs (siRNAs) that actively recruit components of heterochromatin to centromeres. Both centromeric siRNAs and the heterochromatin component Chp1 are components of the RITS (RNA-induced initiation of transcriptional gene silencing) complex, and the association of RITS with centromeres is linked to Dicer activity. In turn, centromeric binding of RITS promotes Clr4-mediated methylation of histone H3 lysine 9 (K9), recruitment of Swi6, and formation of heterochromatin. Similar to centromeres, the mating type locus (Mat) is coated in K9-methylated histone H3 and is bound by Swi6. Here we report that Chp1 associates with the mating type locus and telomeres and that Chp1 localization to heterochromatin depends on its chromodomain and the C-terminal domain of the protein. Another protein component of the RITS complex, Tas3, also binds to Mat and telomeres. Tas3 interacts with Chp1 through the C-terminal domain of Chp1, and this interaction is necessary for Tas3 stability. Interestingly, in cells lacking the Argonaute (Ago1) protein component of the RITS complex, or lacking Dicer (and hence siRNAs), Chp1 and Tas3 can still bind to noncentromeric loci, although their association with centromeres is lost. Thus, Chp1 and Tas3 exist as an Ago1-independent subcomplex that associates with noncentromeric heterochromatin independently of the RNAi pathway.
Clinical and Parasitological Features of Patients with American Cutaneous Leishmaniasis that Did Not Respond to Treatment with Meglumine Antimoniate

Background American cutaneous leishmaniasis (ACL) is a complicated disease producing about 67.000 new cases per year. The severity of the disease depends on the parasite species; however in the vast majority of cases species confirmation is not feasible. WHO suggestion for ACL produced by Leishmania braziliensis, as first line treatment, are pentavalent antimonial derivatives (Glucantime or Sodium Stibogluconate) under systemic administration. According to different authors, pentavalent antimonial derivatives as treatment for ACL show a healing rate of about 75% and reasons for treatment failure are not well known. Methods In order to characterise the clinical and parasitological features of patients with ACL that did not respond to Glucantime, a cross-sectional observational study was carried out in a cohort of 43 patients recruited in three of the Colombian Army National reference centers for complicated ACL. Clinical and paraclinical examination, and epidemiological and geographic information were recorded for each patient. Parasitological, histopathological and PCR infection confirmation were performed. Glucantime IC50 and in vitro infectivity for the isolated parasites were estimated. Results Predominant infecting Leishmania species corresponds to L. braziliensis (95.4%) and 35% of the parasites isolated showed a significant decrease in in vitro Glucanatime susceptibility associated with previous administration of the medicament. Lesion size and in vitro infectivity of the parasite are negatively correlated with decline in Glucantime susceptibility (Spearman: r = (-)0,548 and r = (-)0,726; respectively). Conclusion A negative correlation between lesion size and parasite resistance is documented. L. braziliensis was found as the main parasite species associated to lesion of patients that underwent treatment failure or relapse. The indication of a second round of treatment in therapeutic failure of ACL, produced by L. braziliensis, with pentavalent antimonial derivatives is discussable.
Drawing Connections Across Education: The Freiburg Writing Center Model

A German Academic Exchange Service (Deutscher Akedemischer Austauschdienst, DAAD) visiting position recently brought me to Germany, “the country of poets and thinkers. ” Whenever I hear this phrase, which is intended to highlight the prevalence of literary and philosophical discussion there, I nod and add for myself: “. and a place where one likes to regard poets and thinkers as geniuses and where writing is still generally understood as something that cannot be taught. ” However, considering the increasingly rapid turnover of knowledge and the growing need for multi-functional writing skills for successful knowledge management, including reflective practice and lifelong self-directed learning, the attitude that writing is more of an innate than learned skill has started to change, albeit too slowly. In this article, I will analyze the preconditions for a faster change regarding the redefinition of writing in higher education, on the level of the individual learner and instructor as well as within the frameworks of curriculum and institution. Based on this analysis, I will suggest a model for how to adapt the basic ideas of U.S. writing across the curriculum (WAC) in Germany.
Set connectivity problems in undirected graphs and the directed Steiner network problem

In the <i>generalized connectivity</i> problem, we are given an edge-weighted graph <i>G = (V, E)</i> and a collection <i>D</i> = {(S<sub>1</sub>,T<sub>1</sub>),…, (S<sub>k</sub>,T<sub>k</sub>)} of distinct <i>demands</i>; each demand (S<sub>i</sub>, T<sub>i</sub>) is a pair of disjoint vertex subsets. We say that a subgraph <i>F ⊆ G connects</i> a demand (S<sub>i</sub>, T<sub>i</sub>) when it contains a path with one endpoint in <i>S<sub>i</sub></i> and the other in T<sub>i</sub>. The goal is to identify a minimum weight subgraph that connects all demands in <i>D</i>. Alon et al. (SODA '04) introduced this problem to study online network formation settings and showed that it captures some well-studied problems such as Steiner forest, non-metric facility location, tree multicast, and group Steiner tree. Finding a non-trivial approximation ratio for generalized connectivity was left as an open problem. Our starting point is the first polylogarithmic approximation for generalized connectivity attaining a performance guarantee of <i>O(log<sup>2</sup> n log<sup>2</sup> k)</i>. Here <i>n</i> is the number of vertices in G and <i>k</i> is the number of demands. We also prove that the cut-covering relaxation of this problem has an <i>O(log<sup>3</sup> n log<sup>2</sup> k)</i> integrality gap. Building upon the results for generalized connectivity we obtain improved approximation algorithms for two problems that contain generalized connectivity as a special case. For the <i>directed Steiner network</i> problem, we obtain an <i>O</i>(k<sup>1/2+ε</sup>) approximation, which improves on the currently best performance guarantee of O(k<sup>2/3</sup>) due to Charikar et al. (SODA '98). For the <i>set</i> <i>connector</i> problem, recently introduced by Fukunaga and Nagamochi (IPCO '07), we present a polylogarithmic approximation; this result improves on the previously known ratio which can be Ω(<i>n</i>) in the worst case.
ON CONSERVATIVE SMOOTHERS FOR TURBULENT CONVECTION: AN ALTERNATIVE SIMULATION SHORTCUT

Most turbulent flows can not be computed directly from the Navier-Stokes equations, because they possess far too many scales of motion. The computationally almost numberless small scales result from the nonlinear convective term which allows for the transfer of energy from scales as large as the flow domain to the smallest scales that can survive viscous dissipation. In the quest for a simulation shortcut, we propose to smooth the convective term in such a way that the symmetries that yield the invariance of the energy, enstrophy (in 2D) and helicity are preserved. This requirement yields a class of conservative smoothers. The numerical algorithm used to solve the governing equations also preserves the symmetries and is therefore well-suited to test the proposed simulation shortcut. The simulation shortcut is successfully tested for turbulent channel flow (Reτ = 180).
Credibilist multi-sensors fusion for the mapping of dynamic environment

In this article, we present how, starting from an credibilist multi-object association algorithm we can carry out a multi-sensor fusion algorithm. The tracking algorithm makes a data association between predicted information and observations. These information are imperfect. The algorithm takes into account the inaccuracy and the uncertainty of the data and the reliability of the sensors. Association is realized with the belief theory. This method can be applied to the fusion of several homogeneous data sources. The problem arises when information are heterogeneous. Here, we answer this problem by using a decentralized architecture which breaks up into two stages. The first consists in having at first a local processor to each sensor. This local processing makes it possible to obtain a set of homogeneous data. The second stage uses these homogeneous data to carry out global fusion. This fusion gives a representation and a global view of a dynamic environment around a reference vehicle the most faithful and most reliable by using all available information. Moreover, this very general approach shows the polyvalence of this algorithm which con be in any case-used for multi-object matching, local tracking, multi-sensors fusion and global tracking.
Learning Task Formulations through Situated Interactive Instruction

We present an agent, called RosieTAG, which is implemented in Soar and interacts with an external robotic environment. Rosie learns new games through interactive instruction with a human via restricted natural language. Instead of learning policy or strategy information as is common in other game learners, Rosie learns multiple game formulations (the objects, players, and rules of a game) and then uses its own general strategies to solve them. We describe the structure and functionality of Rosie, and evaluate its competence, generality, communication efficiency, communication accessibility, and ability to continuously learn and accumulate new tasks and new task knowledge.
The Effect of Process Parameters on Weld Quality in Resistance Spot Welding Dual-Phase Steels

In order to reduce vehicle weight and improve crash performance, dual-phase (DP) steels are increasingly used for lightweight auto-body. the high cooling rates in Resistance spot welding (RSW) process will make the nugget very brittle and result in interfacial fracture modes. In this study, a servo resistance welding system is firstly introduced to control process parameters during the welding process. The influences of different process parameters (weld current, weld time and electrode force) on the weld strength, nugget diameter, facture modes and weld indentation are analyzed. Finally, an on-line weld failure mode inspection method is proposed based on servo gun’s feedback characteristics.
Independent Manner − α to Multiple Chemotherapy Agents in an IAP-Dependent but TNF-Small Cell Lung Cancers − SMAC Mimetic ( JP 1201 ) Sensitizes Non

Inhibitors of apoptosis proteins (IAP) are key regulators of apoptosis and are inhibited by the second mitocondrial activator of caspases (SMAC). Previously, a small subset of TNF-a–expressing non–small cell lung cancers (NSCLC) was found to be sensitive to SMAC mimetics alone. In this study, we determined if a SMAC mimetic (JP1201) could sensitize nonresponsive NSCLC cell lines to standard chemotherapy. We found that JP1201 sensitized NSCLCs to doxorubicin, erlotinib, gemcitabine, paclitaxel, vinorelbine, and the combination of carboplatin with paclitaxel in a synergistic manner at clinically achievable drug concentrations. Sensitization did not occur with platinum alone. Furthermore, sensitization was specific for tumor compared with normal lung epithelial cells, increased in NSCLCs harvested after chemotherapy treatment, and did not induce TNF-a secretion. Sensitization also was enhanced in vivowith increased tumor inhibition and increased survival of mice carrying xenografts. These effects were accompanied by caspase 3, 4, and 9 activation, indicating that both mitochondrial and endoplasmic reticulum stress-induced apoptotic pathways are activated by the combination of vinorelbine and JP1201. Chemotherapies that induce cell death through the mitochondrial pathway required only inhibition of X-linked IAP (XIAP) for sensitization, whereas chemotherapies that induce cell death through multiple apoptotic pathways required inhibition of cIAP1, cIAP2, and XIAP. Therefore, the data suggest that IAPtargeted therapy using a SMAC mimetic provides a new therapeutic strategy for synergistic sensitization of NSCLCs to standard chemotherapy agents, which seems to occur independently of TNF-a secretion. Cancer Res; 71(24); 7640–8. 2011 AACR.
Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

The orbitrap mass analyzer combines high sensitivity, high resolution, and high mass accuracy in a compact format. In proteomics applications, it is used in a hybrid configuration with a linear ion trap (LTQ-Orbitrap) where the linear trap quadrupole (LTQ) accumulates, isolates, and fragments peptide ions. Alternatively, isolated ions can be fragmented by higher energy collisional dissociation. A recently introduced stand-alone orbitrap analyzer (Exactive) also features a higher energy collisional dissociation cell but cannot isolate ions. Here we report that this instrument can efficiently characterize protein mixtures by alternating MS and “all-ion fragmentation” (AIF) MS/MS scans in a manner similar to that previously described for quadrupole time-of-flight instruments. We applied the peak recognition algorithms of the MaxQuant software at both the precursor and product ion levels. Assignment of fragment ions to co-eluting precursor ions was facilitated by high resolution (100,000 at m/z 200) and high mass accuracy. For efficient fragmentation of different mass precursors, we implemented a stepped collision energy procedure with cumulative MS readout. AIF on the Exactive identified 45 of 48 proteins in an equimolar protein standard mixture and all of them when using a small database. The technique also identified proteins with more than 100-fold abundance differences in a high dynamic range standard. When applied to protein identification in gel slices, AIF unambiguously characterized an immunoprecipitated protein that was barely visible by Coomassie staining and quantified it relative to contaminating proteins. AIF on a benchtop orbitrap instrument is therefore an attractive technology for a wide range of proteomics analyses.
ATM and p53 Regulate FOXM1 Expression via E2F in Breast Cancer Epirubicin Treatment and Resistance

In this report, we investigated the role and regulation of forkhead box M1 (FOXM1) in breast cancer and epirubicin resistance. We generated epirubicin-resistant MCF-7 breast carcinoma (MCF-7-EPIR) cells and found FOXM1 protein levels to be higher in MCF-7-EPIR than in MCF-7 cells and that FOXM1 expression is downregulated by epirubicin in MCF-7 but not in MCF-7-EPIR cells. We also established that there is a loss of p53 function in MCF-7-EPIR cells and that epirubicin represses FOXM1 expression at transcription and gene promoter levels through activation of p53 and repression of E2F activity in MCF-7 cells. Using p53−/− mouse embryo fibroblasts, we showed that p53 is important for epirubicin sensitivity. Moreover, transient promoter transfection assays showed that epirubicin and its cellular effectors p53 and E2F1 modulate FOXM1 transcription through an E2F-binding site located within the proximal promoter region. Chromatin immunoprecipitation analysis also revealed that epirubicin treatment increases pRB (retinoblastoma protein) and decreases E2F1 recruitment to the FOXM1 promoter region containing the E2F site. We also found ataxia-telangiectasia mutated (ATM) protein and mRNA to be overexpressed in the resistant MCF-7-EPIR cells compared with MCF-7 cells and that epirubicin could activate ATM to promote E2F activity and FOXM1 expression. Furthermore, inhibition of ATM in U2OS cells with caffeine or depletion of ATM in MCF-7-EPIR with short interfering RNAs can resensitize these resistant cells to epirubicin, resulting in downregulation of E2F1 and FOXM1 expression and cell death. In summary, our data show that ATM and p53 coordinately regulate FOXM1 via E2F to modulate epirubicin response and resistance in breast cancer. Mol Cancer Ther; 10(6); 1046–58. ©2011 AACR.
HYBRED: An OCR Document Representation for Classification Tasks

The classification of digital documents is a complex task in a document analysis flow. The amount of documents resulting from the OCR retro-conversion (optical character recognition) makes the classification task harder. In the literature, different features are used to improve the classification quality. In this paper, we evaluate various features on OCRed and non OCRed documents. Thanks to this evaluation, we propose the HYBRED (HYBrid REpresentation of Documents) approach which combines different features in a single relevant representation. The experiments conducted on real data show the interest of this approach.
Measurement of Phase Difference for Micromachined Gyros Driven by Rotating Aircraft

This paper presents an approach for realizing a phase difference measurement of a new gyro. A silicon micromachined gyro was mounted on rotating aircraft for aircraft attitude control. Aircraft spin drives the silicon pendulum of a gyro rotating at a high speed so that it can sense the transverse angular velocity of the rotating aircraft based on the gyroscopic precession principle when the aircraft has transverse rotation. In applications of the rotating aircraft single channel control system, such as damping in the attitude stabilization loop, the gyro signal must be kept in sync with the control signal. Therefore, the phase difference between both signals needs to be measured accurately. Considering that phase difference is mainly produced by both the micromachined part and the signal conditioning circuit, a mathematical model has been established and analyzed to determine the gyro's phase frequency characteristics. On the basis of theoretical analysis, a dynamic simulation has been done for a case where the spin frequency is 15 Hz. Experimental results with the proposed measurement method applied to a silicon micromachined gyro driven by a rotating aircraft demonstrate that it is effective in practical applications. Measured curve and numerical analysis of phase frequency characteristic are in accordance, and the error between measurement and simulation is only 5.3%.
Benzodiazepine use in older adults enrolled in a health maintenance organization.

OBJECTIVES The authors examined patterns of benzodiazepine use in older adults. Specifically, they describe prevalence and incidence of benzodiazepine use during the index year, describe persistence and intensity of benzodiazepine use over a 4-year period; and examine factors associated with benzodiazepine use in the upcoming year. METHODS Authors performed a secondary analysis of data collected as part of a health promotion intervention trial conducted from 1986 to 1992 in older health maintenance organization enrollees (N=1,505). Benzodiazepine use was ascertained from computerized pharmacy records. Demographic characteristics, health status, and health behaviors were ascertained from mailed questionnaires. RESULTS During the index year, the prevalence and incidence of benzodiazepine use was 12.3% and 6.6%, respectively. Of those using during the index year, 16% of new users and 63% of previous users continued to use for the following 3 years. The factors significantly associated with benzodiazepine use in the following year were female gender, high school education, higher chronic disease score, higher levels of self-reported pain and stress, low-to-normal body mass index (BMI), and self-reported nervous disorder. CONCLUSIONS New users had low intensity of use and a low probability of continuing use over the following 3 years. A very small percentage of this sample had evidence of daily use for 4 years. Of concern, benzodiazepines were used by the segment of the sample that were at greatest risk for hip fractures (women with normal/low BMI). Clinicians should assess the need for continued benzodiazepine use at regular intervals.
Salmonella enteritidis gastroenteritis transmitted by intact chicken eggs.

OBJECTIVE To determine the source and to describe the clinical importance of a large outbreak of Salmonella enteritidis gastroenteritis in Tennessee, which is outside the geographic focus of the S. enteritidis pandemic. DESIGN A case-control study and tracing of the source eggs. SETTING A Tennessee community and a large layer farm in Indiana. PATIENTS Case patients ate at the implicated restaurant and subsequently developed S. enteritidis gastroenteritis; controls ate with the case patients, but did not develop gastroenteritis. MEASUREMENTS Eighty-one case patients were identified; 73 (90%) had eaten egg-containing sauces at a local restaurant on a given evening. The eggs were traced to their farm of origin in Indiana. The farm was inspected 5 weeks after the outbreak. MAIN RESULTS Of 24 patients with culture-proved cases, 11 were hospitalized. Hollandaise and bernaise sauces prepared with intact, extra-large, grade-A eggs were strongly associated with illness (P less than 0.001). Salmonella enteritidis was isolated from specimens collected from chickens and the farm. Antimicrobial susceptibility patterns, phage typing, and plasmid profiles of isolates from the farm and from patients were indistinguishable. CONCLUSIONS Salmonella enteritidis infection is a large and growing public health problem that is spreading beyond the northeastern United States. This study shows a direct link between infected poultry flocks and an outbreak of human illness.
Micromagnetic Simulation on Ground State Domain Structures of Barium Hexaferrite (BaFe12O19)

We have systematically investigated the domain structures of Barium Hexaferrite (BaFe12O19) by means of a micromagnetic simulation under zero external magnetic field. A hexagonal-shaped and cylindrical-shaped models are used in this simulation with respect to the diameter variation from 50 nm to 600 nm. A transition domain structure is found from a single-domain (SD) to multi-domain (MD) at a certain diameter. The hexagonal-shaped occurs in diameter 430 nm and cylindrical-shaped in diameter 410 nm. Interestingly, the domain wall of MD structure exhibits a Bloch-wall type. The domain wall width is determined by full width half maximum (FWHM) method from the transverse magnetization component data. The domain wall width from simulation showed close to Kittel’s formula