gebhart/patrepeval huggingface dataset:
Data from PLK1 Phosphorylates PAX3-FOXO1, the Inhibition of Which Triggers Regression of Alveolar Rhabdomyosarcoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Pediatric tumors harbor very low numbers of somatic mutations and therefore offer few targets to improve therapeutic management with targeted drugs. In particular, outcomes remain dismal for patients with metastatic alveolar rhabdomyosarcoma (aRMS), where the chimeric transcription factor PAX3/7-FOXO1 has been implicated but problematic to target. In this report, we addressed this challenge by developing a two-armed screen for druggable upstream regulatory kinases in the PAX3/7-FOXO1 pathway. Screening libraries of kinome siRNA and small molecules, we defined PLK1 as an upstream-acting regulator. Mechanistically, PLK1 interacted with and phosphorylated PAX3-FOXO1 at the novel site S503, leading to protein stabilization. Notably, PLK1 inhibition led to elevated ubiquitination and rapid proteasomal degradation of the PAX3-FOXO1 chimeric oncoprotein. On this basis, we embarked on a preclinical validation of PLK1 as a target in a xenograft mouse model of aRMS, where the PLK1 inhibitor BI 2536 reduced PAX3-FOXO1–mediated gene expression and elicited tumor regression. Clinically, analysis of human aRMS tumor biopsies documented high PLK1 expression to offer prognostic significance for both event-free survival and overall survival. Taken together, these preclinical studies validate the PLK1–PAX3-FOXO1 axis as a rational target to treat aRMS. &lt;i&gt;Cancer Res; 75(1); 98–110. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Gammatella: Visualizing Program-Execution Data for Deployed Software (2004)

Software systems are often released with missing functionality, errors, or incompatibilities that may result in failures in the field, inferior performances, or, more generally, user dissatisfaction. In previous work, some of the authors presented the gamma approach, whose goal is to improve software quality by augmenting software-engineering tasks with dynamic information collected from deployed software. The gamma approach enables analyses that (1) rely on actual field data instead of synthetic in-house data and (2) leverage the vast and heterogeneous resources of an entire user community instead of limited, and often homogeneous, in-house resources. When monitoring a large number of deployed instances of a software product, however, a significant amount of data is collected. Such raw data are useless in the absence of suitable datamining and visualization techniques that support exploration and understanding of the data. In this paper, we present a new technique for collecting, storing, and visualizing program-execution data gathered from deployed instances of a software product. We also present a prototype toolset, Gammatella, that implements the technique. Finally, we show how the visualization capabilities of Gammatella facilitate effective investigation of several kinds of execution-related information in an interactive fashion, and discuss our initial experience with a semi-public display of Gammatella.
Comparison of SVD-MIMO with Antenna-Selection-BLAST Using Linear Receivers under Channel Estimation Errors for ITU Channels (2011)

In wireless communication systems, the spatial multiplexing mode of Multiple Input Multiple Output (MIMO) is known to provide significant gain in spectral efficiency in the high Signal to Noise Ratio (SNR) region. Between the two methods, Singular Value Decomposition (SVD) and Bell labs Layered Space Time (BLAST), for implementing spatial multiplexing, the SVD scheme provides much higher spectral efficiency but it is much more complex to implement than the BLAST scheme. The aim of this work is to present an algorithm for antenna selection, which works together with BLAST method and compare the performance with that of SVD method. The comparison is done considering linear receiver architecture, and that the receiver has noisy channel estimates. The channel model used for performance evaluation is as per International Telecommunication Union (ITU)-specifications. It is shown in this work that, the proposed algorithm used with BLAST is very simple to implement and performs at par with SVD.
Leaching behavior of prototypical corium samples: A step to understand the interactions between the fuel debris and water at the Fukushima Daiichi reactors (2020)

On 11 March 2011, the Great East Japan Earthquake occurred and caused a severe nuclear accident at the Fukushima Daiichi Nuclear Power Station (1F). A policy for corium debris retrieval will be decided in the near future. To this end, debris management after removal from reactors must be optimized. From the viewpoint of cost and waiting for definitive solutions, interim or long-term underwater storage is one of the considered options after debris removal. Leaching data on the long term behavior of debris in water are therefore needed before debris removal. In addition, it is important to understand potential differences in leaching behaviors between debris and Spent Fuel (SF) to get comparative elements. For these reasons, simulated in-vessel and ex-vessel corium debris, fabricated in the Colima experimental facility set up in the PLINIUS platform at CEA Cadarache, were selected and leaching experiments were carried out under oxidizing conditions. In parallel, geochemical modeling was performed to better understand the experimental concentrations, pH evolutions and secondary phase’s formation. Finally, the Fractional Release Rates of the (U, Zr)O2 matrix for the two kinds of samples (in-vessel and ex-vessel) were found to be close to or one order of magnitude lower than that of SF under oxidizing conditions (from 10−6 to 10−7 per day) but the release processes are different. Indeed, the Fraction of Inventory in Aqueous Phase of Mo, Ba, Sr, Rh, La, Nd, Ce and Y tended to be higher than that of uranium and zirconium in this study whatever the element considered. The release of simulating PFs, including low volatile element like trivalent rare earths, does not appear to be fully controlled by that of the (U, Zr)O2 matrix from a macroscopic and average point of view. The FPs could be partially located outside the (U, Zr)O2 solid solution as a function of the corium history (quenching rate and thermal history, chemical interactions…). The location of inventories and their chemical forms are not very well known moreover uncertainties related to heterogeneity are important and may also impact the calculation of the global released fractions over time. For the ex-vessel sample, releases into the solution of the main concrete elements (Si, Ca, Mg) seem well correlated and dissociated from the behavior of the (U, Zr)O2 phase. Further studies are needed especially on real or prototypical corium approaching the conditions of the Fukushima accident. The study of simpler and model systems could also provide information on the reactivity of the (U, Zr)O2 matrix.
Influencing Mechanism of Inherent Aluminum Oxide Film on Coach Peel Performance of Baked Al-Steel RSW (2020)

A traditional resistance spot weld process in combination with Multi-Ring Domed welding electrodes was applied to join AA5754-O to low carbon steel. The coach peel performance of welds was compared between the as-welded (unbaked) and post-paint bake condition (baked). The unbaked joints exhibited button pullout fracture mode, whereas the baked joints were severely weakened and demonstrated an interfacial fracture mode which is attributed to the baking process inducing thermal stress at the dissimilar material interface which cracked the semi-continuous oxide film inclusions at the edge of the solidified aluminum nugget to form a more continuous defect layer across the diameter of the aluminum nugget. These defects act as low energy crack paths under applied loads and reduce joint strength by promoting undesirable interfacial fracture in baked welds.
In Vitro Studies on the Trafficking of Dendritic CellsThrough Endothelial Cells and Extra‐Cellular Matrix (2000)

Dendritic cells (DC) are antigen presenting cells (APC) with the unique ability to initiate an immune response. Immature DC are localized in peripheral tissues where they exert a sentinel function for incoming antigens (Ag). After Ag capture and exposure to inflammatory stimuli DC undergo maturation and migrate to regional lymph nodes where the presentation of antigenic peptides to T lymphocytes takes place. Thus their correct functioning as APC involves localization in tissues and trafficking via the lymph or blood to lymphoid organs. In the present study we have investigated the ability of DC to interact in vitro with human vascular endothelial cells (EC) and extracellular matrix (ECM). DC are differentiated from monocytes by in vitro exposure to GM-CSF and IL-13 for 7 days. In adhesion assays a considerable proportion of DC binds to resting EC monolayers and this adhesion is inhibited by anti-CD11a and CD11b, but not anti-CD11c mAbs. Binding to a natural ECM, derived from cultured EC involves VLA-4 and VLA-5 integrins. In a transmigration assay, 10% of input cells are able to cross the EC monolayer in the absence of exogenous stimuli. The amount of DC transmigrated through a monolayer of EC was increased of 2-3 fold by C-C chemokines RANTES, MIP1alpha, and MIP-1beta. Most importantly, in view of the trafficking pattern of these cells, a significant proportion of DC can migrate in a reverse transmigration assay, i.e. across the endothelial basement membrane and subsequently, across endothelial cells. Upon exposure to immune or inflammatory signals peripheral DC undergo maturation and migration to lymphoid organs. Functional maturation is associated with loss of responsiveness to chemokines present at sites of inflammation (e.g. MIP1alpha, MIP1beta and RANTES) and acquisition of a receptor repertoire which renders these cells responsive to signals which guide their localization in lymphoid organs (e.g. MIP3beta). A better understanding of the molecular basis of DC trafficking may provide molecular and conceptual tools to direct and modulate DC localization as a strategy to upregulate and orient specific immunity.
A Novel Superoxide-producing NAD(P)H Oxidase in Kidney (2001)

During phagocytosis, gp91(phox), the catalytic subunit of the phagocyte NADPH oxidase, becomes activated to produce superoxide, a precursor of microbicidal oxidants. Currently increasing evidence suggests that nonphagocytic cells contain similar superoxide-producing oxidases, which are proposed to play crucial roles in various events such as cell proliferation and oxygen sensing for erythropoiesis. Here we describe the cloning of human cDNA that encodes a novel NAD(P)H oxidase, designated NOX4. The NOX4 protein of 578 amino acids exhibits 39% identity to gp91(phox) with special conservation in membrane-spanning regions and binding sites for heme, FAD, and NAD(P)H, indicative of its function as a superoxide-producing NAD(P)H oxidase. The membrane fraction of kidney-derived human embryonic kidney (HEK) 293 cells, expressing NOX4, exhibits NADH- and NADPH-dependent superoxide-producing activities, both of which are inhibited by diphenylene iodonium, an agent known to block oxygen sensing, and decreased in cells expressing antisense NOX4 mRNA. The human NOX4 gene, comprising 18 exons, is located on chromosome 11q14.2-q21, and its expression is almost exclusively restricted to adult and fetal kidneys. In human renal cortex, high amounts of the NOX4 protein are present in distal tubular cells, which reside near erythropoietin-producing cells. In addition, overexpression of NOX4 in cultured cells leads to increased superoxide production and decreased rate of growth. The present findings thus suggest that the novel NAD(P)H oxidase NOX4 may serve as an oxygen sensor and/or a regulator of cell growth in kidney.
Correct-schema-guided synthesis of steadfast programs (2002)

It can be argued that for (semi-)automated software development, program schemas are indispensable, since they capture not only structured program design principles but also domain knowledge, both of which are of crucial importance for hierarchical program synthesis. Most researchers represent schemas purely syntactically (as higher-order expressions). This means that the knowledge captured by a schema is not formalised. We take a semantic approach and show that a schema can be formalised as an open (first-order) logical theory that contains an open logic program. By using a special kind of correctness for open programs, called steadfastness, we can define and reason about the correctness of schemas. We also show how to use correct schemas to synthesise steadfast programs.
Design and implementation of secure Web-based LDAP management system (2002)

As the Internet grows quickly, more and more services are available. How to provide high quality, convenient, and personalized services to users are the important issues for Internet service providers to keep customers connected to their Web sites. The directory is an important part of Internet technology used to support such needs. It exists in a multitude of applications ranging from operating systems, asset management systems, security systems, etc. Furthermore, The Gartner Group, a market research firm, predicts that 40% to 90% of new software and hardware will be directory related products, at end of the period 2001 to 2003. In the directory industry, we can divide products into 3 fields: directory server, management system, and directory application. The management system is one of the important parts of directory services. The directory management system is focused on non-Web-based systems. While directory services are applied on Internet services, it is necessary to provide a Web-based management interface. This interface will provide the advantages of ubiquity, cross platform, thin client, and reduced TCO (total cost of ownership). We proposed and implemented a Web-based lightweight directory access protocol (LDAP) management architecture to provide such benefits and to manage multiple LDAP servers. We used the standard protocol and popular software of Internet technology usually used to build the system, so the system is easy to be ported and minimized the changes of the original system. In addition, we also considered the security factors while designing and constructing the system.
Bridging Python to Silicon: The SODA Toolchain (2022)

Systems performing scientific computing, data analysis, and machine learning tasks have a growing demand for application-specific accelerators that can provide high computational performance while meeting strict size and power requirements. However, the algorithms and applications that need to be accelerated are evolving at a rate that is incompatible with manual design processes based on hardware description languages. Agile hardware design tools based on compiler techniques can help by quickly producing an application-specific integrated circuit (ASIC) accelerator starting from a high-level algorithmic description. We present the software-defined accelerator (SODA) synthesizer, a modular and open-source hardware compiler that provides automated end-to-end synthesis from high-level software frameworks to ASIC implementation, relying on multilevel representations to progressively lower and optimize the input code. Our approach does not require the application developer to write any register-transfer level code, and it is able to reach up to 364 giga floating point operations per second (GFLOPS)/W efficiency (32-bit precision) on typical convolutional neural network operators.
Forward Backward Syndrome Computation: A Reduced Complexity CRC Code Decoder (2023)

This letter proposes a simplified method for correcting a single-bit error event in a message protected by a CRC code thanks to a new decoding method called Forward-Backward Syndrome Computation. The two key ideas of the letter are to show that: 1) syndrome computation can be performed in any direction (Forward and Backward), 2) consequently, it is possible to create a partition of the received message in a set of disjoint syndromes, thus allowing a direct identification of the error position. Evaluation in terms of number of 2-input binary logic functions shows a complexity reduction by a factor of up to 3 compared to conventional methods.
The junctional adhesion molecule JAM-C regulates polarized transendothelial migration of neutrophils in vivo (2011)

The migration of neutrophils into inflamed tissues is a fundamental component of innate immunity. A decisive step in this process is the polarized migration of blood neutrophils through endothelial cells (ECs) lining the venular lumen (transendothelial migration (TEM)) in a luminal-to-abluminal direction. By real-time confocal imaging, we found that neutrophils had disrupted polarized TEM ('hesitant' and 'reverse') in vivo. We noted these events in inflammation after ischemia-reperfusion injury, characterized by lower expression of junctional adhesion molecule C (JAM-C) at EC junctions, and they were enhanced by blockade or genetic deletion of JAM-C in ECs. Our results identify JAM-C as a key regulator of polarized neutrophil TEM in vivo and suggest that reverse TEM of neutrophils can contribute to the dissemination of systemic inflammation.
Molecular genetic survey of 16 kindreds with hereditary antithrombin III deficiency (1987)

Molecular genetic techniques were utilized to examine antithrombin III (ATIII) gene status in 16 independently ascertained kindreds with hereditary ATIII deficiency. In one of these families antithrombin III deficiency is caused by hemizygosity of the ATIII locus. In the remaining 15 kindreds, two copies of the ATIII gene are present and appear to be grossly normal at the level of whole genome Southern blotting, suggesting that small deletions, insertions or limited nucleotide substitution(s) in the antithrombin III gene, or “trans- acting” defects at other loci involved in the processing, modification, and secretion of biologically active ATIII are responsible for the observed anticoagulant disorders.
Field test of the hybrid photodetector R9792U-40 on the MAGIC camera (2011)

The hybrid photodetector (HPD) R9792U-40 has very high peak quantum efficiency (> 50% at 500 nm), excellent charge resolution and very low after-pulsing probability (500 times less than that of currently used photomulti- pliers (PMTs)). These features will improve the sensitivity, the energy resolution and the energy threshold of the MAGIC telescope. On the other hand, its high photocathode voltage (−8 to −6 kV), relatively short photocathode lifetime, and relatively large temperature dependence of the gain need to be taken care of. In February 2010, 6 HPDs were installed in a corner of the MAGIC-II camera for a field test. Here we report the results of the field test and our future plans.
Making competitive grants programs of the national agricultural research systems work : learning from the Brazilian experience (1998)

In the last few years there has been increasing interest in establishing competitive grants programs in agricultural research in developing countries. In donor funded projects, these programs are often seen as a complement to the ongoing research programs, undertaken through regular long term research funding, but which often pose the risk of being viewed as a panacea, and a substitute for regular long term research funding. Their design and implementation needs to reflect understanding of a complexity of factors needed to make them work effectively. The design of Brazil's competitive grants program in agriculture is drawing extensively on international and domestic experience. This paper briefly reviews the recent Brazilian experience, and offers its full operational manual for review, and possible wider adaptation as appropriate in other countries. The competitive system established and implemented by EMBRAPA (Empresa Brasileira de Pesquisa Agropecuaria) actively seeks to increase competitiveness, and partnerships among participating institutions. Access to grant funding by the entire national agricultural research system, through the process of a competitive system, will enhance the quality of project proposals, and support the improvement of research results and better linkages of research to felt demands. Through partnerships, the Brazil Agricultural Technology Development Project expects to capitalize on the complementarity of Brazilian researchers with those at the global level, and their corresponding institutions. At the national level, a much better and efficient use of available infrastructure (labs, etc.) should be attained.
Removal of volatile organic compounds from soil (2010)

Pollution by petroleum products is a source of volatile organic compounds in soil. Therefore, laboratory column venting experiments were completed in order to investigate the removal of a pure compound (toluene) and a mixture of two (toluene and n-heptane) and five (toluene, n-heptane, ethylbenzene, m-xylene and p-xylene) compounds. The choice of the compounds, as well as their proportion in the mixture, was made on the basis of the real fuel composition. The objective of this study is a comparison between the experimental volatile organic compounds removal results and the computational fluid dynamics (CFDs) analysis. The proposed model for the contaminants transport describes the removal of organic compounds from soil, the contaminants being distributed among four phases: vapor, nonaqueous liquid phase, aqueous and "solid"; the local phase's equilibrium and the ideal behavior of all four phases was found to be accurate enough to describe the interphase mass transfer. The process developed in the lab consists of a heater/boiler that pumps and circulates hot oil through a pipeline that is enclosed in a larger-diameter pipe. This extraction pipe is vertically installed within the contaminated soil up to a certain depth and is welded at the bottom and capped at the top. The number of heat source pipes and extraction wells depends on the type of soil, the type of pollutants, and the moisture content of the soil and the size of the area to be cleaned. The heat source heats the soil, which is transported in the interior part of the soil by means of conduction and convection. This heating of the soil results in vaporization of the gases, which are then driven out of the soil by the extraction well. The extraction well consists of the blower, which sucks the vaporized gases out of the system. Our previous studies have removed higher boiling compounds, such as naphthalene, etc., to a non-detectable level. Thus, the current technology is very promising for removing most of the chemical compounds; and can also remove these high boiling compounds from the saturated zone. The reasonable www.