gebhart/patrepeval huggingface dataset:
Complete nucleotide sequence, genome organization, and biological properties of human immunodeficiency virus type 1 in vivo: evidence for limited defectiveness and complementation (1992)

Previous studies of the genetic and biologic characteristics of human immunodeficiency virus type 1 (HIV-1) have by necessity used tissue culture-derived virus. We recently reported the molecular cloning of four full-length HIV-1 genomes directly from uncultured human brain tissue (Y. Li, J. C. Kappes, J. A. Conway, R. W. Price, G. M. Shaw, and B. H. Hahn, J. Virol. 65:3973-3985, 1991). In this report, we describe the biologic properties of these four clones and the complete nucleotide sequences and genome organization of two of them. Clones HIV-1YU-2 and HIV-1YU-10 were 9,174 and 9,176 nucleotides in length, differed by 0.26% in nucleotide sequence, and except for a frameshift mutation in the pol gene in HIV-1YU-10, contained open reading frames corresponding to 5'-gag-pol-vif-vpr-tat-rev-vpu-env-nef-3' flanked by long terminal repeats. HIV-1YU-2 was fully replication competent, while HIV-1YU-10 and two other clones, HIV-1YU-21 and HIV-1YU-32, were defective. All three defective clones, however, when transfected into Cos-1 cells in any pairwise combination, yielded virions that were replication competent and transmissible by cell-free passage. The cellular host range of HIV-1YU-2 was strictly limited to primary T lymphocytes and monocyte-macrophages, a property conferred by its external envelope glycoprotein. Phylogenetic analyses of HIV-1YU-2 gene sequences revealed this virus to be a member of the North American/European HIV-1 subgroup, with specific similarity to other monocyte-tropic viruses in its V3 envelope amino acid sequence. These results indicate that HIV-1 infection of brain is characterized by the persistence of mixtures of fully competent, minimally defective, and more substantially altered viral forms and that complementation among them is readily attainable. In addition, the limited degree of genotypic heterogeneity observed among HIV-1YU and other brain-derived viruses and their preferential tropism for monocyte-macrophages suggest that viral replication within the central nervous system may differ from that within the peripheral lymphoid compartment in significant and clinically important ways. The availability of genetically and biologically well characterized HIV-1 clones from uncultured human tissue should facilitate future studies of virus-cell interactions relevant to viral pathogenesis and drug and vaccine development.
Supplementary Information Figure S1 from Dissecting Therapeutic Resistance to ERK Inhibition (2023)

&lt;p&gt;Sequencing of HCT116 resistant (HCT116R) cell lines&lt;/p&gt;
Research on Optimization of Vehicle Driving Based on Energy-saving and Low-carbon (2013)

Optimization of vehicle driving can reduce energy consumption and carbon emission. According to differences of vehicle braking mode, two driving situations are proposed. In this context, vehicle energy-consumption models based on energy consumption minimization are built and the soft such as MATLAB is employed to solve the models. By calculating, minimal energy-consumption value and related variable values on different driving distances are got, which contribute to guiding drivers taking energy-consumption driving behaviors. Finally conclusions are drawn by comparing and analyzing results of optimization under two situations.
[Potentiation of the antitumoral effect of electrochemotherapy by immunotherapy with allogeneic cells producing interleukin 2]. (1992)

Electrochemotherapy (ECT) is a new antitumour treatment which consists of delivering electric pulses to the tumour a few minutes after an intravenous injection of bleomycin. The antitumour efficacy of ECT is increased by local injections of interleukin 2 (IL2) in the oedema which appears at the site of the treated tumours. We have shown that tumour cells inoculated in syngeneic mice are rejected if IL2 secreting allo- or xenogeneic cells are co-injected with tumour cells. We report here the large increase of ECT therapeutical efficacy when allogeneic cells secreting IL2 are injected into the peri-tumoural oedema.
Implementation of a model based fault detection and diagnosis for actuation faults of the Space Shuttle main engine (1992)

In a previous study, Guo, Merrill and Duyar, 1990, reported a conceptual development of a fault detection and diagnosis system for actuation faults of the space shuttle main engine. This study, which is a continuation of the previous work, implements the developed fault detection and diagnosis scheme for the real time actuation fault diagnosis of the space shuttle main engine. The scheme will be used as an integral part of an intelligent control system demonstration experiment at NASA Lewis. The diagnosis system utilizes a model based method with real time identification and hypothesis testing for actuation, sensor, and performance degradation faults.
ChemInform Abstract: SYNTHESIS OF 3‐ACYLPYRIDINES UTILIZING A FRIEDEL‐CRAFTS REACTION (1983)

Abstract Die aus (I) zugänglichen l ,4‐Dihydropyridine (IV) werden in 3‐Stellung nach Friedel‐Crafts zu (VI) acyliert und dann mit Schwefel in Naphthalin zu den 3‐Acyl‐pyridinen (VII) dehydriert.
Interleukin-2 (2020)

This chapter discusses the available information regarding the structure, molecular biology, and biology of interleukin-2 (IL-2) and the IL-2-receptor. It also discusses the various pharmacological and toxicological effects associated with the in vitro and in vivo use of IL-2. The primary structure of IL-2 has been deduced in seven mammalian species following the cloning of human, gibbon ape, murine, rat, bovine, ovine, and porcine IL-2 cDNAs. The low affinity IL-2 receptor (IL-2Roc, Tac antigen, P-55, CD25) and the intermediate-affinity receptor can bind IL-2 either separately or together following their noncovalent association at the cell surface to form the high-affinity IL-2 receptor complex. Several parameters relating to the production of IL-2, including type and concentration of mitogenic agents, stimulation with mitogen aloneversus mitogen plus phorbol myristate acetate, and serum concentration necessary to support lymphocyte proliferation, have been examined to establish optimum conditions for IL-2 production by T cells in various animal species.
A New Generation of SnO2 gas sensor for agro-industrial applications (2001)

International audience
trans -Sodium Crocetinate and Diffusion Enhancement (2006)

trans-Sodium crocetinate (TSC) increases the diffusion coefficient of glucose through water by about 25-30%. This is the same percentage increase that TSC causes in the diffusivity of oxygen through water. TSC is also found to induce order in the surrounding water structure through increased hydrogen bonding of the water molecules, and molecular simulations suggest that the increase in diffusivity occurs only in these ordered regions.
Multiplexed Cell Signaling Analysis of Human Breast Cancer Applications for Personalized Therapy (2008)

Phosphoprotein driven cellular signaling events represent most of the new molecular targets for cancer treatment. Application of reverse-phase protein microarray technology for the study of ongoing signaling activity within breast tumor specimens holds great potential for elucidating and profiling signaling activity in real-time for patient-tailored therapy. Analysis of laser capture microdissection primary human breast tumors and metastatic lesions reveals pathway specific profiles and a new way to classify cancer based on functional signaling portraits. Moreover, the data demonstrate the requirement of laser capture microdissection for analysis and reveal the metastasis-specific changes that occur within a new microenvironment. Analysis of biopsy material from clinical trials for targeted therapeutics demonstrates the feasibility and utility of comprehensive signal pathway activation profiling for molecular analysis.
SYNTHESIS OF 3D NANOGRAPHENE WITHIN MESOPOROUS GERMANIUM STRUCTURE (2020)

International audience
Network Analysis of Lung Transcriptomics Reveals a Distinct B-Cell Signature in Emphysema (2016)

Our study identifies enrichment in B cell-related genes in patients with COPD with emphysema that is absent in bronchiolitis. These observations contribute to a better understanding of COPD pathobiology and may open new therapeutic opportunities for patients with COPD.
A Metalloantibody That Irreversibly Binds a Protein Antigen (2007)

Antibody affinity is critically important in therapeutic applications, as well as steady state diagnostic assays. Picomolar affinity antibodies, approaching the association limit of protein-protein interactions, have been discovered for highly potent antigens, but even such high-affinity binders have off-rates sufficient to negate therapeutic efficacy. To cross this affinity threshold, antibodies that tether their targets in a manner other than reversible non-covalent interaction will be required. Here we report the design and construction of an antibody that forms an irreversible complex with a protein antigen in a metal-dependent reaction. The complex resists thermal and chemical denaturation, as well as attempts to remove the coordinating metal ion. Such irreversibly binding antibodies could facilitate the development of next generation "reactive antibody" therapeutics and diagnostics.
Integrated Modeling and Analysis of Automotive Embedded Control Systems with Real-Time Scheduling (2004)

&lt;div class="htmlview paragraph"&gt;As the complexity of automotive embedded software grows, it is desirable to bring as much automation into the development process as possible, as evidenced by efficient code generators from modeling tools such as Simulink. However, the current development process does not pay enough attention to non-functional issues such as real-time requirements. Modeling tools such as Simulink do not allow representation of the target platform, so it is not possible to analyze real-time behavior in the early design stage. The typical approach is to download the executable to the target micro-controller and measure to see if there are any missed deadlines. We describe a tool that can be used to model system-level software and hardware architectures and analyze system timing behavior at early design stages, and assess the impact of the target platform on control system performance.&lt;/div&gt;
Two-dimensional angular correlation study of delocalized positronium in alkali halides (1997)

The two-dimensional angular correlation of positron annihilation radiation (2D-ACAR) from KCl and KI single crystals at low temperatures has been measured. The intensities of the narrow peaks resulting from the Bloch modulation of the delocalized positronium (Ps) are studied. The intensities of the peaks except for those at the momenta corresponding to the (000) and (200) reciprocal-lattice vectors are very low for both KCl and KI. The experimental results for KCl are compared with the calculations made by Zhang and Song. Calculations with simpler approximations are also performed for both KCl and KI.
GIN: A Clustering Model for Capturing Dual Heterogeneity in Networked Data (2015)

Networked data often consists of interconnected multi-typed nodes and links. A common assumption behind such heterogeneity is the shared clustering structure. However, existing network clustering approaches over-simplify the heterogeneity by either treating nodes or links in a homogeneous fashion, resulting in massive loss of information. In addition, these studies are more or less restricted to specific network schemas or applications, losing generality. In this paper, we introduce a flexible model to explain the process of forming heterogeneous links based on shared clustering information of heterogeneous nodes. Specifically, we categorize the link generation process into binary and weighted cases and model them respectively. We show these two cases can be seamlessly integrated into a unified model. We propose to maximize a joint log-likelihood function to infer the model efficiently with Expectation Maximization (EM) algorithms. Experiments on real-world networked data sets demonstrate the effectiveness and flexibility of the proposed method in fully capturing the dual heterogeneity of both nodes and links.
Antitumor activity and suppression of AKT pathway activation by PDK1 inhibitor SNS-391. (2014)

e13560 Background: 3-Phosphatidylinositide-dependent kinase 1 (PDK1) interacts with its substrate kinases after binding phosphatidylinositol (PI). PDK1 also affects downstream targets in a PI-independent manner, causing activation of additional pathways. PDK1 activation of AKT involves both PI-dependent and independent mechanisms, making PDK1 a challenging target for AKT pathway inhibition. Here we describe a novel PDK1 inhibitor, SNS-391, that is highly effective at inhibiting AKT activity with broad anti-tumor activity. Methods: SNS-391 was evaluated in the prostate cancer PC-3 cell line (PTEN null) for inhibition of several signaling pathways and was tested in proliferation assays in over 50 tumor cell lines of prostate, lung, colon, breast, melanoma, and pancreatic origin. Tumor xenograft studies were conducted in prostate, gastric, lung, pancreatic, and colorectal cancer models. Tumor samples were analyzed for pathway inhibition and compound exposure to develop PK/PD relationships. Results: SNS-391 (biochemical kinase assay IC50: 1.8 nM ) showed strong suppression of both AKT-308 (EC50: 87 nM) and AKT-473 phosphorylation in PC-3 cells. PDK1 autophosphorylation was reduced >50%, and downstream AKT pathway inhibition was indicated by suppression of PRAS-40 and S6K phosphorylation. Inhibition of phosphorylation of PI independent substrates IKKβ and RSK2 was observed. SNS-391 caused G1/S arrest and apoptosis. Inhibition of proliferation was seen across tumor cell lines of prostate, lung, colon, breast, melanoma, and pancreatic origin with EC50 < 1 μM. Many cell lines with mutations in PTEN, p53, PI3K, Ras, or Raf were sensitive to SNS-391 treatment. SNS-391 showed strong tumor growth inhibition (TGI 66%-95%) in gastric, lung, pancreatic, and colorectal cancer xenograft models. In the prostate PC-3 xenograft model, SNS-391 (TGI 82%) activity was superior to PI3K inhibitor pictilisib (TGI 58%) and AKT inhibitor MK2206 (TGI 40%). Conclusions: PDK1 inhibitor SNS-391 inhibits both PI-dependent and independent AKT pathways and has broad potential for the treatment of diverse cancers.
Engineering the α-factor in quantum dot-in-a-well lasers (2004)

The linewidth enhancement factor in quantum dot (QD) in a quantum well (QW) lasers was observed to decrease from 2.5 to 1 as result of controlling the QD shape and the composition of the QW.
Extraction of polyphenols from grape seeds by high voltage electrical discharges and extracts concentration by membrane process (2011)

FILTECH 2011, Wiesbaden, Germany, March 22-24, 2011.
3D Optical Interconnect Distributed Crossbar Switching Architecture (2001)

We present the design and implementation of a scalable 3D Optical Interconnect Distributed Crossbar Switching (3DOCS) architecture with small footprint (&lt;70cm2) and high bandwidth (256Gbps). The motivation of 3DOCS, particularly for SMP systems, is discussed.
Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations (2019)

Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P &lt; 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
Size-Dependent Subnanometer Pd Cluster (Pd4, Pd6, and Pd17) Water Oxidation Electrocatalysis (2013)

Water oxidation is a key catalytic step for electrical fuel generation. Recently, significant progress has been made in synthesizing electrocatalytic materials with reduced overpotentials and increased turnover rates, both key parameters enabling commercial use in electrolysis or solar to fuels applications. The complexity of both the catalytic materials and the water oxidation reaction makes understanding the catalytic site critical to improving the process. Here we study water oxidation in alkaline conditions using size-selected clusters of Pd to probe the relationship between cluster size and the water oxidation reaction. We find that Pd4 shows no reaction, while Pd6 and Pd17 deposited clusters are among the most active (in terms of turnover rate per Pd atom) catalysts known. Theoretical calculations suggest that this striking difference may be a demonstration that bridging Pd-Pd sites (which are only present in three-dimensional clusters) are active for the oxygen evolution reaction in Pd6O6. The ability to experimentally synthesize size-specific clusters allows direct comparison to this theory. The support electrode for these investigations is ultrananocrystalline diamond (UNCD). This material is thin enough to be electrically conducting and is chemically/electrochemically very stable. Even under the harsh experimental conditions (basic, high potential) typically employed for water oxidation catalysts, UNCD demonstrates a very wide potential electrochemical working window and shows only minor evidence of reaction. The system (soft-landed Pd4, Pd6, or Pd17 clusters on a UNCD Si-coated electrode) shows stable electrochemical potentials over several cycles, and synchrotron studies of the electrodes show no evidence for evolution or dissolution of either the electrode material or the clusters.
Diagnosing and responding to violations in the positivity assumption (2010)

The assumption of positivity or experimental treatment assignment requires that observed treatment levels vary within confounder strata. This article discusses the positivity assumption in the context of assessing model and parameter-specific identifiability of causal effects. Positivity violations occur when certain subgroups in a sample rarely or never receive some treatments of interest. The resulting sparsity in the data may increase bias with or without an increase in variance and can threaten valid inference. The parametric bootstrap is presented as a tool to assess the severity of such threats and its utility as a diagnostic is explored using simulated and real data. Several approaches for improving the identifiability of parameters in the presence of positivity violations are reviewed. Potential responses to data sparsity include restriction of the covariate adjustment set, use of an alternative projection function to define the target parameter within a marginal structural working model, restriction of the sample, and modification of the target intervention. All of these approaches can be understood as trading off proximity to the initial target of inference for identifiability; we advocate approaching this tradeoff systematically.
Substrate Specificities and Intracellular Distributions of Three N-glycan Processing Enzymes Functioning at a Key Branch Point in the Insect N-Glycosylation Pathway (2012)

Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2) is a key branch point intermediate in the insect N-glycosylation pathway because it can be either trimmed by a processing β-N-acetylglucosaminidase (FDL) to produce paucimannosidic N-glycans or elongated by N-acetylglucosaminyltransferase II (GNT-II) to produce complex N-glycans. N-acetylglucosaminyltransferase I (GNT-I) contributes to branch point intermediate production and can potentially reverse the FDL trimming reaction. However, there has been no concerted effort to evaluate the relationships among these three enzymes in any single insect system. Hence, we extended our previous studies on Spodoptera frugiperda (Sf) FDL to include GNT-I and -II. Sf-GNT-I and -II cDNAs were isolated, the predicted protein sequences were analyzed, and both gene products were expressed and their acceptor substrate specificities and intracellular localizations were determined. Sf-GNT-I transferred N-acetylglucosamine to Man(5)GlcNAc(2), Man(3)GlcNAc(2), and GlcNAc(β1-2)Man(α1-6)[Man(α1-3)]ManGlcNAc(2), demonstrating its role in branch point intermediate production and its ability to reverse FDL trimming. Sf-GNT-II only transferred N-acetylglucosamine to Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2), demonstrating that it initiates complex N-glycan production, but cannot use Man(3)GlcNAc(2) to produce hybrid or complex structures. Fluorescently tagged Sf-GNT-I and -II co-localized with an endogenous Sf Golgi marker and Sf-FDL co-localized with Sf-GNT-I and -II, indicating that all three enzymes are Golgi resident proteins. Unexpectedly, fluorescently tagged Drosophila melanogaster FDL also co-localized with Sf-GNT-I and an endogenous Drosophila Golgi marker, indicating that it is a Golgi resident enzyme in insect cells. Thus, the substrate specificities and physical juxtapositioning of GNT-I, GNT-II, and FDL support the idea that these enzymes function at the N-glycan processing branch point and are major factors determining the net outcome of the insect cell N-glycosylation pathway.
Routine use of the transradial approach in primary percutaneous coronary intervention: procedural aspects and outcomes in 2209 patients treated in a single high-volume centre (2011)

Systematic use of the TRA in PPCI yields low access site crossover, high procedural success rates and excellent procedural performances. It can therefore represent the primary access site in the vast majority of STEMI patients.
Visual analytics for the big data era &#x2014; A comparative review of state-of-the-art commercial systems (2012)

Visual analytics (VA) system development started in academic research institutions where novel visualization techniques and open source toolkits were developed. Simultaneously, small software companies, sometimes spin-offs from academic research institutions, built solutions for specific application domains. In recent years we observed the following trend: some small VA companies grew exponentially; at the same time some big software vendors such as IBM and SAP started to acquire successful VA companies and integrated the acquired VA components into their existing frameworks. Generally the application domains of VA systems have broadened substantially. This phenomenon is driven by the generation of more and more data of high volume and complexity, which leads to an increasing demand for VA solutions from many application domains. In this paper we survey a selection of state-of-the-art commercial VA frameworks, complementary to an existing survey on open source VA tools. From the survey results we identify several improvement opportunities as future research directions.