gebhart/patrepeval huggingface dataset:
Monomeric Class I Molecules Mediate TCR/CD3ε/CD8 Interaction on the Surface of T Cells (2001)

Both CD8 and the TCR bind to MHC class I molecules during physiologic T cell activation. It has been shown that for optimal T cell activation to occur, CD8 must be able to bind the same class I molecule that is bound by the TCR. However, no direct evidence for the class I-dependent association of CD8 and the TCR has been demonstrated. Using fluorescence resonance energy transfer, we show directly that a single class I molecule causes TCR/CD8 interaction by serving as a docking molecule for both CD8 and the TCR. Furthermore, we show that CD3epsilon is brought into close proximity with CD8 upon TCR/CD8 association. These interactions are not dependent on the phosphorylation events characteristic of T cell activation. Thus, MHC class I molecules, by binding to both CD8 and the TCR, mediate the reorganization of T cell membrane components to promote cellular activation.
Synthesis of 4,6-disubstituted- and 4,5,6-trisubstituted-2-phenyl-pyrimidines and their affinity towards A1 adenosine receptors. (1997)

Synthesis and assay of title compounds are reported. The results can support our hypothesis about the possibility that molecules characterized by great flexibility, as the title 2-phenyl-4,5,6-triaminopyrimidines, can better interact with the receptor sites compared with rigid molecules as 2,6,9-trisubstituted 8-azaadenines. Relatively low activity shown by pyrimidine derivatives demonstrated the importance of the bicyclic aromatic system in 8-azaadenines and adenines to give a favourable interaction between a hexogenous molecule and the A1 adenosine receptors.
A MCP1 fusokine with CCR2-specific tumoricidal activity (2011)

Our data demonstrate that GMME1 is a fusokine with a potent, CCR2 receptor-mediated pro-apoptotic effect on tumor cells and could be exploited as a novel biological therapy for CCR2+ malignancies including lymphoid and central nervous system malignancies.
Simulated distillation of petroleum and its products by gas and supercritical fluid chromatography: A review (1994)

Abstract Information about the boiling point distribution of petroleum and its products is obtained either by actual distillation, or by analyses designed to simulate the distillation process. These analytical techniques are called simulated distillations. Simulated distillations are most often performed by gas or supercritical fluid chromatography. This paper reviews the use of gas and supercritical fluid chromatography for simulated distillation, and the development of element‐specific detection coupled with these analyses.
An ATP-Binding Cassette Transporter and Two rRNA Methyltransferases Are Involved in Resistance to Avilamycin in the Producer Organism Streptomyces viridochromogenes Tu57 (2001)

Three different resistance factors from the avilamycin biosynthetic gene cluster of Streptomyces viridochromogenes Tü57, which confer avilamycin resistance when expressed in Streptomyces lividans TK66, were isolated. Analysis of the deduced amino acid sequences showed that AviABC1 is similar to a large family of ATP-binding transporter proteins and that AviABC2 resembles hydrophobic transmembrane proteins known to act jointly with the ATP-binding proteins. The deduced amino acid sequence of aviRb showed similarity to those of other rRNA methyltransferases, and AviRa did not resemble any protein in the databases. Independent expression in S. lividans TK66 of aviABC1 plus aviABC2, aviRa, or aviRb conferred different levels of resistance to avilamycin: 5, 10, or 250 microg/ml, respectively. When either aviRa plus aviRb or aviRa plus aviRb plus aviABC1 plus aviABC2 was coexpressed in S. lividans TK66, avilamycin resistance levels reached more than 250 microg/ml. Avilamycin A inhibited poly(U)-directed polyphenylalanine synthesis in an in vitro system using ribosomes of S. lividans TK66(pUWL201) (GWO), S. lividans TK66(pUWL201-Ra) (GWRa), or S. lividans TK66(pUWL201-Rb) (GWRb), whereas ribosomes of S. lividans TK66 containing pUWL201-Ra+Rb (GWRaRb) were highly resistant. aviRa and aviRb were expressed in Escherichia coli, and both enzymes were purified as fusion proteins to near homogeneity. Both enzymes showed rRNA methyltransferase activity using a mixture of 16S and 23S rRNAs from E. coli as the substrate. Coincubation experiments revealed that the enzymes methylate different positions of rRNA.
Genetically modified filamentous phage as bactericidal agents: a pilot study (2003)

This feasibility study provides a possible strategy for the use of genetically engineered phage as bactericidal agents by optimizing the advantages and minimizing potential risks such as release of pyrogenic cell wall components.
Treatment of Patients With Metastatic Cancer Using a Major Histocompatibility Complex Class II–Restricted T-Cell Receptor Targeting the Cancer Germline Antigen MAGE-A3 (2017)

Purpose Adoptive transfer of genetically modified T cells is being explored as a treatment for patients with metastatic cancer. Most current strategies use genes that encode major histocompatibility complex (MHC) class I-restricted T-cell receptors (TCRs) or chimeric antigen receptors to genetically modify CD8<sup>+</sup> T cells or bulk T cells for treatment. Here, we evaluated the safety and efficacy of an adoptive CD4<sup>+</sup> T-cell therapy using an MHC class II-restricted, HLA-DPB1*0401-restricted TCR that recognized the cancer germline antigen, MAGE-A3 (melanoma-associated antigen-A3). Patients and Methods Patients received a lymphodepleting preparative regimen, followed by adoptive transfer of purified CD4<sup>+</sup> T cells, retrovirally transduced with MAGE-A3 TCR plus systemic high-dose IL-2. A cell dose escalation was conducted, starting at 10<sup>7</sup> total cells and escalating at half-log increments to approximately 10<sup>11</sup> cells. Nine patients were treated at the highest dose level (0.78 to 1.23 × 10<sup>11</sup> cells). Results Seventeen patients were treated. During the cell dose-escalation phase, an objective complete response was observed in a patient with metastatic cervical cancer who received 2.7 × 10<sup>9</sup> cells (ongoing at ≥ 29 months). Among nine patients who were treated at the highest dose level, objective partial responses were observed in a patient with esophageal cancer (duration, 4 months), a patient with urothelial cancer (ongoing at ≥ 19 months), and a patient with osteosarcoma (duration, 4 months). Most patients experienced transient fevers and the expected hematologic toxicities from lymphodepletion pretreatment. Two patients experienced transient grade 3 and 4 transaminase elevations. There were no treatment-related deaths. Conclusion These results demonstrate the safety and efficacy of administering autologous CD4<sup>+</sup> T cells that are genetically engineered to express an MHC class II-restricted antitumor TCR that targets MAGE-A3. This clinical trial extends the reach of TCR gene therapy for patients with metastatic cancer.
Using Reducing Agents to Eliminate Chlorine Dioxide and Chlorite Ion Residuals in Drinking Water (1991)

In an effort to determine the viability of various disinfection alternatives, the Evansville, Ind., Water and Sewer Utility is engaged in a pilot‐plant investigation to compare chlorine dioxide and ozone pretreatment. As a result of increased speculation that the total residual concentration of chlorine dioxide and its inorganic species will soon be regulated, supplemental studies were performed to determine the effectiveness of various reducing agents for reducing or eliminating chlorine dioxide and chlorite ion residuals in finished water. The effectiveness of ferrous iron in achieving the desired reductions is examined along with promising results obtained with sodium thiosulfate. Specific difficulties encountered with the sulfur dioxide–sulfite ion method of chlorite ion reduction are also presented.
Adaptive Coding of Monochrome and Color Images (1977)

An efficient adaptive encoding technique using a new implementation of the Fast Discrete Cosine Transform (FDCT) for bandwidth compression of monochrome and color images is described. Practical system application is attained by maintaining a balance between complexity of implementation and performance. FDCT sub-blocks are sorted into four classes according to level of image activity, measured by the total ac energy within each sub-block. Adaptivity is provided by distributing bits between classes, favoring higher levels of activity over lower levels. Excellent performance is demonstrated in terms of mean square error and direct comparison of original and reconstructed images. Results are presented for both noiseless and noisy transmission at a total rate of 1 bit and 0.5 bit per pixel for a monochrome image and for a total rate of 2 bits and 1 bit per pixel for a color image. In every case the total bit rate includes all overhead required for image reconstruction and bit protection.
Augmenting Shape with Appearance in Vehicle Category Recognition (2006)

Shape is an important cue for generic object recognition but can be insufficient without other cues such as object appearance. We explore a number of ways in which the geometric aspects of an object can be augmented with its appearance. The main idea is to construct a dense correspondence between the interior regions of two shapes based on a shape-based correspondence so that the intensity and gradient distributions can be compared, e.g., using a mutual information paradigm. Three methods for regional alignment are suggested and compared here, based on: (i) propagation of correspondences from the silhouette to parallel curves in the interior, (ii) intersection of line segments anchored on corresponding points on the contour, and (iii) correspondence of shape skeletons. These methods have been implemented and applied to vehicle category recognition from aerial videos under known viewing and illumination conditions. We have constructed a photo-realistic synthetic video database to explore the performance of these methods under controlled conditions. We have also tested these algorithms on real video collected for this purpose from a balloon. Our findings indicate that (i) augmenting shape with appearance significantly increases recognition rate, and (ii) the region correspondence induced by the shape skeleton yields the highest performance.
Selective Precipitation of 14 kDa Stone/Thread Proteins by Concentration of Pancreaticobiliary Secretions (1989)

Concentrated proteins in pancreatic juice could precipitate and plug pancreatic ducts, initiating pancreatic disease. In cystic fibrosis (CF), pancreatic fluid secretion is impaired due to defective anion transport and proteins are hyperconcentrated. To determine whether proteins in pancreatic secretions precipitate selectively or nonspecifically, duodenal secretions were obtained from subjects with and without cystic fibrosis, during pancreatic stimulation with cholecystokinin (CCK) and secretin, dialyzed against phosphate-buffered saline (PBS), and concentrated in stages by ultrafiltration. Precipitates obtained by centrifugation at 15,600 g for 10 min at 4 degrees C were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The only protein band regularly enriched in precipitates from 10 CF and 9 non-CF samples had an Mr of approximately 14,000. Monoclonal antibodies, raised independently in two laboratories against either pancreatic stone protein (PSP) or pancreatic thread protein (PTP), reacted with the Mr 14,000 protein(s). Differential extraction of PTP and PSP by 0.1N HCl and 10% sodium citrate produced Mr 14,000 products that reacted equally with each monoclonal antibody (MAB). Two-dimensional gel electrophoresis demonstrated two Mr 14,000 spots in each extract with pI's of 5.8 and 6.0. Each spot reacted equivalently with the MABs for PSP and PTP. PSP/PTP type proteins are sparingly soluble in pancreatic secretions and could contribute to protein plugging in pancreatic disease.
Contributions of mitochondria to animal physiology: from homeostatic sensor to calcium signalling and cell death (1999)

Over recent years, it has become clear that mitochondria play a central role in many key aspects of animal physiology and pathophysiology. Their central and ubiquitous task is clearly the production of ATP. Nevertheless, they also play subtle roles in glucose homeostasis, acting as the sensor for substrate supply in the transduction pathway that promotes insulin secretion by the pancreatic -cell and that modulates the excitability of the hypothalamic glucose-sensitive neurons involved in appetite control. Mitochondria may also act as sensors of availability of oxygen, the other major mitochondrial substrate, in the regulation of respiration. Mitochondria take up calcium, and the high opacity mitochondrial calcium uptake pathway provides a mechanism that couples energy demand to increased ATP production through the calcium-dependent upregulation of mitochondrial enzyme activity. Mitochondrial calcium accumulation may also have a substantial impact on the spatiotemporal dynamics of cellular calcium signals, with subtle differences of detail in different cell types. Recent work has also revealed the centrality of mitochondrial dysfunction as an irreversible step in the pathway to both necrotic and apoptotic cell death. This review looks at recent developments in these rapidly evolving areas of cell physiology in an attempt to draw together disparate areas of research into a common theme.
Next Generation Short-Term Forecasting of Wind Power – Overview of the ANEMOS Project. (2006)

International audience
Segmentation and tracking of static and moving objects in video surveillance scenarios (2008)

In this paper we present a real-time object tracking system for monocular video sequences with static camera. The workflow is based on a pixel-based foreground detection system followed by foreground object tracking. The foreground detection method performs the segmentation in three levels: Moving Foreground, Static Foreground and Background level. The tracking uses the foreground segmentation for identifying the tracked objects, but minimizes the reliance on the foreground segmentation, using a modified Mean Shift tracking algorithm. Combining this tracking system with the Multi-Level foreground segmentation, we have improved the tracking results using the classification in static or moving objects. The system solves successfully a high percentage of the moving objects occlusions, and most of the occlusions between static and moving objects.
EGF receptor and p185erbB‐2‐specific single‐chain antibody toxins differ in their cell‐killing activity on tumor cells expressing both receptor proteins (1995)

Many human tumors over-express erbB-2 and EGF receptors. The membrane localization of these receptor tyrosine kinases make them appropriate targets for directed tumor therapy. We have used recombinant DNA technology to produce single-chain antibody exotoxin A (scFv-ETA) fusion proteins which specifically bind the erbB-2 and EGF receptors. The scFv portion is composed of the heavy- and light-chain variable domains of monoclonal antibodies which recognize the extracellular portion of each receptor. We have previously described the anti-tumor activity of the bacterially produced scFv(FRP5)-ETA directed to the erbB-2 receptor. In this paper we describe the characteristics of scFv(225)-ETA, a protein which binds the EGF receptor. The bacterially produced recombinant protein binds to the receptor with high affinity and inhibits the in vitro growth of the EGF receptor over-expressing tumor cell lines A431 and MDA-MB468. Combination treatment with scFv-(FRP5)-ETA and scFv(225)-ETA led to an additive inhibitory effect on the in vitro growth of A431 cells. SKBR3 cells expressing low levels of EGF receptor but high levels of p185erbB-2 were not affected by scFv(225)-ETA treatment but were sensitive to scFv(FRP5)-ETA. Stimulation of SKBR3 cells and HCII RI#11 mouse mammary epithelial cells expressing the human erbB-2 with EGF led to an increase in scFv(FRP5)-ETA activity, showing that the EGF-induced activation of erbB-2 can potentiate the action of the erbB-2-directed toxin. Treatment of athymic nude mice with scFv(FRP5)-ETA and the combination of both scFv-ETA proteins led to the transient arrest of growth of established A431 tumors. scFv(225)-ETA treatment alone was the most effective, leading to tumor shrinkage during the course of treatment, whereas treatment with the parental monoclonal antibody 225 led to retarded tumor growth.
BRCA2 Is Ubiquitinated In Vivo and Interacts with USP11, a Deubiquitinating Enzyme That Exhibits Prosurvival Function in the Cellular Response to DNA Damage (2004)

Individuals carrying a germ line mutation of the breast cancer susceptibility gene BRCA2 are predisposed to breast, ovarian, and other types of cancer. The BRCA2 protein has been proposed to function in the repair of DNA double-strand breaks. Using an immunopurification-mass spectrometry approach to identify novel proteins that associate with the BRCA2 gene product, we found that a deubiquitinating enzyme, USP11, formed specific complexes with BRCA2. Moreover, BRCA2 was constitutively ubiquitinated in vivo in the absence of detectable proteasomal degradation. Mitomycin C (MMC) led to decreased BRCA2 protein levels associated with increased ubiquitination, consistent with proteasome-dependent degradation. While BRCA2 could be deubiquitinated by USP11 in transient overexpression assays, a catalytically inactive USP11 mutant had no effect on BRCA2 ubiquitination or protein levels. Antagonism of USP11 function either through expression of this mutant or through RNA interference increased cellular sensitivity to MMC in a BRCA2-dependent manner. All of these results imply that BRCA2 expression levels are regulated by ubiquitination in the cellular response to MMC-induced DNA damage and that USP11 participates in DNA damage repair functions within the BRCA2 pathway independently of BRCA2 deubiquitination.
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. (1994)

I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency of preferred codons is significantly higher at codons conserved for amino acids than at nonconserved codons in 38 genes compared between D. melanogaster and Drosophila virilis or Drosophila pseudoobscura (Z = 5.93, P < 10(-6)). Preferred codon usage is also significantly higher in putative zinc-finger and homeodomain regions than in the rest of 28 D. melanogaster transcription factor encoding genes (Z = 8.38, P < 10(-6)). Mutational alternatives (within-gene differences in mutation rates, amino acid changes altering codon preference states, and doublet mutations at adjacent bases) do not appear to explain this association between synonymous codon usage and amino acid constraint.
Estradiol repression of tumor necrosis factor-α transcription requires estrogen receptor activation function-2 and is enhanced by coactivators (1999)

The tumor necrosis factor-alpha (TNF-alpha) promoter was used to explore the molecular mechanisms of estradiol (E(2))-dependent repression of gene transcription. E(2) inhibited basal activity and abolished TNF-alpha activation of the TNF-alpha promoter. The E(2)-inhibitory element was mapped to the -125 to -82 region of the TNF-alpha promoter, known as the TNF-responsive element (TNF-RE). An AP-1-like site in the TNF-RE is essential for repression activity. Estrogen receptor (ER) beta is more potent than ERalpha at repressing the -1044 TNF-alpha promoter and the TNF-RE upstream of the herpes simplex virus thymidine kinase promoter, but weaker at activating transcription through an estrogen response element. The activation function-2 (AF-2) surface in the ligand-binding domain is required for repression, because anti-estrogens and AF-2 mutations impair repression. The requirement of the AF-2 surface for repression is probably due to its capacity to recruit p160 coactivators or related coregulators, because overexpressing the coactivator glucocorticoid receptor interacting protein-1 enhances repression, whereas a glucocorticoid receptor interacting protein-1 mutant unable to interact with the AF-2 surface is ineffective. Furthermore, receptor interacting protein 140 prevents repression by ERbeta, probably by interacting with the AF-2 surface and blocking the binding of endogenous coactivators. These studies demonstrate that E(2)-mediated repression requires the AF-2 surface and the participation of coactivators or other coregulatory proteins.
Targeted Oncolytic Herpes Simplex Viruses for Aggressive Cancers (2012)

Herpes simplex virus (HSV) is a well-known vector that is often used for gene therapy to treat cancers. The most attractive feature of HSV is its ability to destroy tumors through a distinctive oncolytic mechanism where the virus can destroy cancer cells via cell lysis, a killing function that no anti-cancer drugs can mimic. Importantly, HSV is a safe and effective virus that can be easily manipulated to preferentially replicate in tumor cells. In the last 20 years of reengineering efforts, a number of HSV designs, including the classical G207, have been focused on deleting viral genes in order to render the virus tumor specific. Although such designs can successfully destroy tumor xenografts in animal models, with minimal impact on normal tissues, a common trade-off is the marked attenuation of the virus. This problem is most profound in many clinical tumors, where virus dissemination is often hindered by the difficult cellular and molecular terrain of the human tumor mass. In order to harness all of HSV's replication potential to destroy tumor cells, efforts in our lab, as well as others, last several years have been focused on engineering an oncolytic HSV to target tumor cells without deleting any viral genes, and have since generated highly tumor specific viruses including our transcriptional translational dually regulated HSV (TTDR-HSV). In this review, we will discuss the improvements associated with the newer TTDR-HSV design compared to the classical defective HSV designs such as G207 and tk- HSV. Lastly, we will review additional cellular features of aggressive tumors, such as their immense cellular heterogeneity and volatility, which may serve to hinder the dissemintation of TTDR-HSV. The challenge for future studies would be to explore how TTDRHSV could be redesigned and/or employed with combinatorial approaches to better target and destroy the heterogeneous and dynamic cell populations in the aggressive tumor mass.
One-stop clinic for assessment of risk of chromosomal defects at 12 weeks of gestation (2002)

Prenatal diagnosis of trisomy 21 requires an invasive test in women considered to be at high risk after screening. At present, there are four screening tests. For a 5% false-positive rate, the sensitivities are approximately 30% for maternal age alone, 60-70% for maternal age and second-trimester maternal serum biochemical testing, 75% for maternal age and first-trimester fetal nuchal translucency (NT) scanning, and 90% for maternal age with fetal NT and maternal serum free beta-human chorionic gonadotropin (beta-hCG) and pregnancy-associated plasma protein-A (PAPP-A) at 11-14 weeks. This article examines the methodology of first-trimester screening and summarizes the results from all studies reporting on the implementation of this method.