gebhart/patrepeval huggingface dataset:
Functional expression of the Erwinia uredovora carotenoid biosynthesis gene crtl in transgenic plants showing an increase of β‐carotene biosynthesis activity and resistance to the bleaching herbicide norflurazon (1993)

Among the enzymes involved in carotenoid biosynthesis, phytoene desaturase is considered to be a rate-limiting enzyme in this pathway and is also the target of many bleaching herbicides. This enzyme shows diversity concerning its function and amino acid homology among various organisms. The phytoene desaturase gene crtl of Erwinia uredovora was expressed, the 5'-region of which was fused to the sequence for the transit peptide of a pea Rubisco small subunit, in tobacco plants under the control of the CaMV 35S promoter. This chimeric gene product was targeted into chloroplasts and processed in the transgenic plants. The production and processing of the corresponding protein could be demonstrated by Western blotting. Immunogold localization showed that the location of the gene product Crtl was preferentially in the thylakoids. A radioactive labeling study using the leaves demonstrated enhanced activity for the synthesis of beta-carotene. In addition, the transgenic tobacco acquired elevated resistance to the bleaching herbicide norflurazon.
Structure of the complex group-specific polysaccharide of group B Streptococcus (1987)

The group-specific antigen was isolated from a type Ia group B streptococcal strain and is a complex polysaccharide composed of alpha-L-rhamnopyranosyl, alpha-D-galactopyranosyl, 2-acetamido-2-deoxy-beta-D-glucopyranosyl, D-glucitol, and phosphate residues. The complexity of the group B polysaccharide antigen is evident from the fact that when depolymerized by basic hydrolysis it yielded three structurally related, but nevertheless significantly different, oligosaccharides. These oligosaccharides were obtained in different molar quantities as their monophosphate esters. This evidence strongly suggests that they are linked by phosphodiester bonds in the original group B antigen. If these oligosaccharides are in fact randomly situated throughout the linear polysaccharide, then this type of heterogeneous repeating unit is unusual for a polysaccharide of bacterial origin. However, this structural arrangement of the oligosaccharides has yet to be unambiguously established because the alternate explanation of there being three different polysaccharides in the group B antigen cannot be discounted in the evidence presented here. The oligosaccharides were enzymatically dephosphorylated, and the structures of two of the three oligosaccharides are (formula: see text) Despite their structural differences, the two oligosaccharides are related by the smaller being an integral part of the larger. In the structural analysis of the group B antigen, methylation analysis, periodate oxidation, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, fast atom bombardment mass spectrometry, and various specific chemical and enzymatic degradations were the principal methods used. Of particular interest was the use of an alpha-rhamnosidase to selectively degrade the larger oligosaccharide. This facilitated the assignment of signals in its 1H and 13C NMR spectra.
EFEMP1 Expression Promotes In vivo Tumor Growth in Human Pancreatic Adenocarcinoma (2009)

The progression of pancreatic cancer is dependent on local tumor growth, angiogenesis, and metastasis. EFEMP1, a recently discovered member of the fibulin family, was characterized with regard to these key elements of pancreatic cancer progression. Differential gene expression was assessed by mRNA microarray hybridization in FG human pancreatic adenocarcinoma cells and L3.6pl cells, a highly metastatic variant of FG. In vivo orthotopic tumor growth of EFEMP1-transfected FG cells was examined in nude mice. To assess the angiogenic properties of EFEMP1, vascular endothelial growth factor (VEGF) production of tumor cells, endothelial cell proliferation and migration, and tumor microvessel density were analyzed in response to EFEMP1. Further, tumor cell apoptosis, cell cycle progression, and resistance to cytotoxic agents were quantitated by propidium iodide staining and flow cytometry. In microarray hybridization, EFEMP1 was shown to be significantly up-regulated in L3.6pl cells compared with FG cells. Concordantly, EFEMP1 transfection of FG cells stimulated orthotopic and metastatic tumor growth in vivo. EFEMP1 expression resulted in a stimulation of VEGF production by tumor cells and an increased number of CD31-positive microvessels. Endothelial cell proliferation and migration were not altered by EFEMP1, indicating an indirect angiogenic effect. Further, EFEMP1 expression decreased apoptosis and promoted cell cycle progression in response to serum starvation or exposure to gemcitabine, 5-fluorouracil, and irinotecan. EFEMP1 has protumorigenic effects on pancreatic cancer in vivo and in vitro mediated by VEGF-driven angiogenesis and antiapoptotic mechanisms. Hence, EFEMP1 is a promising candidate for assessing prognosis and individualizing therapy in a clinical tumor setting.
Myelin phagocytosis and remyelination of macrophage‐enriched central nervous system aggregate cultures (2001)

An increased level of myelin basic protein (MBP) degradation peptide 80-89, representative of myelin breakdown, is detected in myelinating foetal rat brain aggregate cultures supplemented with peritoneal macrophages at a time coinciding with the onset of myelination. During the period of myelination, the proportion of activated macrophages/microglia in the aggregates decreases, accompanied by a reduction in the content of MBP degradation products. During the recovery period following a demyelinating episode, the rate of MBP synthesis in antibody-treated standard aggregates was greater than in their medium controls. However, the rate of MBP accumulation was not as efficient in macrophage-enriched aggregates and was associated with persistently raised MBP peptide levels. Thus, as occurs in multiple sclerosis lesions, attempts at remyelination appear to be counterbalanced by macrophage-mediated demyelination, with the continued presence of degraded myelin rendering a local environment that is not fully conducive to remyelination.
<title>Lithographic lens testing: analysis of measured aerial images, interferometric data, and photoresist measurements</title> (1996)

This paper shows and discusses the use of direct aerial image measurements and optical interferometry for the evaluation of advanced i-line lenses. These measurement techniques provide direct information on the image forming capabilities of a stepper lens such that assessments of field curvature, astigmatism and image asymmetry can readily be accomplished. The interaction with the photoresist is shown by directly using the measured aerial image and aberration data into photoresist modeling programs such as Prolith/2 and Solid-C. The link between the optical measurements and the photoresist processes is further established by a comparison of simulated and measured results.
Type-based race detection for Java (2000)

This paper presents a static race detection analysis for multithreaded Java programs. Our analysis is based on a formal type system that is capable of capturing many common synchronization patterns. These patterns include classes with internal synchronization, classes thatrequire client-side synchronization, and thread-local classes. Experience checking over 40,000 lines of Java code with the type system demonstrates that it is an effective approach for eliminating races conditions. On large examples, fewer than 20 additional type annotations per 1000 lines of code were required by the type checker, and we found a number of races in the standard Java libraries and other test programs.
BATTLE OF THE MOUSE CLICKS (1999)

SUBTITLE: CORPORATE SELF-BOOKING VIA THE INTERNET APPEARS TANTALIZINGLY CLOSE BUT OUT OF REACH.
Escherichia coli Diacylglycerol Kinase Is an α-Helical Polytopic Membrane Protein and Can Spontaneously Insert into Preformed Lipid Vesicles (1996)

Escherichia coli diacylglycerol kinase (DAGK) is a 13.2 kDa enzyme which spans the cytoplasmic membrane three times. Functional DAGK was purified to homogeneity using a polyhistidine tag and Ni(II)-chelate chromatography. Transmission Fourier transform infrared spectroscopy (FT-IR) of DAGK in phosphatidylcholine multilayers led to the conclusion that > or = 90 of DAGK's native 121 residues are alpha-helical, consistent with a model in which DAGK consists of two amphipathic alpha-helices and three transmembrane helices. Polarized attenuated total reflection FT-IR studies of DAGK in oriented multilamellae yielded data consistent with a topological arrangement in which the three transmembrane helices are well-aligned with the bilayer normal while the two amphipathic helices are approximately parallel with the membrane plane. The ability of DAGK to spontaneously insert into preformed lipid vesicles was examined using a novel assay system involving DAGK-catalyzed phosphorylation of a fluorescently tagged diacylglycerol. When micellar DAGK is diluted into L alpha-phase vesicles spontaneous insertion of the enzyme is fairly efficient (ca. 30%). DAGK refolding and insertion from delipidated urea-solubilized DAGK into lipid vesicles is also modestly efficient (3.8 +/- 2.1%) above the gel to liquid crystalline phase transition temperature. The insertion studies indicate that the difference in energy barriers (delta delta G++) between pathways leading to catalytically productive folding and insertion of DAGK relative to unproductive pathways is < 4 kcal/mol. However, additional studies carried out with mutant forms of DAGK indicated that the differences between refolding/insertion pathways for DAGK in vivo and in vitro can be significant.
Intrathecal baclofen for intractable spasticity of spinal origin: results of a long-term multicenter study (1993)

A total of 93 patients with intractable spasticity due to either spinal cord injury (59 cases), multiple sclerosis (31 cases), or other spinal pathology (three cases) were entered into a randomized double-blind placebo-controlled screening protocol of intrathecal baclofen test injections. Of the 88 patients who responded to an intrathecal bolus of 50, 75, or 100 micrograms of baclofen, 75 underwent implantation of a programmable pump system for chronic therapy. Patients were followed for 5 to 41 months after surgery (mean 19 months). No deaths or new permanent neurological deficits occurred as a result of surgery or chronic intrathecal baclofen administration. Rigidity was reduced from a mean preoperative Ashworth scale score of 3.9 to a mean postoperative score of 1.7. Muscle spasms were reduced from a mean preoperative score of 3.1 (on a four-point scale) to a mean postoperative score of 1.0. Although the dose of intrathecal baclofen required to control spasticity increased with time, drug tolerance was not a limiting factor in this study. Only one patient withdrew from the study because of a late surgical complication (pump pocket infection). Another patient received an intrathecal baclofen overdose because of a human error in programming the pump. The results of this study indicate that intrathecal baclofen infusion can be safe and effective for the long-term treatment of intractable spasticity in patients with spinal cord injury or multiple sclerosis.
Real-Time Facial Analysis for Virtual Teleconferencing (1996)

Image analysis for a virtual tele-conferencing system is described. Eyes are tracked in real-time using multi-resolution grey-scale correlation. Locating the eyes allows the positions of other facial features to be approximated. The head orientation is calculated by comparing the eye locations in the video images to the positions of the top and sides of the head. The direction and gesture parameters are transmitted to a three dimensional animated +clone+ in a virtual office or virtual conferencing room.
A 5′ RNA element promotes dengue virus RNA synthesis on a circular genome (2006)

The mechanisms of RNA replication of plus-strand RNA viruses are still unclear. Here, we identified the first promoter element for RNA synthesis described in a flavivirus. Using dengue virus as a model, we found that the viral RdRp discriminates the viral RNA by specific recognition of a 5′ element named SLA. We demonstrated that RNA–RNA interactions between 5′ and 3′ end sequences of the viral genome enhance dengue virus RNA synthesis only in the presence of an intact SLA. We propose a novel mechanism for minus-strand RNA synthesis in which the viral polymerase binds SLA at the 5′ end of the genome and reaches the site of initiation at the 3′ end via long-range RNA–RNA interactions. These findings provide an explanation for the strict requirement of dengue virus genome cyclization during viral replication.
24·5% Efficiency silicon PERT cells on MCZ substrates and 24·7% efficiency PERL cells on FZ substrates (1999)

This paper reports the recent improvements in the energy conversion efficiencies of solar cells on magnetically-confined Czochralski grown (MCZ) and float zone (FZ) silicon substrates at the University of New South Wales. A PERT (passivated emitter, rear totally-diffused) cell structure has been used to reduce the cell series resistance from higher resistivity substrates. The total rear boron diffusion in this PERT structure appears to improve the surface passivation quality of MCZ and some FZ substrates. Hence, higher open-circuit voltages were observed for some PERT cells. One of these cells on MCZ substrates demonstrated 24·5% energy conversion efficiency at Sandia National Laboratories under the standard global spectrum (100 mW/cm2) at 25°C. This is the highest efficiency ever reported for a MCZ silicon solar cell. The cells made on MCZ substrates also showed stable cell performance rather than the usually reported unstable performance for boron-doped CZ substrates. Also reported is a PERL (passivated emitter, rear locally-diffused) cell on a FZ substrate of 24·7% efficiency, which is the highest efficiency ever reported for any silicon solar cell. Copyright © 1999 John Wiley & Sons, Ltd.
The "Session Tty" Manager (1988)

In many UNIX systems, it is possible for a program to retain access to the login terminal after the user has logged out. This poses obvious security risks and can also confuse the modem control signals. We solve this for System V by adding a layer of indirection known as the session tty driver. At login time, a session device is linked to the physical terminal. User programs have access to the session device only, and may not open the physical line. Upon logout or carrier drop, the link is severed. New login sessions are given new session devices, and are thus insulated from persistent processes. Use of session devices is controlled by a new system process known as the session manager; by means of suitable plumbing primitives, a "reconnect after line drop" facility can easily be implemented.
Peptide-specific killing of antigen-presenting cells by a recombinant antibody–toxin fusion protein targeted to major histocompatibility complex/peptide class I complexes with T cell receptor-like specificity (1997)

Specificity in the immune system is dictated and regulated by specific recognition of peptide/major histocompatibility complex (MHC) complexes by the T cell receptor. Such peptide/MHC complexes are a desirable target for novel approaches in immunotherapy because of their highly restricted fine specificity. Recently, phage display was used to isolate an antibody that has T cell receptor-like specificity. It recognizes mouse MHC class I H-2Kk molecules complexed with a H-2Kk-restricted influenza virus-derived hemagglutinin peptide (Ha255-262) but does not bind to class I H-2Kk alone, peptide alone, or H-2Kk complexed with other peptides. We have used this antibody to make a recombinant antibody-toxin fusion protein (immunotoxin) and show herein that it specifically kills antigen-presenting cells in a peptide-dependent manner and with T cell receptor-like specificity. We find a striking correlation between the fine specificity of binding of the antibody and the cytotoxic activity of the recombinant immunotoxin. We also show specific killing of influenza virus-infected target cells. The results suggest that it should be possible to develop novel immunotherapeutic strategies against human cancer by making recombinant antibodies that will recognize cancer-related peptides complexed with MHC class I molecules on the surface of cancer cells and using these to deliver toxins, radioisotopes, or cytotoxic drugs to the cancer cells.
Dissecting subunit interfaces in homodimeric proteins (2003)

The subunit interfaces of 122 homodimers of known three-dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single-patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 A2 of the surface of each monomer, contains one or two patches burying 600-1,600 A2, is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein-protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces.
PD-1 expression conditions T cell avidity within an antigen-specific repertoire (2015)

Despite its negative regulatory role on tumor-specific T cells, Programmed cell death 1 (PD-1) is also a marker of activated tumor-infiltrating T cells. In cancer, PD-1 blockade partially reverses T cell dysfunction allowing the amplification of tumor reactive T cells. Here, we investigated the role of PD-1 signaling on effector/memory human T cells specific for shared melanoma antigens, derived from blood. We documented for the first time the existence of melanoma-specific T cell clones unable to express PD-1. This stable feature was due to the persistent methylation of the <i>PDCD1</i> promoter. These PD-1<sup>neg</sup> clones were of lower avidity than their PD-1<sup>pos</sup> counterparts, suggesting that high-affinity-specific T cell clones unable to express PD-1 are not or rarely present in peripheral blood, as they are probably eliminated by negative selection, due to their high reactivity. We also documented the existence of such PD-1<sup>neg</sup> T cell clones in melanoma tumor-infiltrating lymphocytes (TIL), which also exhibited a lower functional avidity than PD-1<sup>pos</sup> TIL clones. This clearly shows that PD-1 expression identifies antigen-specific T cell clonotypes of high functional avidity. Finally, we demonstrated that PD-1 blockade during the <i>in vitro</i> selection process of Melan-A-specific T cells favored the amplification of higher avidity T cell clonotypes. This preferential amplification of high-avidity memory T cells upon PD-1 blockade resonates with the expansion of reactive T cells, including neo-antigen-specific T cells observed in anti-PD-1-treated patients. This feature should also be a useful biomarker of clinical efficiency, while providing new insights for adoptive transfer treatments.
Cytochrome P450 CYP71BE5 in grapevine (Vitis vinifera) catalyzes the formation of the spicy aroma compound (−)-rotundone (2015)

(-)-Rotundone is a potent odorant molecule with a characteristic spicy aroma existing in various plants including grapevines (Vitis vinifera). It is considered to be a significant compound in wines and grapes because of its low sensory threshold and aroma properties. (-)-Rotundone was first identified in red wine made from the grape cultivar Syrah and here we report the identification of VvSTO2 as a α-guaiene 2-oxidase which can transform α-guaiene to (-)-rotundone in the grape cultivar Syrah. It is a cytochrome P450 (CYP) enzyme belonging to the CYP 71BE subfamily, which overlaps with the very large CYP71D family and, to the best of our knowledge, this is the first functional characterization of an enzyme from this family. VvSTO2 was expressed at a higher level in the Syrah grape exocarp (skin) in accord with the localization of (-)-rotundone accumulation in grape berries. α-Guaiene was also detected in the Syrah grape exocarp at an extremely high concentration. These findings suggest that (-)-rotundone accumulation is regulated by the VvSTO2 expression along with the availability of α-guaiene as a precursor. VvSTO2 expression during grape maturation was considerably higher in Syrah grape exocarp compared to Merlot grape exocarp, consistent with the patterns of α-guaiene and (-)-rotundone accumulation. On the basis of these findings, we propose that VvSTO2 may be a key enzyme in the biosynthesis of (-)-rotundone in grapevines by acting as a α-guaiene 2-oxidase.
Analysis of Free Drug Fractions by Ultrafast Immunoaffinity Chromatography (2001)

A chromatographic method was developed for measuring the nonbound (or free) fraction of drugs by using millisecond-scale extractions on small immunoaffinity columns. The design of this system was developed by considering the dissociation rates of (R)- and (S)-warfarin from the binding protein human serum albumin (HSA) and by performing computer simulations of the immunoaffinity extraction of these drugs. The final system was tested by using it to measure the free fractions of (R)- or (S)-warfarin in samples with known concentrations of these agents and HSA. The free warfarin fraction was extracted in 180 ms by a 2.1-mm-i.d. sandwich microcolumn that contained a 1.1-mm layer of an anti-warfarin antibody support. The nonretained peaks from this immunoaffinity column were passed through a series internal surface reversed-phase columns and a fluorescence detector for the analysis of any protein-bound warfarin that remained in the sample. The experimental results were found to have good agreement with those predicted from the known equilibrium constants for the binding of (R)- and (S)-warfarin with HSA. This approach can be modified for other analytes by changing the types of antibodies that are used in the immunoaffinity column and by using an appropriate detector for the nonretained drug fraction.
Digital Low-Pass Differentiation for Biological Signal Processing (1982)

Digital low-pass differentiation is often required in processing various biological or biomechanical data. However, both the nature of biological signals and the use of micro-or minicomputers in such applications imply the need for simple, low-order, and fast differentiation methods, rather than sophisticated high-order algorithms. Responding to this need, we investigate here the low-pass first- and second-order digital differentiation from both theoretical and practical points of view, in order to achieve good and simple algorithms. In contrast with most of the research works previously done in this field, whose main aim was to achieve better accuracy even in the cost of using quite high-order algorithms, we restrict ourselves in this study only to low orders, being interested not only in the accuracy achieved, but also in the simplicity of the algorithm. After discussing the theoretical considerations concerning our optimum low-pass differentiation filters, we present our simple low-order filters and show them to be not only very convenient for use, but also almost optimum.