gebhart/patrepeval huggingface dataset:
Protein folding using inter-residue contact (2005)

Contact maps and contact vectors are representations of a protein structure particularly suitable for computer simulations of protein folding. We first formulate the problem of determining the native state of a protein as one of energy minimization in the space of contact maps or of contact vectors. In order to realize this program we discuss algorithms to explore the portions of contact map space and of contact vector space that correspond to the conformational space of a protein. We then attempt to derive an energy for contact maps or for contact vectors whose ground state corresponds to the native state of a protein and we show that this is an impossible result to achieve. Finally we discuss the possibility of performing protein fold predictions by using database information to predict inter-residue contacts to be used in a restrained energy minimization in the contact map space or in the contact vector space.
Site-Specific N-Glycosylation of Caprine Lysostaphin Restricts its Bacteriolytic Activity TowardStaphylococcus Aureus (2013)

Lysostaphin (LYS) is an anti-staphylococcal prokaryotic polypeptide that has been used to avoid Staphylococcus aureus mastitis through transgenic or viral vector approaches exogenously expressed in dairy animals. However, glycosylation of lysostaphin expressed in mammalian cells results in a loss of bioactivity. Until now, the mechanism of site-specific glycosylation of lysostaphin causing this loss of bioactivity remains unknown. An immortalized caprine mammary epithelial cell line (CMEC-08-D) was used to study recombinant lysostaphin fused with goat β-casein, goat lactoferrin (LF) or prokaryotic signal peptides. These constructs were separately ectopically expressed in CMEC-08-D. Results of site-directed mutagenesis show that Asn(125) but not Asn(232) is the exact glycosylation site of lysostaphin expressed in CMEC-08-D. In addition, the effect of glycosylation of lysostaphin on its staphylolytic activity was identified through bacterial plate assay. The data indicated that wild type and mutated N232Q-lysostaphin (Asn(232) to Gln(232) substitution) lacked staphylolytic activity. In contrast, mutated N125Q (Asn(125) to Gln(125) substitution) and N125Q/N232Q-lysostaphin possessed staphylolytic activity. On the other hand, all mutated lysostaphin showed no change in binding ability to S. aureus. This reveals that N-glycosylation at Asn(125) of lysostaphin expressed in a eukaryotic system greatly decreases lysostaphin bacteriolytic activity but does not affect its binding ability to S. aureus.
RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays (2005)

RNA interference (RNAi) is a process in which double-strand RNA (dsRNA) directs the specific degradation of a corresponding target mRNA. The mediators of this process are small dsRNAs, of approximately 21 bp in length, called small interfering RNAs (siRNAs). siRNAs, which can be prepared in vitro in a number of ways and then transfected into cells, can direct the degradation of corresponding mRNAs inside these cells. Hence, siRNAs represent a powerful tool for studying gene functions, as well as having the potential of being highly specific pharmaceutical agents. Some limitations in using this technology exist because the preparation of siRNA in vitro and screening for siRNAs efficient in RNAi can be expensive and time-consuming processes. Here, we demonstrate that custom oligonucleotide arrays can be efficiently used for the preparation of defined mixtures of siRNAs for the silencing of exogenous and endogenous genes. The method is fast, inexpensive, does not require siRNA optimization and has a number of advantages over methods utilizing enzymatic preparation of siRNAs by digestion of longer dsRNAs, as well as methods based on chemical synthesis of individual siRNAs or their DNA templates.
Oral tolerance to myelin basic protein and natural recovery from experimental autoimmune encephalomyelitis are associated with downregulation of inflammatory cytokines and differential upregulation of transforming growth factor beta, interleukin 4, and prostaglandin E expression in the brain. (1992)

Experimental autoimmune encephalomyelitis (EAE) in the Lewis rat is a self-limited inflammatory process localized to the central nervous system that is induced by the injection of myelin basic protein (MBP) in adjuvant. Oral administration of MBP suppresses EAE, and this suppression is mediated by CD8+ T cells that adoptively transfer protection and suppress both in vitro and in vivo by the release of transforming growth factor (TGF) beta after antigen-specific triggering. Furthermore, oral tolerance to MBP is enhanced by the concomitant oral administration of lipopolysaccharide (LPS). The present study was undertaken to determine whether the disease course in EAE and its suppression by oral tolerization to MBP is associated with distinct patterns of cytokine expression in the target organ. Detailed immunohistology of the brain was performed at the peak of clinical disease (day 14 after immunization) and after recovery (day 18) in control (ovalbumin [OVA]-fed), MBP-fed, and MBP plus LPS-fed animals. Brains from OVA-fed animals at the peak of disease showed perivascular infiltration with activated mononuclear cells which secreted the inflammatory cytokines interleukins (IL) 1, 2, 6, 8, TNF-alpha, and interferon gamma. The inhibitory cytokines TGF-beta and IL-4, and prostaglandin E2 (PGE2) were absent. In MBP orally tolerized animals there was a marked reduction of the perivascular infiltrate and downregulation of all inflammatory cytokines. In addition, there was upregulation of the inhibitory cytokine TGF-beta. In MBP plus LPS orally tolerized animals, in addition to upregulation of TGF-beta and reduction of inflammatory cytokines, there was enhanced expression of IL-4 and PGE2, presumably secondary to activation of an additional population of immunoregulatory cells. In OVA-fed animals that had recovered (day 18), staining for inflammatory cytokines diminished, and there was the appearance of TGF-beta and IL-4. These results suggest that suppression of EAE, either induced by oral tolerization or that which occurs during natural recovery is related to the secretion of inhibitory cytokines or factors that actively suppress the inflammatory process in the target organ.
Evidence for a TCR Affinity Threshold Delimiting Maximal CD8 T Cell Function (2010)

Protective adaptive immune responses rely on TCR-mediated recognition of Ag-derived peptides presented by self-MHC molecules. However, self-Ag (tumor)-specific TCRs are often of too low affinity to achieve best functionality. To precisely assess the relationship between TCR-peptide-MHC binding parameters and T cell function, we tested a panel of sequence-optimized HLA-A(*)0201/NY-ESO-1(157-165)-specific TCR variants with affinities lying within physiological boundaries to preserve antigenic specificity and avoid cross-reactivity, as well as two outliers (i.e., a very high- and a low-affinity TCR). Primary human CD8 T cells transduced with these TCRs demonstrated robust correlations between binding measurements of TCR affinity and avidity and the biological response of the T cells, such as TCR cell-surface clustering, intracellular signaling, proliferation, and target cell lysis. Strikingly, above a defined TCR-peptide-MHC affinity threshold (K(D) < approximately 5 muM), T cell function could not be further enhanced, revealing a plateau of maximal T cell function, compatible with the notion that multiple TCRs with slightly different affinities participate equally (codominantly) in immune responses. We propose that rational design of improved self-specific TCRs may not need to be optimized beyond a given affinity threshold to achieve both optimal T cell function and avoidance of the unpredictable risk of cross-reactivity.
Solubilization and purification of aldehyde‐generating fatty acyl‐CoA reductase from green alga Botryococcus braunii (1995)

Membrane-bound fatty acyl-CoA reductase from the green alga Botryococcus braunii has been solubilized from the microsomal preparation by 0.1% octyl beta-glucoside and purified to near homogeneity by Blue A agarose and palmitoyl-CoA agarose affinity column chromatography. The molecular mass of the enzyme was estimated by SDS-PAGE to be 35 kDa. The enzyme generates fatty aldehyde by reduction of fatty acyl-CoA with NADH as the reductant. The N-terminal amino acid sequence of this protein that represents the first eucaryotic aldehyde-generating reductase to be purified shows high homology with the N-terminus of fatty acid reductase from bacteria.
High power resonant Switched-Capacitor step-down converter (2008)

This paper treats a new type of high power switched-capacitor-DC-DC-converter (SCDDC), which is characterized by resonant switching transitions. This drastically reduces switching losses and opens up the possibility to employ thyristors instead of turn-off power semiconductors. At the same time a larger energy can be transferred per switching cycle and/or the application of the SCDDCs can be extended into the megawatt power range. For operation with high switching frequency thyristors are replaced by IGCTs which allow to avoid a turn-off time in reverse-blocking mode. The new converter topology is extensively analyzed using simulations. To gain practical results a small scale prototype is designed and the operation of the proposed converter is experimentally verified including the resonant operation of IGCTs which results in significantly reduced switching losses.
Vision sensing for intelligent vehicle and highway systems (2002)

The complexity and congestion of current transportation systems often produce traffic situations that jeopardize the safety of the people involved. These situations vary from maintaining a safe distance behind a leading vehicle to safely allowing a pedestrian to cross a busy street. Environmental sensing plays a critical role in virtually all of these situations. Of the sensors available, vision sensors provide information that is richer and more complete than other sensors, making them a logical choice for a multisensor transportation system. In this paper we present robust techniques for intelligent vehicle and highway applications where computer vision plays a crucial role. In particular, we demonstrate that the controlled active vision framework can be utilized to provide a visual sensing modality to a traffic advisory system in order to increase the overall safety margin in a variety of common traffic situations. We have selected two application examples, vehicle tracking and pedestrian tracking, to demonstrate that the framework can provide precisely the type of information required to effectively manage the given situation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Epolones induce erythropoietin expression via hypoxia-inducible factor-1α activation (2000)

Induction of erythropoietin (Epo) expression under hypoxic conditions is mediated by the heterodimeric hypoxia-inducible factor (HIF)-1. Following binding to the 3' hypoxia-response element (HRE) of the Epo gene, HIF-1 markedly enhances Epo transcription. To facilitate the search for HIF-1 (ant)agonists, a hypoxia-reporter cell line (termed HRCHO5) was constructed containing a stably integrated luciferase gene under the control of triplicated heterologous HREs. Among various agents tested, we identified a class of substances called epolones, which induced HRE-dependent reporter gene activity in HRCHO5 cells. Epolones are fungal products known to induce Epo expression in hepatoma cells. We found that epolones (optimal concentration 4-8 micromol/L) potently induce HIF-1 alpha protein accumulation and nuclear translocation as well as HIF-1 DNA binding and reporter gene transactivation. Interestingly, the activity of a compound related to the fungal epolones, ciclopirox olamine (CPX), was blocked after addition of ferrous iron. This suggests that CPX might interfere with the putative heme oxygen sensor, as has been proposed for the iron chelator deferoxamine mesylate (DFX). However, about 10-fold higher concentrations of DFX (50-100 micromol/L) than CPX were required to maximally induce reporter gene activity in HRCHO5 cells. Moreover, structural, functional, and spectrophotometric data imply a chelator:iron stoichiometry of 1:1 for DFX but 3:1 for CPX. Because the iron concentration in the cell culture medium was determined to be 16 micromol/L, DFX but not CPX function can be explained by complete chelation of medium iron. These results suggest that the lipophilic epolones might induce HIF-1 alpha by intracellular iron chelation. (Blood. 2000;96:1558-1565)
Characterization of the Erwinia chrysanthemi osmoprotectant transporter gene ousA (1996)

Growth of Erwinia chrysanthemi in media of elevated osmolarity can be achieved by the uptake and accumulation of various osmoprotectants. This study deals with the cloning and sequencing of the ousA gene-encoded osmoprotectant uptake system A from E. chrysanthemi 3937. OusA belongs to the superfamily of solute ion cotransporters. This osmotically inducible system allows the uptake of glycine betaine, proline, ectoine, and pipecolic acid and presents strong similarities in nucleotide sequence and protein function with the proline/betaine porter of Escherichia coli encoded by proP. The control of ousA expression is clearly different from that of proP. It is induced by osmotic strength and repressed by osmoprotectants. Its expression in E. coli is controlled by H-NS and is rpoS dependent in the exponential phase but unaffected by the stationary phase.
Filtered Back Projection, Adaptive Statistical Iterative Reconstruction, and a Model-based Iterative Reconstruction in Abdominal CT: An Experimental Clinical Study (2012)

The MBIR algorithm considerably improved objective and subjective image quality parameters of routine abdominal multidetector CT images compared with those of ASIR and FBP.
Regions of Drosophila Notch That Contribute to Ligand Binding and the Modulatory Influence of Fringe (2005)

Two glycosyltransferases that transfer sugars to epidermal growth factor (EGF) domains, OFUT1 and Fringe, regulate Notch signaling. To characterize the impact of glycosylation at the 23 consensus O-fucose sites in Drosophila Notch, we conducted deletion mapping and site-specific mutagenesis and then assayed the binding of soluble forms of Notch to cell-surface ligands. Our results support the conclusion that EGF11 and EGF12 are essential for ligand binding, but indicate that other EGF domains also make substantial contributions to ligand binding. Characterization of Notch deletion constructs and O-fucose site mutants further revealed that no single site or region can account for the influence of Fringe on Notch-ligand binding. Additionally, we observed an influence of Fringe on a Notch fragment including only 4 of its 36 EGF domains (EGF10-13). Together, our observations imply that glycosylation influences Notch-ligand interactions through a distributive mechanism that involves local interactions with multiple EGF domains and led us to suggest a structural model for how Notch interacts with its ligands.
Monitoring Lipid Anchor Organization in Cell Membranes by PIE-FCCS (2012)

This study examines the dynamic co-localization of lipid-anchored fluorescent proteins in living cells using pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) and fluorescence lifetime analysis. Specifically, we look at the pairwise co-localization of anchors from lymphocyte cell kinase (LCK: myristoyl, palmitoyl, palmitoyl), RhoA (geranylgeranyl), and K-Ras (farnesyl) proteins in different cell types. In Jurkat cells, a density-dependent increase in cross-correlation among RhoA anchors is observed, while LCK anchors exhibit a more moderate increase and broader distribution. No correlation was detected among K-Ras anchors or between any of the different anchor types studied. Fluorescence lifetime data reveal no significant Förster resonance energy transfer in any of the data. In COS 7 cells, minimal correlation was detected among LCK or RhoA anchors. Taken together, these observations suggest that some lipid anchors take part in anchor-specific co-clustering with other existing clusters of native proteins and lipids in the membrane. Importantly, these observations do not support a simple interpretation of lipid anchor-mediated organization driven by partitioning based on binary lipid phase separation.
Ectopic Expression of Hel-N1, an RNA-Binding Protein, Increases Glucose Transporter (GLUT1) Expression in 3T3-L1 Adipocytes (1997)

3T3-L1 preadipocytes ectopically expressing the mammalian RNA-binding protein Hel-N1 expressed up to 10-fold more glucose transporter (GLUT1) protein and exhibited elevated rates of basal glucose uptake. Hel-N1 is a member of the ELAV-like family of proteins associated with the induction and maintenance of differentiation in various species. ELAV proteins are known to bind in vitro to short stretches of uridylates in the 3' untranslated regions (3'UTRs) of unstable mRNAs encoding growth-regulatory proteins involved in transcription and signal transduction. GLUT1 mRNA also contains a large 3'UTR with a U-rich region that binds specifically to Hel-N1 in vitro. Analysis of the altered GLUT1 expression at the translational and posttranscriptional levels suggested a mechanism involving both mRNA stabilization and accelerated formation of translation initiation complexes. These findings are consistent with the hypothesis that the Hel-N1 family of proteins modulate gene expression at the level of mRNA in the cytoplasm.
Volume sampled voxelization of geometric primitives (1993)

We present a 3-D antialiasing algorithm for voxel-based geometric models. The technique band-limits the continuous object before sampling it at the desired 3-D raster resolution. By precomputing tables of filter values for different types and sizes of geometric objects, the algorithm is very efficient and has a complexity that is linear with the number of voxels generated. The algorithm not only creates voxel models which are free from object space aliasing, but it also incorporates the image space antialiasing information as part of the view independent voxel model. The resulting alias-free voxel models have been used to model synthetic scenes, for discrete ray tracing applications. The discrete ray-traced image is superior in quality to the image generated with a conventional surface-based ray tracer, since silhouettes of objects, shadows, and reflections appear smooth (jaggy-less). In addition, the alias-free models are also suitable for intermixing with sampled datasets, since they can be treated uniformly as one common data representation. >
Dry Reforming of Methane Using Ce-modified Ni Supported on 8%PO4 + ZrO2 Catalysts (2020)

Dry reforming of methane (DRM) was studied in the light of Ni supported on 8%PO4 + ZrO2 catalysts. Cerium was used to modify the Ni active metal. Different percentage loadings of Ce (1%, 1.5%, 2%, 2.5%, 3%, and 5%) were tested. The wet incipient impregnation method was used for the preparation of all catalysts. The catalysts were activated at 700 °C for ½ h. The reactions were performed at 800 °C using a gas hourly space velocity of 28,000 mL (h·gcat)−1. X-ray diffraction (XRD), N2 physisorption, hydrogen temperature programmed reduction (H2-TPR), temperature programmed oxidation (TPO), temperature programmed desorption (TPD), and thermogravimetric analysis (TGA) were used for characterizing the catalysts. The TGA analysis depicted minor amounts of carbon deposition. The CO2-TPD results showed that Ce enhanced the basicity of the catalysts. The 3% Ce loading possessed the highest surface area, the largest pore volume, and the greatest pore diameter. All the promoted catalysts enhanced the conversions of CH4 and CO2. Among the promoted catalysts tested, the 10Ni + 3%Ce/8%PO4 + ZrO2 catalyst system operated at 1 bar and at 800 °C gave the highest conversions of CH4 (95%) and CO2 (96%). The stability profile of Cerium-modified catalysts (10%Ni/8%PO4 + ZrO2) depicted steady CH4 and CO2 conversions during the 7.5 h time on stream.
Study of Air Revitalization System for space station (1989)

&lt;div class="htmlview paragraph"&gt;In closed environments such as space stations, it is necessary to eliminate CO&lt;sub&gt;2&lt;/sub&gt; produced by the metabolisms of crew members, for their life support, and to regenerate the air by supplying O&lt;sub&gt;2&lt;/sub&gt; to make up for the deficiency. If humans are to be in space only a short time, it is in general advantageous to adsorb CO&lt;sub&gt;2&lt;/sub&gt; with lithium hydroxide, and to supply O&lt;sub&gt;2&lt;/sub&gt; from tanks. But when the stay in space is long, it is essential to establish a highly reliable and energy-efficient system to recover CO&lt;sub&gt;2&lt;/sub&gt; in high concentrations and regenerate O&lt;sub&gt;2&lt;/sub&gt; from this recovered CO&lt;sub&gt;2&lt;/sub&gt; &lt;span class="xref"&gt;Fig. 1&lt;/span&gt; shows the system presently conceived, which is roughly divided into the following processes: A process that removes and concentrates CO&lt;sub&gt;2&lt;/sub&gt; from the air; a CO&lt;sub&gt;2&lt;/sub&gt; reduction process that separates carbon from CO&lt;sub&gt;2&lt;/sub&gt; and obtains water; and a water electrolysis process that decomposes water electrically and recovers O&lt;sub&gt;2&lt;/sub&gt;. The process deemed most promising both in terms of low energy consumption and reliability for removing and concentrating CO&lt;sub&gt;2&lt;/sub&gt;. In this process, solid amine removes CO&lt;sub&gt;2&lt;/sub&gt; produced by human metabolisms, desorbs it, then separates and concentrates CO&lt;sub&gt;2&lt;/sub&gt; of high purity.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Bosch reaction, which proceeds at comparatively low temperatures, is thought to be advantageous for the CO&lt;sub&gt;2&lt;/sub&gt; reduction process, and using a solid electrolyte is advantageous for the water electrolysis process.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This research involved several tests, and simulated analysis for these processes to examine the optimum conditions for the effective operation of the system.&lt;/div&gt;
Disseminated Tumor Cells in Lymph Nodes as a Determinant for Survival in Surgically Resected Non–Small-Cell Lung Cancer (1999)

The immunohistochemical detection of disseminated tumor cells in lymph nodes of patients with completely resected NSCLC is an independent prognostic factor for overall survival.
Retinoic acid‐promoted expansion of total cellular ATP pools in 3T3 cells can mediate its stimulatory and growth inhibitory effects (1982)

Exposure of Swiss 3T3 cells to micromolar quantities of beta-all-trans-retinoic acid (RA) results in either inhibition of growth or stimulation of cellular responsiveness to mitogens, depending on the length of treatment. Inhibition of growth is produced by treatment of the cells with RA for at least 48 hours. The total cellular pools of adenosine 5'-triphosphate (ATP) are markedly increased after 48-hour RA treatment and dose dependence studies show a correlation between the expanded ATP pools and the inhibitor effects. The expansion of total cellular ATP pools by retinoic acid occurs throughout the cell cycle and parallels the cell cycle-dependent fluctuations in total cellular ATP pools of untreated cells. Studies of [3H]thymidine incorporation and labeling indices in intact cells and [3H]dTTP incorporation and labeling indices in isolated nuclei of RA-treated and control cultures suggest that cellular acid-soluble nucleotide pools mediate the inhibition of DNA replication in the 48-hour-RA-treated cells. The stimulatory activity of RA for mitogenic responsiveness is demonstrated by treatment of G0/G1-arrested 3T3 cells with micromolar levels of RA for a maximum of 18 hours resulting in the potentiation of phorbol myristate acetate (PMA)-stimulated transition into S phase of the cell cycle. Marked increases in total cellular ATP and UTP pools are produced by 18-hour treatment of G0/G1-arrested cells with RA, before their exposure to PMA.