gebhart/patrepeval huggingface dataset:
The role of L3T4 in T cell activation: L3T4 may be both an Ia-binding protein and a receptor that transduces a negative signal. (1986)

The T cell surface molecules Lyt-2 and L3T4 are strongly correlated with the class of MHC gene product recognized by the T cell bearing them. The L3T4 molecule has been proposed to play a role in enhancing recognition of antigen:Ia by specific T cells. In the present experiments, we have explored the role of L3T4 in T cell activation by examining the effects of the L3T4-specific monoclonal antibody GK1.5 on T cell responses in the presence or absence of class II-MHC gene products. Our studies show that GK1.5 inhibits T cell activation in the absence of class II-MHC gene products, while antibodies to other T cell surface molecules do not transduce negative signals to the same cells. We interpret our results as suggesting a signaling role for L3T4 and, by inference, for Lyt-2 as well. We would propose that L3T4 molecules on the class II-restricted T cell initiate the interaction between the L3T4+ T cell and its class II-MHC gene product bearing target cell (B cell, APC). This initial contact is important in allowing a finite time for antigen, Ia, and the T cell receptor to form an activating complex, which in turn transduces a dominant on signal to the cell. In the absence of specific antigen, or if the class II-bearing cell is of the wrong MHC genotype, so that the antigen:Ia receptor is not aggregated, then the association of L3T4 with class II molecules transduces a net negative signal to the T cell. We suggest that this negative signal is responsible for T cell:target cell deconjugation under these circumstances. Thus, we would propose that L3T4 initiates T cell:Ia-bearing cell interactions and, a finite time later, signals the T cell to discontinue the interaction unless a stimulating level of the antigen:Ia complexes for which the T cell's receptor is specific is present.
Bioorganic chemistry : peptides and proteins (1998)

1. Introduction to Peptides and Proteins 2. Chemical Synthesis of Peptides 3. Total Chemical Synthesis of Proteins 4. Structural Analysis of Proteins 5. Protein Structure 6. Protein Folding 7. Nucleic Acid Interacitve Protein Domains that Require Zinc 8. Understanding the Mechanism and Rates of Enzyme-Catalyzed Proton Transfer Reactions to and from Carbon 9. Site-Directed Mutagenesis 10. The Structural Basis of Antibody Catalysis 11. Peptides Hormones 12. Peptide Mimetics 13. Use of Enzymes in Organic Synthesis 14. Engineered Proteins in Materials Research
An Evolutionary Algorithm for Large Traveling Salesman Problems (2004)

This work proposes an evolutionary algorithm, called the heterogeneous selection evolutionary algorithm (HeSEA), for solving large traveling salesman problems (TSP). The strengths and limitations of numerous well-known genetic operators are first analyzed, along with local search methods for TSPs from their solution qualities and mechanisms for preserving and adding edges. Based on this analysis, a new approach, HeSEA is proposed which integrates edge assembly crossover (EAX) and Lin-Kernighan (LK) local search, through family competition and heterogeneous pairing selection. This study demonstrates experimentally that EAX and LK can compensate for each other's disadvantages. Family competition and heterogeneous pairing selections are used to maintain the diversity of the population, which is especially useful for evolutionary algorithms in solving large TSPs. The proposed method was evaluated on 16 well-known TSPs in which the numbers of cities range from 318 to 13509. Experimental results indicate that HeSEA performs well and is very competitive with other approaches. The proposed method can determine the optimum path when the number of cities is under 10,000 and the mean solution quality is within 0.0074% above the optimum for each test problem. These findings imply that the proposed method can find tours robustly with a fixed small population and a limited family competition length in reasonable time, when used to solve large TSPs.
Front-line Bevacizumab in combination with Oxaliplatin, Leucovorin and 5-Fluorouracil (FOLFOX) in patients with metastatic colorectal cancer: a multicenter phase II study (2007)

The combination of FOLFOX4/bevacizumab appears to be highly effective, well tolerated and merits further evaluation in patients with mCRC.
Synchronization of cell division in microorganisms by percoll gradients (1980)

We describe a method for obtaining synchronously dividing cells of bacteria (Escherichia coli B and K-12 and Bacillus subtilis 168) and fission yeasts (Schizosaccharomyces pombe) by the use of Percoll density gradients.
Serum level of interleukin 6 as a prognosis factor in metastatic renal cell carcinoma. (1992)

Interleukin (IL) 6 was measured in the serum of 138 patients with metastatic renal carcinoma before the initiation of IL-2 treatment. IL-6 was detectable in 66 patients with renal cancer (48%) and in only 8 of 70 normal adults (11%). Serum C reactive protein (CRP) and IL-6 levels are correlated, suggesting that IL-6 is involved in CRP increase in these patients. The interval between diagnosis of the primary tumor and metastasis was shorter in patients with a detectable serum IL-6 and/or serum CRP level greater than 50 mg/liter. Serum IL-6 and CRP levels were higher in subgroups of patients previously defined as having a poor life expectancy according to the Eastern Cooperative Oncology Group criteria. Pretreatment concentrations of IL-6 and CRP were higher in patients who experienced progressive disease after IL-2 treatment. Patients with detectable IL-6 had a shorter survival from the beginning of IL-2 treatment than patients without circulating IL-6 (median, 8 versus 16 months). Similarly, the median survival from the beginning of IL-2 therapy of patients with CRP levels greater than 50 mg/liter was 6 months, compared to 16 months in those with CRP levels below this threshold. None of the 21 patients with serum IL-6 concentrations greater than 300 pg/ml achieved response to any of the three IL-2 regimens. This subgroup has a median survival of 5 months after IL-2 treatment and consisted of 15% of the patients in our series. These results indicate that serum IL-6 and CRP levels are adverse prognosis factors in patients with metastatic renal cell carcinoma. Serum IL-6 level could help in the selection or stratification of the patients in future IL-2 trials.
Latency and throughput tradeoffs in self-timed speed-independent pipelines and rings (1990)

Asynchronous pipelines control the flow of tokens through a sequence of logical stages based on the status of local completion detectors. As in a synchronously clocked circuit, the design of self-timed pipelines can trade off between achieving low latency and high throughput. However, there are more degrees of freedom because of the variances in specific latch and function block styles, and the possibility of varying both the number of latches between function blocks and their connections to the completion detectors. This report demonstrates the utility of a graph-based methodology for analyzing the timing dependencies and uses it to make comparisons of different configurations. It is shown that the extremes for high throughput and low latency differ significantly, the placement of the completion detectors influences timing as much as adding an additional latch, and the choice as to whether or static logic is best is dependent on the cost in complexity of the completion detectors.
Chemical Durability of Silicon Oxycarbide Glasses (2002)

Silicon oxycarbide (SiOC) glasses with controlled amounts of Si—C bonds and free carbon have been produced via the pyrolysis of suitable preceramic networks. Their chemical durability in alkaline and hydrofluoric solutions has been studied and related to the network structure and microstructure of the glasses. SiOC glasses, because of the character of the Si—C bonds, exhibit greater chemical durability in both environments, compared with silica glass. Microphase separation into silicon carbide (SiC), silica (SiO 2 ), and carbon, which usually occurs in this system at pyrolysis temperatures of &gt;1000°–1200°C, exerts great influence on the durability of these glasses. The chemical durability decreases as the amount of phase separation increases, because the silica/silicate species (without any carbon substituents) are interconnected and can be easily leached out, in comparison with the SiOC phase, which is resistant to attack by OH − or F − ions.
Characterization of an immunoglobulin binding protein homolog in the maize floury-2 endosperm mutant. (1991)

The maize b-70 protein is an endoplasmic reticulum protein overproduced in the floury-2 (fl2) endosperm mutant. The increase in b-70 levels in fl2 plants occurs during seed maturation and is endosperm specific. We have used amino acid sequence homology to identify b-70 as a homolog of mammalian immunoglobulin binding protein (BiP). Purified b-70 fractions contain two 75-kilodalton polypeptides with pl values of 5.3 and 5.4. Both 75-kilodalton polypeptides share several properties with BiP, including the ability to bind ATP and localization within the lumen of the endoplasmic reticulum. In addition, both b-70 polypeptides can be induced in maize cell cultures with tunicamycin treatment. Like BiP, the pl 5.3 form of b-70 is post-translationally modified by phosphorylation and ADP-ribosylation. However, modification of the pl 5.4 species was not detected in vitro or in vivo. Although the b-70 gene is unlinked to fl2, b-70 overproduction is positively correlated with the fl2 gene and is regulated at the mRNA level. In contrast, the fl2 allele negatively affects the accumulation of the major endosperm storage proteins. The physical similarity of b-70 to BiP and its association with abnormal protein accumulation in fl2 endoplasmic reticulum may reflect a biological function to mediate protein folding and assembly in maize endosperm.
The potential of a dielectrophoresis activated cell sorter (DACS) as a next generation cell sorter (2016)

Originally introduced by H. A. Pohl in 1951, dielectrophoretic (DEP) force has been used as a striking tool for biological particle manipulation (or separation) for the last few decades. In particular, dielectrophoresis activated cell sorters (DACSes) have been developed for applications in various biomedical fields. These applications include cell replacement therapy, drug screening and medical diagnostics. Since a DACS does not require a specific bio-marker, it is able to function as a biological particle sorting tool with numerous configurations for various cells [e.g. red blood cells (RBCs), white blood cells (WBCs), circulating tumor cells, leukemia cells, breast cancer cells, bacterial cells, yeast cells and sperm cells]. This article explores current DACS capabilities worldwide, and it also looks at recent developments intended to overcome particular limitations. First, the basic theories are reviewed. Then, representative DACSes based on DEP trapping, traveling wave DEP systems, DEP field-flow fractionation and DEP barriers are introduced, and the strong and weak points of each DACS are discussed. Finally, for the purposes of commercialization, prerequisites regarding throughput, efficiency and recovery rates are discussed in detail through comparisons with commercial cell sorters (e.g. fluorescent activated and magnetic activated cell sorters).
Prediction and measurement of particle velocities in ultrasonic standing waves. (2008)

A numerical model has been developed to predict particle trajectories in ultrasonic standing waves. The model includes an electroacoustic model that calculates the characteristics of the one-dimensional standing wave as a function of the input voltage to the piezoelectric transducer driving the cavity. Next, the acoustic radiation force is calculated for particles residing within the water filled cavity. Finally, the particle trajectories are calculated through integration of the equations of motion of the particles. Particle translation is achieved through a periodic sweeping of the excitation frequency. Translational velocities of 6-μm-diameter polystyrene spheres are calculated for a 2-MHz standing wave driven by a PZT-4 transducer. In the experiment a cavity is filled with water and polystyrene particles. A PZT-4 transducer operates near its resonance frequency of 2 MHz. Through a periodic sweeping of the frequency the particles are translated away from the transducer face and ultimately clump together near the rigid reflector at the opposite end. The particle translational velocity is a function of the sweep parameters, i.e., frequency range and sweep period. The calculated particle velocities are then compared to the measured velocities. Needle hydrophone measurements are used to characterize the acoustic standing wave.
Fulminant spontaneous autoimmunity of the central nervous system in mice transgenic for the myelin proteolipid protein-specific T cell receptor (2000)

Proteolipid protein (PLP)-139-151 is the dominant encephalitogenic peptide that induces experimental autoimmune encephalomyelitis (EAE) in SJL (H-2(s)) mice. To examine the contribution of T cell receptor (TCR) specificity in the induction of EAE, we generated transgenic mice expressing the rearranged TCR genes from an encephalitogenic or a nonencephalitogenic PLP-139-151/I-A(s)-specific T cell clone. Both types of transgenic lines developed spontaneous EAE, but, remarkably, the lines expressing the TCR from the nonencephalitogenic clone showed increasingly higher frequencies of disease (60-83%) in progressive SJL backcrosses and could not be propagated on the susceptible background. The T cells from the transgenic mice were not tolerized, because they responded vigorously to the antigen in vitro and mediated EAE when the mice were immunized with antigen. Besides being the only description of a TCR transgenic mice for the PLP-139-151/I-A(s) epitope, the results demonstrate that the TCR from a nonencephalitogenic PLP-specific T cell clone can induce autoimmune disease when expressed appropriately in vivo.
Immunity to influenza in ferrets V. Immunization with inactivated virus in adjuvant 65 (1973)

Ferrets infected with influenza virus A2/Hong Kong/3/68 responded with a febrile reaction; the temperature was elevated by 1.0 degrees C. or greater to a level of 40 degrees C. or more. In addition, relatively high titres of virus were recovered from nasal washings taken 3 days after virus infection, serum antibody was produced, increased nasal protein was detected and nasal washings contained both HI and neutralizing antibody. Of four ferrets immunized with 400 CCA units of inactivated influenza virus A2/Aichi/2/68 in saline, only one produced detectable serum HI antibody, and none produced detectable nasal antibody. These ferrets were subsequently found to be susceptible to intranasal infection with influenza virus A2/Hong Kong/3/68. Thus, the temperature response, the titre of virus recovered from nasal washings and the serum HI antibody response found after virus infection was similar to that found after infection of non-immunized ferrets. However, the increase in protein concentration and the titre of HI and neutralizing antibody found in nasal washings after virus infection was detectably less than that found after virus infection of non-immunized ferrets.Four ferrets were immunized with 400 CCA units of inactivated A2/Aichi/2/68 virus in adjuvant 65, and these ferrets produced relatively high titres of serum HI antibody but no detectable nasal antibody. After subsequent virus infection with influenza virus A2/Hong Kong/3/68, these ferrets showed a modified temperature response, reduced titres of virus in nasal washings compared to that found in nasal washings from non-immunized ferrets, no increase in nasal protein and no detectable nasal HI antibody. Thus, immunization with inactivated virus in adjuvant 65 resulted in a significant modification of the response of ferrets to challenge virus; however, the immunity was not complete, and appreciably less than that found after infection with live homologous virus.
Preoperative serum C-reactive protein level in non-small cell lung cancer. (2007)

The preoperative serum CRP level is an independent and significant indicator predictive of a poor prognosis in patients with NSCLC.
Luteinizing hormone-releasing hormone agonist and transferrin functionalizations enhance nanoparticle delivery in a novel bovine ex vivo eye model. (2006)

The ex vivo bovine eye model is a useful tool in understanding disposition of nanoparticles after topical delivery. The corneal epithelium is a significant barrier for topical nanoparticle delivery to the anterior segment. Surface modification of nanoparticles by conjugating an LHRH agonist or transferrin is a useful approach to provide rapid, efficient delivery of intact nanoparticles into and/or across cornea and conjunctiva.
Rat obesity gene fatty (fa) maps to chromosome 5: evidence for homology with the mouse gene diabetes (db). (1991)

The autosomal recessive mutations fa (rat) and db (mouse) cause obesity syndromes that develop early and ultimately become severe. Although both fa/fa rats and db/db mice have been studied extensively as models of human obesity and diabetes, the molecular bases of these phenotypes remain unknown. We have mapped fa in 50 fa/fa (obese) offspring of a (13M x Brown Norway) F1 fa/+ intercross relative to two molecular markers, Ifa and Glut-1, which flank db on mouse chromosome 4 and which are located on rat chromosome 5. Ifa and Glut-1 are linked to fa, with a gene order, Ifa-fa-Glut-1, that is identical to that for the region around db in the mouse genome. These results place fa on rat chromosome 5 and suggest that db and fa are mutations in homologous genes.
Curcumin activates the haem oxygenase-1 gene via regulation of Nrf2 and the antioxidant-responsive element (2003)

The transcription factor Nrf2, which normally exists in an inactive state as a consequence of binding to a cytoskeleton-associated protein Keap1, can be activated by redox-dependent stimuli. Alteration of the Nrf2-Keap1 interaction enables Nrf2 to translocate to the nucleus, bind to the antioxidant-responsive element (ARE) and initiate the transcription of genes coding for detoxifying enzymes and cytoprotective proteins. This response is also triggered by a class of electrophilic compounds including polyphenols and plant-derived constituents. Recently, the natural antioxidants curcumin and caffeic acid phenethyl ester (CAPE) have been identified as potent inducers of haem oxygenase-1 (HO-1), a redox-sensitive inducible protein that provides protection against various forms of stress. Here, we show that in renal epithelial cells both curcumin and CAPE stimulate the expression of Nrf2 in a concentration- and time-dependent manner. This effect was associated with a significant increase in HO-1 protein expression and haem oxygenase activity. From several lines of investigation we also report that curcumin (and, by inference, CAPE) stimulates ho-1 gene activity by promoting inactivation of the Nrf2-Keap1 complex, leading to increased Nrf2 binding to the resident ho-1 AREs. Moreover, using antibodies and specific inhibitors of the mitogen-activated protein kinase (MAPK) pathways, we provide data implicating p38 MAPK in curcumin-mediated ho-1 induction. Taken together, these results demonstrate that induction of HO-1 by curcumin and CAPE requires the activation of the Nrf2/ARE pathway.
Polymer-Binding Peptides for the Noncovalent Modification of Polymer Surfaces: Effects of Peptide Density on the Subsequent Immobilization of Functional Proteins (2011)

Peptides that specifically bind to polyetherimide (PEI) were selected, characterized, and used for the noncovalent modification of the PEI surface. The peptides were successfully identified from a phage-displayed peptide library. A chemically-synthesized peptide composed of the Thr-Gly-Ala-Asp-Leu-Asn-Thr sequence showed an extremely high binding constant for the PEI films (5.6 × 10(8) M(-1)), which was more than three orders of magnitude greater than that for the reference polystyrene films. The peptide was biotinylated and immobilized onto the PEI films to further immobilize streptavidin (SAv). The amount of SAv bound depended on the density of immobilized peptide. It gradually increased with an increasing density of immobilized peptide and achieved a maximum (2.1 pmol cm(-2)) at a peptide density of 19.8 pmol cm(-2). The ratio of peptide used for immobilizing SAv at the maximum value was only 11%, and was partially due to the low accessibility of SAv to the biotin moieties on the PEI films. Moreover, the amount of SAv bound gradually decreased at higher peptide densities, suggesting that the clustering of the peptides also inhibited the binding of SAv. Furthermore, peptides on the PEI films promoted the uniform immobilization of SAv with less structural denaturing. The immobilized SAv was able to further immobilize probe DNA to hybridize with its complementary DNA. These present results suggest that the density of immobilized peptide has a great impact on the surface modifications using polymer-binding peptides.
Improved Mie scattering algorithms (1980)

Scattering of electromagnetic radiation from a sphere, so-called Mie scattering, requires calculations that can become lengthy and even impossible for those with limited resources. At the same time, such calculations are required for the widest variety of optical applications, extending from the shortest UV to the longest microwave and radar wavelengths. This paper briefly describes new and thoroughly documented Mie scattering algorithms that result in considerable improvements in speed by employing more efficient formulations and vector structure. The algorithms are particularly fast on the Cray-1 and similar vector-processing computers.
Determinants of Inequality in Cameroon: A Regression-Based Decomposition Analysis (2013)

This paper applies the regression-based inequality decomposition approach to explore determinants of income inequality in Cameroon using the 2007 Cameroon household consumption survey. The contribution of each source to measured income inequality is the sum of its weighted marginal contributions in all possible configurations of sources as sanctioned by the Shapley value decomposition rule. Regressed-income sources attributable to education, health, urban residency, household size, fraction of active household members, working in the formal sector and farmland ownership are the main determinants of household income inequality in that order. These results have policy vocation that policy-mix that simultaneously combine efforts targeting human capital consolidation with other policy outlets will have an overall higher effectiveness for both total welfare enhancement and human capital development than when implemented alone. Keywords: Decomposition, Inequality, household Economic well-being and Cameroon BOJE: Botswana Journal of Economics, 11(15), 2-20