gebhart/patrepeval huggingface dataset:
Purification of cartilage-derived growth factor by heparin affinity chromatography. (1985)

Cartilage-derived growth factor (CDGF) was found to bind tightly to columns of immobilized heparin and could be eluted with concentrations of salt in the order of 1.6-1.8 M NaCl. The molecular weight of CDGF was estimated to be 18,000-20,000 by high performance liquid-size exclusion chromatography. The affinity of CDGF for heparin greatly facilitated its purification. Highly purified CDGF active at about 1-2 ng/ml was obtained when crude cartilage extract was applied to heparin-Sepharose and the growth factor activity was recycled over heparin-Sepharose two more times. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and silver stain visualization of highly purified CDGF showed one major polypeptide band with a molecular weight of about 19,000 containing over 95% of the protein and one minor polypeptide band containing the rest of the protein. Only the Mr 19,000 polypeptide was active after elution from the polyacrylamide gel. Although CDGF bound tightly to immobilized heparin, it did not bind to immobilized chondroitin sulfate or hyaluronic acid. In addition, CDGF bound to heparin much more tightly than did platelet-derived growth factor even though these two growth factors had similar isoelectric points of about 10. These results suggest that the binding of CDGF to heparin was due to a specific affinity of the 2 molecules for each other.
Self-aligned carbon nanotube transistors with charge transfer doping (2005)

This letter reports a charge transfer p-doping scheme which utilizes one-electron oxidizing molecules to obtain stable, unipolar carbon nanotube transistors with a self-aligned gate structure. This doping scheme allows one to improve carrier injection, tune the threshold voltage Vth, and enhance the device performance in both the “ON-” and “OFF-” transistor states. Specifically, the nanotube transistor is converted from ambipolar to unipolar, the device drive current is increased by 2–3 orders of magnitude, the device OFF current is suppressed and an excellent Ion∕Ioff ratio of 106 is obtained. The important role played by metal–nanotube contacts modification through charge transfer is demonstrated.
The Major Calpain Isozymes Are Long-lived Proteins (1996)

Calpains are intracellular Ca2+-dependent proteases that are thought to participate in Ca2+-associated signal transduction pathways. It has been proposed that calpains are activated by an autoproteolytic mechanism. If this is true one would expect a relatively short half-life for calpain protein in cells. To test this hypothesis, WI-38 human diploid fibroblasts were pulse-labeled with [35S]methionine, and calpain was immunoprecipitated at various times after chasing with nonradioactive methionine to determine residual radioactivity. The results demonstrated that the two major calpain isozymes, m-calpain and micro-calpain, had metabolic half-lives of approximately 5 days. Calpains were long-lived proteins in several human cell lines, A-431, HeLa, VA-13, C-33A, and TE2 cells. In addition, calpastatin, the calpain-specific inhibitor protein, also had a long metabolic half-life. These observations suggest that the model for calpain activation by autoproteolysis requires re-investigation. Based on a knowledge of calpain metabolic stability, a protocol was devised for chronic exposure of WI-38 cells and HeLa cells to a calpain small subunit antisense oligodeoxyribonucleotide. Depletion of calpain small subunit after 5 or more days of treatment led to inhibition of cell proliferation that could be reversed by removal of antisense oligodeoxyribonucleotide from the culture medium. Together with previous studies, these results indicate a requirement for calpains in mammalian cell proliferation.
A pragmatic approach to trellis-coded modulation (1989)

Since the early 1970s, for power-limited applications, the convolutional code constraint length K=7 and rate 1/2, optimum in the sense of maximum free distance and minimum number of bit errors caused by remerging paths at the free distance, has become the de facto standard for coded digital communication. This was reinforced when punctured versions of this code became the standard for rate 3/4 and 7/8 codes for moderately bandlimited channels. Methods are described for using the same K=7, rate 1/2 convolutional code with signal phase constellations of 8-PSK and 160PSK and quadrature amplitude constellations of 16-QASK, 64-QASK, and 256-QASK to achieve, respectively, 2 and 3, and 2, 4, and 6 b/s/Hz bandwidth efficiencies while providing power efficiency that in most cases is virtually equivalent to that of the best Ungerboeck codes for constraint length 7 or 64 states. This pragmatic approach to all coding applications permits the use of a single basic coder and decoder to achieve respectable coding (power) gains for bandwidth efficiencies from 1 b/s/Hz to 6 b/s/Hz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expansion of Melanoma-specific Cytolytic CD8+ T Cell Precursors in Patients with Metastatic Melanoma Vaccinated with CD34+ Progenitor-derived Dendritic Cells (2004)

Cancer vaccines aim at inducing (a) tumor-specific effector T cells able to reduce/eliminate the tumor mass, and (b) long-lasting tumor-specific memory T cells able to control tumor relapse. We have shown earlier, in 18 human histocompatibility leukocyte antigen (HLA)-A*0201 patients with metastatic melanoma, that vaccination with peptide-loaded CD34-dendritic cells (DCs) leads to expansion of melanoma-specific interferon gamma-producing CD8+ T cells in the blood. Here, we show in 9 out of 12 analyzed patients the expansion of cytolytic CD8+ T cell precursors specific for melanoma differentiation antigens. These precursors yield, upon single restimulation with melanoma peptide-pulsed DCs, cytotoxic T lymphocytes (CTLs) able to kill melanoma cells. Melanoma-specific CTLs can be grown in vitro and can be detected in three assays: (a) melanoma tetramer binding, (b) killing of melanoma peptide-pulsed T2 cells, and (c) killing of HLA-A*0201 melanoma cells. The cytolytic activity of expanded CTLs correlates with the frequency of melanoma tetramer binding CD8+ T cells. Thus, CD34-DC vaccines can expand melanoma-specific CTL precursors that can kill melanoma antigen-expressing targets. These results justify the design of larger follow-up studies to assess the immunological and clinical response to peptide-pulsed CD34-DC vaccines.
Physics and finance (1997)

The workshop will examine the strengths and weaknesses of a number of approaches developed to test evolutionary theories, including: econometric analysis, experiments, and calibrated simulation models. It will also explore the differences and commonalities among the approaches through papers that apply each of the approaches to evolutionary problems.
Studies of whole-body retention and clearance of inhaled noble gases. (1978)

The in vivo measurements of 127Xe and 79Kr clearance from the whole body indicate five components, with biologic half-times ranging from 13 sec to 17.04 h. The slowest component correlated highly with percent total-body fat, the half-time varying between 7.59 and 17.04 for xenon and between 4.20 and 9.62 h for krypton. The long-term retention was localized to regions of high fat content as determined by the coincidence mode of the whole-body counter and images obtained with the scintillation camera. The estimated dose based on the retention data of this study would indicate increased doses to body fat and gonads as compared with those previously calculated. These increased doses are due to the longer retention of noble gases in fat. After 10-min inhalations of a mixture of 127Xe and air and 79Kr and air, approximately one third of the total 127Xe and one fifth of the total 79Kr were transferred to the body tissues, extrapolated back to the start of gas washout. Of this amount, approximately 13% of the 127Xe and approximately 9% of the 79Kr were associated with the slowest component.
Aerosol dispersion in human lung: comparison between numerical simulations and experiments for bolus tests (1997)

Bolus inhalations of 0.87-micron-diameter particles were administered to 10 healthy subjects, and data were compared with numerical simulations based on a one-dimensional model of aerosol transport and deposition in the human lung (J. Appl. Physiol. 77: 2889-2898, 1994). Aerosol boluses were inhaled at a constant flow rate into various volumetric lung depths up to 1,500 ml. Parameters such as bolus half-width, mode shift, skewness, and deposition were used to characterize the bolus and to display convective mixing. The simulations described the experimental results reasonably well. The sensitivity of the simulations to different parameters was tested. Simulated half-width appeared to be insensitive to altered values of the deposition term, whereas it was greatly affected by modified values of the apparent diffusion in the alveolar zone of the lung. Finally, further simulations were compared in experiments with a fixed penetration volume and various flow rates. Comparison showed good agreement, which may be explained by the fact that half-width, mode shift, and skewness were little affected by the flow rate.
Galacto-oligosaccharide Synthesis from Lactose Solution or Skim Milk Using the β-Galactosidase from Bacillus circulans (2012)

The synthesis of galacto-oligosaccharides (GOS) catalyzed by a novel commercial preparation of β-galactosidase from Bacillus circulans (Biolactase) was studied, and the products were characterized by MS and NMR. Using 400 g/L lactose and 1.5 enzyme units per milliliter, the maximum GOS yield, measured by HPAEC-PAD analysis, was 165 g/L (41% w/w of total carbohydrates in the mixture). The major transgalactosylation products were the trisaccharide Gal-β(1→4)-Gal-β(1→4)-Glc and the tetrasaccharide Gal-β(1→4)-Gal-β(1→4)-Gal-β(1→4)-Glc. The GOS yield increased to 198 g/L (49.4% w/w of total carbohydrates) using a higher enzyme concentration (15 U/mL), which minimized the enzyme inactivation under reaction conditions. Using skim milk (with a lactose concentration of 46 g/L), the enzyme also displayed transgalactosylation activity: maximum GOS yield accounted for 15.4% (7.1 g/L), which was obtained at 50% lactose conversion.
In Vivo Photocrosslinking with Unnatural Amino Acid Mutagenesis (2002)

Shining a light on cells allows an intracellular protein to be covalently crosslinked to its in vivo binding partner. Unnatural amino acid mutagenesis is used to introduce a photocrosslinking amino acid into selected sites in monomers of a dimeric complex. In vivo surface-specific photocrosslinking of these monomers (see figure) is demonstrated by purification of the complexes formed and their identification by Western blot. This methodology may be used to elucidate the many varied interactions of proteins within the cell.
Finding the right consumer (2012)

The ultimate goal of advertisers are conversions representing desired user actions on the advertisers' websites in the form of purchases and product information request. In this paper we address the problem of finding the right audience for display campaigns by finding the users that are most likely to convert. This challenging problem is at the heart of display campaign optimization and has to deal with several issues such as very small percentage of converters in the general population, high-dimensional representation of the user profiles, large churning rate of users and advertisers. To overcome these difficulties, in our approach we use two sources of information: a seed set of users that have converted for a campaign in the past; and a description of the campaign based on the advertiser's website. We explore the importance of the information provided by each of these two sources in a principled manner and then combine them to propose models for predicting converters. In particular, we show how seed set can be used to capture the campaign-specific targeting constraints, while the campaign metadata allows to share targeting knowledge across campaigns. We give methods for learning these models and perform experiments on real-world advertising campaigns. Our findings show that the seed set and the campaign metadata are complimentary to each other and both sources provide valuable information for conversion optimization.
Characterization of Membrane-Bound Small GTP-Binding Proteins from Nicotiana tabacum (1995)

We have cloned nine cDNAs encoding small GTP-binding proteins from leaf cDNA libraries of tobacco (Nicotiana tabacum). These cDNAs encode distinct proteins (22-25 kD) that display different levels of identity with members of the mammalian Rab family: Nt-Rab6 with Rab6 (83%), Nt-Rab7a-c with Rab7 (63-70%), and Nt-Rab11a-e with Rab11 (53-69%). Functionally important regions of these proteins, including the "effector binding" domain, the C-terminal Cys residues for membrane attachment, and the four regions involved in GTP-binding and hydrolysis, are highly conserved. Northern and western blot analyses show that these genes are expressed, although at slightly different levels, in all plant tissues examined. We demonstrate that the plant Rab5, Rab6, and Rab11 proteins, similar to their mammalian and yeast counterparts, are tightly bound to membranes and that they exhibit different solubilization characteristics. Furthermore, we show that the yeast GTPase-activating protein Gyp6, shown to be specifically required to control the GTP hydrolysis of the yeast Ypt6 protein, could interact with tobacco GTP-binding proteins. It increases in vitro the GTP hydrolysis rate of the wild-type Nt-Rab7 protein. In addition, it also increases, at different levels, the GTP hydrolysis rates of a Nt-Rab7m protein with a Rab6 effector domain and of two other chimaeric Nt-Rab6/Nt-Rab7 proteins. However, it does not interact with the wild-type Nt-Rab6 protein, which is most similar to the yeast Ypt6 protein.
A high-performance BICMOS Technology with double-polysilicon self-aligned bipolar devices (1987)

A high-performance BICMOS technology is described which incorporates 12-GHz double-polysilicon self-aligned bipolar, fully salicided CMOS devices and 1-µm features. This process is applied to a new BICMOS gate design, called transistor feedback logic (TFL), to fabricate a divide-by-16 frequency divider with a maximum operating frequency of 364 MHz. Availability of uncompromised MOS and bipolar transistors allows a free mix of pure CMOS, pure bipolar, or BICMOS gates on the same chip.
Damage-Associated Molecular Patterns in Inflammatory Diseases (2018)

Damage-associated molecular patterns (DAMPs) are endogenous danger molecules that are released from damaged or dying cells and activate the innate immune system by interacting with pattern recognition receptors (PRRs). Although DAMPs contribute to the host's defense, they promote pathological inflammatory responses. Recent studies have suggested that various DAMPs, such as high-mobility group box 1 (HMGB1), S100 proteins, and heat shock proteins (HSPs), are increased and considered to have a pathogenic role in inflammatory diseases. Here, we review current research on the role of DAMPs in inflammatory diseases, including rheumatoid arthritis, systemic lupus erythematosus, osteoarthritis, atherosclerosis, Alzheimer's disease, Parkinson's disease, and cancer. We also discuss the possibility of DAMPs as biomarkers and therapeutic targets for these diseases.
Low loss etchless silicon photonic waveguides (2009)

We demonstrate low loss silicon waveguides fabricated without any silicon etching. We define the waveguides by selective oxidation which produces ultra-smooth sidewalls with width variations of 0.3 nm. The waveguides have a propagation loss of 0.3 dB/cm at 1.55 microm. The waveguide geometry enables low bending loss of approximately 0.007 dB/bend for a 90 degrees bend with a 50 microm bending radius.
Stress Corrosion Cracking and Life Prediction Evaluation of Austenitic Stainless Steels in Calcium Chloride Solution (1996)

The stress corrosion cracking (SCC) susceptibility of austenitic stainless steels (SS) in calcium chloride (CaCl2) solutions was studied using a constant-load method. Initiation and propagation of stress corrosion cracks were examined using fractography. The distribution of cracks was classified. A physical cracking was introduced, and creep deformation measurements were performed. The steady-state strain rate (ε˙SS) obtained from the corrosion elongation curve (elongation-vs-time curve) showed a linear function of time to failure (tf). This implied that ε˙SS can be applied as a parameter for prediction of tf. Furthermore, ε˙SS below which no failure occurs within a laboratory time scale was estimated. Based on results obtained, the critical values of stress (σ) below which no SCC occurred were evaluated. Based upon creep measurements in a noncorrosive environment, the influence of environment on ε˙SS was more than fivefold. Cracking characteristics were divided into three categories according to the crack initiation distribution. Transgranular cracking predominated at relatively low σ and ε˙SS.
Determination of the sequence of spaE and identification of a promoter in the subtilin (spa) operon in Bacillus subtilis (1992)

An 851-residue open reading frame (ORF) called SpaE has been discovered in the subtilin (spa) operon. Interruption of this ORF with a chloramphenicol acetyltransferase gene destroys the ability of Bacillus subtilis LH45 delta c (a derivative of B. subtilis 168) to produce subtilin, which is an antimicrobial peptide belonging to the class of ribosomally synthesized peptide antibiotics called lantibiotics. SpaE shows strong homology to NisB, which is in the nisin (nis) operon in Lactococcus lactis ATCC 11454. Despite the strong sequence homology between SpaE and NisB, the spaE and nisB genes occupy very different locations in their respective operons, indicating that they have been evolving separately for a long time. Primer extension analysis was employed to identify a promoter upstream from the spaE gene, which appears to define the 5' end of the spa operon, which contains four other ORFs (Y. J. Chung, M. T. Steen, and J. N. Hansen, J. Bacteriol. 174:1417-1422, 1992).
Carboxyl-terminal truncation of recombinant factor XIII A-chains. Characterization of minimum structural requirement for transglutaminase activity. (1994)

A series of truncation mutants lacking 218, 229, 250, and 269 amino acid residues from the carboxyl terminus of blood coagulation factor XIII A-chains (FXIII A), designated as delta K513, delta A502, delta Y481, and delta K462, respectively, were expressed in Escherichia coli to define the minimum structure required for transglutaminase activity. delta K513 and delta A502 displayed a 3.8-4.7-fold reduction in the Kcat with no change in the Km for the glutamine substrate and a 2-fold increase in the Km of the primary amine substrate. There was no detectable transglutaminase activity for either thrombin-activated delta Y481 or delta K462. The rate of ammonia release of thrombin-activated delta K513 and delta A502 was reduced 6- and 4-fold, respectively, whereas ammonia release was not detected for the delta Y481 and delta 462 mutants. The Kact for calcium ions of the delta K513 mutant was similar to recombinant FXIIIa, whereas, it was increased by approximately 3-fold for the delta A502 mutant. The rate of fibrin gamma-chain dimer formation for the delta K513 and delta A502 mutants was reduced by approximately 19-fold. delta K462 did not bind to fibrin, while all of the other thrombin-cleaved mutants were bound. In conclusion, these results documented that the carboxyl-terminal calcium binding domain (Asp468-Glu495) was important for FXIIIa to adopt the correct conformation to ensure that efficient catalysis occurred.
Inducible Amplification of Gene Copy Number and Heterologous Protein Production in the Yeast Kluyveromyces lactis (1999)

Heterologous protein production can be doubled by increasing the copy number of the corresponding heterologous gene. We constructed a host-vector system in the yeast Kluyveromyces lactis that was able to induce copy number amplification of pKD1 plasmid-based vectors upon expression of an integrated copy of the plasmid recombinase gene. We increased the production and secretion of two heterologous proteins, glucoamylase from the yeast Arxula adeninivorans and mammalian interleukin-1beta, following gene dosage amplification when the heterologous genes were carried by pKD1-based vectors. The choice of the promoters for expression of the integrated recombinase gene and of the episomal heterologous genes are critical for the mitotic stability of the host-vector system.
Differential Role of IFN-γ-Inducible Protein 10 kDa in a Cockroach Antigen-Induced Model of Allergic Airway Hyperreactivity: Systemic Versus Local Effects (2002)

The ability of IFN-gamma to antagonize established Th2 type allergic responses is well documented. To investigate the role of IFN-gamma-inducible protein 10 kDa (IP10) in the allergic response, we chose to investigate the effect of IP10 neutralization on an established Th2 response. Systemic neutralization of IP10 at the time of allergen challenge increased airway hyperreactivity as well as airway eosinophil accumulation. Interestingly, IFN-gamma levels were markedly reduced in both the lung and peripheral lymph node following IP10 neutralization. Furthermore, the number of CXCR3(+)CD4(+) T cells was decreased in the peripheral lymph node following neutralization of IP10. Introduction of exogenous IP10 into the airway at the time of allergen challenge also dramatically increased eosinophil accumulation in the airway. Protein levels of IL-4, IL-5, and IL-13 were significantly increased in the lung following exogenous airway administration of IP10 with allergen. Interestingly, airway hyperreactivity was significantly decreased at early time points following concurrent IP10 and allergen challenge but rebounded at 24 and 48 h post allergen challenge. Although IP10 may initially be acting locally to dampen the allergic response, its ability to recruit eosinophils may ultimately supersede any immunomodulatory effect it may have in an established allergic response. These results suggest that while systemic levels of IP10 are beneficial in controlling the allergic response, possibly by regulating cellular trafficking in the lymph node, local administration of exogenous IP10 into an established allergic response may be detrimental.
Exotoxins of Staphylococcus aureus (2000)

This article reviews the literature regarding the structure and function of two types of exotoxins expressed by Staphylococcus aureus, pyrogenic toxin superantigens (PTSAgs) and hemolysins. The molecular basis of PTSAg toxicity is presented in the context of two diseases known to be caused by these exotoxins: toxic shock syndrome and staphylococcal food poisoning. The family of staphylococcal PTSAgs presently includes toxic shock syndrome toxin-1 (TSST-1) and most of the staphylococcal enterotoxins (SEs) (SEA, SEB, SEC, SED, SEE, SEG, and SEH). As the name implies, the PTSAgs are multifunctional proteins that invariably exhibit lethal activity, pyrogenicity, superantigenicity, and the capacity to induce lethal hypersensitivity to endotoxin. Other properties exhibited by one or more staphylococcal PTSAgs include emetic activity (SEs) and penetration across mucosal barriers (TSST-1). A detailed review of the molecular mechanisms underlying the toxicity of the staphylococcal hemolysins is also presented.
Ethnic differences in genetic susceptibility to atopy and asthma. (1999)

The genetics of asthma and atopy is complex, but can be approached by studies of both candidate genes and mapping of susceptibility loci. Genetic factors conferring susceptibility to disease may vary among ethnic groups. We present our experience with some candidate gene studies for asthma and atopy and susceptibility locus mapping for linkage to chromosome 5q.