gebhart/patrepeval huggingface dataset:
Steroid Receptors in Breast Cancer (1979)

Knowledge of the steroid receptor content of human breast cancer is important for proper diagnosis and for deciding the proper treatment for metastatic disease. Few patients whose breast cancers lack estrogen receptor will benefit from endocrine therapy, while more than half of patients with estrophilin-rich cancers will obtain objective remissions. The probability of objective response to endocrine therapy increases with an increase in the quantity of estrogen receptor in the cancer. Furthermore, patients whose cancers have both estrogen and progestin receptors have a better probability of response than patients whose lesions have only one of the receptors present, although even in such cases the response rate is higher than that seen in patients whose tumors lack both receptors. The data currently available suggest that receptor assays carried out on the primary tumor can be used for prediction of subsequent response to endocrine therapy, even at a later time of recurrent disease. Nonetheless, while sequential assays of receptors in lesions from the same patients are likely to be in agreement, when changes occur they tend to be reductions in amount of receptor or loss of receptor during disease progression . Breast cancer patients with receptor-positive tumors appear to have longer disease-free intervals and prolonged survival when compared with patients whose cancers lack ER, but clearly a part of the prolonged survival relates to response to endocrine therapies. Receptor positivity is frequently associated with well-differentiated tumors, while more poorly differentiated cancers, as well as medullary tumors, in general, and possibly cancers with significant lymphocytic infiltration, are more likely to be receptor negative. While there are some problems reproducing the exact quantitative receptor results among various laboratories assaying the same breast cancer, standard biochemical assays are still the only clinically proven and generally accepted procedure for assessing receptor status of a tumor. Histochemical assays based both on the steroid content of a tumor or using steroid-protein fluorescein complexes, while showing some correlation with standard biochemical assays for estrogen receptor, do not appear to detect receptor protein itself and can not be used instead of standard receptor assays. With the recent availability of monoclonal antibodies to the estrogen receptor, newer assays based on immunochemical procedures are under development and can be expected to provide simpler, less expensive, and more useful biochemical as well as immunohistochemical methods for receptor determination.(ABSTRACT TRUNCATED AT 400 WORDS)
Modeling charge injection in MOS analog switches (1987)

Charge injection in MOS switches has been analyzed. The analysis has been extended to the general case of including source resistance and source capacitance. Universal plots of percentage channel charge injected are presented. Normalized variables are used to facilitate usage of the plots. A small-geometry switch, slow switching rate, and small source resistance can help reduce the charge injection effect.
Thermal Decomposition Pathways and Rates for Silane, Chlorosilane, Dichlorosilane, and Trichlorosilane (2001)

Calculations have been carried out for the thermal decomposition of silane, chlorosilane, dichlorosilane, and trichlorosilane. In each case, the stationary point geometries and harmonic frequencies were characterized using CASSCF/derivative methods and the cc-pVDZ basis set. Accurate energetics were obtained by combining the CCSD(T) results using the a-cc-pVTZ basis set with an extrapolation to the basis set limit using the a-cc-pVDZ, a-cc-pVTZ, and a-cc-pVQZ basis sets at the MP2 level. The geometries, energetics, and harmonic frequencies were used to obtain rate constants using conventional transition state theory. The barrier heights obtained in the present work (kcal/mol) are the following: SiH4 → SiH2 + H2 (61.9); SiClH3 → SiClH + H2 (66.7); SiClH3 → SiH2 + HCl (76.9); SiCl2H2 → SiCl2 + H2 (77.2); SiCl2H2 → SiClH + HCl (74.8); SiCl3H → SiCl2 + HCl (72.7). The computed barrier heights are believed to be accurate to within 1 kcal/mol. The rate coefficients obtained in the present work are in fair accord with most of the experimental results.
Finitary Set Theory (2009)

I argue for the use of the adjunction operator (adding a single new element to an existing set) as a basis for building a finitary set theory. It allows a simplified axiomatization for the first-order theory of hereditarily finite sets based on an induction schema and a rigorous characterization of the primitive recursive set functions. The latter leads to a primitive recursive presentation of arithmetical operations on finite sets.
Genetic Polymorphisms of Human Cytosol Glutathione <i>S</i> -Transferases and Prostate Cancer (2007)

Glutathione S-transferases (GSTs) are involved in the metabolism of a wide range of carcinogenic chemicals. In humans, cytosol GSTs are divided into eight classes: alpha (GSTA), mu (GSTM), pi (GSTP), theta (GSTT), tau (GSTZ), sigma (GSTS), omicron (GSTO) and kappa (GSTK). The allelic polymorphism of these enzymes is associated with variations in enzyme activity; hence, it may affect the concentration of activated carcinogenic chemicals in the body. In addition to the metabolism of chemical carcinogens, GSTs metabolize steroid hormones, compounds in the diet and other agents potentially involved in prostate carcinogenesis. Three genetic polymorphisms of GSTs, GSTM1*0 (null), GSTT1*0 (null) and GSTP1 A313G, have been well documented. No consistent associations between GSTM1, GSTT1 or GSTP1 genotypes and prostate cancer have been observed. Recent meta-analysis reports show that these polymorphisms of GSTM1, GSTT1 and GSTP1 are unlikely to be major determinants of susceptibility to prostate cancer.
Closed-form Maker fringe formulas for poled polymer thin films in multilayer structures (2011)

We report new closed-form expressions for Maker fringes of anisotropic and absorbing poled polymer thin films in multilayer structures that include back reflections of both fundamental and second-harmonic waves. The expressions, based on boundary conditions at each interface, can be applied to multilayer structures containing a buffer and a transparent conducting oxide layer, which might enhance multiple reflections of fundamental and second-harmonic waves inside a nonlinear thin film layer. This formulation facilitates Maker fringe analysis for a sample containing additional multilayer structures on either side of a poled polymer thin film. Experimental data and numerical simulations are given to indicate the importance of inclusion of such a reflective layer in analyses for reliable characterization of second-harmonic tensor elements.
Activated factor B (Bb) of the alternative pathway of complement activation cleaves and activates plasminogen. (1981)

Activated Factor B (Bb), the central serine esterase of the alternative pathway of complement activation, exhibits restricted substrate specificity in the complement system for C3 and C5. The results presented here indicate that Bb can cleave and activate plasminogen in an experimental system containing purified plasminogen and Bb; complement cellular intermediate bearing the Bb-enzyme; or cobra venom factor-stabilized Bb-enzyme (CVF,Bb). Cleavage of plasminogen by Factor Bb generated 2 disulfide-linked polypeptides with apparent m.w. of 64,000 and 25,000 to 32,000 (SDS-PAGE). Complement cellular intermediates containing the C3b, Bb-enzyme cleave 40 to 80% of 4.5 micrograms of 125I-labeled plasminogen during 30 min of incubation at 37 degrees C; native Factor B was inactive; and anti-Factor Blg inhibited by 100% the plasminogen cleavage mediated by complement cellular intermediates bearing the Bb-enzyme. Fibrinolytic activity was detected in plasminogen activator (PA) assays when purified plasminogen and 125I-labeled fibrin tubes were incubated with Bb, CVF, Bb, or complement cellular intermediates bearing the C3b,Bb-enzyme: 10 micrograms Bb released 40 to 65% of the 125I-fibrin released by 5 micrograms urokinase in 4 hr at 37 degrees C. Plasminogen activator activity of the C3b,Bb-enzyme was found to be regulated in serum. At dilutions of NHS 1:50, the PA-activity of 1.6 micrograms Bb was 100% inhibited, and at a 1:250 dilution, 50% inhibition was observed. This report describes a novel activity for the Bb-enzyme, which constitutes the C3/C5-convertase of the alternative pathway of complement activation.
Early B cell changes predict autoimmunity following combination immune checkpoint blockade (2018)

Combination checkpoint blockade (CCB) targeting inhibitory CTLA4 and PD1 receptors holds promise for cancer therapy. Immune-related adverse events (IRAEs) remain a major obstacle for the optimal application of CCB in cancer. Here, we analyzed B cell changes in patients with melanoma following treatment with either anti-CTLA4 or anti-PD1, or in combination. CCB therapy led to changes in circulating B cells that were detectable after the first cycle of therapy and characterized by a decline in circulating B cells and an increase in CD21lo B cells and plasmablasts. PD1 expression was higher in the CD21lo B cells, and B cell receptor sequencing of these cells demonstrated greater clonality and a higher frequency of clones compared with CD21hi cells. CCB induced proliferation in the CD21lo compartment, and single-cell RNA sequencing identified B cell activation in cells with genomic profiles of CD21lo B cells in vivo. Increased clonality of circulating B cells following CCB occurred in some patients. Treatment-induced changes in B cells preceded and correlated with both the frequency and timing of IRAEs. Patients with early B cell changes experienced higher rates of grade 3 or higher IRAEs 6 months after CCB. Thus, early changes in B cells following CCB may identify patients who are at increased risk of IRAEs, and preemptive strategies targeting B cells may reduce toxicities in these patients.
Permeabilization of the Mitochondrial Inner Membrane by Short Cecropin‐A–Melittin Hybrid Peptides (1994)

A number of cecropin-A-melittin hybrid peptides have previously been shown to be potent antibacterial agents [Andreu, D., Ubach, J., Boman, A., Wahlin, B., Wade, D., Merrifield, R. B. & Boman, H. G. (1992) FEBS Lett. 296, 190-194]. In the present report we analyze their action on biological systems using rat liver mitochondria as a test system. We demonstrate that the longest peptide, cecropin-A-(1-8)-melittin(1-18) permeabilizes the mitochondrial inner membrane allowing the movement of both charged and non-charged solutes. Concentrations used have already been shown to be bactericidal. This effect is also demonstrated under respiring conditions where succinate oxidation is uncoupled. Shorter analogs also permeabilize mitochondria although at ten-fold higher concentrations. Heparin potentiates the peptide effects at low concentrations, while at high concentration it becomes inhibitory. We propose that the cecropin-melittin analogs disrupt the mitochondrial membrane in a detergent-like mode rather than by creating selective channels as had been previously suggested.
Expression of Properly Folded Human Glutamate Decarboxylase 65 as a Fusion Protein in <i>Escherichia Coli</i> (1997)

Autoantibodies to the islet-cell 65-kDa variant of glutamate decarboxylase (GAD65) are found in most insulin-dependent diabetes mellitus (IDDM) patients many years before the appearance of clinical symptoms of the disease. As IDDM-preventive therapies may be available in the future, an international effort is taking place to develop widely applicable anti-GAD immunochemical tests. These tests would help to detect individuals at risk before the full installation of the disease and to enroll them in prevention programs. Autoantibodies to GAD65 are mostly directed to conformational epitopes, and the enzyme is a complex molecule with a prosthetic group and 15 cysteine residues. Thus, the conformational integrity of GAD65 is essential for an appropriate anti-GAD assay. Isolation of large amounts of GAD65 from pancreas or other tissues is impractical, and no successful production of properly folded GAD65 has been reported in bacteria. Native recombinant GAD65 for immunochemical tests is usually obtained from eukaryotic expression systems. Since the large-scale production of a recombinant protein in an eukaryotic system is expensive and technically difficult, we investigated the expression of GAD65 in Escherichia coli as an alternative. A number of DNA constructs intended to export the enzyme to the periplasmic space or to improve its cytoplasmic solubility were designed and tested. Our results provide a solution to the two main problems associated with the expression of GAD65 in E. coli: misfolding, leading to the formation of inclusion bodies; and the presence of alternative initiation sites for translation that causes the preferential production of truncated variants of GAD65. We describe here the production of properly folded, fully active, and immunochemically competent GAD65 as an N-terminal fusion protein with thioredoxin. An account of the reactivity of the produced protein with sera of six IDDM patients is also presented.
A low-cost two-way radio transceiver (2002)

A few years ago, NCR came to Bell Labs (the research arm of Lucent Technologies) with an unusual challenge. How do you build a two-way digital radio for well under one dollar? After overcoming the initial instinct to laugh it off as an impossible task, we started to investigate various options and architectures. This paper summarizes the technical solutions that went into the final design, which is now part of a successful NCR product offering.
Increase in <i>S</i>-adenosylmethionine decarboxylase in SV-3T3 cells treated with <i>S</i>-methyl-5′-methylthioadenosine (1987)

Treatment of SV-3T3 cells with the spermine synthase inhibitor S-methyl-5'-methylthioadenosine [AdoS+(CH3)2] led to a large increase in the activity of S-adenosylmethionine decarboxylase (AdoMetDC) without affecting ornithine decarboxylase. The elevation of AdoMetDC activity was due to an increased amount of enzyme protein, as demonstrated by radioimmunoassay and by immunoblotting. The increase in AdoMetDC protein was caused by at least three factors: an increase in the amount of translatable mRNA, an increased translation efficiency of the mRNA and an increase in the half-life of the protein. The depletion of spermine brought about by AdoS+(CH3)2 appeared to be responsible for the increased synthesis of AdoMetDC and for part of the decrease in its rate of degradation. An additional stabilization of the enzyme protein was probably due to the binding of AdoS+(CH3)2, which is also a weak inhibitor of AdoMetDC. These results demonstrate the importance of cellular spermine concentrations in regulating the activity of AdoMetDC, which is a key enzyme controlling polyamine synthesis.
Chimeric Smooth Muscle–Specific Enhancer/Promoters (2001)

Gene transfer with adenoviral vectors is an attractive approach for the treatment of atherosclerosis and restenosis. However, because expression of a therapeutic gene in nontarget tissues may have deleterious effects, artery-specific expression is desirable. Although expression vectors containing transcriptional regulatory elements of genes expressed solely in smooth muscle cells (SMCs) have proved efficient to restrict expression of the transgene, their use in the clinical setting can be limited by their reduced strength. In the present study, we show that low levels of transgene expression are obtained with the smooth muscle (SM)-specific SM22alpha promoter compared with the viral cytomegalovirus (CMV) enhancer/promoter. We have generated chimeric transcriptional cassettes containing either a SM (SM-myosin heavy chain) or a skeletal muscle (creatine kinase) enhancer combined with the SM22alpha promoter. With both constructs we observed significantly stronger expression that remains SM-specific. In vivo, reporter gene expression was restricted to arterial SMCs with no detectable signal at remote sites. Moreover, when interferon-gamma expression was driven by one of these two chimeras, SMC growth was inhibited as efficiently as with the CMV promoter. Finally, we demonstrate that neointima formation in the rat carotid balloon injury model was reduced to the same extent by adenoviral gene transfer of interferon-gamma driven either by the SM-myosin heavy chain enhancer/SM22alpha promoter or the CMV promoter. These results indicate that such vectors can be useful for the treatment of hyperproliferative vascular disorders.
DC drift activation energy of LiNbO<sub>3</sub> optical modulators based on thousands of hours of active accelerated aging tests (2002)

Activation energy Ea in the drift of a separate dc bias port of x-cut LiNbO/sub 3/ (LN) optical modulators has been estimated based on thousands of hours of accelerated aging test data. The obtained drift curves show peaking and suggest an absence of catastrophically increasing bias voltages in these x-cut LN modulators. The Ea values calculated from the first positive drift slope, the time to peak and the succeeding negative drift slope were 1.39, 1.25, and 1.47 eV, respectively, suggesting Ea /spl sim/ 1.4 eV.
Maximal oil recovery by simultaneous condensation of alkane and steam (2007)

This paper deals with the application of steam to enhance the recovery from petroleum reservoirs. We formulate a mathematical and numerical model that simulates coinjection of volatile oil with steam into a porous rock in a one-dimensional setting. We utilize the mathematical theory of conservation laws to validate the numerical simulations. This combined numerical and analytical approach reveals the detailed mechanism for thermal displacement of oil mixtures discovered in laboratory experiments. We study the structure of the solution, determined by the speeds and amplitudes of the several nonlinear waves involved. Thus we show that the oil recovery depends critically on whether the boiling-point of the volatile oil is around the water boiling temperature, or much below or above it. These boiling-point ranges correspond to three types of wave structures. When the boiling point of the volatile oil is near the boiling point of water, the striking result is that the speed of the evaporation front is equal or somewhat larger than the speed of the steam condensation front. Thus the volatile oil condenses at the location where the steam condenses too, yielding virtually complete oil recovery. Conversely, if the boiling point is too high or too low, there is incomplete recovery. The condensed volatile oil stays at the steam condensation location because the steam condensation front is a physical shock.
Circular dichroism of twisted photons in non-chiral atomic matter (2017)

We calculate the circular dichroism (CD) for absorption of the twisted photons, or optical vortices, by atoms, caused by atomic excitation into discrete energy levels. The effects of photon spin on the rates and cross sections of atomic photo-excitation are considered. It is demonstrated that although for electric dipole transitions the atomic excitation rates depend on the relative orientation of photon spin and orbital angular momentum (OAM), the resulting CD is zero. However, CD is nonzero for atomic transitions of higher multipolarity, peaking in the optical vortex center, resulting in preferred absorption of the photons with their spins aligned with OAM. The effects remain large in a paraxial limit, where analytic expressions are provided. The predicted spin asymmetries are equivalent to OAM dichroism for the fixed photon spin.
Mechanisms of gold biomineralization in the bacterium <i>Cupriavidus metallidurans</i> (2009)

While the role of microorganisms as main drivers of metal mobility and mineral formation under Earth surface conditions is now widely accepted, the formation of secondary gold (Au) is commonly attributed to abiotic processes. Here we report that the biomineralization of Au nanoparticles in the metallophillic bacterium Cupriavidus metallidurans CH34 is the result of Au-regulated gene expression leading to the energy-dependent reductive precipitation of toxic Au(III)-complexes. C. metallidurans, which forms biofilms on Au grains, rapidly accumulates Au(III)-complexes from solution. Bulk and microbeam synchrotron X-ray analyses revealed that cellular Au accumulation is coupled to the formation of Au(I)-S complexes. This process promotes Au toxicity and C. metallidurans reacts by inducing oxidative stress and metal resistances gene clusters (including a Au-specific operon) to promote cellular defense. As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au(0). Similar particles were observed in bacterial biofilms on Au grains, suggesting that bacteria actively contribute to the formation of Au grains in surface environments. The recognition of specific genetic responses to Au opens the way for the development of bioexploration and bioprocessing tools.
Stochastic modeling as a means of automatic speech recognition. (1975)

Abstract : Automatic recognition of continuous speech involves estimation of a sequence X(1), X(2), X(3), ..., X(T) which is not directly observed (such as the words of a spoken utterance), based on a sequence Y(1), Y(2), Y(3), ..., Y(T) of related observations (such as the sequence of acoustic parameter values) and a variety of sources of knowledge. Formally the author wishes to find the sequence x(1:T) which maximizes the a posteriori probability Pr(x(1:T))=(1:T) Y(1:T) =y(1:T),A,L.P,S), where A,L,P,S represent the acoustic-phonetic, lexical, phonological, and syntactic-semantic knowledge. A speech recognition system must attempt to approximate a solution to this problem, whether or not the system uses a formal stochastic model. The DRAGON speech recognition system models the knowledge sources as probalistic functions of Markov processes. The assumption of the Markov property allows the use of an optimal search strategy. A simplified implementation of the DRAGON system has been developed using knowledge A and L, and some of the knowledge from S.
Mitochondrial Inhibitory Factor 1 (IF1) Is Present in Human Serum and Is Positively Correlated with HDL-Cholesterol (2011)

Altogether, these data support the view that, in humans, circulating IF1 might affect HDL levels by inhibiting hepatic HDL uptake and also impact TG metabolism.
Enhanced Terahertz Detection Efficiency via Grating-Assisted Noncollinear Electro-Optic Sampling (2019)

Efficient, broadband terahertz detection through electro-optic sampling is an enabling technology for numerous applications, including time-resolved spectroscopy of condensed matter systems and fundamental investigations of the quantum vacuum. The technique is inherently sensitive, but ultimately limited by the intrinsic optical properties of the known nonlinear crystals. In this study the authors imprint a phase grating on the surface of a nonlinear crystal, to define a noncollinear detection geometry inside the crystal. This surface grating allows improved phase-matching conditions, which lead to a doubling of detection bandwidth and efficiency.