gebhart/patrepeval huggingface dataset:
Nucleotide sequence of mouse IL-2 receptor cDNA and its comparison with the human IL-2 receptor sequence (1985)

We have cloned cDNA encoding the mouse interleukin-2 (IL-2) receptor from a murine T cell line, CTLL using human IL-2 receptor cDNA as probe. COS 7 cells transfected with the cDNA expressed the antigen recognized by the monoclonal antibody against the murine IL-2 receptor. The cDNA identified 4 species of mRNA (4.5, 3.5, 2.2 and 1.5 kb) of the mouse IL-2 receptor in CTLL cells. Difference in the length of mRNA seems to be ascribed to the variable length of the 3' untranslated sequence. Total nucleotide sequence (approximately 1400 bp) of this cDNA was determined and compared with the human receptor. The nucleotide and amino acid sequences of the IL-2 receptor are 70% and 60%, respectively, homologous in average between the two species. The comparison has revealed several conserved regions localized to particular exons such as transmembrane and cytoplasmic portions, suggesting that these regions are important for receptor function and its regulation.
Influence of inflammatory cells and serum on the performance of implantable glucose sensors (2000)

The objective of this investigation was to evaluate the influence of polymorphonuclear granulocytes on the performance of uncoated and cellulose acetate/Nafion coated amperometric glucose sensors in vitro. The response of these sensors was also investigated in serum. Uncoated and coated sensors showed lower sensitivities to glucose, with a significant drift in sensor output upon exposure to serum or leukocytes. Although the use of a coating resulted in higher sensitivity, the progressive loss of output was not completely prevented. Stimulated granulocytes were shown to excrete components, probably catalase and myeloperoxidase, which consumed the hydrogen peroxide formed by the oxidation of glucose. In addition, adsorbed serum proteins formed a diffusional barrier for glucose. Furthermore, serum was found to contain low-molecular weight components that alone inhibited glucose oxidase activity. Based on preliminary electrochemical results, we postulate that rabbit serum contains oxidizing substrates that compete with molecular oxygen for the acceptance of electrons from the oxidized enzyme. Consequently, future efforts should be aimed at elucidating the mechanisms involved in the interference of unknown serum components with electron transfer. In addition, further investigations have to be performed to develop an outer membrane that minimizes protein adsorption as well as the actions of inflammatory cells.
Immunotherapy with intralesional Candida albicansantigen in resistant or recurrent warts: A study (2013)

The small sample size and lack of control group are the main limitations of the study.
Injection, transport and recombination of charge carriers in organic light-emitting diodes (1998)

Depending on the magnitude of the energy barrier for charge carrier injection from the electrode(s) the current flowing through a light-emitting diode (LED) can be either space charge-limited or injection-limited. The first alternative, reflected in j(E) characteristics obeying Child’s law, requires the electrode to be ohmic. Various injection models are discussed, favoring a hopping description for the escape of a charge carrier from the image charge potential in an energetically disordered system. Information concerning the mobility of charge carriers can be inferred from time of flight studies, from space charge limited currents, as well as from transient absorption due to the momentary space charge stored inside the sample. A simple model, building on the proven validity of Langevin-type electron hole recombination in organic solids, is able to explain the recombination yield in single-layer LEDs as a function of the cell current. A more elaborate analytic theory is described for bilayer systems in which internal energy barriers give rise to charge accumulation and to a concomitant redistribution of the electric field. © 1998 John Wiley & Sons, Ltd.
The SIFT algorithm for fundamental frequency estimation (1972)

In this paper a new method for estimating F <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> , the fundamental frequency of voiced speech versus time, is presented. The algorithm is based upon a simplified version of a general technique for fundamental frequency extraction using digital inverse filtering. It is demonstrated that the simplified inverse filter tracking algorithm (hereafter referred to as the SIFT algorithm) encompasses the desirable properties of both autocorrelation and cepstral pitch analysis techniques. In addition, the SIFT algorithm is composed of only a relatively small number of elementary arithmetic operations. In machine language, SIFT should run in several times real time while with special-purpose hardware it could easily be realized in real time.
Advances, challenges and opportunities in 3D CMOS sequential integration (2011)

3D sequential integration enables the full use of the third dimension thanks to its high alignment performance. In this paper, we address the major challenges of 3D sequential integration: in particular, the control of molecular bonding allows us to obtain pristine quality top active layer. With the help of Solid Phase Epitaxy, we can match the performance of top FET, processed at low temperature (600°C), with the bottom FET devices. Finally, the development of a stable salicide enables to retain bottom performance after top FET processing. Overcoming these major technological issues offers a wide range of applications.
Unmasking PD-1 Resistance by Next-Generation Sequencing (2016)

Monoclonal antibodies that inhibit the programmed death 1 (PD-1)–programmed death ligand 1 (PD-L1) pathway are clinically active against a broad range of tumors; however, even the most susceptible tumors (e.g., melanoma) respond less than half the time because of innate resistance. In this issue of the Journal, Zaretsky et al.1 describe the use of whole-exome sequencing to identify mechanisms of acquired immune resistance in tumors from patients with melanoma who had a relapse after more than 6 months of tumor response to treatment with pembrolizumab. Tumor regression after PD-1–PD-L1 blockade is presumed to be mediated by the activation of tumor-infiltrating . . .
Species-Specific Tropism Determinants in the Human Immunodeficiency Virus Type 1 Capsid (2004)

Retroviral tropism is determined in part by cellular restriction factors that block infection by targeting the incoming viral capsid. Indeed, human immunodeficiency virus type 1 (HIV-1) infection of many nonhuman primate cells is inhibited by one such factor, termed Lv1. In contrast, a restriction factor in humans, termed Ref1, does not inhibit HIV-1 infection unless nonnatural mutations are introduced into the HIV-1 capsid protein (CA). Here, we examined the infectivity of a panel of mutant HIV-1 strains carrying substitutions in the N-terminal CA domain in cells that exhibit restriction attributable to Lv1 or Ref1. Manipulation of HIV-1 CA could alter HIV-1 tropism, and several mutations were identified that increased or decreased HIV-1 infectivity in a target-cell-specific manner. Many residues that affected HIV-1 tropism were located in the three variable loops that lie on the outer surface of the modeled HIV-1 conical capsid. Some tropism determinants, including the CypA binding site, coincided with residues whose mutation conferred on HIV-1 CA the ability to saturate Ref1 in human cells. Notably, a mutation that reverses the infectivity defect in human cells induced by CypA binding site mutation inhibits recognition by Ref1. Overall, these findings demonstrate that exposed variable loops in CA and a partial CypA "coat" can modulate restriction and HIV-1 tropism and suggest a model in which the exposed surface of the incoming retroviral capsid is the target for inhibition by host cell-specific restriction factors.
Quantitative structure-activity relationships for oxidation reactions of organic chemicals in water (2003)

Even in the absence of microbiological mediation, oxidation is one of the most important chemical processes contributing to the degradation of organic contaminants in the aquatic environment. The oxidants that are responsible for these reactions include hydroxyl radical, carbonate radical, organic oxyl and peroxyl radicals, peroxides, excited triplet states of organic chromophores, singlet molecular oxygen, ozone, chlorine dioxide, permanganate, and chromate. Some of these oxidants contribute to natural attenuation of organic contaminants, but many are of greater interest because of their role in engineered remediation technologies. Kinetic studies of these processes have lead to numerous quantitative structure-activity relationships (QSARs). Many of these QSARs are simple empirical correlations to common convenient descriptor variables like Hammett constants (sigma), half-wave oxidation potentials (E1/2), energies of the highest occupied molecular orbital (E(HOMO)) or rate constants for other oxidation reactions. However, several environmentally relevant, aqueous-phase oxidation reactions have been described with QSARs based on theoretical models for electron transfer that were developed by Marcus-Hush and Rehm-Weller. This review summarizes many of the reported QSARs for aquatic oxidations of organic compounds with emphasis on the interrelation between traditional empirical models and the potential for future development of QSARs based on theoretical models.
The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T-DNA (1986)

We used a binary-vector strategy to study the hypervirulence of Agrobacterium tumefaciens A281, an L,L-succinamopine strain. Strain A281 is hypervirulent on several solanaceous plants. We constructed plasmids (pCS65 and pCS277) carrying either the transferred DNA (T-DNA) or the remainder of the tumor-inducing (Ti) plasmid (pEHA101) from this strain and tested each of these constructs in trans with complementary regions from heterologous Ti plasmids. Hypervirulence on tobacco could be reconstructed in a bipartite strain with the L,L-succinamopine T-DNA and the vir region on separate plasmids. pEHA101 was able to complement octopine T-DNA to hypervirulence on tobacco and tomato plants. Nopaline T-DNA was complemented better on tomato plants by pEHA101 than it was by its own nopaline vir region, but not to hypervirulence. L,L-Succinamopine T-DNA could not be complemented to hypervirulence on tobacco and tomato plants with either heterologous vir region. From these results we suggest that the hypervirulence of strain A281 is due to non-T-DNA sequences on the Ti plasmid.
New perspectives on the involvement of mTOR in depression as well as in the action of antidepressant drugs (2015)

Despite the revolution in recent decades regarding monoamine involvement in the management of major depressive disorder (MDD), the biological mechanisms underlying this psychiatric disorder are still poorly understood. Currently available treatments require long time courses to establish antidepressant response and a significant percentage of people are refractory to single drug or combination drug treatment. These issues, and recent findings demonstrating the involvement of synaptic plasticity in the pathophysiological mechanisms of MDD, are encouraging researchers to explore the molecular mechanisms underlying psychiatric disease in more depth. The discovery of the rapid antidepressant effect exerted by glutamatergic and cholinergic agents highlights the mammalian target of rapamycin (mTOR) pathway as a critical pathway that contributes to the efficacy of these pharmacological agents in clinical and pre-clinical research. The mTOR pathway is a downstream intracellular signal that transmits information after the direct activation of α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) and neurotrophic factor receptors. Activation of these receptors is hypothesized to be one of the major axes involved in the synthesis of synaptogenic proteins underlying synaptic plasticity and critical to both the rapid and delayed effects exerted by classic antidepressants. This review focuses on the involvement of mTOR in the pathophysiology of depression and on molecular mechanisms involved in the activity of emerging and classic antidepressant agents.
A Method for Calibrating Diffusion Gradients in Diffusion Tensor Imaging (2007)

The protocol and retrospective correction are shown to be effective. The method may be used for prospective correction if actual diffusion-gradient waveforms are available. The methodology is expandable to general diffusion imaging schemes.
Interfacial properties of coal: a guide to catalyst loading and dispersion for coal conversion (1996)

Electrokinetic and adsorption studies have shown that the loading, dispersion and activities of coal-conversion catalysts can be enhanced by controlling the pH and the charge at the coal-water interface. 2 refs., 5 figs.
Improved Method for Detection of Vibrio parahaemolyticus in Seafood (2001)

We have developed a new, effective procedure for detecting Vibrio parahaemolyticus in seafoods using enrichment and plating onto a chromogenic agar medium. Samples were cultured in salt Trypticase soy broth, which is a nonselective medium, and then a portion of the culture was cultured with salt polymyxin broth, which is a selective medium for V. parahaemolyticus. This two-step enrichment was more effective than the one-step enrichment in salt polymyxin broth alone. The enrichment cultures were then plated onto a new chromogenic agar containing substrates for beta-galactosidase. The V. parahaemolyticus colonies developed a purple color on this growth medium that distinguished them from other related bacterial strains. V. parahaemolyticus was isolated more frequently from naturally contaminated seafood samples using the chromogenic agar than thiosulfate citrate bile salts sucrose agar medium, which is currently used for the isolation of V. parahaemolyticus. Our findings suggest that this new enrichment and isolation scheme is more sensitive and accurate for identifying V. parahaemolyticus in seafood samples than previously used methods.
Factors Associated With Death in Critically Ill Patients With Coronavirus Disease 2019 in the US (2020)

This study identified demographic, clinical, and hospital-level risk factors that may be associated with death in critically ill patients with COVID-19 and can facilitate the identification of medications and supportive therapies to improve outcomes.
Colony Variants of Neisseria Meningitidis Strain 2996 (B: 2b: P1.2): Influence of Class-5 Outer Membrane Proteins and Lipopolysaccharides (1985)

Different colonial morphologies were found among colonies of Neisseria meningitidis strain 2996 (B:2b:P1.2). Examination of cultures, selected on the basis of colony transparency or opacity, revealed that both lipopolysaccharides (LPS) and class-5 outer membrane proteins (OMP) are associated with differences in colonial morphology. Among 13 variants, four LPS variants and two class-5 OMP variants were recognised. All variants were non-fimbriate. The LPS variations were confirmed by immunoprecipitation. In addition to these qualitative variations of LPS, meningococci synthesise LPS of different molecular size depending upon growth phase; larger LPS molecules were found after analysis of stationary-phase cultures than with exponential-phase cultures. These changes did not cause a change in serotyping characteristics. The recognition in this study of intra-strain heterogeneity of meningococcal LPS and class-5 OMPs is important for the understanding of meningococcal pathogenicity. This heterogeneity was also detected in simultaneous isolates from different sites of a patient.
Passive and Active Inclusion of Host Proteins in Human Immunodeficiency Virus Type 1 Gag Particles during Budding at the Plasma Membrane (2004)

Human immunodeficiency virus type 1 particles form by budding at the surface of most cell types. In this process, a piece of the plasma membrane is modified into an enveloped virus particle. The process is driven by the internal viral protein Pr55(gag). We have studied how host proteins in the membrane are dealt with by Pr55(gag) during budding. Are they included in or excluded from the particle? The question was approached by measuring the relative concentrations of host and viral proteins in the envelope of Pr55(gag) particles and in their donor membranes in the cell. We observed that the bulk of the host proteins, including actin and clathrin, were passively included into the virus-like Gag particles. This result suggests that budding by Pr55(gag) proceeds without significant alteration of the original host protein composition at the cell membrane. Nevertheless, some proteins were concentrated in the particles, and a few were excluded. The concentrated proteins included cyclophilin A and Tsg-101. These were recruited to the plasma membrane by Pr55(gag). The membrane-bound cyclophilin A was concentrated into particles as efficiently as Pr55(gag), whereas Tsg-101 was concentrated more efficiently. The latter finding is consistent with a role for Tsg-101 in Gag particle release.
Normalized Mutual Information Feature Selection (2009)

A filter method of feature selection based on mutual information, called normalized mutual information feature selection (NMIFS), is presented. NMIFS is an enhancement over Battiti's MIFS, MIFS-U, and mRMR methods. The average normalized mutual information is proposed as a measure of redundancy among features. NMIFS outperformed MIFS, MIFS-U, and mRMR on several artificial and benchmark data sets without requiring a user-defined parameter. In addition, NMIFS is combined with a genetic algorithm to form a hybrid filter/wrapper method called GAMIFS. This includes an initialization procedure and a mutation operator based on NMIFS to speed up the convergence of the genetic algorithm. GAMIFS overcomes the limitations of incremental search algorithms that are unable to find dependencies between groups of features.
Analytical and micromagnetic modeling for detection of a single magnetic microbead or nanobead by spin valve sensors (2003)

We present a simple analytical model based on the Stoner-Wohlfarth model for the detection of a single magnetic microbead or nanobead by spin valve sensors. Two-dimensional micromagnetic simulations were also performed for the spin valve sensors. It is found that the analytical model fits well with the micromagnetic simulations in the case of the microbead, although it underestimates the effect of a nanobead. Experiments were carried out to detect a single superparamagnetic microbead (Dynabeads/spl reg/ M-280, 2.8 /spl mu/m in diameter) on the fabricated spin valve sensors. The experimental results were found to be consistent with the analytical and micromagnetic models.
Digital quantification of mutant DNA in cancer patients (2006)

In this review, we discuss the clinical utility of mutant DNA quantification in cancer patients in the context of recent technical advances made in digital mutation detection.
The digital baton: a versatile performance instrument (1997)

The Digital Baton is a new electronic instrument which has been designed and built for the performance of computer music. The principle motivation for its design was to create a gestural controller which replicated as closely as possible the feel of a traditional conducting baton while retaining the maximum number of intuitive control parameters for the user. The Digital Baton contains several sensor systems which capture many of the modalities of hand motion and gesture for their application toward both discrete controls and continuous, expressive gestures. Current software for the Digital Baton makes use of its sensing functions in real-time music performance systems.
Directed lysis of experimental cancer byβ‐carotene in liposomes (1991)

The purpose of this study was to extend the knowledge of the antitumor activity of liposomes and to identify, for the first time, the antitumor effect of liposomes with the antioxidant beta-carotene. The administration of the carotenoid encapsulated in in liposomes has the advantages of quantitation, facilitation, and most importantly an increased therapeutic response, resulting in the accentuation of regression of carcinoma in the hamster pouch. Tumors induced after the application of the carcinogen 7,12-dimethylbenz[alpha]anthracene (0.5%) were injected with liposomes composed of phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine in a ratio of 1:1:1 (large unilamellar vesicles). Tumor-bearing animals were divided into four groups, each containing 10 hamsters. The group treated with the liposomes of beta-carotene exhibited a significantly lower tumor burden (approx 5,000-fold difference) than the control tumor group. Electron- and light-micrographic analyses were used to substantiate the gross observations of tumor regression. It was noted that the carcinoma cells endocytozed liposomes in increased numbers compared with normal mucosa treated with liposomes. In addition, non-tumor-bearing hamsters injected with beta-carotene liposomes or liposomes alone did not exhibit any pathological change to the normal mucosa. An inflammatory infiltrate consisting of mononuclear cells, mast cells, and some polymorphonuclear leukocytes was noted, and degranulating polymorphonuclear leukocytes and mast cells and eosinophils predominated in the tumor controls (7,12-dimethylbenz[alpha]anthracene treated only). Notably, not all areas of degenerating dysplasia or early carcinoma exhibited a dense inflammatory response adjacent to the mucosa after the injection of beta-carotene liposomes. The results demonstrate a selective nontoxic therapy to regress experimental oral cancer.
Tryptophans 286 and 288 in the C-terminal Region of Protein B23.1 are Important for Its Nucleolar Localization (2002)

Nucleolar protein B23 can shuttle between the nucleolus and cytoplasm. However, the mechanism involved in the protein moving and staying in the nucleolus is not fully understood. To identify the nucleolar localization signal sequence of protein B23, we examined the subnuclear location of B23.1 mutant proteins fused with green fluorescent protein in HeLa cells. The results suggested that the two C-terminal tryptophan residues (Trp-286 and Trp-288) of protein B23.1 were important in this phenomenon.
Phase II Multicenter Study of the Epidermal Growth Factor Receptor Antibody Cetuximab and Cisplatin for Recurrent and Refractory Squamous Cell Carcinoma of the Head and Neck (2005)

Cetuximab and cisplatin is an active regimen in refractory SCCHN. The relative contribution of cetuximab is better defined in a single-agent trial. Cetuximab did not exacerbate cisplatin toxicity but was associated with skin rash in a majority of patients and occasional serious allergic reactions. Further study of this compound is warranted.
PCR and FISH Detection Extends the Range of Pfiesteria piscicida in Estuarine Waters (1999)

PCR and fluorescent in situ hybridization probes were used to assay for the presence of the dinoflagellate Pfiesteria piscicida in 170 estuarine water samples collected from New York to northern Florida. 20% of samples tested positive for the presence of P. piscicida, including sites where fish kills due to Pfiesteria have occurred and sites where there was no historical evidence of such events. The results extend the known range of P. piscicida northward to Long Island, New York. The results also suggest that P. piscicida is common, and normally benign, inhabitatant of estuarine waters of the eastern US.