gebhart/patrepeval huggingface dataset:
Microstamping on an Activated Polymer Surface:  Patterning Biotin and Streptavidin onto Common Polymeric Biomaterials (2001)

Microstamping on an activated polymer surface (MAPS) is a methodology that enables biomolecules to be patterned on polymers with micrometer spatial resolution. MAPS combines homogeneous surface derivatization of a polymer to introduce a reactive functional group followed by reactive microcontact printing (μCP) of a biological ligand of interest, linked to an appropriate reactive group. We demonstrate here that polyethylene, polystyrene, poly(methyl methacrylate), and poly(ethylene terephthalate) films can be successfully modified to introduce COOH groups on their surfaces, which can be subsequently patterned by reactive μCP of amine-terminated biotin after derivatization of the COOH groups with pentafluorophenol. X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry (TOF-SIMS) confirmed the chemistry of MAPS at each stage of the derivatization of the polymer surfaces and reactive μCP of biotin. Micropatterned biotin surfaces fabricated by MAPS were patterned with streptavidin by exploiting molecular recognition between biotin and streptavidin. The formation of streptavidin patterns was examined by fluorescence microscopy of Alexa488-labeled streptavidin and by TOF-SIMS imaging of 15N-labeled recombinant streptavidin, bound to biotin patterns. The contrast in the streptavidin micropatterns was optimized by examining the effect of blocking agents and streptavidin incubation time. Maximum contrast was obtained for binding of 0.1 μM streptavidin from a buffer containing 0.02% (v/v) Tween 20 detergent for an incubation time of 1 min.
Structural basis for receptor binding heterogeneity of apolipoprotein E from type III hyperlipoproteinemic subjects. (1982)

The three major isoforms of human apolipoprotein E (apo-E2, -E3, and -E4) are coded for by three alleles (epsilon 2, epsilon 3, and epsilon 4) which have a common genetic locus. Previously, we demonstrated that E2, E3, and E4 differ in primary structure from one another at two substitution sites, site A (residue 112) and site B (residue 158). At sites A/B, apo-E2, -E3, and -E4 contain cysteine/cysteine, cysteine/arginine, and arginine/arginine, respectively. We demonstrated that the substitution of cysteine for arginine at site B is at least partly responsible for the defective binding of apo-E2 to human fibroblast low density lipoprotein receptors, compared to the normal binding activity of apo-E3 or -E4. Subjects with the genetic disorder type III hyperlipoproteinemia are phenotypically homozygous for apo-E2, but the binding activity of apo-E to the fibroblast receptor differs considerably from one type III individual to another. We therefore undertook a partial comparative sequence analysis of apo-E2 from three type III subjects whose apo-E displayed this heterogeneity. The subject with the poorest binding apo-E2 was genotypically homozygous for an apo-E allele (epsilon 2); cysteine was found at sites A and B. The subject with the most active apo-E2 was genotypically homozygous for an apo-E allele (epsilon 2); cystine was found at site A and at a new site (site C, residue 145). The epsilon 2 allele specifies a protein that has arginine at site B (residue 158); the epsilon 2 allele specifies a protein that has arginine at site C (residue 145). Therefore, the two alleles differ from one another by cysteine/arginine interchanges at two positions, sites B and C. The third subject, whose apo-E2 displayed binding activity intermediate between the activities of the other two, was genotypically heterozygous, having one epsilon 2 allele and one epsilon 2 allele. The intermediate binding activity of apo-E2 from this subject resulted from having a mixture of severely defective apo-E (specified by epsilon 2) and slightly defective apo-E (specified by epsilon 2).
The molecular rationale of Src inhibition in colorectal carcinomas (2013)

Src has been one of the most studied proto-oncogenes. The cellular Src (c-Src) holds a critical role in several human malignancies and has emerged as a key factor that promotes tumor progression during the multistep process of colorectal cancer (CRC) pathogenesis. The robust activation of Src in CRC of aggressive phenotype and poor prognosis seems to be a subsequent event of a strong link between its deregulated activity and the tumor's cell adhesion properties, invasiveness and metastatic potential. The rarely detected genetic defects drive interest in signaling networks that control Src kinase activity and integrate the association of Src with receptor tyrosine kinases (RTKs), such as the epidermal growth factor receptor (EGFR). Therefore, a dynamic crosstalk is being formed with oncogenic capacity and therapeutic applications, because Src inhibition seems to sensitize previously unresponsive cancer cells to chemotherapy and anti-EGFR inhibitors. The present review explores the molecular basis behind Src inhibition in colorectal carcinomas. Furthermore, preclinical studies and clinical trials of Src inhibitors and combination regimens are discussed, providing new insights for further investigation and new therapeutic strategies.
A poly(dT)-stimulated ATPase activity associated with simian virus 40 large T antigen. (1979)

Highly purified SV40 large T antigen exhibits an ATPase activity which can be stimulated approximately 7-fold by the DNA homopolymer poly(dT). The poly(dT)-stimulated enzyme can hydrolyze various ribonucleotide and deoxyribonucleotide triphosphates, with ATP and dATP serving as the best substrates. Purified large T antigen hydrolyzes ATP to ADP and Pi, with a maximum specific activity of 13.5 mumol of inorganic phosphate released per h per mg of protein. Of the various natural and synthetic polynucleotides tested, poly(dT) was by far the best activator. Long chain poly(dT) molecules are much more effective activators than are short chain length oligo(dT) molecules. The highly purified large T antigen contains no detectable protein kinase activity.
Lymphoid Organs as a Major Reservoir for Human T-Cell Leukemia Virus Type 1 in Experimentally Infected Squirrel Monkeys (Saimiri sciureus): Provirus Expression, Persistence, and Humoral and Cellular Immune Responses (2000)

The aim of this study was to investigate the distribution of human T-cell leukemia virus type 1 (HTLV-1) in various organs of serially sacrificed squirrel monkeys (Saimiri sciureus) in order to localize the reservoir of the virus and to evaluate the relationship between viral expression and the humoral or cellular immune response during infection. Six squirrel monkeys infected with HTLV-1 were sacrificed 6, 12, and 35 days and 3, 6, and 26 months after inoculation, and 20 organs and tissues were collected from each animal. PCR and reverse transcription-PCR (RT-PCR) were performed with gag and tax primers. Proviral DNA was detected by PCR in peripheral blood mononuclear cells (PBMCs) of monkeys sacrificed 6 days after inoculation and in PBMCs, spleens, and lymph nodes of monkeys sacrificed 12 and 35 days and 3, 6, and 26 months after inoculation. Furthermore, tax/rex mRNA was detected by RT-PCR in the PBMCs of two monkeys 8 to 12 days after inoculation and in the spleens and lymph nodes of the monkey sacrificed on day 12. In this animal, scattered HTLV-1 tax/rex mRNA-positive lymphocytes were detected by in situ hybridization in frozen sections of the spleen, around the germinal centers and close to the arterial capillaries. Anti-HTLV-1 cell-mediated immunity was evaluated at various times after inoculation. Anti-p40(Tax) and anti-Env cytolytic T-cell responses were detected 2 months after infection and remained detectable thereafter. When Tax peptides were used, this response appeared to be directed against various Tax epitopes. Our results indicate that squirrel monkeys represent a promising animal model for studying the early events of HTLV-1 infection and for evaluating candidate vaccines against HTLV-1.
Excitatory amino acid transporter 5, a retinal glutamate transporter coupled to a chloride conductance (1997)

Although a glutamate-gated chloride conductance with the properties of a sodium-dependent glutamate transporter has been described in vertebrate retinal photoreceptors and bipolar cells, the molecular species underlying this conductance has not yet been identified. We now report the cloning and functional characterization of a human excitatory amino acid transporter, EAAT5, expressed primarily in retina. Although EAAT5 shares the structural homologies of the EAAT gene family, one novel feature of the EAAT5 sequence is a carboxy-terminal motif identified previously in N-methyl-D-aspartate receptors and potassium channels and shown to confer interactions with a family of synaptic proteins that promote ion channel clustering. Functional properties of EAAT5 were examined in the Xenopus oocyte expression system by measuring radiolabeled glutamate flux and two-electrode voltage clamp recording. EAAT5-mediated L-glutamate uptake is sodium- and voltage-dependent and chloride-independent. Transporter currents elicited by glutamate are also sodium- and voltage-dependent, but ion substitution experiments suggest that this current is largely carried by chloride ions. These properties of EAAT5 are similar to the glutamate-elicited chloride conductances previously described in retinal neurons, suggesting that the EAAT5-associated chloride conductance may participate in visual processing.
Oviductal Sperm Numbers Following Proximal Uterine Horn or Uterine Body Insemination (2000)

For all mares studied, a greater percentage of oviductal sperm were recovered from the ipsilateral oviduct following uterine horn insemination (77.3%) than resulted from uterine body insemination (53.8%). The number of oviductal sperm recovered from reproductively normal mares and mares with delayed uterine clearance was not different. Authors’ Addresses: Dept. of Large Animal Medicine & Surgery, College of Veterinary Medicine (Rigby, Brinsko, Blanchard, Taylor, Varner) and Dept. of Animal Science, Texas A&M University, College Station, TX 77843-4475 (Derczo, Forrest). © 2000 AAEP.
A Double-Blind, Randomized Clinical Trial of Niacinamide 4% versus Hydroquinone 4% in the Treatment of Melasma (2011)

Background. Multiple modalities have been used in the treatment of melasma with variable success. Niacinamide has anti-inflammatory properties and is able to decrease the transfer of melanosomes. Objective. To evaluate the therapeutic effect of topical niacinamide versus hydroquinone (HQ) in melasma patients. Patients and Methods. Twenty-seven melasma patients were randomized to receive for eight weeks 4% niacinamide cream on one side of the face, and 4% HQ cream on the other. Sunscreen was applied along the observation period. They were assessed by noninvasive techniques for the evaluation of skin color, as well as subjective scales and histological sections initially and after the treatment with niacinamide. Results. All patients showed pigment improvement with both treatments. Colorimetric measures did not show statistical differences between both sides. However, good to excellent improvement was observed with niacinamide in 44% of patients, compared to 55% with HQ. Niacinamide reduced importantly the mast cell infiltrate and showed improvement of solar elastosis in melasma skin. Side effects were present in 18% with niacinamide versus 29% with HQ. Conclusion. Niacinamide induces a decrease in pigmentation, inflammatory infiltrate, and solar elastosis. Niacinamide is a safe and effective therapeutic agent for this condition.
FlexMix: A General Framework for Finite Mixture Models and Latent Class Regression inR (2004)

FlexMix implements a general framework for fitting discrete mixtures of regression models in the R statistical computing environment: three variants of the EM algorithm can be used for parameter estimation, regressors and responses may be multivariate with arbitrary dimension, data may be grouped, e.g., to account for multiple observations per individual, the usual formula interface of the S language is used for convenient model specification, and a modular concept of driver functions allows to interface many different types of regression models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models.
A queueing model for analysis of a bursty multiple-access communication channel (1981)

A bursty multiple-access communication channel with constrained total system bandwidth, total average power, and message error rates is considered. A stochastic model for the number of active transmitters is developed. Four schemes for the dynamic assignment of power and coding rate to active transmitters are considered and compared under the expected burst system time criterion. Necessary and sufficient conditions for system operation are given, and all schemes are shown to have the same saturation behavior. Adaptive coding rates are shown to enjoy substantial advantages over fixed coding; adaptive power assignment does not offer advantages over fixed power assignment.
Removal of surfactant and capping agent from Pd nanocubes (Pd-NCs) using tert-butylamine: its effect on electrochemical characteristics (2013)

Synthesis of shape-controlled nanoparticles of precious metals with defined size is well-established in the literature and the control over shape and size is achieved using surfactants and capping agents. However, a clean surface without impurities is required for realistic applications. In the present investigation, palladium nanocubes are synthesized using poly(vinylpyrrolidone) and potassium bromide. A novel method for cleaning the nanoparticle surface, i.e., treatment with tert-butylamine is reported. For comparison, a part of the untreated sample is subjected to the commonly used method of heat-treatment in an oxygen atmosphere for surface cleaning. The XPS and FTIR spectra of the heat-treated sample show incomplete removal of PVP and complete removal of Br− and the XRD pattern suggests oxide formation on the Pd surface. Treatment with tert-butylamine provides a clean surface free of PVP and Br−. Cleanliness of the surface is further confirmed by the voltammograms and ORR activities in 0.1 M HClO4. We conclude that tert-butylamine can be an effective solvent for the removal of PVP and a reagent for Br− ions because of its ability to form a quaternary ammonium salt.
Expression of blood group antigens H-2, Le(y), and sialylated-Le(a) in human colorectal carcinoma. An immunohistochemical study using double-labeling techniques. (1991)

In this study, double-labeling immunohistochemistry was used to gain insight into the coexpression or interrelationship between blood group antigens (BGA) that are differentiation antigens in the normal colon, and BGA that are sequential moieties in the same synthetic pathway. Paired-wise Sialylated-Le(a)/Le(y) and H-2/Le(y) was studied. The Sialylated-Le(a) and Le(y) are synthesized from type 1 and type 2 backbones, respectively. In the normal colon, the Le(y) and Sialylated-Le(a) are expressed by cells at the base and surface of the crypt, respectively, representing undifferentiated and differentiated enterocytes. The H-2 is considered oncofetal in nature, and is considered to be the immediate precursor in the synthesis of Le(y). In individual cancers. Sialylated-Lea and Le(y) were detected in different cancer cells within the same malignant glands, separately in different glands, and in different subcellular compartments of the same cell. Both H-2 and Le(y) were coexpressed in the same individual cells in 92% of cancers expressing both these BGA. In 50% of the cancers, the H-2 and Le(y) also were expressed separately in different malignant glands within individual tumors. These findings indicate that, in colorectal cancers, differentiation antigens (Sialylated Le(a) and Le(y)) are expressed by different individual cells within the same malignant gland somewhat, recapitulating the normal colon crypt. Antigens of different backbones occasionally may be expressed in the same cells but within different subcellular compartments. Precursor accumulation is common in cancers, and antigens in the same synthetic pathway are coexpressed in the same cell. The expression of H-2 and Le(y) in different glands (lack of coexpression) may be explained possibly by aberrant synthesis of Le(y) by an alternate pathway.
Cycloaddition of Oxirane Group with Carbon Dioxide in the Supercritical Homogeneous State (2002)

Cycloaddition of an oxirane group of 2-methyloxirane or 2,2-dimethyloxirane with carbon dioxide was carried out in both supercritical homogeneous and vapor−liquid coexisting regions to produce a cyclic carbonate compound of 4-methyl-1,3-dioxolan-2-one or 4,4-dimethyl-1,3-dioxolan-2-one. The yield of the cyclic carbonate exceeded 95%, when the reaction proceeded in the supercritical uniform condition. On the other hand, the yield was less than 5%, when the reaction occurred in the two-phase region. While almost all kinds of alkali metal halides exhibited the high catalytic activity in a polar liquid solvent, limited numbers of halides were found to have much activity in supercritical carbon dioxide. This might be due to differences in solvent properties such as polarity and dissolving power between the supercritical and liquid solvents. The selective separation of cyclic carbonate from the supercritical mixture of reactants and products was investigated by manipulating the temperature and pressure. When decreasing the temperature and pressure of the effluent from the reactor below the critical temperature and pressure of carbon dioxide, a condensate of cyclic carbonate with a purity of more than 99% was obtained from the outlet stream.
Expression of SV40‐lacZ gene in mouse preimplantation embryos after pronuclear microinjection (1991)

In order to study the expression of an exogenous gene in developing mouse embryos during the preimplantation period, DNA carrying the SV40 early promoter fused with the Escherichia coli beta-galactosidase gene (lacZ) was microinjected into the pronucleus of fertilized mouse eggs. Expression of lacZ gene was detected by staining embryos with 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-gal) as a substrate at pH 7.2. The embryos expressing the lacZ gene showed various intensities of blue staining, all showing a mosaic pattern. The exogenous gene was expressed from the 4-cell stage until the blastocyst stage. The proportion of embryos expressing the lacZ gene was maximal (38%) at the morula stage, and the expression was dependent on the presence of the SV40 promoter.
Self-configuring, Lightweight Sensor Networks for Ubiquitous Computing (2003)

We show that it is possible to extract geometric descriptions of the spaces observed by sensor networks, even if the network consists of sensors that are of very limited ability: such as motion detectors. By using statistical techniques and relying only on the unconstrained patterns generated by the occupants of the building we show how to recover information about sensor geometry. This is important to the ubiquitous computing community since ubiquitous sensors and the context that the provide will only become a reality if the sensors are cheap, low-power, and self-configuring.
Haptic rendering of rigid contacts using impulsive and penalty forces (2005)

A new simulation approach is proposed to improve the stability and the perceived rigidity of contacts during haptic interaction with multirigid body virtual environments. The approach computes impulsive forces upon contact and penalty and friction forces during contact. The impulsive forces are derived using a new multiple collision resolution method that never increases the kinetic energy of the system. When new contacts arise, the impulsive forces generate large hand accelerations without requiring increased contact stiffness and damping. Virtual objects and linkages are regarded as points in the configuration space, and no distinction is made between them in the proposed approach.
Ultra-wideband impulse radar-an overview of the principles (1998)

Over the past decade, extensive research work has been carried out to develop the ultra-wideband (UWB) technology for radar applications, and to resolve the practical challenges in implementing an efficient UWB radar system. In this paper, we present an overview of the basic principles of UWB impulse radar. The focus is on the principles of UWB signal generation, impulse radiation, waveform design, pulse compression, range-velocity resolution (ambiguity function), array beamforming, and radar-target signature.
Research Agenda for Understanding Alzheimer Disease in Diverse Populations: Work Group on Cultural Diversity, Alzheimer's Association (2002)

The emerging evidence of ethnic variations in apolipoprotein polymorphism and Alzheimer disease risk shows that one cannot generalize findings based on a single cultural group too broadly ( Tang et al., 2001). Presence of one apolipoprotein E epsilon 4 allele is a stronger risk factor for Alzheimer disease in whites and Asians than in blacks ( Farrer et al., 1997). Environmental or genetic cofactors may modulate the effects of epsilon 4 on beta-amyloid metabolism differently in different subpopulations ( Shadlen, 1998). Recognizing this, the Alzheimer's Association has extended its goals to strengthen the scientific information base on the interactions of population diversity and Alzheimer disease heterogeneity ( NIA, 1998). This new focus is timely since minority elderly are the most rapidly increasing segment of the elderly population ( Lilienfeld and Perl, 1994, Brookmeyer et al., 1998). In this article, the authors highlight recent progress in research on Alzheimer disease among culturally diverse populations with a special emphasis on gaps in the knowledge base. The authors recommend four priorities for future Alzheimer disease research: (1) determine whether genetic causative factors interact differently in different populations; (2) reexamine the nature and role of cerebral ischemia and infarction and variations in symptom severity of Alzheimer disease; (3) explore the interaction of genes and environmental influences that are protective against Alzheimer disease; and (4) recruit and enroll ethnically diverse subjects in Alzheimer disease clinical trials.
Evaluating Microarray-based Classifiers: An Overview (2008)

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy.
Control of Coherent Acoustic Phonons in InGaN Multiple Quantum Wells (2000)

Using sub-picosecond optical pump-probe techniques, coherent zone-folded longitudinal acoustic phonons (ZFLAPs) were generated and controlled in an InGaN multiple quantum well structure. A one-pump, one-probe differential transmission technique revealed that carriers injected near the barrier band edge were quickly captured into the quantum wells and generated strong coherent ZFLAP oscillations. Two-pump differential transmission was used to generate and control coherent ZFLAP oscillations through the relative timing and amplitude of the two pump pulses. Enhancement and suppression of ZFLAP oscillations were demonstrated, including complete cancellation of generated acoustic phonons for the first time in any material system. Coherent control was used to demonstrate that ZFLAPs are generated differently in InGaN multiple quantum wells than in GaAs/AlAs superlattices.