gebhart/patrepeval huggingface dataset:
Micro-stimulator circuitry design for visual prosthesis based on optic nerve stimulation in artificial vision (2006)

A micro-stimulator circuitry designed for visual prosthesis based on optic nerve stimulation is presented in this paper. This micro-stimulator is capable of providing a wide range of biphasic current pulses with an amplitude from several muA up to 4 mA, a pulse width from 20 musec up to over four hundred musec, and a pulse frequency up to over three hundred Hz. The micro current pulses transmitting to the penetrating multi-electrode-arrays will stimulate optic nerve to elicit phosphenes within visual field. The performances of the proposed micro-stimulator circuitry were studied using the PSPICE program. The simulation results verified the circuit performances are agreed with the expected values
A 30-MHz low-jitter high-linearity CMOS voltage-controlled oscillator (1987)

A fully monolithic voltage-controlled oscillator (VCO) with an on-chip timing capacitor and a maximum oscillation frequency of 30 MHz is reported. Using a novel on-chip servo loop, the VCO displays less than 0.17% nonlinearity in its voltage-frequency transfer function from 1 to 15 MHz without trimming. An improved circuit topology that provides a large swing on the timing capacitor allows the VCO to obtain a cycle-to-cycle jitter of less than 100 p.p.m. The circuit operates on a 5-V supply with a die size of 104 mil/spl times/154 mil.
A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase (2004)

Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.
The accuracy of DNA sequences: Estimating sequence quality (1992)

In this paper we describe a method for the statistical reconstruction of a large DNA sequence from a set of sequenced fragments. We assume that the fragments have been assembled and address the problem of determining the degree to which the reconstructed sequence is free from errors, i.e., its accuracy. A consensus distribution is derived from the assembled fragment configuration based upon the rates of sequencing errors in the individual fragments. The consensus distribution can be used to find a minimally redundant consensus sequence that meets a prespecified confidence level, either base by base or across any region of the sequence. A likelihood-based procedure for the estimation of the sequencing error rates, which utilizes an iterative EM algorithm, is described. Prior knowledge of the error rates is easily incorporated into the estimation procedure. The methods are applied to a set of assembled sequence fragments from the human G6PD locus. We close the paper with a brief discussion of the relevance and practical implications of this work.
Transendothelial migration induces rapid expression on neutrophils of granule-release VLA6 used for tissue infiltration (1997)

Little is known of the mechanisms allowing neutrophils to infiltrate tissue after transendothelial migration. We postulated that VLA6 might be involved in neutrophil infiltration because it revealed as the most expressed beta1 integrins among VLA5, VLA4, and VLA3, which also appeared to define subsets within the blood neutrophil population. Transendothelial migration up-regulated by threefold (5,000 to 15,000 receptors) VLA6 expression on neutrophils. VLA6 up-regulation was transient, peaking in 6 min and returning to baseline in 1 h when tested in response to N-formyl-methionyl-leucyl-phenylalanine. Neutrophil degranulation experiments revealed a steady correlation between expression of VLA6 and granule content release, notably beta-glucuronidase, indicating that VLA6 molecules were preformed and stored mostly in azurophilic granules. Migration across fibroblast monolayers of neutrophils preactivated for VLA6 up-regulation was blocked when they were preincubated with anti-VLA6. However, anti-VLA6 had no effect on transfibroblast migration of non-preactivated neutrophils. These results indicate that VLA6 was functional only on activated neutrophils that used their up-regulated VLA6 to cross fibroblasts. Activation of neutrophils by transendothelial migration induces rapid expression of granule release VLA6 that appears to be a key adhesion mechanism used by a subset of neutrophils to infiltrate tissue.
Mass spectrometry: A tool for the identification of proteins separated by gels (2000)

Mass spectrometry (MS) has become the technique of choice to identify proteins. This has been largely accomplished by the combination of high-resolution two-dimensional (2-D) gel separation with robotic sample preparation, automated MS measurement, data analysis, and database query. Developments during the last five years in MS associated with protein gel separation are reviewed.
Electrochemical polymerization of conducting polymers in living neural tissue (2007)

A number of biomedical devices require extended electrical communication with surrounding tissue. Significant improvements in device performance would be achieved if it were possible to maintain communication with target cells despite the reactive, insulating scar tissue that forms at the device-tissue interface. Here, we report that the conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) can be polymerized directly within living neural tissue resulting in an electrically conductive network that is integrated within the tissue. Nano and microscale PEDOT filaments extend out from electrode sites, presumably forming within extracellular spaces. The cloud of PEDOT filaments penetrates out into the tissue far enough that it should be possible to bypass fibrous scar tissue and contact surrounding healthy neurons. These electrically functional, diffuse conducting polymer networks grown directly within tissue signify a new paradigm for creating soft, low impedance implantable electrodes.
Effects of cryoprotectant concentration and cooling rate on vitrification of aqueous solutions (2006)

Vitrification of aqueous cryoprotectant mixtures is essential in cryopreservation of proteins and other biological samples. Systematic measurements of critical cryoprotective agent (CPA) concentrations required for vitrification during plunge-cooling from T = 295 K to T = 77 K in liquid nitrogen are reported. Measurements on fourteen common CPAs, including alcohols (glycerol, methanol, 2-propanol), sugars (sucrose, xylitol, dextrose, trehalose), polyethylene glycols (ethylene glycol, PEG 200, PEG 2000, PEG 20000), glycols [dimethyl sulfoxide (DMSO), 2-methyl-2,4-pentanediol (MPD)], and salt (NaCl), were performed for volumes ranging over four orders of magnitude from ∼1 nl to 20 µl, and covering the range of interest in protein crystallography. X-ray diffraction measurements on aqueous glycerol mixtures confirm that the polycrystalline-to-vitreous transition occurs within a span of less than 2% w / v in CPA concentration, and that the form of polycrystalline ice (hexagonal or cubic) depends on CPA concentration and cooling rate. For most of the studied cryoprotectants, the critical concentration decreases strongly with volume in the range from ∼5 µl to ∼0.1 µl, typically by a factor of two. By combining measurements of the critical concentration versus volume with cooling time versus volume, the function of greatest intrinsic physical interest is obtained: the critical CPA concentration versus cooling rate during flash-cooling. These results provide a basis for more rational design of cryoprotective protocols, and should yield insight into the physics of glass formation in aqueous mixtures.
Intrauterine infection and spontaneous midgestation abortion: Is the spectrum of microorganisms similar to that in preterm labor? (2000)

Objective To determine whether microorganisms associated with intrauterine infection and preterm labor play a contributing role in midgestation abortion. Methods A 4 year retrospective review of spontaneous midgestation abortions for which autopsy and microbiological cultures of placental and fetal tissue were performed was conducted for a tertiary obstetrics hospital, which included a regional referral service for perinatal and fetal pathology. One hundred twenty-nine spontaneously delivered, nonmacerated, midgestation fetuses or stillbirths (of between 16 and 26 weeks' gestation) and placentas were examined and cultured for aerobic and anaerobic bacteria, yeasts, and genital mycoplasmas. Results Microorganisms were recovered in 85 (66%) cases (57% placentas, 49% fetuses). Among the culture positive cases, 81% had histological chorioamnionitis, 28% fetal pneumonitis, 38% clinical signs of infection, and 62% ruptured membranes at the time of miscarriage. These differed significantly from culture-negative cases (44%, 5%, 13%, and 34%, respectively). Group B streptococcus (GBS) was the most significant pathogen, recovered in 21 cases, 13 as the sole isolate, 94% with chorioamnionitis, and 47% in women with intact membranes. Escherichia coli and Ureaplasma urealyticum (22 and 24 cases, respectively) occurred mostly as mixed infections, with ruptured membranes. GBS, U. urealyticum, and Streptococcus anginosus group were individually associated with chorioamnionitis, Bacteroides/Prevotella and S. anginosus with fetal pneumonitis. The spectrum of microorganisms was similar to that in preterm labor at later gestations; however, GBS appeared to be the most significant pathogen in midgestation miscarriage, especially with intact membranes. Conclusions Unsuspected intrauterine infection underlies many spontaneous midgestation abortions. GBS is a key pathogen in this setting. Infect. Dis. Obstet. Gynecol. 8:220–227, 2000. © 2000 Wiley-Liss, Inc.
Immunization against anthrax with aromatic compound-dependent (Aro-) mutants of Bacillus anthracis and with recombinant strains of Bacillus subtilis that produce anthrax protective antigen (1990)

The safety and efficacy of five prototype, live anthrax vaccines were studied in Hartley guinea pigs and CBA/J and A/J mice. Two of the strains, Bacillus anthracis FD111 and FD112, are Aro- mutants derived by Tn916 mutagenesis of B. anthracis UM23-1. Bacillus subtilis PA1 and PA2 contain a recombinant plasmid, pPA101 or pPA102, respectively, that carries the gene from B. anthracis encoding synthesis of protective antigen (PA). The final strain, B. subtilis PA7, was isolated in this study from B. subtilis DB104 transformed with pPA101. All five strains were less virulent in guinea pigs and A/J and CBA/J mice than the toxinogenic, nonencapsulated B. anthracis veterinary vaccine Sterne strain. A/J and CBA/J inbred mice represent strains that are innately susceptible and resistant, respectively, to the Sterne strain. These differences in susceptibility are due to differences in ability to produce complement component 5. In guinea pigs, immunization with PA1 or PA2 vegetative cells or PA7 spores protected greater than or equal to 95% from an intramuscular spore challenge with the virulent, "vaccine-resistant" B. anthracis Ames strain. Strain PA2 vegetative cells and strain PA7 spores were as effective as the Sterne strain in Sterne-resistant CBA/J mice, protecting 70% of the mice from Ames strain spore challenge. Immunization with FD111 or FD112 vegetative cells fully protected guinea pigs from challenge. Immunization with FD111 cells protected up to 100% of CBA/J mice and up to 70% of A/J mice.
The Components of a Competency Based Elementary Reading Program (1977)

In a competency based reading program, the instructional emphasis is on each student's successful attainment and completion of the specific learning objectives provided. As such, the length of time required for each individual student to complete the objectives may be different.
Phenotypic and functional characterization of c-kit expression during intrathymic T cell development (1992)

We have studied the expression and function of c-kit on subsets of mouse thymocytes. c-kit was primarily expressed on subpopulations of CD4-CD8-CD3- triple negative (TN) cells. The strongest c-kit expression was associated with subsets that represent the least mature TN cells, including CD44+CD25- TN, and a subpopulation of CD25+ TN. These cells were also Thy-1lo, H-2Khi TSA-1hi, HSAlo, B220-, Mac-1-, and Gr-1-. Additionally, the recently described pre-TN thymocyte population (CD4loCD3-CD8-) was also c-kit+. CD25+ TN thymocytes proliferated in the presence of IL-7 and stem cell factor (the ligand for c-kit), and this proliferation was completely inhibited in the presence of anti-c-kit. Furthermore, the addition of anti-c-kit to 2-deoxyguanosine-treated fetal thymic lobes undergoing reconstitution with fetal liver-derived precursor cells inhibited their T cell differentiation potential. These observations indicate an important role for c-kit/stem cell factor interactions during early thymocyte development.
Robust hand gesture recognition based on finger-earth mover's distance with a commodity depth camera (2011)

The recently developed depth sensors, e.g., the Kinect sensor, have provided new opportunities for human-computer interaction (HCI). Although great progress has been made by leveraging the Kinect sensor, e.g. in human body tracking and body gesture recognition, robust hand gesture recognition remains an open problem. Compared to the entire human body, the hand is a smaller object with more complex articulations and more easily affected by segmentation errors. It is thus a very challenging problem to recognize hand gestures. This paper focuses on building a robust hand gesture recognition system using the Kinect sensor. To handle the noisy hand shape obtained from the Kinect sensor, we propose a novel distance metric for hand dissimilarity measure, called Finger-Earth Mover's Distance (FEMD). As it only matches fingers while not the whole hand shape, it can better distinguish hand gestures of slight differences. The extensive experiments demonstrate the accuracy, efficiency, and robustness of our hand gesture recognition system.
Targeting Weak Antigens to CD64 Elicits Potent Humoral Responses in Human CD64 Transgenic Mice (2000)

Previous studies have documented that targeting foreign Ags to IgG FcgammaR leads to enhanced Ag-specific responses in vitro and in vivo. However, the ability to overcome immunologic nonresponsiveness by targeting poorly immunogenic Ags to FcgammaR has not been investigated. To address this question in a simple model, we immunized transgenic mice expressing human CD64 (FcgammaRI) and their nontransgenic littermates with Fab' derived from the murine anti-human CD64 mAb m22. The m22 Fab' served as both the targeting molecule and the Ag. We found that only CD64-expressing mice developed anti-Id titers to m22. Furthermore, chemically linked multimers of m22 Fab', which mediated efficient internalization of the human CD64, were significantly more potent than monomeric m22 F(ab')(2) at inducing anti-Id responses. In all cases, the humoral responses were specific for m22 Id and did not react with other murine IgG1 Fab' fragments. Chemical addition of a second murine Fab' (520C9 anti-human HER2/neu) to m22 Fab' multimers demonstrated that IgG1 and IgG2a anti-Id titers could be generated to 520C9 only in the CD64-expressing mice. These results show that targeting to CD64 can overcome immunological nonresponsiveness to a weak immunogen. Therefore, targeting to CD64 may be an effective method to enhance the activity of nonimmunogenic tumor vaccines.
A Conformational Switch in Escherichia coli 16 S Ribosomal RNA During Decoding of Messenger RNA (1997)

Direct evidence is presented for a conformational switch in 16S ribosomal RNA (rRNA) that affects tRNA binding to the ribosome and decoding of messenger RNA (mRNA). These data support the hypothesis that dynamic changes in rRNA structure occur during translation. The switch involves two alternating base-paired arrangements apparently facilitated by ribosomal proteins S5 and S12, and produces significant changes in the rRNA structure. Chemical probing shows reciprocal enhancements or protections at sites in 16S rRNA that are at or very near sites that were previously crosslinked to mRNA. These data indicate that the switch affects codon-anticodon arrangement and proper selection of tRNA at the ribosomal A site, and that the switch is a fundamental mechanism in all ribosomes.
Non-destructive methods for space charge distribution measurements: what are the differences? (2003)

For more than 25 years, various techniques have been introduced for the nondestructive measurement of the space charge distribution in solid dielectrics. All these techniques can be classified into a set of three methods: (i) the thermal method, (ii) the pressure-wave-propagation method and (iii) the electro-acoustic method. Despite their apparent differences they are based on the same physical idea: the perturbation of the equilibrium between electrostatic and elastic forces in the material induces a response, either electrical or mechanical, which can be analyzed. In this paper, we demonstrate that the information on the material contained in the response is identical whatever the method used. As a consequence the differences between methods stand only in the nature of the perturbation and its physical properties.
Identification of Derivatives of Bisphenol A Diglycidyl Ether and Novolac Glycidyl Ether in Can Coatings by Liquid Chromatography/Ion Trap Mass Spectrometry (2000)

A reversed-phase liquid chromatographic method combined with fluorescence and multiple mass spectrometric detection in series is presented for the separation and structure elucidation of bisphenol A diglycidyl ether (BADGE) and novolac glycidyl ether (NOGE) derivatives. Atmospheric pressure chemical ionization in the positive ion mode and collision induced fragmentation in the ion trap allowed identification of BADGE- and NOGE-related compounds originating from reactions of the glycidyl ethers with bisphenols, solvents, and chain stoppers. Two extracts from food-can coatings were investigated in detail. It was possible to elucidate the structures of many substances and consequently to draw conclusions about the production of the lacquers.
A large annotated corpus for learning natural language inference (2015)

Understanding entailment and contradiction is fundamental to understanding natural language, and inference about entailment and contradiction is a valuable testing ground for the development of semantic representations. However, machine learning research in this area has been dramatically limited by the lack of large-scale resources. To address this, we introduce the Stanford Natural Language Inference corpus, a new, freely available collection of labeled sentence pairs, written by humans doing a novel grounded task based on image captioning. At 570K pairs, it is two orders of magnitude larger than all other resources of its type. This increase in scale allows lexicalized classifiers to outperform some sophisticated existing entailment models, and it allows a neural network-based model to perform competitively on natural language inference benchmarks for the first time.
Splitting and contrary motion of coherent bremsstrahlung peaks in strained-layer superlattices (1991)

The peaks in the spectrum of coherent bremsstrahlung from MeV-GeV electrons in crystalline targets are split into components if the target is a strained-layer superlattice (SLS). We have studied this effect theoretically for an illustrative example; it also entails that when the crystal is rocked, a contrary motion of the split components takes place. Due to their strong dependence on beam orientation relative to a channel axis, these new predicted phenomena should provide a sensitive measure of the strains in SLS layers; but because of the broadening of the photon peaks in thin layers, good observability will be restricted to superlattice layers with a thickness of several hundred Å or more.
KGB: a single buffer for all restriction endonucleases (1988)

Journal Article KGB: a single buffer for all restriction endonucleases Get access Michael McClelland, Michael McClelland Department of Biochemistry and Molecular Biology, University of Chicago920 East 58th St., Chicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar John Hanish, John Hanish Department of Biochemistry and Molecular Biology, University of Chicago920 East 58th St., Chicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Nelson, Michael Nelson Department of Biochemistry and Molecular Biology, University of Chicago920 East 58th St., Chicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Yogesh Patel Yogesh Patel Department of Biochemistry and Molecular Biology, University of Chicago920 East 58th St., Chicago, IL 60637, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 1, 11 January 1988, Page 364, https://doi.org/10.1093/nar/16.1.364 Published: 11 January 1988 Article history Accepted: 06 November 1987 Published: 11 January 1988
S-antigen in the developing retina and pineal gland: a monoclonal antibody study. (1985)

Spleen cells of BALB/c mice, previously immunized with bovine retinal S-antigen, were fused with Sp2/0-Ag14 mouse myeloma cells. Two monoclonal antibodies (MAbs) MAbA9-C6 (IgG2a isotype) and MAbA1-G5 (IgG1 isotype) were selected on the basis of reactivity in an ELISA and immunofluorescent assay. In radioimmunoassay MAbA9-C6 and MAbA1-G5 do not compete and appear to define unrelated epitopes of S-antigen. Both MAbs reacted in the ELISA assay, whereas only MAbA9-C6 bound to S-antigen in fixed tissue sections. Because MAbA9-C6 was useful for immunocytochemistry, it was studied in more detail. MAbA9-C6 bound to all vertebrate retinas tested including human, bovine, guinea pig, and mice. The immunoreactivity of MAbA9-C6 also was studied in the developing rat retina and pineal gland. In the morphologically undifferentiated retina, assessed by conventional light microscopy, there was an incomplete separation of the outer neuroblastic cells. However, in the same retina a distinct zone, corresponding to S-antigen immunoreactivity, was present indicating antigenic differentiation with regard to S-antigen at this stage of retinal development. In the pineal gland, S-antigen immunoreactivity was first observed in the three day old rat and at all stages examined thereafter. The usefulness of these two MAbs in the study of the embryologic development of the retina and of the antigenic epitopes of S-antigen is discussed.