gebhart/patrepeval huggingface dataset:
Efficient Iridium‐Catalyzed CH Functionalization/Silylation of Heteroarenes (2008)

CSi investigation: The efficient iridium-catalyzed CH functionalization/silylation of a wide variety of N-, S-, and O-heteroarenes, including N-unsubstituted indoles, is promoted by 2-norbornene and features a high level of regioselectivity (see scheme; Ts=p-toluenesulfonyl, cod=cyclooctadiene). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z802456_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Camera calibration of the stereo vision measurement system (2008)

Camera calibration is the important step for the stereo vision measurement system. The accuracy of the calibration affects the accuracy of the vision measurement system. The calibration is realized with a planar pattern. The pattern has some spot array with high precision. Stereo vision measurement system captures the images of the calibration pattern at several different orientations. The parameter model is modified as the polynomial model to describe the lens distortion. The calibration experiment demonstrates that the error of 3-D reconstruction is 0.020mm.
Effect of Cromakalim Prodrug 1 (CKLP1) on Aqueous Humor Dynamics and Feasibility of Combination Therapy With Existing Ocular Hypotensive Agents (2017)

CKLP1 lowered intraocular pressure by reducing episcleral venous pressure and lowering distal outflow resistance in the conventional outflow pathway. Owing to this unique mechanism of action, CKLP1 works in an additive manner to lower intraocular pressure with latanoprost, timolol, and Rho kinase inhibitor Y27632.
Improved tumor imaging with radiolabeled monoclonal antibodies by plasma clearance of unbound antibody with anti-antibody column. (1991)

Imaging of tumors by using radiolabeled monoclonal antibodies (MoAs) is hindered by the presence of background activity. To reduce this problem, the authors investigated the process of removing labeled MoAs from plasma at selected times by means of extracorporeal immunoadsorption. In seven patients with either lung or breast carcinoma, an indium-111-labeled murine antibody was intravenously administered. Six to 24 hours later, immunoadsorption was performed by passing the patients' plasma through a goat anti-mouse antibody column connected to a plasma separator. Whole-body computer images were obtained before and after the treatment. Blood pool activity in the images was reduced by an average of 59%, while tumor activity dropped by only 10%. Tumor-to-blood activity ratios therefore more than doubled, improving by an average of 121% between the pre- and posttreatment image sets. Eight of 12 areas of known disease and three areas of unknown but later documented disease were detected after the immunoadsorption process, while the three areas of unknown disease and three of the areas of known disease were not detected in the preclearance images. Thus, the feasibility of using extracorporeal immunoadsorption to improve MoA imaging of tumors was demonstrated.
Electro-Optical Platform for the Manipulation of Live Cells (2002)

The advent of the genome facilitated by the advances in micro- and nanotechnology has revolutionized our understanding of living systems. DNA microarrays, catalytic RNA arrays, and protein arrays are all a consequence of innovations in engineering at the micro- and nanoscales. Here, we extend this paradigm to the fabrication of live mammalian cell arrays that can be used to investigate the state of the cell at the level of an integrated system. Specifically, we describe an electro-optical system that utilizes physical properties of mammalian cells (charge, dielectric permittivity) rather than receptor-mediated adhesion to rapidly pattern and manipulate cells in a microarray format. The platform we describe is an electro-optical method that employs two complementary methods of cell manipulation: (1) electrophoretic arraying of cells in a dc field due to their intrinsic negative surface charge and (2) remote optical manipulation of individual cells by vertical-cavity surface emitting laser driven infrared optical tweezers. The platform is optically transparent and thus enables monitoring of fluorescent reporters of cellular events (e.g., expression of green fluorescent protein) and allows remote optical manipulation of arrayed cells without risk of breaching the aseptic environment. In addition to the experimental manipulation of mammalian cells, we also present a theoretical framework to establish the limitations of the platform we describe. The ability to probe dynamic cellular events in parallel may offer insights into unforeseen biological mechanisms of cellular function and find applications in drug discovery, functional genomics, and tissue engineering.
Intra-follicular and peripheral steroid characteristics during vernal transition in the pony mare. (1991)

This experiment investigated steroid production by ovarian tissues, in vitro, of pony mares during vernal transition from anoestrus to the breeding season. Follicular dynamics were monitored to detect the first, second, third or fourth transition follicle, greater than or equal to 30 mm diameter or the first large post luteal follicle of the breeding season. Twenty-four hours after a large follicle was detected, theca (T) and granulosa (G) tissues were harvested. Separate and co-incubations of these tissues were conducted to determine steroid production in early transition (ET), late transition (LT) and pre-ovulatory (OV) follicles. Peripheral plasma and follicular fluid steroids and gonadotrophins also were assayed. Peripheral plasma oestradiol concentrations increased from ET to LT and again from LT to OV in parallel with tissue production and follicular fluid content. Androgen production increased from LT to OV whereas progesterone production showed no change, thereby indicating a possible failure of 17-alpha steroid hydroxylase in ET follicles. Examination of tissue steroid secretion rates revealed that granulosa was the major site of oestrogen production, whereas theca secreted greater amounts of androgen.
Three-dimensional diffuse optical tomography in the parallel plane transmission geometry: Evaluation of a hybrid frequency domain/continuous wave clinical system for breast imaging (2003)

Three-dimensional diffuse optical tomography (DOT) of breast requires large data sets for even modest resolution (1 cm). We present a hybrid DOT system that combines a limited number of frequency domain (FD) measurements with a large set of continuous wave (cw) measurements. The FD measurements are used to quantitatively determine tissue averaged absorption and scattering coefficients. The larger cw data sets (10(5) measurements) collected with a lens coupled CCD, permit 3D DOT reconstructions of a 1-liter tissue volume. To address the computational complexity of large data sets and 3D volumes we employ finite difference based reconstructions computed in parallel. Tissue phantom measurements evaluate imaging performance. The tests include the following: point spread function measures of resolution, characterization of the size and contrast of single objects, field of view measurements and spectral characterization of constituent concentrations. We also report in vivo measurements. Average tissue optical properties of a healthy breast are used to deduce oxy- and deoxy-hemoglobin concentrations. Differential imaging with a tumor simulating target adhered to the surface of a healthy breast evaluates the influence of physiologic fluctuations on image noise. This tomography system provides robust, quantitative, full 3D image reconstructions with the advantages of high data throughput, single detector-tissue coupling path, and large (1L) imaging domains. In addition, we find that point spread function measurements provide a useful and comprehensive representation of system performance.
Experimental study of electrical breakdown in MEMS devices with micrometer scale gaps (2008)

We present an experimental study of the DC breakdown voltage of MEMS interdigitated aluminum electrodes with gaps ranging from 10 to 500 &mu;m. Unlike most research on MEMS electrodes, that was done at atmospheric pressure, our work has focused on the effect of gas pressure and gas type on the breakdown voltage. A main goal was to identify geometries that favor the creation of low-voltage discharges. Helium, argon and nitrogen pressure was varied from 10<sup>2</sup> to 8.10<sup>4</sup> Pa (1 to 800 mbar). The breakdown voltage was plotted as a function of the Paschen reduced variable P<sub>red</sub> = p·g. For higher values of pressure, p or gap, d (high P<sub>red</sub>), classical Paschen scaling was observed. For lower values of P<sub>red</sub> however, significant deviations were seen, particularly at low pressures. We attribute these differences not to field emission, but to the scale of the mean free path (which explains the higher than predicted voltages), and to the many length scales effectively present in our planar geometry (on-chip and even off-chip, that lead to the superposition of several Paschen curves). Guidelines are proposed for low-pressure operation of MEMS to avoid or to encourage breakdown.
Modulation of GDP Release from Transducin by the Conserved Glu134-Arg135 Sequence in Rhodopsin (1996)

A superfamily of seven-transmembrane helix receptors catalyzes GDP release from heterotrimeric guanine nucleotide-binding proteins (G proteins) to initiate the intracellular signaling cascade. The photoreceptor rhodopsin is a prototypical member of the superfamily that activates the retinal G protein transducin (Gt). The cytoplasmic domain of rhodopsin binds and activates Gt, but residues that stimulate GDP release from Gt have not been identified until now. We show here that the abnormal signal transduction phenotypes of several different mutations affecting the highly conserved Glu134-Arg135 charge pair result from alteration of the GDP release step in the Gt activation cascade. We propose that Glu134 and Arg135 constitute the site that directly provides the signal from rhodopsin to activate GDP release from Gt. Because the Glu/Asp-Arg sequence occurs at a topologically identical location in most of the seven-transmembrane helix receptors, we propose that these residues constitute a switch for signal transfer.
Proton nuclear magnetic resonance spectroscopy and ligand binding dynamics of the Escherichia coli L-arabinose binding protein (1982)

The L-arabinose binding protein (ABP) from Escherichia coli was studied by proton nuclear magnetic resonance spectroscopy (1H NMR). Distinct spectral changes occur when ABP binds its natural ligand, L-arabinose, which involve resonances in the aromatic ring current shifted methyl, bulk methyl, methylene, aromatic, and amide proton regions of the spectra. Several amide resonances can be "protected" from deuterium exchange if L-arabinose is bound to ABP prior to deuterium oxide dialysis. On the basis of the pH dependence of their chemical shifts, two low-field resonances have been tentatively assigned to C2 protons of two of the three histidines present in ABP. These histidyl residues have pK values of 8.0 and 8.6 which support their involvement in ionic interactions observed earlier in the crystallographic analysis. One histidyl residue shows a small chemical shift change upon the addition of arabinose. When ABP binds D-galactose, changes in the spectra occur which are different than those observed when L-arabinose is bound. Binding of L-arabinose and D-galactose to the binding protein (ABP) was considered by equilibrium binding and fluorescence emission spectroscopy. ABP binds L-arabinose and D-galactose with high affinities (Kd's at 6 degrees C of 1.3 x 10(-7) and 1.9 x 10(-7) M, respectively), and both enthalpy and entropy contribute to the ABP-ligand association. When excited at 285 nm, ABP has a fluorescence emission maximum of 340 nm which is quenched and blue shifted (to 337 nm) upon binding L-arabinose. ABP binding D-galactose produced a similar emission shift but no fluorescence quenching.
Appearance of stable glow discharge in air, argon, oxygen and nitrogen at atmospheric pressure using a 50 Hz source (1993)

Unusual glow discharges in air, argon, oxygen and nitrogen at atmospheric pressure can be produced using a 50 Hz source. This technique is introduced on the basis of the idea of a lower dielectric breakdown voltage gas. The electrode system, which is composed of a fine metal wire mesh of specified radius and a dielectric substance, is very useful for plasma surface processes and for chemical reactions in the plasma bulk. The observations of the Lissajous figure of voltage-electric charges and of the current pulse shapes are proposed as a method of distinguishing between the atmospheric pressure glow plasma and the silent electric discharge.
Genome scan of human systemic lupus erythematosus: Evidence for linkage on chromosome 1q in African-American pedigrees (1998)

Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens including DNA, ribosomal P, Ro (SS-A), La (SS-B), and the spliceosome. Etiology is suspected to involve genetic and environmental factors. Evidence of genetic involvement includes: associations with HLA-DR3, HLA-DR2, Fcgamma receptors (FcgammaR) IIA and IIIA, and hereditary complement component deficiencies, as well as familial aggregation, monozygotic twin concordance >20%, lambdas > 10, purported linkage at 1q41-42, and inbred mouse strains that consistently develop lupus. We have completed a genome scan in 94 extended multiplex pedigrees by using model-based linkage analysis. Potential [log10 of the odds for linkage (lod) > 2.0] SLE loci have been identified at chromosomes 1q41, 1q23, and 11q14-23 in African-Americans; 14q11, 4p15, 11q25, 2q32, 19q13, 6q26-27, and 12p12-11 in European-Americans; and 1q23, 13q32, 20q13, and 1q31 in all pedigrees combined. An effect for the FcgammaRIIA candidate polymorphism) at 1q23 (lod = 3.37 in African-Americans) is syntenic with linkage in a murine model of lupus. Sib-pair and multipoint nonparametric analyses also support linkage (P < 0.05) at nine loci detected by using two-point lod score analysis (lod > 2.0). Our results are consistent with the presumed complexity of genetic susceptibility to SLE and illustrate racial origin is likely to influence the specific nature of these genetic effects.
High Circulating Frequencies of Tumor Necrosis Factor Alpha- and Interleukin-2-Secreting Human T-Lymphotropic Virus Type 1 (HTLV-1)-Specific CD4+T Cells in Patients with HTLV-1-Associated Neurological Disease (2003)

Significantly higher frequencies of tumor necrosis factor alpha- and interleukin-2-secreting human T-lymphotropic virus type 1 (HTLV-1)-specific CD4(+) T cells were present in the peripheral blood mononuclear cells of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients than in those of asymptomatic carriers with similar provirus loads. The data suggest that HTLV-1-specific CD4(+) T cells play a role in the pathogenesis of HAM/TSP.
Verification of a model for the piezoelectric d33 coefficient of cellular electret films (2005)

An existing model for the piezoelectric thickness coefficient (d33 coefficient) of cellular polymers is tested with experimental data obtained from two differently manufactured cellular polypropylene (PP) materials. The model assumes the cellular film to consist of plane parallel solid and gaseous layers charged at their interfaces. The cellular PP films are expanded by a pressure treatment. Subsequently, due to viscoelastic relaxation, the thickness of the films decreases, thus causing a change of their Young’s modulus Y with time. The values of Y are obtained from interferometric measurements of the resonance frequency of the films. Together with the measured thickness of the solid layers and air layers in the material, the d33 coefficients can be determined from the model. These values are compared with experimental results for d33 also obtained interferometrically by means of the inverse piezoelectric effect. A very good agreement between the measured and calculated d33 coefficients as a function of film thickness is obtained for all investigated films.
Electronic trading in on-line delivered content (2003)

Electronically traded On-line Delivered Content (ODC) is data, information, and knowledge traded on the Internet or through other on-line means. ODC includes on-line newspapers, magazines, music, education, searchable databases, consulting, and eventually expertise ideas. This paper outlines the growing importance of ODC. It then attempts to position electronic trading in ODC within the wider field of Electronic Commerce. It identifies its distinctive characteristics compared to other forms of trading content as well as electronic trading in physical goods. Important ODC peculiarities are identified and analyzed. Based on the case of a medium-sized specialized publisher, the benefits and problems of moving into the business of electronic trading in ODC are discussed. The paper concludes with an outlook and agenda for further research.
Site-directed mutation of conserved cysteine residues does not inactivate the Streptococcus pyogenes hyaluronan synthase (2001)

Hyaluronan synthase (HAS), the enzyme responsible for the production of hyaluronic acid (HA), is a well-conserved membrane-bound protein in both prokaryotes and eukaryotes. This enzyme performs at least six discrete functions in producing a heterodisaccharide polymer of several million molecular weight and extruding it from the cell. Among the conserved motifs and domains within the Class I HAS family are four cysteine residues. Cysteines in many proteins are important in establishing and maintaining tertiary structure or in the coordination of catalytic functions. In the present study we utilized a combination of site-directed mutagenesis, chemical labeling, and kinetic analyses to determine the importance of specific Cys residues for catalysis and structure of the HA synthase from Streptococcus pyogenes (spHAS). The enzyme activity of spHAS was partially inhibited by cysteine-reactive chemical reagents such as N-ethylmaleimide. Quantitation of the number of Cys residues modified by these reagents, using MALDI-TOF mass spectrometry, demonstrated that there are no stable disulfide bonds in spHAS. The six Cys residues of spHAS were then mutated, individually and in various combinations, to serine or alanine. The single Cys-mutants were all kinetically similar to the wild-type enzyme in terms of their V(max) and K(m) values for HA synthesis. The Cys-null mutant, in which all Cys residues were mutated to alanine, retained approximately 66% of wild-type activity, demonstrating that despite their high degree of conservation within the HAS family, Cys residues are not absolutely necessary for HA biosynthesis by the spHAS enzyme.
Bayesian Unsupervised Batch and Online Speaker Adaptation of Activation Function Parameters in Deep Models for Automatic Speech Recognition (2016)

We present a Bayesian framework to obtain maximum a posteriori (MAP) estimation of a small set of hidden activation function parameters in context-dependent-deep neural network-hidden markov model (CD-DNN-HMM)-based automatic speech recognition (ASR) systems. When applied to speaker adaptation, we aim at transfer learning from a well-trained deep model for a “general” usage to a “personalized” model geared toward a particular talker by using a collection of speaker-specific data. To make the framework applicable to practical situations, we perform adaptation in an unsupervised manner assuming that the transcriptions of the adaptation utterances are not readily available to the ASR system. We conduct a series of comprehensive batch adaptation experiments on the Switchboard ASR task and show that the proposed approach is effective even with CD-DNN-HMM built with discriminative sequential training. Indeed, MAP speaker adaptation reduces the word error rate (WER) to 20.1% from an initial 21.9% on the full NIST 2000 Hub5 benchmark test set. Moreover, MAP speaker adaptation compares favorably with other techniques evaluated on the same speech tasks. We also demonstrate its complementarity to other approaches by applying MAP adaptation to CD-DNN-HMM trained with speaker adaptive features generated through constrained maximum likelihood linear regression and further reduces the WER to 18.6%. Leveraging upon the intrinsic recursive nature in Bayesian adaptation and mitigating possible system constraints on batch learning, we also proposed an incremental approach to unsupervised online speaker adaptation by simultaneously updating the hyperparameters of the approximate posterior densities and the DNN parameters sequentially. The advantage of such a sequential learning algorithm over a batch method is not necessarily in the final performance, but in computational efficiency and reduced storage needs, without having to wait for all the data to be processed. So far, the experimental results are promising.
Prevention and Reversal of Antibody Responses Against Factor IX in Gene Therapy for Hemophilia B (2011)

Intramuscular (IM) administration of an adeno-associated viral (AAV) vector represents a simple and safe method of gene transfer for treatment of the X-linked bleeding disorder hemophilia B (factor IX, F.IX, deficiency). However, the approach is hampered by an increased risk of immune responses against F.IX. Previously, we demonstrated that the drug cocktail of immune suppressants rapamycin, IL-10, and a specific peptide (encoding a dominant CD4(+) T cell epitope) caused an induction of regulatory T cells (Treg) with a concomitant apoptosis of antigen-specific effector T cells (Nayak et al., 2009). This protocol was effective in preventing inhibitory antibody formation against human F.IX (hF.IX) in muscle gene transfer to C3H/HeJ hemophilia B mice (with targeted F9 gene deletion). Here, we show that this protocol can also be used to reverse inhibitor formation. IM injection of AAV1-hF.IX vector resulted in inhibitors of on average 8-10 BU within 1 month. Subsequent treatment with the tolerogenic cocktail accomplished a rapid reduction of hF.IX-specific antibodies to <2 BU, which lasted for >4.5 months. Systemic hF.IX expression increased from undetectable to >200 ng/ml, and coagulation times improved. In addition, we developed an alternative prophylactic protocol against inhibitor formation that did not require knowledge of T cell epitopes, consisting of daily oral administration of rapamycin for 1-month combined with frequent, low-dose intravenous injection of hF.IX protein. Experiments in T cell receptor transgenic mice showed that the route and dosing schedule of drug administration substantially affected Treg induction. When combined with intravenous antigen administration, oral delivery of rapamycin had to be performed daily in order to induce Treg, which were suppressive and phenotypically comparable to natural Treg.
Remodeling by ventricular pacing in hypertrophying dog hearts (2001)

In hypertrophying hearts chronic pacing at the RV apex suppresses the development of hypertrophy in the early-activated apical septum but does not cause additional hypertrophy in late-activated regions, as is the case in non-hypertrophic hearts. The latter suggests that the local growth response is reduced in hypertrophying hearts.