gebhart/patrepeval huggingface dataset:
Remarks on the Vitality of the Human Cornea After Organ Culture (1995)

The purpose of this study was to obtain further information on the viability of organ-cultured human cornea. We thus used a specific staining method for succinate dehydrogenase (SDH), which is located in the membrane system of vital mitochondria. We examined fresh and long-term-cultured human corneas. After an initial incubation period in dextran-free culture medium, corneas were stored in a medium containing dextran. With respect to different appearances of the SDH staining, minimal essential medium without dextran seems to have a positive effect on the condition of epithelial cells. After renewal of the medium, keratocytes showed a brief improvement followed by a delayed deterioration, while the endothelial cells were severely damaged. However, best results for all three cell types were observed on the fourth day in a medium containing dextran. We therefore conclude that these corneas were best suited for transplantation.
Detection of Serum Antibody Responses in Cattle with Natural or Experimental Neospora Infections (1993)

Parasite-specific antibody responses were detected using an indirect fluorescent antibody (IFA) test in cattle that were naturally or experimentally infected with Neospora parasites. The test was developed using Neospora tachyzoites isolated from an aborted bovine fetus and grown in bovine cell cultures (isolate BPA1). In all cases, infections were confirmed by the identification of Neospora tachyzoites and/or bradyzoite cysts in fetal or calf tissues using an immunoperoxidase test procedure. Fifty-five naturally infected cows that aborted Neospora-infected fetuses had titers of 320-5,120 at the time of abortion. The titer of 6 cows that were serologically monitored over a prolonged period decreased to 160-640 within 150 days after they aborted infected fetuses. Two of the cows showed an increase in their Neospora titers during their subsequent pregnancy, and they gave birth to congenitally infected calves that had precolostral titers of 10,240-20,480. Postcolostral titers of these calves and of 4 other calves with congenital Neospora infections were all > or = 5,120, whereas calves with no detectable parasites had titers < or = 160. Two pregnant heifers that were experimentally infected with the BPA1 isolate at approximately 120 days gestation seroconverted to Neospora antigens within 9 days and developed peak titers of 5,120 and 20,480 within 32 days of infection. The fetus taken by caesarean section 32 days postinfection from 1 heifer and the full-term calf born to the other had Neospora titers of 640 and 10,240, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Peptide Conjugation at the 5′-End of Oligodeoxynucleotides Abrogates Toll-Like Receptor 9-Mediated Immune Stimulatory Activity (2009)

Bacterial and synthetic DNA containing unmethylated CpG motifs act as ligands of Toll-like receptor 9 (TLR9). Our earlier studies showed that 5'-accessibility of synthetic oligodeoxynucleotides containing CpG motif (ODN) is required for TLR9-mediated immune stimulatory activity. Blocking the 5'-end of ODN through conjugation to a variety of moieties reduces immune stimulatory activity (Bioconjugate Chem. 2002, 13, 966-974). In the present study, we conjugated a model peptide, a 28-amino-acid-long beta-amyloid peptide, to either the 5'- or the 3'-end of an ODN via C3 and C6 alkyl linkers. We compared the immune stimulatory activity of the resulting conjugates with that of a parent ODN without conjugation in TLR9-transfected cells, mouse spleen cell cultures, and in vivo in mice. ODN with the peptide conjugated at the 3'-end via C3 and C6 linkers had immune stimulatory activity similar to that of the parent ODN in both in vitro and in vivo in mice. On the contrary, conjugation of peptide at the 5'-end of the ODN significantly abrogated immune stimulatory activity. In conclusion, the results presented here demonstrate that peptide/protein conjugation to ODN is optimal at the 3'-end with either C3 or C6 linker and conjugation at the 5'-end leads to significant loss of TLR9-mediated immune stimulation.
Measurement of pitch in speech: An implementation of Goldstein’s theory of pitch perception (1982)

Recent developments in hearing theory have resulted in the rather general acceptance of the idea that the perception of pitch of complex sounds is the result of the psychological pattern recognition process. The pitch is supposedly mediated by the fundamental of the harmonic spectrum which fits the spectrum of the complex sound optimally. The problem of finding the pitch is then equivalent to finding the best harmonic match. Goldstein [J. Acoust. Soc. Am. 54, 1496-1516 (1973)] has described an objective procedure for finding the best fit for stimuli containing relatively few spectral components. He uses maximum likelihood criterion. Application of this procedure to various data on the pitch of complex sounds yielded good results. This motivated our efforts to apply the pattern recognition theory of pitch to the problem of measuring pitch in speech. Although we were able to follow the main line of Goldstein's procedure, some essential changes had to be made. The most important is that in our implementation not all spectral components of the complex sound have to be classified as belonging to the harmonic pattern. We introduced a harmonics sieve to determine whether components are rejected or accepted at a candidate pitch. A simple criterion, based on the components accepted and rejected, led to the decision on which candidate pitch was to be finally selected. The performance and reliability of this psychoacoustically based pitch meter were tested in a LPC-vocoder system.
A Binary Tunnel Field Effect Transistor with a Steep Sub-threshold Swing and Increased ON Current (2010)

A variant tunnel field effect transistor structure called the binary tunnel field effect transistor (BTFET) for low voltage and near ideal switching characteristics is proposed. The BTFET relies on a binary tunneling distance (HIGH and LOW) for its operation to achieve a steep sub-threshold swing with a predicted range of 5 mV/dec. The transition of tunneling distance from HIGH to LOW state is a step-function of the gate voltage with the threshold voltage as a transition voltage. BTFET has a high on-current due to the high gate electric field and a large tunneling cross section area. An orientation dependent non-local band-to-band tunneling model was used to analyze the DC characteristics of the device.
Comprehensive characterization of a general composite waveplate by spectroscopic Mueller matrix polarimetry (2018)

Composite waveplates (CWs) consisting of multiple single waveplates are basic polarization elements and widely used to manipulate the polarized light in optical systems, and their performances affect the final accuracy and precision significantly. This research proposes a method for the comprehensive characterization of an arbitrary CW based on spectroscopic Mueller matrix polarimetry. An analytical model is established to describe a general CW by extending Jones' equivalent theorem with Mueller matrix calculus. In this model, an arbitrary CW is optically equivalent to a cascaded system consisting of a linear retarder with slight diattenuation followed by an optical rotator, and its polarization properties are completely described by four polarization parameters, including the retardance, the fast axis azimuth, the rotation angle, and the diattenuation angle. Analytical relations between the polarization properties, the structure, and the Mueller matrix of the CW are then derived from the established model. By the proposed method, the polarization parameters of an arbitrary CW can be comprehensively characterized over an ultra-wide spectral range via only one measurement. Moreover, the actual structure of the CW, including the thicknesses and fast axis azimuths of the single waveplates, as well as the axis alignment errors, can be completely reconstructed from the polarization spectra. Experiments performed with a house-developed broadband Mueller matrix polarimeter on three typical CWs including a compound zero-order waveplate, an achromatic waveplate and a specially designed biplate have demonstrated the capability of the proposed method.
Synthesis and Antitumor Properties of BQC-Glucuronide, a Camptothecin Prodrug for Selective Tumor Activation (2016)

Major limitations of camptothecin anticancer drugs (toxicity, nonselectivity, water insolubility, inactivation by human serum albumin) may be improved by creating glucuronide prodrugs that rely on beta-glucuronidase for their activation. We found that the camptothecin derivative 5,6-dihydro-4H-benzo[de]quinoline-camptothecin (BQC) displays greater cytotoxicity against cancer cells than the clinically used camptothecin derivatives SN-38 and topotecan even in the presence of human serum albumin. We synthesized the prodrug BQC-glucuronide (BQC-G), which was 4000 times more water soluble and 20-40 times less cytotoxic than BQC. Importantly, even in the presence of human serum albumin, BQC-G was efficiently hydrolyzed by beta-glucuronidase and produced greater cytotoxicity (IC50 = 13 nM) than camptothecin, 9-aminocamptothecin, SN-38, or topotecan (IC50 > 3000, 1370, 48, and 28 nM, respectively). BQC-G treatment of mice bearing human colon cancer xenografts with naturally or artificially elevated beta-glucuronidase activity produced significant antitumor activity, showing that BQC-G is a potent prodrug suitable for selective intratumoral drug activation.
One-Step Production of a Biologically Active Novel Furan Fatty Acid from 7,10-Dihydroxy-8(<i>E</i>)-octadecenoic Acid (2011)

Furan fatty acids (F-acids) gain special attention because they are known to play important roles in biological systems including humans. Specifically, F-acids are known to have strong antioxidant activitis such as radical scavenging activity. Although widely distributed in most biological systems, F-acids are trace components and their biosynthesis is complicated and quite different by sources. On the basis of biochemical study, they are considered to be an essential nutritional factor for mammals and should be provided through the diet. Hence, several studies reported the chemical synthesis of F-acids using chemical catalysts. However, chemical synthesis required complicated multiple steps. In this study was developed a simple one-step synthesis of a novel F-acid, 7,10-epoxyoctadeca-7,9-dienoic acid (EODA), from a dihydroxyl fatty acid, 7,10-dihydroxy-8(E)-octadecenoic acid (DOD), by heat treatment. The structure of EODA was confirmed by GC-MS, NMR, and FTIR analyses, and maximum production yield under the reaction conditions of 90 °C and 24 h reached 80%.
Author response: MicroRNA-146a acts as a guardian of the quality and longevity of hematopoietic stem cells in mice (2013)

Chronic and excessive inflammation can lead to exhaustion of the supply of hematopoietic stem cells and to myeloid malignancies in mice, mimicking important aspects of the myelodysplastic syndrome found in humans.
<i>Artemisia annua</i> L. (Asteraceae) trichome‐specific cDNAs reveal CYP71AV1, a cytochrome P450 with a key role in the biosynthesis of the antimalarial sesquiterpene lactone artemisinin (2006)

Artemisinin, a sesquiterpene lactone endoperoxide derived from the plant Artemisia annua, forms the basis of the most important treatments of malaria in use today. In an effort to elucidate the biosynthesis of artemisinin, an expressed sequence tag approach to identifying the relevant biosynthetic genes was undertaken using isolated glandular trichomes as a source of mRNA. A cDNA clone encoding a cytochrome P450 designated CYP71AV1 was characterized by expression in Saccharomyces cerevisiae and shown to catalyze the oxidation of the proposed biosynthetic intermediates amorpha-4,11-diene, artemisinic alcohol and artemisinic aldehyde. The identification of the CYP71AV1 gene should allow for the engineering of semi-synthetic production of artemisinin in appropriate plant or microbial hosts.
Investigation of effective system designs for transcranial photoacoustic tomography of the brain (2014)

Photoacoustic computed tomography (PACT) holds great promise for transcranial brain imaging. However, the strong reflection, scattering and attenuation of acoustic waves in the skull present significant challenges to developing this method. We report on a systematic computer-simulation study of transcranial brain imaging using PACT. The goal of this study was to identify an effective imaging system design that can be translated for clinical use. The propagation of photoacoustic waves through a model skull was studied by use of an elastic finite-difference time-domain (FDTD) method. The acoustic radiation pattern from a photoacoustic source just beneath the skull was observed with a ring transducer array that was level with the source. The observed radiation pattern was found to contain stronger contributions from waves that were converted to shear waves in skull than longitudinal waves that did not undergo mode conversion. Images reconstructed from the pressure data that contain shear wave components possess better resolution than images reconstructed from the data that only contain the longitudinal wave signals. These observations revealed that the detection system should be designed to capture photoacoustic signals that travel through the skull in the form of shear waves as well as in the form of longitudinal waves. A preliminary investigation on the effect of the presence of absorption in the skull is also reported. This study provides an insight into the wave phenomena in transcranial PACT imaging, as well as a concrete detection design strategy that mitigates the degraded resolution of reconstructed images.
Synthesis and Mechanism of Action of Novel Pyrimidinyl Pyrazole Derivatives Possessing Antiproliferative Activity (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Transmit diversity by antenna selection in CDMA downlink (2002)

We study transmit diversity concepts in DS/CDMA wireless networks with multiple transmit antennas. The previously proposed diversity techniques are reviewed and their performance is compared to a selective transmit diversity (STD) concept, proposed here for CDMA systems. In all the competing concepts the encoded bits are distributed to all transmit antennas, whereas in the proposed concept bit are transmitted only from the best antenna as indicated by a closed loop antenna selection (CL-AS) subchannel from the terminal to the base. We quantify the achievable gains for these transmit diversity concepts with Monte-Carlo simulations.
Acquired Resistance to EGFR Tyrosine Kinase Inhibitors in EGFR-Mutant Lung Cancer: Distinct Natural History of Patients with Tumors Harboring the T790M Mutation (2010)

Among patients with acquired resistance to EGFR TKIs, the presence of T790M defines a clinical subset with a relatively favorable prognosis and more indolent progression. Knowledge of T790M status is therefore important both for the clinical care of these patients and for the optimal design and interpretation of clinical trials in this setting.
Non-invasive measurement of chemotherapy drug concentrations in tissue: preliminary demonstrations of<i>in vivo</i>measurements (1999)

Measurements of the tissue concentrations of two chemotherapy agents have been made in vivo on an animal tumour model. The method used is based on elastic scattering spectroscopy (ESS) and utilizes a fibre-optic probe spectroscopic system. A broadband light source is used to acquire data over a broad range of wavelengths and, therefore, to facilitate the separation of absorptions from various chromophores. The results of the work include measurements of the time course of the drug concentrations as well as a comparison of the optical measurements with high performance liquid chromatography (HPLC) analysis of the drug concentrations at the time of sacrifice. It is found that the optical measurements correlate linearly with HPLC measurements, but give lower absolute values.
A Compact Imaging Detector of Polarization and Spectral Content (1993)

A new type of image detector will simultaneously analyze the polarization of light at all picture elements in a scene. The integrated Dual Imaging Detector (IDID) consists of a polarizing beam splitter bonded to a charge-coupled device (CCD), with signal-analysis circuitry and analog-to-digital converters, all integrated on a silicon chip. The polarizing beam splitter can be either a Ronchi ruling, or an array of cylindrical lenslets, bonded to a birefringent wafer. The wafer, in turn, is bonded to the CCD so that light in the two orthogonal planes of polarization falls on adjacent pairs of pixels. The use of a high-index birefringent material, e.g., rutile, allows the IDID to operate at f-numbers as high as f/3.5. Other aspects of the detector are discussed.
On Periodic Functions as Regularizers for Quantization of Neural Networks (2018)

Deep learning models have been successfully used in computer vision and many other fields. We propose an unorthodox algorithm for performing quantization of the model parameters. In contrast with popular quantization schemes based on thresholds, we use a novel technique based on periodic functions, such as continuous trigonometric sine or cosine as well as non-continuous hat functions. We apply these functions component-wise and add the sum over the model parameters as a regularizer to the model loss during training. The frequency and amplitude hyper-parameters of these functions can be adjusted during training. The regularization pushes the weights into discrete points that can be encoded as integers. We show that using this technique the resulting quantized models exhibit the same accuracy as the original ones on CIFAR-10 and ImageNet datasets.
Online End Point Detection in CMP Using SPRT of Wavelet Decomposed Sensor Data (2005)

Efficient end point detection (EPD) in chemical mechanical planarization (CMP) is critical to quality and productivity of the wafer fabrication process. The cost of over and under polishing, and the cost of ownership of many expensive metrology-based EPD methods have motivated the researchers to seek cost effective and efficient alternatives. This paper presents a novel method for EPD, which uses a sequential probability ratio test (SPRT) on the wavelet decomposed coefficient of friction (CoF) data from the CMP process. The method is made suitable for online application by developing a moving block data processing strategy, which matches the rate of data acquisition. Tests on both oxide and copper metal CMP show that the developed methodology is uniquely capable of identifying the start and finish of the end point event.
Donor CD8+ T Cells Mediate Graft-versus-Leukemia Activity without Clinical Signs of Graft-versus-Host Disease in Recipients Conditioned with Anti-CD3 Monoclonal Antibody (2007)

Donor CD8(+) T cells play a critical role in mediating graft-vs-leukemia (GVL) activity, but also induce graft-vs-host disease (GVHD) in recipients conditioned with total body irradiation (TBI). In this study, we report that injections of donor C57BL/6 (H-2(b)) or FVB/N (H-2(q)) CD8(+) T with bone marrow cells induced chimerism and eliminated BCL1 leukemia/lymphoma cells without clinical signs of GVHD in anti-CD3-conditioned BALB/c (H-2(d)) recipients, but induced lethal GVHD in TBI-conditioned recipients. Using in vivo and ex vivo bioluminescent imaging, we observed that donor CD8(+) T cells expanded rapidly and infiltrated GVHD target tissues in TBI-conditioned recipients, but donor CD8(+) T cell expansion in anti-CD3-conditioned recipients was confined to lymphohematological tissues. This confinement was associated with lack of up-regulated expression of alpha(4)beta(7) integrin and chemokine receptors (i.e., CXCR3) on donor CD8(+) T cells. In addition, donor CD8(+) T cells in anti-CD3-conditioned recipients were rendered unresponsive, anergic, Foxp3(+), or type II cytotoxic T phenotype. Those donor CD8(+) T cells showed strong suppressive activity in vitro and mediated GVL activity without clinical signs of GVHD in TBI-conditioned secondary recipients. These results indicate that anti-CD3 conditioning separates GVL activity from GVHD via confining donor CD8(+) T cell expansion to host lymphohemological tissues as well as tolerizing them in the host.
Estimation of Sparse MIMO Channels with Common Support (2012)

We consider the problem of estimating sparse communication channels in the MIMO context. In small to medium bandwidth communications, as in the current standards for OFDM and CDMA communication systems (with bandwidth up to 20 MHz), such channels are individually sparse and at the same time share a common support set. Since the underlying physical channels are inherently continuous-time, we propose a parametric sparse estimation technique based on finite rate of innovation (FRI) principles. Parametric estimation is especially relevant to MIMO communications as it allows for a robust estimation and concise description of the channels. The core of the algorithm is a generalization of conventional spectral estimation methods to multiple input signals with common support. We show the application of our technique for channel estimation in OFDM (uniformly/contiguous DFT pilots) and CDMA downlink (Walsh-Hadamard coded schemes). In the presence of additive white Gaussian noise, theoretical lower bounds on the estimation of sparse common support (SCS) channel parameters in Rayleigh fading conditions are derived. Finally, an analytical spatial channel model is derived, and simulations on this model in the OFDM setting show the symbol error rate (SER) is reduced by a factor 2 (0 dB of SNR) to 5 (high SNR) compared to standard non-parametric methods - e.g. lowpass interpolation.
SAMTOR is an <i>S</i> -adenosylmethionine sensor for the mTORC1 pathway (2017)

mTOR complex 1 (mTORC1) regulates cell growth and metabolism in response to multiple environmental cues. Nutrients signal via the Rag guanosine triphosphatases (GTPases) to promote the localization of mTORC1 to the lysosomal surface, its site of activation. We identified SAMTOR, a previously uncharacterized protein, which inhibits mTORC1 signaling by interacting with GATOR1, the GTPase activating protein (GAP) for RagA/B. We found that the methyl donor <i>S</i>-adenosylmethionine (SAM) disrupts the SAMTOR-GATOR1 complex by binding directly to SAMTOR with a dissociation constant of approximately 7 μM. In cells, methionine starvation reduces SAM levels below this dissociation constant and promotes the association of SAMTOR with GATOR1, thereby inhibiting mTORC1 signaling in a SAMTOR-dependent fashion. Methionine-induced activation of mTORC1 requires the SAM binding capacity of SAMTOR. Thus, SAMTOR is a SAM sensor that links methionine and one-carbon metabolism to mTORC1 signaling.
Digital video stabilization architecture for low cost devices (2005)

This paper presents a fast video stabilization algorithm that allows a very robust correction of both translational and rotational jitter, while keeping a very low-cost, low-power solution. A binary motion estimation is used in some key areas of the image to obtain a field of vectors, minimizing memory constraints. After a careful removal of the outlier motion vectors, the affine parameters that describe the global rotational and translational motion of the image are extracted. This motion is then properly filtered to retain only its intentional component. Performances of the algorithm and the complexity of a possible software solution in a realistic platform are evaluated.