gebhart/patrepeval huggingface dataset:
Electrical property and stability of electrochemically synthesized polypyrrole films (2004)

Abstract Polypyrrole (PPy) films doped with arylsulfonate dopants were prepared by electrochemical polymerization, to investigate the effects of various dopants on conductivities, thermal stabilities, and morphologies of PPy films. Also, HCl was added to those dopants as a cooperating dopant, to improve conductivity of PPy films. Conductivity of PPy film doped with the mixture of each dopant and HCl was improved. Temperature dependency on conductivity for PPy films doped with various dopants was investigated by heating them from 30 to 300°C. For the film doped with TSA, DBSA, and AQSA, conductivity increased up to 150°C and then rapidly decreased, whereas the conductivity of other films decreased after 200°C as temperature increased up to 300°C. Moreover, the film doped with small size dopant such as TSA and HCl/TSA had an interconnected porous fibrillar‐like morphology. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 91: 3659–3666, 2004
Gibberellins: A Phytohormonal Basis for Heterosis in Maize (1988)

Four commercially important maize parental inbreds and their 12 F(1) hybrids were studied to investigate the role of the phytohormone gibberellin (GA) in the regulation of heterosis (hybrid vigor). All hybrids grew faster than any inbred. In contrast, all inbreds showed a greater promotion of shoot growth after the exogenous application of GA(3). Concentrations of endogenous GA(1), the biological effector for shoot growth in maize, and GA(19), a precursor of GA(1), were measured in apical meristematic shoot cylinders for three of the inbreds and their hybrids by gas chromatography-mass spectrometry with selected ion monitoring; deuterated GAs were used as quantitative internal standards. In 34 of 36 comparisons, hybrids contained higher concentrations of endogenous GAs than their parental inbreds. Preferential growth acceleration of the inbreds by exogenous GA(3) indicates that a deficiency of endogenous GA limits the growth of the inbreds and is thus a cause of inbreeding depression. Conversely, the increased endogenous concentration of GA in the hybrids could provide a phytohormonal basis for heterosis for shoot growth.
Lead Design and Initial Applications of a New Lead for Long‐Term Endovascular Vagal Stimulation (2007)

A new endovascular spiral lead that takes advantage of the anatomy of the cardiac branches of the vagus nerve in the SVC was developed. VNS using ESVL produced significant HR slowing at voltages slightly below the highest pulse generator output of 7.5 V, which may be suitable for long-term implantation.
Analysis and validation of an artifact resistant design for oxygen saturation measurement using photo pletyhsmographic ring sensors (2004)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.
Identification of CD34+ cells in normal and pathological bone marrow biopsies by QBEND10 monoclonal antibody. (1991)

Monoclonal antibody QBEND10 is reactive with the CD34 antigen in aldehyde-fixed, decalcified, paraffin-embedded bone marrow biopsies. In normal bone marrow it stained endothelial cells lining arterioles and capillaries, sinusoidal (littoral) cells and 0.89% of all haemopoietic cells. QBEND10+ mononuclear cells were seen as isolated, randomly distributed mononuclear cells in normal and regenerating bone marrows. Conversely, QBEND10+ cells were increased and present in aggregates of three or more cells in 6/8 cases of acute leukemia; in two cases of CD34-negative leukemia and in two patients after complete remission no aggregates were seen. QBEND10 immunohistochemistry may therefore be useful for diagnosis and follow-up of myeloid leukemias. In addition, increased numbers of CD34+ cells arranged in clusters were seen in 4/9 cases of refractory anemia with excess blasts (RAEB), 1 case of chronic myelomonocytic leukemia, 3/3 cases of RAEB in transformation, and in 3/7 cases of chronic myelogenous leukemia: in all these cases, CD34 staining of the bone biopsy may have prognostic value. QBEND10+ endothelial cells were significantly increased in all the pathological conditions examined (1.43% of all nucleated cells versus 0.80% in normal bone marrow; p = 0.0063), but especially in myeloid leukemias and in two fibrotic syndromes examined.
Protein Engineering of a Viral Cage for Constrained Nanomaterials Synthesis (2002)

Cage architectures based on the cowpea chlorotic mottle virus (see Figure) have been employed to achieve a synthetic mimic of the iron storage protein ferritin. The electrostatic nature of the inner protein surface could be changed by up to 3240 units of charge, while still maintaining a stable cage structure. The spatial isolation within the protein cage prevents bulk aggregation of the mineral particles and results in a stable, mono-disperse colloid.
Correction of Attitude Fluctuation of Terra Spacecraft Using ASTER/SWIR Imagery With Parallax Observation (2007)

Accurate attitude estimation of spacecrafts is the main requirement to provide good geometric performance of remote-sensing imagery. The Advanced Spaceborne Thermal Emission and Reflection Radiometer/short-wave-infrared subsystem has six linear-array sensors arranged in parallel, and each line scans the same ground target with a time interval of 356.238 ms between neighboring bands. The registration performance between bands becomes worse when attitude fluctuation occurs during a time lag between observations. Since the time resolution of the line scan is higher than that of the attitude information provided from the satellite, attitude data are estimated with a high frequency. We succeeded in correcting the image-registration error using the revised attitude information. As a result, the image distortion of 0.2 pixels caused by spacecraft-attitude jitter is reduced to less than 0.08 pixels, showing that band-to-band registration errors of a sensor with parallax observation are available to improve the image distortion caused by attitude fluctuation.
A Pilot Study in Rhesus Macaques to Assess the Treatment Efficacy of a Small Molecular Weight Catalytic Metalloporphyrin Antioxidant (AEOL 10150) in Mitigating Radiation-induced Lung Damage (2013)

The objective of this pilot study was to explore whether administration of a catalytic antioxidant, AEOL 10150 (C48H56C15MnN12), could reduce radiation-induced lung injury and improve overall survival when administered after 11.5 Gy of whole thorax lung irradiation in a non-human primate model. Thirteen animals were irradiated with a single exposure of 11.5 Gy, prescribed to midplane, and delivered with 6 MV photons at a dose rate of 0.8 Gy min. Beginning at 24 h post irradiation, the AEOL 10150 cohort (n = 7) received daily subcutaneous injections of the catalytic antioxidant at a concentration of 5 mg kg for a total of 4 wk. All animals received medical management, including dexamethasone, based on clinical signs during the planned 180-d in-life phase of the study. All decedent study animals were euthanized for failure to maintain saturation of peripheral oxygen > 88% on room air. Exposure of the whole thorax to 11.5 Gy resulted in radiation-induced lung injury in all animals. AEOL 10150, as administered in this pilot study, demonstrated potential efficacy as a mitigator against fatal radiation-induced lung injury. Treatment with the drug resulted in 28.6% survival following exposure to a radiation dose that proved to be 100% fatal in the control cohort (n = 6). Computed tomography scans demonstrated less quantitative radiographic injury (pneumonitis, fibrosis, effusions) in the AEOL 10150-treated cohort at day 60 post-exposure, and AEOL 10150-treated animals required less dexamethasone support during the in-life phase of the study. Analysis of serial plasma samples suggested that AEOL 10150 treatment led to lower relative transforming growth factor-Beta-1 levels when compared with the control animals. The results of this pilot study demonstrate that treatment with AEOL 10150 results in reduced clinical, radiographic, anatomic, and molecular evidence of radiation-induced lung injury and merits further study as a medical countermeasure against radiation-induced pulmonary injury.
Sugar and Signal-Transducer Binding Sites of the Escherichia coli Galactose Chemoreceptor Protein (1988)

D-galactose-binding (or chemoreceptor) protein of Escherichia coli serves as an initial component for both chemotaxis towards galactose and glucose and high-affinity active transport of the two sugars. Well-refined x-ray structures of the liganded forms of the wild-type and a mutant protein isolated from a strain defective in chemotaxis but fully competent in transport have provided a molecular view of the sugar-binding site and of a site for interacting with the Trg transmembrane signal transducer. The geometry of the sugar-binding site, located in the cleft between the two lobes of the bilobate protein, is novel in that it is designed for tight binding and sequestering of either the alpha or beta anomer of the D-stereoisomer of the 4-epimers galactose and glucose. Binding specificity and affinity are conferred primarily by polar planar side-chain residues that form intricate networks of cooperative and bidentate hydrogen bonds with the sugar substrates, and secondarily by aromatic residues that sandwich the pyranose ring. Each of the pairs of anomeric hydroxyls and epimeric hydroxyls is recognized by a distinct Asp residue. The site for interaction with the transducer is about 18 A from the sugar-binding site. Mutation of Gly74 to Asp at this site, concomitant with considerable changes in the local ordered water structures, contributes to the lack of productive interaction with the transmembrane signal transducer.
Purification and characterization of sortase, the transpeptidase that cleaves surface proteins of Staphylococcus aureus at the LPXTG motif (1999)

Surface proteins of Staphylococcus aureus are linked to the bacterial cell wall by sortase, an enzyme that cleaves polypeptides at the threonine of the LPXTG motif. Surface proteins can be released from staphylococci by treatment with hydroxylamine, resulting in the formation of threonine hydroxamate. Staphylococcal extracts, as well as purified sortase, catalyze the hydroxylaminolysis of peptides bearing an LPXTG motif, a reaction that can be inhibited with sulfhydryl-modifying reagents. Replacement of the single conserved cysteine at position 184 of sortase with alanine abolishes enzyme activity. Thus, sortase appears to catalyze surface-protein anchoring by means of a transpeptidation reaction that captures cleaved polypeptides as thioester enzyme intermediates.
A Peptide Inhibitor of Cytomegalovirus Infection from Human Hemofiltrate (2013)

Naturally occurring substances with antimicrobial activity can serve as a starting point for the rational design of new drugs to treat infectious diseases. Here, we screened a library of peptides derived from human hemofiltrate for inhibitory effects on human cytomegalovirus (CMV) infection. We isolated a previously unknown derivative of the neutrophil-activating peptide 2, which we termed CYVIP, for CMV-inhibiting peptide. The peptide blocked infection with human and mouse CMV as well as with herpes simplex virus type 1 in different cell types. We found that CYVIP interferes with virus attachment to the cell surface, and structure-activity relationship studies revealed that positively charged lysine and arginine residues of CYVIP are essential for its inhibitory activity. The N-terminal 29 amino acids of the peptide were sufficient for inhibition, and substitution with an acidic residue further improved its activity. The target structure of CYVIP on the cell surface seems to be the sulfate residues of heparan sulfate proteoglycans, which are known to serve as herpesvirus attachment receptors. Our data suggest that O-sulfation of heparan sulfate is required for binding of CYVIP, and furthermore, that the initial interaction of CMV particles with cells takes place preferentially via 6-O-linked sulfate groups. These findings about CYVIP's mode of action lay the basis for further development of antivirals interfering with attachment of CMV to cells, a crucial step of the infection cycle.
Vector Precoding for Wireless MIMO Systems and its Replica Analysis (2008)

This paper studies a nonlinear vector precoding scheme which inverts the wireless multiple-input multiple-output (MIMO) channel at the transmitter so that simple symbol-by-symbol detection can be used in lieu of sophisticated multiuser detection at the receiver. In particular, the transmit energy is minimized by relaxing the transmitted symbols to a larger alphabet for precoding, which preserves the minimum signaling distance. The so-called replica method is used to analyze the average energy savings with random MIMO channels in the large-system limit. It is found that significant gains can be achieved with complex-valued alphabets. The analysis applies to a very general class of MIMO channels, where the statistics of the channel matrix enter the result via the R-transform of the asymptotic empirical distribution of its eigenvalues. Moreover, we introduce polynomial-complexity precoding schemes for binary and quadrature phase-shift keying in complex channels by using convex rather than discrete relaxed alphabets. In case the number of transmit antennas is more than twice the number of receive antennas, we show that a convex precoding scheme, despite its polynomial complexity, outperforms NP-hard precoding using the popular Tomlinson-Harashima signaling.
Modulation of transcription factor NF-kappa B binding activity by oxidation-reduction in vitro. (1991)

NF-kappa B is a widely used regulator of inducible and tissue-specific gene control. In the cytosol, when complexed to an inhibitory molecule, I kappa B, NF-kappa B is in an inactive form and cannot bind DNA. Activation of cells with appropriate stimuli results in the dissociation of NF-kappa B from I kappa B and its translocation to the nucleus as an active binding protein. We now demonstrate that NF-kappa B binding in vitro can be inhibited by agents that modify free sulfhydryls. Binding is eliminated after treatment with N-ethylmaleimide, an alkylating agent, and diamide, an oxidizing agent. The diamide effect can be reversed by 2-mercaptoethanol. Further, 2-mercaptoethanol acts synergistically with deoxycholate plus Nonidet P-40 in converting inactive cytosolic NF-kappa B to an active DNA-binding form. It is therefore possible that modulation of the redox state of NF-kappa B could represent a post-translational control mechanism for this factor.
NGC: lossless and lossy compression of aligned high-throughput sequencing data (2012)

A major challenge of current high-throughput sequencing experiments is not only the generation of the sequencing data itself but also their processing, storage and transmission. The enormous size of these data motivates the development of data compression algorithms usable for the implementation of the various storage policies that are applied to the produced intermediate and final result files. In this article, we present NGC, a tool for the compression of mapped short read data stored in the wide-spread SAM format. NGC enables lossless and lossy compression and introduces the following two novel ideas: first, we present a way to reduce the number of required code words by exploiting common features of reads mapped to the same genomic positions; second, we present a highly configurable way for the quantization of per-base quality values, which takes their influence on downstream analyses into account. NGC, evaluated with several real-world data sets, saves 33-66% of disc space using lossless and up to 98% disc space using lossy compression. By applying two popular variant and genotype prediction tools to the decompressed data, we could show that the lossy compression modes preserve >99% of all called variants while outperforming comparable methods in some configurations.
Generation of Replication-Competent Hepatitis B Virus Nucleocapsids in Insect Cells (1998)

The double-stranded DNA genome of human hepatitis B virus (HBV) and related hepadnaviruses is reverse transcribed from a pregenomic RNA by a viral polymerase (Pol) harboring both priming and RNA- and DNA-dependent elongation activities. Although hepadnavirus replication occurs inside viral nucleocapsids, or cores, biochemical systems for analyzing this reaction are currently limited to unencapsidated Pols expressed in heterologous systems. Here, we describe cis and trans classes of replicative HBV cores, produced in the recombinant baculovirus system via coexpression of HBV core and Pol proteins from either a single RNA (i.e., in cis) or two distinct RNAs (in trans). Upon isolation from insect cells, cis and trans cores contained Pol-linked HBV minus-strand DNA with 5' ends mapping to the authentic elongation origin DR1 and also plus-strand DNA species. Only trans cores, however, were highly active for the de novo priming and reverse transcription of authentic HBV minus strands in in vitro endogenous polymerase assays. This reaction strictly required HBV Pol but not the epsilon stem-loop element, although the presence of one epsilon, or better, two epsilons, enhanced minus-strand synthesis up to 10-fold. Compared to unencapsidated Pol enzymes, encapsidated Pol appeared to be (i) highly processive, able to extend minus-strand DNAs of 400 nucleotides from DR1 in vitro, and (ii) more active for HBV plus-strand synthesis. These observations suggest possible contributions to the replication process from the HBV core protein. These novel core reagents should facilitate the analysis of HBV replication in its natural environment, the interior of the capsid, and also fuel the development of new anti-HBV drug screens.
Spectral-domain spectrally-encoded endoscopy (2007)

Spectrally-encoded miniature endoscopy uses a single optical fiber and wavelength division multiplexing to obtain macroscopic images through miniature, flexible probes. In turn, it has the potential to enable two- and three-dimensional imaging within the body at locations that are currently difficult to access with conventional endoscopes. Here we present a novel detection scheme for spectrally-encoded endoscopy using spectral-domain interferometry. Compared to previous time-domain configurations, this new detection method results in greater than 1000-fold increase in sensitivity (77 dB), a 6-fold increase in imaging speed (30 volumes per second), and a 2-fold increase in depth range (2.8 mm). We demonstrate spectrally-encoded, spectral-domain detection by conducting video-rate, three-dimensional imaging in a variety of specimens, including the paws of a mouse embryo and excised human ear bones. Our results show that this new technology enables video rate spectrally-encoded endoscopy and will therefore be useful for a variety of minimally invasive medical applications.
Replication of an adenoviral vector controlled by the human telomerase reverse transcriptase promoter causes tumor-selective tumor lysis. (2003)

Telomerase reactivation is a critical step for tumorigenesis, allowing cancer cells to proliferate indefinitely. Taking advantage of this property, we generated an adenovirus vector in which E1 gene expression, and therefore viral replication, is under control of the human telomerase reverse transcriptase (hTERT) promoter. This vector, referred to as Ad5-hTERT-E1, replicated in cancer cells and demonstrated efficient cancer-selective cytolysis in a variety of tumor cell lines, including HT-1080 (fibrosarcoma cells); HeLa (cervical carcinoma cells); A549 (lung carcinoma cells); Hep G2 (hepatocellular carcinoma cells); SCC-4, SCC-25, and SCCLSU-1 (head and neck squamous cell carcinoma cells); T24 (bladder carcinoma); and DU 145 (prostate carcinoma). In contrast, the identical multiplicities of infection of Ad5-hTERT-E1 had no effect on primary cultures of normal human fibroblasts, airway epithelial cells, and bone marrow mesenchymal stem cells. Moreover, a single injection of Ad5-hTERT-E1 into preexisting HT-1080 solid tumors, established s.c. in nu/nu mice, efficiently suppressed tumor growth. Interestingly, this conditionally replicating vector transactivated the replication of an E1-deleted antitumor adenoviral vector, Ad5-RSV-hsvTK, in tumor cells, demonstrating a synergistic antitumor effect in vivo. Combinational injection of a single dose of Ad5-hTERT-E1 and Ad5-RSV-hsvTK vector resulted in significant tumor suppression and regression after ganciclovir treatment. These results suggest that the Ad5-hTERT-E1 vector has potential as a broad-spectrum antitumor agent.
Retinitis pigmentosa and allied diseases: numerous diseases, genes, and inheritance patterns (2002)

Retinitis pigmentosa (RP) and allied diseases are heterogeneous clinically and genetically. Here we summarize the retinal cell types involved in these diseases, the large number of genes that cause them, and the variety of inheritance patterns that the affected families display. Special consideration is given to unusual inheritance patterns. The aggregate carrier frequency for recessive RP alleles may be as high as 10%.
α-Tocopheryl Succinate as a Scaffold to Develop Potent Inhibitors of Breast Cancer Cell Adhesion (2009)

This study is aimed at the pharmacological exploitation of alpha-tocopheryl succinate (1) to develop potent antiadhesion agents. Considering the structural cooperativity between the phytyl chain and the carboxylic terminus in determining the antiadhesion activity, our structural optimization led to compound 5 ([2-(4,8-dimethyl-non-1-enyl)-2,5,7,8-tetramethyl-chroman-6-yloxy]-acetic acid), which exhibited an-order-of-magnitude higher potency than 1 in blocking the adhesion of 4T1 metastatic breast cancer cells to extracellular matrix proteins (IC(50), 0.6 microM versus 10 microM). Evidence indicates that the ability of compound 5 to block cell adhesion and migration was attributable to its effect on disrupting focal adhesion and actin cytoskeletal integrity by facilitating the degradation of focal adhesion kinase. Interactions between tumor cells and the ECM in the tumor microenvironment have been increasingly recognized as critical modulators of the metastatic potential of tumor cells. Consequently, the ability of compound 5 to block such interactions provides a unique pharmacological tool to shed light onto mechanisms that govern cell adhesion and tumor metastasis.
Holographic Notch Filter for Low-Wavenumber Stokes and Anti-Stokes Raman Spectroscopy (1991)

A holographic notch filter with a 15-nm rejection band is used as a Rayleigh line filter for Raman spectroscopy with a single-stage grating spectrograph. The filter is shown to allow acquisition of Stokes and anti-Stokes spectra as close as 72 cm −1 from the exciting line.
Human tumor vaccines and genetic engineering of tumors with cytokine and histocompatibility genes to enhance immunogenicity (1994)

Genetically engineered tumor cells can be used as vaccines in order to stimulate an immune response. To date, tumor cells have been modified in vitro so that they secrete cytokines or express histocompatibility molecules that they naturally fail to express. These tumor cells differ in the types of immune responses they induce and in whether the responses have local or systemic efficacy. Many questions have been raised during the past year, including whether allogeneic or autologous tumor cells should be employed and whether there may be a risk of inducing autoimmune disease along with the antitumor response. Nevertheless, because of the paucity of available therapies for patients with advanced cancer, investigators must attempt to refine the approaches used in order to minimize patient risk while maximizing tumor cell destruction.