gebhart/patrepeval huggingface dataset:
A proteomic approach reveals transient association of reticulocalbin-3, a novel member of the CREC family, with the precursor of subtilisin-like proprotein convertase, PACE4 (2006)

SPCs (subtilisin-like proprotein convertases) are a family of seven structurally related serine endoproteases that are involved in the proteolytic activation of proproteins. In an effort to examine the substrate protein for PACE4 (paired basic amino-acid-cleaving enzyme-4), an SPC, a potent protein inhibitor of PACE4, an alpha1-antitrypsin RVRR (Arg-Val-Arg-Arg) variant, was expressed in GH4C1 cells. Ectopic expression of the RVRR variant caused accumulation of the 48 kDa protein in cells. Sequence analysis indicates that the 48 kDa protein is a putative Ca2+-binding protein, RCN-3 (reticulocalbin-3), which had previously been predicted by bioinformatic analysis of cDNA from the human hypothalamus. RCN-3 is a member of the CREC (Cab45/reticulocalbin/ERC45/calumenin) family of multiple EF-hand Ca2+-binding proteins localized to the secretory pathway. The most interesting feature of the RCN-3 sequence is the presence of five Arg-Xaa-Xaa-Arg motifs, which represents the target sequence of SPCs. Biosynthetic studies showed that RCN-3 is transiently associated with proPACE4, but not with mature PACE4. Inhibition of PACE4 maturation by a Ca2+ ionophore resulted in accumulation of the proPACE4-RCN-3 complex in cells. Furthermore, autoactivation and secretion of PACE4 was increased upon co-expression with RCN-3. Our findings suggest that selective and transient association of RCN-3 with the precursor of PACE4 plays an important role in the biosynthesis of PACE4.
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution (2008)

The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
Stimuli-Responsive Azulene-Based Conjugated Oligomers with Polyaniline-like Properties (2011)

Novel azulene building blocks, prepared via the cycloaddition of thiophene-S,S-dioxides and fulvenes, allow for incorporation of the seven-membered ring of the azulene nucleus directly into the backbone of conjugated materials. This unique mode of incorporation gives remarkably stable, stimuli-responsive materials upon exposure to acid. This simple doping/dedoping strategy provides for effective optical band gap control and on/off fluorescence switching, reminiscent of polyaniline.
PAM4-Reactive MUC1 Is a Biomarker for Early Pancreatic Adenocarcinoma (2007)

The results suggest that expression of the PAM4-reactive antigen may represent an early event in the development of invasive pancreatic adenocarcinoma, and is unrelated to the VNTR peptide core epitopes of MUC1. Detection of this biomarker using immunohistology, in vitro immunoassays, and in vivo antibody-based imaging may provide new opportunities for the early detection and improved diagnosis of pancreatic cancer.
Methods in laboratory investigation. Application of the indirect enzyme-linked immunosorbent assay microtest to the detection and surveillance of human t cell leukemia-lymphoma virus. (1983)

An ELISA assay for the detection of human T cell leukemia-lymphoma virus antibodies in human sera has been developed that has considerable advantages over previous techniques and equals the sensitivity of radioimmunoassay. Tests of normal and antibody-positive sera from leukemia patients indicate that this method should prove useful in the seroepidemiologic research for human T cell leukemia-lymphoma virus in the human population for probing the mode of its transmission and its clinical association with various T cell malignancies.
Fast Three Step Intra Prediction Algorithm for 4x4 blocks in H.264 (2005)

This paper presents a fast three step algorithm for H.264 4/spl times/4 intra prediction. Motivated by the high correlation of RD cost between different prediction directions, in each step of the algorithm, the proposed algorithm efficiently explores the neighborhood direction around the minimum one and thus skips other unlikely ones. Thus, the proposed algorithm can complete 4/spl times/4 intra prediction by only examining 6 modes instead of 9 modes in the full search algorithm. The simulation result shows that the proposed algorithm can maintain a similar PSNR quality to the full search algorithm with only about 1% bit-rate increase.
A structured speech model with continuous hidden dynamics and prediction-residual training for tracking vocal tract resonances (2004)

A novel approach is developed for efficient and accurate tracking of vocal tract resonances, which are natural frequencies of the resonator from larynx to lips, in fluent speech. The tracking algorithm is based on a version of the structured speech model consisting of continuous-valued hidden dynamics and a piecewise-linearized prediction function from resonance frequencies and bandwidths to LPC cepstra. We present details of the piecewise linearization design process and an adaptive training technique for the parameters that characterize the prediction residuals. An iterative tracking algorithm is described and evaluated that embeds both the prediction-residual training and the piecewise linearization design in an adaptive Kalman filtering framework. Experiments on tracking vocal tract resonances in Switchboard speech data demonstrate high accuracy in the results, as well as the effectiveness of residual training embedded in the algorithm. Our approach differs from traditional formant trackers in that it provides meaningful results even during consonantal closures when the supra-laryngeal source may cause no spectral prominences in speech acoustics.
Endothelin-1 Induces CXCL1 and CXCL8 Secretion in Human Melanoma Cells (2005)

The endothelin pathway plays a critical role in melanoma tumor progression by a variety of mechanisms that enhance tumor cell growth, invasion, and metastasis. Here, we investigate the effect of this pathway on CXC chemokine expression in human melanoma cells and melanocytes. As determined by ELISA, endothelin-1 (ET-1) induces CXCL1 and CXCL8 secretion in three human melanoma cell lines in a concentration-dependent fashion. These responses are mediated by the endothelin-B receptor and are sustained over a 40 h time course. ET-1 does not induce CXCL1 secretion in primary human melanocytes but ET-3, an endothelin isoform, induces a low level of CXCL1 secretion in certain cultures. Neither ET-1 nor ET-3 induces secretion of CXCL8 in primary human melanocytes; thus, this response may be specific for melanocytic cells that have undergone malignant transformation. We have previously demonstrated that ET-1 induces changes in the expression of adhesion molecules in melanoma cells such that invasion and metastasis are favored. This study demonstrates that ET-1 additionally induces secretion of CXC chemokines critical for melanoma metastasis and tumor progression.
Media Convergence and the Impact of the Internet on the M&A Activity of Large Media Companies (2010)

This study develops an analytical framework which helpsexplain how media convergence can impact ownership decisions of largemedia companies. It then uses data on nine large U.S. media companies toexamine what impact the Internet and media convergence have had on their M&A activity. The study finds that how a firm conceptualizes theInternet relative to its existing business has a significant impact on M&Aactivity—and understanding investing in the Internet as being more about change than simply growth is key to success.
The synthesis of phenyl(2-3H)glyoxal (1979)

A simple inexpensive method has been developed for the synthesis of [2-3H]acetophenone, which has been converted into phenyl[2-3H]glyoxal. The latter compound has been used to modify arginine residues in alkaline phosphatase from two sources, and also a sialidase.
Human Immunodeficiency Virus Type 1 Quasi Species That Rebound after Discontinuation of Highly Active Antiretroviral Therapy Are Similar to the Viral Quasi Species Present before Initiation of Therapy (2001)

In an effort to identify the sources of the viruses that emerge after discontinuation of therapy, analyses of human immunodeficiency virus (HIV) quasi species were done for 3 patients with sustained levels of HIV RNA of <50 copies/mL for 1-3 years. The sequences found in the rebounding plasma virus were closely related to those of the actively replicating form of viruses present before the initiation of combination therapy. All quasi species found in the rebounding plasma virus were also present in proviral DNA, cell-associated RNA in peripheral blood mononuclear cells (PBMC), and virion RNA derived from PBMC coculture during periods when plasma HIV RNA levels were <50 copies/mL. These findings suggest that the rapid resurgence of plasma viremia observed after discontinuation of therapy and the viruses cocultured from PBMC are derived from a relatively stable pool of the replicating form of virus rather than from activation of a previously latent pool.
Solid Phase Synthesis of Peptide C-Terminal Thioesters by Fmoc/t-Bu Chemistry (1999)

Peptide C-terminal thioesters are key intermediates in a variety of applications, most notably the recently developed native chemical ligation methods for the total chemical synthesis of proteins. So far they have been prepared only by the use of the least prevalent Boc/benzyl solid-phase method on ad hoc prepared resin supports. We describe here a novel method for the solid phase synthesis of thioesters by the most prevalent Fmoc/t-Bu method. The method is based on the use of a 3-carboxypropanesulfonamide safety-catch linker, which is fully stable to repetitive exposure to the basic conditions needed for Fmoc cleavage. Activation with diazomethane or iodoacetonitrile followed by displacement with a suitable thiol produces the thioester in good to excellent yields. The method is also compatible with Boc/benzyl chemistry. Moreover, all the necessary reagents are commercially available.
Characterization of the hierarchical composite properties of cortical bone: A transgenic approach. (1994)

The stability of diclofenac sodium injection was studied by means of a stability-indicating high-performance liquid chromatography assay method that was developed in our laboratory. There was a direct relationship between the peak heights and the concentrations. The percent relative standard deviation based on five injections was 0.9. The products of decomposition and the excipients present in the dosage form did not interfere with the developed assay method. The injection was stable for at least 23 days when stored in clear glass vials at room temperature. Contrary to the recommendation in the literature, the injection may not be stored at the refrigerated temperature. The physcial appearacne and the pH value of the injection did not change during the study period.
A 58.6 mW 30 Frames/s Real-Time Programmable Multiobject Detection Accelerator With Deformable Parts Models on Full HD $1920\times 1080$ Videos (2017)

This paper presents a programmable, energy-efficient, and real-time object detection hardware accelerator for low power and high throughput applications using deformable parts models, with 2x higher detection accuracy than traditional rigid body models. Three methods are used to address the high computational complexity of eight deformable parts detection: classification pruning for 33x fewer part classification, vector quantization for 15x memory size reduction, and feature basis projection for 2x reduction in the cost of each classification. The chip was fabricated in a 65 nm CMOS technology, and can process full high definition 1920 × 1080 videos at 60 frames/s without any OFF-chip storage. The chip has two programmable classification engines (CEs) for multiobject detection. At 30 frames/s, the chip consumes only 58.6 mW (0.94 nJ/pixel, 1168 GOPS/W). At a higher throughput of 60 frames/s, the CEs can be time multiplexed to detect even more than two object classes. This proposed accelerator enables object detection to be as energy-efficient as video compression, which is found in most cameras today.
Conductiong polymer connections for molecular devices (1994)

Ways of connecting molecular devices will be needed if the ideas of molecular electronics are ever to be realized. The potential of conducting polymer nanowires for this purpose is discussed and illustrated with the case of poly(3‐alkylthiophene), which can be made to connect two Pt wires by forming dendrites between them (see Figure). magnified image
Effects of passivation layer on stress relaxation in Cu line structures (2004)

In this study, we investigate the effect of passivation layer on mass transport by measuring stress relaxation in Cu damascene line structures. SiC and SiN/sub x/ passivation layers are investigated and compared with no passivation to examine the bonding effect on mass transport. The observed stress relaxation behavior is analyzed by a kinetic model considering the contribution to mass transport via various diffusion paths including the passivation interface. Results of this study show a significant effect due to the passivation layer that can be attributed to the interfacial chemistry.
Generation and decay of the immune response to a progressive fibrosarcoma. I. Ly-1+2- suppressor T cells down-regulate the generation of Ly-1-2+ effector T cells. (1984)

It was shown that the progressive growth of the immunogenic meth A fibrosarcoma in its semisyngeneic host results in the generation of concomitant immunity to the growth of a tumor implant. The generation of immunity occurred between days 6 and 9 of tumor growth and was associated with the generation of sensitized T cells that were capable, on passive transfer, of causing regression of a 3-d tumor in gamma-irradiated recipients. After day 9 of tumor growth, concomitant immunity and the T cells able to passively transfer it were progressively lost, and this was associated with the generation of splenic suppressor T cells able to suppress the expression of adoptive immunity against an established tumor in T cell-deficient ( TXB ) recipients. The T cells that passively transferred concomitant immunity were shown to be of the Ly-1-2+ phenotype, in contrast to the T cells that transferred suppression, which were shown with the same reagents to be Ly-1+2-. The results are consistent with the hypothesis that the progressive growth of an immunogenic tumor results in the generation of Ly-1-2+-sensitized effector T cells that fail to reach a number sufficient to destroy the tumor because their generation is down-regulated by tumor-induced Ly-1+2- suppressor T cells.
Development of a multiple thin-film semimicro DC-probe for intracerebral recordings (during surgery) (1990)

A thin-film multiple-electrode probe for measuring de potentials at eight sites with interdistances of 1 mm was constructed for the investigation of slow potential changes in deep regions of the human brain during surgery. The thin-film electrodes had to be placed on curved cylinder-shaped surgical instruments with dimensions of 2 mm diameter and 33 cm length used with the Freiburg stereotactic equipment. Several novel technological steps had to be introduced for the solution of the encountered problems: 1) Structuring of the metal layers on curved substrates was accomplished by using flexible masks. 2) Special feed-through technologies had to be invented in order to obtain reliable connections between the thin-film sensors and the copper wires inside the stereotactic instrument. 3) Thin-film Ag-AgCl electrodes had to be formed in order to obtain satisfying recordings of slow potential changes below 10 Hz. Slow potential changes were recorded from different depths in interdistances of only 1 mm with these new miniaturized thin film Ag-AgCl electrodes and bipolar recordings with an electrode interdistance of only 3 mm showed clearly the appearance of Bereitschaftspotentials.
Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon. (1987)

The complete nucleotide sequence of the glucitol (gut) operon in Escherichia coli has been determined. The glucitol-specific Enzyme II and Enzyme III of the phosphoenolpyruvate:sugar phosphotransferase system as well as glucitol-6-phosphate dehydrogenase which are encoded by the gutA, gutB, and gutD genes of the gut operon, respectively, are predicted to consist of 506 (Mr = 54,018), 123 (Mr = 13,306), and 259 (Mr = 27,866) amino acyl residues, respectively. The hydropathic profile of the Enzyme IIgut revealed 7 or 8 long hydrophobic segments which may traverse the cell membrane as alpha-helices as well as 2 or 4 short strongly hydrophobic stretches which may traverse the membrane as beta-structure. The number of amino acyl residues in the sum of the molecular weights of the glucitol Enzyme II-III pair are nearly the same as those of the mannitol Enzyme II. The ratio of hydrophobic to hydrophilic amino acyl residues and the numbers of the hydrophobic segments are also nearly the same for both transport systems. However, no significant homology was found in the nucleotide or amino acyl sequences of the two systems. Glucitol-6-phosphate dehydrogenase was found to exhibit sequence homology with ribitol dehydrogenase. A repetitive extragenic palindromic sequence was found in the 3'-flanking region of the gutD gene, suggesting the presence of a gene downstream from the gutD gene.
The infrared continuum spectrum of x ray illuminated molecular gas (1990)

In starburst galaxies, active galaxies, and the mysterious ultraluminous infrared galaxies, x rays are likely to interact with molecular gas and dust, thereby inducing infrared emission. X ray heated thermal dust will emit the IR continuum, and x ray photoelectrons will excite an IR emission-line spectrum. Here, researchers model the IR continuum emission characteristic of some selected x ray spectral fluxes, in particular the x ray bremsstrahlung characteristic of supernova and stellar wind bubble shocks in dense media and the power law spectra characteristic of active galactic nuclei. These models are part of a larger project to determine the complete IR spectra, lines plus continuum, of x ray sources embedded in molecular gas. They modeled the thermal emission from grains by calculating a grain temperature/size/composition distribution function, f(T,a,Comp.), which accounts for temperature fluctuations by averaging over all grain thermal histories. In determining the grain thermal distribution, researchers account for both direct grain heating (by x ray absorption and subsequent electron energy deposition) and indirect grain heating (by absorption of the UV emission stimulated by non-thermal photo- and Auger electrons in the gas phase). We let the grain size distribution be proportional to a(exp -3.5), and they consider two types of grain composition: graphites, which we assume to be pure carbon, and silicates, which contain all other depleted heavy elements. They derive the grain composition distribution function from solar abundances and interstellar depletion data.
A fourier‐transform infrared spectroscopic study of the hydrolytic stability of silane coupling agents on E‐glass fibers (1980)

Abstract Fourier‐transform (FT) infrared spectroscopy has been applied to the study the hydrothermal degradation of various coupling agents on E‐glass fibers. The coupling agents studied include γ‐methacryloxypropyltrimethoxysilane, vinyltrimethoxysilane, and cyclohexyltrimethoxysilane. The amount of coupling agents on E‐fibers was measured as a function of immersion time in water at 80°C. Structural changes were also followed by obtaining FT‐IR difference spectra of the coupling agent on the glass fiber surface. Silanes desorb quite differently depending on the organofunctional groups. The resistance to desorption is strongly influenced by the organization of the silane interphase as well as the solubility of the silane in water.
A model for the taxol (paclitaxel)/epothilone pharmacophore (1996)

Epothilone is a recently discovered compound that appears to bind at the same microtubule-binding site as the anticancer agent taxol. A model for the pharmacophore common to these structurally dissimilar compounds is presented.
Artificial oxygen carriers (1998)

The clinical availability of artificial oxygen carriers (AOCs) would result in profound alterations in transfusion medical practice. Rapid progress in the scientific and technological development of AOCs has advanced to a critical stage at which safe and effective alternatives to the transfusion of red blood cells are emerging. Haemoglobin- and perfluorocarbon-based oxygen carriers are under current clinical investigation. Artificial oxygen-carrying solutions, by virtue of their acellular structure, can be used to transport oxygen to ischaemic tissues that cannot otherwise be reached by cellular blood components. Organs awaiting transplantation can be preserved for a long time after perfusion with AOCs and tumour susceptibility to chemo- and radiotherapy is increased. The use of AOCs is therefore not confined to their use as red blood cell substitutes, but may find a wide spectrum of interdisciplinary applications.
Approaches to characterize protein-DNA interactions in vivo. (1993)

With the availability of direct genomic footprinting techniques the study of native genomes has been greatly facilitated. This review provides an overview of the techniques involved and gives also a description of the mode of action of different DNA modifying agents which can be used for such methods. These include exonuclease III, deoxyribonuclease, DNase I, micrococcal nuclease, dimethyl sulfate, diethyl sulfate, ethyl methanesulphonate, ethylnitrosourea, diethylpyrocarbonate, bromoacetaldehyde, potassium permanganate, osmium tetroxide, methidiumpropyl-EDTA-iron(II), formaldehyde, psoralen, 1,10 phenanthroline-copper and UV light. We also describe the limitations of the currently existing techniques and give some potential developments.