gebhart/patrepeval huggingface dataset:
Autophagic activity measured in whole rat hepatocytes as the accumulation of a novel BHMT fragment (p10), generated in amphisomes by the asparaginyl proteinase, legumain (2011)

To investigate the stepwise autophagic-lysosomal processing of hepatocellular proteins, the abundant cytosolic enzyme, betaine:homocysteine methyltransferase (BHMT) was used as a probe. Full-length (45 kDa) endogenous BHMT was found to be cleaved in an autophagy-dependent (3-methyladenine-sensitive) manner in isolated rat hepatocytes to generate a novel N-terminal 10-kDa fragment (p10) identified and characterized by mass spectrometry. The cleavage site was consistent with cleavage by the asparaginyl proteinase, legumain and indeed a specific inhibitor of this enzyme (AJN-230) was able to completely suppress p10 formation in intact cells, causing instead accumulation of a 42-kDa intermediate. To prevent further degradation of p10 or p42 by the cysteine proteinases present in autophagic vacuoles, the proteinase inhibitor leupeptin had to be present. Asparagine, an inhibitor of amphisome-lysosome fusion, did not detectably impede either p42 or p10 formation, indicating that BHMT processing primarily takes place in amphisomes rather than in lysosomes. Lactate dehydrogenase (LDH) was similarly degraded primarily in amphisomes by leupeptin-sensitive proteolysis, but some additional leupeptin-resistant LDH degradation in lysosomes was also indicated. The autophagic sequestration of BHMT appeared to be nonselective, as the accumulation of p10 (in the presence of leupeptin) or of its precursors (in the additional presence of AJN-230) proceeded at approximately the same rate as the model autophagic cargo, LDH. The complete lack of a cytosolic background makes p10 suitable for use in a "fragment assay" of autophagic activity in whole cells. Incubation of hepatocytes with ammonium chloride, which neutralizes amphisomes as well as lysosomes, caused rapid, irreversible inhibition of legumain activity and stopped all p10 formation. The availability of several methods for selective targeting of legumain in intact cells may facilitate functional studies of this enigmatic enzyme, and perhaps suggest novel ways to reduce its contribution to cancer cell metastasis or autoimmune disease.
Wavelength-insensitive single-mode fused tapered 1×N couplers (2005)

Summary form only given. This paper reports for the first time on the fabrication of low insertion loss wavelength-insensitive fused tapered 1/spl times/N couplers using a technique simpler than any previously reported. The couplers are assembled by surrounding the throughput fiber with six output fibers. The fibers are then drawn in the same manner as a conventional 1/spl times/2 coupler.
Highly Efficient Tandem Polymer Solar Cells with a Photovoltaic Response in the Visible Light Range (2014)

Highly efficient polymer solar cells with a tandem structure are fabricated by using two excellent photovoltaic polymers and a highly transparent intermediate recombination layer. Power conversion -efficiencies over 10% can be realized with a photovoltaic response within 800 nm.
Nonorthogonal Optical Waveguides and Resonators (1970)

The modes of propagation in optical systems which do not possess meridional planes of symmetry (nonorthogonal systems) are investigated in the case where the effect of apertures and losses can be neglected. The fundamental mode of propagation is obtained with the help of a complex ray pencil concept. An integral transformation of the field, based on a quasi-geometrical optics approximation and a first-order expansion of the point characteristic of the optical system, is given; it shows that the complex (three-dimensional) wavefront of the fundamental mode is transformed according to a generalized “ABCD law.” A simple expression is also obtained for the phase-shift experienced by the beam. The higher order modes of propagation are obtained from a power series expansion of the fundamental mode. These higher order modes are expressed, in oblique coordinates, as the product of the fundamental solution and finite series of Hermite polynomials with real arguments. In the special case of systems with rotational symmetry, these series reduce to the well-known generalized Laguerre polynomials. The theory is applicable to media such as helical gas lenses and optical waveguides suffering from slowly varying deformations in three dimensions. Nonorthogonal resonant systems are also investigated. An expression for the resonant frequencies, applicable to any three-dimensional resonator, is derived. Numerical results are given for the resonant frequencies and the resonant field of a twisted path cavity which exhibits interesting properties: the usual polarization degeneracy is lifted and the intensity pattern of all of the modes possesses a rotational symmetry.
Distinctive Chromosomal Abnormalities in Histologic Subtypes of Non-Hodgkin's Lymphoma (1982)

Using a new high-resolution technique for chromosomal analysis, we have successfully studied biopsy specimens of lymph nodes from 42 of 44 patients with non-Hodgkin's lymphoma and have categorized them using the new international histologic formulation and immunologic markers. Abnormalities of the clonal chromosomes were detected in all 42 patients. Three recurrent chromosomal aberrations were found to correlate with certain histologic types: a translocation between chromosomes 18 and 14 in 16 of 19 patients with follicular lymphomas (small cleaved cell, mixed cell, and large cell); a translocation between chromosomes 8 and 14 in 5 of 6 patients with small noncleaved-cell (non-Burkitt's) or large-cell immunoblastic lymphoma; and a trisomy 12 in 4 of 11 patients with small-cell lymphocytic lymphoma. Our findings suggest that characteristic chromosomal defects occur in certain lymphoma subtypes and that high-resolution chromosomal analysis promises to become an important tool in improving our basic understanding of lymphoid cancers.
Abstract 2010: BTK inhibitor BGB-3111 demonstrates anti-tumor activity in solid tumor models (2017)

Abstract Background BGB-3111 is a novel, irreversible, second generation BTK inhibitor with better selectivity profile and DMPK property compared to ibrutinib. It has demonstrated promising anti-tumor activities in patients with advanced B cell malignancies. Given BTK is expressed in all hematopoietic lineages except for T lymphocytes, it is reasonable to explore the immune modulatory effect of BGB-3111. In this study, we sought to investigate the anti-tumor activity of BGB-3111 in solid tumor models. Methods Cell viability was assessed with Cell Titer Glo® assay and half maximal inhibitory concentrations (IC50) were estimated. In vivo activity was assessed in subcutaneous mouse xenograft models. Treatments were administered by oral gavage and individual body weight and tumor volume was recorded twice weekly. Results In vitro studies showed that MDA-MB-436 cells are insensitive to BGB-3111, which do not expresse BTK. In both human breast cancer MDA-MB-436 and human A431 epidermoid carcinoma subcutaneous xenograft models, the tumor cells were co-injected with peripheral blood mononuclear cells (PBMCs) of healthy donors. In MDA-MB-436 model, BGB-3111 (15 mg/kg, BID) single agent significantly induced tumor growth inhibition (TGI) of 55%, whereas showed no anti-tumor effect if no PBMCs co-injected. Furthermore, co-treatment of BGB-3111 (15 mg/kg, BID) and anti-PD-1 antibody BGB-A317 (10 mg/kg, QW) demonstrated enhanced therapeutic effect in A431 allogeneic model. Interestingly, in BCLU200 and BCLU054 NSCLC primary tumor xenograft models (without PBMC co-injection), BGB-3111 (15 mg/kg, BID) also demonstrated significant anti-tumor activity. Conclusions In summary, BGB-3111 showed interesting activity in solid tumor models, suggesting BTK inhibitor might have potential to be used beyond hematology malignancies. . Citation Format: Nan Hu, Jiye Zhang, Min He, Shuo Zhang, Yong Liu, Lai Wang. BTK inhibitor BGB-3111 demonstrates anti-tumor activity in solid tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2010. doi:10.1158/1538-7445.AM2017-2010
Sniper detection using infrared camera: technical possibilities and limitations (2010)

The paper discusses technical possibilities to build an effective system for sniper detection using infrared cameras. Descriptions of phenomena which make it possible to detect sniper activities in infrared spectra as well as analysis of physical limitations were performed. Cooled and uncooled detectors were considered. Three phases of sniper activities were taken into consideration: before, during and after the shot. On the basis of experimental data the parameters defining the target were determined which are essential in assessing the capability of infrared camera to detect sniper activity. A sniper body and muzzle flash were analyzed as targets. The simulation of detection ranges was done for the assumed scenario of sniper detection task. The infrared sniper detection system was discussed, capable of fulfilling the requirements. The discussion of the results of analysis and simulations was finally presented.
Optical spectra of doubly charged quantum dot molecules in electric and magnetic fields (2008)

We present an experimental and theoretical study of the photoluminescence spectra of individual doubly charged quantum dot molecules. The quantum dot molecules consist of two vertically stacked InAs self-assembled quantum dots in a GaAs Schottky diode structure. We study two cases: (1) the two dots are charged with two electrons coherently coupled through electron tunneling and (2) the two dots are charged with two holes and coherently coupled through hole tunneling. The optically excited states consist of the two charges along with one or two additional electron-hole pairs, i.e., a doubly charged exciton and biexciton. We determine the spin states and the corresponding spectral fine structure and show how this fine structure depends on vertical electric and magnetic fields. We find that the results are in large part qualitatively similar for the two cases. However, when magnetic fields are applied, we find a strong $g$ factor resonance and evidence of a bonding/antibonding reversal for the hole-tunneling case only. We discuss the implications for quantum information processing using spins confined in proximate dots.
Diagnosis of Persistent Bovine Viral Diarrhea Virus Infection by Immunohistochemical Staining of Formalin-Fixed Skin Biopsy Specimens (2000)

The objective of this study was to evaluate the efficacy of immunohistochemical (IHC) staining for diagnosis of persistent bovine viral diarrhea virus (BVDV) infection using formalin-fixed, paraffin-embedded skin biopsy specimens. Skin from 41 of 42 calves shown to be persistently infected (PI) with BVDV by repeated virus isolation more than 3 weeks apart were immunohistochemically positive for BVDV antigen. Positive IHC staining was most pronounced in the keratinocytes and in hair follicle epithelium, hair matrix cells of the hair bulb, and the dermal papilla. All of the skin sections from 10 calves experimentally infected postnatally with BVDV (10(5) median tissue culture infective doses [TCID50]) and biopsied on days 0, 5, 7, and 9 postinfection were negative for viral antigen. Ten calves from a second group experimentally infected with a higher dose of BVDV (10(8) TCID50) were biopsied when viremic between 10 and 14 days postinfection and 4 calves exhibited positive IHC staining for BVDV; however, staining in these skin biopsies was confined to small foci in the nonfollicular epidermis and follicular ostia. This staining was distinct from that observed in skin obtained from PI cattle. Skin biopsy represents an effective method for identifying animals PI with BVDV.
In-vivo multi-nonlinear optical imaging of a living cell using a supercontinuum light source generated from a photonic crystal fiber (2006)

A supercontinuum light source generated with a femtosecond Ti:Sapphire oscillator has been used to obtain both vibrational and two-photon excitation fluorescence (TPEF) images of a living cell simultaneously at different wavelengths. Owing to an ultrabroadband spectral profile of the supercontinuum, multiple vibrational resonances have been detected through coherent anti-Stokes Raman scattering (CARS) process. In addition to the multiplex CARS process, multiple electronic states can be excited due to the broadband electronic two-photon excitation using the supercontinuum, giving rise to a two-photon excitation fluorescence (TPEF) signal. Using a living yeast cell whose nucleus is labeled by green fluorescent protein (GFP), we have succeeded in visualizing organelles such as mitochondria, septum, and nucleus through the CARS and the TPEF processes. The supercontinuum enables us to perform unique multi-nonlinear optical imaging through two different nonlinear optical processes.
The determination of signal coherence length based on signal coherence and gain measurements in deep and shallow water (2002)

Experimental measurements of signal coherence and array signal gain are reviewed for both deep and shallow water sound channels. The signal gain is related to the horizontal coherence length through relationships from the statistical theory of antennas. Signal gain measurements in the transverse direction are proffered as a practical measure of coherence length for both broadband and narrowband signals. Using this technique, measurements at frequencies near 400 Hz are presented that show for the deep water cases lengths on the order of 100 wavelengths can be achieved while in the downward refraction conditions of shallow water waveguides with sand-silt bottoms, lengths on the order of 30 wavelengths are realized. The measurement of broadband and narrowband coherence and correlation functions are discussed with emphasis on the role of partly coherent noise backgrounds, multipath interference effects, and averaging constraints. These results are interpreted with coherence models consistent with sound scattering from the volume and boundaries of the waveguide.
Role of mitochondria in non‐alcoholic fatty liver disease (2007)

Mitochondrial dysfunction is involved in the three stages of the transition from lack of exercise and excessive food intake to insulin resistance, diabetes and non-alcoholic steatohepatitis (NASH). In muscle, lack of exercise, a fat-rich diet, a polymorphism in peroxisome proliferator-activated receptor gamma coactivator-1 (PGC-1), and possibly age-related mitochondrial DNA (mtDNA) mutations may variously combine their effects to decrease PGC-1 expression, mitochondrial biogenesis and fat oxidation. Together with excessive food intake, insufficient fat oxidation causes fat accumulation and cellular stress in myocytes. The activation of Jun N-terminal kinase and protein kinase C-theta triggers the serine phosphorylation and inactivation of the insulin receptor substrate, and hampers the insulin-mediated translocation of glucose transporter-4 to the plasma membrane. Initially, the trend for increased blood glucose increases insulin secretion by pancreatic beta-cells. High plasma insulin levels compensate for insulin resistance in muscle and maintain normal blood glucose levels. Eventually, however, increased uncoupling protein-2 expression and possibly acquired mtDNA mutations in pancreatic beta-cells can blunt glucose-mediated adenosine triphosphate (ATP) formation and insulin secretion, to cause diabetes in some patients. High plasma glucose and/or insulin levels induce hepatic lipogenesis and cause hepatic steatosis. In fat-engorged hepatocytes, several vicious cycles involving tumor necrosis factor-alpha, reactive oxygen species (ROS), peroxynitrite, and lipid peroxidation products alter respiratory chain polypeptides and mtDNA, thus partially blocking the flow of electrons in the respiratory chain. The overreduction of upstream respiratory chain complexes increases mitochondrial ROS and peroxynitrite formation. Oxidative stress increases the release of lipid peroxidation products and cytokines, which together trigger the liver lesions of NASH.
Über die Umsetzung von Phenylcyanacetaldehyd mit Hydrazin Mitt. über Untersuchungen an Acyl‐enaminen (1971)

Abstract Aus Phenylcyanacetaldehyd ( 1 a ) und Hydrazin entsteht neben 3‐Amino‐4‐phenyl‐pyrazol ( 2 a ) das Pyrazolo‐pyrimidin 7 und nicht, wie in der Literatur 2) angegeben, das Azin 3 .
Neighboring Side Chain Effects on Asparaginyl and Aspartyl Degradation:  An Ab Initio Study of the Relationship between Peptide Conformation and Backbone NH Acidity (2001)

The rate of spontaneous degradations of asparagine and aspartyl residues occurring through succinimide intermediates is dependent upon the nature of the residue on the carboxyl side in peptides. For nonglycine residues, we show here that this effect can largely be attributed to the electrostatic/inductive effect of the side chain group on the equilibrium concentration of the anionic form of the peptide bond nitrogen atom that initiates the succinimide forming reaction. However, the rate of degradation of Asn-Gly and Asp-Gly containing peptides is about an order of magnitude greater than predicted solely using this explanation. To understand the nature of the glycine effect, ab initio calculations were performed on model compounds. These calculations indicate that there is little to no change in the stability of the transition state or the tetrahedral intermediate of succinimide formation with Asn-/Asp-Gly and Asn-/Asp-Ala derivatives. However, we have found that the acidity of the backbone peptide nitrogen NH is highly dependent upon the conformation of the molecule. Since glycine residues lack the beta-carbon common to all other protein amino acids, these residues can sample additional regions of conformational space where it is possible to further stabilize the backbone amide anion and thus increase the rate of degradation. These results provide the first rationale for the particular rate enhancement of degradation in peptidyl Asn-/Asp-Gly sequences. The results also can be applied to asparagine and aspartyl residues in proteins where the 3-dimensional structure provides additional constraints on conformation that can either increase or decrease the equilibrium concentration of the backbone amide anion and thus their rate of degradation via succinimide intermediates. Understanding this chemistry will assist attempts to minimize the deleterious effect of aging at the molecular level. The relationship between these results and proton exchange experiments is discussed in the Appendix.
Authors' response (2010)

The paper by Chapman et al 1 reviewing single maintenance and reliever therapy (SMART) in asthma is important in highlighting some of the inadequacies of existing research evaluating this treatment method.
Hypogonadotropic Disorders in Men and Women: Diagnosis and Therapy with Pulsatile Gonadotropin-Releasing Hormone (1986)

Hypogonadotropic hypogonadism (HH) is a clinical syndrome occurring in both sexes which has long puzzled clinicians due to the apparent paradox of nonfunctioning gonads in the face of normal or only slightly lowered levels of circulating gonadotropins. Using frequent sampling of gonadotropin levels as an index of hypothalamic GnRH secretion, we have examined the hypothesis that this group of disorders represents a spectrum of abnormal patterns of the pulsatile release of endogenous GnRH. After a broad, normative data base was established in both men and women for purposes of comparison, it appears that quantifiable abnormalities of GnRH secretion are discernible in both males and females with HH. These abnormalities include a total absence of GnRH secretion, defects of the amplitude and frequency of its secretion, and altered bioactivity of the gonadotropins released. In addition, physiological regimens of hypothalamic replacement therapy with exogenous GnRH, which are fashioned to mimic the normal frequency of endogenous GnRH secretion, result in complete normalization of reproductive function and fertility in hypogonadotropic subjects of both sexes. Thus, the heterogeneous nature of HH, as well as its favorable clinical and biochemical responses to GnRH, suggest that the basic defect in this family of disorders involves a partial or complete inability to synthesize and/or release GnRH from the hypothalamus in a manner compatible with physiological reproductive function. Conversely, these findings imply that maintenance of a physiological amplitude and frequency of endogenous GnRH secretion appear to be essential for normal reproductive function.
Biochemistry and Physiology of Cyclic Nucleotide Phosphodiesterases: Essential Components in Cyclic Nucleotide Signaling (2007)

Although cyclic nucleotide phosphodiesterases (PDEs) were described soon after the discovery of cAMP, their complexity and functions in signaling is only recently beginning to become fully realized. We now know that at least 100 different PDE proteins degrade cAMP and cGMP in eukaryotes. A complex PDE gene organization and a large number of PDE splicing variants serve to fine-tune cyclic nucleotide signals and contribute to specificity in signaling. Here we review some of the major concepts related to our understanding of PDE function and regulation including: (a) the structure of catalytic and regulatory domains and arrangement in holoenzymes; (b) PDE integration into signaling complexes; (c) the nature and function of negative and positive feedback circuits that have been conserved in PDEs from prokaryotes to human; (d) the emerging association of mutant PDE alleles with inherited diseases; and (e) the role of PDEs in generating subcellular signaling compartments.
Mercury‐Glass Interactions in Fluorescent Lamps (1995)

During the operation of a fluorescent lamp mercury chemically combines with various components inside the lamp. For some types of lamps most of the bound mercury is observed to reside in the glass, despite the intervening phosphor layer. This consumption of mercury by the glass only occurs when a mercury/rare‐gas plasma is present. Experiments were performed to isolate the various factors arising from the operation of the plasma in order to determine which ones are important in driving mercury consumption in the glass. These experiments include shielding samples from the plasma, measuring the line‐of‐sight transmission of the phosphor, and applying small radial dc electrical biases to the lamp. In addition, various analytical techniques, including x‐ray photoelectron spectroscopy, Rutherford backscattering, scanning electron microscopy, and thermally stimulated evolution where used to study the glass surface after exposure to a mercury/rare‐gas plasma. From these studies it is postulated that electrochemical effects play a major role in binding mercury to the glass.
Web information extraction (2006)

Along with the continuous development of the Internet technologies, Web pages can provide a huge amount of information resource. It alters the traditional way of preserving and searching information. The queries target to the Web page becomes huge and more and more important. Now a day, search engine is a very popular method to search information on the Web. However, it only presents a list of documents other than the specific answers or piece of knowledge for the user's specific question. Therefore, the data extraction from the Web is becoming a hot topic. In this paper, we investigate the current development in the Web data extraction, the difficulties, and the objectives. In addition, we illustrate and analyze some examples and provide our solution for information extraction from the Web.