gebhart/patrepeval huggingface dataset:
π−π Interactions of Magnesium Phthalocyanine as Evaluated by Energy Partition Analysis (2001)

Magnesium phthalocyanine (MgPc) is a near-IR-active photoconductor used for laser printers. Our recent structure analysis revealed that the MgPc molecule is not flat in the solid state, but the central Mg atom is projected upward, forming a pyramidal structure. On top of the Mg atom along the stacking axis, the aza-methine nitrogen atom is located with a distance of only 2.70 Å. The present arrangement is quite indicative of an appreciable interaction along the stacking axis through the formation of a five-coordinate Mg complex. Therefore, the Mg−N interaction along the molecular stack has been investigated by energy partition analysis based on semiempirical molecular orbital calculations. The Mg−N bond energy along the molecular stack is found to be roughly one-third that of the Mg−N bond in the molecular plane and approximately one-half that of the Mg−O bond of the six-coordinate MgPc complexes, MgPc/(H2O)2(NMP)2 and MgPc/(2-methoxyethanol)2. These results indicate the formation of five-coordinate MgPc complexes along the stacking axis, showing considerable π−π interactions through the central Mg atom.
Large‐scale production and properties of human plasma‐derived activated Factor VII concentrate (2003)

We established a large-scale manufacturing process of human plasma-derived FVIIa concentrate with a high yield, making it possible to provide sufficient FVIIa concentrate for use in haemophiliacs with inhibitory antibodies.
How Noniridescent Colors Are Generated by Quasi‐ordered Structures of Bird Feathers (2010)

We investigate the mechanism of structural coloration by quasi-ordered nanostructures in bird feather barbs. Small-angle X-ray scattering (SAXS) data reveal the structures are isotropic and have short-range order on length scales comparable to optical wavelengths. We perform angle-resolved reflection and scattering spectrometry to fully characterize the colors under directional and omni-directional illumination of white light. Under directional lighting, the colors change with the angle between the directions of illumination and observation. The angular dispersion of the primary peaks in the scattering/reflection spectra can be well explained by constructive interference of light that is scattered only once in the quasi-ordered structures. Using the Fourier power spectra of structure from the SAXS data we calculate optical scattering spectra and explain why the light scattering peak is the highest in the backscattering direction. Under omni-directional lighting, colors from the quasi-ordered structures are invariant with the viewing angle. The non-iridescent coloration results from the isotropic nature of structures instead of strong backscattering.
Intracranial bone marrow transplantation after traumatic brain injury improving functional outcome in adult rats (2001)

On the basis of their findings, the authors assert that BM transplantation improves neurological outcome and that BM cells survive and express nerve cell proteins after TBI.
Overexpression of p42.3 promotes cell growth and tumorigenicity in hepatocellular carcinoma (2013)

p42.3 promotes tumorigenicity and tumor growth in HCC and may be a potential target for future clinical cancer therapeutics.
Cutaneous Blood Perfusion as a Perturbing Factor for Noninvasive Glucose Monitoring (2010)

It is widely accepted that noninvasive glucose monitoring (NIGM) has the potential to revolutionize diabetes therapy. However, current approaches to NIGM studied to date have not yet demonstrated a level of acceptable functionality to allow real-time use, beyond restricted fields of application. A number of reviews have been devoted to the subject of NIGM with different focuses related to challenges and a description of the respective underlying problems. This review is aimed at addressing a fundamental topic in the application of NIGM that seems to have received less attention, by describing the perturbations that result in a reduced functionality of NIGM in daily use. Here we provide a short general introduction to glucose monitoring and a basic illustration of the electromagnetic spectrum with a description of the respective physical mechanisms underlying the measurement techniques. This allows for a better understanding of how these perturbing factors affect the measured properties. Cutaneous blood perfusion is one of the major perturbing factors to NIGM, along with variations in temperature, migration of water, and the effect of attachment of the sensor to the skin. An understanding of the mechanisms underlying perfusion variation over time and within the measured human skin tissue matrix is required to enable a discrimination between glucose-induced effects within the tissue and various biophysical impacts to be made. It is suggested that a plurality of probing frequencies is required to discriminate glucose-related changes from the perturbations. A system designed to perform the measurements in different regions of the electromagnetic spectrum with dedicated sensors (multisensor approach) has the potential to more efficiently and reliably discriminate glucose-related information from perturbations. This can be achieved by combining signals related to measurements with different physical underlying mechanisms of the interaction between the probing field propagation and the tissue to help account for the different sources of perturbations.
Prevention of Autoimmune Diabetes by Ectopic Pancreatic β-Cell Expression of Interleukin-35 (2012)

Interleukin (IL)-35 is a newly identified inhibitory cytokine used by T regulatory cells to control T cell-driven immune responses. However, the therapeutic potential of native, biologically active IL-35 has not been fully examined. Expression of the heterodimeric IL-35 cytokine was targeted to β-cells via the rat insulin promoter (RIP) II. Autoimmune diabetes, insulitis, and the infiltrating cellular populations were analyzed. Ectopic expression of IL-35 by pancreatic β-cells led to substantial, long-term protection against autoimmune diabetes, despite limited intraislet IL-35 secretion. Nonobese diabetic RIP-IL35 transgenic mice exhibited decreased islet infiltration with substantial reductions in the number of CD4(+) and CD8(+) T cells, and frequency of glucose-6-phosphatase catalytic subunit-related protein-specific CD8(+) T cells. Although there were limited alterations in cytokine expression, the reduced T-cell numbers observed coincided with diminished T-cell proliferation and G1 arrest, hallmarks of IL-35 biological activity. These data present a proof of principle that IL-35 could be used as a potent inhibitor of autoimmune diabetes and implicate its potential therapeutic utility in the treatment of type 1 diabetes.
Frequency-dependent magnetoresistance and magnetocapacitance properties of magnetic tunnel junctions with MgO tunnel barrier (2007)

The frequency-dependent impedance of magnetic tunnel junctions (MTJs) with MgO barriers was investigated. The capacitance of the MTJs switches from high to low when the relative electrode magnetizations change from parallel to antiparallel, opposite the resistance change. Additionally, for parallel magnetizations, the capacitance varies with temperature though resistance remains approximately constant. The low frequency resistance and the tunneling magnetoresistance are in agreement with dc values. The capacitance is found to be larger than the expected (geometrical) capacitance, in contrast to MTJs with Al2O3 barriers. These results are explained by screening due to charge and spin accumulation at the interfaces.
High-rate quasi-cyclic LDPC codes for magnetic recording channel with low error floor (2006)

By implementing an FPGA-based simulator, we investigate the performance of high-rate quasi-cyclic (QC) LDPC codes for the magnetic recording channel at very low sector error rates. Results show that error-floor-free performance can be realized by randomly constructed high-rate regular QC-LDPC codes with column weight 4 for sector error rates as low as 10/sup -9/. We also conjecture several rules for designing randomly constructed high-rate regular QC-LDPC codes with low error floor. We also present a decoder architecture that is well suited to achieving high decoding throughput for these high-rate QC-LDPC codes with low error floor.
<title>Solving graph problems with dynamic computation structures</title> (1996)

We introduce dynamic computation structures (DCS), a compilation technique to produce dynamic code for reconfigurable computing. DCS specializes directed graph instances into user-level hardware for reconfigurable architectures. Several problems such as shortest path and transitive closure exhibit the general properties of closed semirings, an algebraic structure for solving directed paths. Motivating our application domain choice of closed semiring problems is the fact that logic emulation software already maps a special case of directed graphs, namely logic netlists, onto arrays of field programmable gate arrays (FPGA). A certain type of logic emulation software called virtual wires further allows an FPGA array to be viewed as a machine-independent computing fabric. Thus, a virtual wires compiler, coupled with front-end commercial behavioral logic synthesis software, enables automatic behavioral compilation into a multi-FPGA computing fabric. We have implemented a DCS front-end compiler to parallelize the entire inner loop of the classic Bellman-Ford algorithm into synthesizable behavioral verilog. Leveraging virtual wire compilation and behavioral synthesis, we have automatically generated designs of 14 to 261 FPGAs from a single graph instance. We achieve speedups proportional to the number of graph edges - - from 10X to almost 400X versus a 125 SPECint SparcStation 10.
Quantitation of HIV-1 RNA in Plasma Predicts Outcome after Seroconversion (1995)

Plasma HIV-1 RNA is a strong, CD4+ T-cell-independent predictor of a rapid progression to AIDS after HIV-1 seroconversion.
Particle manipulation with nonadiabatic ponderomotive forces (2007)

Average, or ponderomotive potentials effectively seen by particles in oscillating fields allow advanced techniques of particle manipulation inaccessible with static potentials. In strongly inhomogeneous fields the ponderomotive force is phase dependent, and the particle dynamics resembles that of a quantum object in a conservative barrier. Probabilistic transmission through a ponderomotive potential is then possible and can be used for particle beam slicing. Resonant fields can also cool and trap particles exhibiting natural oscillations (e.g., Larmor rotation), as well as transmit them asymmetrically; hence, acting as one-way walls. An approximate integral of particle motion is found for this case and a new ponderomotive potential is introduced accordingly.
Extracting Summary Knowledge Graphs from Long Documents (2020)

Knowledge graphs capture entities and relations from long documents and can facilitate reasoning in many downstream applications. Extracting compact knowledge graphs containing only salient entities and relations is important but challenging for understanding and summarizing long documents. We introduce a new text-to-graph task of predicting summarized knowledge graphs from long documents. We develop a dataset of 200k document/graph pairs using automatic and human annotations. We also develop strong baselines for this task based on graph learning and text summarization, and provide quantitative and qualitative studies of their effect.
Trapped whispering-gallery optical modes in white light-emitting diode lamps with remote phosphor (2006)

Three-dimensional ray tracing simulations show that a significant fraction of the phosphorescence emitted in high-power white light-emitting diode lamps with a remote phosphor is trapped as whispering-gallery modes propagating along the circumference of the encapsulant. The whispering-gallery modes, which are a significant optical loss mechanism and occur for multiple shapes of the encapsulation dome, are shown to be sensitively dependent on the diffusivity of the reflector cup employed in the lamp. By employing a diffuse reflector cup, up to 86% of the trapped modes is extracted out from the encapsulant. In addition, it is experimentally demonstrated that the phosphorescence efficiency is improved by up to 12.2% as the diffusivity of the reflector increases. The experimental results are consistent with theoretical ray tracing simulations.
A novel glycosylation phenotype expressed by Lec23, a Chinese hamster ovary mutant deficient in alpha-glucosidase I. (1991)

Lec23 Chinese hamster ovary (CHO) cells have been shown to possess a unique lectin resistance phenotype and genotype compared with previously isolated CHO glycosylation mutants (Stanley, P., Sallustio, S., Krag, S. S., and Dunn, B. (1990) Somatic Cell Mol. Genet. 16, 211-223). In this paper, a biochemical basis for the lec23 mutation is identified. The carbohydrates associated with the G glycoprotein of vesicular stomatitis virus (VSV) grown in Lec23 cells (Lec23/VSV) were found to possess predominantly oligomannosyl carbohydrates that bound strongly to concanavalin A-Sepharose, eluted 3 sugar eq beyond a Man9GlcNAc marker oligosaccharide on ion suppression high pressure liquid chromatography, and were susceptible to digestion with jack bean alpha-mannosidase. Monosaccharide analyses revealed that the oligomannosyl carbohydrates contained glucose, indicating a defect in alpha-glucosidase activity. This was confirmed by further structural characterization of the Lec23/VSV oligomannosyl carbohydrates using purified rat mammary gland alpha-glucosidase I, jack bean alpha-mannosidase, and 1H NMR spectroscopy at 500 MHz. [3H]Glucose-labeled Glc3Man9GlcNAc was prepared from CHO/VSV labeled with [3H]galactose in the presence of the processing inhibitors castanospermine and deoxymannojirimycin. Subsequently, [3H]Glc2Man9GlcNAc was prepared by purified alpha-glucosidase I digestion of [3H]Glc3Man9GlcNAc. When these oligosaccharides were used as alpha-glucosidase substrates it was revealed that Lec23 cells are specifically defective in alpha-glucosidase I, a deficiency not previously identified among mammalian cell glycosylation mutants.
Brain Ischemia Activates β- and γ-Secretase Cleavage of Amyloid Precursor Protein: Significance in Sporadic Alzheimer’s Disease (2012)

Amyloid precursor protein cleavage through β- and γ-secretases produces β-amyloid peptide, which is believed to be responsible for death of neurons and dementia in Alzheimer's disease. Levels of β- and γ-secretase are increased in sensitive areas of the Alzheimer's disease brain, but the mechanism of this process is unknown. In this review, we prove that brain ischemia generates expression and activity of both β- and γ-secretases. These secretases are induced in association with oxidative stress following brain ischemia. Data suggest that ischemia promotes overproduction and aggregation of β-amyloid peptide in brain, which is toxic for ischemic neuronal cells. In our review, we demonstrated the role of brain ischemia as a molecular link between the β- and the γ-secretase activities and provided a molecular explanation of the possible neuropathogenesis of sporadic Alzheimer's disease.
Is the bovine lysosomal phospholipase B-like protein an amidase? (2013)

The main function of lysosomal proteins is to degrade cellular macromolecules. We purified a novel lysosomal protein to homogeneity from bovine kidneys. By gene annotation, this protein is defined as a bovine phospholipase B-like protein 1 (bPLBD1) and, to better understand its biological function, we solved its structure at 1.9 Å resolution. We showed that bPLBD1 has uniform noncomplex-type N-glycosylation and that it localized to the lysosome. The first step in lysosomal protein transport, the initiation of mannose-6-phosphorylation by a N-acetylglucosamine-1-phosphotransferase, requires recognition of at least two distinct lysines on the protein surface. We identified candidate lysines by analyzing the structural and sequentially conserved N-glycosylation sites and lysines in bPLBD1 and in the homologous mouse PLBD2. Our model suggests that N408 is the primarily phosphorylated glycan, and K358 a key residue for N-acetylglucosamine-1-phosphotransferase recognition. Two other lysines, K334 and K342, provide the required second site for N-acetylglucosamine-1-phosphotransferase recognition. bPLBD1 is an N-terminal nucleophile (Ntn) hydrolase. By comparison with other Ntn-hydrolases, we conclude that the acyl moiety of PLBD1 substrate must be small to fit the putative binding pocket, whereas the space for the rest of the substrate is a large open cleft. Finally, as all the known substrates of Ntn-hydrolases have amide bonds, we suggest that bPLBD1 may be an amidase or peptidase instead of lipase, explaining the difficulty in finding a good substrate for any members of the PLBD family.
Update and commentary on the pro-drug bimatoprost and a putative ‘prostamide receptor’ (2009)

The discovery of potent and efficacious intraocular pressure (IOP)-lowering FP-class prostaglandin (PG) analogs has revolutionized the treatment of ocular hypertension, a major risk factor for progression of the blinding disease glaucoma. Three isopropyl ester pro-drugs (i.e., latanoprost, travoprost and unoprostone) and one amide pro-drug (bimatoprost) of w-chain-modified analogs of PGF2α are approved for lowering IOP and treating glaucoma. It is believed that these pro-drugs are sufficiently lipophilic to readily penetrate the cornea/conjunctiva upon topical ocular dosing whereupon they are hydrolyzed with liberation of their respective free acid into the aqueous humor. The free acids of these PGs activate the FP receptors in the ciliary muscle (CM) and trabecular meshwork (TM) and cause the release of matrix metalloproteinases that digest the extracellular matrix. This remodeling within the CM and TM creates new and/or enlarges fluid flow pathways, both uveoscleral and conventional, for aqueous humor efflux, which then leads to lowering of the IOP. While it is generally believed that bimatoprost is a pro-drug and that bimatoprost free acid is the active moiety involved in lowering IOP, some have proposed that bimatoprost exerts its actions via a putative ‘prostamide receptor’. We provide an update on this topic and discuss published data that addresses the debate in this arena.
Mechanisms Of Epoxide Reactions (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleMechanisms Of Epoxide ReactionsR. E. Parker and N. S. IsaacsCite this: Chem. Rev. 1959, 59, 4, 737–799Publication Date (Print):August 1, 1959Publication History Published online1 May 2002Published inissue 1 August 1959https://pubs.acs.org/doi/10.1021/cr50028a006https://doi.org/10.1021/cr50028a006research-articleACS PublicationsRequest reuse permissionsArticle Views9069Altmetric-Citations1060LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
B7DC/PDL2 Promotes Tumor Immunity by a PD-1–independent Mechanism (2003)

B7H1 (PDL1) and B7DC (PDL2) are two new members of the B7 family that can interact with PD-1, a putative negative regulator for immune function. Recent studies have provided evidence for inhibitory functions of both members via PD-1. Meanwhile, compelling evidence exists for costimulatory function of both members. Here we demonstrate that expression of B7DC on the tumor cells promotes CD8 T cell-mediated rejection of tumor cells, at both the induction and effector phase of antitumor immunity. Moreover, B7DC binds to PD-1(-/-) cells and enhances T cell killing in a PD-1-independent mechanism. Our results demonstrate a novel pathway for B7DC to promote tumor immunity and may reconcile the apparently contradictory findings on the function of B7DC.
Theoretical and Practical Aspects of B‐Cell Activation: Murine and Human Systems (1987)

We have reviewed observations which were made during studies of murine and human B-cell responses in vitro. One currently faces difficulties in drawing any clear schema as to which external signals elicit which responses (activation, proliferation, differentiation) in B cells. However, the most potent antigen-dependent or polyclonal B-cell responses in vitro occur when, in addition to various cytokines, accessory cells, serum etc., the cultures contain either a) intact T-helper cells which enter into cell-to-cell contact with B cells, or b) some B-cell "mitogen" (T-independent antigen). Murine B cells activated with LPS and anti-Ig antibodies represent a model for the study of IL2 receptor expression and function. LPS does not act on human B cells. Certain mutant EL-4 thymoma cells are potent activators of murine and human B cells via a direct cell-to-cell interaction. The majority of human B cells can be induced to proliferate and generate a few hundred antibody-secreting cells each in the presence of such thymoma cells and a mixture of cytokines. From a practical point of view, this observation should be useful in a variety of investigations such as the analysis of the human B-cell specificity repertoire.
DNA-mediated Immunization of Glycoprotein 350 of Epstein-Barr Virus Induces the Effective Humoral and Cellular Immune Responses Against the Antigen (2001)

Epstein-Barr virus (EBV) is a human pathogen that is involved in numerous diseases and tumors. Since the EBV infection occurs in the early ages of life, and most of the population is subsequently exposed to EBV, the conventional method of vaccination to induce the prophylactic immunity cannot be considered effective in coping with the virus infection. In this study, we tested whether the injection of a plasmid vector that contained the gene for glycoprotein 350 (gp350), which had been identified as a ligand for virus' adsorption and a target for virus neutralizing antibodies, could induce effective immune responses against the antigen. As a result, the injection of the constructed plasmid vector into mice induced the production of gp350-specific antibodies. A major isotype of the gp350-specific antibodies was IgG1. The antibodies efficiently mediated the antibody-dependent cellular cytotoxicity against the cells expressing the gp350 antigen. In addition, the injection of the constructed plasmid vector stimulated the precursor T cell population that was specific to the gp350 antigen. In addition, gp350-specific cytotoxic T lymphocytes were efficiently stimulated by the injection of the constructed plasmid vector. These results suggested that the injection of the plasmid vector, containing the gp350 gene of Epstein-Barr virus, could be one of the most effective ways to induce both prophylactic and therapeutic vaccinations against the virus infection.