gebhart/patrepeval huggingface dataset:
ChemInform Abstract: An Efficient One‐Pot Synthetic Method for 2,4‐Disubstituted 7‐Arylpyrido[4,3‐d]pyrimidines from 2,4‐Disubstituted 6‐(Arylethynyl)pyrimidine‐5‐carbaldehydes and tert‐Butylamine. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Wavelength-division-multiplexing-based electronic-photonic network for high-speed computing (Conference Presentation) (2020)

This Conference Presentation, "Wavelength-division-multiplexing-based electronic-photonic network for high-speed computing" was recorded at Photonics West 2020 held in San Francisco, California, United States.
Origin of the isotope effect on solid friction (2009)

Friction of hydrogen-passivated surfaces can be reduced by replacing terminating hydrogen atoms with heavier deuteriums. Using molecular-dynamics simulations, we show that this experimentally observed isotope effect can be explained quantitatively by small differences in surface coverage, which are due to isotope-dependent bond stabilities. We also demonstrate that a change in vibrational frequencies alone does not account for an isotope-dependent solid friction in our model system.
Activation of Blood Coagulation Factor X by Arginine-specific Cysteine Proteinases (Gingipain-Rs) from Porphyromonas gingivalis (1997)

The effect of two arginine-specific cysteine proteinases (gingipain Rs) from Porphyromonas gingivalis, a causative bacterium of adult periodontitis, on human blood coagulation was investigated. Activated partial thromboplastin time and prothrombin time were shortened by these proteinases, with a 95-kDa gingipain R containing adhesin domains being 5-fold more efficient in comparison to a 50-kDa gingipain R containing the catalytic domain alone. The 50-kDa enzyme reduced each coagulation time in several plasmas deficient in various coagulation factors, while it was ineffective in factor X-deficient plasma unless reconstituted with this protein. Each proteinase activated factor X in a dose- and time-dependent manner, with Michaelis constants (Km) being found to be lower than the normal plasma factor X concentration, strongly suggesting that factor X activation by gingipain Rs, especially the 95-kDa form which is strongly activated by phospholipids, could occur in plasma. This is the first report of factor X activation by bacterial proteinases and indicates that the gingipain Rs could be responsible for the production of thrombin and, indirectly, with the generation of prostaglandins, interleukin-1, etc., which have been found to be associated with the development of periodontitis induced by P. gingivalis infections. Furthermore, the data support the hypothesis that induction of blood coagulation by bacterial proteinases may be a causative agent in the pathogenesis of disseminated intravascular coagulation in sepsis.
Electrodynamics of metal-dielectric composites and electromagnetic crystals (2000)

A theory that takes into account effects of retardation is developed for calculating the effective dielectric constant and magnetic permeability of metal-dielectric composites and photonic crystals containing a metallic component. The effective parameters depend, in general, on the local microgeometry of composites and electromagnetic crystals. For example, in metal-wire crystals the effective dielectric constant becomes negative at frequencies below the cutoff frequency, which, in the case of a strong skin effect, is determined by the crystal structure only. It is also shown that the effective high-frequency magnetic permeability, which originates from the eddy currents in metal grains or wires, does not vanish, even in systems with no intrinsic magnetism. In metal-dielectric composites, it is shown that the effective dielectric constant has a positive maximum and a negative minimum in the vicinity of the percolation threshold. A new class of photonic crystals is proposed, where both dielectric permittivity and magnetic permeability are negative in optical spectral range.
Constraint-Based Verification (2006)

Constraint-Based Verification covers an emerging field in functional verification of electronic designs, referred to as the "constraint-based verification." The topics are developed in the context of
Therapeutic translation in acute kidney injury: the epithelial/endothelial axis (2014)

Acute kidney injury (AKI) remains a major clinical event with rising incidence, severity, and cost; it now has a morbidity and mortality exceeding acute myocardial infarction. There is also a documented conversion to and acceleration of chronic kidney disease to end-stage renal disease. The multifactorial nature of AKI etiologies and pathophysiology and the lack of diagnostic techniques have hindered translation of preclinical success. An evolving understanding of epithelial, endothelial, and inflammatory cell interactions and individualization of care will result in the eventual development of effective therapeutic strategies. This review focuses on epithelial and endothelial injury mediators, interactions, and targets for therapy.
Experimental analysis of airbag seam design: high-rate shear testing for skin abrasions (2011)

Approximately 66 per cent of all airbag deployments in the USA result in at least one skin injury, with 47 per cent of these skin injuries attributed directly to the airbag deployment. The purpose of the present study was to evaluate the risk of skin abrasions from the airbag fabric seam design by using a new shear testing methodology. High-rate shear loading was performed with a pneumatic impactor that propelled a section of airbag fabric across porcine skin at 85 m/s. Twenty-seven tests (three control and 24 with fabric) were performed using eight different seam designs. A 40 cm × 10 cm section of airbag fabric with each seam was forced across a 5 cm × 5 cm section of fresh porcine skin that was acquired within 2 h post-mortem. No abrasions were observed in the three control tests, but abrasions were observed in all 24 of the tests conducted using airbag fabric. The unturned, sewn seam orientation resulted in significantly more severe abrasions than the woven, unturned seam orientation ( P = 0.01). This new system and results illustrate that different seam designs can result in different skin abrasion risk. Moreover, the data show that severe abrasions can be caused by normal pressures well below the 1.75 MPa injury threshold previously published.
Model for laser damage dependence on thin-film morphology (1993)

The high laser damage thresholds often reported for porous thin films are discussed in terms of point defects or small absorbing inclusions as sites of thin-film damage initiation. The model is based on the internal pressure built up upon laser heating at short times. The competing effects of short pressure relaxation distances and low thermal conductivity inherent in porous films are discussed. The model predicts that at thicknesses less than or equal to the neck or column diameter of a porous film, the effect of lower thermal conductivity should dominate and cause the films to exhibit lower laser damage thresholds than their denser counterparts.
Endoscopic Submucosal Dissection of Extranodal Marginal Zone B-Cell Lymphoma in a Patient With Helicobacter pylori-Associated Gastritis (2015)

Introduction: Primary gastric lymphoma accounts for 3 % of gastric neoplasms and 10% of lymphomas. Multiple studies have demonstrated the association of the gastric lymphomas and H.pylori infection. Although gastric lymphomas are considered a slow growing tumors, natural history and rate of its growth are largely unknown. We are now presenting a 73 year old female with rapidly growing extranodal marginal zone B cell lymphoma treated with endoscopic submucosal dissection and H.pylori eradication. Case: A 73-year old female with history of GERD presented with nausea for several months. On her first EGD a large (20 mm), benign appearing duodenal polyp was found. She was referred to a out hospital for endoscopic removal of this polyp. During removal of duodenal polyp EGD (3 months after her initial EGD), a large (30 mm), flat gastric polyp was found. During follow up EGD in 3 months patient returned for repeat endoscopy, which demonstrated significant increase in size of the gastric polyp - to 50 mm. The lesion was removed en block via endoscopic submucosal dissection (ESD) and pathological examination revealed low grade B cell lymphoma, negative for the t(11;18) translocation and presence of Helicobacter Pylori (H. Pylori) infection in the gastric mucosa. Helicobacter pylori was treated for with triple therapy. On follow up EGD 3 months later the patient had a well-healed scar. Multiple biopsies demonstrated no residual lymphoid infiltrates or H. pylori infection. Discussion: Estimated incidence of extranodal marginal zone B cell lymphoma (previously called MALT lymphoma) in the United States is between 1:30,000 and 1:80,000. Epidemiologic, experimental and clinical data support a strong association between primary gastric MALT lymphoma and H. Pylori infection. H. H.pylori eradication has emerged as the preferred treatment of early stage H.pylori positive disease, due to demonstrated efficacy and excellent long-term outcome. Although MALT lymphomas are considered indolent, slowly growing tumors, in our patient there was rapid progression of disease: from no apparent lesion on first EGD to 30 mm polyp in 3 months and then 50 mm tumor in 3 months. ESD allowed minimally invasive en block removal of the lesion with histologically negative margins. Repeat endoscopy confirmed complete removal of the lymphoma and successful eradication of H. pylori. Conclusion: Primary gastric extranodal marginal zone B-cell lymphomas can rapidly grow in size. ESD combined with H.pylori eradication allows successful management of the lesion.
Next-Generation HydroGel Films as Tissue Sealants and Adhesion Barriers (2003)

This novel in situ formed sprayable hydrogel film has demonstrated a dual function as an effective tissue sealant and as an adhesion barrier in cardiovascular preclinical models. These next generation synthetic biomaterials are currently undergoing clinical investigations.
Conservation of Hydrophobicity within Viral Envelope Glycoproteins Reveals a Putative Hepatitis C Virus Fusion Peptide (2009)

The mechanism(s) by which hepatitis C virus (HCV) enters and infects cells remains unknown. Identifying the HCV fusion peptide(s) and understanding the early stages of infection may provide new opportunities for improved antiviral therapy. The HCV envelope glycoprotein E2 is thought to be a class II fusion protein. Class II fusion proteins are exemplified by the E protein of the tick-borne encephalitis virus (TBEV) and the E1 protein of the Semliki Forest virus (SFV). Analysis of the hydrophobicity profiles of four HCV E2 envelope glycoproteins revealed a region with a conserved three-pronged pattern of hydrophobicity, termed the tridentate (TD) region. The primary sequence of the TD region is highly conserved in all 490 HCV strains currently reported. The known fusion peptide loops of TBEV and SFV share the characteristic TD region hydrophobicity profile and significant sequence conservation in the TD region was identified in the E and E1 glycoproteins of members of the Flaviviridae and Togaviridae families, respectively. The HCV TD region peptides have membranotropic activity; in molecular dynamics (MD) simulations, the HCV TD region peptides insert into in a biomimetic bilayer in a similar manner to the TBEV fusion peptide and the peptides induce effective mixing of lipid membranes in a liposome fusion assay. Together these results indicate that the highly conserved TD region of the HCV E2 protein is a fusion peptide candidate and may be an important factor in the class II fusion mechanism.
On-chip microbial culture for the specific detection of very low levels of bacteria. (2013)

International audience
Inhibition by retinoic acid of type IV collagenolysis and invasion through reconstituted basement membrane by metastatic rat mammary adenocarcinoma cells. (1989)

The activity of type IV collagenase, which enables tumor cells to degrade collagen type IV found in the subendothelial basement membrane, has been correlated with the metastatic potential in several tumor types, including the rat 13762NF mammary adenocarcinoma cell line and its clones. In this study, we examined whether all-trans-retinoic acid (all-trans-RA) and other retinoids, which exhibit antitumor activity in vitro and in vivo, affect the collagenolytic activity of metastatic rat 13762NF mammary adenocarcinoma cells. Cells of the highly metastatic lung-colonizing clone MTF7.T35.3, derived from the 13762NF cell line, were treated for 3 days with 0.1, 1, or 10 microM all-trans-RA, harvested, and seeded on [3H]proline-labeled extracellular matrix deposited by cultured rat lung endothelial cells or on a film of purified [3H]proline-labeled type IV collagen. The amount of radioactivity released into the medium during the subsequent 24 to 72 h was measured, and it was found that all-trans-RA treatment inhibited degradation of extracellular matrix and type IV collagen by 50 to 60%. This effect was observed whether the cells had been treated with all-trans-RA in serum-free medium or in medium supplemented with heat-inactivated or acid-treated fetal bovine serum. The growth of the cells was not inhibited under these conditions, except after treatment with 10 microM all-trans-RA in serum-free medium. The reduction in collagenolytic activity was observed in viable cells as well as in conditioned medium. A 24-h exposure of cells to all-trans-RA was sufficient to cause a 30% decrease in the collagenolytic activity, and this inhibitory effect was reversible. The direct addition of all-trans-RA to conditioned medium had no effect on secreted collagenase activity. The apparent molecular weights of the collagenolytic enzymes were determined by electrophoresis of cell extracts and concentrated conditioned medium in type IV collagen-embedded polyacrylamide gels followed by renaturation and activation of the enzymes within the gels. Two major type IV collagenolytic metalloproteinases exhibiting molecular weights of 64,000 and 88,000, respectively, were detected by this method. These two enzymes were also found to have specificity for gelatin. The Mr 64,000 enzyme could be extracted from viable cells (presumably from the cell membrane) by 2% 1-butanol. Treatment with all-trans-RA decreased the level of these enzymes in the cellular, cell membrane, and conditioned medium compartments.(ABSTRACT TRUNCATED AT 400 WORDS)
Ultrastruetural Evaluation of the Microslicing Method for the Study of Temporal Bone Pathology (1987)

Microslices 3 mm thick from undecalcified human temporal bones were prepared with a special cutting machine and then processed for SEM and TEM in order to evaluate advantages and disadvantages of the microslicing technique for the study of the temporal bone pathology. In the examined microslices there was some mechanical distortion of the membranous labyrinth, detachment of soft tissues from bone and a considerable amount of contamination by bone dust and debris which are circulated during sectioning. For SEM the method therefore has limited value. For TEM a relatively contamination free area can be found some distance from the cutting surface of each microslice.
Macrocyclic polyaminocarboxylates for stable radiometal antibody conjugates for therapy, spect and pet imaging (2023)

A simple method for the synthesis of 1,4,7, 10-tetraazacyclododecane N,N'N",N'"-tetraacetic acid and 1,4,8,11-tetraazacyclotetradecane N,N',N",N'"-tetraacetic acid involves cyanomethylating 1,4,7, 10-tetraazacyclododecane or 1,4,8,11-tetraazacyclotetradecane to form a tetranitrile and hydrolyzing the tetranitrile. These macrocyclic compounds are functionalized through one of the carboxylates and then conjugated to various biological molecules including monoclonal antibodies. The resulting conjugated molecules are labeled with radiometals for SPECT and PET imaging and for radiotherapy.
Bifurcation Analysis of Catalytic Monoliths with Nonuniform Catalyst Loading (2003)

A one-dimensional two-phase model with position-dependent heat- and mass-transfer coefficients and a nonuniform catalyst distribution along the channel is used to present a complete steady-state bifurcation analysis of a catalytic monolith for the case of an exothermic first-order reaction when the feed temperature is taken as the bifurcation variable. It is found that, for typical operating conditions, washcoat diffusion and the species Lewis number have the largest influence on the light-off boundary (in the sense that the metal loading needed to obtain an ignition point in the bifurcation diagram of exit cup-mixing conversion versus inlet fluid temperature varies by a factor of 100 or more as these parameters are varied), followed by solid conduction (factor of 50), nonuniform catalyst distribution (factor of 10), and channel geometry (factor of 5). A nonuniform catalyst distribution with three zones of catalyst loading (with high activity in the middle zone) appears to be the best configuration considering important factors such as the exit fluid conversion, inlet fluid temperature required for ignition, fouling, and transient time required for the monolith to attain the mass-transfer-controlled regime.
Design of efficient modally phase-matched SHG waveguides with automatic differentiation (2022)

Subwavelength grating (SWG) metamaterial structures are excellent platforms for guided-wave nonlinear optics, but their design and optimization are challenging due to the large number of geometric degrees of freedom and the need for compute-intensive 3D simulations. Here, we demonstrate inverse design of χ(2) SWG waveguides using an efficient and accurate differentiable plane-wave expansion (PWE) eigensolver. Our solver, which incorporates sparse iterative algorithms and subpixel smoothing, enables efficient eigensolution and end-to-end differentiation from geometric parameters to the SWG figure of merit, which depends both on the eigenvalues (first-order perturbation theory) and the eigenvectors and group indices (second-order perturbation theory), both in forward- and reverse-mode. We apply this solver to the design and optimization of metamaterial waveguides for two types of backward SHG: idler-reversed and pump-reversed. This approach may find use in designing periodic structures more generally, including nanobeam cavities, slow-light modulators, and vertically coupled resonators.
J0204-1-6 The Relationship between Streaming Potential and Compressive Stress in Bovine Intervertebral Disc (2010)

Intervertebral disc is constructed of nucleus pulposus (NP) and anulus fibrosus (AF). Intervertebral tissue contains a large amount of negatively-charged proteoglycan. When the tissue deforms, streaming potential is induced by liquid flow with positive ion. In this study, the relationship between streaming potential and applied stress in the bovine intervertebral tissue is investigated under confined compression. Column shaped specimens of 5.5 mm diameter and 3 mm thickness were prepared from several tissue of AF, NP and anulus - nucleus transition (AN) region. The loading direction of each specimen was oriented for spinal axial direction, and furthermore, circumferential and radial direction of spine in AF specimens. Although streaming potential was linearity increased by compressive stress in all specimens, linear coefficients k_e were different values in the tissue extracted region. Expect the case of axial loading of NP specimen, k_e showed higher values in faster compression rate condition. In the case of cyclic compression loading, streaming potential was linearly changed with compressive stress values regardless of tissue and load frequency. The linear coefficient k_e was not changed by cyclic number and loading time increases. The coefficient K_e at axial loading of NP specimen which had the highest proteoglycan density showed the highest value in the intervertebral specimens.
The sine-Gordon equation in reversed-field pinch experiments (2004)

The focal point of this paper is a nonlinear model which describes localized magnetohydrodynamic modes in reversed-field pinch experiments. To date, nearly all experimental and theoretical work in this area have relied on the use of Fourier decomposition of spatial variations as a function of time. Moreover, due to the complexity of this nonlinear problem, previous work is restricted to the analysis of a relatively small number of modes. In contrast, the model studied in this paper, based on the sine-Gordon equation, addresses the full nonlinearity, does not rely on Fourier decomposition and does not require the range of the nonlinearity to be small. A specific consequence of working with the full nonlinearity is the existence of solitary waves in dispersive media. These solitary waves, a key part of the model, are used to describe the so-called slinky-mode propagating in the plasma. To this end, a remarkable resemblance is seen between the wave forms obtained from experiments and the mathematical predictions of the model.
Zero-Truncated Poisson Tensor Decomposition for Sparse Count Data (2022)

We propose a novel statistical inference paradigm for zero-inflated multiway count data that dispenses with the need to distinguish between true and false zero counts. Our approach ignores all zero entries and applies zero-truncated Poisson regression on the positive counts. Inference is accomplished via tensor completion that imposes low-rank structure on the Poisson parameter space. Our main result shows that an $\textit{N}$-way rank-R parametric tensor &#120028; ϵ (0, ∞)<sup>$I$Χ∙∙∙Χ$I$</sup> generating Poisson observations can be accurately estimated from approximately $IR^2 \text{log}^2_2(I)$ non-zero counts for a nonnegative canonical polyadic decomposition. Several numerical experiments are presented demonstrating that our zero-truncated paradigm is comparable to the ideal scenario where the locations of false zero counts are known $\textit{a priori}$.
Clinical Isolates of Streptococcus pneumoniae Bind the Complement Inhibitor C4b-Binding Protein in a PspC Allele-Dependent Fashion (2009)

The complement system constitutes an important component of the innate immune system. To colonize their host and/or to cause disease, many pathogens have evolved strategies to avoid complement-mediated bacterial lysis and opsonophagocytosis. In this study, using a collection of 55 clinical isolates of Streptococcus pneumoniae, we demonstrate for the first time that pneumococci bind the complement inhibitor C4b-binding protein (C4BP). C4BP binding seems to be restricted to certain serotypes such as serotype 4, 6B, 7F, and 14, of which the strains of serotype 14 are the strongest binders. We show that bacteria-bound C4BP retains its functional activity and down-regulates the activation of the classical pathway. Thus, this major respiratory pathogen may escape immune recognition and eradication by the complement system. Furthermore, we show that C4BP binding varies between strains but is dependent on the expression of pneumococcal surface protein C, PspC of group 4. The study of the distribution of group 4 pspC locus shows that most of high-binder serotype 14 isolates harbor an allelic variant of group 4 pspC. Using PspC-negative mutant strains, we identified a new allelic variant of PspC (PspC4.4) as a major ligand for C4BP, revealing a new function for this important pneumococcal virulence factor. Thus pneumococci exploit host C4BP for complement evasion in a PspC allele-dependent manner.