gebhart/patrepeval huggingface dataset:
Mechanics properties of metal materials strengthened by accumulative roll bonding process (2007)

Accumulative roll bonding (ARB) industrial experiments of Q235 plain carbon steel and L2 pure Al were carried out with a multi-function hot-rolling mill. The effects of deformation temperature, reduction and cycle pass on the tensile strength, stress-to-strain relation, microhardness and plasticity of these two metal materials were investigated, and the reasons for these effects were analyzed. The results indicated that Q235 plain carbon steel and L2 pure Al could be well-bonded themselves by ARB process without the addition of any strengthening elements, their tensile strength increased, but their plasticity decreased in a certain extent.
Metallotexaphyrins: a new family of photosensitisers for efficient generation of singlet oxygen (1989)

The photophysical properties of a new series of tripyrroledimethine-derived ‘expanded porphyrins’(‘texaphyrins’) are reported; these compounds show strong low energy optical absorptions in the 730–770 nm spectral range as well as a high triplet quantum yield, and act as efficient photosensitizers for the production of singlet oxygen in methanol solution.
Human anti-idiotype antibodies in cancer patients: Is the modulation of the immune response beneficial for the patient? (1984)

Inoculation of human subjects with mouse monoclonal antibody results in the production of anti-idiotype antibody that reacts with the binding site of the monoclonal antibody. This reaction is hapten-inhibited, suggesting that an internal image of the antigen is produced by the anti-idiotype response. The anti-idiotype antibody isolated from sera of three patients showed significant crossreactivity. Patients who developed the anti-idiotype antibody improved clinically and had long remission from their disease. The possible presence of the internal image of cancer antigen on the human immunoglobulin molecule may change the conditions under which the immune system reacts to the tumor antigen and may open new approaches to the control of tumor growth.
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements (2004)

It has been shown that the activity of the hammerhead ribozyme at microM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the microM range of magnesium ion concentration. Disruption of the loop-loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions.
Tenascin-X is a Novel Diagnostic Marker of Malignant Mesothelioma (2009)

Tenascin XB (TNXB) was previously identified as a gene that is more highly expressed in malignant mesothelioma compared with ovarian/peritoneal serous carcinoma based on gene expression array analysis. The objective of this study was to validate this finding at the mRNA and protein levels. Effusions (n = 91; 71 ovarian carcinomas, 10 breast carcinomas, and 10 malignant mesotheliomas) were assayed for TNXB mRNA expression using quantitative polymerase chain reaction. Tenascin-X protein expression was studied in 183 effusions (137 carcinomas of different origin, 37 mesotheliomas, and 9 reactive effusions) and 178 solid lesions (122 ovarian/peritoneal carcinomas and 56 mesotheliomas) using immunohistochemistry. Quantitative polymerase chain reaction analysis showed significantly higher TNXB mRNA level in mesotheliomas compared with ovarian and breast carcinomas (P < 0.001). By immunohistochemistry, tenascin-X protein expression was significantly higher in malignant mesothelioma compared with metastatic carcinoma in effusions (34 of 37 vs. 31 of 137 positive cases; sensitivity = 92% and specificity = 77%; P < 0.001). Reactive mesothelial cells had focal or no tenascin-X expression. Tenascin-X protein was detected in 41 of 56 mesothelioma biopsy specimens and was uniformly absent from all 122 ovarian carcinomas (sensitivity = 73% and specificity = 100%; P < 0.001). Our data suggest that tenascin-X may be a new diagnostic marker of malignant mesothelioma in the differential diagnosis of cancers involving the serosal cavities, particularly in the differential diagnosis between this tumor and ovarian/peritoneal serous carcinoma.
Incorporation of chimeric gag protein into retroviral particles (1990)

The product of the Rous sarcoma virus (RSV) gag gene, Pr76gag, is a polyprotein precursor which is cleaved by the viral protease to yield the major structural proteins of the virion during particle assembly in avian host cells. We have recently shown that myristylated forms of the RSV Gag protein can induce particle formation with very high efficiency when expressed in mammalian cells (J. W. Wills, R. C. Craven, and J. A. Achacoso, J. Virol. 63:4331-4343, 1989). We made use of this mammalian system to examine the abilities of foreign antigens to be incorporated into particles when fused directly to the myristylated Gag protein. Our initial experiments showed that removal of various portions of the viral protease located at the carboxy terminus of the RSV Gag protein did not disrupt particle formation. We therefore chose this region for coupling of iso-1-cytochrome c from Saccharomyces cerevisiae to Gag. This was accomplished by constructing an in-frame fusion of the CYC1 and gag coding sequences at a common restriction endonuclease site. Expression of the chimeric gene resulted in synthesis of the Gag-cytochrome fusion protein and its release into the cell culture medium. The chimeric particles were readily purified by simple centrifugation, and transmission electron microscopy of cells that produced them revealed a morphology similar to that of immature type C retrovirions.
Solvothermal Reduction of Chemically Exfoliated Graphene Sheets (2009)

We have developed a solvothermal reduction method that affords more effective reduction of chemically derived graphene sheets and graphite oxide than low-temperature reduction methods. Solvothermal reduction removed oxygen and defects from graphene sheets, increased the size of sp(2) domains, and produced materials that were as conducting as pristine graphene and exhibited clear intrinsic Dirac behavior.
Designing a Long Acting Erythropoietin by Fusing Three Carboxyl-Terminal Peptides of Human Chorionic GonadotropinβSubunit to theN-Terminal andC-Terminal Coding Sequence (2011)

A new analog of EPO was designed by fusing one and two CTPs to the N-terminal and C-terminal ends of EPO (EPO-(CTP)(3)), respectively. This analog was expressed and secreted efficiently in CHO cells. The in vitro test shows that the activity of EPO-(CTP)(3) in TFI-1 cell proliferation assay is similar to that of EPO-WT and commercial rHEPO. However, in vivo studies indicated that treatment once a week with EPO-(CTP)(3) (15 μg/kg) dramatically increased (~8 folds) haematocrit as it was compared to rHuEPO. Moreover, it was found that EPO-(CTP)(3) is more effective than rHuEPO and Aranesp in increasing reticulocyte number in mice blood. The detected circulatory half-lives of rHuEPO, Aranesp, and EPO-(CTP)(3) following IV injection of 20 IU were 4.4, 10.8, and 13.1 h, respectively. These data established the rational for using this chimera as a long-acting EPO analog in clinics. The therapeutic efficacy of EPO-CTP analog needs to be established in higher animals and in human clinical trials.
Modification of MyD88 mRNA Splicing and Inhibition of IL-1β Signaling in Cell Culture and in Mice with a 2′- O -Methoxyethyl-Modified Oligonucleotide (2006)

A number of proinflammatory cytokines, including IL-1beta, signal through the adaptor protein MyD88. This signaling leads to phosphorylation of IL-1R-associated kinase-1 (IRAK-1) and, ultimately, activation of the NF-kappaB transcription factor. A splice variant of MyD88 (MyD88(S)), which lacks the ability to couple IRAK-1 to NF-kappaB, has been described. A chemically modified antisense oligonucleotide (ASO) that alters the splicing ratio of MyD88 to MyD88(S) in both cell culture and in animals has been identified. The ASO (ISIS 337846) binds to exon II donor sites in the MyD88 pre-mRNA. By manipulating levels of MyD88 splicing, proinflammatory signaling through the IL-1R has been shown to be diminished, both in cell culture and in mouse liver. To our knowledge, this represents the first example of modulation of RNA splicing of an endogenous gene target in animals after systemic ASO dosing and suggests that this mechanism may be useful as a novel modulator of inflammatory stimuli.
Change in liver blood flow and blood content in dogs during direct and reflex alteration of hepatic sympathetic nerve activity. (1977)

A mean decrease of 60% in liver blood volume was recorded by a plethysmographic technique during electrical stimulation of the hepatic nerves in anesthetized, vagotomized dogs. A decrease in pressure in the vascularly isolated carotid sinus to 40 mm Hg, from a mean control of 144 mm Hg, decreased liver blood volume by a mean of 16%; arterial blood pressure increased by a mean of 77 mm Hg. Carotid sinus hypotension was accompanied by respective mean increases of 16% and 1.4% in hepatic arterial and portal venous blood flows, and of 45% and 22% in arterial and portal resistances. Increase in sinus pressure to 240 mm Hg increased liver blood volume by a mean of 20%; arterial blood pressure decreased by 90 mm Hg. Sinus hypertension was accompanied by respective mean decreased of 10% and 1.5% in hepatic arterial and portal venous blood flows, and of 44% and 18% in arterial and portal resistances. Interruption of afferent vagal traffic from cardiopulmonary receptors was maximally effective in decreasing liver blood volume at a carotid sinus pressure of 40 mm Hg and was ineffective at carotid sinus pressures greater than 160 mm Hg. Combined withdrawal of carotid and cardiopulmonary vasomotor inhibition decreased liver blood volume by 42%; of this 37% was due to the cardiopulmonary and 63% to the carotid baroreflex. The study showed the canine liver to function as a blood reservoir by active mobilization of a portion of its blood volume.
Thymic Involution in Aging Prospects for Correction (1992)

The thymus produces several putative thymic hormones: thymosin alpha 1, thymulin, and thymopoietin, which have been reported to circulate and to act on both prothymocytes and mature T cells in the periphery, thus maintaining their commitment to the T cell system. These endocrine influences decline with age and are associated with "thymic menopause" and cellular immune senescence, which contribute to the development of diseases in the aged. Thymus endocrinology is characterized by the action of many hormones and hormone-like substances on the cellular components of the thymus, including thymocytes, thymic epithelial cells, and thymic stromal cells. The intrathymic environment is characterized by a complex network of paracrine, autocrine, and endocrine signals involving both interleukins and thymic peptides, which can be envisioned to operate in a synergistic network to carry the evolving T cell through its stepwise development to a mature T cell. Extrathymic influences regulating the secretory function of thymic epithelial cells and the stepwise evolution of T cells can be ascribed to circulating interleukins, mainly IL1 and IL2, derived from activation and secretion of leukocytes in the periphery. These interleukins act in a synergistic fashion at all levels of T cell development by the induction of high-affinity IL2 receptors and the resultant IL2-dependent proliferative responses. To determine whether exogenous administration of interleukins would induce T lymphocyte development in aged mice, we chemically thymectomized aged mice with a steroid hormone and treated them with mixed interleukins or thymic hormones such as thymosin. We found that mixed interleukins, but not thymosin, restored thymic weight and cellularity and enhanced thymocyte responses to interleukins and mitogen. Thymosin potentiated the effect.
Shade Avoidance Responses. Driving Auxin along Lateral Routes (2000)

To grow and develop optimally, all organisms need to perceive and process information from their environment. As sessile organisms, plants need to sense and respond to external stimuli more than most organisms. Therefore, plants have to adapt their developmental pattern to the environmental changes
Mode of phytochrome B action in the photoregulation of seed germination in Arabidopsis thaliana (1998)

Arabidopsis thaliana seeds imbibed for a short duration show phytochrome B (PhyB)-specific photo-induction of germination. Using this system, the relationship was determined between the amount of PhyB in seeds and photon energy required for PhyB-specific germination in two transgenic Arabidopsis lines transformed with either the Arabidopsis PhyB cDNA (ABO) or the rice PhyB cDNA (RBO). Immunochemical detection of PhyB apoprotein (PHYB) showed that the expression level of PHYB in ABO seeds was at least two times higher than that in the wild-type seeds, but in RBO seeds the PHYB level was indistinguishable from that in wild-type seeds. The photon fluence required for induction and photoreversible inhibition of germination was examined using the Okazaki large spectrograph. At the wavelengths of 400-710 nm, the ABO seeds required significantly less photon fluence than wild-type seeds for induction of germination, whereas the RBO seeds required similar fluence to wild-type seeds. A critical threshold wavelength for either induction or inhibition of germination of ABO seeds shifted towards the longer wavelengths relative to wild-type seeds. By assuming that PhyA and PhyB are similar in their photochemical parameters, amounts of Pfr at each wavelength were calculated. The photon fluence required for 50% germination was equivalent to the fluence generating a Pfr/Ptot ratio of 0.21-0.43 in wild-type seeds, and of 0.035-0.056 in ABO seeds. These results indicate that PhyB-specific seed germination is not strictly a function of the Pfr/Ptot ratio, but is probably a function of the absolute Pfr concentration.
Convergence of the Abscisic Acid, CO2, and Extracellular Calcium Signal Transduction Pathways in Stomatal Guard Cells (1997)

We show that guard cells from Arabidopsis thaliana plants carrying the abscisic acid-insensitive mutations abi1 and abi2 fail to respond to CO2 and extracellular calcium. This demonstrates that the signal transduction pathways for all three stimuli converge on, or close to, the ABI1 and ABI2 gene products.
One hundred data-driven haptic texture models and open-source methods for rendering on 3D objects (2014)

This paper introduces the Penn Haptic Texture Toolkit (HaTT), a publicly available repository of haptic texture models for use by the research community. HaTT includes 100 haptic texture and friction models, the recorded data from which the models were made, images of the textures, and the code and methods necessary to render these textures using an impedance-type haptic interface such as a SensAble Phantom Omni. This paper reviews our previously developed methods for modeling haptic virtual textures, describes our technique for modeling Coulomb friction between a tooltip and a surface, discusses the adaptation of our rendering methods for display using an impedance-type haptic device, and provides an overview of the information included in the toolkit. Each texture and friction model was based on a ten-second recording of the force, speed, and high-frequency acceleration experienced by a handheld tool moved by an experimenter against the surface in a natural manner. We modeled each texture's recorded acceleration signal as a piecewise autoregressive (AR) process and stored the individual AR models in a Delaunay triangulation as a function of the force and speed used when recording the data. To increase the adaptability and utility of HaTT, we developed a method for resampling the texture models so they can be rendered at a sampling rate other than the 10 kHz used when recording data. Measurements of the user's instantaneous normal force and tangential speed are used to synthesize texture vibrations in real time. These vibrations are transformed into a texture force vector that is added to the friction and normal force vectors for display to the user.
Quantum Dots with a Paramagnetic Coating as a Bimodal Molecular Imaging Probe (2005)

MRI detectable and targeted quantum dots were developed. To that aim, quantum dots were coated with paramagnetic and pegylated lipids, which resulted in a relaxivity, r(1), of nearly 2000 mM(-1)s(-1) per quantum dot. The quantum dots were functionalized by covalently linking alphavbeta3-specific RGD peptides, and the specificity was assessed and confirmed on cultured endothelial cells. The bimodal character, the high relaxivity, and the specificity of this nanoparticulate probe make it an excellent contrast agent for molecular imaging purposes.
Desorption electrospray ionization mass spectrometry for the analysis of pharmaceuticals and metabolites (2005)

The performance of desorption electrospray ionization (DESI) in the analysis of a group of pharmaceuticals and their glucuronic acid conjugates is reported. The suitability of different sprayer solvents and different surfaces was examined. In the positive ion mode, water/methanol/trifluoroacetic acid performed best, whereas, in the negative ion mode, water/methanol/ammonium hydroxide was found to be the most suitable spray solvent. Of the surfaces investigated, polymethylmethacrylate (PMMA) was found to give the best performance in terms of sensitivity. Spray solution flow rate and the distance of the sprayer tip from the surface were also found to have significant effects on the signal intensity. Analytes with basic groups efficiently formed the corresponding protonated molecules in the positive ion mode, whereas acidic analytes, such as the glucuronic acid conjugates, formed intense signals due to the deprotonated molecules in the negative ion mode. Ionization of neutral compounds was less efficient and in many cases it was achieved through adduct formation with simple anions or cations.
Modeling effects of oxygen inhibition in mask‐based stereolithography (2011)

Purpose The purpose of this paper is to present a model that can be used to simulate the photopolymerization process in micro‐stereolithography (SL) in order to predict the shape of the cured parts. SL is an additive manufacturing process in which liquid photopolymer resin is cross‐linked and converted to solid with a UV laser light source. Traditional models of SL processes do not consider the complex chemical reactions and species transport occurring during photopolymerization and, hence, are incapable of accurately predicting resin curing behavior. The model presented in this paper attempts to bridge this knowledge gap. Design/methodology/approach The chemical reactions involved in the photopolymerization of acrylate‐based monomers were modeled as ordinary differential equations (ODE). This model incorporated the effect of oxygen inhibition and diffusion on the polymerization reaction. The model was simulated in COMSOL and verified with experiments conducted on a mask‐based micro‐SL system. Parametric studies were conducted to investigate the possibilities to improve the accuracy of the model for predicting the edge curvature. Findings The proposed model predicts well the effect of oxygen inhibition and diffusion on photopolymerization, and the model accurately predicts the cured part height when compared to experiments conducted on a mask‐based SL system. The simulated results also show the characteristic edge curvature as seen in experiments. Research limitations/implications A triacrylate monomer was used in the experiments conducted, so results may be limited to acrylate monomers. Shrinkage was not considered when comparing cured part shapes to those predicted using COMSOL. Originality/value This paper presents a unique and a pioneering approach towards modeling of the photopolymerization reaction in micro‐SL process. This research furthers the development of patent pending film micro‐SL process which can be used for fabrication of custom micro‐optical components.
A method for calling gains and losses in array CGH data (2004)

Array CGH is a powerful technique for genomic studies of cancer. It enables one to carry out genome-wide screening for regions of genetic alterations, such as chromosome gains and losses, or localized amplifications and deletions. In this paper, we propose a new algorithm 'Cluster along chromosomes' (CLAC) for the analysis of array CGH data. CLAC builds hierarchical clustering-style trees along each chromosome arm (or chromosome), and then selects the 'interesting' clusters by controlling the False Discovery Rate (FDR) at a certain level. In addition, it provides a consensus summary across a set of arrays, as well as an estimate of the corresponding FDR. We illustrate the method using an application of CLAC on a lung cancer microarray CGH data set as well as a BAC array CGH data set of aneuploid cell strains.
Assessment and Implication of the Allergic Sensitivity to a Single Dose of Recombinant Human Hyaluronidase Injection (2007)

Animal-extracted injectable hyaluronidases have been used safely for more than 50 years to increase the dispersion and absorption of coadministered drugs and fluids; however, concern still exists about the allergic and immunological risks of these products. Hylenex recombinant, a novel formulation of recombinant human hyaluronidase, has been developed as an alternative to these animal-derived hyaluronidases. Because recombinant human hyaluronidase is a human (nonforeign) protein manufactured into a purer preparation than the animal extracts, it is expected to convey reduced allergic and immunologic risks. The recombinant human hyaluronidase product was well tolerated in this double-blind, placebo-controlled, single-dose study. No allergic reactions were observed among the 100 volunteer subjects who were injected intradermally. These findings supported the US Food and Drug Administration approval of the recombinant human hyaluronidase product.
Commensal bacteria protect against food allergen sensitization (2014)

Environmentally induced alterations in the commensal microbiota have been implicated in the increasing prevalence of food allergy. We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota. By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. Microarray analysis of intestinal epithelial cells from gnotobiotic mice revealed a previously unidentified mechanism by which Clostridia regulate innate lymphoid cell function and intestinal epithelial permeability to protect against allergen sensitization. Our findings will inform the development of novel approaches to prevent or treat food allergy based on modulating the composition of the intestinal microbiota.
KRAS Mutations As an Independent Prognostic Factor in Patients With Advanced Colorectal Cancer Treated With Cetuximab (2008)

These results confirm the high prognostic value of KRAS mutations on response to cetuximab and survival in metastatic CRC patients treated with cetuximab.