gebhart/patrepeval huggingface dataset:
Macrophages in rheumatoid arthritis. (2000)

The abundance and activation of macrophages in the inflamed synovial membrane/pannus significantly correlates with the severity of rheumatoid arthritis (RA). Although unlikely to be the 'initiators' of RA (if not as antigen-presenting cells in early disease), macrophages possess widespread pro-inflammatory, destructive, and remodeling capabilities that can critically contribute to acute and chronic disease. Also, activation of the monocytic lineage is not locally restricted, but extends to systemic parts of the mononuclear phagocyte system. Thus, selective counteraction of macrophage activation remains an efficacious approach to diminish local and systemic inflammation, as well as to prevent irreversible joint damage.
Patch verification via multiversion interprocedural control flow graphs (2014)

Software development is inherently incremental; however, it is challenging to correctly introduce changes on top of existing code. Recent studies show that 15%-24% of the bug fixes are incorrect, and the most important yet hard-to-acquire information for programming changes is whether this change breaks any code elsewhere. This paper presents a framework, called Hydrogen, for patch verification. Hydrogen aims to automatically determine whether a patch correctly fixes a bug, a new bug is introduced in the change, a bug can impact multiple software releases, and the patch is applicable for all the impacted releases. Hydrogen consists of a novel program representation, namely multiversion interprocedural control flow graph (MVICFG), that integrates and compares control flow of multiple versions of programs, and a demand-driven, path-sensitive symbolic analysis that traverses the MVICFG for detecting bugs related to software changes and versions. In this paper, we present the definition, construction and applications of MVICFGs. Our experimental results show that Hydrogen correctly builds desired MVICFGs and is scalable to real-life programs such as libpng, tightvnc and putty. We experimentally demonstrate that MVICFGs can enable efficient patch verification. Using the results generated by Hydrogen, we have found a few documentation errors related to patches for a set of open-source programs.
Bioassay-Guided Isolation of Proanthocyanidins with Antiangiogenic Activities (2012)

The proangiogenic members of the vascular endothelial growth factor (VEGF) family and related receptors play a central role in the modulation of pathological angiogenesis. In order to identify plant compounds able to interfere in the VEGFs/VEGFR-1 (Flt-1) recognition by VEGF family members, the extracts of the aerial parts of Campsiandra guayanensis and Feretia apodanthera were screened by a competitive ELISA-based assay. By using this bioassay-oriented approach five proanthocyanindins, including the new natural compounds (2S)-4',5,7-trihydroxyflavan-(4β→8)-afzelechin (1) and (2S)-4',5,7-trihydroxyflavan-(4β→8)-epiafzelechin (2) and the known geranin B (3), proanthocyanidin A2 (4), and proanthocyanidin A1 (5), were isolated. The study of the antiangiogenic activities of compounds 1-5 using ELISA and SPR assays showed compound 1 as being the most active. The antiangiogenic activity of 1 was also confirmed in vivo by the chicken chorioallantoic membrane assay. Our results indicated 1 as a new antiangiogenic compound inhibiting the interaction between VEGF-A or PlGF and their receptor VEGRF-1.
T-cell receptor peptide immunization leads to enhanced and chronic experimental allergic encephalomyelitis. (1991)

It has previously been reported that synthetic peptides corresponding to sequences derived from T-cell receptor variable regions identified as dominant in the T-cell-mediated autoimmune disease experimental allergic encephalomyelitis in both the mouse and the rat can down-regulate disease in Lewis rats. In contrast to these results, we have found that immunization of Lewis rats with such peptides in complete Freund's adjuvant prior to induction of experimental allergic encephalomyelitis with myelin basic protein leads to responses ranging from profound disease enhancement to lack of disease. In some cases, enhanced disease was followed by a prolonged neurologic deficit that resembles multiple sclerosis more closely than does acute experimental allergic encephalomyelitis. These findings, on the one hand, support previous results showing T-cell receptor peptide-induced modulation of the disease experimental allergic encephalomyelitis and, on the other, indicate that such immunization is not a reliable method for inducing suppression of encephalitogenic effector cells.
Observations of the stable equilibrium and classical diffusion of field reversing relativistic electron coils (1974)

Observations of high current relativistic electron coils are presented and interpreted theoretically. Electron coil self-magnetic field strengths up to almost twice that of the external magnetic field at the mirror center are observed. Lifetimes up to 30 μsec are related to the classical diffusion of electron coils in a stable equilibrium state. The diffusion mechanism is verified as inelastic small angle scattering of the relativistic electrons from a neutral gas background.
Immunological Responses in Women with Human Papillomavirus Type 16 (HPV-16)-Associated Anogenital Intraepithelial Neoplasia Induced by Heterologous Prime-Boost HPV-16 Oncogene Vaccination (2004)

The prime-boost regimen is immunogenic in AGIN patients (humoral and cellular immunity), but there is no simple relationship between induction of systemic HPV-16-specific immunity and clinical outcome. Other factors that may play a role in the eradication of long-term established AGIN lesions need to be determined to identify the patient group that would benefit from immunotherapy with the vaccines used in this study.
Cloning and characterization of the Vibrio cholerae genes encoding the utilization of iron from haemin and haemoglobin (1993)

Vibrio cholerae can utilize haemin or haemoglobin as its sole source of iron. Four haem utilization mutants of a classical strain of V. cholerae were isolated. These mutations were complemented with pHUT1, a cosmid clone isolated from a library of wild-type CA401 DNA. Two independent Tn5 insertions into the cloned sequence disrupted function in all of the complemented mutants. Escherichia coli 1017 transformed with pHUT1 failed to utilize haemin as an iron source; a second plasmid containing a different cloned fragment of V. cholerae DNA (pHUT3) was required in addition to pHUT1 to reconstitute the system in E. coli. Minicell analysis and SDS-PAGE of protein fractions indicate that pHUT10 (a subclone of pHUT1) encodes a 26 kDa inner membrane protein, and pHUT3 encodes a 77 kDa outer membrane protein. Loss of either protein by Tn5 mutagenesis abolishes haem utilization in E. coli. An E. coli hemA mutant that cannot synthesize porphyrins was transformed with the recombinant plasmids to determine whether the plasmids encoded the ability to transport the porphyrin as well as the iron. The transformants grew aerobically in media containing haemin, whereas the parental strain was unable to grow under these conditions. This indicates that V. cholerae haem-iron utilization genes allow transport of the entire haem moiety into the cell.
Increased in vivo glial activation in patients with amyotrophic lateral sclerosis: Assessed with [11C]-PBR28 (2015)

Evidence from human post mortem, in vivo and animal model studies implicates the neuroimmune system and activated microglia in the pathology of amyotrophic lateral sclerosis. The study aim was to further evaluate in vivo neuroinflammation in individuals with amyotrophic lateral sclerosis using [(11)C]-PBR28 positron emission tomography. Ten patients with amyotrophic lateral sclerosis (seven males, three females, 38-68 years) and ten age- and [(11)C]-PBR28 binding affinity-matched healthy volunteers (six males, four females, 33-65 years) completed a positron emission tomography scan. Standardized uptake values were calculated from 60 to 90 min post-injection and normalized to whole brain mean. Voxel-wise analysis showed increased binding in the motor cortices and corticospinal tracts in patients with amyotrophic lateral sclerosis compared to healthy controls (p FWE < 0.05). Region of interest analysis revealed increased [(11)C]-PBR28 binding in the precentral gyrus in patients (normalized standardized uptake value = 1.15) compared to controls (1.03, p < 0.05). In patients those values were positively correlated with upper motor neuron burden scores (r = 0.69, p < 0.05), and negatively correlated with the amyotrophic lateral sclerosis functional rating scale (r = -0.66, p < 0.05). Increased in vivo glial activation in motor cortices, that correlates with phenotype, complements previous histopathological reports. Further studies will determine the role of [(11)C]-PBR28 as a marker of treatments that target neuroinflammation.
Microscopic Study of a Spin-Orbit-Induced Mott Insulator in Ir Oxides (2010)

Motivated by recent experiments of a novel 5d Mott insulator in Sr2IrO4, we have studied the two-dimensional three-orbital Hubbard model with a spin-orbit coupling λ. The variational Monte Carlo method is used to obtain the ground state phase diagram with varying an on-site Coulomb interaction U as well as λ. It is found that the transition from a paramagnetic metal to an antiferromagnetic insulator occurs at a finite U=U(MI), which is greatly reduced by a large λ, characteristic of 5d electrons, and leads to the "spin-orbit-induced" Mott insulator. It is also found that the Hund's coupling induces the anisotropic spin exchange and stabilizes the in-plane antiferromagnetic order. We have further studied the one-particle excitations by using the variational cluster approximation and revealed the internal electronic structure of this novel Mott insulator. These findings are in agreement with experimental observations on Sr2IrO4.
Tumor pretargeting for radioimmunodetection and radioimmunotherapy. (1998)

The limited success of the sole use of monoclonal antibodies for cancer detection and treatment has led to the development of multistep methods using antibodies in conjunction with low molecular weight agents. For tumor pretargeting, it is important to optimize dose and schedule of relevant agents and to understand barriers to targeted delivery. Here, we address these issues for the anti-carcinoembryonic antigen bifunctional antibody-hapten and the streptavidinylated antibody-biotin systems using a recently developed physiologically based pharmacokinetic model.For baseline conditions of a standard 70-kg man with a 20-g tumor embedded in the liver, the model was used in conjunction with the Medical Internal Radiation Dosimetry schema to: estimate absorbed doses in tumor and normal tissues; determine the dose dependence of effector agent accumulation in tumor; simulate tumor-to-background effector agent uptake ratio; and calculate the therapeutic ratio for different antibody forms and radionuclides. Alternative drug administration schemes and variable tumor physiological conditions were considered.Model simulations showed that 131I-labeled biotin with the streptavidinylated F(ab')2 provided the highest therapeutic ratio under the optimized conditions. The simulations also showed that biotin with the bifunctional streptavidinylated immunoglobulin G provided the highest tumor-to-liver uptake ratio during the early period. Sensitivity analysis showed that antibody extravasation was the major factor limiting the accretion of the effector agent in tumor, whereas antigen expression in normal tissues and tumor antigen shedding had little effect on the absorbed doses.Tumor pretargeting should provide a definite advantage over direct antibody targeting with up to a 200% increase in tumor-to-background ratio in radioimmunodetection and up to a 76% increase in tumor-to-bone marrow therapeutic ratio in radioimmunotherapy. Rapid antibody clearance from the bloodstream before effector agent injection is expected to improve the therapeutic ratio marginally (3%-10%). However, continuous plasmapheresis dramatically increased the tumor-to-background ratio by a factor of 10 in RAID and the tumor-to-bone marrow therapeutic ratio by more than 110% for short-lived radionuclides in RAIT. Apart from drastic measures such as extended plasmapheresis, pretargeting selectivity was neither sensitive enough for radioimmunodetection nor effective enough for radioimmunotherapy in patients with typical solid tumors even using the optimized protocols.
Structural and superconducting properties of (Y,Gd)Ba2Cu3O7−δgrown by MOCVD on samarium zirconate buffered IBAD-MgO (2008)

Textured samarium zirconate (SZO) films have been grown by reactive cosputtering directly on an ion beam assisted deposited (IBAD) MgO template, without an intermediate homoepitaxial MgO layer. The subsequent growth of 0.9 µm thick (Y,Gd)Ba2Cu3O7−δ ((Y, Gd)BCO) films by metal organic chemical vapor deposition (MOCVD) yielded well textured films with a full width at half maximum of 1.9° and 3.4° for the out-of-plane and in-plane texture, respectively. Microstructural characterizations of the SZO buffered samples revealed clean interfaces. This indicates that the SZO not only provides a diffusion barrier, but also functions as a buffer for (Y, Gd)BCO grown by MOCVD. The achievement of self-field critical current densities (Jc) of over 2 MA cm−2 at 75.5 K is another proof of the effectiveness of SZO as a buffer on the IBAD-MgO template. The in-field measurements revealed an asymmetric angular dependence of Jc and a shift of the ab-plane maxima due to the tilted nature of the template and (Y,Gd)2O3 particles existing in the (Y, Gd)BCO matrix. The present results are especially important because they demonstrate that high temperature superconducting coated conductors with simpler architecture can be fabricated using commercially viable processes.
Mechanisms underlying the synergistic effect of SU5416 and cisplatin on cytotoxicity in human ovarian tumor cells (2004)

SU5416 is a selective inhibitor of vascular endothelial growth factor (VEGF) receptors with anti-angiogenesis activity for human cancers. We have previously reported that SU5416 sensitizes ovarian cancer cells to cisplatin via suppression of nucleotide excision repair activity. This study sought to gain further insights into the mechanisms underlying the synergistic effect of SU5416 and cisplatin on cytotoxicity in human ovarian tumor cells. Here, we show that SU5416 inhibited the expression of G1 cell cycle checkpoint regulators, p53, p21, p27 and MDM2 in ovarian carcinoma cells. We also demonstrate that SU5416 triggered the apoptosis of these cells, in addition to augmenting the apoptosis induced by cisplatin, as determined by a Sub-G1 profile analysis using a flow cytometer. Furthermore, we show that SU5416-induced apoptosis is associated with a decrease in the expression of the apoptosis inhibitors, MDM2 and Bcl-2, and an increase in the level of NF-kappaB inhibitor, IkappaBalpha. NF-kappaB is an anti-apoptotic transcription factor, which induces the apoptosis inhibitors, Bcl-XL and IAPs (inhibitor of apoptosis proteins), and IkappaBalpha is an inhibitor of NF-kappaB, which binds to the NF-kappaB and retains it in the cytoplasm. Finally, the compound was found to block cisplatin-induced increases in AP-1 expression and JNK activity, as well as Raf-1 protein level in these cells. Together, these results suggest that the chemosensitizing effect of SU5416 on ovarian tumor cells may be mediated, at least in part, through inhibiting G1 checkpoint control and up-regulating the apoptotic response to cisplatin.
Wnt11 expression in rat dental pulp and promotional effects of Wnt signaling on odontoblast differentiation (2013)

Congenital anomalies of wingless-type mouse mammary tumor virus (MMTV) integration site family (Wnt) are frequently accompanied with tooth and dentin abnormality. The aim of this study was to investigate the effects of Wnt signaling on odontoblast differentiation of mouse dental papilla cells (MDPs). Mouse dental papilla cells were cultured in α-modified minimum essential medium containing 10% fetal bovine serum and antibiotics. Odontoblast differentiation was induced by bone morphogenic protein 2 (BMP2), and the expression of odontoblast-specific markers and Wnt-related signaling molecules was analyzed by real-time reverse transcription-polymerase chain reaction and immunohistochemistry. Odontoblast differentiation was evaluated by dentin sialophosphoprotein (Dspp) and dentin matrix protein (DMP) 1 expression. Localization of β-catenin in MDPs was detected by immunocytochemistry using an anti-β-catenin antibody. Dspp expression in MDPs was upregulated in the presence of BMP2. Wnt5a, Wnt11, Lef1 and Tcf4 expression was upregulated in BMP2-treated MDPs. Wnt11 expression was detected in rat dental pulp in vivo, and particularly strong expression of Wnt11 was detected in odontoblasts. Enhanced Dspp and DMP1 expression and alkaline phosphatase activity induced by BMP2 were completely negated by the Wnt antagonist: IWR-1-endo treatment. Nuclear translocation of β-catenin observed in BMP2-treated MDPs was also negated by IWR-1-endo treatment. These results indicate that Wnt signaling upregulates odontoblast marker expression in MDPs, suggesting a promoting effect of Wnt signaling on odontoblast differentiation.
Calidad de vida y funcionamiento psicosocial de las personas con trastornos mentales graves y duraderos (1998)

Some epidemiological studies have associated tea drinking with several health benefits, while other such studies have been inconclusive. The liver enzyme, xanthine oxidase (XO) produces uric acid and reactive oxygen species (ROS) during the catabolism of purines. Excess of the former can lead to gout and of the latter to increased oxidative stress, mutagenesis and possibly cancer. Polyphenols are antioxidants, and it has been suggested that they can reduce oxidative stress by their antioxidant properties. We report here on the inhibition of XO by five tea catechins and two flavones. The Ki values (microM) and types of inhibition were catechin (C) (Ki = 303.95, uncompetitive), epicatechin (EC) (Ki = 20.48, mixed), epigallocatechin (EGC) (Ki = 10.66, mixed), epicatechin gallate (ECg) (Ki = 2.86, mixed) and epigallocatechin gallate (EGCg) (Ki = 0.76, competitive). The Ki of EGCg was similar to that of allopurinol (Ki = 0.30, mixed), the drug of choice for inhibition of XO in gout patients. Thus, tea catechins may act at.an earlier stage than has previously been suspected, by inhibiting ROS production, rather than only neutralizing the already formed ROS. This suggests a new mechanism whereby tea drinking may prevent oxidative stress related diseases, e.g. atherosclerosis and cancer.
Secreted alkaline phosphatase: an internal standard for expression of injected mRNAs in the Xenopus oocyte (1990)

The Xenopus oocyte is widely used to study the various aspects of eukaryotic cell structure and function. It is also being used increasingly in expression cloning of cDNAs encoding proteins for which there are no structural data. One of the drawbacks of the Xenopus oocyte system is that individual oocytes taken at the same time from the same frog vary considerably in the amount of protein synthesized from the same amount of injected mRNA. In this report we describe the preparation and use of the mRNA for a secreted mutant form of human placental alkaline phosphatase as an internal, coinjected standard to monitor translation in oocytes. Secreted alkaline phosphatase can be readily determined in the medium of cultured oocytes by using a standard colorimetric assay. The amounts of alkaline phosphatase secreted into the medium were shown to parallel the level of expression of two membrane proteins. This permits rapid identification and selection of those oocytes that efficiently express injected mRNAs. The procedure yields more precise data and results in an enormous saving of time and expense, especially in investigations that involve complex measurements on individual oocytes.
Fast &#x2113;<inf>1</inf>-minimization algorithms and an application in robust face recognition: A review (2010)

We provide a comprehensive review of five representative ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -minimization methods, i.e., gradient projection, homotopy, iterative shrinkage-thresholding, proximal gradient, and augmented Lagrange multiplier. The repository is intended to fill in a gap in the existing literature to systematically benchmark the performance of these algorithms using a consistent experimental setting. The experiment will be focused on the application of face recognition, where a sparse representation framework has recently been developed to recover human identities from facial images that may be affected by illumination change, occlusion, and facial disguise. The paper also provides useful guidelines to practitioners working in similar fields.
Recombinant human soluble thrombomodulin prevents peripheral HMGB1‐dependent hyperalgesia in rats (2013)

These data suggest that peripheral HMGB1 causes hyperalgesia, and that rhsTM abolishes HMGB1-dependent hyperalgesia, providing novel evidence for therapeutic usefulness of rhsTM as an analgesic.
Improved Splice Site Detection in Genie (1997)

We present an improved splice site predictor for the genefinding program Genie. Genie is based on a generalized Hidden Markov Model (GHMM) that describes the grammar of a legal parse of a multi-exon gene in a DNA sequence. In Genie, probabilities are estimated for gene features by using dynamic programming to combine information from multiple content and signal sensors, including sensors that integrate matches to homologous sequences from a database. One of the hardest problems in genefinding is to determine the complete gene structure correctly. The splice site sensors are the key signal sensors that address this problem. We replaced the existing splice site sensors in Genie with two novel neural networks based on dinucleotide frequencies. Using these novel sensors, Genie shows significant improvements in the sensitivity and specificity of gene structure identification. Experimental results in tests using a standard set of annotated genes showed that Genie identified 86% of coding nucleotides correctly with a specificity of 85%, versus 80% and 84% in the older system. In further splice site experiments, we also looked at correlations between splice site scores and intron and exon lengths, as well as at the effect of distance to the nearest splice site on false positive rates.
Multi-ligand interactions with receptor-like protein tyrosine phosphatase β: implications for intercellular signaling (1998)

Receptor-like protein tyrosine phosphatase beta (RPTP beta) shows structural and functional similarity to cell adhesion molecules (CAMs). It binds to several neuronal CAMs and extracellular matrix (ECM) proteins that combine to form cell-recognition complexes. Here, the authors discuss the implications of such complexes for intercellular signaling, and the regulation of RPTP activity by cell-cell and cell-ECM contact.
Changes in Red Cell Transfusion Practice among Adult Trauma Victims (1998)

Between 1991 and 1995 there have been significant reductions in both the number of trauma patients receiving blood products and the total number of units transfused. These findings may reflect lower or abandoned hemoglobin transfusion triggers and increased awareness of complications related to transfusion.