gebhart/patrepeval huggingface dataset:
Analysis of Structural Components and Molecular Construction of Soybean Soluble Polysaccharides by Stepwise Enzymatic Degradation (2001)

Soybean soluble polysaccharides (SSPS) extracted from soybean cotyledons have a pectin-like structure. The core polysaccharides after treatments with four kinds of hemicellulases and a pectinase contained approximately equal numbers of L-rhamnose and D-galacturonate residues, suggesting the presence of the rhamnogalacturonan (RG) I structure consisting of the diglycosyl repeating unit, -4)-alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1-. The lengths of RG chains were calculated as approximately 15, 28, and 100 diglycosyl repeats. The RG components linked to each other by intervention of galacturonan (GN) chains, constituting the backbone of SSPS. All arabinose residues, which constitute 21% of total SSPS sugars, were found to be in side chains from RG regions, and this was also true for galactose residues, which constitute 50% of total sugars. Of arabinose residues, 94% are present as alpha-1,3- or alpha-1,5-arabinans, and 89% of galactose residues were present as beta-1,4-galactans. Galactan chains are modified with arabinose, xylose, fucose, and glucose at the sites close to the RG regions.
Biological functions of maspin (2006)

Maspin (Mammary Serine Protease Inhibitor) was first reported in 1994 as a serpin with tumor suppressive properties. Maspin was initially isolated through subtractive hybridization and differential display analysis as a 42-kDa protein that is expressed in normal mammary epithelial cells but reduced or absent in breast carcinomas (Zou et al., 1994). Further research led to maspin's characterization as a class II tumor suppressor based on its ability to inhibit cell invasion, promote apoptosis, and inhibit angiogenesis (Sheng et al., 1996; Zhang et al., 2000b; Jiang et al., 2002). Since then, efforts have been made to characterize maspin's tumor suppressive mechanisms. In particular, researchers have studied maspin localization, the regulation of maspin expression, and more recently, maspin protein interactions. By elucidating these mechanisms, researchers are beginning to understand the complex, pleiotropic nature of maspin and the pathways through which maspin exerts its tumor suppressive properties. These new findings not only further enhance our understanding of cancer biology but also provide an avenue to develop maspin's potential as a diagnostic marker for cancer progression, and as a potentially powerful therapeutic agent in the fight against breast cancer.
Evidence That an OX-2-Positive Cell Can Inhibit the Stimulation of Type 1 Cytokine Production by Bone Marrow-Derived B7-1 (and B7-2)-Positive Dendritic Cells (1999)

We reported that hepatic mononuclear, nonparenchymal cells (NPC) can inhibit the immune response seen when allogeneic C57BL/6 dendritic cells (DC) are incubated with C3H spleen responder cells. Cells derived from these cultures transfer increased survival of C57BL/6 renal allografts in C3H mice. We also found that increased expression of OX-2 on DC was associated with inhibition of cytokine production and renal allograft rejection. We explored whether inhibition by hepatic NPC was a function of OX-2 expression by these cells. Fresh C57BL/6 spleen-derived DC were cultured with C3H spleen responder cells and other putative coregulatory cells. The latter were derived from fresh C3H or C57BL/6 liver NPC, or from C3H or C57BL/6 mice treated for 10 days by i.v. infusion of human Flt3 ligand. Different populations of murine bone marrow-derived DC from cultures of bone marrow with IL-4 plus granulocyte-macrophage-CSF were also used as a source of putative regulator cells. Supernatants of all stimulated cultures were examined for functional expression of different cytokines (IL-2, IL-4, IFN-gamma, and TGFbeta). We found that fresh C57BL/6 splenic DC induced IL-2, not IL-4, production. Cells from the sources indicated inhibited IL-2 and IFN-gamma production and promoted IL-4 and TGFbeta production. Inhibition was associated with increased expression of OX-2 on these cells, as defined by semiquantitative PCR and FACS analysis. By size fractionation, cells expressing OX-2 were a subpopulation of NLDC145+ cells. Our data imply a role for cells expressing OX-2 in the regulation of induction of cytokine production by conventional allostimulatory DC.
Structured Generative Models of Natural Source Code (2014)

We study the problem of building generative models of natural source code (NSC); that is, source code written and understood by humans. Our primary contribution is to describe a family of generative models for NSC that have three key properties: First, they incorporate both sequential and hierarchical structure. Second, we learn a distributed representation of source code elements. Finally, they integrate closely with a compiler, which allows leveraging compiler logic and abstractions when building structure into the model. We also develop an extension that includes more complex structure, refining how the model generates identifier tokens based on what variables are currently in scope. Our models can be learned efficiently, and we show empirically that including appropriate structure greatly improves the models, measured by the probability of generating test programs.
Review of Tissue Plasminogen Activator, Ischemic Stroke, and Potential Legal Issues (2008)

The use of tissue plasminogen activator in ischemic stroke is controversial. Many practicing physicians believe that its usefulness is established, while others, including professional specialty societies, are less sanguine. A review of the literature appears to show that the use of tissue plasminogen activator is efficacious and can result in highly improved outcomes for a majority of eligible patients. These findings may implicate important potential legal issues. Informed consent concerns and, potentially, medical malpractice claims may result, particularly in the context of evidence-based practice, pay for performance, and the currently limited use of tissue plasminogen activator for eligible patients.
Computer modeling for the occlusal surface of teeth (2002)

Modeling of the occlusal surface of teeth is an important problem in computer-aided design of dental restorations. The designed shape must fit the existing jaw articulation. Also, the design process must be fast to be practical in clinical applications. In this paper we present techniques for automatic adjustment of the occlusal surface of restorations based on the results of articulation simulation. The shape of restorations is changed to avoid interpenetrations with the opponent teeth during functional jaw movements. The 3-D space mapping method is used which guarantees the surface smoothness and preservation of the main topological features of the occlusal surface. To speedup calculations we use rasterizing graphics hardware for computationally involved collision detection between complex surfaces of teeth.
EEMCO guidance for the assessment of skin topography (1999)

Numerous factors can modify the visibility or the actual dimensions of the skin microrelief and wrinkles. To quantify these changes, several methods, including clinical and non-invasive ones, have been proposed. This article reviews the advantages et drawbacks of all of them and lists some experimental recommendations to make the results of studies using these methods, more reliable.
Randomised phase II trial of S-1 plus oxaliplatin vs S-1 in patients with gemcitabine-refractory pancreatic cancer (2015)

Although SOX showed an advantage in RR, it provided no significant improvement in PFS or OS compared with S-1 alone.
Polymer Architectures via Reversible Addition Fragmentation Chain Transfer (RAFT) Polymerization (2004)

Abstract Various versatile chain transfer agents (CTAs) have been synthesized for reversible addition fragmentation chain transfer (RAFT) polymerzation. Such CTAs have been used to modify hydroxyl containing materials and produce well‐controlled molecular architectures such as amphiphilic copolymer from poly (ethylene glycol), AB block copolymer consisting of a biodegradable segment, poly ( l ‐lactic acid) (PLLA) and grafted copolymers of poly (styrene), poly (methyl methacrylate) and poly (methyl acrylate) from cellulose.
Acamprosate (Calcium Acetylhomotaurinate) Enhances the N‐Methyl‐d‐Aspartate Component of Excitatory Neurotransmission in Rat Hippocampal CA1 Neurons In Vitro (1996)

The taurinate analog acamprosate (calcium acetylhomotaurinate) has received considerable attention in Europe for its ability to prevent relapse in abstained alcoholics. To determine the mechanism of acamprosate actions in the CNS, we superfused acamprosate onto rat hippocampal CA1 pyramidal neurons using an in vitro slice preparation. In current-and voltage-clamp recordings, acamprosate (100 to 100 microM) superfusion had little effect on resting membrane potential or input slope resistance. Acamprosate had no effect on Ca(2+)-dependent action potentials when tetrodotoxin was used to block Na+ spikes. In whole-cell voltage-clamp recordings, and in the presence of tetraethylammonium and Cs+ to block K+ channels, acamprosate had little effect on a Cd(2+)-sensitive inward current likely to be a high voltage-activated Ca2+ current. However, in both current- and voltage-clamp recordings, acamprosate significantly increased the N-methyl-D-aspartate (NMDA) component of excitatory postsynaptic potentials evoked by stimulation of Schaffer collaterals in the stratum radiatum, in the presence of the selective non-NMDA (R,S)-alpha-amino-3-hydroxy-5-methylisoxazole-4-proprionic acid kainate) glutamate receptor antagonist 6-cyano-7-nitro-quinoxaline-2,3-dione and the GABAA receptor antagonist bicuculline. Acamprosate had inconsistent or no effects on the stratum radiatum-evoked non-NMDA component of the excitatory postsynaptic potentials, in the presence of bicuculline and the NMDA antagonist DL-2-amino-5-phosphonovalerate. Acamprosate, on average, had little effect on the late inhibitory postsynaptic potentials thought to be mediated by GABAB receptors. In the presence of tetrodotoxin to block synaptic transmission, acamprosate dramatically increased inward current responses in most CA1 neurons to exogenous NMDA applied by pressure or superfusion, with reversal on washout of acamprosate. These data suggest that acamprosate may act postsynaptically to increase the NMDA component of excitatory transmission to hippocampal CA1 pyramidal neurons. Considering the known interaction of ethanol with NMDA receptors, this acamprosate modulation of NMDA receptor-mediated neurotransmission could provide a mechanism of action underlying the clinical efficacy of acamprosate.
Antiangiogenic Activity of Hypoxylonol C (2014)

Hypoxylonol C (1), isolated from the inedible mushroom Hypoxylon truncatum, exhibited inhibitory activities against the migration and tube formation of HUVECs. A cDNA microarray analysis was performed to investigate the target of hypoxylonol C (1) in HUVECs, and it was found that the genes related to cell cycle and adhesion were down-regulated. The down-regulation of mRNA levels of cell cycle and adhesion genes was confirmed by real-time RT-PCR. Cell cycle arrest and suppression of adhesion molecule expression might be plausible mechanisms of actions for the antiangiogenic activity of hypoxylonol C (1).
Screening and Improvement of an Anti-VEGF DNA Aptamer (2010)

To obtain an aptamer with a high affinity for vascular endothelial growth factor (VEGF), we focused on the receptor-binding domain (RBD) of VEGF as a target epitope. Three rounds of screening gave Vap7, which bound to the VEGF isoforms VEGF(121) and VEGF(165) with K(D) values of 1.0 nM and 20 nM, respectively. Moreover, Vap7 showed specificity within the VEGF family. Secondary structure predictions and circular dicrhoism suggested that Vap7 folds into a G-quadruplex structure. We obtained a mutant aptamer that contains only this region of the aptamer sequence. This truncated mutant (V7t1) bound to both VEGF(121) and VEGF(165) with K(D) values of 1.1 nM and 1.4 nM, respectively. Its sequence was 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3', and it appeared to form a G-quadruplex structure. We also produced an aptamer heterodimer consisting of our previously derived aptamer (del5-1), which binds to the heparin-binding domain of VEGF, linked to V7t1. The resulting heterodimer bound strongly to VEGF(165) with a K(D) value of 4.7 x 10(2) pM.
Multicolor Organic Light-Emitting Diodes Processed by Hybrid Inkjet Printing (1999)

Inkjet printing (IJP) technology is an attractive alternative for producing OLEDs, due to its low-cost, large-area processing, and multicolor addressing capabilities. The problems associated with this technique (pinhole film structure, uneven surfaces) have been overcome by use of the hybrid IJP technique. Here this technique is demonstrated to produce controllable patterning of red-green-blue OLEDs. The LEDs comprise bilayer structures of red and green dopants inkjet-printed onto a film of the blue-emitting semiconducting polymer poly(9-vinylcarbazole), the latter serving as the hole-transport layer.
Very Delayed Infarction after Mild Focal Cerebral Ischemia: A Role for Apoptosis? (1996)

The temporal evolution of cerebral infarction was examined in rats subjected to transient occlusion of both common carotid arteries and the right middle cerebral artery. After severe (90-min) ischemia, substantial right-sided cortical infarction was evident within 6 h and fully developed after 1 day. After mild (30-min) ischemia, no cortical infarction was present after 1 day. However, infarction developed after 3 days; by 2 weeks, infarction volume was as large as that induced by 90-min ischemia. These data suggest that infarction after mild focal ischemia can develop in a surprisingly delayed fashion. Some evidence of neuronal apoptosis was present after severe ischemia, but only to a limited degree. However, 3 days after mild ischemia, neurons bordering the maturing infarction exhibited prominent TUNEL staining, and DNA prepared from the periinfarct area of ischemic cortex showed internucleosomal fragmentation. Furthermore, pretreatment with 1 mg/kg cycloheximide markedly reduced infarction volume 2 weeks after mild ischemia. These data raise the possibility that apoptosis, dependent on active protein synthesis, contributes to the delayed infarction observed in rats subjected to mild transient focal cerebral ischemia.
In Vitro and In Vivo Comparison of Lymphocytes Transduced with a Human CD16 or with a Chimeric Antigen Receptor Reveals Potential Off-Target Interactions due to the IgG2 CH2-CH3 CAR-Spacer (2015)

The present work was designed to compare two mechanisms of cellular recognition based on Ab specificity: firstly, when the anti-HER2 mAb trastuzumab bridges target cells and cytotoxic lymphocytes armed with a Fc receptor (ADCC) and, secondly, when HER2 positive target cells are directly recognized by cytotoxic lymphocytes armed with a chimeric antigen receptor (CAR). To compare these two mechanisms, we used the same cellular effector (NK-92) and the same signaling domain (FcεRIγ). The NK-92 cytotoxic cell line was transfected with either a FcγRIIIa-FcεRIγ (NK-92(CD16)) or a trastuzumab-based scFv-FcεRIγ chimeric receptor (NK-92(CAR)). In vitro, the cytotoxic activity against HER2 positive target cells after indirect recognition by NK-92(CD16) was always inferior to that observed after direct recognition by NK-92(CAR). In contrast, and somehow unexpectedly, in vivo, adoptive transfer of NK-92(CD16) + trastuzumab but not of NK-92(CAR) induced tumor regression. Analysis of the in vivo xenogeneic system suggested that the human CH2-CH3 IgG2 used as a spacer in our construct was able to interact with the FcR present at the cell surface of the few NSG-FcR+ remaining immune cells. This interaction, leading to blockage of the NK-92(CAR) in the periphery of the engrafted tumor cells, stresses the critical role of the composition of the spacer domain.
Long‐term persistence of host cells detected by X‐chromosome gene‐based assay in patients undergoing gender‐mismatched hematopoietic stem cell transplantation (2005)

Using our recently developed human androgen receptor (HUMARA) gene-based chimerism assay, long-term chimerism was investigated in female patients who underwent hematopoietic stem cell transplantation (HCT) with cells from male donors. After restriction digestion of samples, we detected a small number of female-derived cells within a large population of male-derived cells, with a sensitivity from 0.1% to 0.05%. Chimerism was examined in four patients with myeloid malignancies: two patients with acute myeloid leukemia (AML) from myelodysplastic syndrome (MDS), and one patient each with AML M3 and AML M4. All patients underwent myeloablative conditioning regimens and exhibited good clinical results during a median follow-up period of 6.6 years (range, 3.4-7.5 years). Female-derived cells were detected throughout the entire follow-up period in all bone marrow samples, but they became undetectable in the peripheral blood samples of 3 patients. Moreover, the HUMARA band pattern suggests that these residual host cells were normal cells. This study confirms the usefulness of the HUMARA gene-based assay, which showed that patients undergoing HCT frequently show mixed chimerism (MC) for a long period, especially in bone marrow, although the possibility of contamination by host stromal cells cannot be excluded.
Phase I trial of iodine 131-labeled COL-1 in patients with gastrointestinal malignancies: influence of serum carcinoembryonic antigen and tumor bulk on pharmacokinetics. (1996)

131I-COL-1 is well tolerated, except for hematologic toxicity. These data suggest that patients with highly elevated circulating CEA levels and/or increased tumor bulk may clear 131I-labeled COL-1 more rapidly from the circulation and experience less myelosuppression.
Functional disassociation of the central and peripheral fatty acid amide signaling systems (2004)

Fatty acid amides (FAAs) constitute a large class of endogenous signaling lipids that modulate several physiological processes, including pain, feeding, blood pressure, sleep, and inflammation. Although FAAs have been proposed to evoke their behavioral effects through both central and peripheral mechanisms, these distinct signaling pathways have remained experimentally challenging to separate. Here, we report a transgenic mouse model in which the central and peripheral FAA systems have been functionally uncoupled. Mice were generated that express the principle FAA-degrading enzyme FAA hydrolase (FAAH) specifically in the nervous system (FAAH-NS mice) by crossing FAAH(-/-) mice with transgenic mice that express FAAH under the neural specific enolase promoter. FAAH-NS mice were found to possess wild-type levels of FAAs in the brain and spinal cord, but significantly elevated concentrations of these lipid transmitters in peripheral tissues. This anatomically restricted biochemical phenotype correlated with a reversion of the reduced pain sensitivity of FAAH(-/-) mice, consistent with the FAA anandamide producing this effect by acting on cannabinoid receptors in the nervous system. Interestingly, however, FAAH-NS mice still exhibited an antiinflammatory phenotype similar in magnitude to FAAH(-/-) mice, indicating that this activity, which was not blocked by cannabinoid receptor antagonists, was mediated by peripherally elevated FAAs. These data suggest that the central and peripheral FAA signaling systems regulate discrete behavioral processes and may be targeted for distinct therapeutic gain.
Treatment of Rat Arthritides with Clodronate-Containing Liposomes (1995)

Large multilamellar liposomes containing dichloro-methylene-bisphosphonate (clodronate; Clo), a bisphosphonate that becomes toxic when intracellularly concentrated, were used to therapeutically target macrophages (M phi) in rats with established adjuvant arthritis (AA; i.v. on days 10,11,12) or antigen-induced arthritis (AIA; i.v. or i.a. on 3 h, days 1,2). In established AA, i.v. injection of Clo-liposomes led to significant, long-lasting amelioration of clinical parameters, and to reduced destruction of the ankle joint even several weeks after termination of treatment. In the acute phase of established AIA, intravenous treatment induced transient clinical amelioration, but did not counteract joint destruction. I.a. treatment in AIA was ineffective. Systemic treatment with anti-M phi principles induces amelioration of both AA and AIA; the improvement appears more profound in AA, i.e., the model with a more systemic character. Preliminary data indicate that depletion of M phi occurs in the liver rather than in spleen, draining lymph nodes or synovial membrane. In addition, local treatment with the same principle is ineffective in AIA. Therefore, systemic elimination of M phi in different sites may be crucial for effective therapy of arthritis with anti-M phi agents.
Chemoenzymatic elaboration of monosaccharides using engineered cytochrome P450 BM3 demethylases (2009)

Polysaccharides comprise an extremely important class of biopolymers that play critical roles in a wide range of biological processes, but the synthesis of these compounds is challenging because of their complex structures. We have developed a chemoenzymatic method for regioselective deprotection of monosaccharide substrates using engineered Bacillus megaterium cytochrome P450 (P450(BM3)) demethylases that provides a highly efficient means to access valuable intermediates, which can be converted to a wide range of substituted monosaccharides and polysaccharides. Demethylases displaying high levels of regioselectivity toward a number of protected monosaccharides were identified using a combination of protein and substrate engineering, suggesting that this approach ultimately could be used in the synthesis of a wide range of substituted mono- and polysaccharides for studies in chemistry, biology, and medicine.
Resorbable plate-screw systems: clinical applications. (2005)

Owing to their improved polylactic acid/polyglycolic acid ratio resorbable plate-screw systems which contain varying compositions of polylactic acid and polyglycolic acid copolymers are ideal fixation materials used favourably in maxillofacial, craniofacial and orthopedic reconstructive surgery in that they make effective fixation and have further advantages such as biocompatibility, adequate biomechanical resistance against distraction and compression forces in the early postoperative period, longer dwelling time and elimination from the body through physiological routes without causing any foreign body reaction or significant sequaleae.
Bacteria-derived Peptidoglycans Constitute Pathogen-associated Molecular Patterns Triggering Innate Immunity in Arabidopsis (2007)

Pathogen-associated molecular pattern (PAMP)-triggered immunity constitutes the primary plant immune response that has evolved to recognize invariant structures of microbial surfaces. Here we show that Gram-positive bacteria-derived peptidoglycan (PGN) constitutes a novel PAMP of immune responses in Arabidopsis thaliana. Treatment with PGN from Staphylococcus aureus results in the activation of plant responses, such as medium alkalinization, elevation of cytoplasmic calcium concentrations, nitric oxide, and camalexin production and the post-translational induction of MAPK activities. Microarray analysis performed with RNA prepared from PGN-treated Arabidopsis leaves revealed enhanced transcript levels for 236 genes, many of which are also altered upon administration of flagellin. Comparison of cellular responses after treatment with bacteria-derived PGN and structurally related fungal chitin indicated that both PAMPs are perceived via different perception systems. PGN-mediated immune stimulation in Arabidopsis is based upon recognition of the PGN sugar backbone, while muramyl dipeptide, which is inactive in this plant, triggers immunity-associated responses in animals. PGN adds to the list of PAMPs that induce innate immune programs in both plants and animals. However, we propose that PGN perception systems arose independently in both lineages and are the result of convergent evolution.