gebhart/patrepeval huggingface dataset:
Neural Progenitor Cells Lack Immunogenicity and Resist Destruction as Allografts (2003)

Multipotent, self-renewing stem and progenitor cells isolated from the mammalian central nervous system (CNS) have been shown to survive as allografts following transplantation to sites throughout the neuraxis. However, studies of this type shed little light upon the immunologic properties of the cells themselves, primarily because little is learned about the intrinsic immunogenic properties of a cell when it is grafted into an immune-privileged site. We have therefore investigated the immunogenic and antigenic properties of CNS progenitor cells by grafting them into a conventional (i.e., non-immune-privileged) site, namely, beneath the kidney capsule. Our results indicate that allogeneic CNS progenitor cells survive at least 4 weeks in a conventional site, during which time they neither sensitize their hosts nor express detectable levels of major histocompatibility complex (MHC) class I or II. These in vivo data are in accord with flow cytometric results showing that CNS progenitor cells do not express MHC class I or class II, either at baseline or upon differentiation in 10% serum. Exposure to interferon gamma, however, reversibly upregulates expression of these key transplantation antigens. Together, these results reveal CNS progenitor cells to possess inherent immune privilege. Since CNS progenitor cell allografts were rejected beneath the kidney capsule following specific sensitization of the host, CNS progenitor cells were able to display alloantigens, albeit not in an immunogenic form.
Real-time force measurement in double wavelength optical tweezers (2016)

In optical tweezers, the trap stiffness varies across the sample area. To avoid this problem, the force measurement is often performed in a fixed place where the trap stiffness is well determined. However, for some experiments, bringing the sample to the fixed position is problematic. In this paper, we describe a precise and fast procedure for mapping the trap stiffness over the whole sample area. Such a map allows development of a real-time procedure for force measurement at any point of the sample area. The presented method is particularly suitable for measuring forces, for example, in living cells samples.
Protective Effects of Peroxisome Proliferator-Activated Receptor γ Ligand on Apoptosis and Hepatocyte Growth Factor Induction in Renal Ischemia-Reperfusion Injury (2007)

The numbers of cleaved caspase-3 and ssDNA positive cells were decreased in rats treated with troglitazone. The production of HGF mRNA and protein was most intense at 4 hr. The expression of PPAR-gamma and HGF was increased in the group treated with troglitazone compared with the control group. CONCLUSIONS.: Pretreatment of rats with the PPAR-gamma ligand troglitazone decreased apoptotic cell death in renal ischemia-reperfusion injury as a result of the induction of HGF.
Dimeric, trimeric and tetrameric complexes of immunoglobulin G fix complement (1980)

The binding of pure dimers, trimers and tetramers of randomly cross-linked non-immune rabbit immunoglobulin G to the first component and subcomponent of the complement system, C1 and C1q respectively, was studied. These oligomers possessed open linear structures. All three oligomers fixed complement with decreasing affinity in the order: tetramer, trimer, dimer. Complement fixation by dimeric immunoglobulin exhibited the strongest concentration-dependence. No clear distinction between a non-co-operative and a co-operative binding mechanism could be achieved, although the steepness of the complement-fixation curves for dimers and trimers was better reflected by the co-operative mechanism. Intrinsic binding constants were about 10(6)M-1 for dimers, 10(7)M-1 for trimers and 3 X 10(9)M-1 for tetramers, assuming non-co-operative binding. The data are consistent with a maximum valency of complement component C1 for immunoglobulin G protomers in the range 6-18. The binding of dimers to purified complement subcomponent C1q was demonstrated by sedimentation-velocity ultracentrifugation. Mild reduction of the complexes by dithioerythritol caused the immunoglobulin to revert to the monomeric state (S20,w = 6.2-6.5S) with concomitant loss of complement-fixing ability.
Synergistic Inhibition by β2-Agonists and Corticosteroids on Tumor Necrosis Factor-α –Induced Interleukin-8 Release from Cultured Human Airway Smooth-Muscle Cells (2000)

We have previously reported that human airway smooth-muscle (ASM) cells produce abundant interleukin (IL)-8, a major neutrophil chemoattractant involved in asthma exacerbations. Here, we tested the effects of the beta(2)-agonists salbutamol (Salbu) and salmeterol (Salme) on IL-8 release and tumor necrosis factor (TNF)-alpha-induced IL-8 release from ASM cells. We found that TNF-alpha strongly enhanced IL-8 release in a time- and concentration-dependent manner, whereas Salbu, Salme, the direct adenylyl cyclase activator forskolin (FSK), and the cyclic monophosphate (cAMP) analogue 8-bromoadenosine 3',5'-cAMP (8-Br-cAMP) alone weakly stimulated IL-8 release. TNF-alpha (10 ng/ml)-induced IL-8 release was markedly inhibited by the steroids dexamethasone (Dex) (0.1 to 10 microM) and fluticasone (Flut) (0.01 to 1 microM) but unaffected by Salbu, Salme, FSK, or 8-Br-cAMP. However, a combination of Dex (1 microM) or Flut (0.1 microM) with Salbu (10 microM), Salme (1 microM), FSK (10 microM), or 8-Br-cAMP (10 and 100 microM) significantly enhanced the inhibition by Dex or Flut alone. Experiments with KT5720, a selective inhibitor of cAMP-dependent protein kinase A; rolipram, a selective inhibitor of type IV phosphodiesterase; and ICI-118,551, a beta(2)-receptor antagonist, suggested that the synergistic inhibition was mediated by beta(2)-receptor in a cAMP-dependent manner. This novel synergistic interaction of beta(2)-agonists and steroids may partly explain the benefits that result when these agents are combined to treat asthma.
Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules (2003)

Nanoscale alpha-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson-Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5' versus 3' orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson-Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore.
Intraoperative radioimmunodetection of ovarian cancer using monoclonal antibody B72.3 and a portable gamma-detecting probe (1991)

To assess the value of radioimmunoguided surgery in the intraoperative detection of ovarian cancer, we used monoclonal antibody B72.3, radiolabeled with 125I, and a hand-held gamma-detecting probe in 13 women with ovarian cancer undergoing exploratory laparotomy. B72.3, which recognizes a tumor-associated glycoprotein, TAG 72, was injected 12-29 days preoperatively (intraperitoneally in four cases, intravenously in nine, and by both routes in one). Intraoperatively, the abdomen was surveyed with the probe and probe counts were correlated with biopsies and excised specimens studied by routine histologic stains. Probe counts were positive in four of seven evaluable patients with histologically confirmed disease. In three of these four patients, the probe detected cancer in specimens interpreted as normal on frozen histologic sections. The probe also identified microscopic cancer in the one patient who had no gross disease. The specificity of the probe was 70%. Preoperative computed tomography was normal in all patients, including those with tumors as large as 3 cm. This pilot study shows the ability of radioimmunoguided surgery to detect occult ovarian cancer.
Oncostatin M induces detachment and enhances the metastatic capacity of T-47D human breast carcinoma cells (2004)

5042 Oncostatin M (OSM), an IL-6 family cytokine, has previously been shown to inhibit the proliferation of several breast cancer cell lines in vitro. Our studies report additional effects of OSM treatment on the human breast carcinoma cell line T-47D. OSM treatment of T-47D cells for 1 to 3 days alters cell morphology from a normal epithelial phenotype to more mesenchymal phenotype. These changes are followed by a 250% increase in cell detachment after 5 to 8 days of OSM treatment. Detached aggregates of cells are viable and easily readhere to several extracellular matrix components. In addition, immunoblots of concentrated conditioned media collected from OSM-treated T-47D cells showed an increase in the expression of the proteases cathepsin D and cathepsin L, which have been implicated in metastasis. Importantly, OSM treated T-47D cells show an almost 300% increase in invasive capacity as measured by the Matrigel invasion chamber assay. Collectively, these data demonstrate that OSM induces a metastatic phenotype in T-47D cells in vitro, and suggest that OSM could enhance metastasis in vivo. Our results suggest that experimental therapeutic approaches utilizing OSM as a treatment for human breast cancer should proceed with caution, and that OSM itself may be a valid therapeutic target.
Reconstruction Quality and Spectral Content of an Electromagnetic Time-Domain Inversion Algorithm (2006)

A tomographic time-domain reconstruction algorithm for solving the inverse electromagnetic problem is described. The application we have in mind is dielectric breast cancer detection but the results are of general interest to the field of microwave tomography. Reconstructions have been made from experimental and numerically simulated data for objects of different sizes in order to investigate the relation between the spectral content of the illuminating pulse and the quality of the reconstructed image. We have found that the spectral content is crucial for a successful reconstruction. The work has further shown that when imaging objects with different scale lengths it is an advantage to use a multiple step procedure. Low frequency content in the pulse is used to image the large structures and the reconstruction process then proceed by using higher frequency data to resolve small scale lengths. Good agreement between the results obtained from experimental data and simulated data has been achieved.
IL-21 induces death of marginal zone B cells during chronic inflammation (2010)

Interleukin-2 (IL-2) and IL-21 share activities in the control of T- and B-cell maturation, proliferation, function, and survival. However, opposing roles for IL-2 and IL-21 have been reported in the development of regulatory T cells. To dissect unique, redundant, and opposing activities of IL-2 and IL-21, we compared T- and B-cell development and function in mice lacking both IL-2 receptor α (IL-2Rα) and IL-21R (double knockouts [DKO]) with single knockout and wild-type (WT) mice. Similarly to il2ra(-/-) mice, DKO showed reduced numbers of regulatory T cells and, consequently, hyper-activation and proliferation of T cells associated with inflammatory disease (ie, colitis), weight loss, and reduced survival. The absence of IL-2Rα resulted in overproduction of IL-21 by IFN-γ-producing CD4(+) T cells, which induced apoptosis of marginal zone (MZ) B cells. Hence, MZ B cells and MZ B-cell immunoglobulin M antibody responses to Streptococcus pneumoniae phosophorylcholine were absent in il2ra(-/-) mice but were completely restored in DKO mice. Our results highlight key roles of IL-2 in inhibiting IL-21 production by CD4(+) T cells and of IL-21 in negatively regulating MZ B-cell survival and antibody production.
Manipulation of plant metabolic pathways by transcription factors (2009)

Plant metabolites are produced through complex processes that include multiple enzymatic steps, branched pathways and regulation by a number of functionally redundant transcription factors. In addition, plants synthesize and accumulate each metabolite, especially secondary metabolites, in specific tissues and cells during development. Therefore, manipulation of both transcription factors that regulate enzymatic steps of a metabolic pathway (metabolic regulators) and/or that regulate cellular differentiation (developmental regulators) would be an effective strategy for controlling plant metabolites, quantitatively and qualitatively. In this review, we describe the advantages of using transcription factors for metabolic engineering in plants. Transcriptional activators and repressors, including the chimeric repressors generated by CRES-T, are useful tools for the genetic engineering of metabolic pathways. In addition, we propose that the use of both developmental regulators and plant tissue culture technology, in combination with metabolic regulators, would be an effective strategy to increase the productivity of metabolites. We summarize the strategies that have been applied for the detection of regulators and enzyme genes involved in metabolic pathways.
Hypermethylation of MCAM gene is associated with advanced tumor stage in prostate cancer (2008)

Our results suggest that MCAM promoter hypermethylation deserves further attention as a potential diagnostic prostatic DNA marker in human prostate cancer.
Agitation can Induce Differentiation of Human Pluripotent Stem Cells in Microcarrier Cultures (2010)

One of the factors that can impact human embryonic stem cell expansion in stirred microcarrier culture reactors is mechanical stress caused by agitation. Therefore, we have investigated the effects of agitation on human embryonic stem cell growth and expression of pluripotent markers. Agitation of HES-2 cell line in microcarrier cultures in stirred spinner and agitated six-well plates did not affect expression of pluripotent markers, cell viability, and cell doubling times even after seven passages. However, HES-3 cell line was found to be shear sensitive, showing downregulation of three pluripotent markers Oct-4, mAb 84, and Tra-1-60, and lower cell densities in agitated as compared with static cultures, even after one passage. Cell viability was unaffected. The HES-3-agitated cultures showed increased expression of genes and proteins of the three germ layers. We were unable to prevent loss of pluripotent markers or restore doubling times in agitated HES-3 microcarrier cultures by addition of five different known cell protective polymers. In addition, the human induced pluripotent cell line IMR90 was also shown to differentiate in agitated conditions. These results indicate that the effect of agitation on cell growth and differentiation is cell line specific. We assume that the changes in the growth and differentiation of the agitation-sensitive (HES-3) cell line do not result from the effect of shear stress directly on cell viability, but rather by signaling effects that influence the cells to differentiate resulting in slower growth.
Lignin Structural Modifications Resulting from Ethanol Organosolv Treatment of Loblolly Pine (2009)

Milled wood lignin samples from untreated Loblolly pine, post-ethanol organosolv pretreatment, and ethanol organosolv dissolved lignin were isolated and characterized by quantitative 13C and 31P nuclear magnetic resonance (NMR) spectroscopy. β-O-4 linkages are the predominant substructures present in lignin from the starting material, as well as after the pretreatment. During organosolv treatment of Loblolly pine, acid-catalyzed cleavage of β-O-4 linkages and ester bonds were the major mechanisms of lignin cleavage. This degradative pathway results in the formation of a dissolved ethanol organosolv lignin, which is more condensed and has a lower molecular weight than the starting lignin. The residual lignin isolated from the solid pretreated residue was also more condensed. Results from quantitative 13C and 31P NMR show that the residual and dissolved lignin fractions after pretreatment have a higher abundance of phenols and carboxylic acids and lower aliphatic carbon content and may be suitable as antioxidants or other value-added lignin products.
Effect of intravitreal hyaluronidase on the clearance of tritiated water from the vitreous to the choroid. (1985)

The rate of transfer of intravitreally injected tritiated water from the mid vitreous to the choroid is significantly increased after depolymerization of vitreous hyaluronic acid by injected hyaluronidase. The significance of this finding is discussed in relation to such conditions as retinal detachment and reattachment.
A Compact Optical See-Through Head-Worn Display with Occlusion Support (2005)

We are proposing an optical see-through head-worn display that is capable of mutual occlusions. Mutual occlusion is an attribute of an augmented reality display where real objects can occlude virtual objects and virtual objects can occlude real objects. For a user to achieve the perception of indifference between the real and the virtual images superimposed on the real environment, mutual occlusion is a strongly desired attribute for certain applications. This paper presents a breakthrough in display hardware from a mobility (i.e. compactness), resolution, and a switching speed based criteria. Specifically, we focus on the research that is related to virtual objects being able to occlude real objects. The core of the system is a spatial light modulator (SLM) and polarization-based optics which allow us to block or pass certain parts of a scene which is viewed through the head-worn display. An objective lens images the scene onto the SLM and the modulated image is mapped back to the original scene via an eyepiece. We are combining computer generated imagery with the modulated version of the scene to form the final image a user would see.
A SNP discovery method to assess variant allele probability from next-generation resequencing data (2009)

Accurate identification of genetic variants from next-generation sequencing (NGS) data is essential for immediate large-scale genomic endeavors such as the 1000 Genomes Project, and is crucial for further genetic analysis based on the discoveries. The key challenge in single nucleotide polymorphism (SNP) discovery is to distinguish true individual variants (occurring at a low frequency) from sequencing errors (often occurring at frequencies orders of magnitude higher). Therefore, knowledge of the error probabilities of base calls is essential. We have developed Atlas-SNP2, a computational tool that detects and accounts for systematic sequencing errors caused by context-related variables in a logistic regression model learned from training data sets. Subsequently, it estimates the posterior error probability for each substitution through a Bayesian formula that integrates prior knowledge of the overall sequencing error probability and the estimated SNP rate with the results from the logistic regression model for the given substitutions. The estimated posterior SNP probability can be used to distinguish true SNPs from sequencing errors. Validation results show that Atlas-SNP2 achieves a false-positive rate of lower than 10%, with an approximately 5% or lower false-negative rate.
Hemodynamic Consequences of Atrioventricular and Ventriculoatrial Pacing (1978)

The effect of atrial-ventricular versus ventricular pacing and contraction were studied in seven open-chest dogs. Cardiac output, left ventricular, left atrial, right atrial and pulmonary artery pressures were recorded. The right or left ventricular apical areas were consistently superior as ventricular pacing sites. Appearance of cannon A waves within the pre- or ejection period produced a significant decrease in left ventricular and systemic blood pressure, and cardiac output with a concomitant increase in right atrial, ventricular and pulmonary pressures. Prominent "v" waves were also observed during these periods. Reducing the basic driving cycle length from 400 to 300 msec caused a marked deterioration of all hemodynamic parameters with the appearance of mechanical alternans. Random VA conduction or ventricular pacing in the presence of complete AV and VA heart block appeared to offer a more favorable hemodynamic result than constant 1:1 VA conduction. It is concluded that maintenance of a physiologic AV interval permitting atrial contraction to appear outside of pre- or ejection period of ventricular systole is an important determinant or ventricular function during cardiac pacing.
Synthesis of Carbohydrate Methyl Phosphoramidates (2014)

A two-step route for introducing methyl phosphoramidate moieties onto carbohydrates is reported. The approach uses methyl pivolyl H-phosphonate as the phosphorylating reagent to produce an isolable carbohydrate H-phosphonate intermediate that is then oxidized by a Todd-Atherton reaction. The stability of the product methyl phosphoramidates was subsequently evaluated using various deprotection strategies.
Evidence Report on the Treatment of Pain in Cancer Patients (2004)

Pain associated with cancer is of widespread concern. We conducted a systematic review to evaluate the best available evidence on the efficacy of treatments of cancer-related pain. The sources used were MEDLINE, CancerLit, and the Cochrane Library from 1966 through April 2001, as well as bibliographies of meta-analyses and review articles. We selected randomized controlled trials (RCTs) reporting on cancer pain treatment. We recorded the study characteristics, patient and disease characteristics, treatment comparisons, outcome measures, and results. The methodological quality, applicability, and magnitude of treatment effect for each study were graded. We screened 24 822 titles and selected 213 RCTs to address specific questions. RCTs of cancer pain control often enroll few subjects, have low methodological quality, offer little detail about pain characteristics and mechanisms, and involve heterogeneous interventions and outcomes. Nonsteroidal anti-inflammatory drugs (NSAIDs), opioids, selected adjuvant medications, bisphosphonates, radionuclides, external radiation, palliative chemotherapy, and neurolytic celiac plexus block are each efficacious in relieving cancer pain. However, the retrieved RCTs indicate no difference in the analgesic efficacies of NSAIDs versus other NSAIDs, NSAIDs plus opioids versus NSAIDs alone, or NSAIDs versus opioids. Studies of adjuvant medications and behavioral therapies are too few and varied to synthesize. RCTs of the analgesic effects of corticosteroids were not retrieved in our review, although we did conduct supplemental evidence reviews concerning pain control in oral mucositis, acute herpes zoster, or postherpetic neuralgia. RCTs confirm the efficacy of diverse interventions in relieving cancer pain. The optimal initial and subsequent sequence of choices among analgesic drug types cannot be inferred from the retrieved RCTs. Patient preferences, the relative efficacy of different routes of drug administration, the side effects of analgesics, and the relation of pain control to quality of life have not been studied comprehensively. The quantity and quality of scientific evidence on cancer pain relief compare unfavorably with evidence related to treatment of other high-impact conditions, including cancer itself. One contributor to this gap is the heterogeneity of outcomes instruments employed: of 218 retrieved trials, there were 125 distinct pain outcomes assessed. In the current era of patient-centered care, improving the quality and combinability of trials on cancer pain relief should be a high research priority.