gebhart/patrepeval huggingface dataset:
MUC1 and the MUCs: A Family of Human Mucins with Impact in Cancer Biology (2004)

Mucins represent a family of glycoproteins characterized by repeat domains and a dense O-glycosylation. During the last two decades, the gene and peptide structures of various mucins as well as their glycosylation states were partly elucidated. Characteristic tumor-associated alterations of the expression patterns and glycosylation profiles were observed in biochemical, immunochemical, and histological studies and are discussed in the light of efforts to use the most prominent member in this family, MUC1, as a tumor target in anti-tumor strategies. Within this context the present review, focusing on MUC1, describes recent work on the regulation of mucin biosynthesis by cytokines and hormones, the role of mucins in cell adhesion, and their interaction with the immune system. Important aspects of clinical diagnostics based on mucin antigens are discussed, including the application of tumor serum assays and the significance of numerous studies revealing correlations between the expression of peptide cores or mucin-associated carbohydrates and clinicopathological parameters like tumor progression and prognosis.
Physiological role of an endoperoxide in human platelets: hemostatic defect due to platelet cyclo-oxygenase deficiency. (1975)

The endoperoxide prostaglandin G2 (PGG2) induced platelet aggregation as well as the platelet release reaction (release of ADP and serotonin) when added to human platelet-rich plasma. Formation of a metabolite of PGG2 [8-(l-hydroxy-3-oxopropyl)-9,12L-dihydroxy-5,10-heptadecadienoic acid] and a lipoxygenase product [12L-hydroxy-5,8,10,14-eicosatetraenoic acid] accompanied the release reaction caused by aggregating agents such as collagen, ADP, epinephrine, and thrombin. Indomethacin inhibited the release reaction and PGG2 formation induced by these agents but had no effect on PGG2-induced release reaction. The aggregating effect of PGG2 was abolished by furosemide, which is a competitive inhibitor of ADP-induced primary aggregation. These data indicate that the aggregating effect of PGG2 is due to release of ADP and that PGG2 synthesis is required for induction of the release reaction by various aggregating agents. A subject with a hemostatic defect due to abnormal release mechanism [decreased aggregation with epinephrine (second wave) and collagen and normal platelet ADP] had a deficiency of the cyclo-oxygenase that catalyzes formation of PGG2. Normal aggregation and release reaction were obtained with added PGG2. Ii is concluded that the endoperoxide (PGG2) is essential in normal hemostasis because of its role in initiating the release reaction required for aggregation by collagen and the second wave of aggregation caused by, e.g., ADP.
A Cyclopentane, Cyclopentene and Cyclopentanone Annulation Methodology (1984)

Abstract The chemistry derived from the dienolates of 1,2-dicarboxylic acid esters is described. New methods for preparing cyclopentane, cyclopentene and cyclopentanone rings affixed to the diesters are discussed.
Replication of herpes simplex virus type 1 in macrophages from resistant and susceptible mice (1979)

Studies were carried out to determine whether the in vitro capacity of adherent peritoneal cells to replicate herpes simplex virus type 1 (HSV-1) might correlate with the in vivo susceptibility of mice genetically resistant, moderately susceptible, or very susceptible to HSV-1 infection. Unstimulated and proteose peptone-stimulated monolayers restricted viral replication when infected immediately, but replicated HSV-1 when infected after 3 to 7 days of culture. Macrophages from resistant C57Bl/6 mice restricted HSV-1 replication significantly better than cells from susceptible mice. This function did not segregate with resistance, since macrophages from resistant F1 mice failed to restrict HSV-1 replication. Induction of peritoneal exudate cells with thioglycolate yielded cells capable of replicating HSV-1 when infected immediately after plating and after 4 days of culture.
Thiol–ene “click” reactions and recent applications in polymer and materials synthesis: a first update (2014)

This contribution serves as an update to a previous review (<italic>Polym. Chem.</italic>2010,<bold>1</bold>, 17–36) and highlights recent applications of thiol–ene ‘click’ chemistry as an efficient tool for both polymer/materials synthesis as well as modification.
Double‐blind Randomized Controlled Trial of Intranasal Dexmedetomidine Versus Intranasal Midazolam as Anxiolysis Prior to Pediatric Laceration Repair in the Emergency Department (2016)

Intranasal dexmedetomidine is an alternative anxiolytic medication to intranasal midazolam for pediatric laceration repairs, performing similarly in our study, except that patients who received dexmedetomidine had less anxiety at the time of positioning for procedure.
The role of intramuscular lipid in insulin resistance (2003)

There is interest in how altered lipid metabolism could contribute to muscle insulin resistance. Many animal and human states of insulin resistance have increased muscle triglyceride content, and there are now plausible mechanistic links between muscle lipid accumulation and insulin resistance, which go beyond the classic glucose-fatty acid cycle. We postulate that muscle cytosolic accumulation of the metabolically active long-chain fatty acyl CoAs (LCACoA) is involved, leading to insulin resistance and impaired insulin signalling or impaired enzyme activity (e.g. glycogen synthase or hexokinase) either directly or via chronic translocation/activation of mediators such as a protein kinase C (particularly PKC theta and epsilon ). Ceramides and diacylglycerols (DAGs) have also been implicated in forms of lipid-induced muscle insulin resistance. Dietary lipid-induced muscle insulin resistance in rodents is relatively easily reversed by manipulations that lessen cytosolic lipid accumulation (e.g. diet change, exercise or fasting). PPAR agonists (both gamma and alpha) also lower muscle LCACoA and enhance insulin sensitivity. Activation of AMP-activated protein kinase (AMPK) by AICAR leads to muscle enhancement (especially glycolytic muscle) of insulin sensitivity, but involvement of altered lipid metabolism is less clear cut. In rodents there are similarities in the pattern of muscle lipid accumulation/PKC translocation/altered insulin signalling/insulin resistance inducible by 3-5-h acute free fatty acid elevation, 1-4 days intravenous glucose infusion or several weeks of high-fat feeding. Recent studies extend findings and show relevance to humans. Muscle cytosolic lipids may accumulate either by increased fatty acid flux into muscle, or by reduced fatty acid oxidation. In some circumstances muscle insulin resistance may be an adaptation to optimize use of fatty acids when they are the predominant available energy fuel. The interactions described here are fundamental to optimizing therapy of insulin resistance based on alterations in muscle lipid metabolism.
Introduction of α(1,2)‐fucosyltransferase and its effect on a‐Gal epitopes in transgenic pig (1996)

Abstract: Hyperacute rejection (from pig to human) is thought to result from activation of complement initiated by the binding of host natural antibodies to α‐galactosyl (α‐Gal) epitopes of donor endothelial cells. However, α‐Gal epitope shares a common precursor with H antigen in humans. This means that H antigens as well as α‐Gal epitopes are synthesized in a competitive manner by different enzymes. We thought that it would be possible to convert α‐Gal epitopes into H antigens by introducing cDNA of α(1,2)‐fucosyltransferase (α1–2FT) into porcine cells, and so, pig embryos were microinjected with αl‐2FT cDNA. Transgenic pigs that carried α1–2FT were thus established. Cytotoxicity of fibrocytes derived from skin of transgenic pig was measured by 51 Cr release assay, which showed that H antigen‐expressing cells were significantly resistant to a challenge with human sera. These experiments indicate that our method provides a new strategy which contributes to a successful discordant xenotransplantation.
Syntheses of Negative Photochromic Crowned Spirobenzopyrans (2000)

Abstract Two synthetic routes to negative photochromic spirobenzopyrans bearing a monoazacrown moiety at the 8-position were described and compared. Method B gives much higher total yield than method A.
Age at Onset Curves of Retinitis Pigmentosa (2008)

The age at onset curves are quite simple and useful tools that facilitate counseling at an RP clinic. Without them, the recurrence risk would be misleading.
[Expression of programmed cell death 4 and its clinicopathological significance in human pancreatic cancer]. (2005)

Expression of PDCD4 protein is low in human pancreatic cancer and is correlated with the differentiation levels of human pancreatic cancer. PDCD4 may play an important role in the occurrence and development of pancreatic carcinomas.
Genetic control of rheumatoid factor production in the mouse Role of Genes Linked to the Immunoglobulin Heavy Chain Locus and to the Major Histocompatibility Complex (1983)

The influence of Igh-1 and H-2 linked genes on the production of IgG2a-specific rheumatoid factors (RF) by 129/Sv mice was examined. Heterozygous animals carrying the 129 alleles, H-2b and Igh-1a, and either H-2k, H-2a, or Igh-1b (but not Igh-1d or Igh-1e) had considerably reduced RF levels. In contrast, Igh-1b linked genes failed to suppress RF production by MRL/MpJ-lpr mice. This lack of suppression was linked to the lymphoproliferation trait characteristic of these animals.
The Mechanism of Cell Interaction and Response on Decellularized Human Amniotic Membrane: Implications in Wound Healing. (2007)

ACELAGRAFT™ (Celgene Cellular Therapeutics, Cedar Knolls, NJ) was developed as a decellularized and dehydrated human amniotic membrane product (DDHAM). The product has demonstrated potential as a wound healing product with several ongoing preclinical and clinical studies in the area of acute and chronic ulcers. Although the mechanism of action of such a decellularized product has not been examined, a detailed study of the ability of fibroblasts to interact with DDHAM and subsequent cellular responses are presented. These studies indicate that the composition of DDHAM is that of an extracellular matrix (ECM)-like material with high collagen content, retaining key bioactive molecules, such as fibronectin, laminin, glycosaminoglycans (GAGs), and elastin. No cytokines or growth factors were identified as one might expect in a nondecellularized amniotic membrane product. Cell assays show that fibroblasts can recognize fibronectin in DDHAM and bind to it via typical integrin-fibronectin interactions. Fibroblasts secrete fibronectin and can actively assemble the soluble fibronectin into a complex extracellular matrix on DDHAM. Fibroblasts are also stimulated by DDHAM to secrete key proinflammatory(IL-1 and IL-6) and chemotactic cytokines or chemokines (proand IL-8) involved in regulating and enhancing wound repair processes. Microarray gene expression studies on fibroblasts bound to DDHAM show increased expression of key wound healing cytokines. Together, these studies provide insight into the mechanisms by which DDHAM may augment the wound healing process.
A Systematic Assessment of Mitochondrial Function Identified Novel Signatures for Drug-Induced Mitochondrial Disruption in Cells (2014)

Mitochondrial perturbation has been recognized as a contributing factor to various drug-induced organ toxicities. To address this issue, we developed a high-throughput flow cytometry-based mitochondrial signaling assay to systematically investigate mitochondrial/cellular parameters known to be directly impacted by mitochondrial dysfunction: mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species (ROS), intracellular reduced glutathione (GSH) level, and cell viability. Modulation of these parameters by a training set of compounds, comprised of established mitochondrial poisons and 60 marketed drugs (30 nM to 1mM), was tested in HL-60 cells (a human pro-myelocytic leukemia cell line) cultured in either glucose-supplemented (GSM) or glucose-free (containing galactose/glutamine; GFM) RPMI-1640 media. Post-hoc bio-informatic analyses of IC50 or EC50 values for all parameters tested revealed that MMP depolarization in HL-60 cells cultured in GSM was the most reliable parameter for determining mitochondrial dysfunction in these cells. Disruptors of mitochondrial function depolarized MMP at concentrations lower than those that caused loss of cell viability, especially in cells cultured in GSM; cellular GSH levels correlated more closely to loss of viability in vitro. Some mitochondrial respiratory chain inhibitors increased mitochondrial ROS generation; however, measuring an increase in ROS alone was not sufficient to identify mitochondrial disruptors. Furthermore, hierarchical cluster analysis of all measured parameters provided confirmation that MMP depletion, without loss of cell viability, was the key signature for identifying mitochondrial disruptors. Subsequent classification of compounds based on ratios of IC50s of cell viability:MMP determined that this parameter is the most critical indicator of mitochondrial health in cells and provides a powerful tool to predict whether novel small molecule entities possess this liability.
Synthesis of 2-R-1,3-dioxanes, derivatives of functionally substituted aldehydes of vanillin series (2013)

By the condensation of substituted aldehydes of vanillin series with 1,3-propanediol in boiling benzene in the presence of sulfo cation exchanger FIBAN K-1 as catalyst functionally 2-R-substituted 1,3-dioxanes were synthesized.
EP Component Identification and Measurement by Principal Components-Analysis (1995)

Between the acquisition of Evoked Potential (EP) data and their interpretation lies a major problem: What to measure? An approach to this kind of problem is outlined here in terms of Principal Components Analysis (PCA). An important second theme is that experimental manipulation is important to functional interpretation. It would be desirable to have a system of EP measurement with the following characteristics: (1) represent the data in a concise, parsimonous way; (2) determine EP components from the data without assuming in advance any particular waveforms for the components; (3) extract components which are independent of each other; (4) measure the amounts (contributions) of various components in observed EPs; (5) use measures that have greater reliability than measures at any single time point or peak; and (6) identify and measure components that overlap in time. PCA has these desirable characteristics. Simulations are illustrated. PCA's beauty also has some warts that are discussed. In addition to discussing the usual two-mode model of PCA, an extension of PCA to a three-mode model is described that provides separate parameters for (1) waveforms over time, (2) coefficients for spatial distribution, and (3) scores telling the amount of each component in each EP. PCA is compared with more traditional approaches. Some biophysical considerations are briefly discussed. Choices to be made in applying PCA are considered. Other issues include misallocation of variance, overlapping components, validation, and latency changes.
A high-precision camera operation parameter measurement system and its application to image motion inferring (2001)

Information about camera operations such as zoom, focus, pan, tilt and dollying is significant not only for efficient video coding, but also for content-based video representation. In this paper we describe a high-precision camera operation parameter measurement system and apply it to image motion inferring. First, we outline the implemented system which is designed to provide camera operation parameters with a high precision required for image coding applications. Second, we calibrate the camera lens to determine its exact optical properties, A pin-hole camera model with the 2nd order radial lens distortion and a two-image calibration technique are employed. Finally, we use the pan, tilt and zoom parameters measured by the system to infer image motion. The experimental results show that the inferred motion coincides with the actual motion very closely. Compared to the motion analysis techniques that estimate camera motion from video sequences, our approach does not suffer from ambiguity, thus can provide reliable and accurate image global motion. The obtained motion can be applied to image mosaicing, moving object segmentation, object-based image coding, etc.
Requirements for selective recruitment of Ets proteins and activation of mb-1/Ig- gene transcription by Pax-5 (BSAP) (2003)

Pax-5, a member of the paired domain family of transcription factors, is a key regulator of B lymphocyte-specific transcription and differentiation. A major target of Pax-5-mediated activation is the mb-1 gene, which encodes the essential transmembrane signaling protein Ig-alpha. Pax-5 recruits three members of the Ets family of transcription factors: Ets-1, Fli-1 and GABPalpha (with GABPbeta1), to assemble ternary complexes on the mb-1 promoter in vitro. Using the Pax-5:Ets-1:DNA crystal structure as a guide, we defined amino acid requirements for transcriptional activation of endogenous mb-1 genes using a novel cell-based assay. Mutations in the beta-hairpin/beta-turn of the DNA-binding domain of Pax-5 demonstrated its importance for DNA sequence recognition and activation of mb-1 transcription. Mutations of amino acids contacting Ets-1 in the crystal structure reduced or blocked mb-1 promoter activation. One of these mutations, Q22A, resulted in greatly reduced mb-1 gene transcript levels, concurrent with the loss of its ability to recruit Fli-1 to bind the promoter in vitro. In contrast, the mutation had no effect on recruitment of the related Ets protein GABPalpha (with GABPbeta1). These data further define requirements for Pax-5 function in vivo and reveal the complexity of interactions required for cooperative partnerships between transcription factors.
Optimizing OSPF/IS-IS weights in a changing world (2002)

A system of techniques is presented for optimizing open shortest path first (OSPF) or intermediate system-intermediate system (IS-IS) weights for intradomain routing in a changing world, the goal being to avoid overloaded links. We address predicted periodic changes in traffic as well as problems arising from link failures and emerging hot spots.
The Watershed Transformation Applied to Image Segmentation (1992)

Image segmentation by mathematical morphology is a methodology based upon the notions of watershed and homotopy modification. This paper aims at introducing this methodology through various examples of segmentation in materials sciences, electron microscopy and scene analysis.
The RIN: an RNA integrity number for assigning integrity values to RNA measurements (2006)

Our results show the importance of taking characteristics of several regions of the recorded electropherogram into account in order to get a robust and reliable prediction of RNA integrity, especially if compared to traditional methods.
Culm Strength of Barley (1989)

Grass culms are known to differ in breaking strength, but there is little physicochemical data to explain the response. The fourth internode of four brittle and two nonbrittle barley (Hordeum vulgare L.) strains were used for physical and chemical studies of culm strength. Inner and outer culm diameters of brittle strains (3.6 +/- 0.2 and 5.0 +/- 0.1 millimeters) were not significantly different from those of nonbrittle strains (3.9 +/- 0.2 and 5.2 +/- 0.2 millimeters). Maximum bending stress, at which the culm was broken, was 192 +/- 34 g/mm(2) for brittle and 490 +/- 38 g/mm(2) for nonbrittle strains. Wall thickness and cell dimensions of epidermal, sclerenchyma, and parenchyma cells were measured in culm cross sections. The area of cell wall per unit cell area for each tissue was significantly correlated with the maximum bending stress (r = 0.93 for epidermis, 0.90 for sclerenchyma, and 0.84 for parenchyma). Cell walls of brittle culms had 6 to 64% as much cellulose content as those of nonbrittle culms. Maximum bending stress correlated significantly with cellulose content of the cell walls (r = 0.93), but not with the contents of noncellulosic compounds. The lower cellulose content of the brittle culm was significantly correlated with brittleness.
Evaluation of cooling methods for laser dermatology (2000)

Both spray and contact cooling provide efficient skin cooling. The choice of cooling method depends on other factors such as the target depth, cost, safety, and ergonomic factors.
GM-CSF and IL-4 Stimulate Antibody Responses in Humanized Mice by Promoting T, B, and Dendritic Cell Maturation (2012)

Engraftment of human hematopoietic stem cells into immunodeficient mice that lack T cells, B cells, and NK cells results in reconstitution of human blood lineage cells, especially B cells, in the recipient mice. However, these humanized mice do not make any significant level of IgG Ab in response to Ag stimulation. In this study, we show that in humanized mice, B cells are immature, and there is a complete deficiency of CD209(+) (DC-SIGN) human dendritic cells. These defects can be corrected by expression of human GM-CSF and IL-4 in humanized mice. As a result, these cytokine-treated humanized mice produced significant levels of Ag-specific IgG after immunization, including the production of neutralizing Abs specific for H5N1 avian influenza virus. A significant level of Ag-specific CD4 T cell response was also induced. Thus, we have identified defects in humanized mice and devised approaches to correct these defects such that the platform can be used for studying Ab responses and to generate novel human Abs against virulent pathogens and other clinically relevant targets.
Myocardial Wall Thickness and Left Ventricular Geometry in Hypertensives Relationship With Insulin (1997)

In hypertensive patients the presence of left ventricular (LV) hypertrophy has been associated with a more severe degree of insulin resistance. Whether myocardial wall thickness or LV geometry are associated with a different degree of insulin resistance is still unknown in essential hypertensives. For this reason 26 men with new diagnosed essential hypertension were enrolled. All patients underwent echocardiographic examination and euglycemic hyperinsulinemic glucose clamp combined with indirect calorimetry. According to LV mass and relative wall thickness data, all patients were categorized in four groups: 1) patients with a normal geometric LV pattern (n = 8) (PAT = 0); 2) patients with concentric remodeling LV mass (n = 8) (PAT = 1); 3) patients with eccentric LV hypertrophy (n = 3) (PAT = 2); and 4) patients with concentric LV hypertrophy (n = 7) (PAT = 3). All groups were similar for anthropometric characteristics. Patients with normal echocardiographic LV pattern (PAT = 0) had higher whole body glucose disposal (WBGD), oxidative and nonoxidative glucose metabolism, and lower lipid oxidation than patients with abnormal echocardiographic LV patterns (PAT = 1 to 3). Nevertheless, no significant differences among the groups with abnormal echocardiographic patterns were found. After controlling for age, body mass index (BMI), waist/hip ratio (WHR), and mean arterial blood pressure, only sum of the wall thickness was significantly correlated with fasting plasma insulin (r = -0.38, P < .05), WBGD (r = - 0.50, P < .009), and NOGM (r = - 0.48, P < .02). In multivariate analysis, a model made by age, BMI, WHR, systolic and diastolic blood pressure, and WBGD explained 38% of the echocardiographic pattern variability. In this model, WBGD (P < .02) was significantly and independently associated with echocardiographic patterns explaining 19% of the echocardiographic pattern variability. In conclusion, our data demonstrate that in arterial hypertension hyperinsulinemia/insulin resistance mainly affects myocardial wall thickness, whereas only a trivial association with LV geometry occurs.