gebhart/patrepeval huggingface dataset:
Ironman Triathlon Recovery Enhanced By Dietary Supplementation (2007)

BACKGROUND: Protein/carbohydrate beverages have been used to promote immediate post‐exercise recovery, but longer‐term recovery strategies (days to weeks) are used less frequently. PURPOSE: We evaluated the effect of dietary supplementation on recovery and mood state following an Ironman‐distance triathlon. METHODS: Eighteen subjects were randomly assigned to Supplement (S, n=11) or Control (C, n=7). Subjects performed their “normal” post‐race recovery regimen alone (C) or with a morning (AM) and evening (PM) dietary supplement for 14 days following an Ironman‐distance triathlon (2.4 mile swim, 112 mile bike, 26.2 mile run). AM consisted of 5 herbal extracts (Cordyceps, Rhodiola, Eleuthero, Ashwagandha, and Eurycoma) and PM consisted of 8 nutrients (Glutamine, Leucine, Valine, Isoleucine, Papain, Bromelain, Beta‐sitosterol, and Citrus bioflavonoids). The Profile of Mood States (POMS) questionnaire was used to evaluate Tension, Depression, Anger, Vigor, Fatigue, Confusion and Global Mood State at baseline and 2‐weeks. Data were analyzed using unpaired t‐tests with significance set at p &lt; 0.05. RESULTS: S had significantly lower scores for Stress (‐21%, p=0.037), Tension (−54%, p=0.009), Depression (−64%, trend p=0.07), Anger (−62%, p=0.027), Fatigue (−53%, p=0.025) and Confusion (−67%, p=0.001) and higher scores for Vigor (+69%, p=0.001) and Global Mood (+29%, p=0.002) compared to C. CONCLUSIONS: Adequate recovery is important for athletes to support the demands of training and competition, but also for protection from overtraining, illness, and injury. These results strongly indicate that targeted dietary supplementation is effective for enhancing recovery following intense endurance exercise.
Prediction of Mortality in Patients with Cystic Fibrosis (1992)

Patients with cystic fibrosis should be considered candidates for lung transplantation when the FEV1 falls below 30 percent of the predicted value. Female patients and younger patients may need to be considered for transplantation at an earlier stage.
Cutting Edge: CD3 ITAM Diversity Is Required for Optimal TCR Signaling and Thymocyte Development (2017)

For the αβ or γδTCR chains to integrate extracellular stimuli into the appropriate intracellular cellular response, they must use the 10 ITAMs found within the CD3 subunits (CD3γε, CD3δε, and ζζ) of the TCR signaling complex. However, it remains unclear whether each specific ITAM sequence of the individual subunit (γεδζ) is required for thymocyte development or whether any particular CD3 ITAM motif is sufficient. In this article, we show that mice utilizing a single ITAM sequence (γ, ε, δ, ζa, ζb, or ζc) at each of the 10 ITAM locations exhibit a substantial reduction in thymic cellularity and limited CD4<sup>-</sup>CD8<sup>-</sup> (double-negative) to CD4<sup>+</sup>CD8<sup>+</sup> (double-positive) maturation because of low TCR expression and signaling. Together, the data suggest that ITAM sequence diversity is required for optimal TCR signal transduction and subsequent T cell maturation.
A surrogate hepatitis B virus antigenic epitope represented by a synthetic peptide and an internal image antiidiotype antibody. (1986)

The use of molecules that represent single, defined epitopes able to substitute for antigen (i.e. surrogate antigens) offers considerable advantages over the use of native antigen for the precise manipulation of the immune response. We have investigated the immunochemical characteristics of two types of surrogate hepatitis B surface antigen (HBsAg) epitopes: (a) linear and cyclical synthetic peptides representing amino acid residues 139-147, a hydrophilic region corresponding to part of the a determinant of the HBsAg, and (b) four monoclonal antiidiotypes raised against anti-HBs mAb, two of which behave as an internal image of an a determinant. Polyclonal anti-HBs antisera bound the monoclonal antiidiotypes with affinities of the order of 10(8)/M, and to the peptides with greater than 10-fold lower affinities. However, the levels of antibody in the polyclonal antisera for the peptides was greater than for the antiidiotypes. In inhibition RIA, the surrogate antigens show concordance in that the internal image antiidiotypes inhibit the binding of both monoclonal and polyclonal anti-HBs to the linear and cyclical 139-147 peptides. These results imply that surrogate antigens could indeed be useful as potential hepatitis vaccines, but while the antiidiotypes may stimulate B cells of higher affinity, they would react with a more restricted range of B cell reactivities than would the peptides. A future HBV vaccine may thus comprise a synthetic peptide such as cyclical 139-147 or a cluster of monoclonal internal image antiidiotypes.
Field Programmable Port Extender (FPX) User Guide (Version 2.2) (2002)

This manual summarizes how to insert the Field Programmable Port Extender (FPX) into the Washington University Gigabit Switch (WUGS), how to install the NCHARGE control software, how to initialize the system, and how to reprogram a user-defined module into the FPX over the network using the included web-based tools.
Nat Turner Rebellion (2009)

Nat Turner led the last of the great slave rebellions in the United States. In the dark of a summer morning in 1831, he set out with just six comrades. As they marched across Southampton County, Virginia, their ranks grew to about sixty, and an equal number of white people lay dead. The revolt was swiftly crushed but shook slavery in Virginia to its foundations.
The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides (2003)

The biological activity of siRNA seems to be influenced by local characteristics of the target RNA, including local RNA folding. Here, we investigated quantitatively the relationship between local target accessibility and the extent of inhibition of the target gene by siRNA. Target accessibility was assessed by a computational approach that had been shown earlier to be consistent with experimental probing of target RNA. Two sites of ICAM-1 mRNA predicted to serve as accessible motifs and one site predicted to adopt an inaccessible structure were chosen to test siRNA constructs for suppression of ICAM-1 gene expression in ECV304 cells. The local target-dependent effectiveness of siRNA was compared with antisense oligonucleotides (asON). The concentration dependency of siRNA-mediated suppression indicates a >1000-fold difference between active siRNAs (IC50 approximately 0.2-0.5 nM) versus an inactive siRNA (IC50 > or = 1 microM) which is consistent with the activity pattern of asON when relating target suppression to predicted local target accessibility. The extremely high activity of the siRNA si2B (IC50 = 0.24 nM) indicates that not all siRNAs shown to be active at the usual concentrations of >10-100 nM belong to this highly active species. The observations described here suggest an option to assess target accessibility for siRNA and, thus, support the design of active siRNA constructs. This approach can be automated, work at high throughput and is open to include additional parameters relevant to the biological activity of siRNA.
The effect of salicylates on the hemostatic properties of platelets in man (1968)

Ingestion of 1.5 g of aspirin, but not of sodium salicylate, produced a significant prolongation of the bleeding time in six normal male subjects when compared with the effects of a placebo. Similar differences in the effect of the two drugs on platelets was also observed. Aspirin ingestion resulted in impaired platelet aggregation by connective tissue and was associated with a decreased release of platelet adenosine diphosphate (ADP); sodium salicylate had no effect on these values. In vitro, incubation of platelet-rich plasma with an optimum aspirin concentration of 0.50 mmole/liter (0.045 mg/ml) inhibited both the adhesion of platelets to connective tissue and the release of ADP as well as the secondary wave of platelet aggregation produced with ADP or epinephrine; sodium salicylate had no effect on these reactions, which were also normal in patients with von Willebrand's disease. The inhibitory effect produced by ingesting a single 1.8 g dose of aspirin was detectable for 4-7 days at which time salicylate was no longer detectable in the blood, which suggested an irreversible effect on the platelet. Aspirin also inhibited the release of platelet adenosine triphosphate (ATP), but had no effect on the platelet surface charge, available platelet ATP or ADP, or the destruction of ADP by plasma ADPase. These studies lend further support to the hypothesis that ingestion of aspirin, in contrast to sodium salicylate, prolongs the bleeding time by inhibiting the release of platelet ADP, perhaps reflecting the findings in other cell systems which suggest that aspirin alters membrane permeability.
Expression of c-kit mRNA and protein during the differentiation of human hematopoietic progenitor cells. (1993)

To investigate how c-kit and c-kit ligand play a role in the function of hematopoietic stem cells, we determined the expression of c-kit in sorted human hematopoietic stem cells, CD34+CD33- cells and CD34+CD33+ cells. CD34+ cells constituted approximately 1% of the population of gated bone marrow cells and contained colony-forming cells. Two-color analysis by a fluorescence-activated cell sorter (FACS) revealed that about one-third to one-half of the total CD34+ cell population were positive for the CD33 antigen. To analyze the relative accumulation of c-kit mRNA in sorted cells, we used the reverse transcription-polymerase chain reaction (RT-PCR) method, followed by Southern blot analysis. There was a linear relationship between the amount of input RNA and products amplified in the range of 10(3) to 10(5) cells. Using this procedure, we carried out an analysis of c-kit mRNA expression in CD34+CD33-, CD34+CD33+, CD34-CD33+, and CD34-CD33- cells. Enhanced expression for c-kit mRNA was observed solely in CD34+CD33- cells. In contrast, flow cytometry shows that c-kit protein was expressed most abundantly in CD34+CD33+ cells. Colony-forming cells were generated on a human stromal cell layer for 5 weeks initiated with CD34+CD33- cells but not with CD34+CD33+ cells. During co-culture with stromal cells, CD34+CD33- cells differentiated into CD34+CD33+ cells. From these findings, it is concluded that CD34+CD33+ cells are direct progenies of CD34+CD33- cells. In this differentiation pathway, the expression of c-kit mRNA decreased and the c-kit protein increased.
Condensation reaction of 3,4‐dibenzoyl‐1‐methyl‐2,5‐diphenylpyrrole and ‐1‐phenylpyrazole with methylamine derivatives affording pyrrolo [3,4‐c]pyridine and 2H‐pyrazolo[3,4‐c]‐ and [4,3‐c]pyridines (1981)

Abstract The reaction of 3,4‐dibenzoyl‐1‐methyl‐2,5‐diphenylpyrrole ( 1 ) and ‐1‐phenylpyrazole ( 2 ) with methylamines ( 3a‐c ) afforded pyrrolo[3,4‐c]pyridine ( 4 ), and isomeric 2 H ‐pyrazolo[3,4‐ c ]pyridines ( 5a‐c ) and [4,3‐ c ]pyridines ( 6a‐c ), respectively.
Detection of Soluble Fibrin Monomer Complexes in Blood by Means of Protamine Sulphate Test (1968)

Summary In the present paper described is a simple test for detecting soluble fibrin monomer complexes (SFMC) in blood. The test consists in mixing 1% protamine sulphate with diluted oxalated plasma or serum and reading the optical density at 6190 Å. In experiments with dog plasma, enriched with soluble fibrin complexes, it was shown that OD read in PS test is proportional to the amount of fibrin recovered from the precipitate. It was found that SFMC level in plasma increases in rabbits infused intravenously with thrombin and decreases after injection of plasmin with streptokinase. In both cases PS precipitable protein in serum is elevated indicating enhanced fibrinolysis. In healthy human subjects the mean value of OD readings in plasma and sera were found to be 0.30 and 0.11, while in patients with coronary thrombosis they are 0.64 and 0.05 respectively. The origin of SFMC in circulation under physiological and pathological conditions is discussed.
Novel Plant-Microbe Rhizosphere Interaction Involving Streptomyces lydicus WYEC108 and the Pea Plant ( Pisum sativum ) (2002)

A previously undescribed plant-microbe interaction between a root-colonizing Streptomyces species, S. lydicus WYEC108, and the legume Pisum sativum is described. The interaction is potentially of great importance to the health and growth in nature of this nodulating legume. The root-colonizing soil actinomycete S. lydicus WYEC108 influences pea root nodulation by increasing root nodulation frequency, possibly at the level of infection by Rhizobium spp. S. lydicus also colonizes and then sporulates within the surface cell layers of the nodules. Colonization leads to an increase in the average size of the nodules that form and improves the vigor of bacteroids within the nodules by enhancing nodular assimilation of iron and possibly other soil nutrients. Bacteroid accumulation of the carbon storage polymer, poly-beta-hydroxybutyrate, is reduced in colonized nodules. Root nodules of peas taken from agricultural fields in the Palouse hills of northern Idaho were also found to be colonized by actinomycete hyphae. We hypothesize that root and nodule colonization is one of several mechanisms by which Streptomyces acts as a naturally occurring plant growth-promoting bacterium in pea and possibly other leguminous plants.
Vascular Tissue Engineering (2001)

The development of a tissue-engineered blood vessel substitute has motivated much of the research in the area of cardiovascular tissue engineering over the past 20 years. Several methodologies have emerged for constructing blood vessel replacements with biological functionality. These include cell-seeded collagen gels, cell-seeded biodegradable synthetic polymer scaffolds, cell self-assembly, and acellular techniques. This review details the most recent developments, with a focus on core technologies and construct development. Specific examples are discussed to illustrate both the benefits and shortcomings of each methodology, as well as to underline common themes. Finally, a brief perspective on challenges for the future is presented.
EBV Latent Membrane Proteins (LMPs) 1 and 2 as Immunotherapeutic Targets: LMP-Specific CD4+ Cytotoxic T Cell Recognition of EBV-Transformed B Cell Lines (2008)

The EBV-latent membrane proteins (LMPs) 1 and 2 are among only three viral proteins expressed in EBV-associated Hodgkin's lymphoma and nasopharyngeal carcinoma. Since these tumors are HLA class I and class II-positive, the LMPs could serve as both CD8+ and CD4+ T cell targets. In contrast to CD8 responses, very little is known about CD4 responses to LMPs. In this study, we describe CD4+ T cell clones defining four LMP1- and three LMP2-derived peptide epitopes and their restricting alleles. All clones produced Th1-like cytokines in response to peptide and most killed peptide-loaded target cells by perforin-mediated lysis. Although clones to different epitopes showed different functional avidities in peptide titration assays, avidity per se was a poor predictor of the ability to recognize naturally infected B lymphoblastoid cell lines (LCLs) expressing LMPs at physiologic levels. Some epitopes, particularly within LMP1, consistently mediated strong LCL recognition detectable in cytokine release, cytotoxicity, and outgrowth inhibition assays. Using cyclosporin A to selectively block cytokine release, we found that CD4+ T cell cytotoxicity is the key effector of LCL outgrowth control. We therefore infer that cytotoxic CD4+ T cells to a subset of LMP epitopes could have therapeutic potential against LMP-expressing tumors.
Surface Plasmon Resonance of Au Colloid-Modified Au Films:  Particle Size Dependence (1999)

The influence of colloid diameter on the surface plasmon resonance (SPR) response of a colloidal Au modified Au film is described. Adsorption of 30−59 nm diameter colloidal Au on the surface of a 47 nm thick Au film results in dramatic, size-dependent shifts in plasmon angle, minimum reflectance, and curve breadth. Each of these parameters is observed to increase with particle diameter and particle coverage, eventually reaching a plateau when the attenuation of the SPR curve is maximized. The angle of maximum change in reflectance is observed to be independent of particle size; thus, the reflectance at that angle is proposed as a method for quantifying the perturbation induced by a particular size and coverage of colloidal Au. These results are discussed in terms of the detection limits and dynamic range of colloidal Au-amplified SPR biosensing.
Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome (2018)

Pathology images capture tumor histomorphological details in high resolution. However, manual detection and characterization of tumor regions in pathology images is labor intensive and subjective. Using a deep convolutional neural network (CNN), we developed an automated tumor region recognition system for lung cancer pathology images. From the identified tumor regions, we extracted 22 well-defined shape and boundary features and found that 15 of them were significantly associated with patient survival outcome in lung adenocarcinoma patients from the National Lung Screening Trial. A tumor region shape-based prognostic model was developed and validated in an independent patient cohort (n = 389). The predicted high-risk group had significantly worse survival than the low-risk group (p value = 0.0029). Predicted risk group serves as an independent prognostic factor (high-risk vs. low-risk, hazard ratio = 2.25, 95% CI 1.34-3.77, p value = 0.0022) after adjusting for age, gender, smoking status, and stage. This study provides new insights into the relationship between tumor shape and patient prognosis.
Effect of Small-Molecule–Binding Affinity on Tumor Uptake In Vivo : A Systematic Study Using a Pretargeted Bispecific Antibody (2012)

Small-molecule ligands specific for tumor-associated surface receptors have wide applications in cancer diagnosis and therapy. Achieving high-affinity binding to the desired target is important for improving detection limits and for increasing therapeutic efficacy. However, the affinity required for maximal binding and retention remains unknown. Here, we present a systematic study of the effect of small-molecule affinity on tumor uptake in vivo with affinities spanning a range of three orders of magnitude. A pretargeted bispecific antibody with different binding affinities to different DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid)-based small molecules is used as a receptor proxy. In this particular system targeting carcinoembryonic antigen, a small-molecule-binding affinity of 400 pmol/L was sufficient to achieve maximal tumor targeting, and an improvement in affinity to 10 pmol/L showed no significant improvement in tumor uptake at 24 hours postinjection. We derive a simple mathematical model of tumor targeting using measurable parameters that correlates well with experimental observations. We use relations derived from the model to develop design criteria for the future development of small-molecule agents for targeted cancer therapeutics.
Synthesis of Furanophane Derivatives Through [8 + 2]‐Cycloaddition of Dienylisobenzofurans and Alkynes. (2004)

The coupling of various dienylisobenzofurans with dimethyl acetylenedicarboxylate (DMAD) has been examined. In most cases, this reaction proceeds via [8+2]-cycloaddition to afford furan-bridged decatetraene ring systems. The major competing reaction pathway is [4+2]-cycloaddition between DMAD and the isobenzofuran nucleus. Isobenzofuran intermediates were generated using either a chromium carbene-based method or an acid-catalyzed method.
Anoikis in the Cardiovascular System (2003)

Anoïkis is defined as programmed cell death induced by the loss of cell/matrix interactions. Adhesion to structural glycoproteins of the extracellular matrix is necessary for survival of the differentiated adherent cells in the cardiovascular system, including endothelial cells, smooth muscle cells, fibroblasts, and cardiac myocytes. Adhesion is also a key factor for the differentiation of mesenchymal stem cells. In particular, fibronectin is considered a factor of survival and differentiation for many adherent cells. Adhesion generates cell tensional integrity (tensegrity) and repression of apoptotic signals, whereas detachment has the opposite effect. Anoïkis plays a physiological role by regulating cell homeostasis in tissues. However, anoïkis can also be involved in pathological processes, as illustrated by the resistance to anoïkis in cancer and its enhancement in degenerative tissue remodeling. Extracellular mediators of anoïkis include matrix retraction, leading to loss of tensegrity in fibroblasts, pharmacological disengagement of integrins by RGD-like peptides and fragments of fibronectin, and focal adhesion disassembly by fragments of thrombospondin, plasminogen activator-1, and high-molecular-weight kininogen. In addition to binding of the RGD peptide by integrins, the engagement of the heparin binding sites of adhesive glycoproteins with glycosaminoglycans on the cell surface is also involved in the prevention of cell detachment-induced apoptosis. Proteases able to degrade adhesive glycoproteins, such as fibronectin, induce anoïkis of vascular adherent cells. Active proteases can either be secreted directly by inflammatory cells, as elastase and cathepsin G by polymorphonuclear leukocytes, chymase and tryptase by mast cells, and granzymes by lymphocytes, or generated from circulating zymogens by activation in close contact with the cells. This is the case for the pericellular conversion of plasminogen to plasmin, which degrades fibronectin and induces anoïkis of smooth muscle cells. Involvement of proteases has also been proposed in the apoptotic response of cultured adherent cells to serum starvation. Anoïkis is probably involved in pathological remodeling of cardiovascular tissues, including cardiac myocyte detachment in heart failure, deendothelialization and plaque rupture in atherosclerosis, and smooth muscle cell disappearance in aneurysms and varicose veins. The absence of cell adhesion and growth resulting from cleavage of adhesive proteins also represents a major impediment to cellular healing, including the absence of cell recolonization of proteolytically injured tissue and the low efficacy of cell transplantation. However, the exact role of anoïkis in cardiovascular pathologies remains to be further defined.
Assembly of Type IV Collagen (2000)

Type IV collagen includes six genetically distinct polypeptides named alpha1(IV) through alpha6(IV). These isoforms are speculated to organize themselves into unique networks providing mammalian basement membranes specificity and inequality. Recent studies using bovine and human glomerular and testis basement membranes have shown that unique networks of collagen comprising either alpha1 and alpha2 chains or alpha3, alpha4, and alpha5 chains can be identified. These studies have suggested that assembly of alpha5 chain into type IV collagen network is dependent on alpha3 expression where both chains are normally present in the tissue. In the present study, we show that in the lens and inner ear of normal mice, expression of alpha1, alpha2, alpha3, alpha4, and alpha5 chains of type IV collagen can be detected using alpha chain-specific antibodies. In the alpha3(IV) collagen-deficient mice, only the expression of alpha1, alpha2, and alpha5 chains of type IV collagen was detectable. The non-collagenous 1 domain of alpha5 chain was associated with alpha1 in the non-collagenous 1 domain hexamer structure, suggesting that network incorporation of alpha5 is possible in the absence of the alpha3 chain in these tissues. The present study proves that expression of alpha5 is not dependent on the expression of alpha3 chain in these tissues and that alpha5 chain can assemble into basement membranes in the absence of alpha3 chain. These findings support the notion that type IV collagen assembly may be regulated by tissue-specific factors.