gebhart/patrepeval huggingface dataset:
T-Cell Activation Marker Expression on Tumor-Infiltrating Lymphocytes As Prognostic Factor in Cutaneous Malignant Melanoma (2004)

The central role of T cells in antitumor immunity is well established. However, tumor progression, often seen in the presence of substantial lymphocytic infiltration, suggests that these T cells are not capable of mounting an effective immune response to control tumor growth. Evidence has accumulated that T lymphocytes infiltrating human neoplasms are functionally defective, incompletely activated, or anergic. Therefore, when characterizing the immune competent cells within lymphoid infiltrates of tumors, it is important to assess their activation state. We investigated the expression of two T-cell activation markers, interleukin 2 receptor alpha (CD25) and OX40 (CD134), by immunohistochemistry in primary cutaneous melanoma samples of 76 patients and analyzed it in relation to tumor stage and tumor progression (>5 years follow-up), as well as to patients' survival. We found that the degree of infiltration by CD25(+) and intratumoral OX40(+) lymphocytes showed a tendency to decrease in thicker melanomas. The frequency of samples with high numbers of peritumoral CD25(+) and OX40(+) cells was significantly lower (P = 0.0009 and P = 0.0087, respectively) in melanomas developing distant visceral metastases, compared with nonmetastatic or lymph node metastatic tumors. For both activation markers studied, high peritumoral densities were associated with longer survival by univariate analysis (P = 0.0028 and P = 0.0255 for CD25 and OX40, respectively), whereas peritumoral OX40(+) lymphocyte infiltration had an impact on survival also in multivariate analysis (P = 0.035). The results suggest that the presence of lymphocytes expressing the T-cell activation markers CD25 or OX40 shows correlation with tumor progression as well as with patients' survival in cutaneous malignant melanoma.
The PETT series, a new class of potent nonnucleoside inhibitors of human immunodeficiency virus type 1 reverse transcriptase (1995)

To identify the minimal structural elements necessary for biological activity, the rigid tricyclic nucleus of the known human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) inhibitor tetrahydroimidazobenzodiazepinthione was subjected to systematic bond disconnection to obtain simpler structures. A rational selection and testing of modeled analogs containing these potential pharmacophoric moieties led to the discovery of a new series of nonnucleoside inhibitors of RT. The lead compound of this new PETT series of nonnucleoside RT inhibitors, N-(2-phenylethyl)-N'-(2-thiazolyl)thiourea (LY73497), was found to inhibit HIV-1 but not HIV-2 or simian immunodeficiency virus in cell culture at micromolar concentrations. This derivative was also found to inhibit HIV-1 RT. Through an integrated effort involving synthesis and molecular modeling, compounds with nanomolar potency against HIV-1 in cell culture were developed. In these studies, LY300046-HCl was identified as a potent nonnucleoside inhibitor of HIV-1 RT possessing favorable pharmacokinetic properties.
Characterization of transposon mutants of biofilm-producing Staphylococcus epidermidis impaired in the accumulative phase of biofilm production: genetic identification of a hexosamine-containing polysaccharide intercellular adhesin (1994)

The primary attachment to polymer surfaces followed by accumulation in multilayered cell clusters leads to production of Staphylococcus epidermidis biofilms, which are thought to contribute to virulence in biomaterial-related infections. We isolated Tn917 transposon mutants of biofilm-producing S. epidermidis 13-1, which were completely biofilm negative. In pulsed-field gel electrophoresis no obvious deletions of the mutants were noted. The Tn917 insertions of mutants M10 and M11 were located on different EcoRI fragments but on identical 60-kb SmaI and 17-kb BamHI chromosomal fragments. Linkage of transposon insertions of mutants M10 and M11 with the altered phenotype was demonstrated by phage transduction, whereas the several other mutants apparently represented spontaneous variants. In a primary attachment assay with polystyrene spheres, no significant difference between any of the mutants and the wild type could be detected. Cell clustering as an indication of intercellular adhesion, which is a prerequisite for accumulation in multilayered cell clusters, was not detected with any mutant. These results demonstrate that the mutants were impaired in the accumulative phase of biofilm production. Mutants M10 and M11 did not produce detectable amounts of a specific polysaccharide antigen (D. Mack, N. Siemssen, and R. Laufs, Infect. Immun. 60:2048-2057, 1992), whereas substantially reduced amounts of antigen were produced by the spontaneous variants. Hexosamine was determined as the major specific component of the antigen enriched by gel filtration of biofilm-producing S. epidermidis 1457 because almost no hexosamine was detected in material prepared from the isogenic biofilm-negative transductant 1457-M11, which differentiates the antigen from other S. epidermidis polysaccharide components. Our results provide direct genetic evidence for a function of the antigen in the accumulative phase of biofilm production by S. epidermidis by mediating intercellular adhesion.
Lysophosphatidic acid: mitogen and motility factor (2003)

LPA (lysophosphatidic acid), the simplest of al glycerophospholipids, is a potent inducer of cell proliferation, migration and survival. It does so by activating its cognate G-protein-coupled receptors, four of which have been identified. LPA receptors couple to at least three distinct G-proteins and thereby activate multiple signal transduction pathways, particularly those initiated by the small GTPases Ras, Rho and Rac. Our recent work has shown that LPA signals Rac activation via the Tiam1 GDP/GTP exchange factor and thereby stimulates cell migration. Here we discuss recent progress in our understanding of LPA action.
EXTENDING THE UML FOR MODELLING VARIABILITY FOR SYSTEM FAMILIES (2002)

The process of modelling and developing commonality and variability for system families should be supported by suitable methods and notations. The object-oriented methods and their notations, which are used at present, focus on the development of a single system at a time.
Comparison of performance and attitude in traditional and computer conferencing classes (1991)

(1991). Comparison of performance and attitude in traditional and computer conferencing classes. American Journal of Distance Education: Vol. 5, No. 3, pp. 51-64.
Luminescence Resonance Energy Transfer in Heterodinuclear LnIII Complexes for Sensing Biologically Relevant Anions (2010)

Abstract Dinuclear lanthanide(III) complexes of the macrocycles 1,4‐bis[1‐4,7,10‐ tris(carbamoylmethyl)‐1,4,7,10‐tetraazacyclododecane]‐ m ‐xylene ( 1 ) and 1,3‐bis[1‐4,7,10‐tris(carbamoylmethyl)‐1,4,7,10‐tetraazacyclododecane]‐ p ‐xylene ( 2 ) with Ln III = Eu III , Tb III were prepared. Studies using direct excitation ( 7 F 0 → 5 D 0 ) europium(III) luminescence spectroscopy show that several anions including phosphate, methylphosphate, double‐stranded DNA, a DNA hairpin loop, and fluoride bind to both Eu III centers in Eu 2 ( 1 ) in solutions at pH 7.0, 0.100 M NaNO 3 . Recovered luminescence lifetime data is consistent with replacement of water ligands by these anions. There are distinct changes in the relative intensities of Eu III emission peaks for complexes of Eu 2 ( 1 ) and Eu 2 ( 2 ) with phosphate, fluoride, carbonate, and phosphate ester ligands. This suggests that the Eu III dinuclear complexes show promise as ratiometric sensors for these anions. In contrast, the emission peak ratios for the Tb 2 ( 1 ) and Tb 2 ( 2 ) complex show a lower response upon binding of each anionic ligand. Luminescence resonance energy transfer (LRET) studies with mixed Eu III /Nd III complexes show that the phosphate complexes of Ln 2 ( 1 ) or Ln 2 ( 2 ) both have Ln III –Ln III internuclear distances of 7.7 ± 0.9 Å and the methylphosphate complexes of Ln 2 ( 1 ) and Ln 2 ( 2 ) have internuclear distances of 7.8 ± 0.6 and 8.0 ± 0.7 Å, respectively. LRET experiments also show the two lanthanide ion centers in Ln 2 ( 2 ) are 8.4 ± 0.5 Å apart when bound to GC rich duplex DNA. None of the other anions (carbonate, fluoride, DNA hairpins) form complexes that show measurable energy transfer between the lanthanide ions, which is consistent with intranuclear distances &gt;8 Å.
Relationship Between the Axenic Phenotype and Sensitivity to -Aminocarboxylic Acids in Dictyostelium discoideum (1978)

A previous suggestion that sensitivity to ω-aminocarboxylic acids in Dictyostelium discoideum is associated with the ability to grow axenically has been re-evaluated using new axenic strains and axenic derivatives of strain ax3 recombinant for linkage group II. It is now shown that the major gene for ω-aminocarboxylic acid sensitivity, designated oaaA., is not allelic to previously described axenic loci axeA and axeB, but that oaaA is closely linked to, or allelic with a third axenic gene axeC found in strains ax2 and ax3. The axeC phenotype is rapid growth in axenic medium. The oaaA locus is located on linkage group II. Genetic evidence suggests that the strains ax2 and ax3 now in existence share a common genetic background and may not represent independent isolates from the wild-type strain nc4. Studies with 14C-labelled ϵ-aminocaproic acid show that sensitivity to ω-aminocarboxylic acids is correlated with increased myxamoebal permeability to these compounds.
Human cells infected with retrovirus vectors acquire an endogenous murine provirus (1990)

A 5.2-kilobase mouse RNA is expressed in human cells following infection with recombinant retroviruses propagated in mouse NIH 3T3 cells as psi-2 pseudotypes. This RNA is transcribed from a defective mink cell focus-forming provirus and copackaged into virions and integrated into human target cell DNA at a frequency comparable to that of the recombinant retrovirus genome.
The gatekeeper effect of epithelial-mesenchymal transition regulates the frequency of breast cancer metastasis. (2003)

When carcinoma cells metastasize, they change their phenotype to enhance motility. Cells making this switch selectively express S100A4, a p53-associated, calcium-binding protein known in the fibroblast literature as fibroblast-specific protein-1 (FSP1). FSP1 normally acts as a conversion signal for the local formation of tissue fibroblasts by epithelial-mesenchymal transition. We describe here a novel connection between the process of fibroblast development and the acquisition of a metastatic phenotype in genetically engineered mice with mammary carcinoma. More frequent lung metastases were observed in naïve recipients given purified populations of green fluorescent protein (GFP)(+) tumor cells harvested from PyV-mT x FSP1(+/+.GFP) F1 mice compared with GFP(-) tumor cells (P < or = 0.01), where GFP expression is under the control of the FSP1 promoter. The expression of GFP in these metastases reversibly attenuates with the establishment of secondary tumor nodules. Reduced numbers of metastases were also observed in PyV-mT x FSP1(GFP/GFP) F1 mice carrying null alleles for FSP1 (P < or = 0.04) and in PyV-mT x FSP1.Delta TK(+) F1 mice rescued with nucleoside analogues while expressing thymidine kinase under the control of the FSP1 promoter (P < or = 0.01). We propose that epithelial-mesenchymal transition associated with the expression of FSP1 in tumor cells has a functional role in determining the latency of tumor dispersion and may be a convenient therapeutic target for controlling a key initiating event in metastatic progression.
Immobilized enzyme electrodes for glucose determination for the artificial pancreas. (1983)

Immobilized enzymes are useful in the development of techniques for analytical chemistry measurements, primarily because of the specificity of enzymes for given substrates. In the case of glucose an in vivo assay is needed for closed loop operation of an artificial pancreas insulin delivery system. Several enzymatic methods are available for in vitro determinations of glucose, but only two or three of these methods hold any promise of adaptation for in vivo use. The most promising enzymatic approaches include the use of immobilized glucose oxidase in conjunction with 1) an oxygen electrode to give an amperometric output or 2) a reference electrode to give a potentiometric output. The use of glucose oxidase or other D-glucose-specific enzymes in conjunction with sensitive thermistors to measure the heat of reaction may also be a feasible method. The two most promising approaches are described in terms of their feasibility for continuous measurement of blood glucose levels in vivo without the necessity of withdrawing body fluids for the assay.
Gene injection into canine myocardium as a useful model for studying gene expression in the heart of large mammals. (1993)

We have investigated the regulated expression of genes injected into the heart of large mammals in situ. Reporter constructs using the chloramphenicol acetyltransferase gene under the control of muscle-specific beta-myosin heavy chain (beta-MHC) or promiscuous (mouse sarcoma virus) promoters were injected into the canine myocardium. There was a linear dose-response relation between the level of gene expression and the quantity of plasmid DNA injected between 10 and 200 micrograms per injection site. The level of reporter gene expression did not correlate with the amount of injury imposed on the cardiac tissue. There was no regional variation in expression of injected reporter genes throughout the left ventricular wall. By use of both the mouse sarcoma virus and a muscle-specific beta-MHC promoter, reporter gene expression was one to two orders of magnitude greater in the heart than in skeletal muscle. Expression in the left ventricle was threefold higher than in the right ventricle. Chloramphenicol acetyltransferase activity was detected at 3, 7, 14, and 21 days after injection, with maximal expression at 7 days after injection. Statistical analysis of coinjection experiments revealed that coinjection of a second gene construct (Rous sarcoma virus-luciferase) is useful in the control of transfection efficiency in vivo. Furthermore, using reporter constructs containing serial deletions of the 5' flanking region of the beta-MHC gene, we performed a series of experiments that demonstrate the utility of this model in mapping promoter regions and identifying important regulatory gene sequences in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)
Analysis of human blood serum using the off‐line coupling of capillary isoelectric focusing to matrix‐assisted laser desorption/ionization time of flight mass spectrometry (2005)

Off-line coupling of capillary IEF (CIEF) with matrix-assisted laser desorption/ionization mass spectrometry was utilized for the analysis of human blood serum. Serum proteins were initially separated by CIEF, and fractions of the isoelectric separation were eluted sequentially to a MALDI-TOF MS sample target. During pressure elution of the CIEF sample, voltage was maintained across the capillary system utilizing a sheath flow arrangement to minimize band broadening induced by the laminar flow field. Both pI and mass information were obtained from the complex biological sample, similar to traditional 2-DE techniques, and the platform was faster (hours versus days), more automatable, and simpler than 2-DE. The volume of raw sample present in the actual analysis was approximately 100 nL, making this technique well suited for very rare specimens. Additionally, the speed and simplicity of the technology make it an attractive technique for performing initial comparative analyses of complex samples.
Positive selection of mouse NK1+ T cells by CD1-expressing cortical thymocytes. (1995)

Mouse NK1+ T cells constitute a subset of alpha/beta TCR+ T cells that specialize in the rapid production of cytokines, in particular IL-4, and may promote the differentiation of Th2-type CD4 T cells. Their TCRs, like those of a homologous subset of human T cells, use an invariant TCR alpha chain and were recently shown to be specific for the beta 2-microglobulin-associated, MHC class I-like CD1 molecules, which are encoded outside the MHC. In contrast to mainstream thymocytes, which recognize their positively selecting MHC ligand on thymic epithelial cells, positive selection of NK1+ T cells requires their CD1 ligand to be expressed on bone marrow-derived cells. To investigate the nature of the bone marrow-derived cell involved, chimeric mice were constructed with tissues from normal, SCID, and MHC-deficient mice, so that CD1 could be selectively expressed by different subsets of bone marrow-derived cells in the thymus. CD1 expression was also directly assessed using an anti-CD1 mAb, and a CD1-specific T cell hybridoma. The results suggest that immature (CD4+8+ double-positive) cortical thymocytes are the source of CD1 presentation for positive selection of NK1+ T cells.
Evaluation of cimetidine (tagamet). An antagonist of hydrochloric acid secretion. (1977)

Cimetidine, a potent H2-receptor antagonist, has been introduced for the treatment of various conditions associated with acid peptic digestion in the gastrointestinal tract. Preliminary results are encouraging. Adverse reactions do not appear to be substantial; however, the effect of long-term use has yet to be ascertained.
2,7,12,17‐Tetrapropylporphycene—Counterpart of Octaethylporphyrin in the Porphycene Series (1987)

The title compound 1 and its nickel complex fulfill all that was hoped for: Substitution of porphycene with four propyl groups leads (as in the case of porphyrins) to increased solubility and crystallizability. 1 is distinguished by strong NH…N hydrogen bridges and by NH tautomerism. The nickel complex has the expected properties.
Naloxone Induced Micturition in Unanesthetized Paraplegic Cats (1983)

In chronic spinal cats 2 to 10 weeks after transection of the spinal cord at the lower thoracic level (T12-T13), the administration of naloxone, an opiate antagonist, (32-500 micrograms./kg. i.p.), stimulated micturition. The total quantity of urine released after administration of naloxone ranged from 10 to 70 per cent, (mean 39 per cent) of the initial bladder volume. The response to the drug occurred 5 to 10 minutes after injection and was characterized by repeated periodic expulsion of small quantities of urine (5 to 10 ml.) which coincided with a pattern of hind-limb movement which resembled walking behavior. The effects of naloxone persisted for about 1 hour. The motor activity following administration of naloxone was dependent upon activation of bladder afferents since it did not occur when the bladder was empty. Naloxone also facilitated the release of urine induced by stimulation of somatic afferents. With repeated administration of naloxone, tolerance developed which was evident for several days. These observations suggest that an endogenous opiate may have a tonic inhibitory role in regulation of micturition. Pharmacologic manipulation of this putative inhibitory mechanism may facilitate management of neurogenic bladder dysfunction.
Estimation of a Spherical-Head Model from Anthropometry (2001)

An optimal spherical-head model is derived from the high-frequency interaural time difference (ITD) of a population of 25 subjects. Analysis demonstrates that the optimal sphere results in very small lateral angle errors, except near the interaural poles. The spherical-head model is then estimated using the anthropometry of the subjects, based on simple and robust empirical predictive equations. Such a customization greatly decreases objective angular errors that occur when a generic model is used.
An Electrochemically Actuated Micro Dosing System With Improved Dosing Control (1999)

Abstract In this contribution a micromachined electrochemically-actuated micro dosing system is presented, which accurately can manipulate fluids in microsystems in the nanoliter range. The driving force to actively dispense liquids is provided by the electrochemical generation of gas bubbles (hydrogen and oxygen) by the electrolysis of an electrolyte. As these bubbles expand, they indirectly drive liquid out of a liquid filled reservoir, which is in hydraulic contact with the electrolyte in the bubble reservoir. The dosing system consists basically of a micromachined channel/reservoir structure in silicon, realized by dry reactive ion etching (DRIE). On top of this silicon fluidic board, a Pyrex® cover is bonded on which a set of electrodes is structured. These electrodes are applied for the generation of gas bubbles and at the same time, to measure the impedance of the gas/electrolyte mixture that is formed after bubble generation. It will be shown that this measured impedance reflects the gas bubble fraction in the bubble reservoir and that this parameter can be applied in determining the dosed amount of fluid. Besides the integrated sensor/actuator electrodes, measures have been taken to reduce the catalytic back reaction from the hydrogen oxygen gas mixture to water, as have been observed in the past.
Detection of antibodies against SARS-Coronavirus using recombinant truncated nucleocapsid proteins by ELISA. (2008)

Severe acute respiratory syndrome (SARS) is a lifethreatening emerging respiratory disease caused by the coronavirus, SARS-CoV. The nucleocapsid (N) protein of SARS-CoV is highly antigenic and may be a suitable candidate for diagnostic applications. We constructed truncated recombinant N proteins (N1 [1-422 aa], N2 [1- 109 aa], and N3 [110-422 aa]) and determined their antigenicity by Western blotting using convalescent SARS serum. The recombinants containing N1 and N3 reacted with convalescent SARS serum in Western blotting. However, the recombinant with N2 did not. In ELISA using N1 or N3 as the antigens, positive results were observed in 10 of 10 (100%) SARS-CoV-positive human sera. None of 50 healthy sera gave positive results in either assay. These data indicate that the ELISA using N1 or N3 has high sensitivity and specificity. These results suggest that the middle or C-terminal region of the SARS N protein is important for eliciting antibodies against SARS-CoV during the immune response, and ELISA reactions using N1 or N3 may be a valuable tool for SARS diagnosis.
Periostin and lung diseases: Recent advances and molecular structure modeling (2010)

Periostin is overexpressed in many epithelial malignant cancers. Although there were some reviews on the function of periostin related to a variety of cancers, a specific review on lung cancers is not found so far. Therefore, our brief review outlines the recent advances of periostin roles in the development of lung cancers/diseases and analyzes the potential value of periostin as a therapeutic target and diagnostic signal for lung cancer. We first of all searched for previous literature on a representative set of online databases, and outlined the works on periostin expression and lung cancers. We modeled the 3D homologous structure of human periostin based on computational prediction techniques. The resulting model passed the examination of a protein quality check. The fifteen most conserved sites were identified and forty-one active binding sites were detected, which can serve as potential targets for lung cancer therapy.
Acne analysis, grading and computational assessment methods: an overview (2011)

Semi-automated or automated methods based on computational imaging techniques should be devised for acne grade assessment.