gebhart/patrepeval huggingface dataset:
Mr 26,000 antigen of Schistosoma japonicum recognized by resistant WEHI 129/J mice is a parasite glutathione S-transferase. (1986)

Mice of the inbred strain 129/J bred at this Institute (WEHI 129/J) are relatively resistant to chronic infection with the parasitic helminth Schistosoma japonicum. In contrast to more permissive mouse strains such as BALB/c, the WEHI 129/J mice are high responders to a Mr 26,000 adult worm antigen designated Sj26. Cloned cDNAs corresponding to Sj26 have been identified in a S. japonicum phage lambda gt11 amp3 expression library, and their nucleotide sequences have been deduced. The predicted amino acid sequence of the antigen specified by these cDNAs shows striking homology with class mu isozymes of mammalian glutathione S-transferases (RX:glutathione R-transferase, EC 2.5.1.18). Extracts of adult worms contain glutathione S-transferase activity, and affinity chromatography of enzyme activity on glutathione columns leads to the purification of a Mr 26,000 molecule that comigrates with Sj26. Although vaccination studies in mice with a beta-galactosidase-Sj26 fusion protein from Escherichia coli are encouraging, more immunogenic preparations of the antigen are likely to be required to establish the utility of Sj26 as a model vaccine.
Infection with Human Immunodeficiency Virus Type 1 Upregulates DNA Methyltransferase, Resulting in De Novo Methylation of the Gamma Interferon (IFN-γ) Promoter and Subsequent Downregulation of IFN-γ Production (1998)

The immune response to pathogens is regulated by a delicate balance of cytokines. The dysregulation of cytokine gene expression, including interleukin-12, tumor necrosis factor alpha, and gamma interferon (IFN-gamma), following human retrovirus infection is well documented. One process by which such gene expression may be modulated is altered DNA methylation. In subsets of T-helper cells, the expression of IFN-gamma, a cytokine important to the immune response to viral infection, is regulated in part by DNA methylation such that mRNA expression inversely correlates with the methylation status of the promoter. Of the many possible genes whose methylation status could be affected by viral infection, we examined the IFN-gamma gene as a candidate. We show here that acute infection of cells with human immunodeficiency virus type 1 (HIV-1) results in (i) increased DNA methyltransferase expression and activity, (ii) an overall increase in methylation of DNA in infected cells, and (iii) the de novo methylation of a CpG dinucleotide in the IFN-gamma gene promoter, resulting in the subsequent downregulation of expression of this cytokine. The introduction of an antisense methyltransferase construct into lymphoid cells resulted in markedly decreased methyltransferase expression, hypomethylation throughout the IFN-gamma gene, and increased IFN-gamma production, demonstrating a direct link between methyltransferase and IFN-gamma gene expression. The ability of increased DNA methyltransferase activity to downregulate the expression of genes like the IFN-gamma gene may be one of the mechanisms for dysfunction of T cells in HIV-1-infected individuals.
Variation in Marginal Bract Trichome Density in Upland Cotton (2007)

Elimination or reduction of trichomes around the margins of bracts should improve the cleaning efficiency of cotton (Gossypium hirsutum L.) lint. The objective of the study was to establish sampling protocols for measuring marginal bract trichome density by examining variation over fruiting positions of the cotton plant, sampling time, cultivars, and environments. To determine variation of bract and leaf trichome density, plants of six contrasting cultivars in two environments were evaluated. To determine variation in bract trichome density over time, bracts of three contrasting cultivars were sampled from three canopy sites on three dates from two years. To determine variation in bract trichome density over cultivars and environments, bracts were evaluated for multiple cultivars at multiple sites over four years. Bract trichome density tended to increase as leaf trichome density increased and to decline with canopy age. Significant interactions involving sympodial position indicated that bracts should be sampled from the same position. The first-position is suggested. Interactions involving nodes became non-significant by dropping the highest and lowest nodes. Bract trichome density declined with older canopy sites and later sample dates, but variation among cultivars was relatively consistent over locations and years. Although cultivars varied significantly, none of the cultivars had glabrous bracts. A significant cultivar by location interaction in one year became non-significant by dropping a highly stressed location. These data indicate that bract samples should be collected from full-sized, mid-canopy, first-position bolls soon after flower ing ceases and that bract trichome density can be adequately characterized by sampling bracts at one test site. L
Formation of plasma membrane domains in rat hepatocytes and hepatoma cell lines in culture (1988)

In vivo, proteins of the hepatocyte plasma membrane are asymmetrically distributed, making it possible to distinguish a sinusoidal, a lateral and a canalicular domain. The conditions that determine hepatocyte plasma membrane polarity have been investigated in vitro, using three monoclonal antibodies directed against integral membrane proteins, which were characteristic of each domain. The localization of the three antigens was studied by immunolabelling of hepatocytes isolated from adult rat liver, primary monolayer cultures and rat hepatoma cell lines. When hepatocytes were isolated, the three antigens spread over the entire cell surface. The lateral antigen redistributed at lateral sites as soon as cell-cell contacts were established, 4 h after the beginning of primary culture. The sinusoidal and canalicular antigens became asymmetrically distributed after 48 h of primary culture, after the formation of bile canaliculus-like structures. In most of the hepatoma lines studied, the three antigens were expressed, except that the canalicular antigen was fully expressed in differentiated clones only. The lateral antigen was always distributed on the contiguous membranes of clustered hepatoma cells, whereas the sinusoidal and canalicular antigens were localized on the entire plasma membrane. However, in a few cells of some clones in which bile canaliculus-like structures were observed, the canalicular membranes were strongly labelled only with the canalicular antibody. In the absence of bile canalicular formations, in both primary culture and cell lines, the canalicular antigen and, to a lesser extent, the sinusoidal antigen accumulated in the Golgi apparatus, suggesting that their transport to the cell surface was altered in the absence of a bile pole. These results show that in hepatic cells, polarization of the plasma membrane is determined by: (1) the existence of cell-cell contacts, which is correlated with the domain-specific localization of the lateral antigen; and (2) the formation of bile canaliculi, which would trigger the development of an asymmetrical distribution of the sinusoidal and canalicular antigens.
Some clinical aspects in chronic autoimmune thyroiditis associated with thyroid differentiated cancer. (2012)

The coexistence of HT with DTC represents a clinical reality with yet unknown significance. The difficulty of diagnosis imposes the corroboration of different types of investigations. The best diagnostic accuracy seems to be offered by thyroid US and thyroid cytological investigation.
Automated model-based calibration of imaging spectrographs (2012)

Hyper-spectral imaging has gained recognition as an important non-invasive research tool in the field of biomedicine. Among the variety of available hyperspectral imaging systems, systems comprising an imaging spectrograph, lens, wideband illumination source and a corresponding camera stand out for the short acquisition time and good signal to noise ratio. The individual images acquired by imaging spectrograph-based systems contain full spectral information along one spatial dimension. Due to the imperfections in the camera lens and in particular the optical components of the imaging spectrograph, the acquired images are subjected to spatial and spectral distortions, resulting in scene dependent nonlinear spectral degradations and spatial misalignments which need to be corrected. However, the existing correction methods require complex calibration setups and a tedious manual involvement, therefore, the correction of the distortions is often neglected. Such simplified approach can lead to significant errors in the analysis of the acquired hyperspectral images. In this paper, we present a novel fully automated method for correction of the geometric and spectral distortions in the acquired images. The method is based on automated non-rigid registration of the reference and acquired images corresponding to the proposed calibration object incorporating standardized spatial and spectral information. The obtained transformation was successfully used for sub-pixel correction of various hyperspectral images, resulting in significant improvement of the spectral and spatial alignment. It was found that the proposed calibration is highly accurate and suitable for routine use in applications involving either diffuse reflectance or transmittance measurement setups.
Purification and characterization of the major iron-regulated protein expressed by pathogenic Neisseriae. (1987)

This report describes a method to purify the major iron-regulated protein (MIRP) expressed by N. gonorrhoeae and N. meningitidis. This purification procedure involves maximal expression of the MIRP by growing the organisms on iron-limited media; cellular disruption by sonication followed by centrifugal fractionation; selective solubilization of the MIRP with the cationic detergent hexadecyltrimethylammonium bromide; cation-exchange chromatography in the presence of this detergent; and gel filtration chromatography. The MIRP purified by this technique migrates as a single band when analyzed by SDS-PAGE. The purified MIRP displayed an unusually basic isoelectric point, this value being greater than 9.35. Further biochemical analysis revealed the highly conserved nature of this protein isolated from the two pathogenic species of the genus Neisseria. For example, the amino acid composition of the meningococcal and gonococcal MIRPs were nearly identical and amino terminal sequence analysis showed that both shared the identical primary sequence through residue 48. Surprisingly, the first five NH2-terminal residues of the MIRPs exhibited homology with the first five residues of the gonococcal porin, protein I. Purified preparations of the MIRP exhibited a characteristic pink color reminiscent of the basic iron-binding protein lactoferrin. This observation coupled with the property of iron-regulation prompted us to analyze purified MIRP for iron-content. Approximately 0.5 mol iron per 1 mol of MIRP was detected. This study is the first to show that iron is associated with the MIRP, a property that may implicate this protein as playing a direct role in neisserial iron assimilation. While the precise function of the MIRP is not known, the availability of this protein in pure and biologically relevant quantities will allow further studies to elucidate its pathobiologic function.
Single-longitudinal-mode operation of GRIN rod external coupled-cavity semiconductor lasers (1984)

Single-longitudinal-mode laser sources are of great interest for optical communication In the1.3-1.6-μm wavelength range where the data bit rate in a long-haul transmission system is dispersion limited. The passive external cavity approach has been shown effective in achieving slngle-longitudinal-mode operation. The external cavity can be formed by a spherical mirror with focused feedback to the laser1 or a flat mirror coupled to a short (50-80-μm) cavity laser.2 More recently, single- longitudinal-mode operation of conventional In- GaAsP/lnP BH lasers coupled to a short GRIN rod lens with a reflective Au coating at the far end has been demonstrated.3 This paper describes the electrooptical properties of GRIN rod external coupled-cavity (GRECC) lasers and the simplicity of the design.
All-Trans Retinoic Acid Induces Differentiation of Ducts and Endocrine Cells by Mesenchymal/Epithelial Interactions in Embryonic Pancreas (2003)

Retinoids during the embryonic period act as a mesenchymal inducer in many organs, including kidney, lung, central nervous system, and gut. Retinoic acid (RA) demonstrates insulinotropic effects in adult pancreas, but only a limited study has elucidated its role in pancreatic organogenesis. In this study, we have analyzed the existence of RA-signaling machinery in embryonic pancreas and evaluated its role using in vitro tissue culture experiments. Here we show the presence of endogenous retinaldehyde dehydrogenase 2 (RALDH2), the most effective RA-synthesizing enzyme, RA-binding proteins, and RA receptors (RARs) in embryonic pancreatic tissue. RALDH2 is expressed exclusively in the mesenchyme. Exogenously added all-trans-retinoic acid (atRA) in tissue culture experiments stimulated differentiation of endocrine and duct cells and promoted apoptotic cell death of acinar tissue. Furthermore, we demonstrate that atRA upregulates the PDX-1 expression. Taken together, our data suggest that atRA-mediated mesenchymal/epithelial interactions play an important role in determining the cell fate of epithelial cells via regulation of the PDX-1 gene, leading to the proper formation of the endocrine versus exocrine component during pancreatic organogenesis.
Epigenetics of breast cancer (2007)

Since the introduction of systemic adjuvant chemotherapy (ACT) and endocrine therapy in the early 1970s, the determination of risk of recurrence and death from breast cancer became a critical piece of information in the selection of the optimal postoperative treatment strategy. Classical histopathological prognostic factors included tumor size, regional lymph node metastases and number of axillary nodes involved, tumor grade, presence of lymphovascular invasion, and, more recently, estrogen receptor (ER) and progesterone receptor status, measurement of proliferative activity (S-phase fraction, mitotic index, Ki-67), and HER2 overexpression/amplification. As isolated factors, they have limited predictive ability in the case of individual patients. For that reason, prognostic indices were developed. The most successful is Adjuvant!Online, an online nomogram developed by Peter Ravdin. This nomogram incorporates tumor size, axillary nodal status, tumor grade, ER status, age and comorbidity. The nomogram will provide an assessment of recurrence and mortality rates at 10 years, including deaths due to comorbid conditions. In addition, the nomogram also calculates relative and absolute benefit from various adjuvant interventions: tamoxifen, aromatase inhibitors, and first-generation, secondgeneration and third-generation ACT regimens. The prognostic and predictive value of this nomogram has been externally validated, with a margin of error 1%. Over the past decade, high-throughput technologies have been developed based on gene expression profiling. These include between two and a couple of hundred genes, and have the ability to separate patients with excellent outcomes from those with higher risk. One of these prognostic profiles has been externally validated and is currently undergoing testing for clinical utility in a large, multicenter, prospective randomized trial (MINDACT). Another approach was based on prospectively identifying a set of genes from the literature and from the results of gene expression profiling. Mathematical modeling then led to the selection of 16 genes related to cell proliferation, ER-driven genes, HER2 and proteases, as well as five 'housekeeping' genes (OncotypeDx). This assay is based on RT-PCR, is reproducible and applicable to archival, paraffin-embedded material, and has been shown to predict prognosis in patients with lymph-nodenegative, ER-positive primary breast cancer. Further testing indicated that the assay might also predict sensitivity to tamoxifen, or firstgeneration adjuvant chemotherapy. This assay is also under evaluation for clinical utility in a large, multicenter, prospective randomized trial (TailoRx). Whether these multigene predictors of prognosis will have greater utility than Adjuvant!Online remains to be determined. In the meantime, exploratory analyses are ongoing to identify reliable predictors of response to individual drugs and modern combination drug regimens. These are expected to lead to individualized selection of treatment, or personalized medicine.
Thermoreflectance of metal transducers for optical pump-probe studies of thermal properties (2012)

We report measurements of the temperature dependence of the optical reflectivity, dR/dT of fifteen metallic elements at a wavelength of λ = 1.03 μm by time-domain thermoreflectance (TDTR); and the thermoreflectance of thin-films of Pt, Ta, Al, Au, SrRuO(3), and LaNiO(3) over the wavelength range 0.4 < λ < 1.6 μm using variable angle spectroscopic ellipsometry. At λ = 1.03 μm, Al, Ta, Re, Ru, have high values of thermoreflectance, dR/dT > 6∙10(-5) K(-1), and are good choices as optical transducers for TDTR experiments using a Yb:fiber laser oscillator. If low optical reflectivity and the associated high degree of steady-state heating are not a concern, LaNiO(3) provides an exceptionally sensitive thermometer in the infrared; (1/R)(dR/dT) > 2.5∙10(-4) K(-1) in the wavelength range 0.85 < λ < 1.3 μm. This compilation of data will assist in the design and interpretation of optical pump-probe studies of thermal properties.
Shiga toxin 1 induces apoptosis through the endoplasmic reticulum stress response in human monocytic cells (2008)

Shiga toxins (Stxs) expressed by the enteric pathogens Shigella dysenteriae 1 and enterohaemorrhagic Escherichia coli are potent protein synthesis inhibitors. Shiga toxins have also been shown to induce apoptosis in epithelial, endothelial and monocytic cells. The precise relationship between protein synthesis inhibition and induction of apoptosis is not known. We show that stimulation of the myelogenous leukaemia cell line THP-1 with purified Stx1 induced the endoplasmic reticulum (ER) stress response. Stx1 treatment increased activation of the ER stress sensors IRE1, PERK and ATF6. Toxin treatment increased expression of the transcriptional regulator CHOP and the death domain-containing receptor DR5 at mRNA and protein levels. Following Stx1 intoxication, levels of the survival factor Bcl-2 decreased, while secretion of the death-inducing ligand TRAIL increased. Stx1 enzymatic activity was required for optimal activation of PERK and ATF6, but not IRE1. ER stress elicited by Stx1 increased the release of Ca(2+) from ER stores and the activation of the protease calpain. Inhibition of calpain activity led to reductions in Stx1-induced cleavage of procaspase-8 and apoptosis. Collectively, these data suggest that Shiga toxins trigger monocytic cell apoptosis through the ER stress response, the increased expression of DR5 and TRAIL, and activation of caspase-8 via a calpain-dependent mechanism.
Cell proliferation rates in an artificial tissue‐engineered environment (2005)

Worldwide, and particularly in Europe, Japan and the USA, cardiovascular disease is a major killer. It can be treated using tissue or organ transplant surgery, but donor organs may be scarce. Tissue engineering is the integration of engineering principles and biology to produce satisfactory synthetic replacement body parts, using viable cells in a suitable matrix, for regenerative medicine. The aim of this study was to measure and compare cell proliferation kinetics after different time intervals of myofibroblasts in a synthetic matrix, thus to be able to deduce the period that a transplanted-cell population can be expected to survive in a tissue-engineered environment. Porcine aortic wall cells were grown in a porous sponge scaffold, that later could be fashioned into aortic or heart valve substitutes. Freshly acquired cells were seeded on identical sponges and were grown under normal culture conditions for a period of 4 weeks. Seeding concentration was a million cells per sponge. Cells progressively populated the sponges, both covering the surface and infiltrating the depth of the matrix, via sponge pores. Samples were taken at 1 week and at 4 weeks, and the rate of cell proliferation was determined by the metaphase arrest technique. Specimens were also taken for light and electron microscopy to determine whether these transplanted cells were capable of synthesizing their own extracellular matrix.
Effect of gangliosides on activation of the alternative pathway of human complement. (1988)

Liposomes as defined model membranes were used to quantitatively study the effects of specific sialic acid containing glycolipids on activation of the alternative pathway of human C. Liposomes containing dimyristoylphosphatidylethanolamine, cholesterol, and cerebrosides at molar ratios of 1.0/0.75/0.33 activated the alternative pathway in human serum treated with MgEGTA. Activation was measured by C3 conversion and the deposition of total C3 and functional C3b on the liposome surface. The monosialoganglioside GM1, when incorporated into the activating liposome membrane at molar ratios between 10(-5) and 10(-2), inhibited activation in a dose-dependent manner. Sialosylparagloboside also inhibited activation in human serum, and inhibition was completely reversed after neuraminidase treatment. The degree of inhibition by GM1 correlated with the relative amount of GM1 exposed on the liposome surface. Sialic acid did not directly inhibit the binding of C3b when liposomes containing gangliosides were incubated with the purified components C3, B, D, and P. GM1 did inhibit activation when liposomes were incubated with a mixture of purified C3, B, D, P, H, and I. Binding assays with radiolabeled H showed increased binding of H to liposome-bound C3b in the presence of GM1. These results establish the ability of sialic acid on glycolipids to promote H binding to C3b and thereby regulate alternative pathway activation on a defined lipid membrane.
Structure and polymorphism of 18-carbon fatty acyl triacylglycerols: effect of unsaturation and substitution in the 2-position (1987)

The polymorphic behavior of symmetric diacid triacylglycerols (TGs), 1,3-dioleoyl-2-stearoyl (OSO), 2-elaidoyl (OEO), and 2-vaccinoyl (OVO) glycerols were studied by differential scanning colorimetry (DSC) and X-ray diffraction and compared with the corresponding monoacid TGs triolein (OOO), tristearin (SSS), trielaidin (EEE), and trivaccinin (VVV). The monoacid TGs formed a bilayered structure in all the polymorphic forms. On quenching from the melt, the diacid TGs OEO and OVO formed a bilayered (D = 45 A) beta'-phase with the exception of OSO, which formed a hexagonally packed bilayered (D = 52 A) alpha-phase. At -7 degrees C, the alpha-phase of OSO quickly transformed to a bilayered (D = 45 A) beta'-phase. Incubation at the beta'-phase melting temperature transformed OVO, OEO, and OSO into a trilayered (D = 65 A) beta-phase, where the 1,3-dioleoyl chains are segregated from the vaccinoyl, elaidoyl, or stearoyl chains into alternating layers. In summary, when all the acyl chains in a TG are the same (saturated, cis or trans unsaturated), the stable beta-phase packs into a bilayered structure. However, when the 1- and 3-acyl chains are cis unsaturated (bent) and the 2-acyl chain is either saturated or trans-unsaturated (straight), a bilayered beta'-phase can form, but transforms to a stable trilayered beta-phase, where the 2-acyl chains form a layer between two different layers of 1,3-oleoyl chains.