gebhart/patrepeval huggingface dataset:
HtrA1 Is a Novel Antagonist Controlling Fibroblast Growth Factor (FGF) Signaling via Cleavage of FGF8 (2012)

Accumulating evidence suggests that HtrA1 (high-temperature requirement A1) is involved in modulating crucial cellular processes and implicated in life-threatening diseases, such as cancer and neuropathological disorders; however, the exact functions of this protease in vivo remain unknown. Here, we show that loss of HtrA1 function increases fibroblast growth factor 8 (FGF8) mRNA levels and triggers activation of FGF signaling, resulting in dorsalization in zebrafish embryos. Notably, HtrA1 directly cleaves FGF8 in the extracellular region, and this cleavage results in decreased activation of FGF signaling, which is essential for many physiological processes. Therefore, HtrA1 is indispensable for dorsoventral patterning in early zebrafish embryogenesis and serves as a key upstream regulator of FGF signaling through the control of FGF levels. Furthermore, this study offers insight into new strategies to control human diseases associated with HtrA1 and FGF signaling.
Influenza A virus infection activates cholesterol sulfotransferase (SULT2B1b) in the lung of female C57BL/6 mice (2011)

Cytosolic sulfotransferases (SULTs) catalyze the sulfation of hormones, neurotransmitters, and xenobiotics, increasing their water solubility. SULTs are not only important for xenobiotic detoxification but they also play important biological roles in the regulation of the activities of various biosignaling molecules and other cellular functions. In this study, we investigated the effects of influenza A virus lung infection on the expression of SULTs in the lung, brain, and liver of female C57BL/6 mice. Our results demonstrate for the first time that SULT2B1b enzyme activity and protein expression are significantly up-regulated in the lung and brain of female mice in response to lung influenza A virus infection. Real-time quantitative PCR results are consistent with Western blot and enzymatic activity data. In mouse liver, mSULT2B1b is not significantly changed. Enzyme activities, protein expression, and mRNA expression of SULT1A1 and SULT2A1 in the lung, brain, and liver of mice were not significantly affected by the infection. The induction of SULT2B1b may be used to inactivate natural liver X receptor ligands and activate the proliferation of T cells in response to influenza A virus infection in the lung and brain of mice. Our results raise the possibility that regulation of SULT2B1b may influence acquired immune responses to infectious diseases.
Primary extranodal lymphoma.Response to treatment and factors influencing prognosis (1978)

The cumulative 10 year lymphoma experience of a teaching hospital and two of its affiliated institutions was reviewed. From this group, a series of 39 cases of regionally localized primary extranodal lymphomas (Ann Arbor Stages IE and IIE) were selected for study. This group of patients was analyzed for response to initial curative treatment and factors influencing prognosis. The disease-free survival rate following initial treatment is 41% and the rate is 51% if those treated for a single relapse are included. Factors which clearly influence prognosis in this group are stage (extent of disease) at presentation and Rappaport histologic subclassification. The relationships of anatomic site and age to prognosis independent of other factors are unclear. There appears to be an association between sites of involvement in Waldeyer's Ring and the gastrointestinal tract seen both initially and in sites of relapse. An analysis of relapse patterns revealed that 33% of relapses occur as solitary extranodal "skip" recurrences that when treated with radical local treatment may result in long disease-free survival. The latter is one of several findings which suggest that a modification of the current Ann Arbor staging system may be necessary to encompass certain unique features of this group of tumors.
Photoinduced Electron and Energy Transfer in Rigidly Bridged Ru(II)−Rh(III) Binuclear Complexes (1996)

A series of binuclear Ru(II)-Rh(III) complexes of general formula (ttpy)Ru-tpy-(ph)(n)-tpy-Rh(ttpy)(5+) (n = 0-2) have been synthesized, where ttpy = 4'-p-tolyl-2,2':6,2"-terpyridine and tpy-(ph)(n)-tpy represents a bridging ligand where two 2,2':6',2"-terpyridine units are either directly linked together (n = 0) or connected through one (n = 1) or two (n = 2) phenyl spacers in the 4'-position. This series of complexes is characterized by (i) rigid bridge structures and (ii) variable metal-metal distances (11 Å for n = 0, 15.5 Å for n = 1, 20 Å for n = 2). The photophysics of these binuclear complexes has been investigated in 4:1 methanol/ethanol at 77 K (rigid glass) and 150 K (fluid solution) and compared with that of mononuclear [Ru(ttpy)(2)(2+) and Rh(ttpy)(2)(3+)] or binuclear [(ttpy)Ru-tpy-tpy-Ru(ttpy)(4+)] model compounds. At 77 K, no quenching of the Ru(II)-based excited state is observed, whereas energy transfer from excited Rh(III) to Ru(II) is observed for all complexes. At 150 K, energy transfer from excited Rh(III) to Ru(II) is again observed for all complexes, while quenching of excited Ru(II) by electron transfer to Rh(III) is observed, but only in the complex with n = 0. The reasons for the observed behavior can be qualitatively understood in terms of standard electron and energy transfer theory. The different behavior between n = 0 and n = 1, 2 can be rationalized in terms of better electronic factors and smaller reorganizational energies for the former species. The freezing of electron transfer quenching but not of energy transfer, in rigid glasses reflects the different reorganizational energies involved in the two processes. Unusual results arising from multiphotonic and conformational effects have also been observed with these systems.
[Expression of exogenous porcine transforming growth factor beta-1 gene in ES cells and its effect on their differentiation in vitro]. (1995)

A TGF-beta 1 gene expression plasmid was constructed by inserting the porcine 1.7 Kb TGF-beta 1 cDNA into BamHI site of retrovirus vector Dol. The plasmid DNA was introduced into mouse embryonic stem cells (ES-5 line) by calcium phosphate mediated transfection, and transfected ES-5 cells were then selected by stepwise increase in G418 concentration. Finally, we obtained 21 clones that could be stably grown in culture medium with G418 at 500 micrograms/ml and were designated as ES-T cells. Dot blot and Northern analysis of total RNA and polyA+ RNA extracted from those ES-T cells were shown in FIg. 2 and 3, demonstrating that 6 clones could express exogenous porcine TGF-beta 1 mRNA. The stronger hybridized signal in two clones (ES-T6 and ES-T 16) of them were further proved by southern hybridization of genomic DNA from these ES-T cells with 1.7 Kb TGF-beta 1 cDNA probe (Fig. 4). The product of TGF-beta 1 gene overexpression in ES-T 6 cells was shown in Fig. 5 and 6 by SE-LISA for TGF-beta 1 immunoreactivity to TGF-beta 1 antibodies and biological assay for CCL/64 cell growth inhibition, respectively. With respect to some biological characteristics, ES-T 6 cells, like their parent ES-5 cells, retained their pluripotent properties and positive SSEA-1 antigen (Plate I, Fig. 1). ES-T6 cells were expanded and used for studies of in vitro differentiation. Both of ES-T 6 cells and control ES-5 cells could form a lot of simple aggregates and differentiate into embryoid bodies by hanging drop culture for 3 days in the presence of retinoic acid (RA) at 10(-9) mol/L. Then individual embryoid bodies were plated on gelatinized tissue culture wells. On the third day of further culture without RA, a large amounts of epithelial-like and round cells occurred around the embryoid bodies formed either from ES-T 6 cells or ES-5 cells (Plate I, Fig. 4). However, with further culture of embryoid bodies, only the cells differentiated from ES-T6 embryoid bodies could arrange themselves and differentiate into a lot of radially arranged tubular structures (Plate II, Fig. 5). The frequency of tubular structures present in ES-T6 embryoid bodies were about 95.5%, but in ES-5 group there was only about 17.8% cases giving less defined tubular structures (Plate III, Fig. 8).(ABSTRACT TRUNCATED AT 400 WORDS)
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images (2011)

Although confocal microscopes have considerably smaller contribution of out-of-focus light than widefield microscopes, the confocal images can still be enhanced mathematically if the optical and data acquisition effects are accounted for. For that, several deconvolution algorithms have been proposed. As a practical solution, maximum-likelihood algorithms with regularization have been used. However, the choice of regularization parameters is often unknown although it has considerable effect on the result of deconvolution process. The aims of this work were: to find good estimates of deconvolution parameters; and to develop an open source software package that would allow testing different deconvolution algorithms and that would be easy to use in practice. Here, Richardson-Lucy algorithm has been implemented together with the total variation regularization in an open source software package IOCBio Microscope. The influence of total variation regularization on deconvolution process is determined by one parameter. We derived a formula to estimate this regularization parameter automatically from the images as the algorithm progresses. To assess the effectiveness of this algorithm, synthetic images were composed on the basis of confocal images of rat cardiomyocytes. From the analysis of deconvolved results, we have determined under which conditions our estimation of total variation regularization parameter gives good results. The estimated total variation regularization parameter can be monitored during deconvolution process and used as a stopping criterion. An inverse relation between the optimal regularization parameter and the peak signal-to-noise ratio of an image is shown. Finally, we demonstrate the use of the developed software by deconvolving images of rat cardiomyocytes with stained mitochondria and sarcolemma obtained by confocal and widefield microscopes.
Cardiac troponin T in diagnosis of acute myocardial infarction (1991)

Troponin T is a structurally bound protein found in striated muscle cells. We tested concentrations of its cardiac-specific isotype in peripheral venous blood samples serially drawn from 72 patients with confirmed myocardial infarction. Fifty-nine patients received thrombolytic treatment with intravenous streptokinase, urokinase, or recombinant tissue-type plasminogen activator; because of contraindications, the remaining 13 patients did not. Concentrations of troponin T in plasma, measured by an enzyme-linked immunosorbent assay, started increasing within a few hours after the onset of symptoms (median, 4 h; range, 1-10 h). The sensitivity of troponin T for detecting myocardial infarction was 100% from 10 to 120 h after the onset of symptoms; sensitivity on the seventh day after admission was 84%. Concentrations were increased for up to three weeks in some patients with late or high peak values. Successful reperfusion in Q-wave infarction obviously influences the release of troponin T into plasma, with all such cases showing peak values less than or equal to 26 h (median, 14 h) after the onset of symptoms. Troponin T concentrations in these patients returned to within the reference interval more rapidly than in nonreperfused subjects. In the 13 patients without fibrinolytic therapy, troponin T tended to peak approximately 48 h (median) after the onset of chest pain. Troponin T concentrations in patients for whom thrombolysis was unsuccessful resembled those in patients without fibrinolytic therapy. The specificity of the assay was 96% as tested in samples of 96 emergency-room patients. The reference interval (less than 0.5 micrograms/L) was established from samples of 100 healthy blood donors. Troponin T measurements are a specific and sensitive method for the early and late diagnosis of acute myocardial infarction and could, therefore, provide a new criterion in laboratory diagnosis of its occurrence.
Human oncogenes detected by a defined medium culture assay. (1987)

Oncogenes in DNAs from human tumor cell lines have been detected by a new transformation assay. Cellular DNAs are transfected into NIH3T3 murine fibroblasts, and transformed cells are selected by maintaining cell cultures in a defined medium lacking platelet-derived or fibroblast growth factors. DNAs from eight of 17 human tumor cell lines have yielded transformants by this method. Activated cellular ras genes account for three of the transforming activities. The SAOS2 osteosarcoma cell line contains an activated oncogene distinct from 18 known oncogenes. Another cellular oncogene was detected as the consequence of a fortuitous transfection-mediated DNA rearrangement.
Inhibitory DNA Ligands to Platelet-Derived Growth Factor B-Chain (1996)

We have identified a group of DNA molecules that bind to platelet-derived growth factor (PDGF)-AB with subnanomolar affinity from a randomized DNA library using in vitro selection. Individual ligands cloned from the affinity-enriched pool bind to PDGF-AB and PDGF-BB with comparably high affinity (Kd approximately 10(-10) M) and to PDGF-AA with lower affinity (> 10(-8) M), indicating specific recognition of the PDGF B-chain in the context of the hetero- or homodimer. The consensus secondary structure motif for most of the high-affinity ligands is a three-way helix junction with a three-nucleotide loop at the branch point. Photo-cross-linking experiments with 5-iodo-2'-deoxyuridine-substituted ligands establish a point contact between a thymidine nucleotide in the helix junction loop region and phenylalanine 84 of the PDGF-B chain. Representative minimal DNA ligands inhibit the binding of 125I-PDGF-BB but not of 125I-PDGF-AA to PDGF alpha- or beta-receptors expressed in porcine aortic endothelial (PAE) cells in a concentration-dependent manner with half-maximal effects of approximately 1 nM. The same ligands also exhibit a similar inhibitory effect on PDGF-BB-dependent [3H]thymidine incorporation in PAE cells expressing the PDGF beta-receptors. These DNA ligands represent a novel class of specific and potent antagonists of PDGF-BB and, by inference, PDGF-AB.
Integration of the adeno-associated virus genome into cellular DNA in latently infected human Detroit 6 cells (1980)

A clone of human cells (Detroit 6) latently infected by adeno-associated virus (AAV) has been characterized with regard to the status of the viral DNA. In both early (9 to 10) and late (118) passages of the clone, AAV-DNA was recombined with host DNA, at least in some cases as a head-to-tail tandem repeat, via the terminal sequences of the viral genome. However, it was not possible to distinguish between integration into chromosomal DNA and very large plasmids (< 20 x 10(6) molecular weight) which contain both viral and cellular DNA sequences. Although evidence for some modifications of the viral sequence was obtained, most of the integrated sequences appeared to be intact. In some cases sequences of undetermined origin separated adjacent copies of the viral genome. Free copies of the AAV genome were detectable in late passage cells, but not in early passage cells. The orientation of nucleotide sequences present in the free AAV DNA from late passage cells was indistinguishable from that of virion DNA. With the notable exception, the organization of the integrated AAV sequences as determined by restriction enzyme digestion remained constant with continued passage. Digestion with SmaI, which cleaves within the palindromic region of the terminal repetition in AAV DNA, produced reproducibly different patterns when early and late passage DNAs were compared. Several models for rescue of free copies of the genome from the integrated DNA are possible, all of which involve the terminal repetition.
Purification and characterization of a high-molecular-weight outer membrane protein of Moraxella (Branhamella) catarrhalis (1994)

Moraxella (Branhamella) catarrhalis is an important bacterial cause of otitis media in children and lower respiratory tract infections in adults. In this study, we describe the presence of a novel high-molecular-weight outer membrane protein (HMW-OMP). This protein varies from 350 to 720 kDa in apparent molecular mass among strains by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The protein was detected on SDS-PAGE in 13 of 14 strains tested. We developed a monoclonal antibody and polyclonal antisera to this protein. In immunoblot assays, the protein was present in all 14 strains tested. The immunoblot assays suggest that the protein has at least one epitope that is conserved among strains. A purification method using anion-exchange chromatography is described. Treatment of outer membrane preparations and purified protein by heat and reducing agents did not change the apparent molecular mass of the HMW-OMP. Formic acid treatment of outer membrane preparations and purified HMW-OMP produced a single band with an apparent molecular mass of 120 to 140 kDa. We postulate that this may be the monomer of an oligomeric protein. The HMW-OMP, which varies in molecular mass among strains and is antigenically conserved, will be studied further to determine its role in the human immune response and may be useful as a marker in studying strain acquisition in patients.
A Statistical Analysis of Subjective and Objective Methods of Evaluating Fabric Handle (1985)

A survey of the fabric handle preferences of panels of expert judges drawn from the textile and clothing industries of Japan, Australia, New Zealand and India has been undertaken . These data have been analysed using two statistical techniques, the first to select the most reliable judges and the second to analyse national judging characteristics.The technique for selecting the most reliable judges employs a linear model in which each judge's performance is tested against an orthogonal basis of fabric judgment calculated from the assessments of the remaining judges.In an iterative process, the judge whose handle assessments are least explained by all the other expert judges is then sequentially eliminated until 8 of the original 53 judges remain. This final group was comprised of 4 judges from Japan, 3 from Australia and 1 from India . The results for the New Zealand judges indicate that they may include some different characterisitics when assessing fabric handle .The results from a principal component analysis of variance indicate that although a single factor can account for a substantial amount of the observed variability in the data, additional factors are clearly implicated.The three most significant of these additional factors can be related to distinctive national handle preferences by the Japanese, New Zealand and Australian judging panels.
Identification of Peptide and Protein Ligands for the Caveolin-scaffolding Domain (1997)

Caveolin, a 21-24-kDa integral membrane protein, is a principal component of caveolae membranes. We have suggested that caveolin functions as a scaffolding protein to organize and concentrate certain caveolin-interacting proteins within caveolae membranes. In this regard, caveolin co-purifies with a variety of lipid-modified signaling molecules, including G-proteins, Src-like kinases, Ha-Ras, and eNOS. Using several independent approaches, it has been shown that a 20-amino acid membrane proximal region of the cytosolic amino-terminal domain of caveolin is sufficient to mediate these interactions. For example, this domain interacts with G-protein alpha subunits and Src-like kinases and can functionally suppress their activity. This caveolinderived protein domain has been termed the caveolin-scaffolding domain. However, it remains unknown how the caveolin-scaffolding domain recognizes these molecules. Here, we have used the caveolin-scaffolding domain as a receptor to select random peptide ligands from phage display libraries. These caveolin-selected peptide ligands are rich in aromatic amino acids and have a characteristic spacing in many cases. A known caveolin-interacting protein, Gi2alpha, was used as a ligand to further investigate the nature of this interaction. Gi2alpha and other G-protein alpha subunits contain a single region that generally resembles the sequences derived from phage display. We show that this short peptide sequence derived from Gi2alpha interacts directly with the caveolin-scaffolding domain and competitively inhibits the interaction of the caveolin-scaffolding domain with the appropriate region of Gi2alpha. This interaction is strictly dependent on the presence of aromatic residues within the peptide ligand, as replacement of these residues with alanine or glycine prevents their interaction with the caveolin-scaffolding domain. In addition, we have used this interaction to define which residues within the caveolin-scaffolding domain are critical for recognizing these peptide and protein ligands. Also, we find that the scaffolding domains of caveolins 1 and 3 both recognize the same peptide ligands, whereas the corresponding domain within caveolin-2 fails to recognize these ligands under the same conditions. These results serve to further demonstrate the specificity of this interaction. The implications of our current findings are discussed regarding other caveolin- and caveolae-associated proteins.
Recent Advances in the Physiology and Genetics of Amino Acid-Producing Bacteria (1995)

Corynebacterium glutamicum and its close relatives, C. flavum and C. lactofermentum, have been used for over 3 decades in the industrial production of amino acids by fermentation. Since 1984, several research groups have started programs to develop metabolic engineering principles for amino acid-producing Corynebacterium strains. Initially, the programs concentrated on the isolation of genes encoding (deregulated) biosynthetic enzymes and the development of general molecular biology tools such as cloning vectors and DNA transfer methods. With most of the genes and tools now available, recombinant DNA technology can be applied in strain improvement. To accomplish these improvements, it is critical and advantageous to understand the mechanisms of gene expression and regulation as well as the biochemistry and physiology of the species being engineered. This review explores the advances made in the understanding and application of amino acid-producing bacteria in the early 1990s.