gebhart/patrepeval huggingface dataset:
Identification of the Arabidopsis Palmitoyl-Monogalactosyldiacylglycerol Δ7-Desaturase Gene FAD5, and Effects of Plastidial Retargeting of Arabidopsis Desaturases on the fad5 Mutant Phenotype (2004)

Hexadeca 7,10,13-trienoic acid (16:3Delta(7,10,13)) is one of the most abundant fatty acids in Arabidopsis (Arabidopsis thaliana) and a functional component of thylakoid membranes, where it is found as an sn-2 ester of monogalactosyldiacylglycerol. The Arabidopsis fad5 mutant lacks activity of the plastidial palmitoyl-monogalactosyldiacylglycerol Delta7-desaturase FAD5, and is characterized biochemically by the absence of 16:3Delta(7,10,13) and physiologically by reduced chlorophyll content and a reduced recovery rate after photoinhibition. While the fad5 mutation has been mapped, the FAD5 gene was not unambiguously identified, and a formal functional characterization by complementation of fad5 mutant phenotypes has not been reported. Two candidate genes (At3g15850 and At3g15870) predicted to encode plastid-targeted desaturases at the fad5 chromosomal locus were cloned from fad5 plants and sequenced. A nonsense mutation changing codon TGG (Trp-98) into TGA (stop) was identified in At3g15850 (ADS3), whereas the fad5 At3g15870 allele was identical to wild type (after correction of a sequencing error in the published wild-type genomic At3g15870 sequence). Expression of a genomic clone or cDNA for wild-type At3g15850 conferred on fad5 plants the ability to synthesize 16:3Delta(7,10,13) and restored leaf chlorophyll content. Arabidopsis carrying a T-DNA insertion in At3g15870 had wild-type levels of both 16:3Delta(7,10,13) and chlorophyll. Together, these data formally prove that At3g15850 is FAD5. Interestingly, the fad5 phenotype was partially complemented when extraplastidial Delta9-desaturases of the Arabidopsis desaturase (ADS) family were expressed as fusions with a plastidial transit peptide. Tight correlation between leaf 16:3Delta(7,10,13) levels and chlorophyll content suggests a role for plastidial fatty acid desaturases in thylakoid formation.
NF-κB Inducing Kinase, NIK Mediates Cigarette Smoke/TNFα-Induced Histone Acetylation and Inflammation through Differential Activation of IKKs (2011)

Overall, our findings provide a novel role for NIK in CS- and TNFα-induced histone acetylation, especially on histone H3K9.
Robust Locally Weighted Regression and Smoothing Scatterplots (1979)

Abstract The visual information on a scatterplot can be greatly enhanced, with little additional cost, by computing and plotting smoothed points. Robust locally weighted regression is a method for smoothing a scatterplot, (x i , y i ), i = 1, …, n, in which the fitted value at z k is the value of a polynomial fit to the data using weighted least squares, where the weight for (x i , y i ) is large if x i is close to x k and small if it is not. A robust fitting procedure is used that guards against deviant points distorting the smoothed points. Visual, computational, and statistical issues of robust locally weighted regression are discussed. Several examples, including data on lead intoxication, are used to illustrate the methodology.
In vivo binding of active heat shock transcription factor 1 to human chromosome 9 heterochromatin during stress (2002)

Activation of the mammalian heat shock transcription factor (HSF)1 by stress is a multistep process resulting in the transcription of heat shock genes. Coincident with these events is the rapid and reversible redistribution of HSF1 to discrete nuclear structures termed HSF1 granules, whose function is still unknown. Key features are that the number of granules correlates with cell ploidy, suggesting the existence of a chromosomal target. Here we show that in humans, HSF1 granules localize to the 9q11-q12 heterochromatic region. Within this locus, HSF1 binds through direct DNA–protein interaction with a nucleosome-containing subclass of satellite III repeats. HSF1 granule formation only requires the DNA binding competence and the trimerization of the factor. This is the first example of a transcriptional activator that accumulates transiently and reversibly on a chromosome-specific heterochromatic locus.
Amyloid A in systemic amyloidosis associated with cancer. (1982)

Amyloid fibrils from two cases of cancer-associated, systemic amyloidosis with renal cell carcinoma and mesothelioma as the respective underlying disorders were studied. The immunochemical studies suggested strongly that amyloid A comprised a principal fibril component in both cases of cancer-associated amyloidosis. This was definitively proven by amino acid sequence analyses, which revealed structural homology between a purified subcomponent of the amyloid fibrils from both of the two cases of cancer-associated amyloidosis and previously sequenced amyloid A proteins. The chemical composition of the amyloid fibrils from systemic amyloidosis associated with cancer thus corresponded to that seen in amyloidosis reactive to inflammatory diseases and Hodgkin's disease. Amyloid proteins of immunoglobulin light chain type, which are found associated with myelomatosis, macroglobulinemia, and idiopathic (primary) amyloidosis, were not found in the two amyloid preparations. Renal cell carcinoma appears to be an effective stimulator of amyloid formation, while only one case of amyloidosis associated with mesothelioma has been reported previously.
Solid freeform fabrication (1999)

Researchers at Austin have been working on technologies termed solid freeform fabrication (SFF) or, as reported in the popular press, desktop manufacturing, rapid prototyping, and layered manufacturing. Such processes have the potential to produce accurate, structurally sound 3-D renditions of objects designed with computers and manufactured directly from a CAD database, without part-specific tooling or human intervention, and to make them available to the user in minutes or hours. The benefits include greatly reduced prototyping cost and design time and reliability to achieve, in one operation, shapes that would otherwise require multiple operations or in some cases be impossible to produce with standard techniques. Automated manufacturing technologies in general are well suited to large production numbers, but ill suited to low-volume runs. In the latter case, the components are too few to adequately amortize the cost of part-specific tooling; instead, they are typically made by hand at much greater unit cost and longer completion times. Nor is it a completely desirable low-volume option to interface CAD systems with numerically controlled (NC) machining centers-in essence, computer controlled material removal systems-because so much human intervention is involved in producing NC programs and setting up and supervising NC systems. In fact, the low-volume production arena is exactly where SFF slashes cost and time to completion.
Autologous Chondrocytes Used for Articular Cartilage Repair (2001)

Articular cartilage in adults has a poor ability to self-repair after a substantial injury; however, it is not known whether there is a cartilage resurfacing technique superior to the existing techniques. It is not satisfactory that at the beginning of the new millennium, there still is a lack of randomized studies comparing different cartilage repair techniques and there still is little knowledge of the natural course of a cartilaginous lesion. To date, various articular cartilage resurfacing techniques have the potential to improve the repair of cartilage defects and reduce the patient's disability. One such cartilage repair technique is autologous chondrocyte transplantation combined with a periosteal graft. Since the first patient was operated on in 1987, much interest in cartilage repair and cell engineering has emerged. The experience with autologous chondrocyte transplantation during the past 13 years with in vitro chondrocyte expansion, cartilage harvest, and postoperative biopsy technique is discussed, and the latest followup of 213 consecutive patients in different subgroups with 2 to 10 years followup is presented. The technique gives stable long-term results with a high percentage of good to excellent results (84%-90%) in patients with different types of single femoral condyle lesions, whereas patients with other types of lesions have a lower degree of success (mean, 74%).
Determination of acid alpha-glucosidase activity in blood spots as a diagnostic test for Pompe disease. (2001)

The determination of acid alpha-glucosidase activity in dried-blood spots is a useful, noninvasive diagnostic assay for the identification of Pompe disease. With further validation, this procedure could be adapted for use with blood spots collected in newborn-screening programs.
Einleitung (1996)

Nahezu jeder von uns hat einen Begriff der Leistungsbeurteilung, der sich unmittelbar mit eigener schulischer Erfahrung verbindet: die Benotung. Benotung heißt dann überwiegend ein auf Schulfächer und die eigene "Leistung" bezogenes Urteil einzelner Lehrerinnen und Lehrer, ausgedrückt in Zahlen, Ziffern oder den bekannten sechs Adjektiven, die Leistungsqualitäten beschreiben sollen: sehr gut bis ungenügend. In der reformierten gymnasialen Oberstufe kommen seit Mitte der siebziger Jahre Bewertungen nach einem Punktesystem hinzu. In den meisten Fällen gibt sich die schulische Bewertung scheinbar "objektiv", dabei zwängt sie das Lernen und die Leistung des einzelnen vor allem in einen Vergleich zu den Mitschülerinnen und Mitschülern.
Characterization of the Interleukin (IL)-6 Inhibitor IL-6-RFP (2006)

Although fusion proteins of the extracellular parts of receptor subunits termed cytokine traps turned out to be promising cytokine inhibitors for anti-cytokine therapies, their mode of action has not been analyzed. We developed a fusion protein consisting of the ligand binding domains of the IL-6 receptor subunits IL-6Ralpha and gp130 that acts as a highly potent IL-6 inhibitor. Gp130 is a shared cytokine receptor also used by the IL-6-related cytokines oncostatin M and leukemia inhibitory factor. In this study, we have shown that the IL-6 receptor fusion protein (IL-6-RFP) is a specific IL-6 inhibitor that does not block oncostatin M or leukemia inhibitory factor. We characterized the complex of IL-6-RFP and fluorescently labeled IL-6 (YFPIL-6) by blue native PAGE and gel filtration. A 2-fold molar excess of IL-6-RFP over IL-6 was sufficient to entirely bind IL-6 in a complex with IL-6-RFP. As shown by treatment with urea and binding competition experiments, the complex of IL-6 and IL-6-RFP is more stable than the complex of IL-6, soluble IL-6Ralpha, and soluble gp130. By live cell imaging, we have demonstrated that YFP-IL-6 bound to the surface of cells expressing gp130-CFP is removed from the plasma membrane upon the addition of IL-6-RFP. The apparent molecular mass of the IL-6.IL-6-RFP complex determined by blue native PAGE and gel filtration suggests that IL-6 is trapped in a structure analogous to the native hexameric IL-6 receptor complex. Thus, fusion of the ligand binding domains of heteromeric receptors leads to highly specific cytokine inhibitors with superior activity compared with the separate soluble receptors.
ilvB-encoded acetolactate synthase is resistant to the herbicide sulfometuron methyl (1984)

The herbicide sulfometuron methyl is a potent inhibitor of the branched-chain amino acid biosynthetic enzyme acetolactate synthase (ALS) isolated from bacteria, fungi, and plants. However, it did not prevent growth of wild-type Salmonella typhimurium LT2 or Escherichia coli K-12. These species each contain two acetolactate synthase isozymes. Growth of S. typhimurium and E. coli mutants lacking ALS I was prevented by the herbicide, suggesting that activity of the remaining ALS isoenzyme (II or III, respectively) was stopped by sulfometuron methyl. Synthesis of ALS I requires either an relA function or an elevated cyclic AMP level. A relA mutant of S. typhimurium was inhibited by sulfometuron methyl on rich carbon sources that display a basal cyclic AMP level but not on poor carbon sources where the cyclic AMP concentration is elevated. When L-valine, which allosterically inhibits ALS I activity, was added, growth retardation of the relA- strain by sulfometuron methyl was observed on both poor and rich carbon sources. Enzymological analyses indicated that ALS I activities derived from both species were resistant to the herbicide. In contrast, activities of S. typhimurium ALS II and E. coli ALS III were abolished by sulfometuron methyl.
Hemocompatibility improvement of perfusion-decellularized clinical-scale liver scaffold through heparin immobilization (2015)

Whole-liver perfusion-decellularization is an attractive scaffold-preparation technique for producing clinical transplantable liver tissue. However, the scaffold's poor hemocompatibility poses a major obstacle. This study was intended to improve the hemocompatibility of perfusion-decellularized porcine liver scaffold via immobilization of heparin. Heparin was immobilized on decellularized liver scaffolds (DLSs) by electrostatic binding using a layer-by-layer self-assembly technique (/h-LBL scaffold), covalent binding via multi-point attachment (/h-MPA scaffold), or end-point attachment (/h-EPA scaffold). The effect of heparinization on anticoagulant ability and cytocompatibility were investigated. The result of heparin content and release tests revealed EPA technique performed higher efficiency of heparin immobilization than other two methods. Then, systematic in vitro investigation of prothrombin time (PT), thrombin time (TT), activated partial thromboplastin time (APTT), platelet adhesion and human platelet factor 4 (PF4, indicates platelet activation) confirmed the heparinized scaffolds, especially the /h-EPA counterparts, exhibited ultralow blood component activations and excellent hemocompatibility. Furthermore, heparin treatments prevented thrombosis successfully in DLSs with blood perfusion after implanted in vivo. Meanwhile, after heparin processes, both primary hepatocyte and endothelial cell viability were also well-maintained, which indicated that heparin treatments with improved biocompatibility might extend to various hemoperfusable whole-organ scaffolds' preparation.
An analysis of browser domain-isolation bugs and a light-weight transparent defense mechanism (2007)

Browsers' isolation mechanisms are critical to users' safety and privacy on the web. Achieving proper isolations, however, is very difficult. Historical data show that even for seemingly simple isolation policies, the current browser implementations are surprisingly error-prone. Isolation bugs have been exploited on most major browser products. This paper presents a focused study of browser isolation bugs and attacks. We found that because of the intrinsic complexity of browser components, it is impractical to exhaustively examine the browser implementation to eliminate these bugs. In this paper, we propose the script accenting mechanism as a light-weight transparent defense to enhance the current domain isolation mechanism. The basic idea is to introduce domain-specific "accents" to scripts and HTML object names so that two frames cannot communicate/interfere if they have different accents. The mechanism has been prototyped on Internet Explorer. Our evaluations showed that all known attacks were defeated, and the proposed mechanism is fully transparent to existing web applications. The measurement about end-to-end browsing time did not show any noticeable slowdown. We also argue that accenting could be a primitive that is general enough for implementing other domain-isolation policies.
Analysis of Binding Sites in Human C-reactive Protein for FcγRI, FcγRIIA, and C1q by Site-directed Mutagenesis (2005)

Human C-reactive protein (CRP) is a classical, acute phase serum protein synthesized by the liver in response to infection, inflammation, or trauma. CRP binds to microbial antigens and damaged cells, opsonizes particles for phagocytosis and regulates the inflammatory response by the induction of cytokine synthesis. These activities of CRP depend on its ability to activate complement and to bind to Fcgamma receptors (FcgammaR). The goal of this study was to elucidate amino acid residues important for the interaction of CRP with human FcgammaRI (CD64) and FcgammaRIIa (CD32). Several mutations of the CRP structure were studied based on the published crystal structure of CRP. Mutant and wild-type recombinant CRP molecules were expressed in the baculovirus system and their interactions with FcgammaR and C1q were determined. A previous study by our laboratory identified an amino acid position, Leu(176), critical for CRP binding to FcgammaRI and work by others (Agrawal, A., Shrive, A. K., Greenhough, T. J., and Volanakis, J. E. (2001) J. Immunol. 166, 3998-4004) determined several residues important for C1q binding. The amino acid residues important to CRP binding to FcgammaRIIa were previously unknown. This study newly identifies residues Thr(173) and Asn(186) as important for the binding of CRP to FcgammaRIIa and FcgammaRI. Lys(114), like Leu(176), was implicated in binding to FcgammaRI, but not FcgammaRIIa. Single mutations at amino acid positions Lys(114), Asp(169), Thr(173), Tyr(175), and Leu(176) affected C1q binding to CRP. These results further identify amino acids involved in the binding sites on CRP for FcgammaRI, FcgammaRIIa, and C1q and indicate that these sites are overlapping.
Tax proteins of human T-cell leukemia virus type 1 and 2 induce expression of the gene encoding erythroid-potentiating activity (tissue inhibitor of metalloproteinases-1, TIMP-1). (1994)

A growth factor-like activity for erythroid cells (erythroid-potentiating activity) is produced by the T-cells infected with human T-cell leukemia virus type 2 (HTLV-2) (Gasson, J. C., Golde, D. W., Kaufman, S. E., Westbrook, C. A., Hewick, R. M., Kaufmann, R. J., Wong, G. G., Temple, P. A., Leary, A. C., Brown, E. L., Orr, E. C., and Clark, S. C. (1985) Nature 315, 768-771) and is reportedly identical with tissue inhibitors of matrix metalloproteinases-1 (TIMP-1) (Docherty, A. J. P., Lyons, A., Smith, B. J., Wright, E. M., Stephens, P. E., Harris, T. J. R., Murphy, G., and Reynolds, J. J. (1985) Nature 318, 66-69). We found that adult T-cell leukemia cell lines infected with HTLV-1 also express high levels of a TIMP-1 transcript. A viral transactivator of HTLV-1, Tax1, in a human T-cell line (Jurkat), was sufficient to stimulate transcription of the TIMP-1 gene. Deletion and mutation analysis of the TIMP-1 gene promoter showed that the AP-1 binding site in the 38-base pair sequence conserved between the human and mouse genes was essential for activation by Tax1. The transactivator of HTLV-2 also stimulated the promoter through the same cis-element. The reported growth-promoting activity of TIMP-1 against erythroid cells and potentially against HTLV-1-infected T-cells may modulate the clinical course of adult T-cell leukemia.
In Vivo Myogenic Potential of Human CD133+ Muscle-derived Stem Cells: A Quantitative Study (2009)

In recent years, numerous reports have identified in mouse different sources of myogenic cells distinct from satellite cells that exhibited a variable myogenic potential in vivo. Myogenic stem cells have also been described in humans, although their regenerative potential has rarely been quantified. In this study, we have investigated the myogenic potential of human muscle-derived cells based on the expression of the stem cell marker CD133 as compared to bona fide satellite cells already used in clinical trials. The efficiency of these cells to participate in muscle regeneration and contribute to the renewal of the satellite cell pool, when injected intramuscularly, has been evaluated in the Rag2(-/-) gammaC(-/-) C5(-/-) mouse in which muscle degeneration is induced by cryoinjury. We demonstrate that human muscle-derived CD133+ cells showed a much greater regenerative capacity when compared to human myoblasts. The number of fibers expressing human proteins and the number of human cells in a satellite cell position are all dramatically increased when compared to those observed after injection of human myoblasts. In addition, CD133+/CD34+ cells exhibited a better dispersion in the host muscle when compared to human myoblasts. We propose that muscle-derived CD133+ cells could be an attractive candidate for cellular therapy.
Distribution of Environmentally Regulated Genes of Streptococcus suis Serotype 2 among S. suis Serotypes and Other Organisms (2002)

The occurrence of 36 environmentally regulated genes of Streptococcus suis strain 10 among all 35 S. suis serotypes was determined by using hybridization with the amplified genes as probes. In addition, the distribution of these genes among the virulence phenotypes of serotypes 1 and 2 was assessed. Hybridization was also performed with various other streptococcal species and nonstreptococcal bacterial species which may be present in pigs. Interestingly, probe ivs-25/iri-1, similar to agrA and sapR, hybridized only with S. suis serotype 1 and 2 strains with virulent phenotypes and is therefore suitable as a diagnostic parameter. Only one probe was specific for S. suis. This probe's sequence was identical to the epf gene, a putative virulence factor of S. suis. Probe ivs-31 was similar to a virulence factor of S. suis, namely, a gene encoding a fibronectin- and fibrinogen-binding protein. This probe hybridized only with oral streptococci. Nearly half of the probes (45%) hybridized with the oral streptococci (S. oralis, S. milleri, S. sanguis, S. gordonii, and S. mitis) and with Streptococcus pneumoniae. This indicates a close relationship between S. suis, the oral streptococci, and S. pneumoniae with respect to the selected environmentally regulated genes. One probe only hybridized with gram-negative species and therefore seems to be obtained by S. suis from a gram-negative organism by horizontal transfer.
Stable “zeta” peptides that act as potent antagonists of the high-affinity IgE receptor (2002)

Recently we described a family of peptides, unrelated in sequence to IgE, that form stable beta-hairpins in solution and inhibit IgE activity in the microM range [Nakamura, G. R., Starovasnik, M. A., Reynolds, M. E. & Lowman, H. B. (2001) Biochemistry 40, 9828-9835]. Using an expanded set of peptide-phage libraries, we found a simpler motif, X(2)CPX(2)CYX, for binding to the high-affinity IgE receptor. In solution, one of these peptides spontaneously formed a covalent antiparallel dimer. We subsequently linked these monomers in a single-chain construct on phage and optimized receptor binding. Ultimately, peptides with 30 nM affinity were produced. NMR studies showed that the peptide adopts a stable fold consisting of two "zeta" (zeta)-shaped moieties. Structure-activity analyses reveal a single binding site created by the zeta-dimer, with two tyrosine residues important for structural stability and two proline residues important for Fc epsilon RI binding. The peptides inhibit histamine release from cultured cells and are extremely stable in biological fluids. The zeta peptides appear to act as competitive IgE inhibitors and suggest possibilities for design of novel IgE antagonists.
Properties of digital holography based on in-line configuration (2000)

Digital holography for micromeasurement is an active re- search topic. With respect to the requirement of realizing characteriza- tion of micro-scale structures in microelectromechanical systems with high resolution and accuracy, in-line configuration is studied in this paper as the fundamental structure of a digital holography system. A math- ematical model based on Fourier optics is developed to analyze the digital recording mechanism and properties of the system in comparison with those of the commonly used off-axis arrangement. Theoretical analysis and experimental results demonstrate that in-line configuration is advantageous in enhancing the system performance. Besides the re- laxed requirement of spatial resolution on the CCD sensors and the greater flexibility of the system, higher lateral resolution and lower speckle noise can be achieved. © 2000 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(00)01812-2)