gebhart/patrepeval huggingface dataset:
Porous Silicon Films Micropatterned with Bioelements as Supports for Mammalian Cells (2012)

Abstract Porous silicon (pSi) surfaces have been chemically patterned via a UV initiated hydrosilylation reaction of an alkene through a photomask, introducing chemical functionality in the exposed surface areas. A secondary, UV initiated hydrosilylation reaction with a second alkene of different functionality is performed to backfill the silicon hydride terminated regions on the surface, thereby affording patterned porous films with dual, surface chemistry. UV initiated hydrosilylations were performed using the alkene undecylenic acid N‐hydroxysuccinimide (NHS) ester, and the pSi surfaces were stabilized by a second hydrosilylation reaction with a polyethylene glycol (PEG) appended alkene. NHS ester and PEG functionalized surfaces were used for the selective immobilization of the cell adhesion mediator protein fibronectin (FN), in the NHS‐functional regions. Matrix‐assisted laser desorption/ionization mass spectrometry imaging on the protein functionalized pSi surface confirmed the patterned conjugation of the FN to the NHS functionalized regions. Mammalian cells cultured on these surfaces showed attachment that was confined to the patterned areas of FN on the pSi surface.
Identification of Residues Essential for Carbohydrate Recognition by the Insulin-like Growth Factor II/Mannose 6-Phosphate Receptor (2002)

Two distinct mannose 6-phosphate (Man-6-P) receptors (MPRs), the cation-dependent MPR (CD-MPR) and the insulin-like growth factor II/MPR (IGF-II/MPR), recognize a diverse population of Man-6-P-containing ligands. The IGF-II/MPR is a type I transmembrane glycoprotein with a large extracytoplasmic region composed of 15 repeating domains that display sequence identity to each other and to the single extracytoplasmic domain of the CD-MPR. A structure-based sequence alignment of the two distinct Man-6-P-binding sites of the IGF-II/MPR with the CD-MPR implicates several residues of IGF-II/MPR domains 3 and 9 as essential for Man-6-P binding. To test this hypothesis single amino acid substitutions were made in constructs encoding either the N- or the C-terminal Man-6-P-binding sites of the bovine IGF-II/MPR. The mutant IGF-II/MPRs secreted from COS-1 cells were analyzed by pentamannosyl phosphate-agarose affinity chromatography, identifying four residues (Gln-392, Ser-431, Glu-460, and Tyr-465) in domain 3 and four residues (Gln-1292, His-1329, Glu-1354, and Tyr-1360) in domain 9 as essential for Man-6-P recognition. Binding affinity studies using the lysosomal enzyme, beta-glucuronidase, confirmed these results. Together these analyses provide strong evidence that the two Man-6-P-binding sites of the IGF-II/MPR are structurally similar to each other and to the CD-MPR and utilize a similar carbohydrate recognition mechanism.
PEPCOL: a GERCOR randomized phase II study of nanoliposomal irinotecan PEP02 (MM‐398) or irinotecan with leucovorin/5‐fluorouracil as second‐line therapy in metastatic colorectal cancer (2016)

A multicenter, open-label, noncomparative, randomized phase II study (PEPCOL) was conducted to evaluate the efficacy and safety of the irinotecan or PEP02 (MM-398, nanoliposomal irinotecan) with leucovorin (LV)/5-fluorouracil (5-FU) combination as second-line treatment in patients with metastatic colorectal cancer (mCRC). Patients with unresectable mCRC who had failed one prior oxaliplatin-based first-line therapy were randomized toirinotecan with LV/5-FU (FOLFIRI) or PEP02 with LV/5-FU (FUPEP; PEP02 80 mg/m(2) with LV 400 mg/m(2) on day 1 and 5-FU 2400 mg/m(2) on days 1-2). Bevacizumab (5 mg/kg, biweekly) was allowed in both arms. The primary endpoint was 2-month response rate (RR). Fifty-five patients were randomized (FOLFIRI, n = 27; FUPEP, n = 28). In the intent-to-treat population (n = 55), 2-month RR response rate was observed in two (7.4%) and three (10.7%) patients in the FOLFIRI and FUPEP arms, respectively. The most common grade 3-4 adverse events reported in the respective FOLFIRI and FUPEP arms were diarrhea (33% vs. 21%), neutropenia (30% vs. 11%), mucositis (11% vs. 11%), and grade 2 alopecia (26% vs. 25%). FUPEP has activity and acceptable safety profile in oxaliplatin-pretreated mCRC patients.
The electrophoretically ‘slow’ and ‘fast’ forms of the α2-macroglobulin molecule (1979)

alpha 2-Macroglobulin (alpha 2M) was isolated from human plasma by a four-step procedure: poly(ethylene glyco) fractionation, gel chromatography, euglobulin precipitation and immunoadsorption. No contaminants were detected in the final preparations by electrophoresis or immunoprecipitation. The protein ran as a single slow band in gel electrophoresis, and was designated 'S-alpha 2M'. S-alpha 2M bound about 2 mol of trypsin/mol. Treatment of S-alpha 2M with a proteinase or ammonium salts produced a form of the molecule more mobile in electrophoresis, and lacking proteinase-binding activity (F-alpha 2M). The electrophoretic mobility of the F-alpha 2M resulting from reaction with NH4+ salts was identical with that of proteinase complexes. We attribute the change in electrophoretic mobility of the alpha 2M to a conformation change, but there was no evidence of a change in pI or Strokes radius. Electrophoresis of S-alpha 2M in the presence of sodium dodecylsulphate gave results consistent with the view that the alpha 2M molecule is a tetramer of identical subunits, assembled as a non-covalent pair of disulphide-linked dimers. Some of the subunits seemed to be 'nicked' into two-thires-length and one-third-length chains, however. This was not apparent with F-alpha 2M produced by ammonium salts. F-alpha 2M produced by trypsin showed two new bands attributable to cleavage of the subunit polypeptide chain near the middle. Immunoassays of F-alpha 2M gave 'rockets' 12-29% lower than those with S-alpha 2M. The nature of the interactions between subunits in S-alpha 2M and F-alpha 2M was investigated by treating each form with glutaraldehyde before electrophoresis in the presence of sodium dodecyl sulphate. A much greater degree of cross-linking was observed with the F-alpha 2M, indicating that the subunits interact most closely in this form of the molecule. Exposure of S-alpha 2M to 3 M-urea or pH3 resulted in dissociation to the disulphide-bonded half-molecules; these did not show the proteinase-binding activity characteristic of the intact alpha 2M. F-alpha 2M was less easily dissociated than was S-alpha 2M. S-alpha 2M was readily dissociated to the quarter-subunits by mild reduction, with the formation of 3-4 new thiol groups per subunit. Inact reactive alpha 2M could then be regenerated in high yield by reoxidation of the subunits. F-alpha 2M formed by reaction with a proteinase or ammonium salts was not dissociated under the same conditions, although the interchain disulphide bonds were reduced. If the thiol groups of the quarter-subunits of S-alpha 2M were blocked by carboxymethylation, oxidative reassociation did not occur. Nevertheless treatment of these subunits with methylammonium salts or a proteinase caused the reassembly of half-molecules and intact (F-) tetramers. It is emphasized that F-alpha 2M does not have the properties of a denatured form of the protein...
The Two Genes Encoding Starch-Branching Enzymes IIa and IIb Are Differentially Expressed in Barley1 (1998)

The sbeIIa and sbeIIb genes, encoding starch-branching enzyme (SBE) IIa and SBEIIb in barley (Hordeum vulgare L.), have been isolated. The 5' portions of the two genes are strongly divergent, primarily due to the 2064-nucleotide-long intron 2 in sbeIIb. The sequence of this intron shows that it contains a retro-transposon-like element. Expression of sbeIIb but not sbeIIa was found to be endosperm specific. The temporal expression patterns for sbeIIa and sbeIIb were similar and peaked around 12 d after pollination. DNA gel-blot analysis demonstrated that sbeIIa and sbeIIb are both single-copy genes in the barley genome. By fluorescence in situ hybridization, the sbeIIa and sbeIIb genes were mapped to chromosomes 2 and 5, respectively. The cDNA clones for SBEIIa and SBEIIb were isolated and sequenced. The amino acid sequences of SBEIIa and SBEIIb were almost 80% identical. The major structural difference between the two enzymes was the presence of a 94-amino acid N-terminal extension in the SBEIIb precursor. The (beta/alpha)8-barrel topology of the alpha-amylase superfamily and the catalytic residues implicated in branching enzymes are conserved in both barley enzymes.
Oxidation of ethanol in the brain and its consequences. (2006)

Acetaldehyde, a toxic byproduct of alcohol (i.e., ethanol) metabolism, has long been suspected of causing at least some of the central nervous system actions of ethanol. However, the data to support such a hypothesis have been difficult to obtain. One roadblock is the very low blood levels of acetaldehyde following ethanol intake and the finding that even elevated acetaldehyde levels in the blood do not easily gain access to the brain. The recent discovery of the oxidation of ethanol to acetaldehyde in the adult brain may help explain the acute effects of ethanol.
Synthesis and Characterization of Functionalized Poly(ε-caprolactone) Copolymers by Free-Radical Polymerization (1998)

A series of functionalized poly(ε-caprolactone) copolymers, poly(ε-caprolactone-co-vinylphosphonic acid) and poly(ε-caprolactone-co-dimethyl vinylphosphonate), were synthesized by the free-radical copolymerization of 2-methylene-1,3-dioxepane with two vinyl monomers, vinylphosphonic acid and dimethyl vinylphosphonate. The copolymers have ester groups in the backbone as well as pendant functional groups. The structure of each copolymer was established by 1H and 13C NMR as well as IR spectroscopy. Differential scanning calorimetry indicated that the copolymer had a random structure. NMR study showed hydrogen transfer during the copolymerization. The copolymers have different solubility behavior due to the presence of different pendant functional groups.
Hepatic Glucokinase Is Required for the Synergistic Action of ChREBP and SREBP-1c on Glycolytic and Lipogenic Gene Expression (2004)

Hepatic glucokinase (GK) catalyzes the phosphorylation of glucose to glucose 6-phosphate (G6P), a step which is essential for glucose metabolism in liver as well as for the induction of glycolytic and lipogenic genes. The sterol regulatory element-binding protein-1c (SREBP-1c) has emerged as a major mediator of insulin action on hepatic gene expression, but the extent to which its transcriptional effect is caused by an increased glucose metabolism remains unclear. Through the use of hepatic GK knockout mice (hGK-KO) we have shown that the acute stimulation by glucose of l-pyruvate kinase (l-PK), fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and Spot 14 genes requires GK expression. To determine whether the effect of SREBP-1c requires GK expression and subsequent glucose metabolism, a transcriptionally active form of SREBP-1c was overexpressed both in vivo and in primary cultures of control and hGK-KO hepatocytes. Our results demonstrate that the synergistic action of SREBP-1c and glucose metabolism via GK is necessary for the maximal induction of l-PK, ACC, FAS, and Spot 14 gene expression. Indeed, in hGK-KO hepatocytes overexpressing SREBP-1c, the effect of glucose on glycolytic and lipogenic genes is lost because of the impaired ability of these hepatocytes to efficiently metabolize glucose, despite a marked increase in low K(m) hexokinase activity. Our studies also reveal that the loss of glucose effect observed in hGK-KO hepatocytes is associated with a decreased in the carbohydrate responsive element-binding protein (ChREBP) gene expression, a transcription factor suggested to mediate glucose signaling in liver. Decreased ChREBP gene expression, achieved using small interfering RNA, results in a loss of glucose effect on endogenous glycolytic (l-PK) and lipogenic (FAS, ACC) gene expression, thereby demonstrating the direct implication of ChREBP in glucose action. Together these results support a model whereby both SREBP-1c and glucose metabolism, acting via ChREBP, are necessary for the dietary induction of glycolytic and lipogenic gene expression in liver.
A role for angiogenesis in rheumatoid arthritis (1999)

Rheumatoid arthritis (RA) is a chronic debilitating disease characterized by distinct autoimmune, inflammatory and fibrovascular components which lead to synovial proliferation and joint destruction. However, existing treatments specifically target only autoimmune and inflammatory components despite the fact that neovascularization of the inflamed synovium is a hallmark of rheumatoid arthritis. Angiogenesis may contribute to synovial growth, leukocyte recruitment and tissue remodeling, thus potentiating disease progression. Although no therapies currently target angiogenesis, several existing therapies have anti-angiogenic activity. Recent advances in anti-angiogenic strategies in oncology, including the identification of integrin alpha v beta 3 as a crucial effector of angiogenesis, suggest a means to assess the role of angiogenesis in rheumatoid arthritis. Synovial endothelial cells have been shown to express integrin alpha v beta 3, suggesting that these cells may be targeted for angiogenesis inhibition. Prior studies in rat arthritis models have shown benefit after the addition of broad spectrum integrin antagonists. However, formal assessment of integrin-targeted anti-angiogenic activity is now underway. These controlled studies will be important in assessing the efficacy of therapies which target angiogenesis in RA.
Ausbildungsnachweis/Berichtsheft (1999)

Bereits Generationen von Auszubildenden haben sich vor Ihnen darüber geärgert, dass sie ein Berichtsheft führen müssen. Welcher Sinn oder Unsinn steckt hinter dieser Vorschrift?
Dealer collaboration: transforming the value chain through integration and relationships (2004)

The retail and aftermarket in most value chains is highly segmented and can include dealers, distributors, resellers, independent repair shops, parts suppliers, specialized accessory retail stores and content providers. In the automotive industry, the aftermarket value chain is quite large and fragmented. OEMs need to transform the way they do business in order to obtain a share of this aftermarket revenue and provide better quality of service for handling critical product failures. Crucial failure symptom information is lost between the end consumers of products and the manufacturers due to lack of proper collaboration with dealerships and intermediaries offering independent service. Currently, this results in increased warranty costs for manufacturers and customer defection. In this paper, we present an IBM software solution for automotive dealer collaboration, which enhances the OEM-Dealer relationship through contextual collaboration, information integration and transparent process management. The solution is based on open standards such as Web services, J2EE, J2ME, Struts and others.
Antigen-Specific Signaling by a Soluble, Dimeric Peptide/Major Histocompatibility Complex Class II/Fc Chimera Leading to T Helper Cell Type 2 Differentiation (1999)

Interaction between a T cell receptor (TCR) and various ligands, i.e. , anti-TCR antibodies, superantigens, peptides, or altered peptide ligands in the context of major histocompatibility complex (MHC) molecules can trigger different T helper cell (Th) effector functions. Herein, we studied the T cell response induced by a soluble, dimeric peptide/MHC class II chimera, namely hemagglutinin (HA)110-120/I-E(d)alphabeta/Fcgamma2a (DEF). We have previously demonstrated that the soluble DEF molecule binds stably and specifically to HA110-120-specific TCRs expressed by a T cell hybridoma. Administration of DEF in vivo induced differentiation of resting and activated peptide-specific T cells toward a Th2 response, as indicated by the increase of interleukin (IL)-4, IL-10, and specific immunoglobulin (Ig)G1 antibodies and decrease of IL-2, specific IgG2a antibodies, and cytotoxic T lymphocyte activity. In contrast to HA110-120 peptide presented by the DEF molecule to T cells, the nominal synthetic peptide induced a predominant Th1 response, and the PR8 virus-derived HA110-120 peptides induced a mixed Th1/Th2 response. Independent of antigen processing, soluble DEF was almost 2 logs more potent in stimulating cognate T cells than the nominal peptide. Polarization of cognate T cells toward the Th2 response occurred upon interaction of soluble DEF with TCR and CD4 molecules followed by early activation of p56(lck) and ZAP-70 tyrosine kinases, and negative signaling of the signal transducer and activator of transcription (STAT)4 pathway of Th1 differentiation. DEF-like molecules may provide a new tool to study the mechanisms of signaling toward Th2 differentiation and may also provide a potential immunotherapeutic approach to modulate autoreactive T cells toward protective Th2 immune responses.
DNA methylation versus coronary artery disease, a review (2015)

DNA methylation is a chemical modification with methyl, occurring in the DNA sequence. It can be inherited steadily before or after the transcription and the cell division. Recent studies demonstrated that DNA methylation is mediated by some environmental factors, and it is involved in the pathogenic process of coronary artery disease. This paper systematically reviews the relationships between DNA methylation and the biomarkers of coronary artery disease, the relationships between DNA methylation and the primary etiology of coronary artery disease, i.e. atherosclerosis, and the relationships between DNA methylation and the pathogenic genes of coronary artery disease. In addition, the problems related to the current epigenetic studies for coronary heart disease are also addressed. Finally, directions for future studies to unravel the relationship between DNA methylation and coronary artery disease are discussed.


Key words: 
DNA methylation; Coronary aretery disease; Biomarkers; Atherosclerosis
Differential Colonization Dynamics of Cucurbit Hosts by Erwinia tracheiphila (2016)

Bacterial wilt is one of the most destructive diseases of cucurbits in the Midwestern and Northeastern United States. Although the disease has been studied since 1900, host colonization dynamics remain unclear. Cucumis- and Cucurbita-derived strains exhibit host preference for the cucurbit genus from which they were isolated. We constructed a bioluminescent strain of Erwinia tracheiphila (TedCu10-BL#9) and colonization of different cucurbit hosts was monitored. At the second-true-leaf stage, Cucumis melo plants were inoculated with TedCu10-BL#9 via wounded leaves, stems, and roots. Daily monitoring of colonization showed bioluminescent bacteria in the inoculated leaf and petiole beginning 1 day postinoculation (DPI). The bacteria spread to roots via the stem by 2 DPI, reached the plant extremities 4 DPI, and the plant wilted 6 DPI. However, Cucurbita plants inoculated with TedCu10-BL#9 did not wilt, even at 35 DPI. Bioluminescent bacteria were detected 6 DPI in the main stem of squash and pumpkin plants, which harbored approximately 10(4) and 10(1) CFU/g, respectively, of TedCu10-BL#9 without symptoms. Although significantly less systemic plant colonization was observed in nonpreferred host Cucurbita plants compared with preferred hosts, the mechanism of tolerance of Cucurbita plants to E. tracheiphila strains from Cucumis remains unknown.
In situ hybridization evidence for angiotensinogen messenger RNA in the rat proximal tubule. An hypothesis for the intrarenal renin angiotensin system. (1990)

We examined angiotensinogen gene expression in rat kidney by in situ hybridization histochemistry. Using a rat cRNA probe to angiotensinogen, we demonstrated angiotensinogen mRNA to be localized predominantly in the proximal renal tubule, with considerably lesser amounts in distal tubular segments and glomerular tufts. Previous studies have localized renin immunoreactivity to the juxtaglomerular cells, glomerular tufts, and proximal tubules. Such findings provide further evidence for a local tissue renin angiotensin system within the kidney which may influence regional function. Based on our data, we hypothesize that a major site of angiotensin production is the proximal tubule. We postulate that angiotensin synthesized in and/or around the proximal tubule may directly modulate tubular transport of sodium, bicarbonate, and water. In addition to the proximal tubule, the specific localization of the renin angiotensin components elsewhere in the kidney would also support the other proposed regional functions of the intrarenal system, including modulation of tubuloglomerular balance.
Identifying bacterial genes and endosymbiont DNA with Glimmer (2007)

Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmer.
Tissue-Restricted Adaptive Type 2 Immunity Is Orchestrated by Expression of the Costimulatory Molecule OX40L on Group 2 Innate Lymphoid Cells (2018)

The local regulation of type 2 immunity relies on dialog between the epithelium and the innate and adaptive immune cells. Here we found that alarmin-induced expression of the co-stimulatory molecule OX40L on group 2 innate lymphoid cells (ILC2s) provided tissue-restricted T cell co-stimulation that was indispensable for Th2 and regulatory T (Treg) cell responses in the lung and adipose tissue. Interleukin (IL)-33 administration resulted in organ-specific surface expression of OX40L on ILC2s and the concomitant expansion of Th2 and Treg cells, which was abolished upon deletion of OX40L on ILC2s (Il7ra<sup>Cre/+</sup>Tnfsf4<sup>fl/fl</sup> mice). Moreover, Il7ra<sup>Cre/+</sup>Tnfsf4<sup>fl/fl</sup> mice failed to mount effective Th2 and Treg cell responses and corresponding adaptive type 2 pulmonary inflammation arising from Nippostrongylus brasiliensis infection or allergen exposure. Thus, the increased expression of OX40L in response to IL-33 acts as a licensing signal in the orchestration of tissue-specific adaptive type 2 immunity, without which this response fails to establish.
Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro (1990)

Normal replication of Moloney murine leukemia virus (MoMLV) requires the integration of a DNA copy of the viral RNA genome into a chromosome of the host. In this work, we characterize the DNA sequences at the ends of the linear proviral precursor that are required for integration in the presence of MoMLV integration protein in vitro. We found that nine bases of MoMLV DNA at each end of a linear model substrate were sufficient for near-maximal levels of integration and that four bases of MoMLV DNA at each end were sufficient for low levels of correct integration. We also found that a 3'-terminal A residue was preferred for integration. We infer from the limited DNA sequence requirements for integration that factors in addition to DNA sequence direct integration protein to act at the ends of the viral DNA.