gebhart/patrepeval huggingface dataset:
Laccases Associated with Lignifying Vascular Tissues (1998)

Lignin is formed via the oxidative polymerization of monolignols within the plant cell wall matrix. Peroxidases, which are abundant in virtually all cell walls, can oxidize the monolignols in the presence of H2O2, and have long been held to be the principal catalysts for this reaction. Recent evidence shows, however, that laccases (p-diphenol: O2 oxidoreductases, EC 1.10.3.2) secreted into the secondary walls of vascular tissues are equally capable of polymerizing monolignols in the presence of O2. Full-length and partial laccase gene clones recovered from several different species suggest that these enzymes are widely distributed in the plant kingdom, and may generally occur as multiple isozymes within acidic and basic isoform classes. Although expression of antisense laccase gene constructs in transgenic plants has yet to bring about demonstrable alterations in lignin content, ectopic expression of laccase activity in yellow-poplars regenerated from transformed embryogenic cell lines resulted in a severely dwarfed phenotype having fused organs and hardened tissues.
Bloodspot Assay Using HPLC–Tandem Mass Spectrometry for Detection of Barth Syndrome (2007)

HPLC-tandem mass spectrometry analysis of dried bloodspots is an unambiguous screening test for BTHS with potential for rapid screening of neonates suspected of having BTHS, making remote and retrospective diagnosis accessible for a disease that is almost certainly underdiagnosed.
The timing of maize leaf senescence and characterisation of senescence‐related cDNAs (1995)

Leaf senescence was characterised in two Zea mays lines, earlier senescence (ES) and later senescence (LS). Loss of chlorophyll was delayed in LS compared with ES, but the decline in photosynthesis occurred simultaneously in the two lines. Western analysis detected transition points during senescence of both lines when major quantitative and qualitative changes occurred in a number of leaf proteins. Differences in the pattern of translatable mRNAs were apparent earlier than alterations in pigment or protein levels. A cDNA library was constructed using mRNA from ES leaves early in senescence and differential screening was employed to isolate senescence‐related clones. Two senescence‐enhanced cDNAs showed sequence homology with cDNAs for seed proteins ‐ a cysteine protease and a protein‐processing enzyme. These findings suggest that there are similarities between gene expression during seed maturation, germination and leaf senescence. Other senescence‐enhanced cDNAs were related to genes implicated in gluconeogenesis and chlorophyll breakdown.
Purification and Properties of Membrane-Bound Aminopeptidase P from Rat Lung (1995)

The membrane-bound form of aminopeptidase P (aminoacylprolyl-peptide hydrolase) (EC 3.4.11.9) was purified 670-fold to apparent homogeneity from rat lung microsomes. The enzyme was solubilized from the membranes using a phosphatidylinositol-specific phospholipase C. The purification scheme also resulted in homogeneous preparations of dipeptidylpeptidase IV (EC 3.4.14.5) and membrane dipeptidase (EC 3.4.13.19). Aminopeptidase P had a subunit molecular weight of 90,000, which included at least 17% N-linked carbohydrate. The molecular weight by gel permeation chromatography varied from 220,000 to 340,000, depending on the conditions used. The amino acid composition was determined and the N-terminal sequence was found to be X1-Gly2-Pro3-Glu4-Ser5-Leu6-Gly7-Arg8-Glu9-As p10-Val11-Arg12-Asp13-X14-Ser15- Thr16-Asn17-Pro18-Pro19-Arg20-Leu21- X22-Val23-Thr24-Ala25-. Aminopeptidase P cleaved the Arg1-Pro2 bond of bradykinin with a kcat/Km of 5.7 x 10(5) s-1 M-1. N-Terminal fragments of bradykinin including Arg-Pro-Pro, but not Arg-Pro, were also cleaved. The enzyme was shown to have four binding subsites (S1, S1', S2'. S3'), the first three of which must be occupied for hydrolysis to occur. Neuropeptide Y and allatostatin I were hydrolyzed at the Tyr1-Pro2 bond and Ala1-Pro2 bond, respectively. The pH optimum for Arg-Pro-Pro cleavage was 6.8-7.5 in most buffers. The enzyme was most stable in the range of pH 7.0-10.5 in the presence of poly(ethylene glycol). NaCl inhibited activity completely at 2 M. Mn2+ had variable effects on activity, depending on its concentration and the substrate used. Various peptides having an N-terminal Pro-Pro sequence were inhibitory. The enzyme was also inhibited by EDTA, o-phenanthroline, 2-mercaptoethanol, dithiothreitol, p-(chloromercuri)benzenesulfonic acid, apstatin, and captopril. The carboxyalkyl angiotensin-converting enzyme inhibitors, ramiprilat and enalaprilat, inhibited activity in the micromolar range only in the presence of Mn2+.
A release-competent influenza A virus mutant lacking the coding capacity for the neuraminidase active site (2002)

Both influenza A virus surface glycoproteins, the haemagglutinin (HA) and neuraminidase (NA), interact with neuraminic acid-containing receptors. The influenza virus A/Charlottesville/31/95 (H1N1) has shown a substantially reduced sensitivity to NA inhibitor compared with the A/WSN/33 (H1N1) isolate by plaque-reduction assays in Madin-Darby canine kidney (MDCK) cells. However, there was no difference in drug sensitivity in an NA inhibition assay. The replacement of the HA gene of A/WSN/33 with the HA gene of A/Charlottesville/31/95 led to a drastic reduction in sensitivity of A/WSN/33 to NA inhibitor in MDCK cells. Passage of A/Charlottesville/31/95 in cell culture in the presence of an NA inhibitor resulted in the emergence of mutant viruses (delNA) whose genomes lacked the coding capacity for the NA active site. The delNA mutants were plaque-to-plaque purified and further characterized. The delNA-31 mutant produced appreciable yields ( approximately 10(6) p.f.u./ml) in MDCK cell culture supernatants in the absence of viral or bacterial NA activity. Sequence analysis of the delNA mutant genome revealed no compensatory substitutions in the HA or other genes compared with the wild-type. Our data indicate that sialylation of the oligosaccharide chains in the vicinity of the HA receptor-binding site of A/Charlottesville/31/95 virus reduces the HA binding efficiency and thus serves as a compensatory mechanism for the loss of NA activity. Hyperglycosylation of HA is common in influenza A viruses circulating in humans and has the potential to reduce virus sensitivity to NA inhibitors.
A Lateral Mode Flow-through PMMA Ultrasonic Separator (2010)

A flow-through ultrasonic separator constructed entirely from PMMA has been demonstrated for the first time. Continuous extraction of lipids from milk has been achieved. Construction is simple, requiring channels to be embossed at low temperatures (120°C) with a room temperature solvent bond used to close the channel.
GS52 Ecto-Apyrase Plays a Critical Role during Soybean Nodulation (2008)

Apyrases are non-energy-coupled nucleotide phosphohydrolases that hydrolyze nucleoside triphosphates and nucleoside diphosphates to nucleoside monophosphates and orthophosphates. GS52, a soybean (Glycine soja) ecto-apyrase, was previously shown to be induced very early in response to inoculation with the symbiotic bacterium Bradyrhizobium japonicum. Overexpression of the GS52 ecto-apyrase in Lotus japonicus increased the level of rhizobial infection and enhanced nodulation. These data suggest a critical role for the GS52 ecto-apyrase during nodulation. To further investigate the role of GS52 during nodulation, we used RNA interference to silence GS52 expression in soybean (Glycine max) roots using Agrobacterium rhizogenes-mediated root transformation. Transcript levels of GS52 were significantly reduced in GS52 silenced roots and these roots exhibited reduced numbers of mature nodules. Development of the nodule primordium and subsequent nodule maturation was significantly suppressed in GS52 silenced roots. Transmission electron micrographs of GS52 silenced root nodules showed that early senescence and infected cortical cells were devoid of symbiosome-containing bacteroids. Application of exogenous adenosine diphosphate to silenced GS52 roots restored nodule development. Restored nodules contained bacteroids, thus indicating that extracellular adenosine diphosphate is important during nodulation. These results clearly suggest that GS52 ecto-apyrase catalytic activity is critical for the early B. japonicum infection process, initiation of nodule primordium development, and subsequent nodule organogenesis in soybean.
Tissue factor expression in endothelial cells in health and disease (1995)

Plasma tissue factor (TF) antigen can be detected in healthy volunteers and may be significantly increased in patients with disseminated intravascular coagulation (DIC). Plasma TF antigen level in patients with DIC was significantly reduced after therapy. The TF activity of human umbilical vein endothelial cells (HUVEC) cultured with lipopolysaccharide (LPS), cytokines and the medium of cultured mononuclear cells (MNC) was significantly increased. TF expression was induced in HUVEC and MNC by incubation with lipoproteins, suggesting that hyperlipidaemia is a direct risk factor in thrombotic disease. TF activity in HUVEC was significantly increased in the presence of plasma and this activation was higher in patients with thrombotic thrombocytopenic purpura (TTP) and DIC. Enhanced TF production by endothelial cells may be important in the pathogenesis of thrombotic diseases.
Stent Endothelialization (1997)

(1) Local delivery of recombinant protein to the arterial wall is feasible after stent implantation, and (2) local delivery of the endothelial cell mitogen VEGF accelerates stent endothelialization, reducing stent thrombosis. These results thus establish a novel means by which the safety and/or bioactivity of endovascular stents may be further enhanced.
Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) / CRISPR Associated (Cas) Systems (2012)

Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.
Fluorescence enhancement by hydroperoxides based on a change in the intramolecular charge transfer character of benzofurazan (2005)

Strong fluorescence signals were observed after the reaction of novel reagents with hydroperoxides.
Membrane Stiffness of Animal Cells Challenged by Osmotic Stress (2006)

An atomic force microscope equipped with either a spherical indenter (see SEM image) or a conical tip has been utilized to analyze the nanomechanical behavior of living kidney cells under osmotic stress. The Young's modulus of the cells increases with osmolarity of the medium due to immense compaction of the cell. The change of stiffness is highly reversible and depends strongly on the location on the cell surface.
Dihydroaeruginoic acid synthetase and pyochelin synthetase, products of the pchEF, are induced by extracellular pyochelin in Pseudornonas aeruginosa (1998)

The siderophore pyochelin of Pseudomonas aeruginosa is derived from one molecule of salicylate and two molecules of cysteine. Two cotranscribed genes, pchEF, encoding peptide synthetases have been identified and characterized. pchE was required for the conversion of salicylate to dihydroaeruginoate (Dha), the condensation product of salicylate and one cysteine residue and pchF was essential for the synthesis of pyochelin from Dha. The deduced PchE (156 kDa) and PchF (197 kDa) proteins had adenylation, thiolation and condensation/cyclization motifs arranged as modules which are typical of those peptide synthetases forming thiazoline rings. The pchEF genes were coregulated with the pchDCBA operon, which provides enzymes for the synthesis (PchBA) and activation (PchD) of salicylate as well as a putative thioesterase (PchC). Expression of a translational pchE'-'lacZ fusion was strictly dependent on the PchR regulator and was induced by extracellular pyochelin, the end product of the pathway. Iron replete conditions led to Fur (ferric uptake regulator)-dependent repression of the pchE'-'lacZ fusion. A translational pchD'-'lacZ fusion was also positively regulated by PchR and pyochelin and repressed by Fur and iron. Thus, autoinduction by pyochelin (or ferric pyochelin) and repression by iron ensure a sensitive control of the pyochelin pathway in P. aeruginosa.
Controlling Cell Chemistry with Caged Compounds (1993)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Lack of inhibitory effects of the anti‐fibrotic drug imatinib on endothelial cell functions in vitro and in vivo (2008)

Systemic sclerosis (SSc) is a systemic autoimmune disease that is characterized by microangiopathy with progressive loss of capillaries and tissue fibrosis. Imatinib exerts potent anti-fibrotic effects and is currently evaluated in clinical trials. The aim of the present study was to exclude that the anti-fibrotic effects of imatinib are complicated by inhibitory effects on endothelial cell functions, which might augment vascular disease in SSc. Endothelial cells and mice were treated with pharmacologically relevant concentrations of imatinib. The expression of markers of vascular activation was assessed with real-time PCR. Proliferation was analysed with the cell counting experiments and the MTT assay. Apoptosis was quantified with caspase 3 assays, annexin V in vitro and with TUNEL staining in vivo. Migration was studied with scratch and transwell assays. Tube forming was investigated with the matrigel assay. Imatinib did not alter the expression of markers of vascular activation. Imatinib did not increase the percentage of annexin V positive cells or the activity of caspase 3. No reduction in proliferation or metabolic activity of endothelial cells was observed. Imatinib did not affect migration of endothelial cells and did not reduce the formation of capillary tubes. Consistent with the in vitro data, no difference in the number of apoptotic endothelial cells was observed in vivo in mice treated with imatinib. Imatinib does not inhibit activation, viability, proliferation, migration or tube forming of endothelial cells in vitro and in vivo. Thus, treatment with imatinib might not augment further endothelial cell damage in SSc.
In Vitro Import of a Nuclearly Encoded tRNA into the Mitochondrion of Trypanosoma brucei (1999)

All of the mitochondrial tRNAs of Trypanosoma brucei have been shown to be encoded in the nucleus and must be imported into the mitochondrion. The import of nuclearly encoded tRNAs into the mitochondrion has been demonstrated in a variety of organisms and is essential for proper function in the mitochondrion. An in vitro import assay has been developed to study the pathway of tRNA import in T. brucei. The in vitro system utilizes crude isolated trypanosome mitochondria and synthetic RNAs transcribed from a cloned nucleus-encoded tRNA gene cluster. The substrate, composed of tRNA(Ser) and tRNA(Leu), is transcribed in tandem with a 59-nucleotide intergenic region. The tandem tRNA substrate is imported rapidly, while the mature-size tRNA(Leu) fails to be imported in this system. These results suggest that the preferred substrate for tRNA import into trypanosome mitochondria is a precursor molecule composed of tandemly linked tRNAs. Import of the tandem tRNA substrate requires (i) a protein component that is associated with the surface of the mitochondrion, (ii) ATP pools both outside and within the mitochondrion, and (iii) a membrane potential. Dissipation of the proton gradient across the inner mitochondrial membrane by treatment with an uncoupling agent inhibits import of the tandem tRNA substrate. Characterization of the import requirements indicates that mitochondrial RNA import proceeds by a pathway including a protein component associated with the outer mitochondrial membrane, ATP-dependent steps, and a mitochondrial membrane potential.
RNA-Mediated Virus Resistance: Role of Repeated Transgenes and Delineation of Targeted Regions. (1996)

Resistance to cowpea mosaic virus (CPMV) in transgenic Nicotiana benthamiana plants is RNA mediated. In resistant CPMV movement protein (MP) gene-transformed lines, transgene steady state mRNA levels were low, whereas nuclear transcription rates were high, implying that a post-transcriptional gene-silencing mechanism is at the base of the resistance. The silencing mechanism can also affect potato virus X (PVX) RNAs when they contain CPMV MP gene sequences. In particular, sequences situated in the 3[prime] part of the transcribed region of the MP transgene direct elimination of recombinant PVX genomes. Remarkably, successive portions of this 3[prime] part, which can be as small as 60 nucleotides, all tag PVX genomes for degradation. These observations suggest that the entire 3[prime] part of the MP transgene mRNA is the initial target of the silencing mechanism. The arrangement of transgenes in the plant genome plays an important role in establishing resistance because the frequency of resistant lines increased from 20 to 60% when transformed with a transgene containing a direct repeat of MP sequences rather than a single MP transgene. Interestingly, we detected strong methylation in all of the plants containing directly repeated MP sequences. In sensitive lines, only the promoter region was found to be heavily methylated, whereas in resistant lines, only the transcribed region was strongly methylated.
WIDE workflow development methodology (1999)

The development of workflows (WFs) for complex organizations to be interfaced with existing information systems requires a specific methodological approach to guarantee benefits and effectiveness of the final results. In fact, the WF should be well integrated in the organization both from the technical and the organizational point of view. While the characteristics of the Workflow Management System (WFMS) platform adopted in the implementation are relevant to establish the boundary between the workflow system and other related applications, it is also important that the analysis and design phases are developed independently of those characteristics.The WF development methodology proposed in this paper starts with an analysis phase based on UML, adopted for business process descriptions and business goals. The design phase proposes a pattern-based approach to workflow schemas design, based on the WIDE WF model. This model allows a flexible representation of the exceptions which may occur during WF execution. It also considers the interaction of the WF with external applications and information systems. Finally, the paper briefly discusses the mapping to commercial and prototype WFMSs.
Quantitative analysis of animal model lens anatomy: accommodative range is related to fiber structure and organization (2006)

In humans, the mechanism of accommodation at the fiber level involves the controlled realignment of very flattened and flared, rather than tapered fiber-ends at sutures. In this manner, the simultaneous increase in lens thickness and surface curvature in the accommodated state is the result of fiber-ends being overlapped along multiple (9-12) suture branches covering the majority of the anterior and posterior surfaces. The results of this animal study strongly suggest that accommodative range is directly related to quantitative differences in fiber structure and organization in the different suture types. The very broad accommodative range in birds is made possible, at least in part, by the almost complete tapering of fiber-ends at umbilical sutures. In contrast, the essentially negligible accommodative range of animals that have line- and Y-suture lenses is at least partially the result of the fact that these lenses have fibers with very little end taper. Thus, the blunt ends of fibers in line- and Y-suture lenses precludes any significant overlap of end segments to effect accommodation.
Protective effect of 55- but not 75-kD soluble tumor necrosis factor receptor-immunoglobulin G fusion proteins in an animal model of gram-negative sepsis. (1994)

The aim of this study was to compare the ability of both a 55- and 75-kD soluble tumor necrosis factor receptor immunoglobulin G fusion protein (sTNFR-IgG) in protecting against death in a murine model of gram-negative sepsis. Pretreatment with 250 micrograms of the p75 construct delayed but did not avert death in this model, reducing peak bioactive TNF-alpha levels after infection from 76.4 ng ml-1 in control mice to 4.7 ng ml-1 in the treated group (p < 0.05, two-sample t test). However, these low levels of bioactive TNF-alpha persisted in the p75 fusion protein-treated animals compared with the controls and were sufficient to mediate delayed death. In contrast, pretreatment with 200 micrograms of the p55 sTNFR-IgG gave excellent protection against death with complete neutralization of circulating TNF. Studies of the binding of TNF-alpha with the soluble TNFR fusion proteins showed that the p75 fusion construct exchanges bound TNF-alpha about 50-100-fold faster than the p55 fusion protein. Thus, although both fusion proteins in equilibrium bind TNF-alpha with high affinity, the TNF-alpha p55 fusion protein complex is kinetically more stable than the p75 fusion construct, which thus acts as a TNF carrier. The persistent release of TNF-alpha from the p75 fusion construct limits its therapeutic effect in this model of sepsis.
Acylmorphinans. A novel class of potent analgesic agents (1985)

A series of novel 2- and 3-acylmorphinans (8-14) was synthesized in our search for a potent analgesic agent with low addiction potential. The compounds were evaluated for antinociceptive potency and receptor binding affinity. Among these compounds, the levorotatory 3-acetyl-N-(cyclopropylmethyl)morphinan (12) was found to be an orally active analgesic, comparable in potency to morphine (1), yet only weakly able to substitute for morphine (1) in morphine-dependent rats.
Immunoassays : a practical approach (2000)

Analysis by specific binding raising antibodies choosing and characterizing antibodies labels and endpoints solid-phase reagents standard and immunogens optimization validation data processing quality assurance.
Stochastic Complexity (1987)

SUMMARY It is argued that all the useful information in observed data that can be extracted with a selected class of modeled distributions, will be obtained if we calculate the stochastic complexity, defined to be the shortest description length of the data. The same quantity also determines the greatest lower bound for prediction errors when the data are sequentially predicted. An abstract definition of stochastic complexity is given along with two fundamental theorems which justify the notion. Further, three explicit model selection criteria to approximate the stochastic complexity are described and the associated optimal models are interpreted to define asymptotically sufficient statistics for the data.