gebhart/patrepeval huggingface dataset:
Differential mechanisms targeting type 1 plasminogen activator inhibitor and vitronectin into the storage granules of a human megakaryocytic cell line (1996)

Type 1 plasminogen activator inhibitor (PAI-1) and its cofactor vitronectin (Vn) are stored within the alpha-granules of platelets. The two possible sources for their biosynthetic origin are endogenous synthesis in megakaryocytes or endocytosis from plasma. Using ultrastructural and confocal laser scanning microscopic (CLSM) image analysis, we observed that treatment of Dami cells, a human megakaryocytic cell line, with phorbol myristate acetate (PMA) induces the accumulation of PAI-1 and Vn in intracellular storage vacuoles that contain other alpha-granule proteins such as von Willebrand factor. To examine evidence for biosynthesis of PAI-1 and Vn by Dami cells, we immunoprecipitated PAI-1 and Vn from the conditioned media of cells biosynthetically radiolabeled with 35S-methionine in the presence or absence of PMA. In contrast to Hep G2 cells, which synthesize both PAI-1 and Vn, only 35S-PAI-1 was recovered from PMA-treated Dami cells. Reverse transcription-PCR analysis of RNA extracted from resting and PMA-treated Dami cells confirmed that PAI-1 mRNA expression was detectable at low levels in resting cells and induced by PMA treatment. In contrast, Vn mRNA was not detected. We examined binding and internalization (endocytosis) of PAI-1 and Vn by Dami cells using biotinylated analogs (b-PAI-1 and b-Vn). Flow cytometry analysis indicated that the binding of b-Vn to Dami cells was dose-dependent, saturable, and specific for multimeric forms of Vn. Cells were incubated at 4 degrees C or 37 degrees C and endocytosis of b-Vn was shown by probing electrophoretically fractionated cell lysates with 125I-labeled streptavidin. Only cells incubated at 37 degrees C internalized b-Vn. CLSM image analysis confirmed that the b-Vn was internalized and that it colocalized with PAI-1 in storage granules. The binding of b-Vn to cells was inhibited by the presence of PAI-1, and there was no evidence of specific b-PAI-1 binding or uptake to resting or PMA-treated cells. These data suggest that accumulation of PAI-1 in Dami cell storage granules is due to endogenous synthesis and that the accumulation of Vn is due to endocytosis of serum-derived Vn.
A study of field emission microtriodes (1991)

Structures simulating integrated field emission microtriodes have been successfully fabricated and tested. These microtriodes use Spindt-type molybdenum field emission cathodes with the anodes in three different configurations. The anodes are located at a distance d>5 mm, approximately 1.25 mm, and approximately 2-20 mu m from the gate electrode and the emitter tip. The effects of device operation on the performance of the Mo field emission tips operating in close proximity to anodes were presented. A transconductance of 0.5 mS (5 mu S/tip or 12 S/cm/sup 2/) and a cutoff frequency of 0.8 MHz have been measured. Extension of these results indicates that transconductances of 250 mS/mm and cutoff frequencies of 100 GHz may be possible.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Evaluation of the aerodynamic control of the Space Shuttle orbiter and tip-fin controllers (1984)

A feasibility study to assess the benefits/penalties of installing tip-fin controllers on the Space Shuttle orbiter has been conducted. The results from the aerodynamic and stability and control assessment of this study are presented. These results show that using tip-fin controllers with the centerline vertical tail removed provides adequate control for entry. The orbiter basic maneuvering capability is maintained, and symmetrical deflection of the controllers provides adequate speedbrake authority for energy management. Gust analyses of the orbiter with the tip-fin controller configuration have demonstrated no compromise of existing cross-wind landing capability. Six-degree-of-freedom simulations have shown the tip-fin controllers can provide adequate control for entry with no degradation in vehicle capability.
Weldability of pure titanium and AZ31 magnesium alloy by friction stir welding (2007)

Pure titanium and AZ31B magnesium alloy sheets were butt joined by friction stir welding method (FSW) with different joining parameters by tool rotating speed and changing probe position from the joint interface. Al-rich titanium layer with under 2 μm in thickness was formed at a joint interface in pure titanium side in the following FSW conditions (travel speed: 300 mm/min, tool rotating speed: 1500 rpm , probe position: 1.2 mm into titanium). Near the joint interface, the grain of titanium was deformed by both heat effect and stirring force , and vickers hardness of titanium increased to 200 HV 0.05 in comparison with base metal hardness 150 HV 0.05 because of work hardening. However AZ31B showed no obvious hardness change. Tensile strength of the joint increased with changing the prove position into the titanium side and the maximum strength 156 MPa was obtained at probe position of 1.2 mm into titanium side. Fracture occurred in the stir zone of AZ31B.
Remote Afterloading Transurethral Radiotherapy for Prostatic Cancer (1990)

We have developed a technique of transurethral radiotherapy for prostatic cancer using a remote after-loading system. The radioactive source is a cobalt-60 pellet with 3.7-Ci activity. Four patients with adenocarcinoma of the prostate were treated. In all patients, the local tumor response was rapid and satisfactory as judged by physical examination as well as ultrasonography. Serious complications were not seen. A new technique and preliminary clinical results are reported.
A grid layout algorithm for automatic drawing of biochemical networks (2005)

Motivation: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. Results: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. Availability: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ Contact:kurata@bio.kyutech.ac.jp Supplementary information:http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/
Block Distortion in Orthogonal Transform Coding--Analysis, Minimization, and Distortion Measure (1985)

Psychophysical considerations show that the block-shaped distortion peculiar to orthogonal transform coding (OTC) is ten times more objectionable than random noise distortion. Minimizing the blockshaped distortion is considered here by analyzing the process of generation of coding errors, and the required characteristics of the orthogonal transform function (OTF) are clarified. Computer simulations substantiate its validity. Graphical illustration and measures of the block-shaped distortion are proposed and substantiated. With the aid of these measures, one can evaluate the performance of OTC or a new OTF, if proposed, without conducting visual assessment tests.
SECRETION OF EXTRACELLULAR VIRULENCE FACTORS BY PLANT PATHOGENIC BACTERIA (1994)

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for ...Read More
Increased expression of Siglec-1 on peripheral blood monocytes and its role in mononuclear cell reactivity to autoantigen in rheumatoid arthritis (2013)

Elevated Siglec-1 expression in PBMCs and monocytes can potentially serve as a biomarker for monitoring disease activity in RA. Siglec-1 may also play a proinflammatory role in stimulating lymphocyte proliferation and activation in RA.
Connectionist predicate logic model with parallel execution of rule chains (2010)

In this paper, we describe a model for reasoning using forward chaining for predicate logic rules and facts with coarse-coded distributed representations for instantiated predicates in a connectionist frame work. Distributed representations are known to give advantages of good generalization, error correction and graceful degradation of performance under noise conditions. The system supports usage of complex rules which involve multiple conjunctions and disjunctions. The system supports parallel and independent execution of predicate logic rule chains in a connectionist environment. The system solves the variable binding problem in a new way using coarse-coded distributed representations of instantiated predicates. Its performance with regard to generalization on unseen inputs and its ability to exhibit fault tolerance under noise conditions is studied and has been found to give good results.
Cadherins in Cutaneous Biology (1994)

The role of cadherins in cutaneous biology has focused mainly on the classical cadherins, E- and P-cadherin. In this review, roles for cadherins in skin morphogenesis, keratinocyte differentiation, and cancer metastasis are discussed. E-cadherin is expressed on the surfaces of whole epidermal layer cells, and P-cadherin is expressed only on the surfaces of basal cells. Ultrastructural studies have shown that E-cadherin is distributed on the cytoplasmic membranes of keratinocytes with a condensation in the intercellular space of the desmosomes. During human skin development, P-cadherin expression is spatiotemporally controlled and closely related to the segregation of basal layers as well as to the arrangement of epidermal cells into eccrine ducts. In human skin diseases, E-cadherin expression is markedly reduced on the acantholytic cells of tissues in pemphigus and also in Darier's disease. Keratinocytes cultured in high calcium produce a much more intense immunofluorescence of intercellular E- and P-cadherin than do cells grown in low calcium. Ultrastructural studies show that E-cadherin on the cytoplasmic membrane of the keratinocytes is shifted to desmosomes under physiological conditions and therein expresses an adhesion function is association with other desmosomal cadherins. Cell adhesion molecules are now considered to play significant roles in the cellular connections of cancers and metastatic cells. Reduced expression of E-cadherin on invasive neoplastic cells has been demonstrated for cancers of the stomach, liver, breast, and several other organs. This reduced expression of E-cadherin is observed in squamous cell carcinoma and Paget's disease. Soluble E-cadherins in sera are elevated in various skin diseases, including bullous pemphigoid, pemphigus vulgaris and psoriasis, but not in patients with burns. Markedly high levels in soluble E-cadherin are demonstrated in patients with metastatic cancers.
BIPES, a cost-effective high-throughput method for assessing microbial diversity (2010)

Pyrosequencing of 16S rRNA (16S) variable tags has become the most popular method for assessing microbial diversity, but the method remains costly for the evaluation of large numbers of environmental samples with high sequencing depths. We developed a barcoded Illumina paired-end (PE) sequencing (BIPES) method that sequences each 16S V6 tag from both ends on the Illumina HiSeq 2000, and the PE reads are then overlapped to obtain the V6 tag. The average accuracy of Illumina single-end (SE) reads was only 97.9%, which decreased from ∼99.9% at the start of the read to less than 85% at the end of the read; nevertheless, overlapping of the PE reads significantly increased the sequencing accuracy to 99.65% by verifying the 3' end of each SE in which the sequencing quality was degraded. After the removal of tags with two or more mismatches within the medial 40-70 bases of the reads and of tags with any primer errors, the overall base sequencing accuracy of the BIPES reads was further increased to 99.93%. The BIPES reads reflected the amounts of the various tags in the initial template, but long tags and high GC tags were underestimated. The BIPES method yields 20-50 times more 16S V6 tags than does pyrosequencing in a single-flow cell run, and each of the BIPES reads costs less than 1/40 of a pyrosequencing read. As a laborsaving and cost-effective method, BIPES can be routinely used to analyze the microbial ecology of both environmental and human microbiomes.
Membrane Synthesis, Specific Lipid Requirements, and Localized Lipid Composition Changes Associated with a Positive-Strand RNA Virus RNA Replication Protein (2003)

Multifunctional RNA replication protein 1a of brome mosaic virus (BMV), a positive-strand RNA virus, localizes to the cytoplasmic face of endoplasmic reticulum (ER) membranes and induces ER lumenal spherules in which viral RNA synthesis occurs. We previously showed that BMV RNA replication in yeast is severely inhibited prior to negative-strand RNA synthesis by a single-amino-acid substitution in the ole1w allele of yeast Delta9 fatty acid (FA) desaturase, which converts saturated FAs (SFAs) to unsaturated FAs (UFAs). Here we further define the relationships between 1a, membrane lipid composition, and RNA synthesis. We show that 1a expression increases total membrane lipids in wild-type (wt) yeast by 25 to 33%, consistent with recent results indicating that the numerous 1a-induced spherules are enveloped by invaginations of the outer ER membrane. 1a did not alter total membrane lipid composition in wt or ole1w yeast, but the ole1w mutation selectively depleted 18-carbon, monounsaturated (18:1) FA chains and increased 16:0 SFA chains, reducing the UFA-to-SFA ratio from approximately 2.5 to approximately 1.5. Thus, ole1w inhibition of RNA replication was correlated with decreased levels of UFA, membrane fluidity, and plasticity. The ole1w mutation did not alter 1a-induced membrane synthesis, 1a localization to the perinuclear ER, or colocalization of BMV 2a polymerase, nor did it block spherule formation. Moreover, BMV RNA replication templates were still recovered from cell lysates in a 1a-induced, 1a- and membrane-associated, and nuclease-resistant but detergent-susceptible state consistent with spherules. However, unlike nearby ER membranes, the membranes surrounding spherules in ole1w cells were not distinctively stained with osmium tetroxide, which interacts specifically with UFA double bonds. Thus, in ole1w cells, spherule-associated membranes were locally depleted in UFAs. This localized UFA depletion helps to explain why BMV RNA replication is more sensitive than cell growth to reduced UFA levels. The results imply that 1a preferentially interacts with one or more types of membrane lipids.
ChemInform Abstract: Palladium‐Catalyzed Synthesis of 3‐Alkylphthalides via Carbonylative Cyclization of o‐Bromobenzaldehyde with 1,3‐Dicarbonyl Compounds. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quality Control Certification of RNA Aptamer‐Based Detection (2013)

Aptamers are single-stranded DNA or RNA molecules with a defined tertiary structure for molecular recognition. Numerous RNA aptamers with excellent binding affinity and specificity have been reported; they constitute an attractive reservoir of molecular recognition elements for biosensor development. However, RNA is relatively unstable owing to spontaneous hydrolysis and nuclease degradation. Thus, RNA aptamer-based biosensors are prone to producing false-positive signals. Here, we present an RNA aptamer biosensor design strategy that utilises an internal control to distinguish target binding from false-positive signals. The sequence of a chosen RNA aptamer is expanded so that it can form three consecutive short RNA-DNA duplexes with 1) a quencher-labelled DNA strand (Q(1)DNA), 2) a dual-fluorophore-labelled DNA strand (F(1)DNAF(2)) and 3) another quencher-labelled DNA strand (Q(2)DNA). The addition of a target releases Q(2)DNA from the duplex assembly, and produces the expected positive signal from F(2). However, the authenticity of target recognition is validated only if no signal is generated from F(1). We have successfully engineered two fluorescent reporters by using an RNA aptamer that binds thrombin and one that binds theophylline. Both reporters show the expected binding affinity and specificity, and are capable of reporting system malfunction when treated with nucleases and chemical denaturants. This strategy provides a simple and reliable way to ensure high-quality detection when RNA aptamers are employed as molecular-recognition elements.
Non-hydroxamate Histone Deacetylase Inhibitors (2005)

A number of histone deacetylase (HDAC) inhibitors have been developed as anticancer agents and most of them are hydroxamic acid derivatives, typified by suberoylanilide hydroxamic acid (SAHA), Trichostatin A (TSA) and NVP-LAQ824. However, hydroxamic acids have been associated with poor pharmacokinetics and severe toxicity. In addition, although isozyme-selective HDAC inhibitors are considered useful not only as tools for probing the biology of an enzyme but as drugs with low toxicity, many of the hydroxamate HDAC inhibitors do not distinguish well among the HDAC isozymes. Thus, there has been considerable interest in developing non-hydroxamate HDAC inhibitors. To date, small fatty acids, o-aminoanilides, electrophilic ketones, N-formyl hydroxylamines, thiols and mercaptoamides have been reported as non-hydroxamate HDAC inhibitors, and some of them show antiproliferative activity comparable to hydroxamates. Interestingly, hydroxamate HDAC inhibitors such as SAHA and TSA do not discriminate well among the HDAC isozymes whereas many non-hydroxamate HDAC inhibitors have shown selectivity. These non-hydroxamate HDAC inhibitors should pave the way for the development of tools for biological research and new medicines with few side effects. In this review, we introduce non-hydroxamate HDAC inhibitors describing their design, enzyme inhibition, cancer cell growth inhibition and isozyme selectivity.
The pizzicato knee-joint energy harvester: characterization with biomechanical data and the effect of backpack load (2012)

The reduced power requirements of miniaturized electronics offer the opportunity to create devices which rely on energy harvesters for their power supply. In the case of wearable devices, human-based piezoelectric energy harvesting is particularly difficult due to the mismatch between the low frequency of human activities and the high-frequency requirements of piezoelectric transducers. We propose a piezoelectric energy harvester, to be worn on the knee-joint, that relies on the plucking technique to achieve frequency up-conversion. During a plucking action, a piezoelectric bimorph is deflected by a plectrum; when released due to loss of contact, the bimorph is free to vibrate at its resonant frequency, generating electrical energy with the highest efficiency. A prototype, featuring four PZT-5H bimorphs, was built and is here studied in a knee simulator which reproduces the gait of a human subject. Biomechanical data were collected with a marker-based motion capture system while the subject was carrying a selection of backpack loads. The paper focuses on the energy generation of the harvester and how this is affected by the backpack load. By altering the gait, the backpack load has a measurable effect on performance: at the highest load of 24kg, a minor reduction in energy generation (7%) was observed and the output power is reduced by 10%. Both are so moderate to be practically unimportant. The average power output of the prototype is 2.06±0.3mW, which can increase significantly with further optimization.
Kinetic Analysis of the Oxidative Conversion of the [4Fe-4S] <sup>2+</sup> Cluster of FNR to a [2Fe-2S] <sup>2+</sup> Cluster (2004)

The ability of FNR to sense and respond to cellular O(2) levels depends on its [4Fe-4S](2+) cluster. In the presence of O(2), the [4Fe-4S](2+) cluster is converted to a [2Fe-2S](2+) cluster, which inactivates FNR as a transcriptional regulator. In this study, we demonstrate that approximately 2 Fe(2+) ions are released from the reaction of O(2) with the [4Fe-4S](2+) cluster. Fe(2+) release was then used as an assay of reaction progress to investigate the rate of [4Fe-4S](2+) to [2Fe-2S](2+) cluster conversion in vitro. We also found that there was no detectable difference in the rate of O(2)-induced cluster conversion for FNR free in solution compared to its DNA-bound form. In addition, the rate of FNR inactivation was monitored in vivo by measuring the rate at which transcriptional regulation by FNR is lost upon the exposure of cells to O(2); a comparison of the in vitro and in vivo rates of conversion suggests that O(2)-induced cluster conversion is sufficient to explain FNR inactivation in cells. FNR protein levels were also compared for cells grown under aerobic and anaerobic conditions.
Binding of Autotaxin to Integrins Localizes Lysophosphatidic Acid Production to Platelets and Mammalian Cells (2011)

Autotaxin (ATX) is a secreted lysophospholipase D that generates the bioactive lipid mediator lysophosphatidic acid (LPA). We and others have reported that ATX binds to integrins, but the function of ATX-integrin interactions is unknown. The recently reported crystal structure of ATX suggests a role for the solvent-exposed surface of the N-terminal tandem somatomedin B-like domains in binding to platelet integrin αIIbβ(3). The opposite face of the somatomedin B-like domain interacts with the catalytic phosphodiesterase (PDE) domain to form a hydrophobic channel through which lysophospholipid substrates enter and leave the active site. Based on this structure, we hypothesize that integrin-bound ATX can access cell surface substrates and deliver LPA to cell surface receptors. To test this hypothesis, we investigated the integrin selectivity and signaling pathways that promote ATX binding to platelets. We report that both platelet β1 and β3 integrins interact in an activation-dependent manner with ATX via the SMB2 domain. ATX increases thrombin-stimulated LPA production by washed platelets ~10-fold. When incubated under conditions to promote integrin activation, ATX generates LPA from CHO cells primed with bee venom phospholipase A(2), and ATX-mediated LPA production is enhanced more than 2-fold by CHO cell overexpression of integrin β(3). The effects of ATX on platelet and cell-associated LPA production, but not hydrolysis of small molecule or detergent-solubilized substrates, are attenuated by point mutations in the SMB2 that impair integrin binding. Integrin binding therefore localizes ATX activity to the cell surface, providing a mechanism to generate LPA in the vicinity of its receptors.