gebhart/patrepeval huggingface dataset:
Mechanism of endothelial cell shape change and cytoskeletal remodeling in response to fluid shear stress (1996)

Endothelium exposed to fluid shear stress (FSS) undergoes cell shape change, alignment and microfilament network remodeling in the direction of flow by an unknown mechanism. In this study we explore the role of tyrosine kinase (TK) activity, intracellular calcium ([Ca2+]i), mechanosensitive channels and cytoskeleton in the mechanism of cell shape change and actin stress fiber induction in bovine aortic endothelium (BAE). We report that FSS induces beta-actin mRNA in a time- and magnitude-dependent fashion. Treatment with quin2-AM to chelate intracellular calcium release and herbimycin A to inhibit TK activity abolished BAE shape change and actin stress fiber induction by FSS, while inhibition of protein kinase C with chelerythrine had no effect. Altering intermediate filament structure with acrylamide did not affect alignment or F-actin induction by FSS. Examining the role of the BAE cytoskeleton revealed a critical role for microtubules (MT). MT disruption with nocodazole blocked both FSS-induced morphological change and actin stress fiber induction. In contrast, MT hyperpolymerization with taxol attenuated the cell shape change but did not prevent actin stress fiber induction under flow. Mechanosensitive channels were found not to be involved in the FSS-induced shape change. Blocking the shear-activated current (IK.S) with barium and the stretch-activated cation channels (ISA) with gadolinium had no effect on the shear-induced changes in morphology and cytoskeleton. In summary, FSS has a profound effect on endothelial shape and F-actin network by a mechanism which depends on TK activity, intracellular calcium, and an intact microtubule network, but is independent of protein kinase C, intermediate filaments and shear- and stretch-activated mechanosensitive channels.
Control of Serotonergic Function in Medial Prefrontal Cortex by Serotonin-2A Receptors through a Glutamate-Dependent Mechanism (2001)

We examined the in vivo effects of the hallucinogen 4-iodo-2,5-dimethoxyamphetamine (DOI). DOI suppressed the firing rate of 7 of 12 dorsal raphe (DR) serotonergic (5-HT) neurons and partially inhibited the rest (ED(50) = 20 microg/kg, i.v.), an effect reversed by M100907 (5-HT(2A) antagonist) and picrotoxinin (GABA(A) antagonist). DOI (1 mg/kg, s.c.) reduced the 5-HT release in medial prefrontal cortex (mPFC) to 33 +/- 8% of baseline, an effect also antagonized by M100907. However, the local application of DOI in the mPFC increased 5-HT release (164 +/- 6% at 100 microm), an effect antagonized by tetrodotoxin, M100907, and BAY x 3702 (5-HT(1A) agonist) but not by SB 242084 (5-HT(2C) antagonist). The 5-HT increase was also reversed by NBQX (AMPA-KA antagonist) and 1S,3S-ACPD (mGluR 2/3 agonist) but not by MK-801 (NMDA antagonist). AMPA mimicked the 5-HT elevation produced by DOI. Likewise, the electrical-chemical stimulation of thalamocortical afferents and the local inhibition of glutamate uptake increased the 5-HT release through AMPA receptors. DOI application in mPFC increased the firing rate of a subgroup of 5-HT neurons (5 of 10), indicating an enhanced output of pyramidal neurons. Dual-label fluorescence confocal microscopic studies demonstrated colocalization of 5-HT(1A) and 5-HT(2A) receptors on individual cortical pyramidal neurons. Thus, DOI reduces the activity of ascending 5-HT neurons through a DR-based action and enhances serotonergic and glutamatergic transmission in mPFC through 5-HT(2A) and AMPA receptors. Because pyramidal neurons coexpress 5-HT(1A) and 5-HT(2A) receptors, DOI disrupts the balance between excitatory and inhibitory inputs and leads to an increased activity that may mediate its hallucinogenic action.
Optimum Reflectivity Design of Laser Diode Facets and Recording Medium for an Integrated Flying Optical Head (1993)

A reflectivity design of an integrated optical head is presented based on basic design quantities such as laser diode efficiency, write-erase power margin, phase-change medium sensitivity, and permissible read power. We obtain a reflectivity of R 1 \fallingdotseq0.7 for the laser diode facet that faces the photodetector, R 2 =0.01 for the same diode facet that faces the medium, 0.21≥ R 3 h ≥0.14 for the medium, and a reflectivity difference between the two medium reflectivity states of R 3 h - R 3 l \fallingdotseq0.05.
DNA-Directed Assembly of Bienzymic Complexes from In Vivo Biotinylated NAD(P)H:FMN Oxidoreductase and Luciferase (2002)

Spatially controlled assembly of enzyme conjugates can be applied to signal amplification systems for biosensors, or synthesis of novel catalysts for enzyme process technology. Artificial bienzymic systems comprised of two enzymes, NAD(P)H-FMN oxidoreductase and luciferase (represented as blue and orange spheres, respectively, in the schematic representation) were assembled by means of DNA hybridization and streptavidin–biotin interaction. Supporting information for this article is available on the WWW under http://www.chembiochem.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis (2002)

The covalent attachment of ubiquitin is an important determinant for selective protein degradation by the 26S proteasome in plants and animals. The specificity of ubiquitination is often controlled by ubiquitin-protein ligases (or E3s), which facilitate the transfer of ubiquitin to appropriate targets. One ligase type, the SCF E3s are composed of four proteins, cullin1/Cdc53, Rbx1/Roc1/Hrt1, Skp1, and an F-box protein. The F-box protein, which identifies the targets, binds to the Skp1 component of the complex through a degenerate N-terminal approximately 60-aa motif called the F-box. Using published F-boxes as queries, we have identified 694 potential F-box genes in Arabidopsis, making this gene superfamily one of the largest currently known in plants. Most of the encoded proteins contain interaction domains C-terminal to the F-box that presumably participate in substrate recognition. The F-box proteins can be classified via a phylogenetic approach into five major families, which can be further organized into multiple subfamilies. Sequence diversity within the subfamilies suggests that many F-box proteins have distinct functions and/or substrates. Representatives of all of the major families interact in yeast two-hybrid experiments with members of the Arabidopsis Skp family supporting their classification as F-box proteins. For some, a limited preference for Skps was observed, suggesting that a hierarchical organization of SCF complexes exists defined by distinct Skp/F-box protein pairs. Collectively, the data shows that Arabidopsis has exploited the SCF complex and the ubiquitin/26S proteasome pathway as a major route for cellular regulation and that a diverse array of SCF targets is likely present in plants.
Increased sex chromosome expression and epigenetic abnormalities in spermatids from male mice with Y chromosome deletions (2009)

During male meiosis, the X and Y chromosomes are transcriptionally silenced, a process termed meiotic sex chromosome inactivation (MSCI). Recent studies have shown that the sex chromosomes remain substantially transcriptionally repressed after meiosis in round spermatids, but the mechanisms involved in this later repression are poorly understood. Mice with deletions of the Y chromosome long arm (MSYq-) have increased spermatid expression of multicopy X and Y genes, and so represent a model for studying post-meiotic sex chromosome repression. Here, we show that the increase in sex chromosome transcription in spermatids from MSYq- mice affects not only multicopy but also single-copy XY genes, as well as an X-linked reporter gene. This increase in transcription is accompanied by specific changes in the sex chromosome histone code, including almost complete loss of H4K8Ac and reduction of H3K9me3 and CBX1. Together, these data show that an MSYq gene regulates sex chromosome gene expression as well as chromatin remodelling in spermatids.
Correction of Mismatches in a Time-Interleaved Analog-to-Digital Converter in an Adaptively Equalized Digital Communication Receiver (2008)

In this paper, techniques to overcome the errors caused by the offset, gain, sample-time, and bandwidth mismatches among time-interleaved analog-to-digital converters in a high-speed baseband digital communication receiver are presented. The errors introduced by these mismatches are corrected using least-mean-square adaptation implemented in digital-signal-processing blocks. Gain, sample-time, and bandwidth mismatches are corrected by modifying the operation of the adaptive receive equalizer itself to minimize the hardware overhead. Simulation results show that the gain, offset, sample-time, and bandwidth mismatches are sufficiently corrected for practical digital communication receivers.
Clinical applications of the histoculture drug response assay. (1995)

There is a need for a clinically useful drug-response assay for cancer patients to individualize their chemotherapy. Collagen sponge-gel-supported histoculture has been shown to maintain tissue architecture and function in vitro and has been utilized to develop the histoculture drug-response assay (HDRA) for individualizing chemotherapy. In order to evaluate the HDRA with the 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide end point for clinical use, chemosensitivity to mitomycin C, doxorubicin, 5-fluorouracil, and cisplatin of 107 advanced gastric and 109 advanced colorectal cancers was determined in vitro in a correlative clinical trial. Two hundred eight (96.3%) of 216 of the patient specimens were evaluable in the HDRA. Thirty-eight patients with remaining measurable lesions after surgery were evaluable for comparison of the effects of chemotherapy in the HDRA with clinical outcome. Their overall response in the HDRA to all four drugs correlated to published historical data. Twenty-nine patients were treated with drugs shown to be ineffective in the HDRA, and all 29 cases showed clinical chemoresistance. In nine patients treated with drugs shown to be effective in the HDRA, six showed clinical chemoresponse and three showed arrest of disease progression. The correlation rate of the assay to clinical drug-sensitivity response was thus calculated to be 92.1% (35/38), with 100% (29/29) true-negative and 66.7% (6/9) true-positive rates, 100% (6/6) sensitivity, and 90.6% (29/32) specificity. Thirty-two patients with stage III and IV gastric cancer without remaining measurable tumor lesions after surgery were treated with mitomycin C and a fluoropyrimidine adjuvantly. The survival rate of 10 patients whose tumors were sensitive to either mitomycin C and/or 5-fluorouracil in the assay was significantly (P < 0.005) better than that of 22 patients whose tumors were shown to be insensitive to both drugs. Twenty-nine patients with stage III and IV colorectal cancer without remaining measurable tumor lesions after surgery were treated with fluoropyrimidines adjuvantly. The recurrence-free survival rate of 7 patients whose tumors were sensitive to 5-fluorouracil in the assay was significantly (P < 0.05) better than that of 22 patients whose tumors were insensitive. Thus the HDRA with the 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide end point should be of clinical value to choose optimal chemotherapy for response as well as for survival.
In vivo administration of purified human interleukin 2. II. Half life, immunologic effects, and expansion of peripheral lymphoid cells in vivo with recombinant IL 2. (1985)

Purified recombinant human interleukin 2 (RIL 2) derived from E. coli containing the inserted gene encoding for IL 2 was administered to 20 patients with a variety of malignancies. Toxicity was dose related and included fever, chills, malaise, arthralgias, myalgias, and unexpectedly, weight gain related to marked fluid retention. All patients receiving more than 10(5) U/kg total cumulative dose developed evidence of fluid retention, and all patients requiring discontinuance of RIL 2 (11/20) received total doses of between 2.54 X 10(5) U/kg to 15.4 X 10(5) U/kg. The limiting dose with this preparation was 3000 U/kg/hr by continuous administration or 10(6) U/kg by bolus administration. IL 2 was rapidly cleared from the plasma, with a half life of 6.9 min, and a later delayed clearance was consistent with a two-compartment model, with slower release from the extravascular space back into the plasma compartment. A marked change in lymphoid cells in the periphery was noted with an early depletion of all lymphoid cells, followed by an expansion of such cells with continuous IL 2 administration. A twofold to 16-fold expansion of total lymphoid cells in the peripheral blood could be demonstrated. TAC+ cells representing up to 25% of the circulating peripheral blood mononuclear cells could be demonstrated with 3 wk of continuous RIL 2 administration. Interferon-gamma levels increased in patients treated with IL 2. Precursors of lymphokine-activated killer cells generated under standard conditions were depleted within 2 to 3 min after IL 2 administration, but repopulated the peripheral blood after 7 to 10 days of continuous IL 2 administration. No tumor regression was seen in any of the cancer patients treated with IL 2 alone.
Design and fabrication of a pdms microfluidic probe and perfusion chamber for microfluidic experiments with organotypic brain slices (2008)

Microfluidic systems are increasingly being used for the culture and study of dissociated cells because they facilitate drug screening and chemotaxis studies using minute amounts of chemicals. However, microfluidics have not been adopted for brain slices because of the challenges associated with the culture conditions necessary for maintaining the integrity of the slices. Here, we present a microfluidic system comprising a perfusion chamber compatible with confocal microscopy and a transparent microfluidic probe (MFP) for local microperfusion of organotypic brain slices for epilepsy studies.
The Effect of Chemical Functionalization on Mechanical Properties of Nanotube/Polymer Composites (2003)

The effects of the chemical functionalization of a carbon nanotube embedded in a nanotube/polyethylene composite on the bulk elastic properties are presented. Constitutive equations are established for both functionalized and non-functionalized nanotube composites systems by using an equivalent-continuum modeling technique. The elastic properties of both composites systems are predicted for various nanotube lengths, volume fractions, and orientations. The results indicate that for the specific composite material considered in this study, most of the elastic stiffness constants of the functionalized composite are either less than or equal to those of the non-functionalized composite.
Unique membrane‐interacting properties of the immunostimulatory cationic peptide KLKL5KLK (KLK) (2008)

We have monitored the effects of KLKL(5)KLK (KLK), a derivative of a natural cationic antimicrobial peptide (CAP) on isolated membrane vesicles, and investigated the partition of the peptide within these structures. KLK readily interacted with fluorescent dyes entrapped in the vesicles without apparent pore formation. Fractionation of vesicles revealed KLK predominantly in the membrane. Peptide-treated vesicles appeared with generally disorganized bilayers. While KLK showed no effect on osmotic resistance of human erythrocytes, dramatic decrease in core and surface membrane fluidity was observed in peptide-treated erythrocyte ghosts as measured by fluorescence anisotropy. Finally, CD spectroscopy revealed lipid-induced random coil to beta-sheet and beta-sheet to alpha-helix conformational transitions of KLK. Together with the oligonucleotide oligo-d(IC)(13) [ODN1a], KLK functions as a novel adjuvant, termed IC31. Among other immunological effects, KLK appears to facilitate the uptake and delivery of ODN1a into cellular compartments, but the nature of KLK's interaction with the cell surface and other membrane-bordered compartments remains unknown. Our results suggest a profound membrane interacting property of KLK that might contribute to the immunostimulatory activities of IC31.
Lossless wideband audio compression : prediction and transform (2004)

Das Ziel dieser Dissertation ist die Untersuchung von verlustfreier Audiokompression. Im Bereich der verlustfreien Kompression teilt sich die Forschung in zwei große Entwicklungsabschnitte, nämlich Signalmodellierung und Codierungsverfahren. Die Signal-modellierung befasst sich mit dem Verstehen des Quellsignals, während sich die Codierung mit dem speziellen Problem der effizienten Repräsentation von Einzelsymbolen befaßt. Der Fokus dieser Dissertation liegt auf der Evaluation und Entwicklung von Signalmodellierungstechniken für die verlustfreie Kompression. Mit Bezug auf die Modellierungsmethode zur Dekorrelation des Signals fallen die Datenkompressionssysteme in zwei Kategorien, nämlich die prädiktive Modellierung und die auf Transformation basierende Modellierung. In der Dissertation wurden beide Kategorien aus der Sicht verlustfreier Kompression ausführlich untersucht. Der erste Beitrag der Dissertation ist der Erforschung von Audiokompressionssystemen einschließlich der verlustbehafteten Kompressionssysteme gewidmet. Bei der prädiktiven Modellierung werden die verschiedenen Strukturen der Linear-Prädiktionsfilter durch Vorlage der fundamentalen autoregressiven Modellierung vorgestellt. Die Prädiktionsfilter einschließlich der Ansätze zur Modellierung des nicht-stationären Signals und adaptiven Linear-Prädiktionsfiltern werden vorgestellt, und deren Effizienz im Experiment mit einem prototypischen verlustfreien Audiokompressionssystem evaluiert. Bezüglich der Transformationsbasierten Modellierung werden zwei prominente Codierungsmethoden beschrieben, die auf Subbandtransformation basieren, nämlich Laplacian Pyramide und Subbandcodierung, beschrieben, und die Entwurfsverfahren für perfekt rekonstruierbare Multirate-Filterbänke werden dargestellt. Die Effizienz linearer Prädiktion von Vollbandsignalen und Subbandsignalen wird theoretisch untersucht und empirisch validiert. Die Wavelet-Transformation wird nach verschiedenen Aspekten gründlich untersucht, um die theoretische Verknüpfung zwischen der Wavelet-Transformation und der Multirate-Filterbank zu diskutieren. Theoretische und praktische Aspekte von reversiblen Transformationen werden in Zusammenhang mit S-Transformation, S+P Transformation, und RTS Transformation untersucht. Die Liftingmethode, die die biorthogonalen Wavelets realisiert, wird untersucht. Um eine reversible Wavelet-Transformation zu konstruieren, wird das mit Ganzzahlen operierende Liftingsystem durch Abrundungsverfahren entwickelt. Dessen Funktion wird durch Anwendung auf die verlustfreie Audiokompression validiert. Zum Schluss sind einige wichtige Untersuchungsergebnisse der Dissertation mit Vorschlägen für zukünftige Forschungsarbeiten zusammengefasst.
ZAP-70 Compared with Immunoglobulin Heavy-Chain Gene Mutation Status as a Predictor of Disease Progression in Chronic Lymphocytic Leukemia (2004)

Although the presence of an unmutated IgV(H) gene is strongly associated with the expression of ZAP-70, ZAP-70 is a stronger predictor of the need for treatment in B-cell CLL.
Recent Performance of the Dual-Resistivity MWD Tool (1990)

Summary The dual-resistivity MWD tool uses sections of the drill collar as electrodes and provides two independent resistivity measurements: a principal well-focused lateral measurement of the current flowing radially from a defined segment of the drill collar and a secondary axial or bit measurement of the current flowing from a defined portion of the lower bottomhole assembly (BHA). In oil-based muds, a single (bit) measurement is made of the current flowing to the formation through the drill bit.
Ultrasound Microbubble Destruction Imaging in Acute Middle Cerebral Artery Stroke (2004)

MDI is a qualitative method that can rapidly detect perfusion changes in acute stroke. When combined with other ultrasound techniques and PWI, it may well be valuable in the care of stroke unit patients, eg, as a screening method and for follow-up assessments of perfusion deficits.
The loop problem in proteins: A monte carlo simulated annealing approach (1993)

A Monte Carlo simulated annealing (MCSA) algorithm was used to generate the conformations of local regions in bovine pancreatic trypsin inhibitor (BPTI) starting from random initial conformations. In the approach explored, only the conformation of the segment is computed; the rest of the protein is fixed in the known native conformation. Rather than follow a single simulation exhaustively, computer time is better used by performing multiple independent MCSA simulations in which different starting temperatures are employed and the number of conformations sampled is varied. The best computed conformation is chosen on the basis of lowest total energy and refined further. The total energy used in the annealing is the sum of the intrasegment energy, the interaction energy of the segment with the local surrounding region, and a distance constraint to generate a smooth connection of the initially randomized segment with the rest of the protein. The rms deviations between the main-chain conformations of the computed segments in BPTI and those of the native x-ray structure are 0.94 A for a 5-residue alpha-helical segment, 1.11 A for a 5-residue beta-strand segment, and 1.03, 1.61, and 1.87 A for 5-, 7-, and 9-residue loop segments. Side-chain deviations are comparable to the main-chain deviations for those side chains that interact strongly with the fixed part of the protein. A detailed view of the deviations at an atom-resolved level is obtained by comparing the predicted segments with their known conformations in the crystal structure of BPTI. These results emphasize the value of predetermined fixed structure against which the computed segment can nest.
A new alkaloid AM-2282 of Streptomyces origin taxonomy, fermentation, isolation and preliminary characterization. (1977)

AM-2282, a new alkaloid has been isolated from cultures of Streptomyces sp. AM-2282 by solvent extraction and silica gel chromatography. The compound exhibits a strong absorption maximum at 292 nm and shows antimicrobial activity against fungi and yeast. The LD50 of its hydrochloride (i.p. in mice) is 6.6 mg/kg. The molecular formula of AM-2282 has been determined as C28H26N4O3. The producing strain, AM-2282 was classified as a new species and the name, Streptomyces staurosporeus AWAYA, TAKAHASHI and OMURA, nov. sp. is proposed.
Reexamination of a Battlefield Trauma Golden Hour Policy (2017)

Therapy, level III.