gebhart/patrepeval huggingface dataset:
Viability and membrane integrity of spermatozoa after dilution and flow cytometric sorting in the presence or absence of seminal plasma (1996)

Boar, bull and ram spermatozoa were examined after staining with the DNA-permeant Hoechst 33342 fluorochrome and flow cytometric sorting in the presence or absence of seminal plasma. Spermatozoa were assessed for viability with flow cytometry using the live cell nucleic acid stain SYBR-14 and propidium iodide (PI), and for membrane integrity using fluorescein isothiocyanate-conjugated Pisum sativum (FITC-PSA) and PI; motility and acrosome integrity were estimated by microscopy. Flow cytometric sorting was compared with pipette dilution of boar and bull spermatozoa into: (1) medium [boar: Test buffer containing 2% yolk (TY) or Beltsville thawing solution (BTS); bull: TY or HEPES buffer containing 0.1% bovine serum albumin (HEPES-BSA)] with or without 10% (v/v) seminal plasma; or (2) an empty tube containing no medium. Sorted spermatozoa were either not centrifuged or centrifuged before assessment during a 4-h holding period. The viability, motility and membrane integrity of boar, bull and ram spermatozoa centrifuged after sorting were also examined when seminal plasma was present or absent from the staining extender and/or the TY collection medium. The results indicate that the viability and membrane integrity of spermatozoa in vitro would be improved if: (1) seminal plasma (10%) was routinely included in the BTS and HEPES-BSA staining extenders for boar spermatozoa and ram spermatozoa, respectively, when used in preparation for flow cytometric sorting; and (2) 10% and 50% seminal plasma were included in the TY collection medium for boar or bull spermatozoa and ram spermatozoa respectively.
Vascular permeability induced by VEGF family members in vivo: Role of endogenous PAF and NO synthesis (2006)

We previously reported that vascular endothelial growth factor (VEGF) increases vascular permeability through the synthesis of endothelial platelet-activating factor (PAF), while others reported the contribution of nitric oxide (NO). Herein, we addressed the contribution of VEGF receptors and the role played by PAF and NO in VEGF-induced plasma protein extravasation. Using a modified Miles assay, intradermal injection in mice ears of VEGF-A(165), VEGF-A(121), and VEGF-C (1 microM) which activate VEGFR-2 (Flk-1) receptor increased vascular permeability, whereas a treatment with VEGFR-1 (Flt-1) analogs; PlGF and VEGF-B (1 microM) had no such effect. Pretreatment of mice with PAF receptor antagonist (LAU8080) or endothelial nitric oxide synthase (eNOS) inhibitor (L-NAME) abrogated protein extravasation mediated by VEGF-A(165). As opposed to PAF (0.01-1 microM), treatment with acetylcholine (ACh; up to 100 microM; inducer of NO synthesis) or sodium nitroprusside (SNP; up to 1 microM; NO donor) did not induce protein leakage. Simultaneous pretreatment of mice with eNOS and protein kinase A (PKA) inhibitors restored VEGF-A(165) vascular hyperpermeability suggesting that endogenous NO synthesis leads to PKA inhibition, which support maintenance of vascular integrity. Our data demonstrate that VEGF analogs increase vascular permeability through VEGFR-2 activation, and that both endogenous PAF and NO synthesis contribute to VEGF-A(165)-mediated vascular permeability. However, PAF but not NO directly increases vascular permeability per se, thereby, suggesting that PAF is a direct inflammatory mediator, whereas NO serves as a cofactor in VEGF-A(165) proinflammatory activities.
Multivalent Carbocyanine Molecular Probes:  Synthesis and Applications (2004)

Synergistic multivalent interactions can amplify desired chemical or biological molecular recognitions. We report a new class of multicarboxylate-containing carbocyanine dye constructs for use as optical scaffolds that not only serve as fluorescent antennas but also participate in structural assembly of the multivalent molecular construct. Three generations of carboxylate-terminating multivalent near-infrared carbocyanine probes from a dicarboxylic acid precursor dye (cypate) were prepared via its imino diacetic acid derivatives. Conjugation of the probes with D-(+)-glucosamine afforded dendritic arrays of the carbohydrates on an inner NIR chromophore core. All the multicarboxylate probes and their glucosamine conjugates have similar NIR spectral properties because conjugation occurred at distal positions to the inner chromophore core, thereby providing consistent and predictable spectral properties for their biological applications. Although light-induced photodamage equally affected the precursor dye, multicarboxylate probes, and their glucosamine derivatives, we observed that octacarboxylcypate (multivalent probe) was remarkably stable in different mediums at physiologically relevant temperatures relative to cypate, especially in basic mediums. Biodistribution studies in tumor-bearing nude mice show that all the glucosamine conjugates localized in the tumor but cypate was almost exclusively retained in the liver at 24 h postinjection. The tumor uptake does not correlate with the number of glucosamine tether on the multicarboxylate probe. Overall, the triglucosamine derivative appears to offer the best balance between high tumor uptake and low retention in nontarget tissues. These results suggest that multivalent molecular beacons are useful for assessing the beneficial effects of multivalency and for optimizing the biological and chemical properties of tissue-specific molecular probes.
The tumor vascular targeting agent combretastatin A–4-phosphate induces reorganization of the actin cytoskeleton and early membrane blebbing in human endothelial cells (2002)

Combretastatin A-4-phosphate (CA-4-P) is a tubulin-binding compound currently in clinical trial as a tumor vascular-targeting agent. In endothelial cells, CA-4-P is known to cause microtubule depolymerization, but little is known about its subsequent effects on cell morphology and function. Here, we demonstrate that within minutes of endothelial cell exposure to CA-4-P, myosin light chain (MLC) was phosphorylated, leading to actinomyosin contractility, assembly of actin stress fibers, and formation of focal adhesions. These cytoskeletal alterations appeared to be a consequence of Rho activation, as they were abolished by either the Rho inhibitor C3 exoenzyme or Rho-kinase inhibitor Y-27632. In response to CA-4-P, some cells rapidly assumed a blebbing morphology in which F-actin accumulated around surface blebs, stress fibers misassembled into a spherical network surrounding the cytoplasm, and focal adhesions appeared malformed. Blebbing was associated with decreased cell viability and could be inhibited by Rho/Rho-kinase inhibitors or by blocking the CA-4-P-mediated activation of stress-activated protein kinase-2/p38. The extracellular-regulated kinases 1 and 2 (ERK-1/2) were shown to protect against blebbing since blebbing was attenuated on ERK-1/2 stimulation and was up-regulated by specific inhibition of ERK-1/2 activation. The use of MLC kinase (MLCK) and myosin adenosine triphosphatase inhibitors led us to propose a role for MLCK and myosin activity independent of MLC phosphorylation in regulating the blebbing process. CA-4-P-mediated contractility and blebbing were associated with a Rho-dependent increase in monolayer permeability to dextrans, suggesting that such functional changes may be important in the rapid response of the tumor endothelium to CA-4-P in vivo.
A novel knowledge-based approach to design inorganic-binding peptides (2007)

A bioinformatics approach was developed to classify peptides selected by in vivo techniques according to their inorganic solid-binding properties. Our approach performs all-against-all comparisons of experimentally selected peptides with short amino acid sequences that were categorized for their binding affinity and scores the alignments using sequence similarity scoring matrices. We generated novel scoring matrices that optimize the similarities within the strong-binding peptide sequences and the differences between the strong- and weak-binding peptide sequences. Using the scoring matrices thus generated, a given peptide is classified based on the sequence similarity to a set of experimentally selected peptides. We demonstrate the new approach by classifying experimentally characterized quartz-binding peptides and computationally designing new sequences with specific affinities. Experimental verifications of binding of these computationally designed peptides confirm our predictions with high accuracy. We further show that our approach is a general one and can be used to design new sequences that bind to a given inorganic solid with predictable and enhanced affinity.
『소문(素問),맥요정미론(脈要精微論)』의 촌관척(寸關尺) 장부배속(臟腑配屬)에 대한 고찰 (2009)

In 『Maekyojeongmiron(脈要精微論)』, Jangbu(臟腑) is assigned to Chon·Gwan·Cheok(寸關尺) in according to the position. Kidney[腎] is assigned to the backward area of Cheok. Abdominal cavity[腹中] is assigned to the middle area of Cheok. Hypochondrium[季脇] is assigned to the forward area of Cheok. Liver[肝] is assigned to the backward area of left Gwan. Diaphragm[격] is assigned to the forward area of left Gwan. Stomach[胃] is assigned to the backward area of right Gwan. Spleen[脾] is assigned to the forward area of right Gwan. Heart[心] is assigned to the backward area of left Chon. Central part of the chest[전中] is assigned to the forward area of left Chon. Lung[肺] is assigned to the backward area of right Chon. Thoracic cavity[胸中] is assigned to the forward area of right Chon. This method of assignment is simple and useful in clinic.
Expression of the c‐myc gene as a predictor of chemotherapy response and a prognostic factor in patients with ovarian cancer (2004)

The present study was conducted to determine whether and how expression of the c-myc gene is related to the response to chemotherapy in patients with epithelial ovarian cancer. This study includes 101 consecutive patients with stage Ic to IV epithelial ovarian cancer who underwent primary surgery followed by platinum-based chemotherapy. Immunohistochemical studies were performed to detect Ki-67 and ARF proteins. Apoptotic cells were identified by the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate biotin nick-end labeling method. Mutation of the p53 gene was screened by polymerase chain reaction (PCR)-single strand conformation polymorphism analysis and confirmed by direct sequencing. mRNA expression of c-myc was determined by means of reverse transcription-PCR. Apoptotic index (AI) and ARF labeling index (LI) were significantly increased and Ki-67 LI was decreased after chemotherapy in patients from whom specimens could be obtained before and after chemotherapy. AI, ARF LI, and Ki-67 LI were not related to p53 gene status. A significant correlation between expression of c-myc and ARF LI was observed. Of 38 patients with measurable lesion, 23 (60.5%) responded to chemotherapy and 15 (39.5%) did not. Tumors with the wild-type p53 gene responded significantly better to chemotherapy than did tumors with the mutation. Responders showed a higher expression of c-myc than nonresponders (468 +/- 76 vs. 187 +/- 68). The receiver operating characteristic (ROC) curve according to chemoresponse demonstrated that the cut-off value of c-myc expression was 200. Patients with c-myc expression of more than 200 had a better 5-year survival rate (69.8% vs. 43.5%; 101 patients). Multivariate analysis revealed that c-myc expression was an independent prognostic factor. Our results suggest that the expression of c-myc gene is related to chemoresponse and might be a useful prognostic factor in patients with epithelial ovarian cancer.
A hybrid architecture for text classification (2003)

SKIS, a prototype system that allows for the construction and use of text classification applications, is discussed. SKIS uses a combination of knowledge-based techniques, statistical techniques, morphological processing, and relevance feedback learning techniques to perform text classification. SKIS has been used to construct a prototype text classification application for the routing of customer service requests within customer support centers. The SKIS run-time architecture, the development and knowledge maintenance environment, and how SKIS is used are described. The benefits of combining knowledge-based and statistical techniques for text classification are discussed. SKIS is compared with other text classification systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
L-Amino Acids Regulate Parathyroid Hormone Secretion (2004)

Parathyroid hormone (PTH) secretion is acutely regulated by the extracellular Ca(2+)-sensing receptor (CaR). Thus, Ca(2+) ions, and to a lesser extent Mg(2+) ions, have been viewed as the principal physiological regulators of PTH secretion. Herein we show that in physiological concentrations, l-amino acids acutely and reversibly activated the extracellular Ca(2+)-sensing receptor in normal human parathyroid cells and inhibited parathyroid hormone secretion. Individual l-amino acids, especially of the aromatic and aliphatic classes, as well as plasma-like amino acid mixtures, stereoselectively mobilized Ca(2+) ions in normal human parathyroid cells in the presence but not the absence of the CaR agonists, extracellular Ca(2+) (Ca(2+)(o)), or spermine. The order of potency was l-Trp = l-Phe > l-His > l-Ala > l-Glu > l-Arg = l-Leu. CaR-active amino acids also acutely and reversibly suppressed PTH secretion at physiological ionized Ca(2+) concentrations. At a Ca(2+)(o) of 1.1 mm and an amino acid concentration of 1 mm, CaR-active amino acids (l-Phe = l-Trp > l-His = l-Ala), but not CaR-inactive amino acids (l-Leu and l-Arg), stereoselectively suppressed PTH secretion by up to 40%, similar to the effect of raising Ca(2+)(o) to 1.2 mm. A physiologically relevant increase in the -fold concentration of the plasma-like amino acid mixture (from 1x to 2x) also reversibly suppressed PTH secretion in the Ca(2+)(o) concentration range 1.05-1.25 mm. In conclusion, l-amino acids acutely and reversibly activate endogenous CaRs and suppress PTH secretion at physiological concentrations. The results indicate that l-amino acids are physiological regulators of PTH secretion and thus whole body calcium metabolism.
TNF initiates E-selectin transcription in human endothelial cells through parallel TRAF-NF-kappa B and TRAF-RAC/CDC42-JNK-c-Jun/ATF2 pathways (1997)

TNF acts on the E-selectin gene promoter at three kappa B elements and at a variant cAMP-responsive element that binds ATF2/c-Jun. In human endothelial cells, TNF rapidly induces N-terminal domain phosphorylation of both c-Jun and ATF2. Transient overexpression of N-terminal truncated c-Jun or catalytically inactive Jun N-terminal kinase (JNK) 1 and 2 inhibits TNF-induced transcription of an E-selectin but not a kappa B promoter-reporter gene. Transient overexpression of the TRAF2 adaptor protein can activate NF-kappaB and endogenous JNK, whereas N-terminal truncated TRAF2 protein blocks TNF-induced NF-kappa B and JNK activation as well as E-selectin promoter-reporter gene transcription. Transient overexpression of RAC1 or CDC42, but not RAS, constitutively activates JNK and augments TNF-induced E-selectin transcription. Finally, transient overexpression of catalytically inactive JNK or truncated TRAF2 partially inhibits endogenous E-selectin protein expression in human endothelial cells. These data suggest that TNF activates parallel TRAF-NF-kappa B and TRAF-RAC/CDC42-JNK-c-Jun/ATF2 pathways to initiate E-selectin transcription.
Botulinum Toxin for the Treatment of Hyperfunctional Lines of the Face (1993)

Based on this initial pilot study, botulinum toxin may be an important new option for the treatment of patients with hyperfunctional facial lines.
Transducers of life and death: TNF receptor superfamily and associated proteins. (1996)

Signal transduction pathways which are initiated by members of the TNF superfamily utilize receptors which are devoid of intrinsic catalytic activity. Isolation and characterization of death domain (TNF-RI, Fas, TRADD, FADD/MORT-1, RIP) and TRAF domain-containing proteins (TRAF-1, TRAF-2, TRAF-3) have partially bridged a large molecular gap within one of several signaling pathways which originate at the plasma membrane and terminate in the nucleus. The ability of these two protein families to selectively dimerize and bind to related receptors allows them to govern diverse cellular responses which culminate in cellular proliferation, differentiation, effector functions, and apoptosis.
Nuclear Magnetic Resonance Logging While Drilling (NMR-LWD): From an Experiment to a Day-to-Day Service for the Oil Industry (2010)

NMR T2 distribution measurement is our chosen everyday method for NMR logging while drilling oil and gas wells. This method yields straightforward preparation and execution of the job as well as a normally easy interpretation of the measured data. For instance, gas and light oil discrimination against water is feasible by direct observation of the T2 distribution. A condition for this measurement method is a NMR logging tool that hardly moves while drilling and in addition uses a small static magnetic field gradient and short inter-echo time TE to be motion tolerant. Using data compression techniques, we can transmit by mud pulse telemetry the T2 distribution in real time from the borehole to the surface. This enables the drilling operator to use the NMR data for real-time decisions such as geosteering.
A Simple Algorithm for Finding Maximal Network Flows and an Application to the Hitchcock Problem (1957)

The network-flow problem, originally posed by T . Harris of the Rand Corporation, has been discussed from various viewpoints in ( 1; 2; 7; 16 ). The problem arises naturally in the study of transportation networks; it may be stated in the following way. One is given a network of directed arcs and nodes with two distinguished nodes, called source and sink, respectively. All other nodes are called intermediate. Each directed arc in the network has associated with it a nonnegative integer, its flow capacity. Source arcs may be assumed to be directed away from the source, sink arcs into the sink. Subject to the conditions that the flow in an arc is in the direction of the arc and does not exceed its capacity, and that the total flow into any intermediate node is equal to the flow out of it, it is desired to find a maximal flow from source to sink in the network, i.e., a flow which maximizes the sum of the flows in source (or sink) arcs. Thus, if we let P 1 be the source, P n the sink, we are required to find x ij ( i , j =1, . . . , w ) which maximize
TheBmdsxtransgene including trimmed introns is sex-specifically spliced in tissues of the silkworm, Bombyx mori (2005)

Bmdsx is an orthologue of the sex-determining gene doublesex (dsx) and known to be sex-specifically expressed in various tissues of the silkworm, Bombyx mori. Its pre-mRNA is sex-specifically spliced and encodes female-specific or male-specific polypeptides. The open reading frame of Bmdsx consists of 5 exons, of which exons 3 and 4 are female-specific and its pre-mRNA was known to undergo default processing to generate the female-type mRNA. Previous reports have shown that the mechanism of splicing of the doublesex gene is different in Drosophila melanogaster and Bombyx mori. However, intron 4 is so long that it is difficult to identify the intronic cis-element(s) required for male-specific splicing of Bmdsx pre-mRNA using Bmdsx minigenes whose introns are shortened in various manners. As a first step toward discovery of the cis-element, the Bmdsx mini gene, which consisted of exon 1 and 5 and internally shortened introns 2 to 4, was constructed, and transgenic silkworms expressing this construct were generated. Bmdsx pre-mRNA transcribed derived from transgene was sex-specifically spliced. This result shows that the mini gene contained the information necessary for the correct regulation of alternative splicing.
RTL Synthesis: From Logic Synthesis to Automatic Pipelining (2015)

Design automation has been one of the main propellers of the semiconductor industry with logic synthesis being one of the core technologies in this field. This article reviews the evolution of logic synthesis until the advent of techniques for automatic pipelining based on elastic timing, either synchronous or asynchronous. The emergence of these techniques can enable a productive interaction with tools that can do microarchitectural exploration of complex designs.
Electrical neurostimulation with imbalanced waveform mitigates dissolution of platinum electrodes (2016)

This observation provides an opportunity to re-evaluate the charge-balanced waveform as the primary option for sustainable neural stimulation.
The Human Papillomavirus Type 16 E6 Oncoprotein Can Down-Regulate p53 Activity by Targeting the Transcriptional Coactivator CBP/p300 (1999)

The transforming proteins of the small DNA tumor viruses, simian virus 40 (SV40), adenovirus, and human papillomavirus (HPV) target a number of identical cellular regulators whose functional abrogation is required for transformation. However, while both adenovirus E1A and SV40 large T transforming properties also depend on the targeting of the transcriptional coactivator CBP/p300, no such interaction has been described for the HPV oncoprotein E6 or E7. Here, we demonstrate that the HPV-16 E6 protein, previously shown to facilitate the degradation of p53 in a complex with E6-associated protein (E6AP), also targets CBP/p300 in an interaction involving the C-terminal zinc finger of E6 and CBP residues 1808 to 1826. Furthermore, this interaction is limited to E6 proteins of high-risk HPVs associated with cervical cancer that have the capacity to repress p53-dependent transcription. An HPV-16 E6 mutant (L50G) that binds CBP/p300, but not E6AP, is still capable of down-regulating p53 transcriptional activity. Thus, HPV E6 proteins possess two distinct mechanisms by which to abrogate p53 function: the repression of p53 transcriptional activity by targeting the p53 coactivator CBP/p300, and the removal of cellular p53 protein through the proteosome degradation pathway.
Studies on the Role of Sialic Acid in the Physical and Biological Properties of Erythropoietin (1972)

Crude erythropoietin was subjected to isoelectric focusing over the pH ranges 3–10 and 3–5. All the biological activity was located between pH 3.5 and 4.0. The erythropoietin activity displayed heterogeneity, being divided into three or four peaks within this pH range. Asialoerythropoietin, prepared by acid or enzymic hydrolysis, focused in the pH gradient between pH 5.0 and 6.5 and displayed a similar degree of heterogeneity. Partially desialated erythropoietin focused over a range of intermediate pH values. The large shift in pI on desialation and the demonstration of intermediate partially desialated species suggest a high content of sialic acid in erythropoietin. All desialated species of erythropoietin having isoelectric points greater than 4.0 were without in vivo biological activity. Oxidation of asialoerythropoietin with galactose oxidase completely restored in vivo biological activity.