gebhart/patrepeval huggingface dataset:
Elastin‐Like Polypeptides as a Purification Tag for Recombinant Proteins (2010)

This unit presents a recombinant protein purification method that employs an elastin-like polypeptide (ELP) as a purification tag. ELPs undergo a sharp and reversible phase transition when heated above their lower critical solution temperature. ELPs retain this behavior when they are fused to a protein, and thereby provide a simple method to isolate a recombinant ELP fusion protein from cell contaminants by cycling the solution through the insoluble and soluble phase of the ELP fusion protein using a procedure that is termed Inverse Transition Cycling. This method does not require the use of chromatography, so it is cost-effective, easy to scale up, and easy to multiplex.
HOTPAPER (2008)

The popularity of camera phones enables many exciting multimedia applications. In this paper, we present a novel technology and several applications that allow users to interact with paper documents, books, and magazines. This interaction is in the form of reading and writing electronic information, such as images, web urls, video, and audio, to the paper medium by pointing a camera phone at a patch of text on a document. Our application does not require any special markings, barcodes, or watermarks on the paper document. Instead, we propose a document recognition algorithm that automatically determines the location of a patch of text in a large collection of document images given a small document image. This is very challenging because the majority of phone cameras lack autofocus and macro capabilities and they produce low quality images and video. We developed a novel algorithm, Brick Wall Coding (BWC), that performs image-based document recognition using the mobile phone video frames. Given a document patch image, BWC utilizes the layout, i.e. relative locations, of word boxes in order to determine the original file, page, and the location on the page. BWC runs real-time (4 frames per second) on a Treo 700w smartphone with a 312 MHz processor and 64MB RAM. Using our method we can recognize blurry document patch frames that contain as little as 4-5 lines of text and a video resolution as low as 176x144. We performed experiments by indexing 4397 document pages and querying this database with 533 document patches. Besides describing the basic algorithm, this paper also describes several applications that are enabled by mobile phone-paper interaction, such as inserting electronic annotations to paper, using paper as a tangible interface to collect and communicate multimedia data, and collaborative homework.
Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes (2012)

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.
Cloning of PRV-1, a novel member of the uPAR receptor superfamily, which is overexpressed in polycythemia rubra vera (2000)

Polycythemia vera (PV) is a clonal stem cell disorder characterized by hyperproliferation of the erythroid, myeloid, and megakaryocytic lineages. Although it has been shown that progenitor cells of patients with PV are hypersensitive to several growth factors, the molecular pathogenesis of this disease remains unknown. To investigate the molecular defects underlying PV, we used subtractive hybridization to isolate complementary DNAs (cDNAs) differentially expressed in patients with PV versus normal controls. We isolated a novel gene, subsequently named PRV-1, which is highly expressed in granulocytes from patients with PV (n = 19), but not detectable in normal control granulocytes (n = 21). Moreover, PRV-1 is not expressed in mononuclear cells from patients with chronic myelogenous leukemia (n = 4) or acute myelogenous leukemia (n = 5) or in granulocytes from patients with essential thrombocythemia (n = 4) or secondary erythrocytosis (n = 4). Northern blot analysis showed that PRV-1 is highly expressed in normal human bone marrow and to a much lesser degree in fetal liver. It is not expressed in a variety of other tissues tested. Although PRV-1 is not expressed in resting granulocytes from normal controls, stimulation of these cells with granulocyte colony-stimulating factor induces PRV-1 expression. The PRV-1 cDNA encodes an open reading frame of 437 amino acids, which contains a signal peptide at the N-terminus and a hydrophobic segment at the C-terminus. In addition, PRV-1 contains 2 cysteine-rich domains homologous to those found in the uPAR/Ly6/CD59/snake toxin-receptor superfamily. We therefore propose that PRV-1 represents a novel hematopoietic receptor. (Blood. 2000;95:2569-2576)
An experimental 4-Mbit CMOS EEPROM with a NAND-structured cell (1989)

A 5-V-only high-density (512 K*8 bit) electrically erasable and programmable read-only memory (EEPROM) has been designed and fabricated by using a NAND-structured cell with 1.0- mu m design rules. The average cell area per bit is 12.9 mu m/sup 2/. Block erasing, successive programming, and random reading are achieved using a newly developed NAND-cell control circuit. Typical erasing time is 1.0 ms and page-programming time is 4.0 ms, equivalent to 1.0 mu s/bit. A dynamic sensing system is introduced to sense the small cell current. Typical read access time is 1.6 mu s. The die size is 10.7*15.3 mm/sup 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
CCN1 expression in interleukin-6 deficient mouse kidney in experimental model of heart failure (2013)

Chronic heart failure often leads to worsening of the renal function. Mediators of this process include inflammatory and neuroendocrine factors. CCN1 (Cyr 61), a member of growth factor-inducible immediate early genes, which modulates inflammation and fibrogenesis, is excreted with urine in the early phase of acute renal injury and may be involved in the pathogenesis of the cardiorenal syndrome. The aim of the study was to evaluate CCN1 protein abundance and localization in the kidney of IL-6-deficient C57BL/6J (IL-6 KO) mice and respective wild-type (WT) animals in basal conditions and in animals with chronic heart failure twelve weeks after myocardial infarction. Age- and sex-matched mice from both strains subjected to sham operation served as controls. One group of WT animals subjected to myocardial infarction was treated with antagonist of AT1 receptor telmisartan over 12 weeks. Abundance and localization of CCN1 protein in kidney were assessed with Western blotting and immunohistochemistry, respectively. In all groups the strongest immunohistochemical reaction for CCN1 was observed in distal convoluted tubules and in smaller arteries, however, the total expression of CCN1 protein was lower in IL-6 KO mice in comparison to WT animals. The main difference in CCN1 distribution between the examined genotypes was lack of reaction in internal renal medulla and very weak reaction in proximal convoluted tubules in IL-6 KO mice. Experimental heart failure only slightly attenuated the expression of CCN1 protein in the kidney of WT mice and had no effect in IL-6 KO mice. Although, blockade of AT1 receptor did not alter CCN1 protein expression in kidneys of WT mice after myocardial infarction, it significantly changed its CCN1 distribution in the renal tubular system.
Characterization of the regulatory elements in the promoter of the human elongation factor-1 alpha gene. (1994)

Most eukaryotic cells abundantly express polypeptide chain elongation factor-1 alpha (EF-1 alpha), an enzyme which catalyzes the GTP-dependent binding of aminoacyl-tRNA to ribosomes. In this study, a series of deletion and scanning mutations was introduced in the promoter region of human EF-1 alpha chromosomal gene. Mutated promoters were fused to the bacterial chloramphenicol acetyltransferase gene, and their promoter activity was determined in human HeLa cells. These analyses indicated that both the 5'-flanking region and the first intron of the EF-1 alpha gene are essential for its promoter activity. The region responsible in the intron contains several Sp1 and Ap1 elements which seem to have additive effects on its promoter activity. In the 5'-flanking region, two cis-elements (EFP1 and EFP2) which work interdependently were identified. Gel shift assay with EFP1 and EFP2 elements indicated that several nuclear factors bind to EFP1 and EFP2, and one of the three retarded bands with EFP2 could be super-shifted with the anti-Sp1 antibody. These results indicate that Sp1 or its related factor cooperatively enhances the expression of the EF-1 alpha gene in the 5' flanking region.
Detection of interleukin 8 biological activity in synovial fluids from patients with rheumatoid arthritis and production of interleukin 8 mRNA by isolated synovial cells (1990)

Abstract The presence of neutrophils in the synovial joint of patients with rheumatoid arthritis (RA) is thought to be due to the activity of chemotactic factors released by activated cells in the joint. We have shown in this report, for the first time, the abundance of one such factor, interleukin 8 (IL 8), in the synovial fluid of patients both with RA and other non‐RA joint diseases, and the spontaneous production of IL8 mRNA by RA synovial cells in culture. There was no correlation between the levels of chemotactic activity and IL8 protein, suggesting that other factors with similar neutrophil chemotactic activity are also present in the synovial fluid exudate. In support of this concept neither the level of chemotactic activity nor IL8 protein levels correlated with neutrophil or leukocyte infiltration, indicating that the mechanism of migration into the inflammatory environment of the joint is complex. Such migration is likely to be due to a number of chemotactic signals in addition to IL8, which may either synergize with, or inhibit, the action of IL8.
Parametric array in air (1975)

An experimental investigation of the parametric array in air was conducted using a circular piston transducer which produced spherically spreading, collinear, primary beams at frequencies of 18.6 and 23.6 kHz. Since source levels were not strong (about 110 dB re 0.0002 μbar at 1 ft), the 5−kHz difference frequency signal generated by the parametric array was relatively weak. Because of space limitations, all measurements were made in the nearfield of the array. Spurious difference frequency signals resulting from intermodulation distortion in the receiving system were suppressed by judicious choice of electronic components and by the addition of an acoustical filter in front of the microphone. The classic properties of the parametric array were observed. The 5−kHz beam was narrow, and no minor lobes were evident. The propagation curve first increased with increasing range, reached a broad maximum, and then gradually decreased. Theoretical predictions were based on a perturbation solution of Burgers’ equation and on the integral solution of the inhomogeneous wave equation. Comparison of measured results with these predictions conclusively demonstrated the existence of the parametric array in air. Beam patterns and propagation data obtained for the second−harmonic and sum−frequency signals also confirmed theoretical predictions. Subject Classification: 25.35.
Antitnf-a strategy: Present status of this therapeutic paradigm (2004)

Tumor necrosis factor-alpha (TNF-a), a proinflammatory cytokine is involved in the pathophysiology of a number of disorders including Crohn’s disease, rheumatoid arthritis, ankylosing spondylitis and psoriatic arthritis. AntiTNF-a strategies target this pathogenic element to provide clinical benefit. The various strategies are in preliminary stage of experimentation and much remains to be elucidated before these are applied clinically. Though antiTNF-a therapy is currently approved only for rheumatoid arthritis and Crohn’s disease, the future of this therapeutic paradigm holds much promise. The number of official indications for strategies against this biologic agent are likely to increase to include congestive heart failure, psoriasis, asthma, septic shock, stroke and malignancy. This will make it a truly broad spectrum therapeutic weapon currently available to us.
Hybrid evolutionary search method based on clusters (2001)

Presents a hybrid evolutionary search method based on clusters (HESC). The method is specifically designed to enhance the search efficiency while alleviating the problem of premature convergence inherent in standard evolutionary search methods (SES). It involves the simultaneous evolution of a main species and an additional fast mutating species. A hybrid search method which includes a local parallel single agent search and a global multiagent evolutionary search is carried out for the main species. Effective utilization of the search history is achieved with the clustering and training of a fuzzy ART neural network (ART NN) during the search. The advantages of HESC include: (1) guaranteed population diversity at each generation; (2) effective integration of local search for the exploitation of important regions and the global search for the exploration of the entire space; and (3) fast exploration ability of the fast mutating species and migration from the additional species to the main species. Those advantages have been confirmed with experiments in which hard optimization problems were successfully solved with HESC.
Identification of recurring patterns in fractionated atrial electrograms using new transform coefficients (2012)

Transform coefficients computed from ensemble averages can be used to succinctly quantify synchronized patterns present in AF data. The technique is useful to automatically detect recurrent patterns in CFAE that are embedded in interference without user bias. This quantitation can be implemented in real-time to map the AF substrate prior to and during catheter ablation.
Prolonged Half‐Life in the Circulation of a Chemical Conjugate Between a Pro‐Urokinase Derivative and Human Serum Albumin (1995)

Pro‐urokinase is a natural plasminogen activator that displays a clot‐lysis activity through a fibrin‐dependent mechanism. It seems to be a promising agent for the treatment of coronary thrombosis. Like tissue‐type plasminogen activator and two‐chain urokinase‐type plasminogen activator, pro‐urokinase has a very short half‐life in circulation. It has been described that conjugation of serum albumin with pro‐urokinase in plasma may occur that could protect this protein from degradation. In this study we describe the insertion of an extra cysteine residue in the N‐terminal end of des‐(C11–K135)‐pro‐urokinase (Δ125‐proUK), a pro‐urokinase deletion mutant lacking amino acids 11–135. We have expressed and purified the new mutein [H5K, S9C, N10T]des‐(C11‐K135)‐pro‐urokinase (Cys‐Δ125‐pro‐urokinase) and chemically conjugated it with serum albumin via the extra cysteine of Cys‐Δ125‐pro‐urokinase. The purified conjugate obtained has a lower specific amidolytic activity (72000 U/mg) than unconjugated Cys‐Δ125‐pro‐urikinase (240000 U/mg) due to its higher molecular mass and has a similar fibrinolytic activity in a clot lysis test to that of Δ125‐pro‐urokinase. We established an ELISA to measure the concentration of the conjugate in plasma and to follow the pharmacokinetics of the conjugate in monkeys after bolus injection. The conjugate displays significant lysis of human plasma clots in vivo and a dramatic increase of the half‐life in the circulation, with respect to pro‐urokinase and Δ125‐pro‐urokinase. Therefore, preliminary biological characterisation of this conjugate indicates that it could be a good candidate to inject as a bolus, compared with the infusion regimen needed with pro‐urokinase.
Mesoporous Silica Nanoparticles for Reducing Hemolytic Activity Towards Mammalian Red Blood Cells (2008)

The hemolytic properties of amorphous silica and MCM-41-type mesoporous silica nanoparticles (MSNs) with rabbit red blood cells (RBCs) are compared. The amorphous silica exhibits a high hemolytic activity toward the RBCs. In contrast, a high biocompatibility between the MSNs and the RBCs is observed. The low hemolytic activity of the MSNs offers promising potential for various in vivo biotechnological applications. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Sequencing of Lp-PLA2-encoding PLA2G7 gene in 2000 Europeans reveals several rare loss-of-function mutations (2011)

Elevated plasma levels of lipoprotein-associated phospholipase A(2) (Lp-PLA2) activity have been shown to be associated with increased risk of coronary heart disease and an inhibitor of this enzyme is under development for the treatment of that condition. A Val279Phe null allele in this gene, that may influence patient eligibility for treatment, is relatively common in East Asians but has not been observed in Europeans. We investigated the existence and functional effects of low frequency alleles in a Western European population by re-sequencing the exons of PLA2G7 in 2000 samples. In all, 19 non-synonymous single-nucleotide polymorphisms (nsSNPs) were found, 14 in fewer than four subjects (minor allele frequency <0.1%). Lp-PLA2 activity was significantly lower in rare nsSNP carriers compared with non-carriers (167.8±63.2 vs 204.6±41.8, P=0.01) and seven variants had enzyme activities consistent with a null allele. The cumulative frequency of these null alleles was 0.25%, so <1 in 10,000 Europeans would be expected to be homozygous, and thus not potentially benefit from treatment with an Lp-PLA2 inhibitor.
Observations on Parturition in Crossbred Pony Mares (1972)

SUMMARY No previous account of parturition in the pony mare is to be found in the literature. The paper describes 24 cases of foaling in 13 crossbred pony mares. The mean gestation length was 339 days, and colt foals were carried four days longer than filly foals. All the mares were stabled at the time of foaling and all except one gave birth during the night. Parturition was short and no dystocia was noted. All the foals were presented anteriorly, in dorsal position and normal posture. First stage labour was not easy to assess in some cases but appeared shorter than in the larger breeds. Second stage labour lasted about 12 minutes and the afterbirths were passed at 60 (5–180) minutes. The newly born foals rested for a short period and were able to stand by 32 minutes and took 65 minutes to the time of first suck. The first meconium was passed at 145 minutes, and the time of first micturition was 8.5 hours. RÉSUMÉ On ne peut trouver dans la littérature aucun compte rendu de la mise bas chez le poney. Cet article décrit 24 cas de poulinage chez 13 poulinières poneys de croisement. La durée moyenne de la gestation fur de 339 jours et les poulains de sexe mâle furent en moyenne portés quatre jours de plus que les pouliches. Toutes les juments furent mises au box à l'époque présumée de la mise bas et toutes, à l'exception d'une, accouchèrent la nuit. La mise bas fut brève et aucune dystocie ne fut constatée. Tous les poulains avaient une présentation antèrieure normale. Le premier temps du travail ne fut pas toujours aiséà identifier mais paru plus bref que chez les grandes races. Le deuxième temps du travail dura en moyenne 12 minutes et l'expulsion des enveloppes eut lieu entre 5 et 180 minutes après la mise bas, moyenne 60 minutes. Les nouveaux nés se reposèrent durant une brève période, se tenaient debout après 32 minutes en moyenne et têtaient pour la première fois eprès 65 minutes en moyenne. Le début de l'explusion du meconium se produisit après 145 minutes, la première miction s'effectuait après 8 heures et demie. ZUSAMMENFASSUNG In der Literatur ist keine Beschreibung der Geburt bei der Ponystute zu finden. Der Artikel bezieht sich auf 24 Geburten bei 13 nicht rein gezüchteten Ponystuten. Die durchschnittliche Trächtigkeitsdauer war 339 Tage, wobei die Hengstfohlen vier Tage länger getragen wurden als Stutfohlen. Alle Stuten befanden sich für die Geburt im Stall und fohlten mit einer Ausnahme während der Nacht ab. Der Geburtsvorgang selber dauerte kurze Zeit und Dystokie kam nicht vor. Alle Fohlen wurden in Vorderendlage, oberer Stellung und normaler Haltung geboren. Die Eröffnungswehen waren in einigen Fällen nicht leicht zu erkennen, schienen aber weniger lang zu dauern als bei grösseren Equiden. Die Austreibungsphase dauerte etwa 12 Minuten und die Nachgeburt ging nach 60 (5–180) Minuten ab. Die neugeborenen Fohlen ruhten während kurzer Zeit, standen nach 32 Minuten und saugten nach 65 Minuten zum ersten Mal. Das erste Meconium ging nach 145 Minuten ab und der erste Harnabsatz fand nach 8 1/2 Stunden statt.