gebhart/patrepeval huggingface dataset:
The I‐Ceu I endonuclease: purification and potential role in the evolution of Chlamydomonas group I introns (1994)

During genetic crosses between the interfertile green algae Chlamydomonas eugametos and Chlamydomonas moewusii, the I-CeuI endonuclease encoded by the fifth group I intron (CeLSU.5) in the C. eugametos chloroplast large subunit rRNA gene mediates the mobility of this intron by introducing a double-strand break near the insertion site of the intron in the corresponding C. moewusii intronless allele. To characterize the biochemical properties of this endonuclease, we have purified I-CeuI and determined the optimal reaction conditions for cleavage. I-CeuI activity is maximal at 50 degrees C, pH 10.0, 2.5 mM MgCl2 and in the absence of NaCl. Unlike the well-characterized I-SceI endonuclease, I-CeuI remains stable following preincubation in the absence of substrate. We discuss the role that homing endonucleases may have played in the evolution of Chlamydomonas chloroplast group I introns.
Platelet aggregation monitoring with a newly developed quartz crystal microbalance system as an alternative to optical platelet aggregometry (2010)

The objective of this study was to establish a new test system for the monitoring of platelet aggregation during extracorporeal circulation (ECC) procedures. Even though extensive progress has been made in improving the haemocompatibility of extracorporeal circulation devices, activation of blood coagulation, blood platelets and inflammatory responses are still undesired outcomes of cardiopulmonary bypass. This study deals with an approach towards a platelet aggregation measuring system using a newly developed quartz crystal microbalance (QCM) system. Since QCM is a rarely used technique in the field of blood analytics, the challenge was to transfer the well established methods of aggregometry to the new test system. In a QCM system, either bare gold or fibrinogen-coated sensors were incubated with ADP or arachidonic acid (AA) stimulated platelet rich plasma. For negative controls the GPIIb/IIIa inhibitory antibody abciximab (Reopro®) was used as an inhibitor of platelet aggregation. During incubation, the frequency shifts of the sensors were recorded. The results gained from the QCM system were compared to results gained by optical platelet aggregometry (born aggregometry). For additional visualization of platelet adhesion to the sensor surfaces, fluorescent microscopy and scanning electron microscopy were used. The QCM sensor was able to detect platelet aggregation in both uncoated and fibrinogen coated sensors. The measuring curves of aggregation measurements and controls were clearly distinguishable from each other in terms of frequency shifts and kinetics. For aggregation measurements and inhibited controls the therapeutic diagnosis of platelet function is identical between aggregometer and QCM data. In future, QCM based measuring devices may become an alternative to established point of care methods for rapid bedside testing of platelet aggregation.
Clonal relatedness of Shiga-like toxin-producing Escherichia coli O101 strains of human and porcine origin (1995)

Shiga-like toxin (SLT)-producing Escherichia coli (SLTEC) O101 has recently been associated with hemorrhagic colitis and hemolytic-uremic syndrome in humans. In this study, SLTEC O101 strains from humans and pigs were characterized for clonal relatedness by nucleotide sequence analysis of their slt genes, DNA finger-printing of genomic DNA, and determination of virulence factors. The slt genes of five E. coli O101 strains were cloned and sequenced. For all strains, the deduced amino acid sequences of the B subunits were identical to those of the SLT-IIe present in the classical SLTEC O139 strains that cause edema disease in pigs. The A subunit revealed more than 99% homology to that of SLT-IIe. DNA fingerprinting revealed a high degree of genetic relatedness between the human and porcine O101 isolates. None of the O101 strains investigated had virulence factors frequently found in porcine (F107 fimbriae or heat-stable or heat-labile enterotoxins) or human SLTEC strains (eaeA or enterohemorrhagic E. coli hemolysin). The absence of virulence factors typical of SLT-I- and SLT-II-producing E. Coli together with the presence of SLT-IIe, a toxin previously seen only in porcine E. coli, suggests a new pathogenic mechanism for E. coli O101 infection of humans. For diagnostic purposes, we recommend the use of PCR primers and DNA probes complementary to slt-IIe to correctly identify such strains and to further evaluate their role in human diseases.
The adipsin-acylation stimulating protein system and regulation of intracellular triglyceride synthesis. (1993)

We have previously characterized an activity from human plasma that markedly stimulates triglyceride synthesis in cultured human skin fibroblasts and human adipocytes. Based on its in vitro activity we named the active component acylation stimulating protein (ASP). The molecular identity of the active serum component has now been determined. NH2-terminal sequence analysis, ion spray ionization mass spectroscopy, and amino acid composition analysis all indicate that the active purified protein is a fragment of the third component of plasma complement, C3a-desArg. As well, reconstitution experiments with complement factors B, D, and complement C3, the components necessary to generate C3a, have confirmed the identity of ASP as C3a. ASP appears to be the final effector molecule generated by a novel regulatory system that modulates the rate of triglyceride synthesis in adipocytes.
Inhibition of pneumococcal autolysis in lysis-centrifugation blood culture (1986)

The recovery of Streptococcus pneumoniae from the Isolator lysis-centrifugation blood culture has been low in many studies. The poor survival of pneumococci was not due to toxicity of the Isolator medium but to autolysis before plating. This autolysis was completely inhibited by adding 10 mM phosphorylcholine to the Isolator medium.
NrCAM expression in papillary thyroid carcinomas (2008)

Many controversies remain, in particular, the relative place of bland embolization versus chemoembolization, the clinical benefit of drug-eluting bead chemoembolization (DEB-TACE) over conventional chemoembolization (cTACE), as well as the real place of radioembolization in general setting as well as innovative applications, such as radiation segmentectomy and radiation lobectomy.
Hypoxia-inducible factor 1α protein expression is controlled by oxygen-regulated ubiquitination that is disrupted by deletions and missense mutations (2000)

Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that mediates cellular and systemic homeostatic responses to reduced O(2) availability in mammals, including angiogenesis, erythropoiesis, and glycolysis. HIF-1 activity is controlled by the O(2)-regulated expression of the HIF-1alpha subunit. Under nonhypoxic conditions, HIF-1alpha protein is subject to ubiquitination and proteasomal degradation. Here we report that missense mutations and/or deletions involving several different regions of HIF-1alpha result in constitutive expression and transcriptional activity in nonhypoxic cells. We demonstrate that hypoxia results in decreased ubiquitination of HIF-1alpha and that missense mutations increase HIF-1alpha expression under nonhypoxic conditions by blocking ubiquitination.
Concave Reagents, 5 Bimacrocyclic 1,10‐Phenanthroline Cyclophanes (1990)

The addition of lithium aryls 3 to 1,10‐phenanthroline ( 2 ), functionalization of the rearomatized bisadduct 8b to the tetraphenol 8d , and cyclization of 8d with two equivalents of an α,ω‐ditosylate 9 led to a highly symmetrical, conformer‐free bimacrocyclic 1,10‐phenanthroline 10a in which the basic and coordinating region possesses a concave shielding.
Hormones and Hemodynamics in Heart Failure (1999)

Heart failure is a major cause of cardiovascular mortality and morbidity, resulting in more than 1 million hospitalizations per year, and is the most common hospital-discharge diagnosis among patients older than 65 years.1 In recent years, much has been learned about the pathophysiology of heart failure, particularly in the area of fluid and electrolyte metabolism, and this will be the focus of the present review.Regulation of Body-Fluid VolumeThere is considerable evidence in support of a unifying hypothesis of the regulation of body-fluid volume that is applicable to patients with edematous disorders such as cardiac failure, to patients with . . .
User Simulation Model: overview & validation - Capturing human behaviour in the built environment using RFID (2006)

This paper presents the validation setup for the user simulation model as part of the ongoing research project called User Simulation of Space Utilisation (USSU). The aim of this research project is to develop an overall model for the simulation of human movement and utilization of space capacity in office buildings. In this model, two aspects are essential: the interaction between the building occupants while performing their activities and the way to model these activities in space.
Simultaneous and Mapping With Sparse Extended Information (2014)

In this paper we describe a scalable algorithm for the simultaneous mapping and localization (SLAM) problem. SLAM is the problem of acquiring a map of a static environment with a mobile robot. The vast majority of SLAM algorithms are based on the extended Kalman filter (EKF). In this paper we advocate an algorithm that relies on the dual of the EKF, the extended information filter (EIF). We show that when represented in the information form, map posteriors are dominated by a small number of links that tie together nearby features in the map. This insight is developed into a sparse variant of the EIF, called the sparse extended information filter (SEIF). SEIFs represent maps by graphical networks of features that are locally interconnected, where links represent relative information between pairs of nearby features, as well as information about the robot's pose relative to the map. We show that all essential update equations in SEIFs can be executed in constant time, irrespective of the size of the map. We also provide empirical results obtained for a benchmark data set collected in an outdoor environment, and using a multi-robot mapping simulation.
Abstract 1771: Therapeutic management of pancreatic cancer using a novel drug, Minnelide (2010)

Abstract Background: Pancreatic cancer, the fourth-leading cause of cancer-related deaths in the United States, is one of the most malignant and aggressive forms of cancer, with a 5-year survival of &amp;lt;5%. We have previously shown that triptolide, a diterpenoid isolated from Tripterygium wilfordii, inhibits HSP70 expression leading to cell death in pancreatic cancer cells and reduces the growth as well as loco-regional spread of pancreatic tumors in an orthotopic model. The drawback of the use of triptolide in the clinic is its insolubility in water, requiring the presence of organic solvents. We therefore developed a prodrug of triptolide named Minnelide which is water soluble and converts to the parent compound both in vitro and in vivo. Aim: To evaluate the efficacy of Minnelide as a potential therapeutic agent for pancreatic cancer. Methods: Pancreatic cancer cells of varying metastatic potential (MIA PaCa-2/S2-VP10/S2-013) were incubated with different concentrations of Minnelide (100-200 nM) or vehicle (control). Cell viability was measured using an MTT-based assay, and apoptosis assessed using annexin V staining and caspase 3/9 activation at different time intervals. HSP70 expression was measured in lysates from Minnelide-treated cells by western blot. In vivo efficacy of the drug was measured by implanting tumor cells into the pancreas of nude mice which were then treated with either vehicle or Minnelide for different periods of time, and at different stages of tumor formation. Results: Minnelide decreased the cell viability of the three different human pancreatic cancer cell lines tested in a dose- and time-dependent manner. Furthermore, cell death was associated with annexin V positivity and activation of caspase 3/9. Minnelide repressed HSP70 protein expression at 100nM, supporting our previous results which show that HSP70 plays an important role in tumor progression. In the in vivo orthotopic mouse model, Minnelide dramatically decreased tumor size, loco-regional spread of tumor and extended survival, both in the early (7 days post-inoculation) and late (28 days post-inoculation) stages of pancreatic cancer. Importantly, toxic studies have shown that Minnelide at the concentrations required for tumor regression is not toxic to the animal. Conclusion: Minnelide is a potent anti-cancer agent, both in vitro and in vivo, causing cell death via apoptosis and tumor regression in vivo. It holds great promise as a novel single-agent therapeutic strategy against pancreatic cancer. We are currently in the process of initiating Phase I clinical trials for this drug. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1771.
Evidence for a Mechanism of Repression of Heat Shock Factor 1 Transcriptional Activity by a Multichaperone Complex (2001)

In the absence of stress, human heat shock factor 1 (hHSF1) is in its unactivated form. hHSF1 polypeptide is in a dynamic heterocomplex with Hsp90 and is incapable of specifically binding DNA. When cells are stressed, heterocomplex assembly is disrupted. Unbound hHSF1 homotrimerizes, acquires DNA binding activity, and concentrates in the nucleus, but remains transcriptionally inactive. A subsequent reaction converts this inactive, trimeric form into the active, hyperphosphorylated transcription factor. Subsequent to the stressful event, hHSF1 is deactivated and eventually returned to its unactivated form. Evidence is presented herein that trimeric hHSF1 has the propensity to dynamically associate with an Hsp90-immunophilin-p23 complex through its regulatory domain. Formation of this heterocomplex results in repression of the transcriptional activity of trimeric hHSF1. Stress-denatured proteins effectively compete with trimeric hHSF1 for Hsp90-immunophilin-p23 complex, counteracting assembly of the heterocomplex and repression of hHSF1 transcriptional activity. This repression mechanism may be required for a proportional transcriptional response to stress. Formation of the heterocomplex may also represent the first step toward returning the hHSF1 to its unactivated form.
mkpkg: A software packaging tool (1998)

mkpkg is a tool that helps software publishers create installation packages. Given software that is ready for distribution, mkpkg helps the publisher develop a description of the software package, including manifests, dependencies, and post-install customizations. mkpkg automates many of the painstaking tasks required of the publisher, such as determining the complete package manifest and dependencies of the executables on shared libraries. Using mkpkg, a publisher can generate software packages for complex software such as TeX with only a few minutes effort. mkpkg has been implemented on HP-UX using Tcl/Tk and provides both graphical and command line interfaces. It builds product-level packages for Software Distributor (SD-UX).
Comparison of G-CSF with GM-CSF for mobilizing peripheral blood progenitor cells and for enhancing marrow recovery after autologous bone marrow transplant. (1994)

Primed peripheral blood progenitor cells (PBPC) with hematopoietic growth factors enhance marrow engraftment after autologous bone marrow transplantation (BMT). G-CSF and GM-CSF stimulate the production of PBPC; both cytokines alone also stimulate neutrophil recovery after autologous BMT. Little data exist comparing these two cytokines. We prospectively studied G-CSF and GM-CSF in autologous BMT. Forty-four consecutive patients with either Hodgkin's disease or non-Hodgkin's lymphoma underwent autologous BMT using both PBPC and autologous marrow. The autologous BMT preparative regimen was CBV (VP-16 2400 mg/m2, CY 1800 mg/m2 i.v. four times daily for 4 days, BCNU 600 mg/m2). Sixteen patients received G-CSF 5 micrograms/kg sc daily for 8 days for mobilization of PBPC and received G-CSF 16 micrograms/kg i.v. four times daily after autologous BMT. Twenty-eight patients received GM-CSF to mobilize PBPC (14 patients received 250 micrograms/m2 sc daily for 8 days; 14 patients received 125 micrograms/m2 sc twice daily for 8 days) and GM-CSF (250 micrograms/m2 i.v. four times daily) after autologous BMT. Patients underwent three to five pheresis procedures to harvest at least 3 x 10(8) nucleated cells/kg. Patients receiving G-CSF had higher peripheral WBC counts than did those receiving GM-CSF. Total numbers of mononuclear cells, total CD34+ cells and total CD34+/33-negative cells were similar in the two treatment groups. The patients receiving G-CSF after autologous BMT experienced a more rapid engraftment of both neutrophils (9 days vs 13 days, p = 0.0001) and platelets (14 days vs 18 days, p = 0.027) than did patients receiving GM-CSF after transplant.(ABSTRACT TRUNCATED AT 250 WORDS)
Realistic Cost Estimating for Manufacturing (1989)

This revised edition contains material on the use of software, organization strategies in cost estimating, new types of costs, learning curves, and much more. Topics presented include manufacturing costs, standard vs. actual costs, cost in relation to product volume, analysis, types of estimates, cost estimating controls, cost requests from other departments, evaluating supplier quotes, calculating selling prices, and much more.
Harnessing Syk Family Tyrosine Kinases as Signaling Domains for Chimeric Single Chain of the Variable Domain Receptors: Optimal Design for T Cell Activation (1998)

T cells of tumor bearers often show defective TCR-mediated signaling events and, therefore, exhibit impaired immune responses. As such, patients with heavy tumor burden are often not amenable to adoptive T cell therapy. To overcome this limitation, we have developed a chimeric receptor that joins an extracellular single chain Fv (scFv) of a specific Ab for Ag recognition to an intracellular protein tyrosine kinase (PTK) for signal propagation. Stimulation through the scFv-PTK receptor should bypass defective TCR-proximal events and directly access the T cell's effector mechanisms. In this study we describe the optimization of a scFv-PTK configuration, leading to complete T cell activation. The cytosolic PTK Syk is superior to its family member, Zap-70, for intracellular signaling. As a transmembrane (TM) domain, CD4 performs better than CD8 when plastic-immobilized Ag serves as a stimulator. However, when APC are used to trigger chimeric receptors, the need for a flexible spacer between the scFv and TM domains becomes apparent. The CD8alpha-derived hinge successfully performs this task in chimeric scFv-Syk receptors regardless of its cysteine content. A cytotoxic T cell hybridoma expressing chimeric receptor genes composed of scFv-CD8(hinge)-CD8(TM)-Syk or scFv-CD8(hinge)-CD4(TM)-Syk is efficiently stimulated to produce IL-2 upon interaction with APC and specifically lyses appropriate target cells in a non-MHC-restricted manner.
Growth factor purification and delivery systems (PADS) for therapeutic angiogenesis (2015)

PADS represent a new method of both purification and in vivo stabilization of recombinant growth factors. The use of this system could permit recombinant growth factors to become viable options for therapeutic angiogenesis in a number of disease models.
CO 2 -limitation-inducible Green Recovery of fatty acids from cyanobacterial biomass (2011)

Using genetically modified cyanobacterial strains, we engineered a Green Recovery strategy to convert membrane lipids into fatty acids for economical and environmentally sustainable biofuel production. The Green Recovery strategy utilizes lipolytic enzymes under the control of promoters induced by CO(2) limitation. Data indicate that strains of the cyanobacterium Synechocystis sp. PCC6803 engineered for Green Recovery underwent degradation of membrane diacylglycerols upon CO(2) limitation, leading to release of fatty acids into the culture medium. Recovered fatty acid yields of 36.1 × 10(-12) mg/cell were measured in one of the engineered strains (SD239). Green Recovery can be incorporated into previously constructed fatty-acid-secretion strains, enabling fatty acid recovery from the remaining cyanobacterial biomass that will be generated during fatty acid biofuel production in photobioreactors.
Intracellular Expression of Bacillus Subtilis Phytase phyC in Pichia Pastoris (2004)

The Bacillus phytase is very suitable to be used in animal feed particularly in carp feed,because its optimum pH is at the neutral range and it has the excellent thermostability.At present,all the expressions of Bacillus phytase were reported in prokaryotic expression systems such as Bacillus and Escherichia coli,but the yield was very limited.So,the eukaryotic P. pastoris may be another better expression system due to its highly efficient expression for heterogenous protein.As the foundation of secretory expression in P. pastoris,the intracellular expression of Bacillus phytase was reported firstly in P. pastoris.In this study,the phyC encoding phytase from Bacillus subtilis WHNB02 without signal peptide sequence was amplified by polymerase chain reaction (PCR).The phyC fragment was sequenced and cloned into pPIC3.5K expression vector of P. pastoris.The pPIC3.5KphyC plasmid was linearized and transformed into Pichia Pastoris GS115 strain by electroporation.Positive strain was screened and purified by culturing on MD plate and MM plate.Furthermore,it was cultured and induced by 0.5% methanol.SDS-PAGE analysis shows that phytase is expressed intracellularly,and the yield comes to 24% of the total soluble protein and its molecular weight is 42.01 KD.The enzymatic analysis shows that the expression product has the biological activity of native phytase,its optimum reaction pH and temperature is 7.5 and 70 ℃,respectively.Moreover,its residual activity with treatment at 90 ℃ for 10 min is 42%.All of these properties are better than the native phytase from Bacillus subtilis.
Nitroxide TEMPOL impairs mitochondrial function and induces apoptosis in HL60 cells (2001)

The piperidine nitroxide TEMPOL induces apoptosis in a number of tumor cell lines through free radical-dependent mechanisms. As mitochondria play a major role in apoptosis as both source and target for free radicals, the present study focuses on mitochondrial effects of TEMPOL in a human promyelocytic leukemic cell line (HL-60). On 24-h exposure to TEMPOL, the following alterations were observed: 1) decrease in both the intracellular and mitochondrial glutathione pools; 2) impairment of oxidative phosphorylation; and 3) decrease in mitochondrial membrane potential. In addition, TEMPOL was found to specifically target complex I of the respiratory chain, with minor effects on complexes II and IV, suggesting that mitochondrial effects might play a role in TEMPOL-induced oxidative stress and apoptosis, and that TEMPOL might sensitize tumor cells to the pro-apoptotic effects of cytotoxic agents.