gebhart/patrepeval huggingface dataset:
Induction of Tubular Peroxisomes by UV Irradiation and Reactive Oxygen Species in HepG2 Cells (1999)

Peroxisomes in the human hepatoblastoma cell line HepG2 exhibit a high degree of plasticity. Whereas in confluent cultures they appear as small (0.1-0.3 micrometer) spherical particles, they undergo dramatic changes, forming elongated tubules measuring up to 5 micrometer on separation of cells and cultivation at low density. We recently showed that several growth factors, including nerve growth factor (NGF), induce the formation of tubular peroxisomes and that this induction is sensitive to K 252b, a specific tyrosine kinase inhibitor, suggesting the involvement of this signal transduction pathway. Because tyrosine kinase is also involved in signal transduction via the reactive oxygen species (ROS), we have analyzed in this study the effects of UV irradiation, H(2)O(2), and oxygen on tubulation of peroxisomes. UVC irradiation induced a significant increase in formation of tubular peroxisomes (40-50% of cells) and this effect was dose-dependently inhibited by pretreatment with N-acetyl cysteine, confirming the involvement of ROS in the UV effect. Furthermore, H(2)O(2) also directly induced the tubulation of peroxisomes, although to a lesser extent. Finally, cultivation under hypoxic conditions (1.5% O(2)) drastically reduced the inducing effect of fetal calf serum on tubulation of peroxisomes, suggesting the involvement of oxygen-mediated signaling. Taken together, our observations indicate that ROS induce the tubulation of peroxisomes in HepG2 cells. Because peroxisomes harbor most of the enzymes for catabolism of ROS, the tubulation and expansion of the peroxisome compartment could have a cell rescue function against the destructive effects of ROS.
Conformance Testing with TTCN (2000)

Service Primitives (ASPs). Conceptually, IUT and LT provide their service by exchanging Protocol Data Units (PDUs). In practice, the PDUs are encoded in ASPs of the underlying service, i.e. PDUs will not be exchanged directly. However, CTMF allows to abstract from the encoding of PDUs, i.e. allows to specify the exchange of PDUs in abstract test cases. Therefore, it is not necessary to distinguish between ASP and PDU explicitly, and hence, only the term PDU is used. As shown in the figure, Test Coordination Procedures (TCP) can be used to coordinate the actions of LT and UT. This might be necessary if LT and UT are realized in separate tester processes. The figure presents the conceptual test architecture only. In practice, several variations of the conceptual test architecture are used. The test methods defined in CTMF are local, distributed, coordinated and remote test method. They differ in the possibilities to coordinate LT and UT and the ability to control and observe 2) Only a f...
Novel method to extract large amounts of bacteriocins from lactic acid bacteria (1992)

Antimicrobial peptides, bacteriocins, produced by lactic acid bacteria were adsorbed on the cells of producing strains and other gram-positive bacteria. pH was a crucial factor in determining the degree of adsorption of these peptides onto cell surfaces. In general, between 93 and 100% of the bacteriocin molecules were adsorbed at pHs near 6.0, and the lowest (< or = 5%) adsorption took place at pH 1.5 to 2.0. On the basis of this property, a novel isolation method was developed for bacteriocins from four genera of lactic acid bacteria. By using this method we made preparations of pediocin AcH, nisin, sakacin A, and leuconocin Lcm1 that were potent and concentrated. This method produced a higher yield than isolation procedures, which rely on precipitation of the bacteriocins from the cell-free culture liquor. It is simple and can be used to produce large quantities of bacteriocins from lactic acid bacteria to be used as food biopreservatives.
Controlling Charge States of Peptides through Inductive Electrospray Ionization Mass Spectrometry (2011)

A novel ionization device for controlling the charge states of peptides based on an inductive elecrospray ionization technique was developed. This ion source keeps the major capabilities of electrospray ionization (ESI) which is compatible with liquid separation techniques (such as liquid chromatography (LC) and capillary electrophoresis (CE)) and can be potentially used to control the charge states of peptides accurately by simply varying the AC voltage applied. In comparison with conventional ESI, inductive ESI successfully simplifies the mass spectrum by reducing the charge states of peptide to a singly charged one, as well as eliminating the adduct ions.
Photocatalytic activity of colloidal CdS nanoparticles with different capping ligands (2009)

We report on the synthesis and characterization of cadmiumsulfide quantum dots (CdS-QDs) with three different types of capping ligands, mercaptoacetic acid (CdS-MAA), cysteamine, and 2-mercaptoethanesulfonic acid (CdS-CM), or tiopronin (CdS-TPN). All three types of QDs generate reactive oxygen species (ROS), in particular, superoxide- and hydroxyl radicals, upon irradiation with UV light. The ROS were analyzed using electron paramagnetic resonance (EPR) spectroscopy. Moreover, the hydroxyl radical generation from the three different QDs was monitored using a terephthalate-based fluorimetric assay. The three QDs were then used as photocatalyst to trigger the peroxidase activity of horseradish peroxidase.
Clinical tolerance in allogeneic hematopoietic stem cell transplantation (2011)

Allogeneic hematopoietic stem cell transplantation (HSCT) has been a curative therapeutic option for a wide range of immune hematologic malignant and non-malignant disorders including genetic diseases and inborn errors. Once in the host, allogeneic transplanted cells have not only to ensure myeloid repopulation and immunological reconstitution but also to acquire tolerance to host human leukocyte antigens via central or peripheral mechanisms. Peripheral tolerance after allogeneic HSCT depends on several regulatory mechanisms aimed at blocking alloimmune reactivity while preserving immune responses to pathogens and tumor antigens. Patients transplanted with HSCT represent an ideal model system in humans to identify and characterize the key cellular and molecular players underlying these mechanisms. The knowledge gained from these studies has allowed the development of novel therapeutic strategies aimed at inducing long-term peripheral tolerance, which can be applicable not only in allogeneic HSCT but also in autoimmune diseases and solid-organ transplantation. In the present review, we describe Type 1 regulatory T cells, initially discovered and characterized in chimeric patients transplanted with human leukocyte antigen-mismatched HSCT, and how their presence correlates to tolerance induction and maintenance. Furthermore, we summarize different cell therapy approaches with regulatory T cells, designed to facilitate tolerance induction, minimizing pharmaceutical interventions.
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences (2011)

We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.
The Systems Biology of Glycosylation (2004)

Glycosylation can have a profound influence on the function of a variety of eukaryotic cells. In particular, it can affect signal transduction and cell-cell communication properties and thus shape critical cell decisions, including the regulation of differentiation and apoptosis. Regulation of glycosylation has multiple layers of complexity, both structural and functional, which make its experimental and theoretical analysis difficult to perform and interpret. Novel research methodologies provided by systems biology can help to address many outstanding issues and integrate glycosylation with other metabolic and cell regulation processes. Here we review the toolbox available for biochemical systems analysis of glycosylation.
Nociceptors: the sensors of the pain pathway (2010)

Specialized peripheral sensory neurons known as nociceptors alert us to potentially damaging stimuli at the skin by detecting extremes in temperature and pressure and injury-related chemicals, and transducing these stimuli into long-ranging electrical signals that are relayed to higher brain centers. The activation of functionally distinct cutaneous nociceptor populations and the processing of information they convey provide a rich diversity of pain qualities. Current work in this field is providing researchers with a more thorough understanding of nociceptor cell biology at molecular and systems levels and insight that will allow the targeted design of novel pain therapeutics.
Pemafibrate, a novel selective peroxisome proliferator-activated receptor alpha modulator, improves the pathogenesis in a rodent model of nonalcoholic steatohepatitis (2017)

The efficacy of peroxisome proliferator-activated receptor α-agonists (e.g., fibrates) against nonalcoholic fatty liver disease (NAFLD)/nonalcoholic steatohepatitis (NASH) in humans is not known. Pemafibrate is a novel selective peroxisome proliferator-activated receptor α modulator that can maximize the beneficial effects and minimize the adverse effects of fibrates used currently. In a phase-2 study, pemafibrate was shown to improve liver dysfunction in patients with dyslipidaemia. In the present study, we first investigated the effect of pemafibrate on rodent models of NASH. Pemafibrate efficacy was assessed in a diet-induced rodent model of NASH compared with fenofibrate. Pemafibrate and fenofibrate improved obesity, dyslipidaemia, liver dysfunction, and the pathological condition of NASH. Pemafibrate improved insulin resistance and increased energy expenditure significantly. To investigate the effects of pemafibrate, we analysed the gene expressions and protein levels involved in lipid metabolism. We also analysed uncoupling protein 3 (UCP3) expression. Pemafibrate stimulated lipid turnover and upregulated UCP3 expression in the liver. Levels of acyl-CoA oxidase 1 and UCP3 protein were increased by pemafibrate significantly. Pemafibrate can improve the pathogenesis of NASH by modulation of lipid turnover and energy metabolism in the liver. Pemafibrate is a promising therapeutic agent for NAFLD/NASH.
Non-blocking binary search trees (2010)

This paper describes the first complete implementation of a non-blocking binary search tree in an asynchronous shared-memory system using single-word compare-and-swap operations. The implementation is linearizable and tolerates any number of crash failures. Insert and Delete operations that modify different parts of the tree do not interfere with one another, so they can run completely concurrently. Find operations only perform reads of shared memory.
Expression of serotonin receptors and role of serotonin in human prostate cancer tissue and cell lines (2004)

This is the first study demonstrating an overexpression of 5-HTR subtypes 1A and 1B in PC cells, especially in high-grade tumors. Moreover, 5-HT stimulates proliferation of PC cells and 5-HTR1A antagonists inhibit proliferation. Thus, we propose that 5-HT has an important role in tumor progression, especially in the androgen-independent state of the disease. The design of specific antagonists for this type of receptor might be useful for the growth control of androgen-independent tumors.
Novel High Performance ansa-Zirconocene Catalysts for Isospecific Polymerization of Propylene (1999)

Abstract The introduction of furyl groups to the position next to the silylene bridge of an ansa-zirconocene catalyst was found to remarkably enhance the catalytic activity and the molecular weight of PP during the isospecific polymerization of propylene.
Exploiting the genome (1998)

In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.
Inhibition of acute myeloid leukemia cell growth by mono-specific and bi-specific anti-CD33 × anti-CD64 antibodies (2004)

Bi-specific anti-CD33 x anti-CD64 antibodies (BsAb) mediated more potent and longer-lasting inhibition of proliferation of human leukemia cell lines and primary acute myeloid leukemia (AML) samples compared to mono-specific anti-CD33 mAb. There were no differences between these two antibodies in cellular internalization over time. The inhibitory effect of BsAb was mimicked by a mouse IgG2a subclass mono-specific anti-CD33 mAb. These findings indicate that enhanced inhibition of proliferation was caused by simultaneous ligation of both CD33 and CD64 molecules. We conclude that inhibition of leukemia cell growth initiated by BsAb during prolonged exposure may have therapeutic value for the treatment of AML.
The Role of Allogenic Amniotic Membrane in Burn Treatment (2008)

Amniotic membrane (AM) has been used in burns for nearly 100 years. The purpose of this article is to give a comprehensive review of the English literature published in the last two decades (1987--2007) to present the current state of this therapy form. Three medical databases (PubMed, Medline, The Cochrane Library) and specific burn journals were electronically screened for relevant articles using carefully selected retrieval strategies and keywords (AM, amnion grafts, burns, wound dressing, amnion banking). Bibliographies of relevant articles were analyzed for additional pertinent publications. After exclusion of articles which referred to the use of AM in reconstructive and ophthalmologic surgery, the inquiry yielded 31 relevant articles in English language dealing with AM and burns. There was no publication fulfilling the criteria of evidence level I, 6 articles had evidence level II, 10 had evidence level III, 6 had evidence level IV, and 9 were merely narrative (level V). The review testifies to--in view of good tissue practice--heightened use of processed AM in burns, especially in the last decade. Randomized clinical trials favored the use of amnion in burns in the first place for promotion of wound healing and in the second place for its comfortable and less dressing changes. Antimicrobial effects, pain relief, reduction of fluid, and scar formation were demonstrated additionally.
The Effect of Ablation Electrode Length and Catheter Tip to Endocardial Orientation on Radiofrequency Lesion Size in the Canine Right Atrium (2002)

Although the determinants of radiofrequency lesion size have been characterized in vitro and in ventricular tissue in situ, the effects of catheter tip length and endocardial surface orientation on lesion generation in atrial tissue have not been studied. Therefore, the dimensions of radiofrequency lesions produced with 4-, 6-, 8-, 10-, and 12-mm distal electrode lengths were characterized in 26 closed-chested dogs. The impact of parallel versus perpendicular catheter tip/endocardial surface orientation, established by biplane fluoroscopy and/or intracardiac echocardiography, on lesion dimensions was also assessed. Radiofrequency voltage was titrated to maintain a steady catheter tip temperature of 75 degrees C for 60 seconds. With a perpendicular catheter tip/tissue orientation, the lesion area increased from 29 +/- 7 mm2 with a 4-mm tip to 42 +/- 12 mm2 with the 10-mm tip, but decreased to 29 +/- 8 mm2 with ablation via a 12-mm tip. With a parallel distal tip/endocardial surface orientation, lesion areas were significantly greater: 54 +/- 22 mm2 with a 4-mm tip, 96 +/- 28 mm2 with a 10-mm tip and 68 +/- 24 mm2 with a 12-mm tip (all P < 0.001 vs perpendicular orientation). Lesion lengths and apparent volumes were larger with parallel, compared to perpendicular tip/tissue orientations, although lesion depth was independent of catheter tip length with both catheter tip/tissue orientations. Electrode edge effects were not observed with any tip length. Direct visualization using intracardiac ultrasound guidance was subjectively helpful in insuring an appropriate catheter tip/tissue interface needed to maximize lesion size. Although atrial lesion size is critically dependent on catheter tip length, it is more influenced by the catheter orientation to the endocardial surface. This information may also be helpful in designing electrode arrays for the creation of continuous linear lesions for the elimination of complex atrial tachyarrhythmias.
Pivotal Study of Iodine I 131 Tositumomab for Chemotherapy-Refractory Low-Grade or Transformed Low-Grade B-Cell Non-Hodgkin’s Lymphomas (2001)

A single course of iodine I 131 tositumomab was significantly more efficacious than the LQC received by extensively pretreated patients with chemotherapy-refractory, low-grade, or transformed low-grade NHL and had an acceptable safety profile.
The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues–Which Methods Are Useful When? (2007)

Museums and pathology collections around the world represent an archive of genetic material to study populations and diseases. For preservation purposes, a large portion of these collections has been fixed in formalin-containing solutions, a treatment that results in cross-linking of biomolecules. Cross-linking not only complicates isolation of nucleic acid but also introduces polymerase "blocks" during PCR. A wide variety of methods exists for the recovery of DNA and RNA from archival tissues, and although a number of previous studies have qualitatively compared the relative merits of the different techniques, very few have undertaken wide scale quantitative comparisons. To help address this issue, we have undertaken a study that investigates the quality of nucleic acids recovered from a test panel of fixed specimens that have been manipulated following a number of the published protocols. These include methods of pre-treating the samples prior to extraction, extraction and nucleic acid purification methods themselves, and a post-extraction enzymatic repair technique. We find that although many of the published methods have distinct positive effects on some characteristics of the nucleic acids, the benefits often come at a cost. In addition, a number of the previously published techniques appear to have no effect at all. Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims.
Amylolytic enzymes: molecular aspects of their properties. (2001)

The present review describes the structural features of alpha-amylase, beta-amylase and glucoamylase that are the best known amylolytic enzymes. Although they show similar function, i.e. catalysis of hydrolysis of alpha-glucosidic bonds in starch and related saccharides, they are quite different. alpha-Amylase is the alpha --> alpha retaining glycosidase (it uses the retaining mechanism), and beta-amylase together with glucoamylase are the alpha --> beta inverting glycosidases (they use the inverting mechanism). While beta-amylase and glucoamylase form their own families 14 and 15, respectively, in the sequence-based classification of glycoside hydrolases, alpha-amylase belongs to a large clan of three families 13, 70 and 77 consisting of almost 30 different specificities. Structurally both alpha-amylase and beta-amylase rank among the parallel (beta/alpha)8-barrel enzymes, glucoamylase adopts the helical (alpha/alpha)6-barrel fold. The catalytic (beta/alpha)8-barrels of alpha-amylase and beta-amylase differ from each other. The only common sequence-structural feature is the presence of the starch-binding domain responsible for the binding and ability to digest raw starch. It is, however, present in about 10% of amylases and behaves as an independent evolutionary module. A brief discussion on structure-function and structure-stability relationships of alpha-amylases and related enzymes is also provided.
Driver Information and Traffic Telematics - The Comprehensive Concept by the Mannesmann Group (1996)

&lt;div class="htmlview paragraph"&gt;Traffic Telematics of the Mannesmann group is based on the use and linking of bi-directional mobile data telecommunication and position determination via satellite. The existing infrastructures can be used to realize a multitude of traffic telematics services, which cover a wide spectrum, from information services and emergency calls to individual dynamic route guidance and the closed feedback loop of traffic situation analysis and traffic control.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Three elements are needed for a traffic telematics system to be effective:&lt;/div&gt; &lt;div class="htmlview paragraph"&gt; &lt;ul class="list disc"&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;a center that provides the necessary services,&lt;/div&gt; &lt;/li&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;a mobile telecommunications network capable of transmitting both speech and data,&lt;/div&gt; &lt;/li&gt; &lt;li class="list-item"&gt;&lt;div class="htmlview paragraph"&gt;a vehicle information system that provides the man-machine interface and determines the vehicle's position.&lt;/div&gt; &lt;/li&gt; &lt;/ul&gt; &lt;/div&gt;
Serum Calcium and Magnesium in Schizophrenia: Relationship to Clinical Phenomena and Neuroleptic Treatment (1978)

Serum calcium and magnesium were studied in drug-free and neuroleptic-treated schizophrenic patients. Calcium and magnesium were not significantly different in 31 unmedicated schizophrenic patients compared with normal controls. Serum calcium was altered, however, in two subgroups: (1) Patients who remitted after neuroleptic withdrawal were significantly lower in calcium than those who did not remit; (2) catatonic schizophrenic patients appeared to have an increased calcium at the onset of catatonic stupor. Patients treated with pimozide were found to have a significant decreased in both calcium and magnesium compared with their drug-free values. These same patients showed a similar decrease in both electrolytes during treatment with fluphenazine, a structurally different neuroleptic drug.
Molecular cloning and chemical synthesis of a region of platelet glycoprotein IIb involved in adhesive function. (1987)

Membrane glycoprotein (GP) IIb-IIIa is a component of a platelet adhesive protein receptor. A region of the heavy chain of GPIIb, defined by the monoclonal antibody PMI-1, is involved in adhesion receptor function. We have localized and chemically synthesized this region of GPIIb. A cDNA clone that directs the synthesis of a fusion protein reactive with the PMI-1 antibody was isolated from a phage lambda gt11 expression library constructed with mRNA from an erythroleukemia (HEL) cell line. The deduced amino acid sequence of this clone indicates that it spans the light-heavy chain junction of GPIIb and contains a portion of the carboxyl terminus of the heavy chain and the amino terminus of the light chain. The PMI-1 epitope was found to be contained within a 9-kDa staphylococcal V8 protease fragment of GPIIb, and such a fragment was predicted within the putative heavy-chain sequence. A computerized antigen prediction program identified a single sequence with a high probability of containing a continuous epitope. A synthetic 17-residue peptide containing this sequence binds PMI-1 and inhibits PMI-1 binding to GPIIb-IIIa. The peptide-antibody complex has an approximate Kd of 1.2 microM, which compares to a Kd of 0.95 microM for PMI-1 binding to GPIIb. The region containing the PMI-1 epitope shows no similarity to corresponding regions of two other adhesion receptors, indicating that this portion of GPIIb may function in activities unique to the platelet receptor.