gebhart/patrepeval huggingface dataset:
On Immunity Against Infections and Vaccines: Credo 2004 (2004)

Resistance of vertebrate hosts against infections comprises important natural or innate resistance combined with adaptive immune responses of T and B cells. Viruses, bacteria or classical parasites all probe the limit of immune responses and of immunity. They, therefore, offer an excellent opportunity to assess the biology, physiology and molecular aspects of immune responses and help in characterizing the three basic parameters of immunology-- specificity, tolerance and memory. Various experiments are summarized that indicate that the rules of antiviral, antitumour, antiorgan graft and of autoimmune responses are basically the same. The practical specificity repertoire of T and B cells is probably in the order of 10(4)-10(5) specificities expressed by T cells or by neutralizing antibodies. Tolerance is best defined by rules of reactivity to eliminate infections while avoiding destruction of normal cells by complete elimination of T cells that are specific for antigens persisting within the blood and lymphatic (lymphohaemopoietic) system. Induction of a T-cell response is the result of antigens newly entering lymph nodes or spleen, initially in a local fashion and exhibiting an optimal distribution kinetics within the lymphohaemopoietic system. Antigen staying outside lymphatic tissues are immunologically ignored (e.g. are non-events). Thus immune reactivity is regulated by antigen dose, time and relative distribution kinetics. Memory is the fact that a host is resistant against disease caused by reinfection with the same agent. Memory correlates best with antigen-dependent maintenance of elevated antibody titres in serum and mucosal secretions, or with an antigen-driven activation of T cells, such that they are protective immediately against peripheral reinfections in solid tissues. While antibodies transferred from mother to offspring are a prerequisite for the survival of otherwise unprotected immuno-incompetent offsprings, activated memory T cells cannot be transmitted. Thus, attenuation of infections in newborns and babies by maternal antibodies is the physiological correlate of man-made vaccines. T cells not only play an essential role in maintaining T-help-dependent memory antibody titres, but also in controlling the many infections that persist in a host at rather low levels (such as tuberculosis, measles and HIV).
Real-time monitoring and control of glucose and lactate concentrations in a mammalian cell perfusion reactor (1997)

On-line monitoring and control of cell culture fermentation is important for optimal and consistent production of biologicals. In this work, glucose and lactate concentrations are monitored on-line using a commercially available analyzer (Model 2700, Yellow Springs Instruments, Yellow Springs, OH) during batch and perfusion hybridoma cell fermentation. Cell free samples from the reactor are obtained using a 0.45 mum hollow fiber filtering system placed in a circulation loop. The samples were analyzed at specified times and the data are collected on a computer. A process control strategy was developed to control the concentrations of glucose and lactate in a perfusion reactor where the feed rate is adjusted to maintain their concentrations at desired set points. Hybridoma cells (A10G10) were cultivated in a high density perfusion culture where cell density increased from 2 to 14 million cells/mL. During this period the control algorithm successfully adjusted the perfusion rate while maintaining constant glucose and lactate concentrations. Glucose consumption and lactate accumulation rates as well as net lactate yield on glucose were monitored continuously during perfusion culture. These metabolic rates were observed to be independent of cell concentration and were used for the estimation of viable cell density in the reactor. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 372-378, 1997.
Supplements in Human Islet Culture: Human Serum Albumin is Inferior to Fetal Bovine Serum (2012)

Culture of human islets before clinical transplantation or distribution for research purposes is standard practice. At the time the Edmonton protocol was introduced, clinical islet manufacturing did not include culture, and human serum albumin (HSA), instead of fetal bovine serum (FBS), was used during other steps of the process to avoid the introduction of xenogeneic material. When culture was subsequently introduced, HSA was also used for medium supplementation instead of FBS, which was typically used for research islet culture. The use of HSA as culture supplement was not evaluated before this implementation. We performed a retrospective analysis of 103 high-purity islet preparations (76 research preparations, all with FBS culture supplementation, and 27 clinical preparations, all with HSA supplementation) for oxygen consumption rate per DNA content (OCR/DNA; a measure of viability) and diabetes reversal rate in diabetic nude mice (a measure of potency). After 2-day culture, research preparations exhibited an average OCR/DNA 51% higher (p < 0.001) and an average diabetes reversal rate 54% higher (p < 0.05) than clinical preparations, despite 87% of the research islet preparations having been derived from research-grade pancreata that are considered of lower quality. In a prospective paired study on islets from eight research preparations, OCR/DNA was, on average, 27% higher with FBS supplementation than that with HSA supplementation (p < 0.05). We conclude that the quality of clinical islet preparations can be improved when culture is performed in media supplemented with serum instead of albumin.
Recent improvements of the ProDom database of protein domain families (1999)

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).
Retroviral insertional activation of the Fli-3 locus in erythroleukemias encoding a cluster of microRNAs that convert Epo-induced differentiation to proliferation (2007)

MicroRNAs (miRNAs) are a newly discovered class of posttranscriptional regulatory noncoding small RNAs. Recent evidence has shown that miRNA misexpression correlates with progression of various human cancers. Friend erythroleukemia has been used as an excellent system for the identification and characterization of oncogenes and tumor suppressor genes involved in neoplastic transformation. Using this model, we have isolated a novel integration site designated Fli-3, from a Friend murine leukemia virus (F-MuLV)-induced erythroleukemia. The Fli-3 transcription unit is a murine homologue of the human gene C13orf25 that includes a region encoding the mir-17-92 miRNA cluster. C13orf25 is the target gene of 13q31 chromosomal amplification in human B-cell lymphomas and other malignancies. The erythroleukemias that have acquired either insertional activation or amplification of Fli-3 express higher levels of the primary or mature miRNAs derived from mir-17-92. The ectopic expression of Fli-3 in an erythroblastic cell line switches erythropoietin (Epo)-induced differentiation to Epo-induced proliferation through activation of the Ras and PI3K pathways. Such a response is associated with alteration in the expression of several regulatory factors, such as Spi-1 and p27 (Kip1). These findings highlight the potential of the Fli-3 encoding mir-17-92 in the development of erythroleukemia and its important role in hematopoiesis.
Isotropic Total Variation Regularization of Displacements in Parametric Image Registration (2016)

Spatial regularization is essential in image registration, which is an ill-posed problem. Regularization can help to avoid both physically implausible displacement fields and local minima during optimization. Tikhonov regularization (squared l<sub>2</sub> -norm) is unable to correctly represent non-smooth displacement fields, that can, for example, occur at sliding interfaces in the thorax and abdomen in image time-series during respiration. In this paper, isotropic Total Variation (TV) regularization is used to enable accurate registration near such interfaces. We further develop the TV-regularization for parametric displacement fields and provide an efficient numerical solution scheme using the Alternating Directions Method of Multipliers (ADMM). The proposed method was successfully applied to four clinical databases which capture breathing motion, including CT lung and MR liver images. It provided accurate registration results for the whole volume. A key strength of our proposed method is that it does not depend on organ masks that are conventionally required by many algorithms to avoid errors at sliding interfaces. Furthermore, our method is robust to parameter selection, allowing the use of the same parameters for all tested databases. The average target registration error (TRE) of our method is superior (10% to 40%) to other techniques in the literature. It provides precise motion quantification and sliding detection with sub-pixel accuracy on the publicly available breathing motion databases (mean TREs of 0.95 mm for DIR 4D CT, 0.96 mm for DIR COPDgene, 0.91 mm for POPI databases).
The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race (2007)

Increasingly complex networks of small RNAs act through RNA-interference (RNAi) pathways to regulate gene expression, to mediate antiviral responses, to organize chromosomal domains, and to restrain the spread of selfish genetic elements. Historically, RNAi has been defined as a response to double-stranded RNA. However, some small RNA species may not arise from double-stranded RNA precursors. Yet, like microRNAs and small interfering RNAs, such species guide Argonaute proteins to silencing targets through complementary base-pairing. Silencing can be achieved by corecruitment of accessory factors or through the activity of Argonaute itself, which often has endonucleolytic activity. As a specific and adaptive regulatory system, RNAi is used throughout eukarya, which indicates a long evolutionary history. A likely function of RNAi throughout that history is to protect the genome from both pathogenic and parasitic invaders.
Alice Frost Kennedy - a tribute (1997)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Self-Aligned Nanotube–Nanowire Phase Change Memory (2012)

A central issue of nanoelectronics concerns their fundamental scaling limits, that is, the smallest and most energy-efficient devices that can function reliably. Unlike charge-based electronics that are prone to leakage at nanoscale dimensions, memory devices based on phase change materials (PCMs) are more scalable, storing digital information as the crystalline or amorphous state of a material. Here, we describe a novel approach to self-align PCM nanowires with individual carbon nanotube (CNT) electrodes for the first time. The highly scaled and spatially confined memory devices approach the ultimate scaling limits of PCM technology, achieving ultralow programming currents (~0.1 μA set, ~1.6 μA reset), outstanding on/off ratios (~10(3)), and improved endurance and stability at few-nanometer bit dimensions. In addition, the powerful yet simple nanofabrication approach described here can enable confining and probing many other nanoscale and molecular devices self-aligned with CNT electrodes.
The role of neutrophils in inflammation. (1998)

It has long been noted that inflammation underlies asthma. It is now recognized that there is marked heterogeneity in the stimuli that can cause or aggravate this inflammation, the cells that are involved in the response and the consequences in terms of both pathology and symptoms. The prime role of eosinophilic inflammation in the pathogenesis of asthma is acknowledged in this paper, but the potential role of neutrophilic inflammation to underlie symptoms and physiological changes that are characteristic of asthma is highlighted. A minority group of patients appear to have asthma from clinical signs, but their airway secretions do not contain eosinophils. Their response to treatment is unlike that of patients with typical eosinophilic airway inflammation in that they do not respond to steroid therapy. Published data from in vitro and animal work provide a conceptual framework to explain these observations. The refinement of the technique of examining sputum cellular content to assess airway inflammation provides an opportunity to identify and study this subgroup of patients.
A miniature inspection robot negotiating pipes of widely varying diameter (2004)

The purpose of this research is to realize a small robot which can negotiate pipes whose diameter varies widely during the robot's course. A new in-pipe locomotion mechanism named "snaking drive" is proposed in this paper and its potential and fundamental characteristics are shown with experimental data of the prototype model. First, in the sections 2 to 5, the basic traveling characteristics of the snaking drive mechanism are discussed: a theoretical formula of the fundamental characteristics and control algorithm are derived, the motions of the robot are simulated on a PC, and the prototype model was designed, developed, and tested. Next, in the sections 6 and 7, additional control algorithms for the front link are derived. They are necessary for steering at T-branches and L-bends of pipes, and also for camera view stabilization. Their performances are also shown by software simulation and experiments. The prototype robots moved in pipes whose diameter varies between 55 mm to 331 mm with the maximum speed of 22 mm/s. The paper also shows that the prototype negotiates T-branches and L-bends of pipes with inspection capability through a camera mounted on the robot.
Transient Transfection and Expression in the Obligate Intracellular Parasite Toxoplasma gondii (1993)

Toxoplasma gondii is a protozoan pathogen that produces severe disease in humans and animals. This obligate intracellular parasite provides an excellent model for the study of how such pathogens are able to invade, survive, and replicate intracellularly. DNA encoding chloramphenicol acetyltransferase was introduced into T. gondii and transiently expressed with the use of three vectors based on different Toxoplasma genes. The ability to introduce genes and have them efficiently and faithfully expressed is an essential tool for understanding the structure-function relation of genes and their products.
NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues ofArabidopsis (2007)

Wood is formed by the successive addition of secondary xylem, which consists of cells with a conspicuously thickened secondary wall composed mainly of lignin and cellulose. Several genes involved in lignin and cellulose biosynthesis have been characterized, but the factors that regulate the formation of secondary walls in woody tissues remain to be identified. In this study, we show that plant-specific transcription factors, designated NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis thaliana. In nst1-1 nst3-1 double knockout plants, the secondary wall thickenings in interfascicular fibers and secondary xylem, except for vascular vessels, were completely suppressed without affecting formation of cells destined to be woody tissues. Conversely, as shown previously for NST1, overexpression of NST3 induced ectopic secondary wall thickenings in various aboveground tissues. Furthermore, the expression of chimeric repressors derived from NST1 and NST3 suppressed secondary wall thickenings in the presumptive interfascicular fibers. Because putative orthologs of NST1 and NST3 are present in the genome of poplar, our results suggest that they are also key regulators of the formation of secondary walls in woody plants and could be used as a tool for the genetic engineering of wood and its derivatives.
Outsider-witness practices: some answers to commonly asked questions (2003)

This paper offers an introduction to, and clarification of, some of the intricacies of outsider witnesses. Outsider witness is a therapeutic practice commonly engaged with by those interested in narrative therapy.
Investigation into the future of RFID in biomedical applications (2003)

This paper focuses on the future of RFID systems for biomedical applications. It discusses current technology, restrictions and applications and also illustrates possible future development for the technology. This report gives the reader an idea of what research has been done to date and draws some conclusions about where further development is needed. We focus mainly on actuator devices and introduce some of the concepts for RFID sensors. Radio Frequency Identification or RFID is a technology that has evolved from the development of magnetic bar code systems. Unlike magnetic bar codes, passive RFID can be used in extreme climatic conditions and unlike conventional bar coding does not require wiring or the tags to be within close proximity of the reader. In RFID technology there are two main components, they are an Interrogator and a label/transponder. The interrogator sends coded RF signals to the label in the form of radio frequency waves. The label receives this RF energy and uses it to power its circuit as well as interpreting the energy as some form of instruction. In this report we focus mainly on the label/transponder and assume that the relevant RF energy has been correctly encoded and sent.
Immunotherapeutic potential in murine tumor models of polyinosinic-polycytidylic acid and poly-L-lysine solubilized by carboxymethylcellulose. (1985)

The systemic administration of multiple, nontoxic doses of polyinosinic-polycytidylic acid and poly-L-lysine solubilized by carboxymethylcellulose [poly(I,C)-LC] eradicated established experimental and spontaneous pulmonary metastases. Optimal immunotherapy was schedule dependent, requiring three to five injections of poly(I,C)-LC per week for a minimum of 4 weeks; in addition, therapeutic efficiency was partially dosage independent. Immunotherapy by poly(I,C)-LC was found to be limited by tumor burden, although when combined with chemotherapy as a debulking regimen it resulted in increased survival with protocols in which poly(I,C)-LC alone was insufficient. These data suggest that the systemic administration of poly(I,C)-LC may provide a successful adjuvant therapeutic modality against cancer metastasis.
The Evolution of Molecular Computation (1995)

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Mapping of cellular protein-binding sites on the products of early-region 1A of human adenovirus type 5. (1988)

The binding sites for the 300-, 107-, and 105-kilodalton cellular proteins which associate with human adenovirus type 5 E1A products were studied with E1A deletion mutants. All appeared to bind to the amino-terminal half of E1A products in regions necessary for oncogenic transformation. These results suggest that these cellular species may be important for the biological activity of E1A products.
T cell immunodominance is dictated by the positively selecting self-peptide (2014)

Naive T cell precursor frequency determines the magnitude of immunodominance. While a broad T cell repertoire requires diverse positively selecting self-peptides, how a single positively selecting ligand influences naive T cell precursor frequency remains undefined. We generated a transgenic mouse expressing a naturally occurring self-peptide, gp250, that positively selects an MCC-specific TCR, AND, as the only MHC class II I-E(k) ligand to study the MCC highly organized immunodominance hierarchy. The single gp250/I-E(k) ligand greatly enhanced MCC-tetramer(+) CD4(+) T cells, and skewed MCC-tetramer(+) population toward V11α(+)Vβ3(+), a major TCR pair in MCC-specific immunodominance. The gp250-selected V11α(+)Vβ3(+) CD4(+) T cells had a significantly increased frequency of conserved MCC-preferred CDR3 features. Our studies establish a direct and causal relationship between a selecting self-peptide and the specificity of the selected TCRs. Thus, an immunodominant T cell response can be due to a dominant positively selecting self-peptide. DOI: http://dx.doi.org/10.7554/eLife.01457.001.
In vivo thrombin inhibition enhances and sustains arterial recanalization with recombinant tissue-type plasminogen activator. (1990)

The effects of heparin and the synthetic competitive thrombin inhibitor (2R,4R)-4-methyl-1-[N2-(3-methyl-1,2,3,4-tetrahydro-8-quinolinesulfon yl)-L-arginyl]-2-piperidinecarboxylic acid monohydrate (Argatroban) on thrombolysis with recombinant tissue-type plasminogen activator (rt-PA) was studied in groups of six or seven rabbits with arterial thrombosis. The model consisted of a whole-blood clot produced in a 1-cm isolated femoral arterial segment with superimposed endothelial damage and distal high-grade stenosis. rt-PA was injected as an intravenous bolus of 0.45 mg/kg body wt at 15-minute intervals until recanalization, or up to a maximum of four boluses. In seven rabbits given an intravenous injection of 17 mg/kg aspirin, rt-PA induced transient reflow in only one animal. In seven rabbits that received intravenous heparin (200 units/kg over 60 minutes), rt-PA administration produced reflow in five animals, which was persistent in two rabbits. Combined administration of aspirin and heparin in seven rabbits was associated with similar rt-PA-induced recanalization. rt-PA administration in six rabbits given intravenous Argatroban (100 micrograms/kg/min for 60 minutes) caused recanalization in five, with persistent patency in three. In six rabbits given aspirin and Argatroban, rt-PA caused recanalization in all, with persistent patency in five animals. Reflow occurred significantly more rapidly with Argatroban (14 +/- 7 minutes) than with heparin (35 +/- 11 minutes), reflow was obtained with fewer boluses of rt-PA in combination with Argatroban (median value of one bolus) than with heparin (median value, three boluses), and reocclusion after reflow was less frequent with Argatroban (0 of 11 versus 5 of 10 rabbits). Furthermore, the degree of thrombolysis determined by pathological analysis was significantly more extensive with Argatroban than with heparin, and patency persisted during a 3-hour observation period, despite elimination of Argatroban from the circulation. Thus, Argatroban, relative to heparin, enhances and sustains thrombolysis with rt-PA. It may offer promise as an adjunctive agent for thrombolytic therapy of arterial thrombosis.
Global Text Matching for Information Retrieval (1991)

An approach is outlined for the retrieval of natural language texts in response to available search requests and for the recognition of content similarities between text excerpts. The proposed retrieval process is based on flexible text matching procedures carried out in a number of different text environments and is applicable to large text collections covering unrestricted subject matter. For unrestricted text environments this system appears to outperform other currently available methods.