gebhart/patrepeval huggingface dataset:
A murine model for antibody-directed targeting of vascular endothelial cells in solid tumors. (1992)

An attractive approach to the therapy of solid tumors would be to target cytotoxic agents or coagulants to the vasculature of the tumor rather than to the tumor cells themselves. This strategy has 3 advantages: (a) it should be applicable to many types of solid tumors because all require a blood supply for survival and growth; (b) the target endothelial cells are directly accessible through the blood and are normal cells, making the outgrowth of resistant mutants unlikely; and (c) there is an in-built amplification mechanism because thousands of tumor cells are reliant on each capillary for nutrients and oxygen. Despite its theoretical attractions, the approach of tumor vascular targeting has not been testable because antibodies that recognize tumor vascular endothelial cell antigens with adequate specificity are currently not available. In this study, we developed a model system in which to investigate the antibody-directed targeting of vascular endothelial cells in solid tumors in mice. A neuroblastoma transfected with the mouse interferon-gamma gene, C1300(Mu gamma), was grown in antibiotic-treated BALB/c nude mice. The interferon-gamma secreted by the tumor induces the expression of major histocompatibility complex Class II antigens on the tumor vascular endothelium. Class II antigens are absent from the vasculature of normal tissues, although they are present on B-lymphocytes, cells of monocyte/macrophage lineage, and some epithelial cells. Anti-Class II antibody administered i.v. strongly stains the tumor vasculature, whereas an antitumor antibody directed against a major histocompatibility complex Class I antigen of the tumor allograft produces classical perivascular tumor cell staining. This model should enable the theoretical superiority of tumor vascular targeting over conventional tumor cell targeting to be tested.
A single representation to support assembly and process planning in feature-based design machined parts (1999)

The need for a product model that can support the modelling requirements of a broad range of applications leads to the application of a feature-based model within a computer aided design environment. An important requirement in feature-based design for manufacture is that a single feature representation should be capable of concurrently supporting a number of different applications. Assembly and process planning are seen as two crucial manufacturing applications and a formal structure for their representation in a feature-based design system is presented. This research addresses two basic questions relating to the lack of a unified definition for features and the establishment of a feature-based representation for assembly. Thus the concept of designing with features is extended by incorporating assembly and process planning information with the geometrical and topological details of component parts. A prototype system has been implemented using an object-oriented programming technique which provides a convenient method for adding functionality to the geometric reasoning process of features and the complex relationships between the parts that make up the assembly. The feature-based model is embedded in the ACIS object-oriented solid modeller kernel.
pp60c-src tyrosine kinase, myristylation, and modulatory domains are required for enhanced mitogenic responsiveness to epidermal growth factor seen in cells overexpressing c-src. (1989)

In previous studies examining the potential role of pp60c-src in cellular proliferation, we demonstrated that C3H10T1/2 murine embryo fibroblasts overexpressing transfected chicken genomic c-src displayed an epidermal growth factor (EGF)-induced mitogenic response which was 200 to 500% of the response exhibited by parental control cells (Luttrell et al., Mol. Cell. Biol. 8:497-501, 1988). In order to examine specific structural and functional requirements for pp60c-src in this event, 10T1/2 cells were transfected with chicken c-src genes encoding pp60c-src deficient in tyrosine kinase activity (pm430), myristylation, (pm2A), or a domain hypothesized to modulate the interaction with substrates or regulatory components (dl155). Neomycin-resistant clonal cell lines overexpressing each of the mutated c-src genes were assayed for EGF mitogenic responsiveness by measuring [3H]thymidine incorporation into acid-precipitable material or into labeled nuclei. The results were compared with those obtained with lines overexpressing the cDNA form of wild-type (wt) c-src or control cells transfected with the neomycin resistance gene only. As previously described for cells overexpressing wt genomic c-src (Luttrell et al., 1988), clones overexpressing wt cDNA c-src also exhibited enhanced EGF mitogenic responses ranging from approximately 300 to 400% of the control cell response. In contrast, clones overexpressing unmyristylated, modulation-defective, or kinase-deficient c-src not only failed to support an augmented response to EGF but also exhibited EGF responses lower than that of the control cells. Furthermore, there were no significant differences in the mitogenic responses to 10% fetal calf serum among any of the cells tested. These results indicate that pp60(c-scr) can potentiate mitogenic signaling generated by EGF but not all growth factors. This potentiation requires the utilization of pp60(c-scr) myristylation, and modulatory and tyrosine kinase domains and can me mediated by cDNA-encoded as well as by genome-encoded wt pp60(c-scr).
Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents (2013)

Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
Microglia Overexpressing the Macrophage Colony-Stimulating Factor Receptor Are Neuroprotective in a Microglial-Hippocampal Organotypic Coculture System (2005)

Microglia with increased expression of the macrophage colony-stimulating factor receptor (M-CSFR; c-fms) are found surrounding plaques in Alzheimer's disease (AD) and in mouse models for AD and after ischemic or traumatic brain injury. Increased expression of M-CSFR causes microglia to adopt an activated state that results in proliferation, release of cytokines, and enhanced phagocytosis. To determine whether M-CSFR-induced microglial activation affects neuronal survival, we assembled a coculture system consisting of BV-2 microglia transfected to overexpress the M-CSFR and hippocampal organotypic slices treated with NMDA. Twenty-four hours after assembly of the coculture, microglia overexpressing M-CSFR proliferated at a higher rate than nontransfected control cells and exhibited enhanced migration toward NMDA-injured hippocampal cultures. Surprisingly, coculture with c-fms-transfected microglia resulted in a dramatic reduction in NMDA-induced neurotoxicity. Similar results were observed when cocultures were treated with the teratogen cyclophosphamide. Biolistic overexpression of M-CSFR on microglia endogenous to the organotypic culture also rescued neurons from excitotoxicity. Furthermore, c-fms-transfected microglia increased neuronal expression of macrophage colony-stimulating factor (M-CSF), the M-CSFR, and neurotrophin receptors in the NMDA-treated slices, as determined with laser capture microdissection. In the coculture system, direct contact between the exogenous microglia and the slice was necessary for neuroprotection. Finally, blocking expression of the M-CSF ligand by exogenous c-fms-transfected microglia with a hammerhead ribozyme compromised their neuroprotective properties. These results demonstrate a protective role for microglia overexpressing M-CSFR in our coculture system and suggest under certain circumstances, activated microglia can help rather than harm neurons subjected to excitotoxic and teratogen-induced injury.
Chimeric proteins composed of Jun and CREB define domains required for interaction with the human T-cell leukemia virus type 1 Tax protein (1995)

The regulation of human T-cell leukemia virus type 1 (HTLV-1) long terminal repeat gene expression is dependent on three cis-acting elements known as 21-bp repeats and the transactivator protein Tax. Mutagenesis has demonstrated that sequences in each of the 21-bp repeats can be divided into three domains designated A, B, and C. Tax stimulates the binding of CREB to the B domain, which is essential for Tax activation of HTLV-1 gene expression. In this study, we demonstrate that Tax will stimulate the binding of CREB to the HTLV-1 21-bp repeats but does not stimulate CREB binding to the consensus cyclic AMP response element (CRE) element found in the somatostatin promoter. However, Tax stimulates CREB binding to a consensus CRE in the context of the 21-bp repeats, indicating the importance of these sequences in stimulating CREB binding. To determine the mechanism by which Tax stimulates CREB binding and determine potential interactions between Tax and CREB, we used the mammalian two-hybrid system in conjunction with in vitro binding and gel retardation assays. Two-hybrid analysis indicated that mutations in either the basic or leucine zipper region of CREB prevented interactions with Tax. Since several studies have demonstrated that Tax will also stimulate the binding of a variety of different basic region-leucine zipper proteins to their cognate binding sites, we assayed whether chimeric proteins composed of portions of CREB and another basic region-leucine zipper protein, Jun, could be used to map domains required for interactions with Tax. These studies were possible because we did not detect in vivo or in vitro interactions between Tax and Jun. The amino acid sequence of the CREB basic region and a portion of its leucine zipper were required for both in vivo and in vitro interactions with Tax and increased binding of CREB to the 21-bp repeats in response to Tax. These studies define the domains in CREB required for both in vivo and in vitro interactions by the HTLV-1 Tax protein.
Marine stabilized multiband satellite terminal (2003)

The need to provide high speed data to and from vessels at sea provides a challenging design task for the satellite professional. The task of stabilizing the antenna mount on a moving platform as well as the capability to operate on more than one frequency band presents multiple challenges to the terminal designer. A team of companies have joined together to design and produce the next generation in marine stabilized multiband satellite communications terminal. Austin Info systems, Inc. (AIS) teamed with Maritime Telecommunications Network (MTN), Orbit CT&T Marine Division, and Ki Company to produce the 106M4S3 Satellite Terminal. The system consists of a 2.7-meter carbon fiber reflector system using the AIS patented multiband feed technology. The system provides continuous transmit and receive capability in C-band and Ku-band without the need for mechanical changeout of the feed assembly. The C-band is also provided with selectable circular or linear polarization. The system is supplied with dual band satellite electronics. The system uses X over Y pedestal technology to eliminate cable wrap. The system is capable of being provided in a single or dual terminal configuration. A complete monitor and control system is provided from below decks. Although originally designed for operation in C and Ku bands the system is capable of being expanded to provide coverage of other bands including X and Ka bands. This paper provides details of the design and operation of the system.
Biometric image processing and recognition (1998)

Biometric-based identification and verification systems are poised to become a key technology, with applications including controlling access to buildings and computers, reducing fraudulent transactions in electronic commerce, and discouraging illegal immigration. There are at least eight image-based biometrics that are being actively considered. In image-based biometrics, the biometrie signature is acquired as an image and the image is processed using techniques from computer vision, image understanding, and pattern recognition. We consider two promising image-based biometrics, faces and fingerprints. For each, we provide a critical assessment of the state of the art, suggest future research directions, and identify technological challenges.
Electrophysiological measures of acute cerebral ischaemia (2005)

A method of EEG analysis is described which provides new insights into EEG pathology in cerebral ischaemia. The method is based on a variant of detrended fluctuation analysis (DFA), which reduces short (10 s) segments of spontaneous EEG time series to two dimensionless scaling exponents. The spatial variability of each exponent is expressed in terms of its statistical moments across EEG channels. Linear discriminant analysis combines the moments into concise indices, which distinguish normal and stroke groups remarkably well. On average over the scalp, stroke patients have larger fluctuations on the longest time scales. This is consistent with the notion of EEG slowing, but extends that notion to a wider range of time scales. The higher moments show that stroke patients have markedly reduced variability over the scalp. This contradicts the notion of a purely focal EEG scalp topography and argues instead for a highly distributed effect. In these indices, subacute patients appear further from normal than acute patients.
PURIFICATION AND CHARACTERIZATION OF GUINEA PIG LYMPHOTOXIN PRODUCED BY LYMPH NODE CELLS STIMULATED BY PHYTOHEMAGGLUTININ (1975)

Guinea pig lymphotoxin (LT) produced by stimulation of lymph node cells with Phaseolus vulgaris phytohemagglutinin was purified approximately 1,000-fold in specific activity by ammonium sulfate fractionation, DEAE-Sephadex column chromatography, and gel filtration on Sephadex G-100. The properties of LT tested at the various stages of purification revealed that the LT was a heat-sensitive, protease-sensitive proteinaceous substance, and its approximate molecular weight was estimated to be 50,000 by means of gel filtration. The most purified fraction (Fr. D) was found to be devoid of the activities of migration inhibitory and mitogenic factors, clearly indicating that these activities are mediated by different substances.
HOW ANTIBIOTIC-PRODUCING ORGANISMS AVOID SUICIDE (1989)

Synthese sur la resistance aux antibiotiques chez les microorganismes producteurs: 1) Modification de l'antibiotique; 2) Resistance au niveau de la cible de l'antibiotique; 3) Divers mecanismes de resistance chez les Actinomycetes; 4) Regulation de la resistance
Can hammerhead ribozymes be efficient tools to inactivate gene function? (1994)

In order to improve hammerhead ribozyme efficiency and specificity, we have analyzed, both in vitro and in vivo, the activity of a series of ribozyme/substrate combinations that have the same target sequence but differ in the length of the ribozyme/substrate duplex or in their structure, i.e., the total length of the RNA. In vitro, we have found that optimal kcat/Km (at 37 degrees C) is obtained when the ribozyme/substrate duplex has a length of 12 bases, which according to the base composition represents a calculated free energy of binding of -16 kcal/mol. We discuss the importance of this value for ribozyme specificity and present strategies that may improve it. Increasing the length of the duplex from 14 to 17 bases (from -19 to -26 kcal/mol) produces a reduced ribozyme activity which is probably due to a slower rate of product dissociation. In addition, inclusion of either the substrate or the ribozyme in a long transcript produces a reduction (10 fold) of the kcat/Km, probably because of a different accessibility of the target sequence. In vivo, the activity of the trans-acting ribozyme was extremely low and detected in only one case: with a ribozyme/substrate duplex length of 13 bases and with both ribozyme and substrate embedded in short RNAs expressed at a very high level. The similarity of the results obtained in vitro and in vivo indicates that it is possible to use an in vitro system to optimize ribozymes which are to be used in vivo. Satisfactory results were obtained in vivo only with cisacting ribozymes. Altogether these results suggest that the ribozyme/substrate hybridization step is the limiting step in vivo and therefore it is not clear if ribozymes represent an improvement over antisense RNAs.
An integrated approach to goal-directed obstacle avoidance under dynamic constraints for dynamic environments (2003)

Whenever robots are installed in populated environments, they need appropriate techniques to avoid collisions with unexpected obstacles. Over the past years several reactive techniques have been developed that use heuristic evaluation functions to choose appropriate actions whenever a robot encounters an unforeseen obstacle. Whereas the majority of these approaches determines only the next steering command, some additionally consider sequences of possible poses. However, they generally do not consider sequences of actions in the velocity space. Accordingly, these methods are not able to slow down the robot early enough before it has to enter a narrow passage. In this paper we present a new approach that integrates path planning with sensor-based collision avoidance. Our algorithm simultaneously considers the robot's pose and velocities during the planning process. We employ different strategies to deal with the huge state space that has to be explored. Our method has been implemented and tested on real robots and in simulation runs. Extensive experiments demonstrate that our technique can reliably control mobile robots moving at high speeds.
Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq (2019)

This study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals.
Modification of the glass transitions of polymers by high-pressure gas solubility (2005)

Abstract The newly developed VW- pVT technique for simultaneously measuring the solubility of a gas in a polymer and the concomitant change of volume of the polymer has been used to estimate the solubilities of N 2 , CO 2 , and two hydrofluorocarbons, HFC-134a and HFC-152a, in polystyrene (PS). In conjunction with these solubility data, Chow’s model has been used to calculate the change of the glass-transition temperature of the polymer resulting from gas sorption. The performance of this model for predicting the glass-transition temperature shift is then discussed.
Plant expression, lyophilisation and storage of HBV medium and large surface antigens for a prototype oral vaccine formulation (2012)

Current immunisation programmes against hepatitis B virus (HBV) increasingly often involve novel tri-component vaccines containing-together with the small (S-HBsAg)-also medium and large surface antigens of HBV (M- and L-HBsAg). Plants producing all HBsAg proteins can be a source of components for a potential oral 'triple' anti-HBV vaccine. The objective of the presented research was to study the potential of M/L-HBsAg expression in leaf tissue and conditions of its processing for a prototype oral vaccine. Tobacco and lettuce carrying M- or L-HBsAg genes and resistant to the herbicide glufosinate were engineered and integration of the transgenes was verified by PCR and Southern hybridizations. M- and L-HBsAg expression was confirmed by Western blot and assayed by ELISA at the level of micrograms per g of fresh weight. The antigens displayed a common S domain and characteristic domains preS2 and preS1 and were assembled into virus-like particles (VLPs). Leaf tissues containing M- and L-HBsAg were lyophilised to produce a starting material of an orally administered vaccine formula. The antigens were distinctly sensitive to freeze-drying conditions and storage temperature, in the aspect of stability of S and preS domains and formation of multimeric particles. Efficiency of lyophilisation and storage depended also on the initial antigen content in plant tissue, yet M-HBsAg appeared to be approximately 1.5-2 times more stable than L-HBsAg. The results of the study provide indications concerning the preparation of two other constituents, next to S-HBsAg, for a plant-derived prototype oral tri-component vaccine against hepatitis B.
An odyssey from breast to bone: Multi‐step control of mammary metastases and osteolysis by matrix metalloproteinases (1999)

Development of metastases distant to the primary site of solid tumors marks late stages of tumor progression. Almost all malignant mammary tumors are carcinomas arising from the breast epithelium, but the morphological and molecular alterations in the mammary stroma surrounding the premalignant and the growing tumor contribute to its conversion into neoplastic tissue. Two parameters are critical for initiation of the metastatic process and access of tumor cells to the circulation. These are the ability of tumor cells to invade the basement membrane and the stroma, and the neovascularization of breast tumor tissue. A major site for development of distant metastases is the skeleton. After colonizing the bone, tumor cells promote a cascade of events leading to recruitment of osteoclasts and subsequent osteolytic bone destruction. A ubiquitous theme of neoplastic progression of breast tumors is the overproduction of matrix metalloproteinases. In this review, we summarize the recent insights into the functional consequences of matrix metalloproteinase expression and activation during malignant conversion in the breast, and after bone colonization. The current literature supports the hypothesis that matrix metalloproteinases play a key role in the metastatic expansion of most, if not all, mammary tumors and in the ensuing bone loss.