gebhart/patrepeval huggingface dataset:
Cell Density Modulates Protein-tyrosine Phosphorylation (1998)

The growth of normal cells is arrested at saturating cell density in a process termed contact inhibition. An understanding of how cells communicate their contact with one another is critical for determining how cancers develop and spread. Because the molecular details of how fibroblasts communicate density changes are unclear, we examined cell density itself as a source of signaling events rather than examine specific receptors. A technique was developed to measure tyrosine phosphorylation acutely as a function of cell density. The tyrosine phosphorylation of a number of proteins was found to be modified in response to cell density. Three of these proteins were identified as Src, paxillin, and focal adhesion kinase (FAK), all of which show an increase in their tyrosine phosphate levels with increasing density. All of these proteins are found in focal adhesions, and both FAK and paxillin are believed to be localized exclusively in focal adhesions. Thus, changing cell density alters tyrosine phosphorylation of focal adhesion components.
Statistical Physics of Macromolecules (1995)

T he appellation "dirt physics" was given to three schools of physicists who, during the 1970s, began to work on questions related to the statics and dynamics of complex long-chain molecules.This work was called dirt physics because no one could imagine where the "physics" was or even what the general physics principles were.General principles as well as specific new results were found though, in abundance, by members of all three schools (and other "camp followers," including this reviewer).One substantial school grew up in the UK around Sir Sam Edwards, who in the 1960s had already recognized the uncanny parallels between quantum field theory and
Putting computing in context (2005)

Context-aware computing exposes a unique tension in how information about human context is modeled and used. On the one hand, approaches that use loosely structured information have been shown to be useful in situations where humans are the final consumers of contextual information; these approaches have found favor in many CSCW applications. On the other hand, more rigidly structured information supports machine interpretation and exchange; these approaches have been explored in the ubiquitous computing community. The system presented here, dubbed Intermezzo, represents an exploration of a space between these two extremes. Intermezzo combines a loose data structuring with a number of unique features designed to allow applications to embed specialized semantic interpretations of data into the infrastructure, allowing them to be reused by other applications. This approach can enable the construction of applications that can take advantage of rich, layered interpretations of context without requiring that they understand all aspects of that context. This approach is explored through the creation of two higher-level services that provide context-enhanced session management and context-enhanced access control.
Prospects for mTOR Inhibitor Use in Patients with Polycystic Kidney Disease and Hamartomatous Diseases (2010)

Mammalian target of rapamycin (mTOR) is the core component of two complexes, mTORC1 and mTORC2. mTORC1 is inhibited by rapamycin and analogues. mTORC2 is impeded only in some cell types by prolonged exposure to these compounds. mTOR activation is linked to tubular cell proliferation in animal models and human autosomal dominant polycystic kidney disease (ADPKD). mTOR inhibitors impede cell proliferation and cyst growth in polycystic kidney disease (PKD) models. After renal transplantation, two small retrospective studies suggested that mTOR was more effective than calcineurin inhibitor-based immunosuppression in limiting kidney and/or liver enlargement. By inhibiting vascular remodeling, angiogenesis, and fibrogenesis, mTOR inhibitors may attenuate nephroangiosclerosis, cyst growth, and interstitial fibrosis. Thus, they may benefit ADPKD at multiple levels. However, mTOR inhibition is not without risks and side effects, mostly dose-dependent. Under certain conditions, mTOR inhibition interferes with adaptive increases in renal proliferation necessary for recovery from injury. They restrict Akt activation, nitric oxide synthesis, and endothelial cell survival (downstream from mTORC2) and potentially increase the risk for glomerular and peritubular capillary loss, vasospasm, and hypertension. They impair podocyte integrity pathways and may predispose to glomerular injury. Administration of mTOR inhibitors is discontinued because of side effects in up to 40% of transplant recipients. Currently, treatment with mTOR inhibitors should not be recommended to treat ADPKD. Results of ongoing studies must be awaited and patients informed accordingly. If effective, lower dosages than those used to prevent rejection would minimize side effects. Combination therapy with other effective drugs could improve tolerability and results.
IMGT-ONTOLOGY 2012 (2012)

Immunogenetics is the science that studies the genetics of the immune system and immune responses. Owing to the complexity and diversity of the immune repertoire, immunogenetics represents one of the greatest challenges for data interpretation: a large biological expertise, a considerable effort of standardization and the elaboration of an efficient system for the management of the related knowledge were required. IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) has reached that goal through the building of a unique ontology, IMGT-ONTOLOGY, which represents the first ontology for the formal representation of knowledge in immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets that rely on the seven axioms of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope: "IDENTIFICATION," "DESCRIPTION," "CLASSIFICATION," "NUMEROTATION," "LOCALIZATION," "ORIENTATION," and "OBTENTION." The concepts of identification, description, classification, and numerotation generated from the axioms led to the elaboration of the IMGT(®) standards that constitute the IMGT Scientific chart: IMGT®standardized keywords (concepts of identification), IMGT® standardized labels (concepts of description), IMGT® standardized gene and allele nomenclature (concepts of classification) and IMGT unique numbering and IMGT Collier de Perles (concepts of numerotation). IMGT-ONTOLOGY has become the global reference in immunogenetics and immunoinformatics for the knowledge representation of immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) proteins of humans and other vertebrates, proteins of the immunoglobulin superfamily (IgSF) and MH superfamily (MhSF), related proteins of the immune system (RPI) of vertebrates and invertebrates, therapeutic monoclonal antibodies (mAbs), fusion proteins for immune applications (FPIA), and composite proteins for clinical applications (CPCA).
Gallic acid causes inactivating phosphorylation of cdc25A/cdc25C-cdc2 via ATM-Chk2 activation, leading to cell cycle arrest, and induces apoptosis in human prostate carcinoma DU145 cells (2006)

We recently reported that gallic acid is a major active agent responsible for grape seed extract activity in DU145 human prostate carcinoma cells. The present study was conducted to examine its efficacy and associated mechanism. Gallic acid treatment of DU145 cells resulted in a strong cell growth inhibition, cell cycle arrest, and apoptotic death in a dose- and time-dependent manner, together with a decrease in cyclin-dependent kinases and cyclins but strong induction in Cip1/p21. Additional mechanistic studies showed that gallic acid induces an early Tyr(15) phosphorylation of cell division cycle 2 (cdc2). Further upstream, gallic acid also induced phosphorylation of both cdc25A and cdc25C via ataxia telangiectasia mutated (ATM)-checkpoint kinase 2 (Chk2) activation as a DNA damage response evidenced by increased phospho-histone 2AX (H2A.X) that is phosphorylated by ATM in response to DNA damage. Time kinetics of ATM phosphorylation, together with those of H2A.X and Chk2, was in accordance with an inactivating phosphorylation of cdc25A and cdc25C phosphatases and cdc2 kinase, suggesting that gallic acid increases cdc25A/C-cdc2 phosphorylation and thereby inactivation via ATM-Chk2 pathway following DNA damage that induces cell cycle arrest. Caffeine, an ATM/ataxia telangiectasia-rad3-related inhibitor, reversed gallic acid-caused ATM and H2A.X phosphorylation and cell cycle arrest, supporting the role of ATM pathway in gallic acid-induced cell cycle arrest. Additionally, gallic acid caused caspase-9, caspase-3, and poly(ADP)ribose polymerase cleavage, but pan-caspase inhibitor did not reverse apoptosis, suggesting an additional caspase-independent apoptotic mechanism. Together, this is the first report identifying gallic acid efficacy and associated mechanisms in an advanced and androgen-independent human prostate carcinoma DU145 cells, suggesting future in vivo efficacy studies with this agent in preclinical prostate cancer models.
ROUGE: A Package for Automatic Evaluation of Summaries (2004)

ROUGE stands for Recall-Oriented Understudy for Gisting Evaluation. It includes measures to automatically determine the quality of a summary by comparing it to other (ideal) summaries created by humans. The measures count the number of overlapping units such as n-gram, word sequences, and word pairs between the computer-generated summary to be evaluated and the ideal summaries created by humans. This paper introduces four different ROUGE measures: ROUGE-N, ROUGE-L, ROUGE-W, and ROUGE-S included in the ROUGE summarization evaluation package and their evaluations. Three of them have been used in the Document Understanding Conference (DUC) 2004, a large-scale summarization evaluation sponsored by NIST. 1
Cellular networking: a carrier's perspective (2003)

The author discusses interim and long-term approaches to intersystem networking. Several interim solutions have been identified and are being offered to provide validation, call deliver, and hand-off for cellular users. It is projected that implementation of more sophisticated system interface standards which will allow 'seamless' operation between cellular, landline, and other communications systems will be the next step. A figure representing the cellular SS7 network of the future is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of ribonucleolytic toxin restrictocin in Escherichia coli: purification and characterization (1996)

Restrictocin is a toxin produced by the fungus Aspergillus restritus. The DNA coding for restrictocin was isolated from the host by polymerase chain reaction and cloned into a T7 promoter-based expression vector. The protein was overproduced in Escherichia coli and remained insoluble in the cell in the form of inclusion bodies. Recombinant restrictocin was purified in large amounts, by a simple denaturation-renaturation protocol involving a redox system, with typical yields of 45 mg/l of original culture. Restrictocin could be secreted into the bacterial medium using ompA, pelB and LTB signal sequences. Among the three signal sequences, ompA was found to be the most efficient in secreting the recombinant protein. The protein secreted into the extracellular medium was properly processed as evident by the amino-terminal sequencing. Recombinant restrictocin was readily purified to homogeneity from either the medium or inclusion bodies by simple chromatographic techniques and was found to be functionally as active as the native fungal protein in inhibiting the eukaryotic translation.
Differential neuronal activity in segments of globus pallidus in Parkinsonʼs disease patients (1994)

Microelectrode trajectories through the globus pallidus of 6 Parkinson's disease (PD) patients yielded neurophysiological 'landmarks' which enabled the identification of neurones located in the external segment (GPe) and internal segments, exterior (GPi,e) and interior (GPi,i) of globus pallidus and the surrounding borders (Bor). Firing rate histograms and inter-spike interval time histograms were constructed for neurones in each region. The neuronal activity in GPi,i was higher than in the other segments, and a high degree of bursting was found in GPe and GPi neurones. This profile of neuronal activity is similar to that observed in monkeys treated with MPTP, suggesting that the observed level of activity of neurones in GPi,i is excessive, and contributes to the bradykinesia and rigidity of PD patients.
Cloning of a Retinoic Acid-sensitive mRNA Expressed in Cartilage and during Chondrogenesis (1996)

Retinoic acid (RA) is known to play a role in various aspects of skeletal development in vivo, including morphogenesis, growth plate maturation, and apoptosis. In cell culture, RA treatment of chondrocytes suppresses the differentiated phenotype characterized by production of type II collagen and aggrecan. In an effort to discover molecules involved in regulation of the chondrocyte phenotype or related to developmental processes such as chondrogenesis, mRNAs from bovine chondrocytes cultured with and without RA were amplified by reverse transcription-polymerase chain reaction (PCR) and compared by differential display. PCR products whose expression was inhibited by RA treatment were cloned. One cDNA encodes a molecule we call cartilage-derived retinoic acid-sensitive protein (CD-RAP), and its properties are described here. The full-length bovine CD-RAP mRNA was cloned after amplification by the rapid amplification of cDNA ends procedure, and a part of the rat CD-RAP mRNA was amplified by reverse transcription-PCR using sequence-specific primers. The bovine CD-RAP mRNA contains an open reading frame of 130 amino acids. CD-RAP mRNA expression, as determined by Northern blot analysis and in situ hybridization, was present only in cartilage primordia and cartilage. The inhibition of CD-RAP mRNA expression by RA in vitro was time- and dose-dependent and was tested over concentrations from 10(-8) to 10(-6) M. Southern blot analysis of genomic DNA indicated that CD-RAP was encoded by a single copy gene and that no other genes were closely related. What appears to be the human homologue of CD-RAP was recently isolated and cloned from a melanoma cell line and shown to function as a growth inhibitory protein (Blesch, A., Boberhoff, A.-K., Apfel, R., Behl, C., Hessdoerfer, B., Schmitt, A., Jachimcza, P., Lottspeich, F., Buettner, R., and Bogdahn, U. (1994) Cancer Res. 54, 5695-5701). Neither CD-RAP nor this protein showed any homology to known proteins. We speculate that, in vivo, CD-RAP functions during cartilage development and maintenance.
Wind Farm Connections to the ETSA Utilities Network (2003)

This paper is entitled 'Wind Farm Connections to the ETSA Utilities Network'. The paper outlines: a brief background to wind generation; an overview of the supply/demand balance in SA; a brief overview of the ETSA Utilities Network; some of the publicly announced proposed wind farm projects in SA; and an outline of the process for connection to the ETSA Utilities Network. ETSA Utilities is a privately owned 50/50 partnership of Cheung Kong Infrastructure and Hong Kong Electric. The business was formed in 1999 after the privatisation of the former publicly owned ETSA Corporation. ETSA Utilities has a 200 year lease over the distribution assets it manages in SA. The ETSA Utilities network covers some, but not all, of the areas in SA where wind farms have been proposed. In general, significant Network augmentation and extension is required for the connection of embedded wind generators. This is principally because the distribution network was never designed with the connection of embedded wind generators in mind. The capital cost of a wind farm is typically in the order of $1,550/kW. Operating and maintenance costs are generally 1.5% of the total capital cost of the wind farm across its life span. Wind generation has an insignificant impact on firm generation capacity in SA because of the variability of the wind. Therefore wind generation should have minimal impact on fossil fuel generation planning. The value of wind farms to defer transmission line expenditure is negligible. The converse is true however because more transmission lines will be required in SA to connect wind farms that are generally proposed remote from load centres. There are many commercial and technical issues involved with the network connection of wind farms. The achievement of NEC and ETSA Utilities' quality of supply requirements, in particular voltage control conditions, can determine the selection of wind turbines and their ability to be Code compliant. The issue of 'first in, best dressed' or constraint according to output with a connection to the Network where there is limited capacity can create Network access issues. This is a looming issue in SA where there are several wind farm proposals to be connected to the same existing Network. The existing Network can only be uprated to a certain extent and beyond this significant Network augmentation is required. ETSA Utilities has an obligation under the NEC to offer a connection to all generators that submit Connection Applications and can meet the NEC compliance requirements. Generally, a process detailed in the NEC, Chapter 5 is followed to connect wind farms. Each connection is unique and requires steady state and dynamic stability analysis to determine the impact of the wind farm on the shared Network. It can take up to 12 months to complete a wind farm connection project barring delays associated with planning approvals and plant and equipment supplies.
Osmotic Effectors and DNA Structure: Effect of Glycine on Precipitation of DNA by Multivalent Cations (1995)

We have investigated the effect of glycine (an organic osmolyte) on DNA precipitation induced by spermine4+, spermidine3+ and Tb3+ addition, using circular dichroism (CD), UV spectroscopy (UV), and electric linear dichroism (ELD) techniques. DNA precipitation by the three compounds is perturbed by glycine: more spermine4+, spermidine3+ and Tb3+ must be added to obtain the same extent of precipitation as compared to the behaviour in absence of this organic osmolyte. It seems that glycine has a general effect on the DNA environment. Calculations based on experimental results and Manning's counterion condensation theory show that glycine could modify the electrostatic environment of DNA as a consequence of a change in dielectric constant.
Voltage dependent gate capacitance and its impact in estimating power and delay of CMOS digital circuits with low supply voltage (2000)

Gate capacitance has complex voltage dependency on terminal voltages but the impact of this voltage dependency of gate capacitance on power and delay has not been fully investigated, especially, in low-voltage, low-power designs. Introducing an effective gate capacitance, CG, effit is shown that the power and delay of CMOS digital circuit can be estimated accurately. CG, effis a strong function of VTH/VDDand VTH/VDDtends to increase in low-voltage region. Hence, the effective capacitance (relative to oxide capacitance, CG, eff, is decreasing in low-voltage low-power designs. Therefore, considering CG, effin accurate power and delay) estimation becomes more important in the future.
Effect of Melatonin on L-Tryptophan- and Apomorphine- Stimulated Growth Hormone Secretion in Man (1979)

The effect of subacute melatonin (250 mg every 8 h over a period of 40 h) and placebo treatment on L-tryptophan- and apomorphine-stimulated GH secretion was tested in 13 volunteers. Melatonin premedication significantly reduced the GH response to peroral L-tryptophan loading, suggesting that melatonin affects GH secretion in man by interfering with serotonergic transmission. In the apomorphine test, no significant difference in GH response was observed after melatonin when compared to placebo treatment. This suggests that dopaminergic mechanisms do not have a central role in mediating actions of melatonin on the hypothalamic-pituitary axis. It is further proposed that melatonin influences GH secretion at a suprahypophyseal level.
Recyclable high-performance epoxy based on transesterification reaction (2017)

A repeatedly recyclable thermoset network with strength and stiffness similar to conventional epoxy achieved healing efficiency as high as 88.1%.
Separation Methods in Membrane Proteomics -Integration of Aqueous Two-Phase Partitioning for Enrichment and Pre-Fractionation (2005)

The study of the protein complement of a genome is called proteomics. Proteomics can be defined as identification, quantification and characterization of a total set of proteins expressed at different time-points or under different cellular states to provide global information about biological processes. The study of membrane proteins is a challenging area in the development of proteomic research. Despite their importance in biology and medicine, membrane proteins are remarkably underrepresented in the majority of current proteomic studies, which is largely due to poor solubility in aqueous solutions and thus incompatibility with the traditional separation method, two-dimensional gel electrophoresis. This stresses the need for finding efficient strategies for enrichment and pre-fractionation, and development of novel high-resolution separation techniques for progress of membrane proteomics. In this thesis, aqueous two-phase partitioning has been studied for enrichment and pre-fractionation of proteins to facilitate membrane proteomes analysis. Aqueous two-phase partitioning is a method used in different bioseparation applications for initial recovery of biomolecules mainly based on their surface properties. A number of different aqueous two-phase systems have been used and evaluated with a wide variety of proteomic separation and identification techniques. Detergent/polymer aqueous two-phase partitioning was shown to be efficient for pre-fractionation of yeast mitochondrial proteins. Furthermore, the structural integrity of multi-subunit membrane protein complexes was maintained in the detergent/polymer two-phase partitioning experiments. The importance of screening experimental conditions for optimized extraction of membrane proteins was demonstrated by the efficient and non-denaturing solubilization obtained by the combination of zwitterionic and non-ionic detergents. Metal affinity two-phase partitioning was investigated for selective enrichment of inner membrane vesicles from E. coli and provided a rapid enrichment compared to traditional sucrose gradient centrifugation. PEG/dextran two-phase partitioning was employed for rapid and efficient enrichment of plasma membranes from human peripheral blood mononuclear cells. The identification of a number of unique signature peptides derived from nine cell surface-specific CD-antigens showed that the proposed strategy can potentially be used for proteomic monitoring of disease reactions and therapeutic treatment on membrane bound cell surface proteins. In conclusion, reduction of sample complexity is a key issue in all proteomic studies but especially so in membrane proteomics. The use of aqueous two-phase partitioning for enrichment and pre-fractionation combined with efficient high-resolution separation techniques will provide a useful approach for membrane proteins and membrane protein complexes in future proteomic studies.