gebhart/patrepeval huggingface dataset:
Carbon nanotube electronics – moving forward (2012)

Single-walled carbon nanotubes (SWNTs) possess fascinating electrical properties and offer new entries into a wide range of novel electronic applications that are unattainable with conventional Si-based devices. The field initially focused on the use of individual or parallel arrays of nanotubes as the channel material for ultra-scaled nanoelectronic devices. However, the challenge in the deterministic assembly has proven to be a major technological barrier. In recent years, solution deposition of semiconductor-enriched SWNT networks has been actively explored for high performance and uniform thin-film transistors (TFTs) on mechanically rigid and flexible substrates. This presents a unique niche for nanotube electronics by overcoming their limitations and taking full advantage of their superb chemical and physical properties. This review focuses on the large-area processing and electronic properties of SWNT TFTs. A wide range of applications in conformal integrated circuits, radio-frequency electronics, artificial skin sensors, and displays are discussed--with emphasis on large-area systems where nm-scale accuracy in the assembly of nanotubes is not required. The demonstrations show SWNTs' immense promise as a low-cost and scalable TFT technology for nonconventional electronic systems with excellent device performances.
Integrated-layer packet radio study for AHS (2002)

The design issues and the performance evaluation of packet radio communication systems for automated highway systems (AHS) are presented. The main focus is on the analysis and interaction between the physical and the link-access layers of a packet radio system that can accommodate communication between vehicles and roadside infrastructure as well as between vehicles. We discuss the information flow requirements of AVCS (advanced vehicle control systems) and ATMIS (advanced traffic management and information systems) services and we present preliminary results from the performance evaluation of four multiple access schemes (slotted-ALOHA, reservation-ALOHA, TDMA, and CDMA).
Relational Databases for Querying XML Documents: Limitations and Opportunities (1999)

XML is fast emerging as the dominant standard for representing data in the World Wide Web. Sophisticated query engines that allow users to effectively tap the data stored in XML documents will be crucial to exploiting the full power of XML. While there has been a great deal of activity recently proposing new semistructured data models and query languages for this purpose, this paper explores the more conservative approach of using traditional relational database engines for processing XML documents conforming to Document Type Descriptors (DTDs). To this end, we have developed algorithms and implemented a prototype system that converts XML documents to relational tuples, translates semi-structured queries over XML documents to SQL queries over tables, and converts the results to XML. We have qualitatively evaluated this approach using several real DTDs drawn from diverse domains. It turns out that the relational approach can handle most (but not all) of the semantic...
TheN–methyl D–aspartate receptor glycine site and D–serine metabolism: an evolutionary perspective (2004)

The N-methyl D-aspartate (NMDA) type of glutamate receptor requires two distinct agonists to operate. Glycine is assumed to be the endogenous ligand for the NMDA receptor glycine site, but this notion has been challenged by the discovery of high levels of endogenous d-serine in the mammalian forebrain. I have outlined an evolutionary framework for the appearance of a glycine site in animals and the metabolic events leading to high levels of D-serine in brain. Sequence alignments of the glycine-binding regions, along with the scant experimental data available, suggest that the properties of invertebrate NMDA receptor glycine sites are probably different from those in vertebrates. The synthesis of D-serine in brain is due to a pyridoxal-5'-phosphate (B(6))-requiring serine racemase in glia. Although it remains unknown when serine racemase first evolved, data concerning the evolution of B(6) enzymes, along with the known occurrences of serine racemases in animals, point to D-serine synthesis arising around the divergence time of arthropods. D-Serine catabolism occurs via the ancient peroxisomal enzyme d-amino acid oxidase (DAO), whose ontogenetic expression in the hindbrain of mammals is delayed until the postnatal period and absent from the forebrain. The phylogeny of D-serine metabolism has relevance to our understanding of brain ontogeny, schizophrenia and neurotransmitter dynamics.
Xenopus VegT RNA is localized to the vegetal cortex during oogenesis and encodes a novel T-box transcription factor involved in mesodermal patterning (1996)

An RNA localized to the vegetal cortex of Xenopus oocytes encodes a novel T-box protein (VegT) capable of inducing either dorsal or posterior ventral mesoderm at different times in development. VegT is a nuclear protein and its C-terminal domain can activate transcription in a yeast reporter assay, observations consistent with VegT functioning as a transcription factor. Zygotic expression is dynamic along the dorsoventral axis, with transcripts first expressed in the dorsal marginal zone. By the end of gastrulation, VegT is expressed exclusively in posterior ventral and lateral mesoderm and is excluded from the notochord. Later expression is confined to a subset of Rohon-Beard cells, a type of primary sensory neuron. In animal cap assays, VegT is capable of converting prospective ectoderm into ventral lateral mesoderm. Such ectopic expression of VegT induces its own expression as well as that of Xwnt-8 in caps, suggesting that a Wnt pathway may be involved. Mis-expression of VegT in dorsal animal blastomeres fated to contribute to brain suppresses head formation. Our results suggest that VegT is a localized transcription factor, which operates sequentially in several developmental pathways during embryogenesis, including dorsoventral and posterior patterning of mesoderm.
A molecular inversion probe assay for detecting alternative splicing (2010)

The asMIP assay provides a sensitive, accurate and multiplexed means for measuring pre-mRNA splicing. Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies.
Constitutive expression of the Wilms tumor suppressor gene WT1 in F9 embryonal carcinoma cells induces apoptotic cell death in response to retinoic acid. (1996)

The product of the Wilms tumor suppressor gene, WT1, is thought to be a tissue specific transcription factor regulating cell growth and differentiation. To elucidate the function of WT1 in cellular differentiation, we examined the changes in the level of WT1 expression during retinoic acid induced-differentiation of embryonal carcinoma F9 cells into parietal endoderm cells. We found that, in response to retinoic acid addition, the expression of WT1 increased significantly after 12--24 h of incubation, then decreased and finally disappeared after 4 days, by which time most of the cells had differentiated into primitive endoderm cells. To examine the significance of these changes in WT1 expression, we established cell lines constitutively expressing one of the WT1 splicing variants. These cell lines showed a phenotype very similar to parental F9 cells in the absence of retinoic acid. However, in the presence of retinoic acid, they failed to differentiate into primitive endoderm cells and underwent apoptotic death 36 h after the addition of retinoic acid. These results suggest that downregulation of WT1 expression is necessary for normal differentiation of F9 cells into parietal endoderm cells.
Neuropilins: structure, function and role in disease (2008)

NRPs (neuropilins) are co-receptors for class 3 semaphorins, polypeptides with key roles in axonal guidance, and for members of the VEGF (vascular endothelial growth factor) family of angiogenic cytokines. They lack a defined signalling role, but are thought to mediate functional responses as a result of complex formation with other receptors, such as plexins in the case of semaphorins and VEGF receptors (e.g. VEGFR2). Mutant mouse studies show that NRP1 is essential for neuronal and cardiovascular development, whereas NRP2 has a more restricted role in neuronal patterning and lymphangiogenesis, but recent findings indicate that NRPs may have additional biological roles in other physiological and disease-related settings. In particular, NRPs are highly expressed in diverse tumour cell lines and human neoplasms and have been implicated in tumour growth and vascularization in vivo. However, despite the wealth of information regarding the probable biological roles of these molecules, many aspects of the regulation of cellular function via NRPs remain uncertain, and little is known concerning the molecular mechanisms through which NRPs mediate the functions of their various ligands in different cell types.
Inflammatory response to cardiopulmonary bypass (1998)

This article reviews the roles of the contact and complement systems and of neutrophils and monocytes in the inflammatory response to cardiopulmonary bypass and open heart operation. These blood proteins and cells, together with other blood elements, produce the vasoactive and cytotoxic substances and microemboli that cause the morbidity associated with cardiopulmonary bypass and open heart operation.
Clopidogrel resistance: current aspects and future directions. (2011)

D ual antiplatelet therapy combi­ ning aspirin and clopidogrel is the standard care for patients who have acute coronary syndromes (ACS) or are undergoing percutaneous coronary in­ tervention (PCI), according to the current ACC/AHA and ESC guidelines. How­ ever, despite the administration of dual antiplatelet therapy, some patients do de­ velop recurrent cardiovascular ischemic events, with stent thrombosis being the most catastrophic. It is well established that the antiplatelet response to clopido­ grel varies widely among patients. Pa­ tients who display little attenuation of platelet reactivity under clopidogrel thera­ py are recognized as low­ or non­respond­ ers, or clopidogrel­resistant. This review focuses on the methods used to identify patients with low clopidogrel responsive­ ness, the underlying mechanisms, clinical significance and current therapeutic strat­ egies to overcome clopidogrel resistance.
Location-aware type ahead search on spatial databases (2011)

Users often search spatial databases like yellow page data using keywords to find businesses near their current location. Typing the entire query is cumbersome and prone to errors, especially from mobile phones. We address this problem by introducing type-ahead search functionality on spatial databases. Like keyword search on spatial data, type-ahead search needs to be location-aware, i.e., with every letter being typed, it needs to return spatial objects whose names (or descriptions) are valid completions of the query string typed so far, and which rank highest in terms of proximity to the user's location and other static scores. Existing solutions for type-ahead search cannot be used directly as they are not location-aware. We show that a straight-forward combination of existing techniques for performing type-ahead search with those for performing proximity search perform poorly. We propose a formal model for query processing cost and develop novel techniques that optimize that cost. Our empirical evaluations on real and synthetic datasets demonstrate the effectiveness of our techniques. To the best of our knowledge, this is the first work on location-aware type-ahead search.
Cell cycle-independent death of prostate adenocarcinoma is induced by the trk tyrosine kinase inhibitor CEP-751 (KT6587). (1998)

Advanced prostate cancer remains largely incurable, primarily because the very low growth fraction present in these tumors makes them generally resistant to treatment with standard chemotherapeutic agents that target cell division. Effective therapies should therefore induce death of prostate cancer cells, independent of their growth rate. trkA, the high-affinity tyrosine kinase-linked receptor for nerve growth factor, has been implicated in prostatic cancer growth and may represent a molecular target for therapeutic agents. At low mg/kg doses, the trk tyrosine kinase inhibitor CEP-751 (KT6587) inhibits prostatic cancer growth in nine different animal models independent of the tumor growth rate, androgen sensitivity, metastatic ability, or state of tumor differentiation. CEP-751 is selective for cancerous versus normal prostate cells and affects the growth of only a limited number of nonprostate tumors. Importantly, CEP-751 induces cell death of prostate cancer cells in a cell cycle-independent fashion and, therefore, represents a novel therapeutic approach to the management of both hormone-dependent and hormone-independent prostate cancer.
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. (1987)

A chemically modified phage T7 DNA polymerase has three properties that make it ideal for DNA sequencing by the chain-termination method. The enzyme is highly processive, catalyzing the polymerization of thousands of nucleotides without dissociating. By virtue of the modification the 3' to 5' exonuclease activity is eliminated. The modified polymerase efficiently uses nucleotide analogs that increase the electrophoretic resolution of bands in gels. Consequently, dideoxynucleotide-terminated fragments have highly uniform radioactive intensity throughout the range of a few to thousands of nucleotides in length. There is virtually no background due to terminations at pause sites or secondary-structure impediments. Processive synthesis with dITP in place of dGTP eliminates band compressions, making possible the unambiguous determination of sequences from a single orientation.
Performance evaluation of texture measures with classification based on Kullback discrimination of distributions (2002)

This paper evaluates the performance both of some texture measures which have been successfully used in various applications and of some new promising approaches. For classification a method based on Kullback discrimination of sample and prototype distributions is used. The classification results for single features with one-dimensional feature value distributions and for pairs of complementary features with two-dimensional distributions are presented.
Discrimination of Complex Mixtures by a Colorimetric Sensor Array: Coffee Aromas (2010)

The analysis of complex mixtures presents a difficult challenge even for modern analytical techniques, and the ability to discriminate among closely similar such mixtures often remains problematic. Coffee provides a readily available archetype of such highly multicomponent systems. The use of a low-cost, sensitive colorimetric sensor array for the detection and identification of coffee aromas is reported. The color changes of the sensor array were used as a digital representation of the array response and analyzed with standard statistical methods, including principal component analysis (PCA) and hierarchical clustering analysis (HCA). PCA revealed that the sensor array has exceptionally high dimensionality with 18 dimensions required to define 90% of the total variance. In quintuplicate runs of 10 commercial coffees and controls, no confusions or errors in classification by HCA were observed in 55 trials. In addition, the effects of temperature and time in the roasting of green coffee beans were readily observed and distinguishable with a resolution better than 10 degrees C and 5 min, respectively. Colorimetric sensor arrays demonstrate excellent potential for complex systems analysis in real-world applications and provide a novel method for discrimination among closely similar complex mixtures.
microRNA‐497 inhibits invasion and metastasis of colorectal cancer cells by targeting vascular endothelial growth factor‐A (2016)

Thus our results provide evidence that miR-497 might function as a metastasis suppressor in CRC. Targeting miR-497 may provide a strategy for blocking its metastasis.
RNA hairpin loops repress protein synthesis more strongly than hammerhead ribozymes (1999)

A general study has been carried out to determine how well hammerhead ribozymes might reduce levels of specific protein synthesis in living cells, compared with RNA hairpin loops as stable but noncleaving controls. Four different experiments are described. First, a wide variety of hammerhead ribozymes, as well as hairpin loops, was cloned into a gene-expression cassette for beta-galactosidase, upstream of the coding sequences for that reporter gene, and expressed from plasmids in several strains of Escherichia coli. The results show that ribozymes, when acting intramolecularly in E. coli, do not significantly reduce the amount of protein synthesized from any construct. As a control, long RNA hairpin loops do greatly reduce the amount of protein made. Secondly, we studied the transcription-translation of these same plasmids in a cell extract from E. coli. Once again, hammerhead ribozymes show no effect on levels of beta-galactosidase, whereas long RNA hairpin loops produce a strong reduction, by apparent attentuation at the level of translation. Thirdly, we added an SV40 promoter to each plasmid, in order to study the effects of these gene-regulators on protein synthesis in Chinese hamster ovary cells. Here active intramolecular ribozymes produce a slight reduction in beta-galactosidase, whereas long RNA hairpin loops produce an even stronger reduction than before. Those hairpin loops apparently induce degradation of their own mRNA in Chinese hamster ovary cells, by a mechanism not seen in E. coli. Finally, analyses of total RNA by S1-trimming show that hammerhead ribozymes will self-cleave a mRNA by a total of no more than 45-50% in E. coli, compared with 70-80% in vitro. Other analyses using Northern blotting were unable to detect any ribozyme cleavage in E. coli or Chinese hamster ovary cells. In summary, the ability of hammerhead ribozymes to reduce protein synthesis appears weak or nonexistent in all the cellular systems tested. By comparison, long RNA hairpin loops reduce protein synthesis strongly: by an apparent attentuation mechanism in E. coli or by a novel degradation of their own mRNA in Chinese hamster ovary cells.
A capacitively loaded PIFA for compact mobile telephone handsets (1997)

A capacitively loaded planar inverted-F antenna (PIFA) is proposed and studied. It is found that the capacitive load reduces the resonance length of the PIFA from /spl lambda//4 to less than /spl lambda//S. A design with a bandwidth of 178 MHz centered at 1.8 GHz is provided to demonstrate that compact antennas for mobile telephone handsets can be constructed using this approach. The finite-difference time-domain (FDTD) method is used in the study and experimental verification is also provided.
Numerical Optimization of Advanced Monolithic Microcoolers for High Heat Flux Microelectronics (2015)

This study considers the optimization of a complex micro-scale cooling geometry that represents a unit-cell of a full heat sink microstructure. The configuration consists of a channel with a rectangular cross section and a hydraulic diameter of 100 μm, where the fluid flows between two cooling fins connected by rectangular crossbars (50 × 50 μm). A previous investigation showed that adding these crossbars at certain locations in the flow can increase the heat transfer in the microchannel, and in the present work we perform an optimization to determine the optimal location and number of crossbars. The optimization problem is defined using 12 discrete design parameters, which represent 12 crossbars at different locations in the channel that can either be turned off and become part of the fluid domain, or turned on and become part of the solid domain. The optimization was done using conjugate heat transfer computational fluid dynamics (CFD) simulations using Fluent 15.0. All possible 4096 configurations were simulated for one set of boundary conditions. The domain was discretized using about 1 million nodes combined for the fluid and solid domains and the computational time was around 1 CPU hour per case. The results show that further improvements in heat transfer are feasible at an optimized pressure drop. The results cover a range of pressure drops from 25 kPa to almost 90 kPa and the heat transfer coefficient varies from 60 to 120 kW/m2K. The configurations on the Pareto front show the trend that crossbars closer to the maximal fluid-solid interface result in a more optimal performance than crossbars positioned farther away. In addition to performing simulations for all possible configurations, the potential of using a genetic algorithm to identify the configurations that define the Pareto front was explored, demonstrating that a 80% reduction in computational time can be achieved. The results of this study demonstrate the significant increase in performance that can be obtained through the use of computational tools and optimization algorithms for the design of single phase cooling devices.
Safeguards for Cell Cooperation in Mouse Embryogenesis Shown by Genome-Wide Cheater Screen (2013)

Ensuring cooperation among formerly autonomous cells has been a central challenge in the evolution of multicellular organisms. One solution is monoclonality, but this option still leaves room for exploitative behavior, as it does not eliminate genetic and epigenetic variability. We therefore hypothesized that embryonic development must be protected by robust regulatory mechanisms that prevent aberrant clones from superseding wild-type cells. Using a genome-wide screen in murine induced pluripotent stem cells, we identified a network of genes (centered on p53, topoisomerase 1, and olfactory receptors) whose down-regulation caused the cells to replace wild-type cells in vitro and in the mouse embryo--without perturbing normal development. These genes thus appear to fulfill an unexpected role in fostering cell cooperation.
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition (1991)

The reversible folding and unfolding of barley chymotrypsin inhibitor 2 (CI2) appears to be a rare example in which both equilibria and kinetics are described by a two-state model. Equilibrium denaturation by guanidinium chloride and heat is completely reversible, and the data can be fitted to a simple two-state model involving only native and denatured forms. The free energy of folding in the absence of denaturant, delta GH2O, at pH 6.3, is calculated to be 7.03 +/- 0.16 and 7.18 +/- 0.43 kcal mol-1 for guanidinium chloride and thermal denaturation, respectively. Scanning microcalorimetry shows that the ratio of the van't Hoff enthalpy of denaturation to the calorimetric enthalpy of denaturation does not deviate from unity, the value observed for a two-state transition, over the pH range 2.2-3.5. The heat capacity change for denaturation is found to be 0.789 kcal mol-1 K-1. The rate of unfolding of CI2 is first order and increases exponentially with increasing guanidinium chloride concentration. Refolding, however, is complex and involves at least three well-resolved phases. The three phases result from heterogeneity of the unfolded form due to proline isomerization. The fast phase, 77% of the amplitude, corresponds to the refolding of the fraction of the protein that has all its prolines in a native trans conformation. The rate of this major phase decreases exponentially with increasing guanidinium chloride concentration. The unfolding and refolding kinetics can also be fitted to a two-state model.(ABSTRACT TRUNCATED AT 250 WORDS)