gebhart/patrepeval huggingface dataset:
Minimum Sum-Squared Residue Co-clustering of Gene Expression Data (2004)

Microarray experiments have been extensively used for simultaneously measuring DNA expression levels of thousands of genes in genome research. A key step in the analysis of gene expression data is the clustering of genes into groups that show similar expression values over a range of conditions. Since only a small subset of the genes participate in any cellular process of interest, by focusing on subsets of genes and conditions, we can lower the noise induced by other genes and conditions — a co-cluster characterizes such a subset of interest. Cheng and Church [3] introduced an effective measure of co-cluster quality based on mean squared residue. In this paper, we use two similar squared residue measures and propose two fast k-means like co-clustering algorithms corresponding to the two residue measures. Our algorithms discover k row clusters and l column clusters simultaneously while monotonically decreasing the respective squared residues. Our co-clustering algorithms inherit the simplicity, efficiency and wide applicability of the k-means algorithm. Minimizing the residues may also be formulated as trace optimization problems that allow us to obtain a spectral relaxation that we use for a principled initialization for our iterative algorithms. We further enhance our algorithms by an incremental local search strategy that helps avoid empty clusters and escape poor local minima. We illustrate co-clustering results on a yeast cell cycle dataset and a human B-cell lymphoma dataset. Our experiments show that our co-clustering algorithms are efficient and are able to discover coherent co-clusters.
<b><i>I</i></b>–<b><i>V</i></b>characteristics and photocurrents of a He corona discharge under flow conditions (2004)

I-V characteristics of a helium corona discharge are discussed for both positive and negative modes. Experimental measurements confirm Townsend's theory for only a part of the I-V characteristic. The flow effect has been correlated to a pressure variation inside the discharge chamber, which in turn gives rise to a corona current change. Corona discharges produce UV radiation through excitation and recombination processes. Currents produced by electron extraction from a stainless steel surface located 74 mm away from the discharge have been measured. Corona currents in the range of 1-7 muA induce currents on the metallic target of 10-30 pA (positive corona), whereas currents of 15-50 muA give rise to 60-140 pA (negative corona).
Blends of Crystallizable Polybutadiene Isomers (1993)

Abstract Precipitated blends of two crystallizable polybutadiene (PBD) isomers were characterized in terms of crystallization and phase behavior, morphology, and tensile mechanical properties. The isomers are syndiotactic 1,2 PBD ( M v =32.5 kg/mol) and trans 1,4 PBD ( M v =425 kg/mol). The blends exhibit heterogeneous behavior over the full range of composition. Using a solvent precipitation method, blends are obtained with heterogeneity on the order of 1 µm. Tensile properties of these semicrystalline blends are generally intermediate between those of the corresponding semicrystalline homopolymers, with some enhancement at approximately 10% 1,2 PBD content. Comparisons are made with previously reported data on amorphous PBD blends.
Scheduling and Power Allocation in a Cognitive Radar Network for Multiple-Target Tracking (2011)

We propose a cognitive radar network (CRN) system for the joint estimation of the target state comprising the positions and velocities of multiple targets, and the channel state comprising the propagation conditions of an urban transmission channel. We develop a measurement model for the received signal by considering a finite-dimensional representation of the time-varying system function which characterizes the urban transmission channel. We employ sequential Bayesian filtering at the receiver to estimate the target and the channel state. We propose a hybrid Bayesian filter that operates by partitioning the state space into smaller subspaces and thereby reducing the complexity involved with high-dimensional state space. The feedback loop that embodies the radar environment and the receiver enables the transmitter to employ approximate greedy programming to find a suitable subset of antennas to be employed in each tracking interval, as well as the power transmitted by these antennas. We compute the posterior Cramer-Rao bound (PCRB) on the estimates of the target state and the channel state and use it as an optimization criterion for the antenna selection and power allocation algorithms. We use several numerical examples to demonstrate the performance of the proposed system.
Carbon Dioxide Capture and Use: Organic Synthesis Using Carbon Dioxide from Exhaust Gas (2013)

A carbon capture and use (CCU) strategy was applied to organic synthesis. Carbon dioxide (CO2) captured directly from exhaust gas was used for organic transformations as efficiently as hyper-pure CO2 gas from a commercial source, even for highly air- and moisture-sensitive reactions. The CO2 capturing aqueous ethanolamine solution could be recycled continuously without any diminished reaction efficiency.
Evaluation of Horizontal Wells Using LWD Propagation Resistivity and Laterolog-Type Resistivity Logs (2006)

Abstract Today, highly deviated and horizontal wells are commonly drilled for better drainage of oil reservoirs. Evaluation of horizontal wells is a challenging task. Traditionally, propagation LWD resistivity logs were interpreted with simplified models. These interpretation methods included using charts, databases, and fast inversion or deconvolution algorithms for resolution enhancement. Many of these traditional methods have limitations in evaluating horizontal wells, particularly when fresh mud is used and borehole size is enlarged. Under these difficult conditions, additional information regarding the formation around borehole will help to reduce the uncertainties in formation evaluation. Theoretical study has shown that a particular LWD laterolog type tool, known as a "toroidal type" LWD resistivity tool, brings in additional information with significant bearing on practical formation evaluation. The additional information makes it possible in horizontal wells to study formation anisotropy and invasion effects with greater confidence. This paper briefly introduces the operating physics of the two types of LWD resistivity tools (propagation vs. toroidal). The paper also introduces the modeling methods we have developed. Limitations and advantages of propagation phase resistivity and laterolog type focused resistivity are studied in a horizontal well drilled with fresh mud. Conventionally, when relative dip angle between borehole and formation exceeds 80 degrees, this well can be regarded as a horizontal well. We will show how the combination of the two types of resistivity tools facilitates horizontal well evaluation in wells drilled with fresh or salty mud.
Deficiency in ubiquitin ligase TRIM2 causes accumulation of neurofilament light chain and neurodegeneration (2008)

TRIM RING finger proteins have been shown to play an important role in cancerogenesis, in the pathogenesis of some human hereditary disorders, and in the defense against viral infection, but the function of the majority of TRIM proteins remains unknown. Here, we show that TRIM RING finger protein TRIM2, highly expressed in the nervous system, is an UbcH5a-dependent ubiquitin ligase. We further demonstrate that TRIM2 binds to neurofilament light subunit (NF-L) and regulates NF-L ubiquitination. Additionally, we show that mice deficient in TRIM2 have increased NF-L level in axons and NF-L-filled axonal swellings in cerebellum, retina, spinal cord, and cerebral cortex. The axonopathy is followed by progressive neurodegeneration accompanied by juvenile-onset tremor and ataxia. Our results demonstrate that TRIM2 is an ubiquitin ligase and point to a mechanism regulating NF-L metabolism through an ubiquitination pathway that, if deregulated, triggers neurodegeneration.
Loss of Neurons in the Hippocampus and Cerebral Cortex of AMSH-Deficient Mice (2001)

AMSH, a molecule that associates with STAM1, is involved in the in vitro cell growth signaling mediated by interleukin 2 and granulocyte-macrophage colony-stimulating factor. To investigate the in vivo functional role of AMSH, we have generated AMSH-deficient mice by gene targeting. The AMSH-deficient mice were morphologically indistinguishable from their littermates at birth, and histopathological examinations revealed normal morphogenesis in all tissues tested. However, all the AMSH-deficient mice exhibited postnatal growth retardation and died between postnatal day 19 (P19) and P23. Examination of brain sections at P6 demonstrated significant loss of neurons and apoptotic cells in the CA1 subfield of the hippocampus. Brain atrophy developed by P16 and was accompanied by complete loss of the CA1 neurons in the hippocampus and marked atrophy of the cerebral cortex. Furthermore, AMSH-deficient hippocampal neuronal cells were unable to survive in vitro, even in the presence of several stimulatory cytokines, while AMSH-deficient cerebellar neurons, thymocytes, and embryonic fibroblasts survived normally. Taken together, these observations indicate that AMSH is an essential molecule for the survival of neuronal cells in early postnatal mice.
Using Process Models with Expert Systems to Aid Process Control Operators (1985)

Expert systems technology seems to have great promise as a medium through which the expertise of master process control operators may be made available as a tool for the average operator. However, fulfillment of this promise will depend upon the extent to which expert systems can be of immediate use to operators in the performance of their critical job duties, and provide them with help that is not more readily available through other approaches. In this paper, we describe how expert systems might be applied to the process control operator's various duties, in order to identify the technical advances needed for the full potential of expert systems technology to be realized. Next, we describe how process models of various types may be used in conjunction with expert systems in order to meet some of these needs, and advance the state-of-the-art in the applications of expert systems to process control. Finally, we list several criteria for choosing near-term expert systems development projects, in light of these considerations.
Endothelial Progenitor Cells: More Than an Inflammatory Response? (2004)

The formation of new capillaries (angiogenesis) may be of clinical importance in facilitating reperfusion and regeneration of hibernating cardiac tissue after myocardial infarction and in microvascular ischemia. Evidence is accumulating that as part of the response to hypoxia, bone marrow-derived circulating endothelial progenitor cells (CEPs) are mobilized and subsequently differentiate into proper endothelial cells. There are also indications that such CEPs can facilitate endothelial repair and angiogenesis in vivo. It is not clear yet, however, whether these CEPs are essential for these adaptive processes or what the relative contribution of CEP is compared with that of other mononuclear inflammatory cells that are mobilized to areas of ischemia. Moreover, there are still many uncertainties about how cardiovascular risk factors alter CEP function. Particularly when therapeutically mobilizing CEPs, a further understanding of this issue is essential to assess the risk of potentially harmful side effects of altered CEP function.
NY-ESO-1 immunotherapy for multiple myeloma (2006)

Most patients with poor-prognosis myeloma (abnormal metaphase cytogenetics) achieve excellent responses with tandem transplants, but the remissions are not durable. Novel interventions such as immunotherapy may eradicate the residual chemotherapy-resistant disease. Immunotherapy targeting weak antigens such as myeloma idiotype or tumor lysate has failed to produce clinically meaningful responses. We previously reported that the NY-ESO-1 antigen is expressed in >60% of poor-prognosis myeloma at diagnosis. Since NY-ESO-1 is highly immunogenic and is not expressed in most normal tissues, it is an ideal target for anti-myeloma immunotherapy. NY-ESO-1 based therapies are already being tested in clinical trials for a multitude of tumors. This review discusses the potential of NY-ESO-1 immunotherapy to improve outcome for myeloma.
Thermodynamics and kinetics of self-discharge in graphite-lithium electrodes (2003)

Li/EC-DMC-LiPF/sub 6//Li/sub x/C/sub 6/ half-cells were discharged to 0V vs. Li/sup +//Li then stored at temperatures ranging between 50 and 85/spl deg/C for times between 1 and 12 days. The remaining capacity was measured by galvanostatic delithiation. The time evolution of the open-circuit voltage (OCV) was also monitored during storage. The activation energy of the self-discharge reaction was determined independently from the temperature dependence of the reaction rate constant and from analysis of the OCV curves. It was found to be approximately 50 kJ.mol/sup -1/. Most of the capacity losses were recoverable after further charge/discharge cycling. The remarkable thermal stability of Li/sub x/C/sub 6/ electrode is related to the protective role of the solid electrolyte interphase (SEI). The SEI evolves to more stable composition during aging due to an increase of its insoluble inorganic part.
Enhanced Tolerance to Photooxidative Stress of Transgenic <italic>Nicotiana tabacum</italic> with High Chloroplastic Glutathione Reductase Activity (1993)

A gene from Escherichia coli that encodes glutathione reductase was connected to a gene for a chloroplastic transit-peptide and the 35S promoter of cauliflower mosaic virus. This chimeric gene was introduced into tobacco cells for generation of transgenic plants. Expression of the transgene in leaf cells and accumulation of the product of its translation in chloroplasts of the transgenic plants were confirmed immunochemically. Leaves of some transgenic plants had activities of glutathione reductase that were about 3-fold higher than those of control plants. These transgenic plants exhibited lower susceptibility both to paraquat and to sulfur dioxide in the light than the control plants in terms of the extent of visible foliar damage. These results suggest that the chloroplastic glutathione reductase, a component of the system for scavenging active oxygen, plays a role in the resistance of plants to photooxidative stress caused by paraquat or sulfur dioxide.
Single-molecule correlated chemical probing of RNA (2014)

Complex higher-order RNA structures play critical roles in all facets of gene expression; however, the through-space interaction networks that define tertiary structures and govern sampling of multiple conformations are poorly understood. Here we describe single-molecule RNA structure analysis in which multiple sites of chemical modification are identified in single RNA strands by massively parallel sequencing and then analyzed for correlated and clustered interactions. The strategy thus identifies RNA interaction groups by mutational profiling (RING-MaP) and makes possible two expansive applications. First, we identify through-space interactions, create 3D models for RNAs spanning 80-265 nucleotides, and characterize broad classes of intramolecular interactions that stabilize RNA. Second, we distinguish distinct conformations in solution ensembles and reveal previously undetected hidden states and large-scale structural reconfigurations that occur in unfolded RNAs relative to native states. RING-MaP single-molecule nucleic acid structure interrogation enables concise and facile analysis of the global architectures and multiple conformations that govern function in RNA.
Antimicrobial Activity of the Investigational Pleuromutilin Compound BC-3781 Tested against Gram-Positive Organisms Commonly Associated with Acute Bacterial Skin and Skin Structure Infections (2012)

ABSTRACT BC-3781 is a novel semisynthetic pleuromutilin antimicrobial agent developed as an intravenous and oral therapy for acute bacterial skin and skin structure infections (ABSSSI) and respiratory tract infections (RTI). BC-3781 and comparator agents were tested by the broth microdilution method against 1,893 clinical Gram-positive organisms predominantly causing ABSSSI. BC-3781 exhibited potent activity against methicillin-resistant Staphylococcus aureus (MIC 50/90 , 0.12/0.25 μg/ml), coagulase-negative staphylococci (MIC 50/90 , 0.06/0.12 μg/ml), β-hemolytic streptococci (MIC 50/90 , 0.03/0.06 μg/ml), viridans group streptococci (MIC 50/90 , 0.12/0.5 μg/ml), and Enterococcus faecium (including vancomycin-nonsusceptible strains) (MIC 50/90 , 0.12/2 μg/ml). Compared with other antibiotics in use for the treatment of ABSSSI, BC-3781 displayed the lowest MICs and only a minimal potential for cross-resistance with other antimicrobial classes.
N,N'-Dimethyl-N,N'-dinitrosoterephthalamide Blowing Agent Preparation, Properties, and General Applications (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTN,N'-Dimethyl-N,N'-dinitrosoterephthalamide Blowing Agent Preparation, Properties, and General ApplicationsMack F. FullerCite this: Ind. Eng. Chem. 1957, 49, 4, 722–730Publication Date (Print):April 1, 1957Publication History Published online1 May 2002Published inissue 1 April 1957https://pubs.acs.org/doi/10.1021/ie50568a038https://doi.org/10.1021/ie50568a038research-articleACS PublicationsRequest reuse permissionsArticle Views150Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Identifying Significantly Impacted Pathways and Putative Mechanisms with iPathwayGuide (2017)

iPathwayGuide is a gene expression analysis tool that provides biological context and inferences from data generated by high-throughput sequencing. iPathwayGuide utilizes a systems biology approach to identify significantly impacted signaling pathways, Gene Ontology terms, disease processes, predicted microRNAs, and putative mechanisms based on the given differential expression signature. By using a novel analytical approach called Impact Analysis, iPathwayGuide considers the role, position, and relationships of each gene within a pathway, which results in a significant reduction in false positives, as well as a better ability to identify the truly impacted pathways and putative mechanisms that can explain all measured gene expression changes. It is a Web-based, user-friendly, interactive tool that does not require prior training in bioinformatics. The protocols in this unit describe how to use iPathwayGuide to analyze a single contrast between two phenotypes (any number of samples), and provide guidance on how to interpret the results obtained from iPathwayGuide. Even though iPathwayGuide has powerful meta-analysis capabilities, these are not covered in this unit. © 2017 by John Wiley & Sons, Inc.
C8/119S Mutation of Major Mite Allergen Derf-2 Leads to Degenerate Secondary Structure and Molecular Polymerization and Induces Potent and Exclusive Th1 Cell Differentiation (2000)

Hyposensitization therapy for atopic diseases has been conducted for decades but suffered from many problems including anaphylactic reactions. We previously developed a mutant protein of the major mite allergen Derf-2, C8/119S, which showed reduced binding to IgE. The C8/119S mutant was shown to exhibit more efficient hyposensitizing effect than Derf-2 in the animal model of allergic bronchial asthma. In the present study, we indicate that C8/119S exhibits markedly augmented immunogenicity for the proliferation of Derf-2-specific human T cells and T cell clones irrespective of the epitope specificity as compared with Derf-2. Furthermore, C8/119S has induced potent and almost exclusive differentiation of Th1 cells from the peripheral blood of atopic patients in vitro. Neither Ag dosage effect nor absence of B cell-mediated Ag presentation could fully account for these effects. C8/119S has been indicated to lose the characteristic beta-barrel structure as judged by circular dichroism spectroscopic analysis and to polymerize solubly in physiological condition. Heating of Derf-2 also caused less stable molecular aggregation, but it hardly affected the secondary structure and failed to induce such a polarity toward the Th1 cell differentiation. These results have indicated that the degenerate secondary structure of C8/119S leading to stable molecular polymerization is primarily responsible for the marked increase in T cell-immunogenicity and the induction of exclusive Th1 cell differentiation in atopic patients. It has been suggested strongly that the recombinant C8/119S protein can provide an effective Ag with the least risk of anaphylaxis for allergen immunotherapy against house dust mite in human.
960 Gb/s Optical Backplane Ecosystem Using Embedded Polymer Waveguides and Demonstration in a 12G SAS Storage Array (2013)

An optical backplane ecosystem is described and demonstrated that is capable of multi-Tb/s bandwidth and is based on embedded polymer waveguides, passive optical backplane connectors, and midboard optical transceivers with bandwidth up to 28 Gb/s per lane. These systems provide the highest bandwidth-density, lowest power consumption, while maintaining the signal integrity. Ecosystems built around this architecture will provide the bandwidth-density required for next generation fabric interconnect for storage, switching, and routing applications in future high capacity generations of Data Centers and HPC systems. To demonstrate the applicability of this technology, it was used to provide embedded optical connectivity within a functional data storage enclosure.
Fahrerlose Transportfahrzeuge ohne Leitlinien - eine neue Dimension ım Materialfluß (1991)

Article Fahrerlose Transportfahrzeuge ohne Leitlinien - eine neue Dimension ım Materialfluß was published on December 1, 1991 in the journal Zeitschrift für wirtschaftlichen Fabrikbetrieb (volume 86, issue 12).
Vanadium-Catalyzed Oxidative Intramolecular Coupling of Tethered Phenols: Formation of Phenol-Dienone Products (2020)

A mild and efficient method for the vanadium-catalyzed intramolecular coupling of tethered free phenols is described. The corresponding phenol-dienone products are prepared directly in good yields with low catalyst loadings. Electronically diverse tethered phenol precursors are well tolerated, and the catalytic method was effectively applied as the key step in syntheses of three natural products and a synthetically useful morphinan alkaloid precursor.