gebhart/patrepeval huggingface dataset:
Efficient steady-state analysis based on matrix-free Krylov-subspace methods (1995)

Gaussian-elimination based shooting-Newton methods, a commonly used approach for computing steady-state solutions, grow in computational complexity like N 3 , where N is the number of circuit equations. Just using iterative methods to solve the shooting-Newton equations results in an algorithm which is still order N 2 because of the cost of calculating the dense sensitivity matrix. Below, a matrix-free Krylov-subspace approach is presented, and the method is shown to reduce shooting-Newton computational complexity to that of ordinary transient analysis. Results from several examples are given to demonstrate that the matrix-free approach is more than ten times faster than using iterative methods alone for circuits with as few as 400 equations.
Identification of a 79-kDa Heparin-binding Fibroblast Growth Factor (FGF) Receptor in Rat Hepatocytes and Its Correlation with the Different Growth Responses to FGF-1 between Hepatocyte Subpopulations (1996)

We reported previously that the potency of heparin-binding fibroblast growth factor-1 (FGF-1) as a mitogen for rat hepatocytes in primary culture is as high as that of epidermal growth factor (EGF) and hepatocyte growth factor. To gain insight into the pathophysiological significance of FGF-1 in hepatocyte growth, we analyzed the cooperative mitogenicity of FGF-1 and EGF. Results from a nuclear labeling assay using [3H]thymidine suggest that most hepatocytes in primary culture consist of two cell populations that differ in response to FGF-1; one is an FGF-1-responsive cell population, and the other is an EGF-responsive (but not FGF-1-responsive) cell population. On the other hand, autoradiographic analysis of 125I-FGF-1 binding demonstrated that high affinity FGF receptors were homogeneously distributed on the surface of all hepatocytes. Cross-linking 125I-FGF-1 to the nonstimulated hepatocyte surface indicated that the high affinity FGF receptors comprise two FGF receptors that differ in molecular mass (128 and 79 kDa). Furthermore, the 79-kDa receptor was preferentially down-regulated when the hepatocytes were stimulated with EGF or hepatocyte growth factor. These data suggest that the abundant expression of the 79-kDa FGF receptor on some populations of hepatocytes is involved in their lack of response to FGF-1. The 128- and 79-kDa FGF receptors were assigned as FGFR2 using an antibody specific to the ectodomain of FGFR2, whereas the 79-kDa receptor was not reactive to the antibody against the carboxyl terminus of FGFR2. This 79-kDa FGF receptor was not tyrosine-phosphorylated in response to FGF-1 stimulation, while the 128-kDa FGF receptor was recognized by anti-phosphotyrosine antibody under the same conditions. Also, the heterodimer of 79- and 128-kDa FGF receptors was less tyrosine-phosphorylated than the homodimer of 128-kDa FGF receptors. These data suggest that the 79-kDa FGF receptor inhibits the function of the 128-kDa FGF receptor through their heterodimerization. Thus, we surmise that the difference in response to FGF-1 between the cell populations of normal rat hepatocytes was caused by the different levels of the 79-kDa FGF receptor in each cell population.
Through-Space Polar-.pi. Effects on the Acidity and Hydrogen-Bonding Capacity of Carboxylic Acids (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThrough-Space Polar-.pi. Effects on the Acidity and Hydrogen-Bonding Capacity of Carboxylic AcidsChao-Tsen Chen and Jay S. SiegelCite this: J. Am. Chem. Soc. 1994, 116, 13, 5959–5960Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ja00092a053https://doi.org/10.1021/ja00092a053research-articleACS PublicationsRequest reuse permissionsArticle Views682Altmetric-Citations61LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Testing the Prognostic Accuracy of the Updated Pediatric Sepsis Biomarker Risk Model (2014)

The updated version of PERSEVERE estimates mortality probability reliably in a heterogeneous test cohort of children with septic shock and provides information over and above a physiology-based scoring system.
DNA-binding properties of the Hin recombinase (1989)

The recombinase of the Salmonella inversion system, Hin, mediates site-specific recombination between two 26 base pairs (bp) inverted repeat sequences (hixL and hixR) which flank a 993-bp DNA segment. We have investigated Hin recognition of, and association with, the hix recombination sites. Nuclease and chemical protection studies with linear and supercoiled DNA substrates demonstrate that Hin initially binds hixL and hixR independently of binding of the other protein components of the inversion system, Fis and HU. DNA-binding assays with mutant recombination sites and methylation interference experiments indicate that the critical bases for Hin recognition of its DNA-binding site are within an 8-bp sequence covering adjacent major and minor grooves of the DNA helix in each of the 12-bp half-sites of the hix recombination sites. The nature of the Hin-hix complexes in these binding studies and the results of gel filtration assays with purified Hin suggests that Hin binds the recombination sites as a dimer. The implications of the nature of the interactions of Hin with its recombination sites on the mechanism of the recombination reaction and on the novel features of DNA recognition by Hin are discussed.
Expression of prokaryotic 1‐deoxy‐d‐xylulose‐5‐phosphatases in Escherichia coli increases carotenoid and ubiquinone biosynthesis (1999)

Isopentenyl diphosphate (IPP) acts as the common, five-carbon building block in the biosynthesis of all isoprenoids. The first reaction of IPP biosynthesis in Escherichia coli is the formation of 1-deoxy-D-xylulose-5-phosphate, catalysed by 1-deoxy-D-xylulose-5-phosphate synthase (DXPS). E. coli engineered to produce lycopene, was transformed with dxps genes cloned from Bacillus subtilis and Synechocystis sp. 6803. Increases in lycopene levels were observed in strains expressing exogenous DXPS compared to controls. The recombinant strains also exhibited elevated levels of ubiquinone-8. These increases corresponded with enhanced DXP synthase activity in the recombinant E. coli strains.
C2SM: a mobile system for detecting and 3D mapping of chemical, radiological, and nuclear contamination (2009)

CBRN Crime Scene Modeler (C2SM) is a prototype mobile CBRN mapping system for First Responders in events where Chemical, Biological, Radiological and Nuclear agents where used. The prototype operates on board a small robotic platform, increases situational awareness of the robot operator by providing geo-located images and data, and current robot location. The sensor suite includes stereo and high resolution cameras, a long wave infra red (thermal) camera and gamma and chemical detectors. The system collects and sends geo-located data to a remote command post in near real-time and automatically creates 3D photorealistic model augmented with CBRN measurements. Two prototypes have been successfully tested in field trials and a fully ruggedised commercial version is expected in 2010.
Mechanism and subcellular localization of secretory IgM polymer assembly. (1994)

The predominant functions of secreted IgM, complement fixation and transcytosis across epithelial barriers via the poly(Ig) receptor, are properties of IgM polymers; thus, the mechanisms that regulate oligomerization are critical to immune function. We have developed methods to assess the mechanism and subcellular location of IgM polymer formation. Using denaturing agarose/SDS-polyacrylamide gel electrophoresis and sucrose gradient fractionation, we demonstrate that IgM polymers are assembled in a stepwise fashion in which primary intermediates, including heavy chain-light chain complexes, are sequentially incorporated. Assembly intermediates include both covalent and non-covalent components, suggesting that IgM subunit interactions precede covalent assembly. IgM polymers are assembled from primary intermediates containing immature N-linked oligosaccharides. Polymerization is insensitive to brefeldin A and occurs at temperatures that inhibit protein transport along the secretory pathway. Together, these data demonstrate that IgM polymerization occurs early in the secretory pathway, most likely in the endoplasmic reticulum. These results are consistent with a model in which secretory IgM represents an oligomeric protein that is retained in the endoplasmic reticulum and does not mature along the secretory pathway until complete assembly is achieved.
Dynamin, endocytosis and intracellular signalling (Review) (1996)

Dynamin is a neuronal phosphoprotein and a GTPase enzyme which mediates late stages of endocytosis in both neural and non-neural cells. Current knowledge about dynamin is reviewed with particular emphasis on its structure and regulation with respect to phosphorylation, protein-protein interactions and phospholipid binding. The major themes are the biochemical regulation of dynamin, its effects on dynamin's GTPase activity and how this might relate to assembling the 'fission ring' that brings about vesicle retrieval. Dynamin I is an isoform of the enzyme primarily located in the central and peripheral nervous systems, where it is enriched in areas of abundant synaptic contacts. Dynamin I undergoes protein-protein interactions via its proline-rich domain at the C-terminus and these can elevate its N-terminal GTPase activity. Dynamin I interacts with multiple proteins in the nerve terminal, including SH3 domain-containing proteins such as amphiphysin and potentially with other proteins such as betagamma subunits. These regulate its role in endocytosis by targeting dynamin I to specific subcellular locations of retrieval. Dynamin I is phosphorylated in vivo by PKC and dephosphorylated on depolarization and calcium influx into nerve terminals in parallel with the coupled events of exocytosis and endocytosis. In late stages of synaptic vesicle retrieval dynamin I undergoes stimulated assembly into a collar, or fission ring, that surrounds the neck of recycling synaptic vesicles. Activation of GTP hydrolysis probably then generates the free synaptic vesicle, which can be refilled with neurotransmitters. This targeting and assembly may involve sequential steps including recruitment of AP-2 to synaptotagmin on the synaptic vesicle, and recruitment of amphiphysin, dynamin I, and synaptojanin. In addition to synaptic vesicle retrieval, dynamin has been associated with intracellular events mediated by growth factor receptors, insulin receptors and the beta-adrenergic receptor. This is likely to reflect targeting of these receptors for endocytosis soon after their activation. However, does it also suggest a broader role for dynamin in other aspects of intracellular signalling pathways?
Location-based authentication: Grounding cyberspace for better security (1996)

Cyberspace is often characterized as a virtual world that transcends space. People log into computers and transact business electronically without regard to their own geographic location or the locations of the systems they use. A consequence of this lack of grounding in the physical world is that actions can take place over modems and computer networks without anyone knowing exactly where they originated.
Spatial and temporal distribution of bovine herpesvirus 1 transcripts (1989)

Northern (RNA) blot analysis was used to determine the spatial and temporal distribution of bovine herpesvirus 1 (BHV-1) transcripts. Total RNA was isolated from Madin-Darby bovine kidney cells which had been infected with BHV-1.2b strain K22 or BHV-1.1 strain Jura in the presence or absence of metabolic inhibitors. Cloned restriction fragments representing the entire genome of strain K22 were labeled with 32P and hybridized to immobilized RNA. A total of 54 BHV-1 transcripts were found, ranging in size from 0.4 to larger than 8 kilobases (kb). The inverted repeat regions and an adjacent segment of the unique large part of the BHV-1 genome encoded three major immediate-early (IE) transcripts and one minor IE transcript enriched after cycloheximide treatment of infected cells. Late transcripts were identified by drastically reduced abundance after cytosine arabinoside (araC) treatment. Twelve late transcripts were encoded mainly by the unique long genome region, with a cluster of four transcripts located on HindIII fragment K (map units 0.677 to 0.733). The 21 transcripts unaffected by araC treatment were defined as early; they showed dispersed locations over the whole genome, with a cluster on the unique short sequence. The 17 remaining transcripts could not be classified unambiguously as early or late by these techniques. The IE transcript with a size of 4.2 kb exhibited homology with the single IE gene of pseudorabies virus, and the IE transcript with a size of 2.9 kb was encoded in part by the genome region known to be transcriptionally active during latency.
Computer-Assisted Orthopedic Surgery With Individual Templates and Comparison to Conventional Operation Method (2001)

This cadaveric study has shown that overall operation time including the fluoroscopy time can be shortened by using the individual template for the pedicle bore. The individual template is an alternative to the computer-assisted navigation systems with a good cost-performance ratio without excessive technical workload on the physicians or the surgical personnel. Further investigations must be conducted to validate the clinical applicability of this system.
A Neural Network based Real Time Hand Gesture Recognition System (2012)

Hand Gesture is habitually used in every day life style. It is so natural way to communicate. Hand gesture recognition method is widely used in the application area of Controlling mouse and/or keyboard functionality, mechanical system, 3D World, Manipulate virtual objects, Navigate in a Virtual Environment, Human/Robot Manipulation and Instruction Communicate at a distance. This paper introduces a real time hand gesture recognition system. This system consists of three stages: image acquisition, feature extraction, and recognition. In the first stage input image of hand gestures are acquiesced by digital camera in approximate frame rate. In second stage a rotation, translation, scaling and orientation invariant feature extraction method has been introduce to extract the feature of the input image based on moment feature extraction method. Finally, a neural network is used to recognize the hand gestures. The performance of the system tested on real data. Based on the experimental results, we noted that this system shows satisfactory performance in hand gesture recognition.
Dose adjustment of allopurinol according to creatinine clearance does not provide adequate control of hyperuricemia in patients with gout. (2006)

Adherence to published allopurinol dosing guidelines led to suboptimal control of hyperuricemia in this population of patients with gout. Further work is required to clarify the safety and efficacy of allopurinol dose escalation, particularly in patients with renal impairment.
Assessment of Options for Selective 1-Butanol Recovery from Aqueous Solution (2009)

The microbial production of 1-butanol occurs in aqueous fermentation broth, with up to ∼20 g/L of product. Efficient recovery of butanol from this dilute aqueous phase determines, to a large extent, the efficiency of the production process. Starting from the thermodynamic (phase) properties of butanol and water systems, this paper presents a structured approach to determine the key characteristics of various butanol recovery methods. Analysis of reported separations, combined with fundamental phase properties, has resulted in both the characterization of the selectivity of recovery and estimations of the energy requirement during product recovery for a variety of recovery methods. Energy-efficient systems for the recovery of butanol from aqueous solution are pervaporation- and adsorption-based techniques. The applied method predicts the recovery energy requirement for both techniques to be <4 MJ/kg of butanol, which, on an energy basis, is similar to ∼10% of the internal combustion energy of butanol.
Activation of canonical wnt pathway promotes differentiation of mouse bone marrow‐derived MSCs into type II alveolar epithelial cells, confers resistance to oxidative stress, and promotes their migration to injured lung tissue in vitro (2012)

The differentiation of mesenchymal stem cells (MSCs) into type II alveolar epithelial (AT II) cells in vivo and in vitro, is critical for reepithelization and recovery in acute lung injury (ALI), but the mechanisms responsible for differentiation are unclear. In the present study, we investigated the role of the canonical wnt pathway in the differentiation of mouse bone marrow-derived MSCs (mMSCs) into AT II cells. Using a modified co-culture system with murine lung epithelial-12 (MLE-12) cells and small airway growth media (SAGM) to efficiently drive mMSCs differentiation, we found that GSK 3β and β-catenin in the canonical wnt pathway were up-regulated during differentiation. The levels of surfactant protein (SP) C, SPB, and SPD, the specific markers of AT II cells, correspondingly increased in mMSCs when Wnt3a or LiCl was added to the co-culture system to activate wnt/β-catenin signaling. The expression of these factors was depressed to some extent by inhibiting the pathway with the addition of DKK 1. The differentiation rate of mMSCs also depends on their abilities to accumulate and survive in inflammatory tissue. Our results suggested that the activation of wnt/β-catenin signaling promoted mMSCs migration towards ALI mouse-derived lung tissue in a Transwell assay, and ameliorated the cell death and the reduction of Bcl-2/Bax induced by H(2) O(2), which simultaneously caused reduced GSK 3β and β-catenin in mMSCs. These data supports a potential mechanism for the differentiation of mMSCs into AT II cells involving canonical wnt pathway activation, which may be significant to their application in ALI.
Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma (2015)

Magnetic Resonance Imaging (MRI) has been routinely used for the diagnosis and treatment of breast cancer. However, the relationship between the MRI tumor phenotypes and the underlying genetic mechanisms remains under-explored. We integrated multi-omics molecular data from The Cancer Genome Atlas (TCGA) with MRI data from The Cancer Imaging Archive (TCIA) for 91 breast invasive carcinomas. Quantitative MRI phenotypes of tumors (such as tumor size, shape, margin, and blood flow kinetics) were associated with their corresponding molecular profiles (including DNA mutation, miRNA expression, protein expression, pathway gene expression and copy number variation). We found that transcriptional activities of various genetic pathways were positively associated with tumor size, blurred tumor margin, and irregular tumor shape and that miRNA expressions were associated with the tumor size and enhancement texture, but not with other types of radiomic phenotypes. We provide all the association findings as a resource for the research community (available at http://compgenome.org/Radiogenomics/). These findings pave potential paths for the discovery of genetic mechanisms regulating specific tumor phenotypes and for improving MRI techniques as potential non-invasive approaches to probe the cancer molecular status.
cataract surgical problem (2001)

Journal of Cataract & Refractive Surgery: October 2001 - Volume 27 - Issue 10 - p 1539 doi: 10.1016/S0886-3350(01)01134-8
Major Human Cytomegalovirus Structural Protein pp65 (ppUL83) Prevents Interferon Response Factor 3 Activation in the Interferon Response (2004)

We have identified a cytomegalovirus virion protein capable of modulating the rapid induction of an interferon-like response in cells that follows virus binding and penetration. Functional genomics revealed a role for the major cytomegalovirus structural protein, pp65 (ppUL83), in counteracting this response. The underlying mechanism involves a differential impact of this structural protein on the regulation of interferon response factor 3 (IRF-3). In contrast, NF-kappaB is activated independent of pp65, and neither STAT1 nor STAT3 becomes activated by either virus. pp65 is sufficient to prevent the activation of IRF-3 when introduced alone into cells. pp65 acts by inhibiting nuclear accumulation of IRF-3 and is associated with a reduced IRF-3 phosphorylation state. Thus, this investigation shows that the major structural protein of cytomegalovirus is committed to the modulation of the IRF-3 response, a primary mediator of the type I interferon response. By subverting IRF-3, the virus escapes throwing a central alarm devoted to both immediate antiviral control and regulation of the immune response.
Exogenous Bcl‐xl fusion protein spares neurons after spinal cord injury (2005)

Spinal cord injury (SCI) induces neuronal death, including apoptosis, which is completed within 24 hr at and around the impact site. We identified early proapoptotic transcriptional changes, including upregulation of proapoptotic Bax and downregulation of antiapoptotic Bcl-xL, Bcl-2, and Bcl-w, using Affymetrix DNA microarrays. Because Bcl-xL is the most robustly expressed antiapoptotic Bcl-2 molecule in adult central nervous system, we decided to characterize better the effect of SCI on Bcl-xL expression. We found Bcl-xL expressed robustly throughout uninjured spinal cord in both neurons and glia cells. We also found Bcl-xL localized in different cellular compartments: cytoplasmic, mitochondrial, and nuclear. Bcl-xL protein levels decreased in the cytoplasm and mitochondria 2 hr after SCI and persisted for 24 hr. To test the contribution of proapoptotic decreases in Bcl-xL to neuronal death, we augmented endogenous Bcl-xL levels by administering Bcl-xL fusion protein (Bcl-xL FP) into injured spinal cords. Bcl-xL FP significantly increased neuronal survival, suggesting that SCI-induced changes in Bcl-xL contribute considerably to neuronal death. Because Bcl-xL FP increases survival of dorsal horn neurons and ventral horn motoneurons, it could become clinically relevant in preserving sensory and motor functions after SCI.