gebhart/patrepeval huggingface dataset:
Reconstruction and representation of 3D objects with radial basis functions (2001)

We use polyharmonic Radial Basis Functions (RBFs) to reconstruct smooth, manifold surfaces from point-cloud data and to repair incomplete meshes. An object's surface is defined implicitly as the zero set of an RBF fitted to the given surface data. Fast methods for fitting and evaluating RBFs allow us to model large data sets, consisting of millions of surface points, by a single RBF — previously an impossible task. A greedy algorithm in the fitting process reduces the number of RBF centers required to represent a surface and results in significant compression and further computational advantages. The energy-minimisation characterisation of polyharmonic splines result in a “smoothest” interpolant. This scale-independent characterisation is well-suited to reconstructing surfaces from non-uniformly sampled data. Holes are smoothly filled and surfaces smoothly extrapolated. We use a non-interpolating approximation when the data is noisy. The functional representation is in effect a solid model, which means that gradients and surface normals can be determined analytically. This helps generate uniform meshes and we show that the RBF representation has advantages for mesh simplification and remeshing applications. Results are presented for real-world rangefinder data.
Unusual Porphyrin Analog Promises Many Applications (1988)

RETURN TO ISSUEPREVNewsNEXTUnusual Porphyrin Analog Promises Many ApplicationsSTEPHEN STINSONCite this: Chem. Eng. News 1988, 66, 32, 26–27Publication Date (Print):August 8, 1988Publication History Published online8 November 2010Published inissue 8 August 1988https://pubs.acs.org/doi/10.1021/cen-v066n032.p026https://doi.org/10.1021/cen-v066n032.p026newsACS PublicationsCopyright © 1988 AMERICAN CHEMICAL SOCIETYArticle Views10Altmetric-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 SUBJECTS:Cancer therapy,Coordination chemistry,Metals,Organic chemistry,Pyrroles Get e-Alerts
A Pyruvated Mannose-Specific Xanthan Lyase Involved in Xanthan Degradation by Paenibacillus alginolyticus XL-1 (1999)

The xanthan-degrading bacterium Paenibacillus alginolyticus XL-1, isolated from soil, degrades approximately 28% of the xanthan molecule and appears to leave the backbone intact. Several xanthan-degrading enzymes were excreted during growth on xanthan, including xanthan lyase. Xanthan lyase production was induced by xanthan and inhibited by glucose and low-molecular-weight enzymatic degradation products from xanthan. A xanthan lyase with a molecular mass of 85 kDa and a pI of 7.9 was purified and characterized. The enzyme is specific for pyruvated mannosyl side chain residues and optimally active at pH 6.0 and 55 degrees C.
The influence of natural products upon drug discovery (Antiquity to late 1999) (2000)

The first page of this article is displayed as the abstract.
Insulin receptor and epidermal growth factor receptor dephosphorylation by three major rat liver protein-tyrosine phosphatases expressed in a recombinant bacterial system (1992)

Protein-tyrosine phosphatases (PTPases) play an essential role in the regulation of signal transduction mediated by reversible protein-tyrosine phosphorylation. In order to characterize individual rat hepatic PTPases that might have specificity for autophosphorylated receptor tyrosine kinases, we isolated cDNA segments encoding three PTPases (PTPase 1B, LAR and LRP) that are expressed in insulin-sensitive liver and skeletal muscle tissue, and evaluated their catalytic activity in vitro. The intrinsic PTPase activities of the full-length PTPase 1B protein and the cytoplasmic domains of LAR and LRP were studied by expression of recombinant cDNA constructs in the inducible bacterial vector pKK233-2 using extracts of a host strain of Escherichia coli that lacks endogenous PTPase activity. Each of the cloned cDNAs dephosphorylated a cognate phosphopeptide derived from the regulatory region of the insulin receptor. Despite having only 30-39% sequence identity in their catalytic domains, LAR and PTPase 1B had similar relative activities between the peptide substrate and intact insulin receptors, and also displayed similar initial rates of simultaneous dephosphorylation of insulin and epidermal growth factor (EGF) receptors. In contrast, LRP exhibited a higher rate of dephosphorylation of both intact receptors relative to the peptide substrate, and also dephosphorylated EGF receptors more rapidly than insulin receptors. These studies indicate that three PTPases with markedly divergent structures have the catalytic potential to dephosphorylate both insulin and EGF receptors in intact cells and that redundant PTPase activity may occur in vivo. For these PTPases to have specific physiological actions in intact cells, they must be influenced by steric effects of the additional protein segments of the native transmembrane enzymes, cellular compartmentalization and/or interactions with regulatory proteins.
Mild β+(−87)‐thalassemia CACCC box mutation is associated with elevated fetal hemoglobin expression in cis (1994)

The beta zero-thalassemia codon 39 nonsense mutation predominant in Sardinia is severe, and homozygotes are transfusion dependent. Two-thirds of beta zero 39 alleles are linked to A gamma T (haplotype II). One-fourth are linked to A gamma I (haplotypes I and IX), as is the mild beta +-thalassemia -87 C-->G mutation (haplotype VIII). beta +/beta zero-Thalassemia VIII/II compound heterozygotes have significantly higher A gamma I:A gamma T (23:7) than beta zero-thalassemia I/II (24:20) or IX/II (16:17) cases. This suggests that the beta + -87 mutation is associated with elevated gamma expression in cis, which may contribute to the lack of transfusion-dependence in beta +/beta zero cases.
Greater Clinical Benefit of More Intensive Oral Antiplatelet Therapy With Prasugrel in Patients With Diabetes Mellitus in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel–Thrombolysis in Myocardial Infarction 38 (2008)

Subjects with DM tended to have a greater reduction in ischemic events without an observed increase in TIMI major bleeding and therefore a greater net treatment benefit with prasugrel compared with clopidogrel. These data demonstrate that the more intensive oral antiplatelet therapy provided with prasugrel is of particular benefit to patients with DM.
Characterization of IMiDs (Immunomodulating Agents) Induced “Flare Reaction” in Patients with Chronic Lymphocytic Leukemia (CLL) and Correlation with Changes in Serum Cytokine Levels. (2005)

Abstract Introduction: Several cytokines (including TNF-alpha, IL-6 and VEGF) are reported to play a critical role in the pathogenesis of CLL cells. Targeting the tumor microenvironment through modulation of the cytokine milieu thus is a potential way to treat CLL. In 2 separate clinical studies we investigated the role of IMiDs (thalidomide and lenalidomide) either in combination with standard chemotherapy (thalidomide + fludarabine, FT) or single agent (lenalidomide, L) in pts with previously untreated or relapsed/refractory CLL, respectively. In these studies we observed tumor flare reaction not previously reported. In this report we describe the clinical characteristics of this side effect, its management and correlation with changes in serum cytokine levels. Flare Reaction (FR): CLL pts treated with IMiDs were noted to have tender increase in lymph nodes size starting within 24–48 hours of initiating therapy with or without erythema and rash. Some patients also increased their total white cell as well as absolute lymphocyte count (ALC). Results: A total of 48 pts (20 on FT and 28 on lenalidomide) are collectively treated on 2 clinical trials. Median age was------, -----had limited stage (0-II) and ----- has advance Rai stage (III, IV). ------(%) on the FT and 22 (78.5%) on the L developed a FR, which was noted as early as 24 hours after initiation of therapy (median 48 hours). Most pts resolved FR by day 14. A comparison of serum cytokine level at day 0 and 7 was done in 10 pts (9 with FR) treated with L. An increase in TNF-a (n=4), MIG (n=6), IP-10 (n=8), IL-8 (n=7) and IL-10 (n=6) was noted at day 7. Management: FR was treated with ibuprofen 400 mg q 6 hr with addition of oral morphine (or agents of equivalent potency) for improved pain control. Conclusion: FR is a new side effect noted in CLL pts treated with IMiDs that is fairly well managed by anti-inflammatory agent along with aggressive pain control. Higher incidence is noted with L. There seems to be no correlation of FR with clinical response to therapy. Identification of the FR is important to avoid confusion with disease progression. An increase in levels of inflammatory cytokine was noted in all pts treated with L which may explain the underlying mechanism of this phenomenon.
Ion-exchanged glass waveguides: a review (1988)

Passive glass waveguides made by ion-exchange technique are potential candidates for integrated optics (IO) applications. The authors review the advantages in the technology as applied to fabrication of useful single-mode structures. Progress in process, fabrication, modeling, and waveguide performance using different monovalent cation systems and glass compositions is described with emphasis on fiber-compatible single-mode structures prepared from molten baths. It is shown how a systematic study allows a correlation between the process parameters and the waveguide characteristics so desirable in assuring reproducible characteristics of the devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RNA Amplification Results in Reproducible Microarray Data with Slight Ratio Bias (2002)

Microarray expression analysis demands large amounts of RNA that are often not available. RNA amplification techniques have been developed to overcome this prcblem, but limited data are available regarding the reproducibility and maintenance of original transcript ratios. We optimized and validated two amplification techniques: a modified in vitro transcription for the linear amplification of 3 microg total RNA and a SMART PCR-based technique for the exponential amplification of 50 ng total RNA. To determine bias between transcript ratios, we compared the expression profiles in mouse testis versus spleen between the two amplification methods and a standard labeling protocol, using microarrays containing 4596 cDNAs spotted in duplicate. With each method, replicate hybridizations were highly reproducible. However, when comparing the amplification methods to standard labeling, correlation coefficients were lower. Twelve genes that exhibited inconsistent or contradictory expression ratios among the three methods were verified by quantitative RT-PCR. The amplification methods showed slightly more discrepancies in the expression ratios when compared to quantitative RT-PCR results but were more sensitive in terms of detecting expressed genes. In conclusion, although amplification methods introduce slight changes in the transcript ratios compared to standard labeling, they are highly reproducible. For small sample size, in vitro transcription is the preferred method, but one should never combine different labeling strategies within a single study.
Development and validation of a plasma-based melanoma biomarker suitable for clinical use (2018)

In Australia, more money is spent on skin cancer than any other malignancy. Despite this, the mortality rate of melanoma, the deadliest form, has steadily increased over the past 50 years. Diagnostic imprecision and a lack of complimentary molecular biomarkers are partially responsible for this lack of progress. Whole-microRNAome profiling was performed on plasma samples from 32 patients with histologically confirmed melanoma and 16 normal controls. A classification algorithm was trained on these data and independently validated on multiple previously published microRNA data sets, representing (i) melanoma patient- and normal-blood, (ii) melanoma and nevi biopsy tissue, and (iii) cell lines and purified exosomes. 38 circulating microRNAs had biologically and statistically significant differences between melanoma and normal plasma samples (MEL38). A support vector machine algorithm, trained on these markers, showed strong independent classification accuracy (AUC 0.79–0.94). A majority of MEL38 genes have been previously associated with melanoma and are known regulators of angiogenesis, metastasis, tumour suppression, and treatment resistance. MEL38 exhibits disease state specificity and robustness to platform and specimen-type variation. It has potential to become an objective diagnostic biomarker and improve the precision and accuracy of melanoma detection and monitoring.
Host‐guest interactions in gas phase chemical sensing of permethyl‐6I‐alkenoylamino‐6I‐deoxy‐β‐cyclodextrin derivatized porous silicon (2007)

Abstract Porous silicon surface was modified by photochemically activated hydrosilylation reaction with permethyl‐6 I ‐alkenoylamino‐6 I ‐deoxy‐β‐cyclodextrins. In the presence of controlled amounts of various organic molecules in gas phase photoluminescence response from this derivatized porous silicon revealed formation of host‐guest complexes between β‐cyclodextrin and detected molecules. The strongest modification of photoluminescence response was observed for aromatic compounds that have optimal molecular size for strong interaction with β‐cyclodextrin cavity. For low concentrations of aromatic molecules we observed PL enhancement most probably due to electron transfer from β‐cyclodextrin‐analyte complex to porous silicon. For higher concentrations – after saturation of the β‐cyclodextrin sites – a combined response with dominant PL quenching was observed. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR–aceEF–Ipd operon of Escherichia coli (1995)

The repressor of the pdhR-aceEF-lpd operon of Escherichia coli, PdhR, was amplified to 23% of total cell protein and purified to homogeneity by heparin-agarose and cation-exchange chromatography. The purified protein is a monomer (M(r) 29,300) which binds specifically to DNA fragments containing the pdh promoter (Ppdh) in the absence of pyruvate. The pdh operator was identified by DNase I footprinting as a region of hyphenated dyad symmetry, +11AATTGGTaagACCAATT+27, situated just downstream of the transcript start site. In vitro transcription from Ppdh was repressed > 1000-fold by PdhR and this repression was antagonized in a concentration-dependent manner by its co-effector, pyruvate. Studies on RNA polymerase binding at Ppdh showed that RNA polymerase protects the -44 to +21 region in the absence of PdhR, but no RNA polymerase binding or protection upstream of +9 could be detected in the presence of PdhR. It is concluded that PdhR represses transcription by binding to an operator site centred at +19 such that effective binding of RNA polymerase is prevented.
The first application of a chemiluminescence probe, 2‐methyl‐6‐[P‐methoxyphenyl]‐3,7‐dihydroimidazo[1,2‐α]pyrazin‐3‐one (MCLA), for detecting O2− production, in vitro, from Kupffer cells stimulated by phorbol myristate acetate (1993)

The purpose of this study was to investigate the generation of superoxide anion radical, O2-, by Kupffer cells in vivo in rat liver. Phorbol myristate acetate (PMA) was infused into perfused rat liver which had been continuously infused with 2-methyl-6-[p-methoxyphenyl]-3,7-dihydroimidazo- [1,2-a]pyrazin-3-one (MCLA, a highly sensitive luminescence reagent for O2-) and the MCLA luminescence from the liver surface was detected with a sensitive photon counter. Under identical conditions, but without MCLA infusion, PMA and nitro blue tetrazolium were infused to verify generation of O2- by formation of formazan deposition. Based on MCLA luminescence and formazan deposition, both dependent on the O2- reaction, we have concluded that liver Kupffer cells generate O2- in vivo in response to stimuli such as PMA. Further, the generation of O2- by Kupffer cells may be by the same mechanism as displayed by macrophages.
Photoisomerization mechanism of the rhodopsin chromophore: picosecond photolysis of pigment containing 11-cis-locked eight-membered ring retinal. (1993)

The primary photochemical event in rhodopsin is an 11-cis to 11-trans photoisomerization of its retinylidene chromophore to form the primary intermediate photorhodopsin. Earlier picosecond studies have shown that no intermediate is formed when the retinal 11-ene is fixed through a bridging five-membered ring, whereas a photorhodopsin-like intermediate is formed when it is fixed through a flexible seven-membered ring. Results from a rhodopsin analog formed from a retinal with locked 11-ene structure through the more flexible eight-membered ring (Ret8) are described. Incubation of bovine opsin with Ret8 formed two pigments absorbing at 425 nm (P425) and 500 nm (P500). P425, however, is an artifact because it formed from thermally denatured opsin or other proteins and Ret8. Excitation of P500 with a picosecond green pulse led to formation of two intermediates corresponding to photo- and bathorhodopsins. These results demonstrate that an appearance of early intermediates is dependent on the flexibility of the 11-ene and that the photoisomerization of P500 proceeds by stepwise changes of chromophore-protein interaction, which in turn leads to a relaxation of the highly twisted all-trans-retinylidene chromophore in photorhodopsin.
Calcium Ionophore Increases Amyloid .beta. Peptide Production by Cultured Cells (1994)

Amyloid beta peptide (A beta) is released into the media of a variety of cells in culture during normal metabolism. The discovery of several missense mutations within or flanking the A beta region of the beta amyloid precursor protein (beta APP) in familial Alzheimer's disease provides strong evidence for a role of altered processing of beta APP in the pathogenesis of this disorder. The cellular mechanisms that regulate the relative utilization of the secretory pathway, which causes beta APP to be cleaved within the A beta domain, and the alternative proteolytic pathway, which produces intact A beta, are unknown. It is hypothesized that a number of neurodegenerative diseases, including Alzheimer's disease, are characterized by abnormal calcium metabolism. We investigated the effect of disordered calcium homeostasis on A beta production in human kidney 293 cells transfected with beta APP cDNA. A beta immunoprecipitated from the conditioned media of cells was compared to immunoprecipitated full-length and secreted forms of beta APP in both metabolic labeling and pulse-chase labeling paradigms. The calcium ionophore A23187 consistently increased the production of A beta approximately 3-fold. This effect was dependent on the presence of extracellular calcium in intact cells. Caffeine also increased A beta production, possibly through release of calcium from intracellular stores. The increase in A beta was cAMP-independent, and it was not mediated by a protein kinase C-dependent pathway, as treatment with phorbol esters decreased A beta levels. The effects of the ionophore on beta APP maturation and phosphorylation were also established. We conclude that elevation of intracellular calcium levels has an important effect on beta APP maturation and proteolytic processing and substantially enhances the production and release of the amyloidogenic A beta peptide.
Ad hoc networking with directional antennas: a complete system solution (2005)

Directional antennas offer tremendous potential for improving the performance of ad hoc networks. Harnessing this potential, however, requires new mechanisms at the medium access and network layers for intelligently and adaptively exploiting the antenna system. While recent years have seen a surge of research into such mechanisms, the problem of developing a complete ad hoc networking system, including the unique challenge of real-life prototype development and experimentation has not been addressed. In this paper, we present utilizing directional antennas for ad hoc networking (UDAAN). UDAAN is an interacting suite of modular network- and medium access control (MAC)-layer mechanisms for adaptive control of steered or switched antenna systems in an ad hoc network. UDAAN consists of several new mechanisms-a directional power-controlled MAC, neighbor discovery with beamforming, link characterization for directional antennas, proactive routing and forwarding-all working cohesively to provide the first complete systems solution. We also describe the development of a real-life ad hoc network testbed using UDAAN with switched directional antennas, and we discuss the lessons learned during field trials. High fidelity simulation results, using the same networking code as in the prototype, are also presented both for a specific scenario and using random mobility models. For the range of parameters studied, our results show that UDAAN can produce a very significant improvement in throughput over omnidirectional communications.