gebhart/patrepeval huggingface dataset:
Preferential Binding of 3,3‘-Diethyloxadicarbocyanine to Triplex DNA (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPreferential Binding of 3,3'-Diethyloxadicarbocyanine to Triplex DNAJinsong Ren and Jonathan B. ChairesView Author Information Department of Biochemistry University of Mississippi Medical Center 2500 N. State St., Jackson, Mississippi 39216-4505 Cite this: J. Am. Chem. Soc. 2000, 122, 2, 424–425Publication Date (Web):December 31, 1999Publication History Received28 September 1999Published online31 December 1999Published inissue 1 January 2000https://pubs.acs.org/doi/10.1021/ja9934955https://doi.org/10.1021/ja9934955rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views436Altmetric-Citations51LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Assays,Genetics,Ligands,Nucleic acids,Selectivity Get e-Alerts
Distribution of glucagon receptors on hormone-specific endocrine cells of rat pancreatic islets. (1996)

Glucagon is insulinotropic, but it remains uncertain whether the insulinotropic action is mediated directly by glucagon receptors expressed on beta-cells or by cross-binding to the insulinotropic glucagon-like peptide-1 (GLP-1) receptor known to be expressed on beta-cells. Binding of [125I]glucagon to GLP-1 receptors and not to glucagon receptors has been reported in tumor-derived beta-cells (15). The objectives of the current study were to use receptor-binding techniques and a glucagon receptor-specific antiserum to determine whether glucagon receptors are present on beta-cells. Specific binding (7.2 +/- 0.8%) of [125I]GLP-1 to beta TC-3 cells was displaced equivalently with GLP-1 and exendin-(9-39) )Kd = 0.9 and 0.4 nM. respectively), whereas approximately 700-fold higher concentrations of glucagon were required for equal displacement (Kd = 400 nM). Binding of [125I]glucagon to beta TC-3 cells (approximately 1%) was displaced equivalently with 1 microM glucagon, GLP-1, or exendin-(9-39). These observations support earlier findings that beta TC-3 cells do not express functional glucagon receptors. However, specific binding of [125I]glucagon was observed on INS-1 cells (2.3 +/- 0.2%); this was displaced with glucagon (Kd = 1 nM), but not 1 microM GLP-1 or exendin-(9-39). To examine the distribution of glucagon receptors on native beta-cells, dispersed cultured rat islets were immunostained for glucagon, somatostatin, or insulin in combination with a polyclonal rabbit antiserum raised to an extracellular portion of the glucagon receptor (KD-14). The glucagon receptor antiserum colocalized staining with approximately 97% of immunoreactive insulin cells, 9% of immunoreactive glucagon cells, and 11% of immunoreactive somatostatin cells. Perfusion of the rat pancreas with concentrations of glucagon as low as 10(-12) M resulted in significant insulin release. These results suggest that whereas the tumor-derived beta-cell line beta TC-3 does not express functional glucagon receptors, INS-1 cells and isolated rat pancreatic beta-cells have specific glucagon receptors, as do a subpopulation of alpha- and delta-cells. A model is proposed for the role of glucagon in islet hormone secretion during feeding and fasting.
Physiological and pharmacological implications of peptide transporters, PEPT1 and PEPT2 (2000)

The H+/peptide co-transporters PEPT1 and PEPT2 mediate the cellular uptake of small peptides and peptide-like drugs from the glomerular filtrates. In the present study, we investigated the physiological and pharmacological implications of both transporters. (i) Comparison of the substrate affinity of PEPT1 and PEPT2 indicated that PEPT2 had higher affinity than PEPT1 for most substrates. (ii) The transport characteristics of beta-lactam antibiotics in the renal brush border membrane vesicles were well correlated with those in a PEPT2-expressing transfectant. These results suggested that PEPT2 predominantly contributed to reabsorption of beta-lactam antibiotics in the kidney at therapeutic concentrations. (iii) In rats with chronic renal failure, glycylsarcosine (Gly-Sar) uptake by the renal brush border membranes vesicles was maintained, whereas Na+-dependent glucose uptake was markedly reduced. It is therefore speculated that the function of peptide transporters is tolerant to chronic renal failure.
Speech Privacy in Buildings (1962)

Obtaining adequate speech privacy in modern buildings is one of the important goals of the architect and consultant. This paper deals with the development of a rating method which takes into account the several factors influencing speech privacy. Our work in this area began with a brief laboratory study. The results indicated that speech privacy is related to speech intelligibility rather than to level. The initial experiments were supplemented with an analysis of about 40 case histories representing about 400 pairs of spaces in different kinds of buildings. There appears to be good correlation between the articulation index of intruding speech sound and the reactions of building occupants.
Nonlocal regularization on weighted patches for image deconvolution (2012)

Regularization-based methods have been found widespread application in image deconvolution. Local regularization approaches have made outstanding performance for edge maintain, such as total variation regularization. However, they have weakness in textures preserving. To handle images of hybrid edges and textures, we propose an iterative regularization method that utilizes weighted patches along with nonlocal means filtering. The weighted patches allow us to preserve textures as well as edges. The iterative form in the regularization provides improvement in detail restoration. This nonlocal regularization method reveals favorable recovery of structures in images, especially for textures and edges. Experiment results confirm such superiority with comparison to local regularization methods.
Cationic Methyl- and Chlorotitanium Phosphinimide Complexes (2005)

A variety of donor-stabilized cationic complexes of the form [Cp(NPt-Bu3)TiMe(L)][MeB(C6F5)3] and [Cp(NPt-Bu3)TiMe(L)][B(C6F5)4] (L = Py, 4-EtPy, 4-t-BuPy, NC5H4NMe2, PMe3, Pn-Bu3, PPh3, P(p-MeC6H4)3)have been prepared and characterized. Prolonged storage in CH2Cl2 solution resulted in chloride for methyl exchange to afford species of the form [CpTi(NPt-Bu3)Cl(L)][B(C6F5)4], [{CpTi(NPt-Bu3)Me}2(μ-Cl)][B(C6F5)4], and [CpTi(NPt-Bu3)(μ-Cl)]2[MeB(C6F5)3]2. The byproduct salt [(o-MeC6H4)3PCH2Cl][B(C6F5)4] was obtained from reactions employing the sterically demanding donor phosphine P(o-MeC6H4)3, suggesting transient generation of the cation [CpTi(NPt-Bu3)Cl(CH2Cl2)]+. Analogous reactivity was not seen in C6H5Cl, although the species [{CpTi(NPt-Bu3)Me}2(μ-Me)][B(C6F5)4] could be formed in this solvent. The isolated zwitterionic complex TiCp(NPt-Bu3)Me(μ-MeB(C6F5)3) readily performs insertion chemistry into the Ti−methyl bonds with diisopropylcarbodiimide and diphenylacetylene substrates to afford the cationic species [CpTi(NPt-Bu3)((Ni-Pr)2CMe)][MeB(C6F5)3], [TiCp(NPt-Bu3)(PhCCPh(Me))][MeB(C6F5)3], and [TiCp(NPt-Bu3)(PhCCPh(Me))(PMe3)][MeB(C6F5)3]. The implications of this chemistry are considered.
Evaluation of acid‐labile S‐protecting groups to prevent Cys racemization in Fmoc solid‐phase peptide synthesis (2013)

Phosphonium and uronium salt-based reagents enable efficient and effective coupling reactions and are indispensable in peptide chemistry, especially in machine-assisted SPPS. However, after the activating and coupling steps with these reagents in the presence of tertiary amines, Fmoc derivatives of Cys are known to be considerably racemized during their incorporation. To avoid this side reaction, a coupling method mediated by phosphonium/uronium reagents with a weaker base, such as 2,4,6-trimethylpyridine, than the ordinarily used DIEA or that by carbodiimide has been recommended. However, these methods are appreciably inferior to the standard protocol applied for SPPS, that is, a 1 min preactivation procedure of coupling with phosphonium or uronium reagents/DIEA in DMF, in terms of coupling efficiency, and also the former method cannot reduce racemization of Cys(Trt) to an acceptable level (<1.0%) even when the preactivation procedure is omitted. Here, the 4,4'-dimethoxydiphenylmethyl and 4-methoxybenzyloxymethyl groups were demonstrated to be acid-labile S-protecting groups that can suppress racemization of Cys to an acceptable level (<1.0%) when the respective Fmoc derivatives are incorporated via the standard SPPS protocol of phosphonium or uronium reagents with the aid of DIEA in DMF. Furthermore, these protecting groups significantly reduced the rate of racemization compared to the Trt group even in the case of microwave-assisted SPPS performed at a high temperature.
The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily (2001)

The phospholipase D (PLD) superfamily is a diverse group of proteins that includes enzymes involved in phospholipid metabolism, a bacterial toxin, poxvirus envelope proteins, and bacterial nucleases. Based on sequence comparisons, we show here that the tyrosyl-DNA phosphodiesterase (Tdp1) that has been implicated in the repair of topoisomerase I covalent complexes with DNA contains two unusual HKD signature motifs that place the enzyme in a distinct class within the PLD superfamily. Mutagenesis studies with the human enzyme in which the invariant histidines and lysines of the HKD motifs are changed confirm that these highly conserved residues are essential for Tdp1 activity. Furthermore, we show that, like other members of the family for which it has been examined, the reaction involves the formation of an intermediate in which the cleaved substrate is covalently linked to the enzyme. These results reveal that the hydrolytic reaction catalyzed by Tdp1 occurs by the phosphoryl transfer chemistry that is common to all members of the PLD superfamily.
Use of a Vacuum Assisted Closure device in pilonidal disease (2003)

Pilonidal disease is a debilitating condition that can be difficult to treat. This case report shows how Vacuum Assisted Closure, which can be used on an outpatient basis, led to full wound healing in a patient with a recurrent form of this disease
Measurements of the sheet resistance and conductivity of thin epitaxial graphene and SiC films (2010)

Single postdielectric resonators operating on their quasi TE011 modes were used for the measurement of the surface resistance and conductivity of graphene films grown on semi-insulating SiC substrates. With this technique the surface resistance was measured with an uncertainty of ±5% and the conductivity was evaluated with an uncertainty equal to the uncertainty in determining the film thickness. The room temperature conductivity of the graphene films proved to be in the range 5×106 to 6.4×106 S/m.
Discoordinate expression of stromelysin, collagenase, and tissue inhibitor of metalloproteinases-1 in rheumatoid human synovial fibroblasts. Synergistic effects of interleukin-1 and tumor necrosis factor-alpha on stromelysin expression. (1990)

Primary and passaged human synovial fibroblasts isolated from rheumatoid pannus were treated with recombinant interleukin-1 (IL-1) alpha or beta, tumor necrosis factor-alpha (TNF), or phorbol myristate acetate (PMA) to determine the effects of these stimuli on the relative expression of stromelysin, collagenase, and tissue inhibitor of metalloproteinases (TIMP). The steady-state mRNA levels for these genes and glyceraldehyde-3-phosphate dehydrogenase were determined on Northern blots. Immunoblot analyses of the conditioned media using monoclonal antibodies generated against recombinant human stromelysin, collagenase, or TIMP showed that protein levels reflected the corresponding steady-state mRNA levels. The results revealed that 1) stromelysin and collagenase were not always coordinately expressed; 2) IL-1 was more potent than TNF or PMA in the induction of stromelysin expression; 3) neither IL-1 nor TNF significantly affected TIMP expression; 4) PMA induced both metalloproteinase and TIMP expression; and 5) the combination of IL-1 plus TNF had a synergistic effect on stromelysin expression. Dose response and time course experiments demonstrated that the synergistic effect of IL-1 plus TNF occurred at saturating concentrations of each cytokine and lasted for 7 days. In summary, the ability of IL-1 and TNF to preferentially induce stromelysin and collagenase expression, versus TIMP, may define a pivotal role for these cytokines in the pathogenesis of rheumatoid arthritis.
SILAC‐based quantitative proteomic analysis of gastric cancer secretome (2012)

We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
DNA-Templated Ag Nanocluster Formation (2004)

The high affinity of Ag+ for DNA bases has enabled creation of short oligonucleotide-encapsulated Ag nanoclusters without formation of large nanoparticles. Time-dependent formation of cluster sizes ranging from Ag1 to Ag4/oligonucleotide were observed with strong, characteristic electronic transitions between 400 and 600 nm. The slow nanocluster formation kinetics enables observation of specific aqueous nanocluster absorptions that evolve over a period of 12 h. Induced circular dichroism bands confirm that the nanoclusters are associated with the chiral ss-DNA template. Fluorescence, absorption, mass, and NMR spectra all indicate that multiple species are present, but that their creation is both nucleotide- and time-dependent.
Consumer Engagement in Virtual Power Plants through Gamification (2020)

Virtual power plants (VPPs) are defined as an aggregator of different types of energy resources and flexibility, coordinated by VPP owner through a smart control system. A correct establishment of a VPP will result in reduced electricity costs for the consumers within the VPP. One of the key aspect of VPP’s success is the consumer engagement in order to manage their flexibilities effectively. Gamification is an efficient way of learning and engagement, which can efficiently change the behavior of consumers towards participating in programs provided by VPPs for energy cost reduction. In this paper, a gamification-based approach for consumer engagement is proposed and a methodology based on Fogg’s behavior model and Kim’s model on player types is developed to examine the suitability of available gamification applications for energy saving/efficiency in the context of a VPP. Seven gamification applications are analyzed and evaluated based on the developed methodology and the results are provided.
PatchMatch-Based Automatic Lattice Detection for Near-Regular Textures (2015)

In this work, we investigate the problem of automatically inferring the lattice structure of near-regular textures (NRT) in real-world images. Our technique leverages the PatchMatch algorithm for finding k-nearest-neighbor (kNN) correspondences in an image. We use these kNNs to recover an initial estimate of the 2D wallpaper basis vectors, and seed vertices of the texture lattice. We iteratively expand this lattice by solving an MRF optimization problem. We show that we can discretize the space of good solutions for the MRF using the kNNs, allowing us to efficiently and accurately optimize the MRF energy function using the Particle Belief Propagation algorithm. We demonstrate our technique on a benchmark NRT dataset containing a wide range of images with geometric and photometric variations, and show that our method clearly outperforms the state of the art in terms of both texel detection rate and texel localization score.
Fast parallel construction of high-quality bounding volume hierarchies (2013)

We propose a new massively parallel algorithm for constructing high-quality bounding volume hierarchies (BVHs) for ray tracing. The algorithm is based on modifying an existing BVH to improve its quality, and executes in linear time at a rate of almost 40M triangles/sec on NVIDIA GTX Titan. We also propose an improved approach for parallel splitting of triangles prior to tree construction. Averaged over 20 test scenes, the resulting trees offer over 90% of the ray tracing performance of the best offline construction method (SBVH), while previous fast GPU algorithms offer only about 50%. Compared to state-of-the-art, our method offers a significant improvement in the majority of practical workloads that need to construct the BVH for each frame. On the average, it gives the best overall performance when tracing between 7 million and 60 billion rays per frame. This covers most interactive applications, product and architectural design, and even movie rendering.
Stimulation of the DNA-dependent Protein Kinase by RNA Polymerase II Transcriptional Activator Proteins (1995)

The DNA-dependent protein kinase (DNA-PK) phosphorylates RNA polymerase II and a number of transcription factors. We now show that the activity of DNA-PK is directly stimulated by certain transcriptional activator proteins, including the human heat shock transcription factor 1 (HSF1) and a transcriptionally active N-terminal 147 amino acid GAL4 derivative. Stimulation of DNA-PK activity required specific sequences in the activator proteins outside the minimal DNA binding domains. The stimulation of DNA-PK activity also required DNA and was greater with DNA containing relevant activator binding sites. Comparison of different HSF binding fragments showed that optimal stimulation occurred when two HSF binding sites were present. Stimulation with HSF and GAL4 was synergistic with Ku protein, another regulator of DNA-PK activity. DNA-PK is tightly associated with the transcriptional template, and an increase in its activity could potentially influence transcription through the phosphorylation of proteins associated with the transcription complex.
TURN TAP: Temporal Unit Regression Network for Temporal Action Proposals (2017)

Temporal Action Proposal (TAP) generation is an important problem, as fast and accurate extraction of semantically important (e.g. human actions) segments from untrimmed videos is an important step for large-scale video analysis. We propose a novel Temporal Unit Regression Network (TURN) model. There are two salient aspects of TURN: (1) TURN jointly predicts action proposals and refines the temporal boundaries by temporal coordinate regression: (2) Fast computation is enabled by unit feature reuse: a long untrimmed video is decomposed into video units, which are reused as basic building blocks of temporal proposals. TURN outperforms the previous state-of-the-art methods under average recall (AR) by a large margin on THUMOS-14 and ActivityNet datasets, and runs at over 880 frames per second (FPS) on a TITAN X GPU. We further apply TURN as a proposal generation stage for existing temporal action localization pipelines, it outperforms state-of-the-art performance on THUMOS-14 and ActivityNet.
Dynamic Model and Experimental Investigation of a Pneumatic Proportional Pressure Valve (2004)

A nonlinear dynamic model of a Honeywell Lucifer-type EPP3 J-21-U-100-10 (now Parker P3P-R) pneumatic proportional pressure valve is formulated by modeling the valve's main internal mechatronic devices in order to simulate its dynamic behavior in the time and frequency domains, for several operating conditions and different downstream loads. Mechatronic design and functionality of this valve are carefully analyzed by considering the conditions of its internal devices for each of the three standard working configurations of a three-way proportional valve. The main physical parameters introduced in formulating the dynamic model were identified by means of an experimental investigation. Finally, the experimental and simulated diagrams in the time and frequency domains are compared in order to validate the proposed model, which can be used as a general approach for modeling any pneumatic proportional pressure valve featuring a similar mechatronic design and internal structure.
p15INK4BCpG Island Methylation in Primary Acute Leukemia Is Heterogeneous and Suggests Density as a Critical Factor for Transcriptional Silencing (1999)

The promoter region of the cyclin-dependent kinase inhibitor p15(INK4B) contains a CpG island that is hypermethylated in many hematologic malignancies. To explore the relationship between patterns of methylation and gene transcription, we used bisulfite genomic sequencing to obtain a detailed analysis of methylation in acute leukemia, leukemia cell lines, and normal lymphocytes. The entire CpG island region of p15 was largely devoid of methylation in normal lymphocytes, but methylation of varying density was found in primary acute leukemia. Methylation density was generally conserved between the alleles from each sample, but marked heterogeneity for the specific CpG sites methylated was observed. Patterns of methylation were compared and expression assessed with reverse-transcriptase polymerase chain reaction (RT-PCR). The density of methylation within the CpG island, and not any specific location, correlates best with transcriptional loss. Leukemias with methylation of approximately 40% of the CpG dinucleotides on each allele had complete gene silencing, with variable, but diminished expression with less dense CpG island methylation. Our results suggest that the transcriptional silencing of p15 in conjunction with aberrant hypermethylation is best understood as an evolutionary process that involves progressively increasing methylation of the entire p15 CpG island.
Microvascular protection is essential for successful neuroprotection in stroke (2012)

Currently, the best way of neuroprotection for acute ischemic stroke appears to be restoration of blood flow to the ischemic area by thrombolysis. Unfortunately, a short therapeutic time window as well as thrombolysis-induced bleeding and edema limit the use of recanalization therapies. Here, we review the evidence suggesting that ischemia/reperfusion-induced microvascular injury plays a critical role in determining tissue survival after recanalization in focal cerebral ischemia by disrupting the blood-brain barrier integrity and promoting microcirculatory clogging. Among many complex mechanisms of the ischemia-reperfusion injury, overproduction of oxygen and nitrogen radicals on the microvascular wall appears to significantly contribute to these pathological processes. These developments bring about the exciting possibility that effective suppression of oxidative/nitrative stress during pharmacological or interventional re-opening of the occluded artery may significantly improve the outcome of recanalization therapies in stroke patients by improving microcirculatory reflow as well as by preventing hemorrhagic conversion and vasogenic edema. They also point to the critical (but partly neglected) importance of the microcirculation in neuroprotection.