gebhart/patrepeval huggingface dataset:
Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMolecular Fluorescence, Phosphorescence, and Chemiluminescence SpectrometryAleeta M. Powe†, Susmita Das‡, Mark Lowry‡, Bilal El-Zahab‡, Sayo O. Fakayode§, Maxwell L. Geng∥, Gary A. Baker⊥, Lin Wang⊗, Matthew E. McCarroll⊗, Gabor Patonay○, Min Li‡, Mohannad Aljarrah‡, Sharon Neal#, and Isiah M. Warner*‡View Author Information Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901-4409, Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, and Department of Chemistry, University of Delaware, Newark, Delaware 19716* To whom correspondence should be addressed.†University of Louisville.‡Louisiana State University.§Winston-Salem State University.∥University of Iowa.⊥Oak Ridge National Laboratory.⊗Southern Illinois University.○Georgia State University.#University of Delaware.Cite this: Anal. Chem. 2010, 82, 12, 4865–4894Publication Date (Web):May 26, 2010Publication History Published online26 May 2010Published inissue 15 June 2010https://pubs.acs.org/doi/10.1021/ac101131phttps://doi.org/10.1021/ac101131preview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views9563Altmetric-Citations46LEARN 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 SUBJECTS:Fluorescence,Fluorescence detection,Fluorescence imaging,Fluorescence spectroscopy,Probes Get e-Alerts
XBP-1 and the UPRosome: Mastering Secretory Cell Function (2008)

A unique feature of secretory cells is the proliferation of the endoplasmic reticulum (ER) and Golgi network. The high demand imposed by protein synthesis and folding in secretory cells constitutes an endogenous source of stress due to the accumulation of toxic misfolded intermediaries. Adaptation to ER stress is mediated by the activation of a complex signal transduction pathway known as the unfolded protein response (UPR). Evidence from genetic manipulation of the UPR supports the notion that components of the pathway are essential to sustain the function of secretory cells. Expression of the UPR transcriptional factor X-Box binding protein-1 (XBP-1) is essential for the proper function of plasma B cells and exocrine cells of pancreas and salivary glands. Active XBP-1 is generated by the direct processing of its mRNA by the ER stress sensor IRE1α through the formation of a complex signaling platform at the ER membrane, here termed as UPRosome. XBP-1 controls the expression of genes involved in almost every aspect of the secretory pathway including folding, protein quality control, ER translocation, glycosylation, and remodeling of ER and Golgi structure. In this article we discuss recent advances in understanding the mechanisms through which XBP-1 controls secretory cell function and the possible involvement of this pathway in disease conditions related to irreversible ER damage. Current therapeutic strategies to modulate ER function are also discussed.
Dynamic DNA Hybridization on a Chip Using Paramagnetic Beads (1999)

Dynamic DNA hybridization is presented as an approach to perform gene expression analysis. The method is advantageous because of its dynamic supplies of both DNA samples and probes. The approach was demonstrated on a microfluidic platform by incorporating paramagnetic beads as a transportable solid support. A glass chip was fabricated to allow simultaneous interrogation of eight DNA target samples by DNA probes. DNA targets were immobilized on beads via streptavidin-biotin conjugation or base pairing between oligonucleotide residues. The DNA/bead complex was introduced into the device in which hybridization took place with a complementary probe. The hybridized probe was then removed by heat denaturation to allow the DNA sample to be interrogated again by another probe with a different sequence of interest. A pneumatic pumping apparatus was constructed to transport DNA probes and other reagents into the microfluidic device while hydrostatic pumping was used for the introduction of paramagnetic beads with samples. After investigating three types of paramagnetic beads, we found Dynabeads Oligo(dT)25 best suited this application. Targets on the beads could be sequentially interrogated by probes for 12 times, and the hybridization signal was maintained within experimental variation. Demonstration of specific hybridization reactions in an array format was achieved using four synthesized DNA targets in duplicate and five probes in sequence, indicating the potential application of this approach to gene expression analysis.
Interleukin 6: a possible marker of disease activity in adult onset Still's disease. (1997)

Acute phase proteins and IL-6 are useful markers of disease activity in AOSD.
Advertising communications & promotion management (1997)

Part 1: AC&P and marketing objectives advertising communications and promotion marketing objectives and budget. Part 2: target audience selection and action ojectives behavioural sequence model for specific targetting. Part 3: communication objectives and positioning communication objectives choosing a positioning strategy. Part 4: creative strategy the creative idea creative execution tactics - branding and low-involvement persuasion creative execution tactics - high involvement persuasion attention and structure of ads. Part 5: integrated communication strategy corporate advertising comunications manufacturer's promotions retailer's promotions direct marketing promotions. Part 6: media strategy advertisng and IMC media selection media strategy - the reach pattern and effective frequency media plan implementation. Part 7: advertising research and evaluation advertisng strategy research concept communications and promotion plan.
The Exchangeability of Amino Acids in Proteins (2005)

The comparative analysis of protein sequences depends crucially on measures of amino acid similarity or distance. Many such measures exist, yet it is not known how well these measures reflect the operational exchangeability of amino acids in proteins, since most are derived by methods that confound a variety of effects, including effects of mutation. In pursuit of a pure measure of exchangeability, we present (1) a compilation of data on the effects of 9671 amino acid exchanges engineered and assayed in a set of 12 proteins; (2) a statistical procedure to combine results from diverse assays of exchange effects; (3) a matrix of "experimental exchangeability" values EX(ij) derived from applying this procedure to the compiled data; and (4) a set of three tests designed to evaluate the power of an exchangeability measure to (i) predict the effects of amino acid exchanges in the laboratory, (ii) account for the disease-causing potential of missense mutations in the human population, and (iii) model the probability of fixation of missense mutations in evolution. EX not only captures useful information on exchangeability while remaining free of other effects, but also outperforms all measures tested except for the best-performing alignment scoring matrix, which is comparable in performance.
Improved Frame Mode Selection for AMR-WB+ Based on Decision Tree (2008)

In this letter, we propose a coding mode selection method for the AMR-WB+ audio coder based on a decision tree. In order to reduce computation while maintaining good performance, decision tree classifier is adopted with the closed loop mode selection results as the target classification labels. The size of the decision tree is controlled by pruning, so the proposed method does not increase the memory requirement significantly. Through an evaluation test on a database covering both speech and music materials, the proposed method is found to achieve a much better mode selection accuracy compared with the open loop mode selection module in the AMR-WB+.
SigFree: a signature-free buffer overflow attack blocker (2006)

Abstract—We propose SigFree, an online signature-free out-of-the-box application-layer method for blocking code-injection buffer overflow attack messages targeting at various Internet services such as web service. Motivated by the observation that buffer overflow attacks typically contain executables whereas legitimate client requests never contain executables in most Internet services, SigFree blocks attacks by detecting the presence of code. Unlike the previous code detection algorithms, SigFree uses a new data-flow analysis technique called code abstraction that is generic, fast, and hard for exploit code to evade. SigFree is signature free, thus it can block new and unknown buffer overflow attacks; SigFree is also immunized from most attack-side code obfuscation methods. Since SigFree is a transparent deployment to the servers being protected, it is good for economical Internet-wide deployment with very low deployment and maintenance cost. We implemented and tested SigFree; our experimental study shows that the dependency-degree-based SigFree could block all types of code-injection attack packets (above 750) tested in our experiments with very few false positives. Moreover, SigFree causes very small extra latency to normal client requests when some requests contain exploit code. Index Terms—Intrusion detection, buffer overflow attacks, code-injection attacks. Ç 1
Rabbits generated from fibroblasts through nuclear transfer (2006)

Somatic cell nuclear transfer offers new opportunities for genetic engineering and genome preservation in mammalian animal species. We show that, in addition to cumulus cells, cultured adult rabbit fibroblasts are also capable of supporting full-term development after nuclear transfer. Nuclear transfer embryos constructed using serum-starved fibroblasts showed a significantly higher developmental rate than non-starved fibroblasts through preimplantation stages. A total of 467 nuclear transfer embryos were transferred into the oviducts of pseudo pregnant mothers. Eight of the 20 surrogate rabbits carried the pregnancy to term and five of them gave birth naturally to a total of nine rabbits. However, all of the offspring died before postnatal day 10. A Caesarean section was performed on three surrogates, giving birth to a total of five rabbits, three of them survived and grew into healthy adults. DNA analyses confirmed that these rabbits were genetically identical to the donor male rabbit. The present study demonstrates that rabbits can be cloned from adult fibroblasts after culture.
Important roles of PI3Kγ in osteoclastogenesis and bone homeostasis (2010)

G protein-coupled receptor-regulated PI3Kgamma is abundantly expressed in myeloid cells and has been implicated as a promising drug target to treat various inflammatory diseases. However, its role in bone homeostasis has not been investigated, despite the fact that osteoclasts are derived from myeloid lineage. We therefore carried out thorough bone phenotypic characterization of a PI3Kgamma-deficient mouse line and found that PI3Kgamma-deficient mice had high bone mass. Our analyses further revealed that PI3Kgamma deficiency did not affect bone formation because no significant changes in osteoblast number and bone formation rate were observed. Instead, the lack of PI3Kgamma was associated with decreased bone resorption, as evidenced by decreased osteoclast number in vivo and impaired osteoclast formation in vitro. The decreased osteoclast formation was accompanied by down-regulated expression of osteoclastogenic genes, compromised chemokine receptor signaling, and an increase in apoptosis during osteoclast differentiation. Together, these data suggest that PI3Kgamma regulates bone homeostasis by modulating osteoclastogenesis. Our study also suggests that inhibition of PI3Kgamma, which is being considered as a potential therapeutic strategy for treating chronic inflammatory disorders, may result in an increase in bone mass.
The toxicity of acetaminophen and N-acetyl-p-benzoquinone imine in isolated hepatocytes is associated with thiol depletion and increased cytosolic Ca2+. (1985)

The effects of acetaminophen and its major toxic metabolite, N-acetyl-p-benzoquinone imine (NAPQI), have been investigated in hepatocytes isolated from 3-methylcholanthrene-pretreated and -untreated rats, respectively. The two compounds produced qualitatively similar changes although the quinone imine was toxic with shorter incubations periods and at lower doses. Both agents caused an elevation of cytosolic Ca2+, assessed by phosphorylase a activity, which was accompanied by the concomitant appearance of plasma membrane blebs. A loss of mitochondrial Ca2+ was also observed. This disruption of Ca2+ homeostasis always preceded cell death. Studies with NAPQI showed that low doses were able to cause complete Ca2+ release from isolated liver mitochondria which was accompanied by pyridine nucleotide oxidation and preceded membrane damage. NAPQI also produced a rapid, dose-dependent depletion of both cytosolic and mitochondrial reduced glutathione as well as a loss of protein-bound SH groups. This loss of protein thiols may have been responsible for the observed inhibition of the high-affinity Ca2+-ATPase activity of the plasma membrane fraction isolated from NAPQI-treated cells. In addition, NAPQI inhibited microsomal Ca2+ uptake which would further contribute to the elevation in cytosolic Ca2+. Our results suggest that acetaminophen and N-acetyl-p-benzoquinone imine exert their cytotoxic effects via a disruption of Ca2+ homeostasis secondary to the depletion of soluble and protein-bound thiols. This mechanism may prove to be of general applicability to a variety of hepatotoxins.
Recovering of weather degraded images based on RGB response ratio constancy (2015)

Images captured under bad weather conditions suffer from poor contrast and visibility. These effects are noticeable for haze, mist, fog, or dust storms. We have proposed a recovering method for images captured for several adverse weather conditions based on the RGB response ratio constancy under illuminant changes. This algorithm improves the visibility, contrast, and color in degraded images with low computational times. We obtain results similar to those from previously published deweathering methods but with no prior information about the image content or atmospheric parameters needed.
Timing and crosstalk driven area routing (1998)

We present a timing and crosstalk driven router for the chip assembly task that is applied between global and detailed routing. Our new approach aims to process the crosstalk and timing constraints by ordering nets and tuning wire spacing in a quantitative way. Our graph-based optimizer preroutes wires on the global routing grids incrementally in two stages - net order assignment and space relaxation. The timing delay of each critical path is calculated taking into account interconnect coupling capacitance. The objective is to reduce the delays of critical nets with negative timing slack values, by tuning net ordering and adding extra wire spacing. It shows a remarkable 8.4-25% delay reduction for MCNC benchmarks for wire geometric ratio=2.0, against a 33% delay reduction if interconnect interference disappear.
Mechanism of action of a new antitumor agent, carbetimer. (1986)

Carbetimer, an intermediate molecular-weight-derivatized copolymer of maleic anhydride and ethylene, has been shown to possess significant antineoplastic activity in the stem cell assay. We have examined the antitumor activity of carbetimer in vivo and in vitro against HM5-Carb/S and M21, both primary human melanoma cell lines sensitive and resistant to carbetimer, respectively. The mechanism of action of carbetimer in HM5-Carb/S has been determined. Mice bearing palpable sensitive tumors were treated with 10% lethal doses of carbetimer (1500 mg/kg i.p.). The tumor nucleotide profile was determined 4 hours later. Uridine and cytidine nucleoside triphosphates were reduced by 36.6 and 58.2%, respectively. In a similar experiment using carbetimer-resistant tumor, there was no change in the tumor pool sizes of uridine and cytidine nucleoside triphosphate pools in carbetimer- or saline-treated animals. Following 24-h exposure of the cells to 1000 microM concentration of carbetimer, the carbetimer-sensitive cells were pulsed with [14C]uridine, cytidine, or thymidine for 30 min. Pyrimidine nucleotides, in particular triphosphates, were reduced significantly as compared to the saline-treated control. Similar treatment of carbetimer-resistant cells resulted in no change in the pool sizes of the nucleotides. [14C]Bicarbonate flux studies demonstrated that [14C]CO2 conversion into UMP and CMP was increased 200 and 140% of control in the carbetimer-sensitive cells treated with 1000 microM carbetimer; however, a similar treatment of the resistant cells showed no change in the pool sizes of the nucleotide. Examination of pyrimidine salvage enzymes demonstrated that, in the sensitive cells, carbetimer treatment reduced the specific activity of uridine, cytidine, and thymidine kinase by 46, 37, and 60%. In a similar study using resistant cells, the specific activities were reduced 7 and 0%, respectively. In the restitution studies coincubation of carbetimer-sensitive cells with carbetimer and uridine resulted in essentially the reversal of carbetimer cytotoxicity. Thus, carbetimer inhibits the growth of the sensitive cells by inhibiting the uptake and metabolism of performed nucleosides both in vivo and in vitro.
Pharmacodynamic evaluation of the epidermal growth factor receptor inhibitor OSI-774 in human epidermis of cancer patients. (2003)

OSI-774 exerted pharmacodynamic effects in skin tissues of 30-50% of patients treated with the agent. Up-regulation of p27, which is a downstream effect of EGFR inhibition, was dose related. Although there was a significant decrement in phospho-EGFR (Tyr1173), it was not related to the administered dose of OSI-774. On the basis of these findings and the relatively simple and reliable method to measure p27 expression, this biomarker appears to be the most promising and is being evaluated in Phase II studies as a predictor of clinical outcome.
Spaced Noninvasive Brain Stimulation (2014)

Neuroplasticity is critical for learning, memory, and recovery of lost function following neurological damage. Noninvasive brain stimulation (NIBS) techniques can induce neuroplastic changes in the human cortex that are behaviorally relevant, raising the exciting possibility that these techniques might be therapeutically beneficial for neurorehabilitation following brain injury. However, the short duration and instability of induced effects currently limits their usefulness. To date, trials investigating the therapeutic value of neuroplasticity-inducing NIBS have used either single or multiple treatment sessions, typically repeated once-daily for 1 to 2 weeks. Although multiple stimulation sessions are presumed to have cumulative effects on neuroplasticity induction, there is little direct scientific evidence to support this "once-daily" approach. In animal models, the repeated application of stimulation protocols spaced using relatively short intervals (typically of the order of minutes) induces long-lasting and stable changes in synaptic efficacy. Likewise, learning through spaced repetition facilitates the establishment of long-term memory. In both cases, the spacing interval is critical in determining the outcome. Emerging evidence in healthy human populations suggests that the within-session spacing of NIBS protocols may be an effective approach for significantly prolonging the duration of induced neuroplastic changes. Similar to findings in the animal and learning literature, the interval at which spaced NIBS is applied seems to be a critical factor influencing the neuroplastic response. In this Point of View article, we propose that to truly exploit the therapeutic opportunities provided by NIBS, future clinical trials should consider the optimal spacing interval for repeated applications.
Molecular and immunohistochemical investigation of protein kinase a regulatory subunit type 1A (PRKAR1A) in odontogenic myxomas (2005)

Odontogenic myxomas are rare benign neoplasms affecting the jaw. Myxomas of bones and other sites occur as part of Carney complex (CNC), a multiple neoplasia syndrome caused by mutations in the PRKAR1A gene, which codes for the regulatory subunit of protein kinase A (PKA). In the present study, 17 odontogenic myxomas from patients without CNC were screened for PRKAR1A mutations and PRKAR1A protein expression by immunohistochemistry (IHC). Mutations of the coding region of the PRKAR1A gene were identified in 2 tumors; both these lesions showed no or significantly decreased immunostaining of PRKAR1A in the tumor compared to that in the surrounding normal tissue. One mutation (c.725C>A) led to a nonconservative amino acid substitution in a highly conserved area of the gene (A213D); the other was a single base-pair deletion that led to a frameshift (del774C) and a stop codon 11 amino acids downstream of the mutation site; both tumors were heterozygous for the respective mutations. Of the remaining tumors, 7 of the 15 without mutations showed almost no PRKAR1A in the tumor cells, whereas IHC showed that the protein was abundant in nontumorous cells. We concluded that PRKAR1A may be involved by its down-regulation in the pathogenesis of odontogenic myxomas caused by mutations and/or other genetic mechanisms. Of the sporadic, nonfamilial tumors associated with PRKAR1A mutations, the odontogenic type was the first myxomatous lesion found to harbor somatic PRKAR1A sequence changes.