gebhart/patrepeval huggingface dataset:
Deregulation of the hedgehog signalling pathway: a possible role for the PTCH and SUFU genes in human rhabdomyoma and rhabdomyosarcoma development (2005)

The naevoid basal cell carcinoma syndrome (NBCCS) is caused by mutations in the hedgehog receptor PTCH gene. It is characterized by developmental defects and a predisposition to the development of certain tumours, such as basal cell carcinoma, medulloblastoma and meningioma, and potentially fetal rhabdomyomas and embryonal rhabdomyosarcomas. This study aimed to analyse PTCH status in an NBCCS patient with fetal rhabdomyoma and to investigate whether deregulation of hedgehog signalling, as shown by altered expression of hedgehog pathway components and/or genetic imbalances, is a general finding in sporadic rhabdomyomas and rhabdomyosarcomas. The NBCCS patient had a novel PTCH germ-line mutation, 1370insT, and developed a fetal rhabdomyoma that harboured a 30 bp in-frame deletion in the second allele resulting in homozygous inactivation of PTCH. Sporadic rhabdomyomas and rhabdomyosarcomas showed overexpression of PTCH (43/43) and GLI1 (41/43) mRNA, as determined by in situ hybridization, indicating ongoing active hedgehog signalling. Immunohistochemical staining revealed a subgroup of fetal rhabdomyomas and embryonal rhabdomyosarcomas (12/34) lacking PTCH immunoreactivity. Four of nine informative fetal rhabdomyomas and embryonal rhabdomyosarcomas showed loss of heterozygosity (LOH) in the PTCH region with two of these (one fetal rhabdomyoma and one embryonal rhabdomyosarcoma) also showing LOH in the SUFU region. These findings suggest that haploinsufficiency for the two tumour suppressor genes PTCH and SUFU, which are both active in the same signalling pathway, may be important for tumour development. Based on our results we propose that the pathogenesis of rhabdomyoblastic tumours, particularly fetal rhabdomyomas and embryonal rhabdomyosarcomas, involves deregulation of the hedgehog signalling pathway.
Wnt-3A Enhances Bone Morphogenetic Protein-2-mediated Chondrogenesis of Murine C3H10T1/2 Mesenchymal Cells (2002)

We have recently reported the chondrogenic effect of bone morphogenetic protein-2 (BMP-2) in high density cultures of the mouse multipotent mesenchymal C3H10T1/2 cell line and have shown the functional requirement of the cell-cell adhesion molecule N-cadherin in BMP-2-induced chondrogenesis in vitro (Denker, A. E., Nicoll, S. B., and Tuan, R. S. (1995) Differentiation 59, 25-34; Haas, A. R., and Tuan, R. S. (1999) Differentiation 64, 77-89). Furthermore, BMP-2 treatment also results in an increased protein level of beta-catenin, a known N-cadherin-associated Wnt signal transducer (Fischer, L., Haas, A., and Tuan, R. S. (2001) Signal Transduction 2, 66-78), suggesting functional cross-talk between the BMP-2 and Wnt signaling pathways. We have observed previously that BMP-2 treatment up-regulates expression of Wnt-3A in high density cultures of C3H10T1/2 cells. To assess the contribution of Wnt-3A to BMP-2-mediated chondrogenesis, we have generated C3H10T1/2 cell lines overexpressing Wnt-3A and various forms of glycogen synthase kinase-3beta (GSK-3beta), an immediate cytosolic component of the Wnt signaling pathway, and examined their response to BMP-2. We show that overexpression of either Wnt-3A or kinase-dead GSK-3beta enhances BMP-2-mediated chondrogenesis. Furthermore, Wnt-3A overexpression results in decreases in both N-cadherin and GSK-3beta protein levels, whereas Wnt-3A as well as kinase-dead GSK-3beta overexpression increase total and nuclear levels of both beta-catenin and LEF-1. Direct cross-talk between Wnts and BMP-2 was also indicated by the up-regulated interaction between beta-catenin and SMAD-4 in response to BMP-2. These results suggest that Wnt-3A acts in a manner opposite to that of other Wnts, such as Wnt-7A, which were previously identified as inhibitory to chondrogenesis, and is the first BMP-2-regulated, chondrogenesis-enhancing member of the Wnt family.
Effect of treatment of chronic periodontitis on levels of serum markers of acute‐phase inflammatory and vascular responses (2003)

Improvement in periodontal health did not influence the levels of vascular markers.
Long-Term Storage of DNA-Free RNA for use in Vaccine Studies (2007)

RNA replicons represent potential vaccine delivery vehicles, but are considered too unstable for such use. This study examined the recovery, integrity and function of in vitro transcribed replicon RNA encoding hepatitis C virus (HCV) proteins. To remove residual template DNA, the RNA was digested with TURBO DNase followed by RNeasy DNase set and purified through an RNeasy column. The RNA was freeze-dried in distilled water or trehalose, stored under nitrogen gas for up to 10 months and analyzed at different time points. The recovery of RNA stored at < or = 4 degrees C that was freeze-dried in distilled water varied between 66% to zero of that recovered from RNA freeze-dried in 10% trehalose, a figure that depended on the duration of storage. In contrast, the recovery of the RNA stored in trehalose was consistently high for all time points. After recovery, both RNAs were translationally competent and expressed high levels of proteins after transfection, although the level of expression from the trehalose-stored RNA was consistently higher. Thus the addition of trehalose permitted stable storage of functional RNA at 4 degrees C for up to 10 months and this permits the development of RNA vaccines, even in developing countries where only minimum storage conditions (e.g., 4 degrees C) can be achieved.
CASHEW KERNELS CLASSIFICATION USING TEXTURE FEATURES (2011)

Cashew is a commercial commodity that plays a major role in earning foreign revenue among export commodities in India. The purpose of this research work is to explore image processing techniques and approaches on Indian cashew
variety identification based on their kernels. Colour is an important quality factor for grading, marketing, and end users. Our primary objective is to develop a cost-effective intelligent model to identify the cashew kernels.
Colour features in the RGB (red-green-blue) colour space are extracted and computed. A feed-forward neural network is
trained to classify sample cashew kernels. An intelligent classification system based on computer vision system can be
developed for automated grading and sorting to speed up the classification of cashew kernels. This will solve the major
problems of many of the cashew export industries also, gives justice to the cashew growing farmers in accurate grading. The classification system is evaluated on cashew kernels of 6 different grades. The result of our study shows that, the system gives about 80% classification rate.
Implications of Psoriasis as a New Disease (1999)

It is noted that psoriasis appears not to have been described until the return of explorers from the New World back to the Old. Thus, it is suggested that in fact psoriasis is a new disease to the Old World. One implication of this is that any infectious agent which is a candidate cofactor in the pathogenesis of psoriasis must itself be new to the Old World after the time of the explorers.
<title>Infrared spectroscopic detection of ions and free radicals in discharge plasmas</title> (1993)

High-resolution infrared spectroscopy of molecular ions and free radicals has witnessed a dramatic progress in the past ten years. Spectroscopic identification and characterization of transient species are of great importance for understanding elementary processes in discharge plasmas. Infrared spectroscopy of molecular ions is a relatively new field. Nevertheless, up to the present time, more than 50 species (including negative ions) have been identified and the spectroscopic constants have been determined. In this presentation, some of the more recent results are reviewed, and a new observation of the infrared spectra of D<SUB>3</SUB> and formation mechanism of triatomic hydrogen radicals in hydrogen discharge plasma are discussed.
Optical Design of Intraocular Lenses. I. On-Axis Performance (1989)

The theoretical effect of intraocular lens shape on on-axis performance of model pseudophakic eyes was investigated. Image quality criteria included the magnitude of spherical aberration (both wave and longitudinal), spot diagrams, and the modulation transfer function. For eyes with corneal asphericities encompassing most of the population (Q greater than or equal to -0.5), the optimum lens form is close to being plano-convex, with the more curved surface facing the cornea.
Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. (2003)

Sedolisins (serine-carboxyl peptidases) are proteolytic enzymes whose fold resembles that of subtilisin; however, they are considerably larger, with the mature catalytic domains containing approximately 375 amino acids. The defining features of these enzymes are a unique catalytic triad, Ser-Glu-Asp, as well as the presence of an aspartic acid residue in the oxyanion hole. High-resolution crystal structures have now been solved for sedolisin from Pseudomonas sp. 101, as well as for kumamolisin from a thermophilic bacterium, Bacillus novo sp. MN-32. The availability of these crystal structures enabled us to model the structure of mammalian CLN2, an enzyme which, when mutated in humans, leads to a fatal neurodegenerative disease. This review compares the structural and enzymatic properties of this newly defined MEROPS family of peptidases, S53, and introduces their new nomenclature.
Status on Iterative Transform Phase Retrieval Applied to the GBT Data (2007)

This slide presentation reviews the use of iterative transform phase retrieval in the analysis of the Green Bank Radio Telescope (GBT) Data. It reviews the NASA projects that have used phase retrieval, and the testbed for the algorithm to be used for the James Webb Space Telescope. It shows the comparison of phase retrieval with an interferometer, and reviews the two approaches used for phase retrieval, iterative transform (ITA) or parametric (non-linear least squares model fitting). The concept of ITA Phase Retrieval is reviewed, and the application to Radio Antennas is reviewed. The presentation also examines the National Radio Astronomy Observatory (NRAO) data from the GBT, and the Fourier model that NRAO uses to analyze the data. The challenge for ITA phase retrieval is reviewed, and the coherent approximation for incoherent data is shown. The validity of the approximation is good for a large tilt. There is a review of the proof of concept of the Phase Review simulation using the input wavefront, and the initial sampling parameters estimate from the focused GBT data.
A DFT‐GIAO and DFT‐NBO study of polar substituent effects on NMR 17O chemical shifts in some rigid polycyclic alkanes (2010)

Abstract 17 O NMR shieldings of 3‐substituted(X)bicyclo[1.1.1]pentan‐1‐ols ( 1 , Y = OH), 4‐substituted(X)bicyclo[2.2.2]octan‐1‐ols ( 2 , Y = OH), 4‐substituted(X)‐bicyclo[2.2.1]heptan‐1‐ols ( 3 , Y = OH), 4‐substituted(X)‐cuban‐1‐ols ( 4 , Y = OH) and exo ‐ and endo ‐ 6‐substituted(X) exo ‐bicyclo[2.2.1]heptan‐2‐ols ( 5 and 6 , Y = OH, respectively), as well as their conjugate bases ( 1 – 6 , Y = O − ), for a set of substituents (X = H, NO 2 , CN, NC, CF 3 , COOH, F, Cl, OH, NH 2 , CH 3 , SiMe 3 , Li, O − , and NH ) covering a wide range of electronic substituent effects were calculated using the DFT‐GIAO theoretical model at the B3LYP/6‐311 + G(2d, p) level of theory. By means of natural bond orbital (NBO) analysis various molecular parameters were obtained from the optimized geometries. Linear regression analysis was employed to explore the relationship between the calculated 17 O SCS and polar field and group electronegativity substituent constants ( σ F and σ χ , respectively) and also the NBO derived molecular parameters (oxygen natural charge, Q n , occupation numbers of the oxygen lone pairs, n o , and occupancy of the CO antibonding orbital, σ * CO (occup)). In the case of the alcohols ( 1 – 6 , Y = OH) the 17 O SCS appear to be governed predominantly by the σ χ effect of the substituent. Furthermore, the key determining NBO parameters appear to be n o and σ * CO (occup). Unlike the alcohols, the calculated 17 O SCS of the conjugate bases ( 1 – 6 , Y = O − ), except for system 1 , do not respond systematically to the electronic effects of the substituents. An analysis of the SCS of 1 (Y = O − ) raises a significant conundrum with respect to their origin. Copyright © 2010 John Wiley &amp; Sons, Ltd.
TAK-652 Inhibits CCR5-Mediated Human Immunodeficiency Virus Type 1 Infection In Vitro and Has Favorable Pharmacokinetics in Humans (2005)

The first small-molecule CCR5 antagonist, TAK-779, could not be developed as an anti-human immunodeficiency virus type (anti-HIV-1) agent because of its poor oral bioavailability. TAK-652 is an orally bioavailable TAK-779 derivative with potent anti-HIV-1 activity. TAK-652 inhibited the binding of RANTES (regulated on activation, normal T-cell expressed and secreted), macrophage inflammatory protein 1alpha (MIP-1alpha), and MIP-1beta to CCR5-expressing cells at nanomolar concentrations. TAK-652 could also suppress the binding of monocyte chemotactic protein 1 (MCP-1) to CCR2b-expressing cells. However, its inhibitory effect on ligand binding to other chemokine receptors was limited. TAK-652 was active against CCR5-using (R5) HIV-1 but totally inactive against CXCR4-using (X4) HIV-1. The compound was active against R5 HIV-1 clinical isolates containing reverse transcriptase and protease inhibitor-resistant mutations, with a mean 50% effective concentration (EC50) and EC90 of 0.061 and 0.25 nM, respectively. In addition, recombinant R5 viruses carrying different subtype (A to G) envelope proteins were equally susceptible to TAK-652. A single oral administration of TAK-652 up to 100 mg was safe and well tolerated in humans. The compound displayed favorable pharmacokinetics, and its plasma concentration was 7.2 ng/ml (9.1 nM) even 24 h after the administration of 25 mg. Thus, TAK-652 is a promising candidate as a novel entry inhibitor of HIV-1.
The neuroendocrine chaperone 7B2 can enhance in vitro POMC cleavage by prohormone convertase PC2 (1995)

We previously showed that the neuroendocrine polypeptide 7B2 transiently interacts with prohormone convertase PC2 in the secretory pathway of neuroendocrine cells. Here we demonstrate that the processed, but not the intact, form of 7B2 can enhance the in vitro cleavage of newly synthesized prohormone proopiomelanocortin (POMC) in lysates of Xenopus intermediate pituitary cells. PC2 is presumably the cleavage enzyme involved since intact 7B2 abolishes the enhancing effect of processed 7B2 and is known to act as a specific inhibitor of PC2. Furthermore, processed 7B2 stimulates in vitro POMC cleavage by immunopurified Xenopus PC2. Our results indicate that 7B2 can display chaperone activity towards PC2.
Human p53 and CDC2Hs Genes Combine To Inhibit the Proliferation of Saccharomyces cerevisiae (1992)

Human wild-type and mutant p53 genes were expressed under the control of a galactose-inducible promoter in Saccharomyces cerevisiae. The growth rate of the yeast was reduced in cells expressing wild-type p53, whereas cells transformed with mutant p53 genes derived from human tumors were less affected. Coexpression of the normal p53 protein with the human cell cycle-regulated protein kinase CDC2Hs resulted in much more pronounced growth inhibition that for p53 alone. Cells expressing p53 and CDC2Hs were partially arrested in G1, as determined by morphological analysis and flow cytometry. p53 was phosphorylated when expressed in the yeast, but differences in phosphorylation did not explain the growth inhibition attributable to coexpression of p53 and CDC2Hs. These results suggest that wild-type p53 has a growth-inhibitory activity in S. cerevisiae similar to that observed in mammalian cells and suggests that this yeast may provide a useful model for defining the pathways through which p53 acts.
The Prevalence of Hepatitis C Virus Infection in the United States, 1988 through 1994 (1999)

In the United States, about 2.7 million persons are chronically infected with HCV. People who use illegal drugs or engage in high-risk sexual behavior account for most persons with HCV infection.
Cyclopentene annulation via intramolecular addition of diazoketones to 1,3-dienes. Applications to the synthesis of cyclopentanoid terpenes (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclopentene annulation via intramolecular addition of diazoketones to 1,3-dienes. Applications to the synthesis of cyclopentanoid terpenesTomas Hudlicky, Francis F. Koszyk, Toni M. Kutchan, and Jagdish P. ShethCite this: J. Org. Chem. 1980, 45, 25, 5020–5027Publication Date (Print):December 1, 1980Publication History Published online1 May 2002Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/jo01313a003https://doi.org/10.1021/jo01313a003research-articleACS PublicationsRequest reuse permissionsArticle Views2268Altmetric-Citations120LEARN 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
Immune response in prostate cancer. (2005)

Surprisingly perhaps for a tumor where there is such clear proof of a primary hormonal basis to its development, there is emerging evidence that all elements playing a key role in prostate cancer somehow affect the host immune system. This review turns the spotlight on some previously unsuspectable aspects, able to interact with the immune system in prostate cancer patients PSA, sex hormones, inflammatory infiltrates, cytokines, growth factors, neoformed blood vessels, neurotransmitters and neurotrophins, cigarette smoking, diet, therapeutic approaches. The concept of exploiting the immune system to combat cancer is not new, but only nowadays immunotherapy is a reality. Prostate cancer is an excellent target, involved in an increasing number of clinical immunotherapeutic trials. The main current purpose is to overcome the host immune tolerance of tumor cells. The most recent progresses in gene, monoclonal antibody and vaccine therapies are reported.
Combinatorial Chemistry A Tool for the Discovery of New Catalysts. (2001)

The discovery of new reactions and catalysts has always presented an intriguing challenge to scientists. With the rise of combinatorial chemistry, a new method has emerged that holds considerable promise to facilitate the task since it allows for the simultaneous generation and testing of a large number of compounds. The crucial difficulty lies in establishing general technologies for rapid and reliable screening of libraries to determine the catalytic activity of their members. Several recent publications have addressed this question by using infrared thermography, colorimetric assays and fluorescence spectroscopy. These techniques have not only been applied successfully to the high-throughput screening of parallel compound arrays but also to the screening of one-bead-one-compound libraries. This demonstrates that combinatorial chemistry possesses indeed the potential to establish itself as a powerful tool for the discovery of new catalysts. This review describes the methodologies used so far for the detection of catalytic events and will place particular emphasis on the on-bead screening of one-bead-one-compound libraries.
Clock buffer chip with multiple target automatic skew compensation (1995)

This paper describes the application of a digital delay locked loop that compensates for variable delays on the clock chip, printed circuit board clock traces, and the clock systems on multiple ASICs. For a computer system consisting of nine PC boards ("modules") plugged into a back plane with two clock chips per board and six ASICs per clock chip, a locking range of 25-150 MHz was achieved with a maximum skew in the system of less than 1 ns.
The MPEG-4 fine-grained scalable video coding method for multimedia streaming over IP (2001)

Real-time streaming of audiovisual content over the Internet is emerging as an important technology area in multimedia communications. Due to the wide variation of available bandwidth over Internet sessions, there is a need for scalable video coding methods and (corresponding) flexible streaming approaches that are capable of adapting to changing network conditions in real time. In this paper, we describe a new scalable video-coding framework that has been adopted recently by the MPEG-4 video standard. This new MPEG-4 video approach, which is known as Fine-Granular-Scalability (FGS), consists of a rich set of video coding tools that support quality (i.e., SNR), temporal, and hybrid temporal-SNR scalabilities. Moreover, one of the desired features of the MPEG-J FGS method is its simplicity and flexibility in supporting unicast and multicast streaming applications over IF.
Functional Domains for Amelogenin Revealed by Compound Genetic Defects (2003)

We have previously used the yeast two-hybrid assay and multiple in vitro methodologies to show that amelogenin undergoes self-assembly involving two domains (A and B). Using transgenic animals, we show that unique enamel phenotypes result from disruptions to either the A- or B-domain, supporting the role of amelogenin in influencing enamel structural organization. By crossbreeding, animals bearing two defective amelogenin gene products have a more extreme enamel phenotype than the sum of the defects evident in the individual parental lines. At the nanoscale level, the forming matrix shows alteration in the size of the amelogenin nanospheres. At the mesoscale level of enamel structural hierarchy, 6-week-old enamel exhibits defects in enamel rod organization caused by perturbed organization of the precursor organic matrix. These studies reflect the critical dependency of amelogenin self-assembly to form a highly organized enamel organic matrix, and that amelogenins engineered to be defective in self-assembly produce compound defects in the structural organization of enamel.
Total Synthesis of (−)-Rhazinilam:  Asymmetric C−H Bond Activation via the Use of a Chiral Auxiliary (2002)

The antitumor agent (-)-rhazinilam was synthesized in three major steps, namely the pyrrole synthesis, selective C[bond]H bond activation, and direct macrolactam formation. The key step involved asymmetric C[bond]H bond functionalization (dehydrogenation) of the diethyl group segment in intermediate 6. This was achieved by the attachment of chiral platinum complexes to the proximal nitrogen atom. A high degree of selectivity (60-75% ee) was achieved via the use of oxazolinyl ketone chiral auxiliaries.