gebhart/patrepeval huggingface dataset:
Electronic interaction between photoexcited poly(p-phenylene vinylene) and carbon nanotubes (2000)

We have studied the electronic interaction between photoexcited poly(p-phenylene vinylene) (PPV) and multiwall carbon nanotubes (MWNT's) using photoluminescence (PL) and photoinduced absorption (PIA) spectroscopy. We have found that the MWNT's strongly interact with the photoexcited PPV, while there is no significant interaction in the ground state. The \ensuremath{\pi} conjugation of PPV was slightly reduced in the composite, reflecting the nanoscopic structural influence of the MWNT's. On the basis of its temperature and frequency dependence, the PIA spectrum was found to originate from the same species as the pure PPV film, namely, triplet excitons formed in PPV via intersystem crossing. We have concluded that the predominant electronic interaction is the nonradiative energy transfer of singlet excitons from the PPV to the MWNT's.
Recognition of ECG Patterns Using Artificial Neural Network (2006)

In this paper, the artificial neural network method was used for electrocardiogram (ECG) pattern recognition. Four types of ECG patterns were chosen from the MIT-BIH database to be recognized, including normal sinus rhythm, premature ventricular contraction, atrial premature beat and left bundle branch block beat. ECG morphology and R-R interval features were performed as the characteristic representation of the original ECG signals to be fed into the neural network models. Three types of artificial neural network models, SOM, BP and LVQ networks were separately trained and tested for ECG pattern recognition and the experimental results of the different models have been compared. The SOM network exhibited the best performance and reached an overall accuracy of 95.5%, and the BP and LVQ network reached 92.5% and 91.5%
Genetic evidence for an essential role of brassinosteroids in plant development (1996)

Summary Brassinosteroids which show high structural similarity to animal steroid hormones elicit a variety of growth responses when exogeneously applied to plant tissues. Thus far however, the function of endogeneous brassinosteroids in higher plants has been unclear. This paper describes three extremely dwarfed Arabidopsis thaliana mutants, cbb1 ( dwf1‐6 ), cbb2 and cbb3 , which are impared in cell elongation controlled by brassinosteroids. While cbb1 ( dwf1‐6 ) and cbb3 can be phenotypically normalized to wild‐type by feeding with brassinosteroids indicating deficiencies of brassinosteroid biosynthesis, cbb2 is brassinosteroid‐insensitive and defines a function required for further metabolic conversion necessary for biological activity or for perception/signal transduction of these growth‐regulating plant steroid hormones. Expression of the meri5 and TCH4 genes is low in all three cbb mutants and can be restored to wild‐type levels by brassinosteroid treatment in the cbb1 ( dwf1‐6 ) and cbb3 mutants but are unaffected in the cbb2 mutant. These data indicate that brassinosteroids are essential for proper plant development and play an important role in the control of cell elongation.
The Comprehensive Microbial Resource (2001)

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.
Expression of Human Thyrotropin in Cell Lines with Different Glycosylation Patterns Combined with Mutagenesis of Specific Glycosylation Sites (1995)

We used a novel approach to study the role of the Asn-linked oligosaccharides for human thyrotropin (hTSH) activity. Mutagenesis of Asn (N) within individual glycosylation recognition sequences to Gln (Q) was combined with expression of wild type and mutant hTSH in cell lines with different glycosylation patterns. The in vitro activity of hTSH lacking the Asn alpha 52 oligosaccharide (alpha Q52/TSH beta) expressed in CHO-K1 cells (sialylated oligosaccharides) was increased 6-fold compared with wild type, whereas the activities of alpha Q78/TSH beta and alpha/TSH beta Q23 were increased 2-3-fold. Deletion of the Asn alpha 52 oligosaccharide also increased the thyrotropic activity of human chorionic gonadotropin, in contrast to previous findings at its native receptor. The in vitro activity of wild type hTSH expressed in CHO-LEC2 cells (sialic acid-deficient oligosaccharides), CHO-LEC1 cells (Man5GlcNAc2 intermediates), and 293 cells (sulfated oligosaccharides) was 5-8-fold higher than of wild type from CHO-K1 cells. In contrast to CHO-K1 cells, there was no difference in the activity between wild type and selectively deglycosylated mutants expressed in these cell lines. Thus, in hTSH, the oligosaccharide at Asn alpha 52 and, specifically, its terminal sialic acid residues attenuate in vitro activity, in contrast to the previously reported stimulatory role of this chain for human chorionic gonadotropin and human follitropin activity. The increased thyrotropic activity of alpha Q52/CG beta suggests that receptor-related mechanisms may be responsible for these differences among the glycoprotein hormones. Despite their increased in vitro activity, alpha Q52/TSH beta, and alpha Q78/TSH beta from CHO-K1 cells had a faster serum disappearance rate and decreased effect on T4 production in mice. These findings highlight the importance of individual oligosaccharides in maintaining circulatory half-life and hence in vivo activity of hTSH.
Efficient Gene Transfer into Primary Human CD8 + T Lymphocytes by MuLV-10A1 Retrovirus Pseudotype (2000)

Efficient and stable gene transfer into primary human T lymphocytes would greatly improve their use for adoptive transfer to treat acquired disorders, viral diseases, and cancer. We have constructed retroviral vector pseudotypes of amphotropic murine leukemia viruses (A-MuLV, MuLV-10A1), gibbon ape leukemia virus (GaLV), and feline endogenous virus (RD114) containing the enhanced green fluorescent protein (GFP) as a marker gene. Transduction of primary human CD8+ T lymphocytes by the different GFP-retrovirus pseudotypes revealed the superiority of MuLV-10A1 in comparison with A-MuLV, GaLV, and RD114, respectively. The superior transduction efficacy of CD8+ T cells by MuLV-10A1 correlates with a longer half-life of this pseudotype in comparison with A-MuLV and, as shown by interference analysis with the human T cell line HUT78, by the utilization of both the A-MuLV receptor (Pit2) and the GaLV receptor (Pit1) for cell entry.
The relationship among tumor architecture, pharmacokinetics, pharmacodynamics, and efficacy of bortezomib in mouse xenograft models (2009)

Understanding a compound's preclinical pharmacokinetic, pharmacodynamic, and efficacy relationship can greatly facilitate its clinical development. Bortezomib is a first-in-class proteasome inhibitor whose pharmacokinetic/pharmacodynamic parameters are poorly understood in terms of their relationship with efficacy. Here we characterized the bortezomib pharmacokinetic/pharmacodynamic/efficacy relationship in the CWR22 and H460 xenograft models. These studies allowed us to specifically address the question of whether the lack of broad bortezomib activity in solid tumor xenografts was due to insufficient tumor penetration. In vivo studies showed that bortezomib treatment resulted in tumor growth inhibition in CWR22 xenografts, but not in H460 xenografts. Using 20S proteasome inhibition as a pharmacodynamic marker and analyzing bortezomib tumor exposures, we show that efficacy was achieved only when suitable drug exposures drove proteasome inhibition that was sustained over time. This suggested that both the magnitude and duration of proteasome inhibition were important drivers of efficacy. Using dynamic contrast-enhanced magnetic resonance imaging and high-resolution computed tomographic imaging of vascular casts, we characterized the vasculature of CWR22 and H460 xenograft tumors and identified prominent differences in vessel perfusion, permeability, and architecture that ultimately resulted in variations in bortezomib tumor exposure. Comparing and contrasting the differences between a bortezomib-responsive and a bortezomib-resistant model with these techniques allowed us to establish a relationship among tumor perfusion, drug exposure, pharmacodynamic response and efficacy, and provided an explanation for why some solid tumor models do not respond to bortezomib treatment.
Targeting the RET Pathway in Thyroid Cancer (2009)

The RET (rearranged during transfection) protooncogene encodes a single pass transmembrane receptor that is expressed in cells derived from the neural crest and the urogenital tract. As part of a cell-surface complex, RET binds glial derived neurotrophic factor (GDNF) ligands in conjunction with GDNF-family alpha co-receptors (GFRalpha). Ligand-induced activation induces dimerization and tyrosine phosphorylation of the RET receptor with downstream activation of several signal transduction pathways. Activating germline RET mutations play a central role in the development of the multiple endocrine neoplasia (MEN) syndromes MEN2A, MEN2B, and familial medullary thyroid carcinoma (FMTC) and also in the development of the congenital abnormality Hirschsprung's disease. Approximately 50% of patients with sporadic MTC have somatic RET mutations, and a significant portion of papillary thyroid carcinomas result from chromosomal inversions or translocations, which activate RET (RET/PTC oncogenes). The RET protooncogene has a significant place in cancer prevention and treatment. Timely thyroidectomy in kindred members who have inherited a mutated RET allele, characteristic of MEN2A, MEN2B, or FMTC, can prevent MTC, the most common cause of death in these syndromes. Also, recently developed molecular therapeutics that target the RET pathway have shown activity in clinical trials of patients with advanced MTC, a disease for which there has been no effective therapy.
Organs-on-chips: Progress, challenges, and future directions (2017)

The National Institutes of Health Microphysiological Systems (MPS) program, led by the National Center for Advancing Translational Sciences, is part of a joint effort on MPS development with the Defense Advanced Research Projects Agency and with regulatory guidance from FDA, is now in its final year of funding. The program has produced many tangible outcomes in tissue chip development in terms of stem cell differentiation, microfluidic engineering, platform development, and single and multi-organ systems-and continues to help facilitate the acceptance and use of tissue chips by the wider community. As the first iteration of the program draws to a close, this Commentary will highlight some of the goals met, and lay out some of the challenges uncovered that will remain to be addressed as the field progresses. The future of the program will also be outlined. Impact statement This work is important to the field as it outlines the progress and challenges faced by the NIH Microphysiological Systems program to date, and the future of the program. This is useful information for the field to be aware of, both for current program stakeholders and future awardees and partners.
Characterization of SMOC-2, a modular extracellular calcium-binding protein (2003)

We have isolated the novel gene SMOC-2, which encodes a secreted modular protein containing an EF-hand calcium-binding domain homologous to that in BM-40. It further consists of two thyroglobulin-like domains, a follistatin-like domain and a novel domain found only in the homologous SMOC-1. Phylogenetic analysis of the calcium-binding domain sequences showed that SMOC-1 and -2 form a separate group within the BM-40 family. The human and mouse SMOC-2 sequences are coded for by genes consisting of 13 exons located on chromosomes 6 and 17, respectively. Analysis of recombinantly expressed protein showed that SMOC-2 is a glycoprotein with a calcium-dependent conformation. Results from Northern blots and reverse transcription PCR revealed a widespread expression in many tissues.
Concise total synthesis of (+)-gliocladins B and C (2012)

The first total synthesis of (+)-gliocladin B is described. Our concise and enantioselective synthesis takes advantage of a new regioselective Friedel-Crafts-based strategy to provide an efficient multigram-scale access to the C3-(3'-indolyl)hexahydropyrroloindole substructure, a molecular foundation present in a significant subset of epipolythiodiketopiperazine natural alkaloids. Our first-generation solution to (+)-gliocladin B involved the stereoselective formation of (+)-12-deoxybionectin A, a plausible biosynthetic precursor. Our synthesis clarified the C15 stereochemistry of (+)-gliocladin B and allowed its full structure confirmation. Further studies of a versatile dihydroxylated diketopiperazine provided a concise and efficient synthesis of (+)-gliocladin B as well as access to (+)-gliocladin C.
Providing personalized recommendation for attending events based on individual interest profiles (2015)

In this article we present a framework to extract user interests from social network profiles such as Facebook to personalize recommendations about products and services. Matching users’ interests as keywords with product attributes as keywords, performed by currently available personalization systems, has a very low recall, so more general category-based frameworkis needed. It turns out that substantial reasoning about products and their categories is required to match a taxonomy of theowner of products and services, with that of a user, as expressed in a public profile. To handle inconsistencies between the setaxonomies, a mapping of one into another is expressed as a Defeasible Logic program (DeLP), where a potential mapping can bedefeated by other ones if relevant information becomes available. Events and things to do are recommended at StubHub.com and www.facebook.com/StubHub/ so that the reader can observe the system at a scale. Also, we present content management system which supports personalized recommendation is outlined.
The LPP1 and DPP1 Gene Products Account for Most of the Isoprenoid Phosphate Phosphatase Activities inSaccharomyces cerevisiae (1999)

Two genes in Saccharomyces cerevisiae, LPP1 and DPP1, with homology to a mammalian phosphatidic acid (PA) phosphatase were identified and disrupted. Neither single nor combined deletions resulted in growth or secretion phenotypes. As observed previously (Toke, D. A., Bennett, W. L., Dillon, D. A., Wu, W.-I., Chen, X., Ostrander, D. B., Oshiro, J., Cremesti, A., Voelker, D. R., Fischl, A. S., and Carman, G. M. (1998) J. Biol. Chem. 273, 3278-3284; Toke, D. A., Bennett, W. L., Oshiro, J., Wu, W.-I., Voelker, D. R., and Carman, G. M. (1998) J. Biol. Chem. 273, 14331-14338), the disruption of DPP1 and LPP1 produced profound losses of Mg2+-independent PA phosphatase activity. The coincident attenuation of hydrolytic activity against diacylglycerol pyrophosphate prompted an examination of the effects of these disruptions on hydrolysis of isoprenoid pyrophosphates. Disruption of either LPP1 or DPP1 caused respective decreases of about 25 and 75% in Mg2+-independent hydrolysis of several isoprenoid phosphates by particulate fractions isolated from these cells. The particulate and cytosolic fractions from the double disruption (lpp1Delta dpp1Delta) showed essentially complete loss of Mg2+-independent hydrolytic activity toward dolichyl phosphate (dolichyl-P), dolichyl pyrophosphate (dolichyl-P-P), farnesyl pyrophosphate (farnesyl-P-P), and geranylgeranyl pyrophosphate (geranylgeranyl-P-P). However, a modest Mg2+-stimulated activity toward PA and dolichyl-P was retained in cytosol from lpp1Delta dpp1Delta cells. The action of Dpp1p on isoprenyl pyrophosphates was confirmed by characterization of the hydrolysis of geranylgeranyl-P-P by the purified protein. These results indicate that LPP1 and DPP1 account for most of the hydrolytic activities toward dolichyl-P-P, dolichyl-P, farnesyl-P-P, and geranylgeranyl-P-P but also suggest that yeast contain other enzymes capable of dephosphorylating these essential isoprenoid intermediates.
Learning to combine foveal glimpses with a third-order Boltzmann machine (2010)

We describe a model based on a Boltzmann machine with third-order connections that can learn how to accumulate information about a shape over several fixations. The model uses a retina that only has enough high resolution pixels to cover a small area of the image, so it must decide on a sequence of fixations and it must combine the “glimpse ” at each fixation with the location of the fixation before integrating the information with information from other glimpses of the same object. We evaluate this model on a synthetic dataset and two image classification datasets, showing that it can perform at least as well as a model trained on whole images. 1
Dynamic force microscopy study of 3,4,9,10-perylenetetracarboxylic dianhydride on KBr(001) (2005)

A scanning force microscope operated in the dynamic force mode has been used to analyze the arrangement of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecules on a KBr(001) surface. The molecules do not form a close-packed layer but crystallites with the shape of truncated pyramids. Even after depositing only 0.3 molecular layers of PTCDA, these crystallites have a height of 20--30 molecular layers. We have been able to resolve individual molecules of the top layer and on some of the crystallites facets. The results agree with the known ``herringbone'' structure of the bulk. A comparison of the experimentally observed contrast to a simple force field calculation based on semiempirical interaction potentials is given.
A novel pyridopyrimidine inhibitor of abl kinase is a picomolar inhibitor of Bcr-abl-driven K562 cells and is effective against STI571-resistant Bcr-abl mutants. (2003)

Inhibition of the constitutively active Bcr-abl tyrosine kinase(TK) by STI571 has proven to be a highly effective treatment for chronic myelogenous leukemia (CML). However, STI571 is only transiently effective in blast crisis, and drug resistance emerges by amplification of or development of mutational changes in Bcr-abl. We have screened a family of TK inhibitors of the pyrido [2,3-d]pyrimidine class, unrelated to STI571, and describe here a compound with substantial activity against STI-resistant mutant Bcr-abl proteins. This compound, PD166326, is a dual specificity TK inhibitor and inhibits src and abl in vitro with IC(50)s of 6 and 8 nM respectively. PD166326 inhibits the growth of K562 cells with IC(50) of 300 pM, leading to apoptotic G(1) arrest, whereas non-Bcr-abl cell types require >1000 times higher concentrations. We tested the effects of PD166326 on two of the clinically observed STI571-resistant Bcr-abl mutants. PD166326 potently inhibits the E255K mutant Bcr-abl protein and the growth of Bcr-ablE255K-driven cells. The T315I mutant Bcr-abl protein, which is mutated within the ATP-binding pocket, is resistant to PD166326; however, the growth of Bcr-ablT315I-driven cells is partially sensitive to this compound, likely through the inhibition of Bcr-abl effector pathways. These findings show that TK drug resistance is a structure-specific phenomenon and can be overcome by TK inhibitors of other structural classes, suggesting new approaches for future anticancer drug development. PD166326 is a prototype of a new generation of anti-Bcr-abl compounds with picomolar potency and substantial activity against STI571-resistant mutants.
Mini‐review: Transendothelial migration of leukocytes: through the front door or around the side of the house? (2004)

Leukocyte adhesion to the endothelial cells lining the vessel wall and the subsequent migration of the leukocytes into the underlying tissue are key elements of both innate and adaptive immunity. Leukocyte extravasation is generally believed to take place through small gaps at intercellular endothelial cell junctions -- the paracellular route. This view has, however, been repeatedly challenged by morphological studies demonstrating leukocyte migration through the endothelial cells themselves -- the transcellular pathway. On the basis of the current experimental evidence, we propose consideration that both pathways are equally possible for a leukocyte's journey from the apical surface of the endothelium to its basal side.
The homologous regulators ANR of Pseudornonas aeruginosa and FNR of Escherichia coli have overlapping but distinct specificities for anaerobically inducible promoters (1996)

The anaerobic transcriptional regulator ANR induces the arginine deiminase and denitrification pathways in Pseudomonas aeruginosa during oxygen limitation. The homologous activator FNR of Escherichia coli, when introduced into an anr mutant of P. aeruginosa, could functionally replace ANR for anaerobic growth on nitrate but not for anaerobic induction of arginine deiminase. In an FNR-positive E. coli strain, the ANR-dependent promoter of the arcDABC operon, which encodes the enzymes of the arginine deiminase pathway, was not expressed. To analyse systematically these distinct induction patterns, a lacZ promoter-probe, broad-host-range plasmid containing various -40 regions (the ANR/FNR recognition sequences) and -10 promoter sequences was constructed. These constructs were tested in P. aeruginosa and in E. coli expressing either ANR or FNR. In conjunction with the consensus -10 hexamer of E. coli sigma 70 RNA polymerase (TATAAT), the consensus FNR site (TTGAT ..... ATCAA) was recognized efficiently by ANR and FNR in both hosts. By contrast, when promoters contained the Arc box (TTGAC .... ATCAG), which is found in the arcDABC promoter, or a symmetrical mutant FNR site (CTGAT .... ATCAG), ANR was a more effective activator than was FNR. Conversely, an extended 22 bp, fully symmetrical FNR site allowed better activation with FNR than with ANR. Combination of the arc promoter -10 sequence (CCTAAT) with the Arc box or the consensus FNR site resulted in good ANR-dependent expression in P. aeruginosa but gave practically no expression in E. coli, suggesting that RNA polymerase of P. aeruginosa differs from the E. coli enzyme in -10 recognition specificity. In conclusion, ANR and FNR are able to activate the RNA polymerases of P. aeruginosa and E. coli when the -40 and -10 promoter elements ae identical or close to the E. coli consensus sequences.