gebhart/patrepeval huggingface dataset:
Transcriptional Targeting to Anterior Pituitary Lactotrophic Cells Using Recombinant Adenovirus Vectors in Vitro and in Vivo in Normal and Estrogen/Sulpiride-Induced Hyperplasic Anterior Pituitaries* (2000)

The use of pituitary cell type-specific promoters is a powerful molecular tool to achieve pituitary cell type-specific transcriptional targeting of transgenes encoded by viral vectors. It has recently been proposed that transcriptional targeting of therapeutic genes could be harnessed as a gene therapy strategy for the treatment of pituitary disease. We describe the successful use of the human PRL promoter (hPrl) encoded within recombinant adenovirus vectors to target transgene expression of Herpes Simplex Virus Type 1-Thymidine Kinase (HSV1-TK) or beta-galactosidase to lactotrophic cells in vitro and in vivo. Functionally, the restriction of expression of HSV1-TK to lactotrophic tumor cells, using the hPrl promoter, resulted in the cell type-specific induction of apoptosis in the lactotrophic GH3 tumor cell line, in the presence of ganciclovir (GCV). In the corticotrophic AtT20 cell line, we detected neither HSV1-TK expression, nor apoptosis in the presence of GCV. The hPrl promoter encoded within a recombinant adenoviral vector also restricted transgene expression to lactotrophic cells in primary anterior pituitary (AP) cultures, and importantly, within the anterior pituitary gland in vivo. When the HSV1-TK driven by hPrl promoter was used in an in vivo model ofestrogen/sulpiride lactotroph induced hyperplasia within the AP in situ, the treatment was not effective in either reducing the weight of the gland, the number of lactotrophic cells within the transduced area in vivo, or the circulating PRL levels. This is in contrast to the human cytomegalovirus promoter (hCMV) driving expression of HSV1-TK in the same experimental paradigm, which was effective in reducing pituitary weight and circulating PRL levels. Our results have important implications in the design of gene therapy strategies for pituitary tumors. We demonstrate that both the choice of the in vivo animal model, i.e. adenoma in the AP gland in situ, and the particular gene therapy strategy chosen, i.e. use of strong ubiquitous promoters vs. weaker but cell type-specific promoters, determine the experimental therapeutic outcome.
Synonymous codon usage and selection on proteins (2004)

Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein sequences from their synonymous codon usage (Plotkin and Dushoff 2003, Plotkin et al 2004a). Here we provide a theoretical foundation for this approach. We derive the expected frequencies of synonymous codons as a function of the strength of selection, the mutation rate, and the effective population size. We analyze the conditions under which we can expect to draw inferences from biased codon usage, and we estimate the time scales required to establish and maintain such a signal. Our results indicate that, over a broad range of parameters, synonymous codon usage can reliably distinguish between negative selection, positive selection, and neutrality. While the power of volatility to detect negative selection depends on the population size, there is no such dependence for the detection of positive selection. Furthermore, we show that phenomena such as transient hyper-mutators in microbes can improve the power of volatility to detect negative selection, even when the typical observed neutral site heterozygosity is low.
Metal-assisted aldol condensation of chiral .alpha.-halogenated imide enolates: a stereocontrolled chiral epoxide synthesis (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal-assisted aldol condensation of chiral .alpha.-halogenated imide enolates: a stereocontrolled chiral epoxide synthesisAhmed. Abdel-Magid, Lendon N. Pridgen, Drake S. Eggleston, and Ivan. LantosCite this: J. Am. Chem. Soc. 1986, 108, 15, 4595–4602Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://doi.org/10.1021/ja00275a054RIGHTS & PERMISSIONSArticle Views1032Altmetric-Citations103LEARN 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 InReddit PDF (1 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
sst2 Somatostatin Receptor Mediates Negative Regulation of Insulin Receptor Signaling through the Tyrosine Phosphatase SHP-1 (1998)

We have previously reported in Chinese hamster ovary (CHO) cells expressing sst2 that activation of the sst2 somatostatin receptor inhibits insulin-induced cell proliferation by a mechanism involving stimulation of a tyrosine phosphatase activity. Here we show that the tyrosine phosphatase SHP-1 was associated with the insulin receptor (IR) at the basal level. Activation of IR by insulin resulted in a rapid and transient increase of tyrosine phosphorylation of IR, its substrates IRS-1 and Shc, and also of SHP-1. This was then followed by a rapid dephosphorylation of these molecules, which was related to the insulin-induced increase of SHP-1 association to IR and of SHP-1 activity. On the other hand, addition to insulin of the somatostatin analogue, RC160, resulted in a higher and faster increase of SHP-1 association to IR directly correlated with an inhibition of phosphorylation of IR and its substrates, IRS-1 and Shc. RC160 also induced a higher and more sustained increase in SHP-1 activity. Furthermore, RC160 completely suppressed the effect of insulin on SHP-1 phosphorylation. Finally, in CHO cells coexpressing sst2 and a catalytically inactive mutant SHP-1, insulin as well as RC160 could no longer stimulate SHP-1 activity. Overexpression of the SHP-1 mutant prevented the insulin-induced signaling to be terminated by dephosphorylation of IR, suppressed the inhibitory effect of RC160 on insulin-induced IR phosphorylation, and abolished the cell proliferation modulation by insulin and RC160. Our results suggest that SHP-1 plays a role in negatively modulating insulin signaling by association with IR. Furthermore, somatostatin inhibits the insulin-induced mitogenic signal by accelerating and amplifying the effect of SHP-1 on the termination of the insulin signaling pathway.
Genes differentially expressed in prostate cancer (2004)

Because of the heterogeneity of prostate cancer knowledge about the genes involved in prostate carcinogenesis is still very limited. Previously, the use of novel high‐throughput technologies offered the possibility to investigate broad gene expression profiles and thus helped to improve understanding of the molecular basis of prostate disease. Many candidate genes have been identified so far which have a more or less strong effect on prostate cancer. This vast number of gene expression changes show that it is unlikely that only one gene promotes prostate cancer. Conversely, it seems more likely that a broad network of molecular changes is involved in the complex cascade of events which lead to tumour formation and progression, respectively. A few of these novel molecular targets are currently under clinical evaluation. This paper gives an overview of several interesting candidate genes which may be useful as improved biomarkers for diagnosis or as targets for developing novel treatment methods.
Role of erbB2 in breast cancer chemosensitivity (2000)

The erbB2 gene, which encodes a transmembrane growth factor receptor, is overexpressed in approximately 30% of breast cancers. Overexpressing this gene makes breast cancers resistant to certain chemotherapeutic agents. In this article, we review what is known about ErbB2-mediated chemoresistance and the controversies surrounding it. We also examine the antiapoptotic function of erbB2 as one of the molecular mechanisms of ErbB2-mediated Taxol resistance and describe several emerging strategies for overcoming intrinsic ErbB2-mediated chemoresistance. Finally, we discuss future avenues for studies of chemosensitivity in ErbB2-overexpressing breast cancers that may lead to the development of effective biology-based treatment strategies. BioEssays 22:673–680, 2000. © 2000 John Wiley & Sons, Inc.
Analysis of the proteomic profile of chronic pressure ulcers (2012)

Analysis of the proteomic profile of pressure ulcers over time is a critical step in the identification of biomarkers of healing or nonhealing in pressure ulcers. The wound fluid from 32 subjects with 42 pressure ulcers was evaluated over 6 weeks at 15 time points. Samples specific to both the interior and the periphery of the wound bed were collected. Antibody screening arrays, isobaric tags for relative and absolute quantitation with mass spectrometry and multiplexed microarrays were used to characterize wound fluid and results were correlated with clinical outcome. Twenty-one proteins were found to distinguish between healed and chronic wounds and 19 proteins were differentially expressed between the interior and periphery of wounds. Four proteins, pyruvate kinase isozymes M1/M2, profilin-1, Ig lambda-1 chain C regions, and Ig gamma-1 chain C region, were present in lower levels for periphery samples when compared to interior samples and six proteins, keratin, type II cytoskeletal 6A (KRT6A), keratin, type I cytoskeletal 14, S100 calcium binding proteins A7, alpha-1-antitrypsin precursor, hemoglobin subunit alpha, and hemoglobin subunit beta, were present in higher levels in periphery samples when compared with interior samples. S100 calcium binding protein A6, S100 calcium binding protein A7, and soluble receptor for advanced glycation end-products had higher levels in the periphery of chronic wounds vs. the interior in planar arrays. A significant temporal trend was noted for monokine induced by gamma interferon (MIG), synonomous with chemokine (C-X-C motif) ligand 9 (CXCL9), which increased as wounds healed and remained nearly constant for ulcers that were not approaching closure.
DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. (2002)

We identified DD3(PCA3) as one of the most prostate cancer-specific genes at present (M. J. Bussemakers et al. Cancer Res., 59: 5975-5979, 1999). Consequently, DD3(PCA3) is an interesting candidate for use as a diagnostic and/or prognostic marker. In this study we developed a method for the accurate quantification of DD3(PCA3) mRNA, using real-time quantitative reverse transcription-PCR. DD3(PCA3) was expressed at low levels in normal prostate but not in 21 selected other normal tissues, blood, or 39 tumor samples other than prostate. The diagnostic and prognostic value of DD3(PCA3) in normal, hyperplastic, and malignant prostate tissues was determined and compared with another promising tumor marker for prostate cancer, telomerase reverse transcriptase (hTERT gene), the expression of which is related to telomerase activity. Sensitivity and specificity estimates for both genes were calculated as the area under the receiver-operating characteristics curve (AUC-ROC). DD3(PCA3) (AUC-ROC, 0.98) demonstrated better diagnostic efficacy than hTERT (AUC-ROC, 0.88). Moreover, the median increase in mRNA expression in tumor tissues compared with nonmalignant prostate tissues was much higher for DD3(PCA3) (34-fold) than for hTERT (6-fold). In tumor tissues, the median expression of DD3(PCA3) was much higher than hTERT (5849 versus 10 normalized mRNA copies). A significant relationship was observed only between tumor stage and hTERT gene expression. We conclude that expression of the DD3(PCA3) gene is a very sensitive and specific marker for the detection of prostate tumor cells in a high background of normal (prostate) cells. Consequently, DD3 measurements may be used for clinical application in prostate needle biopsies or bodily fluids such as blood, ejaculate, urine, or prostate massage fluid.
Stimuli-induced Pulsatile or Triggered Release Delivery Systems for Bioactive Compounds (2007)

As is frequently found in the living body, many vital functions are regulated by pulsed or triggered release of bioactive substances at a specific site and time. Thus it is important to develop new drug delivery devices to achieve pulsed delivery of a certain amount of drugs in order to mimic the function of the living systems to minimize the undesired side effects. The pulsed or triggered delivery systems are designed to alter their rate of drug delivery in response to stimuli such as changes in a specific molecule, a magnetic or electric field, temperature, light or mechanical forces. Such systems are suitable for the release of therapeutics that benefit from non-constant plasma concentrations. In this article, several types of drug delivery systems which cause the pulsed or triggered release of bioactive compounds due to certain external stimuli, mostly focuses on thermally-, electrically- and magnetically- induced release are described in detail. The recent patents on various delivery systems which release the active compounds only with the external stimuli are described in detail. Keywords: Pulsatile release, triggered release, bioactive compounds, reservoir devices, thermo-responsive, electro-responsive
Whangamata Beachcare - Evaluation of a Participatory Approach to Common Property Management (1997)

Beachcare is a community participation dune management program in the Waikato region of the North Island of New Zealand. The groups aim to promote sustainable coastal management by design and implementation of appropriate dune management programmes, to act as a vehicle for promoting increased community awareness and participation, and to promote a dune care ethic in the wider community. This paper presents an evaluation of the effectiveness of one of these groups, Whangamata Beachcare, in promoting increased community awareness and appropriate attitudinal and behavioural changes. Despite the fact that this group is the one experiencing the most difficulties in the Waikato Region, community surveys revealed a high level of support (>97%) for community based coastal management and a high level of willingness to be involved in (37%) and informed about (53%) such work. Also, considerable dissatisfaction with the present level of community participation in coastal management. There is also evidence, that despite present limitations, the group has impacted positively on community awareness of coastal management issues and has promoted appropriate changes in community attitudes and behaviour - particularly among local residents. Overall, the survey results indicate strong community desire and support for common property management regimes such as Beachcare and also suggest that such management approaches have considerable potential to facilitate increased community ownership of and responsibility for coastal management. However, it is also clear from the surveys that Whangamata Beachcare has to address a number of issues if it is to realise the potential of community participation in common property management. In the current political climate of increasing privatisation of public resources, the Beachcare program stands as an example of what can be achieved by facilitating public involvement and consultation in common property management.
Specificity and function of immunoglobulin superfamily NK cell inhibitory and stimulatory receptors (1997)

Human NK cells express clonally distributed receptors specific for HLA-A, -B and -C molecules. These receptors belong to the immunoglobulin superfamily and can be functionally distinguished as inhibitory or stimulatory. Inhibitory receptors block NK-cell-mediated cytotoxicity upon binding to HLA class I ligands. This function is mediated by phosphorylation of cytoplasmic tyrosines, which recruit the protein tyrosine phosphatase SHP-1. Stimulatory receptors also bind HLA class I, lack cytoplasmic tyrosine-based motifs, and trigger NK cytotoxicity and proliferation. Both types of receptor are characterized by a limited diversity allowing for recognition of distinct class I supertypic epitopes. This limited diversity is counterbalanced by the expression of different combinations of inhibitory and stimulatory receptors with self and/or non-self HLA class I specificities on distinct NK cell clones. This peculiar strategy allows NK cells to detect loss of MHC class I molecules on autologous transformed and virally infected cells with maximal sensitivity.
Acoustic control of suspended particles in micro fluidic chips (2004)

A method to separate suspended particles from their medium in a continuous mode at microchip level is described. The method combines an ultrasonic standing wave field with the extreme laminar flow properties obtained in a silicon micro channel. The channel was 750 microm wide and 250 microm deep with vertical side walls defined by anisotropic wet etching. The suspension comprised "Orgasol 5 microm" polyamide spheres and distilled water. The channel was perfused by applying an under pressure (suction) to the outlets. The channel was ultrasonically actuated from the back side of the chip by a piezoceramic plate. When operating the acoustic separator at the fundamental resonance frequency the acoustic forces were not strong enough to focus the particles into a well defined single band in the centre of the channel. The frequency was therefore changed to about 2 MHz, the first harmonic with two pressure nodes in the standing wave, and consequently two lines of particles were formed which were collected via the side outlets. Two different microchip separator designs were investigated with exit channels branching off from the separation channel at angles of 90 degrees and 45 degrees respectively. The 45 degrees separator displayed the most optimal fluid dynamic properties and 90% of the particles were gathered in 2/3 of the original fluid volume.
Sequence conservation in the α and β subunits of pyruvate dehydrogenase and its similarity to branched‐chain α‐keto acid dehydrogenase (1991)

Amino acid sequence comparison of 8 alpha and 6 beta subunits of the alpha-keto acid dehydrogenase (E1) component of the pyruvate dehydrogenase complex and branched-chain alpha-keto acid dehydrogenase complex form multiple species was performed by computer analysis. In addition to 2 previously recognized regions of homology in the alpha subunit, a 3rd region of extensive homology was identified in E1 alpha, and may be one of the sites involved in subunit interaction. E1 beta contains 4 regions of extensive homology. Region 1 contains 10 amino acids that are homologous to a 10-amino acid stretch in Escherichia coli E1. Regions 2 and 3 have sequence homologies with other dehydrogenases suggesting that these regions may be involved in catalysis.
Template-based learning of grasp selection (2012)

The ability to grasp unknown objects is an important skill for personal robots, which has been addressed by many present and past research projects, but still remains an open problem. A crucial aspect of grasping is choosing an appropriate grasp configuration, i.e. the 6d pose of the hand relative to the object and its finger configuration. Finding feasible grasp configurations for novel objects, however, is challenging because of the huge variety in shape and size of these objects. Moreover, possible configurations also depend on the specific kinematics of the robotic arm and hand in use. In this paper, we introduce a new grasp selection algorithm able to find object grasp poses based on previously demonstrated grasps. Assuming that objects with similar shapes can be grasped in a similar way, we associate to each demonstrated grasp a grasp template. The template is a local shape descriptor for a possible grasp pose and is constructed using 3d information from depth sensors. For each new object to grasp, the algorithm then finds the best grasp candidate in the library of templates. The grasp selection is also able to improve over time using the information of previous grasp attempts to adapt the ranking of the templates. We tested the algorithm on two different platforms, the Willow Garage PR2 and the Barrett WAM arm which have very different hands. Our results show that the algorithm is able to find good grasp configurations for a large set of objects from a relatively small set of demonstrations, and does indeed improve its performance over time.
Direct Synthesis of Amides from Alcohols and Amines with Liberation of H 2 (2007)

Given the widespread importance of amides in biochemical and chemical systems, an efficient synthesis that avoids wasteful use of stoichiometric coupling reagents or corrosive acidic and basic media is highly desirable. We report a reaction in which primary amines are directly acylated by equimolar amounts of alcohols to produce amides and molecular hydrogen (the only products) in high yields and high turnover numbers. This reaction is catalyzed by a ruthenium complex based on a dearomatized PNN-type ligand [where PNN is 2-(di-tert-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine], and no base or acid promoters are required. Use of primary diamines in the reaction leads to bis-amides, whereas with a mixed primary-secondary amine substrate, chemoselective acylation of the primary amine group takes place. The proposed mechanism involves dehydrogenation of hemiaminal intermediates formed by the reaction of an aldehyde intermediate with the amine.
B-1 and B-2 Cell–Derived Immunoglobulin M Antibodies Are Nonredundant Components of the Protective Response to Influenza Virus Infection (2000)

We have studied the role of secreted immunoglobulin (Ig)M in protection from infection with influenza virus and delineated the relative contributions of B-1 versus B-2 cell-derived IgM in this process. Mice deficient in secreted IgM but capable of expressing surface IgM and secreting other Ig classes show significantly reduced virus clearance and survival rates compared with wild-type controls. Irradiation chimeras in which only either B-1 or B-2 cells lack the ability to secrete IgM show mortality rates similar to those of mice in which neither B-1 nor B-2 cells secrete IgM. Dependence on both sources of IgM for survival is partially explained by findings in allotype chimeras that broadly cross-reactive B-1 cell-derived natural IgM is present before infection, whereas virus strain-specific, B-2 cell-derived IgM appears only after infection. Furthermore, lack of IgM secreted from one or both sources significantly impairs the antiviral IgG response. Reconstitution of chimeras lacking B-1 cell-derived IgM only with IgM-containing serum from noninfected mice improved both survival rates and serum levels of virus-specific IgG. Thus, virus-induced IgM must be secreted in the presence of natural IgM for efficient induction of specific IgG and for immune protection, identifying B-1 and B-2 cell-derived IgM antibodies as nonredundant components of the antiviral response.