gebhart/patrepeval huggingface dataset:
Selective hydrogenations promoted by copper catalysts. 1. Chemoselectivity, regioselectivity, and stereoselectivity in the hydrogenation of 3-substituted steroids (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective hydrogenations promoted by copper catalysts. 1. Chemoselectivity, regioselectivity, and stereoselectivity in the hydrogenation of 3-substituted steroidsNicletta Ravasio and Michele RossiCite this: J. Org. Chem. 1991, 56, 13, 4329–4333Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/jo00013a054https://doi.org/10.1021/jo00013a054research-articleACS PublicationsRequest reuse permissionsArticle Views745Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
RhoA‐kinase and myosin II are required for the maintenance of growth cone polarity and guidance by nerve growth factor (2006)

Growth cones are highly polarized and dynamic structures confined to the tips of axons. The polarity of growth cones is in part maintained by suppression of protrusive activity from the distal axon shaft, a process termed axon consolidation. The mechanistic basis of axon consolidation that contributes to the maintenance of growth cone polarity is not clear. We report that inhibition of RhoA-kinase (ROCK) or myosin II resulted in unstable consolidation of the distal axon as evidenced by increased filopodial and lamellipodial extension. Furthermore, when ROCK or myosin II was inhibited lamellipodia formed at the growth cone migrated onto the axon shaft. Analysis of EYFP-actin dynamics in the distal axon revealed that ROCK negatively regulates actin polymerization and initiation of protrusive structures from spontaneously formed axonal F-actin patches, the latter being an effect attributable to ROCK-mediated regulation of myosin II. Inhibition of ROCK or myosin II blocked growth cone turning toward NGF by preventing suppression of protrusive activity away from the source of NGF, resulting in aborted turning responses. These data elucidate the mechanism of growth cone polarity, provide evidence that consolidation of the distal axon is a component of guidance, and identify ROCK as a negative regulator of F-actin polymerization underlying protrusive activity in the distal axon.
Gene expression of neural cell adhesion molecule L1 in malignant gliomas and biological significance of L1 in glioma invasion. (1996)

Neural cell adhesion molecule L1 is a member of the immunoglobulin superfamily that is expressed in the nervous system. Its functions have been mainly studied in vitro using premature neuronal cells. We show that all glioma cells tested, as well as normal glia cells, express a short type of L1, L1cs mRNA. The expression of L1 protein in glioma cells was confirmed by Western blotting and flow cytometric analysis. Migration assay showed that C6 glioma cells were stimulated to migrate to soluble L1 and L1cs released from L1- or L1cs-transfected fibroblast cells. The L1-stimulated migration was significantly inhibited by antibody that recognizes the immunoglobulin C2-like domain of L1. However, antibodies that recognize the fibronectin type III-like domain and the cytoplasmic (IC) domain of L1 had no effect on migration. Our in vivo migration study demonstrated the migration of L1 on C6 glioma cells that had been transfected in rat brains. These results suggest that L1cs expressed on glioma cells may play an important role in the adhesion and migration of glioma cells by homophilic binding (probably through the extracellular immunoglobulin C2 domain of L1) and that L1cs participates in tumor invasion along neuronal fibers.
Fast label-free multilayered histology-like imaging of human breast cancer by photoacoustic microscopy (2017)

The goal of breast-conserving surgery is to completely remove all of the cancer. Currently, no intraoperative tools can microscopically analyze the entire lumpectomy specimen, which results in 20 to 60% of patients undergoing second surgeries to achieve clear margins. To address this critical need, we have laid the foundation for the development of a device that could allow accurate intraoperative margin assessment. We demonstrate that by taking advantage of the intrinsic optical contrast of breast tissue, photoacoustic microscopy (PAM) can achieve multilayered histology-like imaging of the tissue surface. The high correlation of the PAM images to the conventional histologic images allows rapid computations of diagnostic features such as nuclear size and packing density, potentially identifying small clusters of cancer cells. Because PAM does not require tissue processing or staining, it can be performed promptly and intraoperatively, enabling immediate directed re-excision and reducing the number of second surgeries.
T cell priming by dendritic cells: thresholds for proliferation, differentiation and death and intraclonal functional diversification (2002)

The variables that influence priming of human naive CD4+ T cells by dendritic cells (DC) were dissected in vitro by analyzing the response to the bacterial superantigen toxicshock syndrome toxin or to alloantigens. We show that under conditions that force DC-T cell interactions a single DC can prime up to 20 naive T cells. Moreover, the strength of antigenic stimulation, as determined by DC numbers, antigen dose, TCR avidity and duration of DC-T cell interactions, drives the progressive differentiation of proliferating T cells from a non-effector CCR7+ stage, to an effector CCR7- stage and, eventually, to cell death. We also show that the proliferating CCR7+ and CCR7- populations share clonotypic sequences, demonstrating that the two cell fates can be generated within a single clone. Taken together these results indicate that the strength of antigenic stimulation regulates T cell progression through thresholds of proliferation, differentiation and death. However, the random nature of DC-T cell encounters introduces a critical stochastic element in T cell stimulation, which leads to the generation of cells endowed with distinct homing potentials and effector functions within a given T cell clone.
Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis (2002)

Fabrication of high density oligonucleotide arrays using metal on glass photolithographic masks is inflexible and expensive. Maskless methods using computer-controlled projection have been proposed and implemented, but associated stray light effects on photodirected oligonucleotide synthesis and their analysis have not been reported. We have developed a theoretical approach: it predicts that the stray light content of the output of digital micromirror devices and other spatial light modulators of similar performance (contrast ratio approximately 400) will cause extensive random base insertions. For example, use of a digital micromirror device for synthesis of a 20mer array will result in the majority of oligonucleotide chains being 21mers or 22mers. This chain lengthening effect of stray light would not be preventable when synthesis involves a directly photosensitive 5'-blocking group. If the 5'-blocking group is acid labile and released with photogenerated acid, the presence of low concentrations of weak base will prevent the effect of stray light. We have demonstrated experimentally the anticipated chain lengthening effect of stray light on photoacid-dependent synthesis of oligonucleotides and prevention of the effect by low concentrations of n-octylamine. The application of these findings should facilitate the development of maskless fabrication and availability of high density and high fidelity user-designed arrays for research applications.
Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics (2012)

The rigorous testing of hypotheses on suitable sample cohorts is a major limitation in translational research. This is particularly the case for the validation of protein biomarkers; the lack of accurate, reproducible, and sensitive assays for most proteins has precluded the systematic assessment of hundreds of potential marker proteins described in the literature. Here, we describe a high-throughput method for the development and refinement of selected reaction monitoring (SRM) assays for human proteins. The method was applied to generate such assays for more than 1000 cancer-associated proteins, which are functionally related to candidate cancer driver mutations. We used the assays to determine the detectability of the target proteins in two clinically relevant samples: plasma and urine. One hundred eighty-two proteins were detected in depleted plasma, spanning five orders of magnitude in abundance and reaching below a concentration of 10 ng/ml. The narrower concentration range of proteins in urine allowed the detection of 408 proteins. Moreover, we demonstrate that these SRM assays allow reproducible quantification by monitoring 34 biomarker candidates across 83 patient plasma samples. Through public access to the entire assay library, researchers will be able to target their cancer-associated proteins of interest in any sample type using the detectability information in plasma and urine as a guide. The generated expandable reference map of SRM assays for cancer-associated proteins will be a valuable resource for accelerating and planning biomarker verification studies.
Photochemical decomposition of geminal diazides. I. Dimethyl diazidomalonate (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemical decomposition of geminal diazides. I. Dimethyl diazidomalonateKevin M. Moriarty, Jonathan M. Kliegman, and Catherine. ShovlinCite this: J. Am. Chem. Soc. 1967, 89, 23, 5958–5959Publication Date (Print):November 1, 1967Publication History Published online1 May 2002Published inissue 1 November 1967https://pubs.acs.org/doi/10.1021/ja00999a042https://doi.org/10.1021/ja00999a042research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-Citations31LEARN 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
Synchronous selection of homing peptides for multiple tissues byin vivophage display (2006)

In vivo phage display is a technology used to reveal organ-specific vascular ligand-receptor systems in animal models and, recently, in patients, and to validate them as potential therapy targets. Here, we devised an efficient approach to simultaneously screen phage display libraries for peptides homing to any number of tissues without the need for an individual subject for each target tissue. We tested this approach in mice by selecting homing peptides for six different organs in a single screen and prioritizing them by using software compiled for statistical validation of peptide biodistribution specificity. We identified a number of motif-containing biological candidates for ligands binding to organ-selective receptors based on similarity of the selected peptide motifs to mouse proteins. To demonstrate that this methodology can lead to targetable ligand-receptor systems, we validated one of the pancreas-homing peptides as a mimic peptide of natural prolactin receptor ligands. This new comprehensive strategy for screening phage libraries in vivo provides an advantage over the conventional approach because multiple organs internally control for organ selectivity of each other in the successive rounds of selection. It may prove particularly relevant for patient studies, allowing efficient high-throughput selection of targeting ligands for multiple organs in a single screen.
The Fluid Mechanics of Large Blood Vessels (1980)

1. Physiological introduction 2. Propagation of the pressure pulse 3. Flow patterns and wall shear stress in arteries I Straight tubes 4. Flow patterns and wall shear stress in arteries II. Curved tubes 5. Flow patterns and wall shear stress in arteries III. Branched tubes and flow instability 6. Flow in collapsible tubes.
Reversal of T4 RNA ligase (1982)

Unexpected products detected in oligoribonucleotide synthesis reactions catalyzed by T4 RNA ligase are shown to be a result of a partial reversal of the enzyme reaction. A transfer assay for the reversal of the third step in the RNA ligase reaction mechanism and an exchange assay for the reversal of both the second and third steps are described. Reversal is confirmed by the formation of the expected covalent intermediates, adenylylated donor and adenylyl ligase, from a reaction containing 5'-AMP, unadenylylated ligase, and the tetranucleotide (Ap)3Cp. In the reverse reaction, RNA ligase shows a strong preference for hydrolysis of the 3'-terminal phosphodiester bonds of oligoribonucleotides which terminate in a 3'-phosphate. Several strategies are discussed to minimize the effects of reversal in the enzymatic synthesis of oligoribonucleotides.
The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A (1997)

Development of effective drugs against the rhinovirus (HRV) responsible for the common cold remains a challenge because there are over 100 serotypes. This process could be significantly aided by an understanding of the atomistic mechanism by which such drugs work. We suggest that the most effective drugs against HRV-1A act by stiffening the pentamer channel of the viral coat through which the RNA is released, preventing the steps leading to uncoating. Using molecular dynamics methods we tested this Pentamer Channel Stiffening Model (PCSM) by examining the changes in strain energy associated with opening the pentamer channel through which the RNA is released. We find that the PCSM strain correlates well with the effectiveness of the WIN (Sterling-Winthrop) drugs for HRV-1A. To illustrate the use of the PCSM to predict new drugs and to prioritize experimental tests, we tested three modifications of the WIN drugs that are predicted to be nearly as effective (for HRV-1A) as the best current drug.
Cyclic hydroxamic-acid-containing peptide 31, a potent synthetic histone deacetylase inhibitor with antitumor activity. (2001)

Cyclic hydroxamic-acid-containing peptide 1 (CHAP1), designed as a hybrid of trichostatin A and trapoxin, is a lead compound for the development of potent inhibitors of histone deacetylase (HDAC). In this study, we synthesized a series of CHAP derivatives and evaluated their biological activities by monitoring the potency of their inhibition of HDAC activity, their ability to augment the expression of MHC class-I molecules in B16/BL6 cells, and their effect on cell proliferation. A structure-activity relationship study using these three assay systems revealed several requirements of their structure for the strong inhibition of HDAC not only in the cell-free situation, but also in cells. When the structures of CHAP derivatives are represented as cyclo(-Asu(NHOH)-AA(2)-AA(3)-Pro or Pip-)(n), where Asu(NHOH) and Pip are zeta-hydroxamide-alpha-aminosuberic acid and pipecolic acid, respectively, (a) the tetrapeptide structure (n = 1) was better than the octapeptide one (n = 2); (b) AA(2) and AA(3) should be hydrophobic; and (c) the combination of amino acid chirality should be LDLD for the strongest inhibition of HDAC in cells (LDLD > LLLD, LDLL > LLDL). cyclo(-L-Asu(NHOH)-D-Tyr(Me)-L-Ile-D-Pro-) or CHAP31 was selected as one of the strongest CHAPs, and its biological activity was characterized further. CHAP31 was much more stable in the presence of cultured cells (t(1/2) > 3000 h) than trichostatin A (t(1/2) = 14.7 h) or trapoxin A (t(1/2) = 2.10 h). CHAP31 exhibited antitumor activity in C57BL x DBA/2 F(1) (BD2F(1)) mice bearing B16/BL6 tumor cells. Furthermore, CHAP31 inhibited the growth in four of five human tumor lines implanted into nude mice. These results suggest CHAP31 to be promising as a novel therapeutic agent for cancer treatment.
Investigation of the synthesis of ortho-substituted tetraphenylporphyrins (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInvestigation of the synthesis of ortho-substituted tetraphenylporphyrinsJonathan S. Lindsey and Richard W. WagnerCite this: J. Org. Chem. 1989, 54, 4, 828–836Publication Date (Print):February 1, 1989Publication History Published online1 May 2002Published inissue 1 February 1989https://pubs.acs.org/doi/10.1021/jo00265a021https://doi.org/10.1021/jo00265a021research-articleACS PublicationsRequest reuse permissionsArticle Views8398Altmetric-Citations623LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Chapter 1 Vehicle routing (1995)

This chapter presents the most important algorithms that have been developed for model of the vehicle routing problem. However, before plunging into the mathematical development, it will be helpful to consider some examples of vehicle routing problems and various practical issues that arise in the use of vehicle routing models. Vehicle routing problems are all around us in the sense that many consumer products such as soft drinks, beer, bread, snack foods, gasoline and pharmaceuticals are delivered to retail outlets by fleets of trucks whose operation fits the vehicle routing model. Other examples of vehicle routing problems include the delivery of liquefied industrial gases and the collection of milk from farms for transportation to a processing center. Many companies have reported successful implementation of mathematical algorithms to optimize trucking operations including Air Products and Chemicals, Chevron, DuPont, Edward Don and Company etc. Two approaches have been taken to providing geographic information. The first approach is easy to implement and thus preferred if it is accurate enough. It consists of assigning coordinates to each customer and assuming that the travel distance between customers is the Euclidean distance between their coordinate pairs. Cost is taken to be proportional to distance. The distance is often scaled up by a factor to compensate for roads that deviate from a straight-line path between customers. The second approach obtains travel distances by applying a shortest route algorithm to a computerized network model of the road system.
Demonstration of Sufficient Control for Two Rounds of Quantum Error Correction in a Solid State Ensemble Quantum Information Processor (2011)

We report the implementation of a 3-qubit quantum error-correction code on a quantum information processor realized by the magnetic resonance of carbon nuclei in a single crystal of malonic acid. The code corrects for phase errors induced on the qubits due to imperfect decoupling of the magnetic environment represented by nearby spins, as well as unwanted evolution under the internal Hamiltonian. We also experimentally demonstrate sufficiently high-fidelity control to implement two rounds of quantum error correction. This is a demonstration of state-of-the-art control in solid state nuclear magnetic resonance, a leading test bed for the implementation of quantum algorithms.
Proteomic analysis of RCL2 paraffin‐embedded tissues (2008)

Histopathological diagnosis in most of the world's hospitals is based upon formalin-fixed and paraffin-embedded (FFPE) tissues. Although this standard fixation and embedding procedure keeps the tissue in excellent form for morphological and immunohistological analysis, FFPE is inappropriate for nucleic acids and protein studies. We investigated the potential value of RCL2, a new non-toxic fixative, for sparing proteins preserved in paraffin-embedded tissues. Normal colonic mucosa tissue was fixed in RCL2 prior to paraffin embedding (RCL2P), and then processed for quality and quantity of protein conservation, as compared to frozen and FFPE tissues using complementary proteomic analysis approaches. Using 4 different protein extraction protocols, RCL2P tissue consistently showed the highest protein yield. Similar protein patterns were observed with RCL2P and frozen tissues using mono and bi-dimensional electrophoresis. Moreover, membrane, cytoplasmic and nuclear proteins, as well as phosphorylated proteins, were successfully detected using western-blot. Furthermore, protein patterns observed by mass spectrometry analysis after laser-captured microdissection were found to be identical for frozen and RCL2-fixed tissues. At last, immunohistochemistry using various antibodies showed comparable results between both tissue storage methods. We concluded that RCL2 has great potential for performing both morphological and molecular analyses on the same archival paraffin-embedded tissue sample, and can be a new method for investigating protein biomarkers.
New aspects in the treatment of immunomediated diseases. (1992)

The following constitutes a summary of lectures delivered during the session "New aspects in the treatment of immunomediated diseases" which was held during the 25th Annual Scientific Meeting of the European Society for Clinical Investigation in Pisa, Italy on 6th April 1991. The aim of this session was to present and discuss some of the novel therapeutic modalities currently being employed either in experimental models or in phase I clinical studies.