gebhart/patrepeval huggingface dataset:
The abundant retinal protein of the Chlamydomonas eye is not the photoreceptor for phototaxis and photophobic responses (2001)

The chlamyopsin gene (cop) encodes the most abundant eyespot protein in the unicellular green alga Chlamydomonas reinhardtii. This opsin-related protein (COP) binds retinal and was thought to be the photoreceptor controlling photomovement responses via a set of photoreceptor currents. Unfortunately, opsin-deficient mutants are not available and targeted disruption of non-selectable nuclear genes is not yet possible in any green alga. Here we show that intron-containing gene fragments directly linked to their intron-less antisense counterpart provide efficient post-transcriptional gene silencing (PTGS) in C. reinhardtii, thus allowing an efficient reduction of a specific gene product in a green alga. In opsin-deprived transformants, flash-induced photoreceptor currents (PC) are left unchanged. Moreover, photophobic responses as studied by motion analysis and phototaxis tested in a light-scattering assay were indistinguishable from the responses of untransformed wild-type cells. We conclude that phototaxis and photophobic responses in C. reinhardtii are triggered by an as yet unidentified rhodopsin species.
MODELING OF LIQUID HYDROCARBON FUEL PRODUCTION FROM PALM OIL VIA CATALYTIC CRACKING USING MCM-41 AS CATALYST (2015)

The objective of this study was to determine the reaction kinetics of the catalytic cracking of palm oil over MCM-41 as a catalyst at the higher C/O ratio and WHSV. The kinetic values obtained from this study can be used further for industrial purpose. In this study, palm oil was cracked using MCM-41 as a catalyst in a fixed bed micro-reactor. The experiment was conducted at the atmospheric pressure, with reaction temperature of 623.15 K, 673.15, and 723.15 K, Weight Hourly Space Velocity (WHSV) of 15, 17.5, 20, 22.5, 25, 27.5, and 30 h-1, and C/O (catalyst/oil) ratio of 1:32.5. The kinetic model used in this study was the three-lump model developed by Weekman, which involves parallel cracking of palm oil to Organic Liquid Product (OLP) and gas plus coke, with consecutive cracking of the OLP to gas plus coke. The model can represent the experimental data fairly well. From the study, the rate constant values k1, k2, k3 for reaction temperature of 623.15 K were found to be 9.499, 1.8967 and 0.15565 h-1, respectively. For reaction temperature of 673.15 K, the rate constant values were 20.0674, 3.9725 and 0.6330 h-1. For reaction temperature of 723.15 K, the rate constant values were 28.5494, 5.1498 and 0.6768 h-1. Using the Arrhenius equation, the activation energy is 41.5000, 37.7800 and 12.7437 kJ/mol for E1, E2, and E3, respectively. The pre-exponential factor k10, k20, and k30 obtained using the same equations were 30091.6, 2971.14 and 5.82 h-1, respectively.
Isomerisation of allyl ethers catalysed by the cationic iridium complex [Ir(cyclo-octa-1,5-diene)(PMePh2)2]PF6. A highly stereoselective route to trans-propenyl ethers (1978)

Allyl alkyl (and aryl) ethers are isomerised by H2-activated [Ir(cyclo-octa-1,5-diene)(PMePh2)2]PF6 in tetrahydrofuran or dioxan at room temperature to the corresponding trans-propenyl ethers (yields 95%; stereoselectivity 97%).
Complete Nucleotide Sequences of Two Adjacent Early Vaccinia Virus Genes Located Within the Inverted Terminal Repetition (1982)

The proximal part of the 10,000-base pair (bp) inverted terminal repetition of vaccinia virus DNA encodes at least three early mRNAs. A 2,236-bp segment of the repetition was sequenced to characterize two of the genes. This task was facilitated by constructing a series of recombinants containing overlapping deletions; oligonucleotide linkers with synthetic restriction sites provided points for radioactive labeling before sequencing by the chemical degradation method of Maxam and Gilbert (Methods Enzymol. 65:499-560, 1980). The ends of the transcripts were mapped by hybridizing labeled DNA fragments to early viral RNA and resolving nuclease S1-protected fragments in sequencing gels, by sequencing cDNA clones, and from the lengths of the RNAs. The nucleotide sequences for at least 60 bp upstream of both transcriptional initiation sites are more than 80% adenine . thymine rich and contain long runs of adenines and thymines with some homology to procaryotic and eucaryotic consensus sequences. The gene transcribed in the rightward direction encodes an RNA of approximately 530 nucleotides with a single open reading frame of 420 nucleotides. Preceding the first AUG, there is a heptanucleotide that can hybridize to the 3' end of 18S rRNA with only one mismatch. The derived amino acid sequence of the protein indicated a molecular weight of 15,500. The gene transcribed in the leftward direction encodes an RNA 1,000 to 1,100 nucleotides long with an open reading frame of 996 nucleotides and a leader sequence of only 5 to 6 nucleotides. The derived amino acid sequence of this protein indicated a molecular weight of 38,500. The 3' ends of the two transcripts were located within 100 bp of each other. Although there are adenine . thymine-rich clusters near the putative transcriptional termination sites, specific AATAAA polyadenylic acid signal sequences are absent.
Potential anti-Parkinson drugs designed by receptor mapping (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotential anti-Parkinson drugs designed by receptor mappingYvonne C. Martin, Charles H. Jarboe, Ruth A. Krause, Kathleen R. Lynn, Daniel Dunnigan, and James B. HollandCite this: J. Med. Chem. 1973, 16, 2, 147–150Publication Date (Print):February 1, 1973Publication History Published online1 May 2002Published inissue 1 February 1973https://pubs.acs.org/doi/10.1021/jm00260a014https://doi.org/10.1021/jm00260a014research-articleACS PublicationsRequest reuse permissionsArticle Views209Altmetric-Citations17LEARN 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
A Convenient Method for C-Azanucleosides Synthesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTA Convenient Method for C-Azanucleosides SynthesisMasataka Yokoyama, Takahiro Akiba, Yoshie Ochiai, Atsuya Momotake, and Hideo TogoView Author Information Department of Chemistry, Faculty of Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba City, Japan Cite this: J. Org. Chem. 1996, 61, 17, 6079–6082Publication Date (Web):August 23, 1996Publication History Received18 March 1996Published online23 August 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo960523ihttps://doi.org/10.1021/jo960523ibrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views853Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alkyls,Carbohydrates,Column chromatography,Cytosine,Mixtures Get e-Alerts
A Randomized Trial of E5510 versus Aspirin in Patients with Transient Ischemic Attacks (1995)

In a randomized double-blind trial, the Study Group compared the efficacy of E5510, a novel antiplatelet agent, and aspirin in preventing the recurrence of transient ischemic attacks (TIA). In total, 227 patients who suffered from TIA in the twelve weeks prior to the study were enrolled. They were randomly allocated to three treatment groups, ie, 71 patients in the E5510 4 mg group, 77 patients in the E5510 2 mg group, and 79 patients in the aspirin 324 mg group, and were treated for twelve to twenty-four weeks. The incidence of recurrent TIA or stroke was 21.5% in the aspirin group and was significantly lower in the E5510 groups, being 8.5% in the 4 mg group (P < 0.05) and 11.7% in the 2 mg group (P < 0.05). Adverse events were observed in 5 cases in the 4 mg group, in 8 cases in the 2 mg group, and in 10 cases in the aspirin group, but none of them were serious. Since safety was judged to be comparable among the three groups, E5510 appears to be an antiplatelet agent for the treatment of TIA with a clinical benefit over aspirin.
Remarks about protein structure precision (1999)

Full-matrix least squares is taken as the basis for an examination of protein structure precision. A two-atom protein model is used to compare the precisions of unrestrained and restrained refinements. In this model, restrained refinement determines a bond length which is the weighted mean of the unrestrained diffraction-only length and the geometric dictionary length. Data of 0.94 A resolution for the 237-residue protein concanavalin A are used in unrestrained and restrained full-matrix inversions to provide standard uncertainties sigma(r) for positions and sigma(l) for bond lengths. sigma(r) is as small as 0.01 A for atoms with low Debye B values but increases strongly with B. The results emphasize the distinction between unrestrained and restrained refinements and between sigma(r) and sigma(l). Other full-matrix inversions are reported. Such inversions require massive calculations. Several approximate methods are examined and compared critically. These include a Fourier map formula [Cruickshank (1949). Acta Cryst. 2, 65-82], Luzzati plots [Luzzati (1952). Acta Cryst. 5, 802-810] and a new diffraction-component precision index (DPI). The DPI estimate of sigma(r, Bavg) is given by a simple formula. It uses R or Rfree and is based on a very rough approximation to the least-squares method. Many examples show its usefulness as a precision comparator for high- and low-resolution structures. The effect of restraints as resolution varies is examined. More regular use of full-matrix inversion is urged to establish positional precision and hence the precision of non-dictionary distances in both high- and low-resolution structures. Failing this, parameter blocks for representative residues and their neighbours should be inverted to gain a general idea of sigma(r) as a function of B. The whole discussion is subject to some caveats about the effects of disordered regions in the crystal.
Nerve growth factor: Increased angiogenesis without improved nerve regeneration (1991)

Nerve growth factor (NGF) and laminin are important factors for neural development and regeneration. We examined the effects of increasing the local concentration and duration of action of NGF and laminin on peripheral nerve regeneration in the adult mouse sciatic nerve. A Silastic (silicone rubber) channel with intraluminal NGF solution was secured between transected nerve ends. The second channel tested, formed from a polysaccharide called chitosan, was prepared with NGF and laminin in the channel walls and provided a sustained release of NGF. At six weeks post-implantation, no improvement in nerve regeneration was identified in those channels prepared with NGF when comparing electromyographic thresholds (microA), maximum potentials (mV), nerve diameter, myelin sheath thickness, myelinated axon counts, or diameter. However, increased angiogenesis was demonstrated within the chitosan and Silastic channels prepared with NGF compared to those channels without NGF. Silastic exhibited minimal inflammation. Chitosan was associated with inflammation in many nerve channels.
Quantification of gliadin levels to the picogram level by flow cytometry (2005)

There is a growing concern that gliadin, even when present in gluten-free foods within the limit fixed by the Codex Alimentarius, over the long term may become toxic to patients with celiac disease. The techniques described in this study provide an opportunity to further decrease the acceptable limit of gliadin in gluten-free foods.
Neuron-to-neuron wild-type Tau protein transfer through a trans-synaptic mechanism: relevance to sporadic tauopathies (2014)

Taken together, these results support a novel mechanism for Tau protein transfer compared to previous reports based on transgenic models with mutant cDNA. It also demonstrates that mutant Tau proteins are not suitable for the development of experimental models helpful to validate therapeutic intervention interfering with Tau spreading.
Polymeric integrated circuits and light-emitting diodes (2002)

All-polymer flexible integrated circuits have been fabricated using a potentially low-cost technology. Combination with commodity anti-theft stickers has led to functional radio frequent identification transponders. Polymeric light-emitting diodes (PLEDs) opened the way to cost efficient, large area display-applications. Directions for further enhancement of their performance are presented.
Aromatic retinoic acid analogs. Synthesis and pharmacological activity (1981)

Aromatic analogues of (all-E)- and 13(Z)-retinoic acids have been synthesized as potential chemopreventive agents for the treatment of epithelial cancer. In the E series, (1E,3E)-1-(4-carboxyphenyl)-2-methyl-4-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1,3- butadiene (7a), its ethyl ester 5a, and the epoxy ethyl ester 14 displayed excellent activity in the assay for the inhibition of tumor promotor-induced mouse epidermal ornithine decarboxylase, while (1E,3E)-1-(4-carboethoxy-3-methylphenyl)-2-methyl-4-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1,3-butadiene (5b) was inactive. The 13(Z) analogues, (E)-1-(2-carboxyphenyl)-4-methyl-6-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1,3,5-he xatriene (19) and (E)-1-(2-hydroxyphenyl)-4-methyl-6-(2,6,6-trimethyl-1-cyclohexen-1-yl)-1,3,5-he xatriene (27), had minimal activity.
Nonmyristoylated p60v-src fails to phosphorylate proteins of 115-120 kDa in chicken embryo fibroblasts. (1988)

We have used anti-phosphotyrosine antibodies to identify a large number of tyrosine phosphoproteins in Rous sarcoma virus (RSV)-transformed chicken embryo fibroblasts. Most of these proteins were found in the 100,000 X g supernatant when cells were separated into soluble and particulate fractions; however, one group of proteins, of 115-120 kDa, was found in the particulate fraction. The phosphotyrosine content of the 115- to 120-kDa proteins was greatly reduced in chicken embryo fibroblasts infected with mutants of RSV (NY314 and SD10) encoding nonmyristoylated forms of the viral src gene product that do not associate with cellular membranes. Since RSV mutants NY314 and SD10 do not transform cells, phosphorylation of this group of 115- to 120-kDa membrane proteins may be related to the process of transformation.
Differentiation of a stem cell line toward a neuronal phenotype (1991)

This study examined the morphology and the development of inward currents in the course of differentiation of a stem cell toward a neuronal phenotype. Using the P19 embryonal cell line, whole-cell current profiles of P19 cells before, during and after retinoic acid-induced differentiation were matched with their morphology as well as with the expression of neuron-specific enolase-like immunoreactivity. Prior to and during the initial 48 hr of retinoic acid treatment, P19 cells either lacked detectable currents or expressed a voltage-dependent outward potassium current, did not display neuron-like morphology and did not express neuron-specific enolase-like immunoreactivity. Upon completion of retinoic acid treatment, the current profile of fully differentiated P19 cells was hallmarked by a large voltage-dependent inward current which consisted of a sodium current and a smaller cobalt-sensitive calcium component, in addition to the potassium current observed earlier. Such cells invariably emitted neurites and displayed neuron-specific enolase-like immunoreactivity. Interestingly, coupling was prevalent among P19 cells in the undifferentiated state but was absent in the fully differentiated cultures. In studying cells undergoing neuronal differentiation, these results underscore the importance of taking into account both electrical properties and morphological considerations in determining the degree of differentiation.
PSY/JD: An Advisory System for Legal Aspects of Decision Making in the Psychiatric Emergency Room (1990)

The application of legal knowledge to clinical decision making receives little attention in the traditional medical-school curriculum. Physicians-in-training often feel unprepared to handle clinical situations that involve contact with the judicial system. PSY/JD is a prototype rule-based expert system for advising psychiatrists on the legal aspects of emergency-room admissions, discharges, and referrals. The difficulties encountered in designing a rule-based representation for knowledge at the interface between law and psychiatry present opportunities for exploring case-based representations and other techniques which may facilitate the incorporation of commonsense knowledge into computer-based reasoning systems.
Protocol for the examination of specimens from patients with ductal carcinoma in situ of the breast. (2009)

Authors Susan C. Lester, MD, PhD, FCAP* Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts Shikha Bose, MD, FCAP Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California Yunn-Yi Chen, MD, PhD, FCAP Department of Pathology, UCSF Medical Center, San Francisco, California James L. Connolly, MD, FCAP Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts Monica de Baca, MD, FCAP Physicians Laboratory, Sioux Falls, South Dakota Patrick L. Fitzgibbons, MD, FCAP Department of Pathology, St. Jude Medical Center, Fullerton, California Daniel F. Hayes, MD, Department of Medical Oncology, University of Michigan Medical Center, Ann Arbor, Michigan Celina Kleer, MD, FCAP Department of Pathology, University of Michigan Medical Center, Ann Arbor, Michigan Frances P. O’Malley, MD, FCAP Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, University of Toronto, Ontario, Canada David L. Page, MD, FCAP Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee Barbara L. Smith, MD, PhD Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts Donald L. Weaver, MD, FCAP Department of Pathology, College of Medicine and Vermont Cancer Center, University of Vermont, Burlington, Vermont Eric Winer, MD Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts Jean F. Simpson, MD, FCAP† Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee For the Members of the Cancer Committee, College of American Pathologists
The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway (2004)

The primary mechanism of EGF-induced stimulation of the PI-3 kinase/Akt anti-apoptotic pathway occurs via the docking protein Gab1. However, in cells expressing ErbB3, EGF and neuroregulin can stimulate PI-3 kinase and Akt activation in a Gab1-dependent or Gab1-independent manner.
Pseudomonas aeruginosa killing of Caenorhabditis elegans used to identify P. aeruginosa virulence factors (1999)

We reported recently that the human opportunistic pathogen Pseudomonas aeruginosa strain PA14 kills Caenorhabditis elegans and that many P. aeruginosa virulence factors (genes) required for maximum virulence in mouse pathogenicity are also required for maximum killing of C. elegans. Here we report that among eight P. aeruginosa PA14 TnphoA mutants isolated that exhibited reduced killing of C. elegans, at least five also exhibited reduced virulence in mice. Three of the TnphoA mutants corresponded to the known virulence-related genes lasR, gacA, and lemA. Three of the mutants corresponded to known genes (aefA from Escherichia coli, pstP from Azotobacter vinelandii, and mtrR from Neisseria gonorrhoeae) that had not been shown previously to play a role in pathogenesis, and two of the mutants contained TnphoA inserted into novel sequences. These data indicate that the killing of C. elegans by P. aeruginosa can be exploited to identify novel P. aeruginosa virulence factors important for mammalian pathogenesis.
Studying the use of popular destinations to enhance web search interaction (2007)

We present a novel Web search interaction feature which, for a given query, provides links to websites frequently visited by other users with similar information needs. These popular destinations complement traditional search results, allowing direct navigation to authoritative resources for the query topic. Destinations are identified using the history of search and browsing behavior of many users over an extended time period, whose collective behavior provides a basis for computing source authority. We describe a user study which compared the suggestion of destinations with the previously proposed suggestion of related queries, as well as with traditional, unaided Web search. Results show that search enhanced by destination suggestions outperforms other systems for exploratory tasks, with best performance obtained from mining past user behavior at query-level granularity.
Human Nuclear NAD + ADP-Ribosyltransferase(polymerizing): Organization of the Gene (1989)

Human nuclear NAD+: protein ADP-ribosyltransferase(polymerizing) [pADPRT; poly(ADP-ribose)poly-merase; EC 2.4.2.30] is a DNA-dependent protein-modifying enzyme composed of several domains important for DNA binding, automodification, and NAD binding. We report that the human pADPRT gene is 43 kb in length and is split into 23 exons. All the intron-exon boundaries correspond to a canonical splice consensus sequence. Each of the four metal coordinating sites putatively forming the two zinc fingers of the DNA-binding domain is encoded separately. The automodification domain and the NAD-binding domain are coded for by 4 and 12 exons, respectively.