gebhart/patrepeval huggingface dataset:
Chemical Biology of Lipidated Proteins (2011)

Many signaling proteins such as the members of the Ras superfamily of GTPases are posttranslationally modified by covalent attachment of lipid groups, which is crucial for the correct localization and function of these proteins. Numerous lipidated proteins are oncogens often found mutated in several human cancers. Therefore, several therapeutic strategies have been developed based on the inhibition of the enzymes involved in these lipidation steps. Here, we will summarize the results on protein lipidation inhibition, mainly focusing on the small molecules targeting the isoprenylation and acylation of proteins.
Mitochondrial succinic-semialdehyde dehydrogenase of the γ-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants (2003)

The gamma-aminobutyrate (GABA) shunt is a metabolic pathway that bypasses two steps of the tricarboxylic acid cycle, and it is present in both prokaryotes and eukaryotes. In plants the pathway is composed of the calcium/calmodulin-regulated cytosolic enzyme glutamate decarboxylase and the mitochondrial enzymes GABA transaminase and succinic-semialdehyde dehydrogenase (SSADH). The activity of the GABA shunt in plants is rapidly enhanced in response to various biotic and abiotic stresses. However the physiological role of this pathway remains obscure. To elucidate its role in plants, we analyzed Arabidopsis T-DNA knockout mutants of SSADH, the ultimate enzyme of the pathway. Four alleles of the ssadh mutation were isolated, and these exhibited a similar phenotype. When exposed to white light (100 micromol of photons per m2 per s), they appear dwarfed with necrotic lesions. Detailed spectrum analysis revealed that UV-B has the most adverse effect on the mutant phenotype, whereas photosynthetic active range light has a very little effect. The ssadh mutants are also sensitive to heat, as they develop necrosis when submitted to such stress. Moreover, both UV and heat cause a rapid increase in the levels of hydrogen peroxide in the ssadh mutants, which is associated with enhanced cell death. Surprisingly, our study also shows that trichomes are hypersensitive to stresses in ssadh mutants. Our work establishes a role for the GABA shunt in preventing the accumulation of reactive oxygen intermediates and cell death, which appears to be essential for plant defense against environmental stress.
Small cell lung cancer, endocrine cells of the fetal bronchus, and other neuroendocrine cells express the Leu-7 antigenic determinant present on natural killer cells (1985)

Small cell lung cancer is distinguished from other lung cancer histologic types by possessing a variety of neuroendocrine properties. Anti-Leu-7 is a monoclonal antibody that recognizes a 110,000-dalton molecular weight glycoprotein initially described on natural killer cells and subsequently reported on a variety of normal and malignant neural and neuroendocrine cell types. We have found intense anti-Leu-7 binding to a large number of small cell lung cancers, while other lung cancer types were negative or showed only weak and focal binding. Other antigens expressed by natural killer cells, lymphocytes, and monocytes were never or less often expressed on small cell lung cancer cells. In addition, we report for the first time anti-Leu-7 binding by carcinoids, carotid body tumors, pheochromocytomas, endocrine cells of the fetal bronchus and the adult intestine, and select pancreatic islet cells. Anti-Leu-7 binding by small cell lung cancer is consistent with a derivation from pulmonary precursor cells, and anti-Leu-7 staining is clinically useful for the identification of human neuroendocrine tumors of the amine precursor uptake and decarboxylation (“APUD”) type.
Scandium(III) Triflate-Catalyzed Friedel−Crafts Alkylation Reactions (1997)

The Sc(OTf)3-catalyzed Friedel−Crafts alkylation reaction with an alcohol, an arenecarbaldehyde or an arenecarbaldehyde acetal as the alkylating agent affords a diarylmethane or an allylbenzene derivative highly selectively. The salient feature of this reaction is that only a catalytic amount of Sc(OTf)3 can effect the reaction. Furthermore, Sc(OTf)3 is recoverable and reusable after the synthetic reaction. The Sc(OTf)3-catalyzed benzylation using an arenecarbaldehyde and 1,3-propanediol or their acetal affords diarylmethane as a sole product in excellent yields in sharp contrast to the original Friedel−Crafts reaction. Since no reaction occurs in the absence of 1,3-propanediol, the reaction is considered to proceed through a redox process including a hydride shift. The hydride shift mechanism is strongly supported by the experimental evidence. The reaction of benzaldehyde with benzene in the presence of 1,3-propanediol-1,1,3,3,-d4 gives rise to the deuterium incorporation into the benzylic carbon of diphenylmethane. Worthy of note is that 1,3-propanediol acts as the hydride source. Herein, diphenylmethyl 3-hydroxypropyl ether is assumed to be the most likely intermediate. In this reaction, Sc(OTf)3 catalyst effectively promotes initial acetal formation, electrophilic aromatic substitution, and successive intramolecular hydride transfer.
Enhanced expression of CD71, transferrin receptor, on immature reticulocytes in patients with paroxysmal nocturnal hemoglobinuria (2009)

Erythroid cells in the marrow express CD71, transferrin receptor, and reticulocytes released from the marrow lose their expression during maturation. The immature reticulocyte fraction, the proportion of reticulocytes with the highest content of RNA, has been determined by hematology analysis. In the present study, we examined CD71 expression on immature reticulocytes by flow cytometry (FCM) in paroxysmal nocturnal hemoglobinuria (PNH) patients with reticulocytosis. We modified 'reticulocyte-gated FCM' to multi-color FCM, i.e. RNA/CD71, RNA-CD59 or CD59/CD71/CD45. In PNH, in addition to the increased number of immature reticulocytes (%CD71-positive), a more immature phenotype in regard to both CD71 intensity and RNA content levels was demonstrated. In seven PNH patients studied, %CD71-positive reticulocytes were significantly increased at 32.2 +/- 11.9% (n = 10, normal 10.4 +/- 3.5%, P = 0.002). RNA content levels (assessed by mean fluorescence index, MFI) in CD71-positive reticulocytes were significantly increased at 812.0 +/- 215.2 MFI in PNH (n = 10, normal 508 +/- 86.1 MFI, P = 0.002). These data indicate that stimulated erythropoietic conditions induce the release of more immature reticulocytes to the peripheral blood than ordinary erythropoietic conditions. CD71 intensity on immature reticulocytes was well correlated with their RNA content levels, indicating the usefulness of CD71 as an immature reticulocyte marker.
Inhibition of the Androgen Receptor as a Novel Mechanism of Taxol Chemotherapy in Prostate Cancer (2009)

Taxol chemotherapy is one of the few therapeutic options for men with castration-resistant prostate cancer (CRPC). However, the working mechanisms for Taxol are not fully understood. Here, we showed that treatment of 22Rv1, a PTEN-positive CRPC cell line, with paclitaxel and its semisynthetic analogue docetaxel decreases expression of the androgen receptor (AR)-activated genes prostate-specific antigen (PSA) and Nkx3.1 but increases expression of the AR repression gene maspin, suggesting that Taxol treatment inhibits AR activity. This was further supported by the observation that the activity of AR luciferase reporter genes was inhibited by paclitaxel. In contrast, paclitaxel treatment failed to inhibit AR activity in the PTEN-null CRPC cell line C4-2. However, pretreatment of C4-2 cells with the phosphoinositide 3-kinase inhibitor LY294002 restored paclitaxel inhibition of the AR. Treatment of 22Rv1 xenografts in mice with docetaxel induced mitotic arrest and a decrease in PSA expression in tumor cells adjacent to vascular vessels. We further showed that paclitaxel induces nuclear accumulation of FOXO1, a known AR suppressive nuclear factor, and increases the association of FOXO1 with AR proteins in the nucleus. FOXO1 knockdown with small interfering RNA attenuated the inhibitory effect of paclitaxel on AR transcriptional activity, expression of PSA and Nkx3.1, and cell survival. These data reveal a previously uncharacterized, FOXO1-mediated, AR-inhibitory effect of Taxol in CRPC cells that may play an important role in Taxol-mediated inhibition of CRPC growth.
Ultrabroadband chirped mirrors for femtosecond lasers (1997)

We report on the performance of widely tunable femtosecond and continuous-wave Ti:sapphire lasers that use a newly developed ultrabroadband mirror set. The mirrors exhibit high reflectivity (R > 99%) and smooth variation of group delay versus frequency over a wavelength range from 660 to 1060 nm. Mode-locked operation with pulse durations of 85 fs was achieved from 693 to 978 nm with only one set of ultrabroadband mirrors.
THE LINKAGE OF GLUCOSE IN COLIPHAGE NUCLEIC ACIDS1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE LINKAGE OF GLUCOSE IN COLIPHAGE NUCLEIC ACIDS1Elliot VolkinCite this: J. Am. Chem. Soc. 1954, 76, 22, 5892–5893Publication Date (Print):November 1, 1954Publication History Published online1 May 2002Published inissue 1 November 1954https://pubs.acs.org/doi/10.1021/ja01651a117https://doi.org/10.1021/ja01651a117research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations68LEARN 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
Ion Channels and Gap Junctions: Their Role in Erectile Physiology, Dysfunction, and Future Therapy. (1999)

A flurry of research and clinical activity during this past decade has documented that the tonicity and synchronicity of the corporal smooth muscle cells of the penis are major determinants of erectile capacity and function. Specifically, the effects of diverse and bifurcating intracellular signal transduction pathways on the activity of nonjunctional ion channels such as potassium (K(+)), calcium (Ca(2+)), and chloride (C(1-)) govern the former, whereas intercellular communication through gap junctions provides the anatomic substrate for the latter. Recent studies at the tissue, cellular, subcellular, and molecular levels have verified this supposition and provided important insight into how subtle alterations in the balance between contraction and relaxation of the corporal smooth muscle cells can predispose a man to erectile failure. This report reviews the available information concerning the participation of gap junctions and K(+), Ca(2+), and C(1-) channels in the erectile process and describes their importance as potential molecular targets for the future therapy of erectile dysfunction (ED). It is argued that a major goal should now be to proceed on at least two fronts simultaneously: (1) to capitalize on these new mechanistic insights by developing novel treatments for ED centered on the modulation of ion channel activity; and (2) simultaneously to take advantage of the unique therapeutic opportunities afforded by the presence and ubiquitous distribution of gap junction channels in the human corpora. One strategy that fulfils both criteria will be briefly reviewed, that is, gene therapy with the maxi-K(+) channel subtype.
Globally and locally consistent image completion (2017)

We present a novel approach for image completion that results in images that are both locally and globally consistent. With a fully-convolutional neural network, we can complete images of arbitrary resolutions by filling-in missing regions of any shape. To train this image completion network to be consistent, we use global and local context discriminators that are trained to distinguish real images from completed ones. The global discriminator looks at the entire image to assess if it is coherent as a whole, while the local discriminator looks only at a small area centered at the completed region to ensure the local consistency of the generated patches. The image completion network is then trained to fool the both context discriminator networks, which requires it to generate images that are indistinguishable from real ones with regard to overall consistency as well as in details. We show that our approach can be used to complete a wide variety of scenes. Furthermore, in contrast with the patch-based approaches such as PatchMatch, our approach can generate fragments that do not appear elsewhere in the image, which allows us to naturally complete the images of objects with familiar and highly specific structures, such as faces.
Efficient Natural Language Response Suggestion for Smart Reply (2017)

This paper presents a computationally efficient machine-learned method for natural language response suggestion. Feed-forward neural networks using n-gram embedding features encode messages into vectors which are optimized to give message-response pairs a high dot-product value. An optimized search finds response suggestions. The method is evaluated in a large-scale commercial e-mail application, Inbox by Gmail. Compared to a sequence-to-sequence approach, the new system achieves the same quality at a small fraction of the computational requirements and latency.
An Improved Synthesis of Homocitrate (1998)

Monoethyl malonate (1) and tert-butyl alcohol are esterified by catalysis with dicyclohexylcarbodiimide and 4-dimethylaminopyridine to yield ethyl t-butyl malonate (2). The ethoxymagnesio derivative (3) of the ester is condensed with b-carbomethoxypropionyl chloride to give the triester (4), which is decomposed by heating under vacuum in the presence of b-naphthalensulfonic acid to give ethyl methyl β-ketoadipate (5). Compound 5 is reacted with hydrogen cyanide,followed by hydrolysis of the cyanohydrin to give the free acid (6). Compound 6 is converted to homocitrate (7) by the use of an improved procedure.
Dual-mask model-based proximity correction for high-performance 0.10-μm CMOS process (2001)

Selective strong phase shift mask techniques, whereby a phase-shift mask exposure is followed by a binary mask exposure to define a single pattern, present unique capabilities and problems. First, there is the proper exposure balance and alignment of the two masks. Second, there is the challenge of performing optical proximity correction that will account for two overlaying exposure models and masks. This is further complicated by the need to perform multiple biasing and adjustments that are often required for development processes. In this paper, we present results for applying a new OPC correction technique to a dual exposure binary and phase-shift mask that have been used for development of 100 nm CMOS processes. The correction recipe encompasses two models that were anchored to optimized processes (exposure, NA, and ?). The correction to the masks also utilized boolean techniques to perform selective biasing without destroying the original hierarchical structure. CMOS technology utilizes isolation with pitches of active device regions below 0.4 ?m. The effective gate length on silicon is in the range of 0.08 to 0.18 ?m. Patterning of trench openings and gate regions are accomplished using deep-UV lithography.
Thalidomide in actinic prurigo (1983)

Fourteen patients suffering from actinic prurigo were treated with thalidomide. Eleven patients showed lasting improvement on the drug and three of these remained symptom-free after discontinuing therapy. No major side-effects were observed. Thalidomide is an effective drug in the treatment of actinic prurigo but it must be used with adequate contraception in women of child-bearing age.
Parallel Polarization EPR Characterization of the Mn(III) Center of Oxidized Manganese Superoxide Dismutase (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTParallel Polarization EPR Characterization of the Mn(III) Center of Oxidized Manganese Superoxide DismutaseKristy A. Campbell, Emine Yikilmaz, Christopher V. Grant, Wolfgang Gregor, Anne-Frances Miller, and R. David BrittView Author Information Department of Chemistry, University of California Davis, California 95616 Departments of Chemistry and Biophysics The Johns Hopkins University,3400 North Charles Street Baltimore, Maryland 21218 Cite this: J. Am. Chem. Soc. 1999, 121, 19, 4714–4715Publication Date (Web):May 1, 1999Publication History Received22 January 1999Revised25 March 1999Published online1 May 1999Published inissue 1 May 1999https://pubs.acs.org/doi/10.1021/ja9902219https://doi.org/10.1021/ja9902219rapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1039Altmetric-Citations74LEARN 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:Electron paramagnetic resonance spectroscopy,Magnetic properties,Quantum mechanics,Temperature dependence,Transition metals Get e-Alerts
CCured: type-safe retrofitting of legacy software (2005)

This article describes CCured, a program transformation system that adds type safety guarantees to existing C programs. CCured attempts to verify statically that memory errors cannot occur, and it inserts run-time checks where static verification is insufficient.CCured extends C's type system by separating pointer types according to their usage, and it uses a surprisingly simple type inference algorithm that is able to infer the appropriate pointer kinds for existing C programs. CCured uses physical subtyping to recognize and verify a large number of type casts at compile time. Additional type casts are verified using run-time type information. CCured uses two instrumentation schemes, one that is optimized for performance and one in which metadata is stored in a separate data structure whose shape mirrors that of the original user data. This latter scheme allows instrumented programs to invoke external functions directly on the program's data without the use of a wrapper function.We have used CCured on real-world security-critical network daemons to produce instrumented versions without memory-safety vulnerabilities, and we have found several bugs in these programs. The instrumented code is efficient enough to be used in day-to-day operations.
[Digital analysis of pulmonary nodules--potential usefulness of computer-aided diagnosis for differentiation of benign from malignant nodules]. (1995)

Digital analysis of 80 plain chest radiographs was done to differentiate benign from malignant pulmonary nodules. Each of 80 radiographs had a solitary pulmonary nodule, of which 40 were benign and the other 40 were malignant. Radiographic features of nodules were visually evaluated. Frequencies of the radiographic features described below were significantly different between benign and malignant nodules: irregular shape, vague density, well-defined contour, spicular formation, and vascular convergene. To digitally evaluate the density characteristics, two kinds of concentric circular windows were used, to allow analysis of intra-nodular, marginal and surrounding regions of the nodules. Seventeen digital parameters were obtained by computerized analysis with the windows. There were significant differences in six digital parameters; three of density gradient (one of intra-nodular and two of marginal regions), one DCF-N (directional contrast filter for nodule) output of intra-nodular region, and two of density entropy values of intra-nodular and surrounding regions. Density gradient parameters of marginal regions are believed to represent the features of nodular shape and spicula formation. With these six parameters, 70% of benign nodules and 85% of malignant nodules were correctly discriminated. These results suggest that computer-aided diagnosis may be used to differentiate benign from malignant nodules.
Dental Fluorosis : A Handbook for Health Workers (1989)

Fluorides, caries and dental fluorosis - a historical perspective the features of dental fluorosis indices for measuring dental fluorosis diagnosis of dental fluorosis and the problems of differential diagnosis reporting findings and interpretation of data Factors affecting the prevalence and severity of dental fluorosis dental fluorosis and dental caries the treatment of dental fluorosis defluoridation of drinking waters dental fluorosis and the use of fluorides in caries prevention.
Places: A 10 Million Image Database for Scene Recognition (2017)

The rise of multi-million-item dataset initiatives has enabled data-hungry machine learning algorithms to reach near-human semantic classification performance at tasks such as visual object and scene recognition. Here we describe the Places Database, a repository of 10 million scene photographs, labeled with scene semantic categories, comprising a large and diverse list of the types of environments encountered in the world. Using the state-of-the-art Convolutional Neural Networks (CNNs), we provide scene classification CNNs (Places-CNNs) as baselines, that significantly outperform the previous approaches. Visualization of the CNNs trained on Places shows that object detectors emerge as an intermediate representation of scene classification. With its high-coverage and high-diversity of exemplars, the Places Database along with the Places-CNNs offer a novel resource to guide future progress on scene recognition problems.