gebhart/patrepeval huggingface dataset:
Survey on the attention based RNN model and its applications in computer vision (2016)

The recurrent neural networks (RNN) can be used to solve the sequence to sequence problem, where both the input and the output have sequential structures. Usually there are some implicit relations between the structures. However, it is hard for the common RNN model to fully explore the relations between the sequences. In this survey, we introduce some attention based RNN models which can focus on different parts of the input for each output item, in order to explore and take advantage of the implicit relations between the input and the output items. The different attention mechanisms are described in detail. We then introduce some applications in computer vision which apply the attention based RNN models. The superiority of the attention based RNN model is shown by the experimental results. At last some future research directions are given.
RNA Interference and Small Interfering RNAs (2001)

Double-stranded RNA (dsRNA) activates the sequence-specific degradation of homologous mRNAs in animal and plant cells by a process known as RNA interference (RNAi). The mediators of mRNA degradation are 21–23-nt small interfering ribonucleoprotein particles (siRNPs) which are produced from dsRNA by an RNase III-like processing reaction (see schematic picture). RNAi has rapidly become an invaluable tool for functional genomics and siRNAs are promising candidates for future biomedical applications.
Observation of quantum collapse and revival in a one-atom maser (1987)

The dynamics of the interaction of a single Rydberg atom with a single mode of an electromagnetic field in a superconducting cavity was investigated. Velocity-selected atoms were used and the evolution of the atomic inversion as atom and field exchange energy was observed. The quantum collapse and revival predicted by the Jaynes-Cummings model were demonstrated experimentally for the first time. The evaluation of the dynamic behavior of the atoms allows us to determine the statistics of the few photons in the cavity.
Clinical manifestations and treatment of Menkes disease and its variants (1999)

The clinical manifestations of classical Menkes disease, mild Menkes disease and occipital horn syndrome are reviewed. Menkes disease is a neurodegenerative disease with X-linked recessive inheritance. Orally administered copper accumulates in the intestine, resulting in the failure of copper absorption. The primary metabolic defect that causes copper accumulation in the intestine is present in almost all extrahepatic tissues. The blood, liver and brain are in a state of copper deficiency, which is due to defective copper absorption. The characteristic features, including neurological disturbances, arterial degeneration and hair abnormalities, can be explained by the decrease in cuproenzyme activities. DNA-based diagnosis is now possible. Mild Menkes disease and occipital horn syndrome, which show milder forms than Menkes disease, have been identified as genetic disorders resulting from mutations in the Menkes disease gene. Because the clinical spectrum of Menkes disease is wide, males with mental retardation and connective tissue abnormalities should be evaluated for biochemical evidence of defective copper transport. The treatment accepted currently is parenteral administration of copper. When treatment is started in patients with classical Menkes disease above the age of 2 months, it does not improve the neurological degeneration. When the treatment is initiated in newborn babies affected with this disease, the neurological degeneration can be prevented in some, but not all, cases. Moreover, early treatment cannot improve non-neurological problems, such as connective tissue laxity. Therefore, alternative therapies for Menkes disease and occipital horn syndrome should be studied.
Isolation and characterization of the lantibiotic salivaricin A and its structural gene salA from Streptococcus salivarius 20P3 (1993)

A bacteriocin-like inhibitory substance, salivaricin A, was purified from cultures of Streptococcus salivarius 20P3 and was shown by ion spray mass spectrometry to have a molecular mass of 2,315 +/- 1.1 Da. Amino acid composition analysis demonstrated the presence of lanthionine, indicating that salivaricin A may be a member of the lantibiotic class of antibiotic substances. The sequence of eight amino acids at the N terminus of the molecule was determined by Edman degradation, and mixed oligonucleotide probes based on part of this sequence (GSGWIA) were used to detect the salivaricin A structural gene. A 6.2-kb EcoRI fragment of chromosomal DNA from strain 20P3 that hybridized with the probes was cloned, and the hybridizing region was further localized to a 379-bp DraI-AluI fragment. Analysis of the nucleotide sequence of this fragment indicated that salivaricin A is synthesized as a 51-amino-acid prepeptide that is posttranslationally modified and cleaved to give a biologically active 22-residue peptide containing one lanthionine and two beta-methyllanthionine residues. The secondary structure of presalivaricin A was predicted to be similar to that of type A lantibiotics, with a hydrophilic alpha-helical leader sequence and a propeptide region with potential for beta-turn formation and a lack of alpha-helicity. The sequence around the cleavage site of presalivaricin A differed from that of other type A lantibiotics but was similar to that of several bacteriocin-like inhibitory substances produced by lactic acid bacteria.
Effect of Convalescent Plasma on Mortality among Hospitalized Patients with COVID-19: Initial Three-Month Experience (2020)

ClinicalTrials.gov Identifier: NCT04338360.
Cytochrome P-450 55A1 (P-450dNIR) acts as nitric oxide reductase employing NADH as the direct electron donor. (1993)

Cytochrome P-450dNIR (P-450dNIR), involved in the fungal denitrification by Fusarium oxysporum, was purified to homogeneity. The cytochrome P-450 (P-450) exhibited a potent nitric oxide (NO) reductase activity to form nitrous oxide (N2O) employing NADH but not NADPH as the sole effective electron donor. The apparent maximum turnover rate against NO was estimated as high as 31,500 min-1. The stoichiometry of the reaction between NO:NADH:N2O was 2:1:1. The reaction required neither an artificial electron-carrying mediator nor other proteinaceous components. An anaerobic incubation of ferric P-450dNIR.NO complex, but not of free ferric P-450dNIR, resulted in rapid reduction of the P-450, indicating that P-450dNIR.NO complex was reduced directly by NADH. Spectral changes during catalytic turnover indicated that decomposition of the ferrous P-450.NO complex might be rate-limiting. The reaction was not inhibited by carbon monoxide at all, suggesting that the free ferrous P-450 is not formed during turnover. On the basis of these results a possible reaction mechanism was considered. The present results demonstrated not only the unique reaction catalyzed by P-450, but also the first P-450-dependent reaction where the electron transport from NAD(P)H to P-450 is not supported by other components. Now that the physiological function of P-450 55A1 (P-450dNIR) has been found, we propose to alter the trivial name to P-450nor.
Biosynthetic production of 13C-labeled amino acids with site-specific enrichment. (1982)

We have developed two Escherichia coli strains for the production of specifically labeled amino acids suitable for high resolution nuclear magnetic resonance experiments. The 13C atoms from the enriched carbon sources, [1-13C]lactate, [1,4-13C2]succinate, and [1-13C]-acetate, are incorporated into the amino acids producing multilabeled molecules with relatively few instances of adjacent enriched carbons. This greatly simplifies the resultant spectra as compared to the extensively spin-coupled spectra of uniformly enriched samples. No isotopic enrichment was found at carbon positions expected to be unenriched by consideration of the major biosynthetic pathways. Utilizing 90% enriched precursors, most positions were enriched to approximately 85% except for those positions derived from acetate and those affected by the carbon interchange of the pentose phosphate shunt. In both of these cases, the enrichment level fell to 70%. The only result enrichment at the delta-methyl carbon of isoleucine. For the bacterial strain in question, the main pathway of isoleucine biosynthesis appears not to be from threonine but from an alternate precursor, possibly glutamate.
Effect of amniotic fluid on cationic lipid mediated transfection and retroviral infection. (1996)

In preparation for foetal gene therapy by intra-amniotic gene application, we have investigated the effect of amniotic fluid on several gene transfer systems. In vitro lipofection of embryonically derived 3T3 cells by several of the tested cationic lipids decreases in the presence of human amniotic fluid, while two formulations, Lipid 67 and Tfx-50, remain highly active. As some body fluids are known to inactivate most retroviral vectors, we investigated the influence of amniotic fluid on the efficiency of infection of 3T3 cells by murine leukaemia virus (MoMLV)-based vectors, including amphotropic and ecotropic retrovirus, and a vesicular stomatitis virus G (VSV-G) glycoprotein pseudotyped retroviral vector. All showed a decrease of infectivity from 21 to 56% in the presence of amniotic fluid. The ecotropic retrovirus is the most infectious under normal conditions as well as in amniotic fluid. Our results suggest that intra-amniotic injection may allow efficient gene transfer using either amniotic fluid-resistant cationic lipids or ecotropic retroviral vectors in a murine in vivo model for foetal gene therapy. The VSV-G-pseudotyped vector, although displaying a decrease of infectivity, remains of great interest for gene delivery, because of its broad host range and because of the high virus titers achievable. Finally, a baculovirus-based vector shows no decrease of its infectivity and does not seem to be affected by amniotic fluid but has only low infectivity on the tested foetal fibroblast cell line.
PCR amplification of anEscherichia coligene using mixed primers containing deoxyinosine at ambiguous positions in degenerate amino acid codons (1990)

Journal Article PCR amplification of an Escherichia coli gene using mixed primers containing deoxyinosine at ambiguous positions in degenerate amino acid codons Get access Rajkumar V. Patil, Rajkumar V. Patil Department of Biological Chemistry, University of MichiganAnn Arbor, MI 48109–0606, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Eugene E. Dekker Eugene E. Dekker * Department of Biological Chemistry, University of MichiganAnn Arbor, MI 48109–0606, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 10, 25 May 1990, Page 3080, https://doi.org/10.1093/nar/18.10.3080 Published: 25 May 1990 Article history Received: 10 April 1990 Published: 25 May 1990
Insulin exerts neuroprotection by counteracting the decrease in cell‐surface GABAA receptors following oxygen–glucose deprivation in cultured cortical neurons (2004)

A loss of balance between excitatory and inhibitory signaling leads to excitoxicity, and contributes to ischemic cell death. Reduced synaptic inhibition as a result of dysfunction of the ionotropic GABAA receptor has been suggested as one of the major causes for this imbalance, although the underlying mechanisms remain poorly understood. In the present study, we investigated whether oxygen-glucose deprivation (OGD), an ischemia-like challenge, alters cell-surface expression of GABAA receptors in cultured hippocampal neurons, and thereby leads to excitotoxic cell death. Using cell culture ELISA as a cell surface receptor assay, we found that OGD produced a marked decrease in cell surface GABAA receptors, without altering the total amount of receptors. Furthermore, the reduction could be prevented by inhibition of receptor endocytosis with hypertonic sucrose treatment. Notably, insulin significantly limited OGD-induced changes in cell-surface GABAA receptors. In parallel, insulin protected cultured neurons against both glutamate toxicity and OGD, as assayed by mitochondrial reduction of Alamar Blue. Importantly, insulin-mediated neuroprotection was eliminated when bicuculline, a GABAA receptor antagonist, was co-applied with insulin during OGD. Together, our results strongly suggest that ischemia-like insults decrease cell surface GABAA receptors in neurons via accelerated internalization, and that insulin provides neuroprotection by counteracting this reduction.
Structural characteristics of 2'-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations (1998)

The structure and physical properties of 2'-sugar substituted O -(2-methoxyethyl) (MOE) nucleic acids have been studied using molecular dynamics simulations. Nanosecond simulations on the duplex MOE[CCAACGTTGG]-r[CCAACGUUGG] in aqueous solution have been carried out using the particle mesh Ewald method. Parameters for the simulation have been developed from ab initio calculations on dimethoxyethyl fragments in a manner consistent with the AMBER 4.1 force field database. The simulated duplex is compared with the crystal structure of the self-complementary duplex d[GCGTATMOEACGC]2, which contains a single modification in each strand. Structural details from each sequence have been analyzed to rationalize the stability imparted by substitution with 2'- O -(2-methoxyethyl) side chains. Both duplexes have an A-form structure, as indicated by several parameters, most notably a C3' endo sugar pucker in all residues. The simulated structure maintains a stable A-form geometry throughout the duration of the simulation with an average RMS deviation of 2.0 A from the starting A-form structure. The presence of the 2' substitution appears to lock the sugars in the C3' endo conformation, causing the duplex to adopt a stable A-form geometry. The side chains themselves have a fairly rigid geometry with trans , trans , gauche +/- and trans rotations about the C2'-O2', O2'-CA', CA'-CB' and CB'-OC' bonds respectively.
X Box-Binding Protein 1 Regulates Angiogenesis in Human Pancreatic Adenocarcinomas (2009)

We propose that the IRE1alpha-XBP-1 branch of the UPR modulates a complex proangiogenic, VEGF-independent response that depends on signals received from the tumor microenvironment.
[P53 antibodies: a new method for the analysis of alterations of the p53 gene: application to breast cancer]. (1996)

Alterations in the p53 gene are found in 20% to 40% of breast cancers and are generally associated with factors of adverse prognostic significance. In most instances, point mutations modify the confirmation of p53, causing the gene to accumulate in the nuclei of tumor cells. These alterations can be detected via molecular analysis or immunohistochemical methods. More recent studies have demonstrated that accumulation of the p53 protein in tumor cells may induce an immune response with presence of anti-p53 antibodies in the serum of cancer patients. Assaying serum anti-p53 antibody is a new approach to investigation of the status of the p53 gene in a tumor.
Immunochemical Studies on Blood Groups. XXXIV. Structures of Some Oligosaccharides Produced by Alkaline Degradation of Blood Group A, B, and H Substances* (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImmunochemical Studies on Blood Groups. XXXIV. Structures of Some Oligosaccharides Produced by Alkaline Degradation of Blood Group A, B, and H Substances*Kenneth O. Lloyd, Elvin A. Kabat, Espriela J. Layug, and Flavio GruezoCite this: Biochemistry 1966, 5, 5, 1489–1501Publication Date (Print):May 1, 1966Publication History Published online1 May 2002Published inissue 1 May 1966https://pubs.acs.org/doi/10.1021/bi00869a007https://doi.org/10.1021/bi00869a007research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations120LEARN 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
Selective patterning of covalent molecular grafting on doped amorphous silicon templates (2010)

Abstract Linear alkene molecules have been covalently immobilized on amorphous silicon surfaces. The larger thermal reactivity of n + ‐doped vs. nominally undoped a‐Si:H surfaces towards perfluorodecene (PFD) molecules in the gas phase has been exploited to investigate a selective patterning of molecular grafting on a previously defined template of doped / undoped regions. PFD has been chosen to obtain hydrophobic monomolecular layers with fluorine labelling, useful for photoelectron spectroscopy (XPS) and NanoSIMS imaging. The template was obtained by growing undoped a‐Si:H on top of n + a‐Si‐H, and defining 40 μm‐edge patterns of undoped a‐Si:H by reactive ion etching in a (CF 4 , O 2 ) mixture. After native oxide removal, the patterned surface was exposed to PFD at 230 °C. NanoSIMS images, taken at increasing Cs + irradiation doses, show the expected 19 F and 28 Si contrast on as‐grafted surfaces; this contrast disappears after ∼340 seconds Cs + irradiation, corresponding to the desorption of the PFD monomolecular layer. (© 2010 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Drug Abuse: Hedonic Homeostatic Dysregulation (1997)

Understanding the neurobiological mechanisms of addiction requires an integration of basic neuroscience with social psychology, experimental psychology, and psychiatry. Addiction is presented as a cycle of spiralling dysregulation of brain reward systems that progressively increases, resulting in compulsive drug use and a loss of control over drug-taking. Sensitization and counteradaptation are hypothesized to contribute to this hedonic homeostatic dysregulation, and the neurobiological mechanisms involved, such as the mesolimbic dopamine system, opioid peptidergic systems, and brain and hormonal stress systems, are beginning to be characterized. This framework provides a realistic approach to identifying the neurobiological factors that produce vulnerability to addiction and to relapse in individuals with a history of addiction.
Hierarchical Gecko‐Like Adhesives (2008)

The role of hierarchy in gecko-like adhesive surfaces is presented. Experiments on two-level structured surfaces with micropillars of different dimensions demonstrate that hierarchy does not seem to positively influence adhesion of structured surfaces to planar substrates, but may be relevant when stiff materials or rough substrates come into play, where adaptability of the adhesive structure is required for successful contact. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Towards total scene understanding: Classification, annotation and segmentation in an automatic framework (2009)

Given an image, we propose a hierarchical generative model that classifies the overall scene, recognizes and segments each object component, as well as annotates the image with a list of tags. To our knowledge, this is the first model that performs all three tasks in one coherent framework. For instance, a scene of a `polo game' consists of several visual objects such as `human', `horse', `grass', etc. In addition, it can be further annotated with a list of more abstract (e.g. `dusk') or visually less salient (e.g. `saddle') tags. Our generative model jointly explains images through a visual model and a textual model. Visually relevant objects are represented by regions and patches, while visually irrelevant textual annotations are influenced directly by the overall scene class. We propose a fully automatic learning framework that is able to learn robust scene models from noisy Web data such as images and user tags from Flickr.com. We demonstrate the effectiveness of our framework by automatically classifying, annotating and segmenting images from eight classes depicting sport scenes. In all three tasks, our model significantly outperforms state-of-the-art algorithms.
Tumour necrosis factor inhibitors (2005)

The cytokine, tumour necrosis factor-alpha (TNF-alpha) plays a key role in the pathogenesis of many chronic inflammatory and rheumatic diseases, in particular, Crohn's disease, rheumatoid arthritis, ankylosing spondylitis and psoriatic arthritis. Controlled trials have shown that the TNF inhibitors (etanercept, infliximab and adalimumab) significantly reduce symptoms and signs, improve function and quality of life, and reduce radiologically evident damage in patients with rheumatoid diseases. For reasons that are not entirely clear, etanercept does not work in Crohn's disease. Injection site and intravenous reactions and increased risk of infection (in particular, reactivation of tuberculosis) are associated with the use of these agents. Increased risk of lymphoproliferative disease, the development of lupus-like syndromes and demyelination, including optic neuritis and reactivation of multiple sclerosis, are under evaluation in long-term follow-up studies. The TNF inhibitors are expensive (about $18 000 per year), and in some patients need to be given continuously to maintain benefit, even in the presence of other immunosuppressive therapy.
Isolation of histamine-producing Lactobacillus buchneri from Swiss cheese implicated in a food poisoning outbreak (1985)

A histamine-producing strain of Lactobacillus buchneri was isolated from Swiss cheese that had been implicated in an outbreak of histamine poisoning. It produced up to 4,070 nmol of histamine per ml in MRS broth supplemented with 0.1% histidine. The identification of this isolate was based on its biochemical, bacteriological, and DNA characterizations.