gebhart/patrepeval huggingface dataset:
LSTM neural networks for language modeling (2012)

Neural networks have become increasingly popular for the task of language modeling.Whereas feed-forward networks only exploit a fixed context length to predict the next word of a sequence, conceptually, standard recurrent neural networks can take into account all of the predecessor words.On the other hand, it is well known that recurrent networks are difficult to train and therefore are unlikely to show the full potential of recurrent models.These problems are addressed by a the Long Short-Term Memory neural network architecture.In this work, we analyze this type of network on an English and a large French language modeling task.Experiments show improvements of about 8 % relative in perplexity over standard recurrent neural network LMs.In addition, we gain considerable improvements in WER on top of a state-of-the-art speech recognition system.
Structure of the α and β heavy chains of the outer arm dynein from Chlamydomonas flagella (1989)

The photoaffinity analogs 2-azidoadenosine 5'-tri(di)-phosphate (2-N3AT(D)P) and 8-azidoadenosine 5'-triphosphate (8-N3ATP) have been used to probe the substructural organization of the nucleotide binding pockets within the alpha and beta heavy chains of the outer arm dynein from Chlamydomonas flagella. Both 2-N3ATP and 8-N3ATP are competitive inhibitors of dynein ATP hydrolysis, and both analogs are themselves hydrolyzed by the alpha-beta dimer. Following vanadate-dependent photolysis at the V1 site (by UV irradiation in the presence of Mg2+, ATP, and vanadate), both probes exclusively labeled the larger fragment from the alpha chain. In contrast, within the beta chain the predominant insertion sites for the two analogs were located on opposite sides of the V1 site. Therefore, the hydrolytic pockets of these two molecules have different substructures. Vanadate-dependent photolysis of the alpha and beta chains at the V2 sites (by UV irradiation in the presence of vanadate and Mn2+) profoundly affected the predominant modification sites; for example, following photolysis at the V2a site neither fragment of the alpha chain was photolabeled by 2-N3ATP or 8-N3ATP. Based on the photolabeling patterns obtained, the single V2 site within the beta chain is predicted to be analogous to the V2b site within the alpha chain. The results support the hypothesis that the V2 sites occur within the ATP binding pockets, and indicate that these functional domains are composed of portions of the heavy chains which are linearly separated by up to at least 100,000 daltons. Thus, the central region of each dynein heavy chain must be extensively folded so as to bring the widely separated photocleavage and photolabeling sites together within a single catalytic unit.
Cloning and expression of rat liver CTP: phosphocholine cytidylyltransferase: an amphipathic protein that controls phosphatidylcholine synthesis. (1990)

CTP:phosphocholine cytidylyltransferase (EC 2.7.7.15) is a key regulatory enzyme in the synthesis of phosphatidylcholine in higher eukaryotes. This enzyme can interconvert between an inactive cytosolic form and an active membrane-bound form. To unravel the structure of the transferase and the mechanism of its interaction with membranes, we have cloned a cytidylyltransferase cDNA from rat liver by the oligonucleotide-directed polymerase chain reaction. Transfection of the rat clone into COS cells resulted in a 10-fold increase in cytidylyltransferase activity and content. The activity of the transfected transferase was lipid-dependent. The central portion of the derived protein sequence of the rat clone is highly homologous to the previously determined yeast cytidylyltransferase sequence [Tsukagoshi, Y., Nikawa, J. & Yamashita, S. (1987) Eur. J. Biochem. 169, 477-486]. The rat protein sequence lacks any signals for covalent lipid attachment and lacks a hydrophobic domain long enough to span a bilayer. However, it does contain a potential 58-residue amphipathic alpha-helix, encompassing three homologous 11-residue repeats. We propose that the interaction of cytidylyltransferase with membranes is mediated by this amphipathic helix lying on the surface with its axis parallel to the plane of the membrane such that its hydrophobic residues intercalate the phospholipids.
How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography (2015)

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization.
Fractal geometry of music. (1990)

Music critics have compared Bach's music to the precision of mathematics. What "mathematics" and what "precision" are the questions for a curious scientist. The purpose of this short note is to suggest that the mathematics is, at least in part, Mandelbrot's fractal geometry and the precision is the deviation from a log-log linear plot.
Cutaneous response to recombinant interleukin 2 in human immunodeficiency virus 1-seropositive individuals. (1990)

We report that 11 human immunodeficiency virus 1 (HIV-1)-seropositive patients, including three AIDS patients, were able to generate a cellular immune response to the intradermal injection of low doses (2-10 micrograms) of recombinant interleukin 2 (rIL-2). A dose-dependent zone of induration appeared at the site of injection, peaked at 24 hr, and was accompanied by the local accumulation of T cells, monocytes, and Langerhans cells. Despite the reductions in the CD4+ T-cell counts in the peripheral blood of most patients, CD4+ T-cells could still be mobilized with rIL-2 injections into the skin. The total number of immigrant cells was equivalent to those in HIV-1-seronegative patients, although the CD4+/CD8+ ratio of the dermal population was reduced. In response to rIL-2, major histocompatibility complex (MHC) class II antigen was expressed on the surface of keratinocytes, Langerhans cells, lymphocytes, and macrophages. In addition, the gamma interferon (IFN-gamma)-induced protein IP-10 rapidly appeared in dermal inflammatory cells and keratinocytes. A majority of HIV-1-seropositive patients demonstrated low or absent responses to common skin-test antigens. Those with positive zones of induration were often defective in the cellular expression of the IFN-gamma-induced MHC class II antigen. The simultaneous administration of rIL-2 and soluble antigen at widely separated cutaneous sites led to an enhancement of skin-test antigen reactivity in seropositive patients. The results suggest that local administration of rIL-2 to seropositive patients may act systemically, stimulating cellular immunity to recall antigens, and thus may be of potential benefit in the defense against opportunistic pathogens encountered in HIV-1 infection.
Isolation of a cDNA encoding CD33, a differentiation antigen of myeloid progenitor cells. (1988)

A cDNA clone encoding the human myeloid Ag CD33 was isolated from a U937 cDNA library after three rounds of transient expression in COS cells and enrichment by panning. COS cells transfected with the isolated clone expressed a surface protein recognized by the anti-CD33 mAb MY9, L1B2, and L4F3, having mass similar to but slightly smaller than the mass of CD33 expressed on myeloid cells. CD33 transcripts were found constitutively expressed in several myeloid progenitor cell lines. The cDNA sequence predicts a 40-kDa polypeptide with the typical features of a glycosylated integral membrane protein. The extracellular part of CD33 contains two Ig-like domains which are highly related to the first two domains of the neural cell myelin-associated glycoprotein and the B cell Ag CD22.
Nonsteroidal Antiinflammatory Agents, XVIII: C‐5 Functionalized 6,7‐Diphenyl‐2,3‐dihydro‐1H‐pyrrolizines as Inhibitors of Bovine Cyclooxygenase and 5‐Lipoxygenase (1994)

6-(4-Chlorophenyl)-7-phenyl-2,3-dihydro-1H-pyrrolizines with functional groups at position 5 of the heterocyclic moiety were synthesized and tested. To determine their antiinflammatory activity bovine blood was used as enzyme source for the cyclooxygenase and 5-lipoxygenase, respectively. The iminoxy acetic acid derivative and the iminotetrazole selectively inhibit the 5-lipoxygenase, all the other compounds show medium or low affinity to the active sites of cyclooxygenase and 5-lipoxygenase. In general all compounds inhibit 5-lipoxygenase more effectively than cyclooxygenase. Concerning the inhibition of 5-lipoxygenase the most active compounds found are equipotent to the corresponding propionic acid compounds, but they aren't well balanced dual inhibitors as shown for the carboxylic derivatives. A structure activity relationship and the enzyme selectivity are discussed.
Cloning and characterization of a receptor-class phosphotyrosine phosphatase gene expressed on central nervous system axons in Drosophila melanogaster. (1991)

We have cloned and characterized cDNAs coding for a receptor-class phosphotyrosine phosphatase gene from Drosophila melanogaster. The gene maps to the polytene chromosome bands 99A7-8. The cDNA clones code for a polypeptide of 1301 amino acids with a predicted molecular mass of 145 kDa. The extracellular domain includes two fibronectin-type III-like domains. The cytoplasmic region contains two tandemly repeated phosphotyrosine phosphatase-like domains. Residues shown crucial for catalytic activity are absent in the second domain. This Drosophila receptor-class phosphotyrosine phosphatase polypeptide is expressed on axons of the embryonic central nervous system.
Design of an Electrochemical Cell Making Syngas (CO + H2) from CO2 and H2O reduction at Room Temperature (2007)

Abstract not Available.
Elements Upstream of the AAUAAA within the Human Immunodeficiency Virus Polyadenylation Signal Are Required for Efficient Polyadenylation In Vitro (1992)

Recent in vivo studies have identified specific sequences between 56 and 93 nucleotides upstream of a polyadenylation [poly(A)] consensus sequence, AAUAAA, in human immunodeficiency virus type 1 (HIV-1) that affect the efficiency of 3'-end processing at this site (A. Valsamakis, S. Zeichner, S. Carswell, and J. C. Alwine, Proc. Natl. Acad. Sci. USA 88:2108-2112, 1991). We have used HeLa cell nuclear extracts and precursor RNAs bearing the HIV-1 poly(A) signal to study the role of upstream sequences in vitro. Precursor RNAs containing the HIV-1 AAUAAA and necessary upstream (U3 region) and downstream (U5 region) sequences directed accurate cleavage and polyadenylation in vitro. The in vitro requirement for upstream sequences was demonstrated by using deletion and linker substitution mutations. The data showed that sequences between 56 and 93 nucleotides upstream of AAUAAA, which were required for efficient polyadenylation in vivo, were also required for efficient cleavage and polyadenylation in vitro. This is the first demonstration of the function of upstream sequences in vitro. Previous in vivo studies suggested that efficient polyadenylation at the HIV-1 poly(A) signal requires a spacing of at least 250 nucleotides between the 5' cap site and the AAUAAA. Our in vitro analyses indicated that a precursor containing the defined upstream and downstream sequences was efficiently cleaved at the polyadenylation site when the distance between the 5' cap and the AAUAAA was reduced to at least 140 nucleotides, which is less than the distance predicted from in vivo studies. This cleavage was dependent on the presence of the upstream element.
Polypeptide Hormone‐Receptor Interactions: The Structure and Receptor Binding of Insulin and Glucagon (1978)

Insulin is a small globular protein with a well defined tertiary structure which is closely similar in all species with the exception of certain hystricomorphs such as the guinea pig. Insulin-like growth factor is homologous with insulin and probably has an insulin-like tertiary structure. In contrast glucagon is not a globular protein. It exists as an equilibrium population of conformers with low helix content at physiological concentrations but attains a largely helical conformation on association to trimers. The receptor binding of insulin depends critically on the correct three-dimensional juxtaposition of groups (A1, A21, B25, etc) and involves both hydrophobic and polar interactions. In insulin-like growth factor part of the insulin receptor region is thought to be buried in extra peptide, so explaining its weak binding to insulin receptors. In contrast the glucagon receptor complex probably involves largely hydrophobic contacts which are possible when a helical conformer is formed.
Angiogenesis in the brain during development: the effects of vascular endothelial growth factor and angiopoietin-2 in an animal model (2005)

Some of these observations may provide insight into how one may develop a better model of brain arteriovenous malformations.
Early growth and coronary heart disease in later life: longitudinal study (2001)

Irrespective of size at birth, low weight gain during infancy is associated with increased risk of coronary heart disease. After age 1 year, rapid weight gain is associated with further increase in risk, but only among boys who were thin at birth. In these boys the adverse effects of rapid weight gain on later coronary heart disease are already apparent at age 3 years. Improvements in fetal, infant, and child growth could lead to substantial reductions in the incidence of coronary heart disease.
Targeting Costimulatory Molecules to Improve Antitumor Immunity (2012)

The full activation of T cells necessitates the concomitant activation of two signals, the engagement of T-cell receptor by peptide/major histocompatibility complex II and an additional signal delivered by costimulatory molecules. The best characterized costimulatory molecules belong to B7/CD28 and TNF/TNFR families and play crucial roles in the modulation of immune response and improvement of antitumor immunity. Unfortunately, tumors often generate an immunosuppressive microenvironment, where T-cell response is attenuated by the lack of costimulatory molecules on the surface of cancer cells. Thus, targeting costimulatory pathways represent an attractive therapeutic strategy to enhance the antitumor immunity in several human cancers. Here, latest therapeutic approaches targeting costimulatory molecules will be described.
Depletion Mode Oxide TFT Shift Register for Variable Frame Rate AMOLED Displays (2015)

This letter demonstrates a shift register circuit at the backplane of depletion mode oxide thin-film transistors (TFTs), which can cover variable frame rates for low-power active matrix organic light emitting diode (AMOLED) displays. The proposed scheme focuses on the stable gate control of a pull-up TFT by securing the charging and discharging paths at the wide operating frequency range. In a prototype high-definition (HD: 1366 × 768) AMOLED panel, it is ensured that fabricated shift registers operate at the wide frame frequency range from 1 to 240 Hz. The measured current consumptions are 30, 4, 6, and 5.8 mA for four clock signals, VGH of 24 V, VGL1 of -6 V, and VGL2 of -14 V at a frame rate of 120 Hz.
On double-link failure recovery in WDM optical networks (2003)

Network survivability is a crucial requirement in high-speed optical networks. Typical approaches of providing survivability have considered the failure of a single component such as a link or a node. We consider a failure model in which any two links in the network may fail in an arbitrary order. Three loopback methods of recovering from double-link failures are presented. The first two methods require the identification of the failed links, while the third one does not. However, precomputing the backup paths for the third method is more difficult than for the first two. A heuristic algorithm that pre-computes backup paths for links is presented. Numerical results comparing the performance of our algorithm with other approaches suggests that it is possible to achieve 100% recovery from double-link failures with a modest increase in backup capacity.
Flip-Flop HSV-BAC: bacterial artificial chromosome based system for rapid generation of recombinant herpes simplex virus vectors using two independent site-specific recombinases. (2006)

Our Flip-Flop HSV-BAC system enables rapid generation of HSV vectors carrying transgene inserts. By introducing a tumor-specific-promoter-driven ICP4 cassette into pM24-BAC using this system, one should be able to generate transcriptionally-targeted oncolytic HSV vectors. We believe this system will greatly facilitate the screening of a plethora of clinically useful tumor-specific promoters in the context of oncolytic HSV vectors.
ChemInform Abstract: Synthesis, Anti‐Parasitic and Anti‐Fungal Activities of Arylalkyl‐ and Arylvinylthiazolines. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fourier transform channeled spectropolarimetry in the MWIR (2007)

A complete Fourier Transform Spectropolarimeter in the MWIR is demonstrated. The channeled spectral technique, originally developed by K. Oka, is implemented with the use of two Yttrium Vanadate (YVO(4)) crystal retarders. A basic mathematical model for the system is presented, showing that all the Stokes parameters are directly present in the interferogram. Theoretical results are compared with real data from the system, an improved model is provided to simulate the effects of absorption within the crystal, and a modified calibration technique is introduced to account for this absorption. Lastly, effects due to interferometer instabilities on the reconstructions, including nonuniform sampling and interferograms translations, are investigated and techniques are employed to mitigate them.
The Human Genome Browser at UCSC (2002)

As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
Graph Matching Networks for Learning the Similarity of Graph Structured Objects (2019)

This paper addresses the challenging problem of retrieval and matching of graph structured objects, and makes two key contributions. First, we demonstrate how Graph Neural Networks (GNN), which have emerged as an effective model for various supervised prediction problems defined on structured data, can be trained to produce embedding of graphs in vector spaces that enables efficient similarity reasoning. Second, we propose a novel Graph Matching Network model that, given a pair of graphs as input, computes a similarity score between them by jointly reasoning on the pair through a new cross-graph attention-based matching mechanism. We demonstrate the effectiveness of our models on different domains including the challenging problem of control-flow-graph based function similarity search that plays an important role in the detection of vulnerabilities in software systems. The experimental analysis demonstrates that our models are not only able to exploit structure in the context of similarity learning but they can also outperform domain-specific baseline systems that have been carefully hand-engineered for these problems.
Phosphoinositide 3‐kinase δ inhibitor as a novel therapeutic agent in asthma (2008)

Multiple signal transduction pathways are involved in airway inflammation with one of the key signalling pathways being phosphoinositide 3-kinase (PI3K). Numerous components of the PI3K pathway play an important role in the expression and activation of inflammatory mediators, inflammatory cell recruitment, immune cell function, airway remodelling and corticosteroid insensitivity in asthma. More recently studies exploring the specific roles of different PI3K catalytic subunit isoforms in asthma have been initiated. Several of these have highlighted the importance of p110delta isoform as a novel target for therapeutic intervention in asthma. In this review the biological role of PI3Ks, especially PI3Kdelta, are highlighted and the therapeutic potential of selective PI3Kdelta inhibitor in asthma discussed.
Efficient Access Control for Distributed Hierarchical File Systems (2005)

To determine whether a user can access a file in a hierarchical file system a traversal of the directory hierarchy is required in order to check access control for all the parent directories. This traversal can be especially expensive in a distributed system where the files may be on separate devices. We present two approaches for representing the complete access control for a file and its parent directories such that it can be stored locally with each file in order to avoid traversal. We use the well-known CNF and DNF (conjunctive and disjunctive normal form) formats to store permission and ownership information compactly for the entire path to a file. An examination of the structure of an existing large shared file system demonstrates the efficacy of our solution.