gebhart/patrepeval huggingface dataset:
Sequence to Sequence Learning with Neural Networks (2014)

Deep Neural Networks (DNNs) are powerful models that have achieved excel-lent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-TermMemory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from theWMT’14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM’s BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the pas-sive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM’s performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier. 1
Longest prefix matching using bloom filters (2003)

We introduce the first algorithm that we are aware of to employ Bloom filters for Longest Prefix Matching (LPM). The algorithm performs parallel queries on Bloom filters, an efficient data structure for membership queries, in order to determine address prefix membership in sets of prefixes sorted by prefix length. We show that use of this algorithm for Internet Protocol (IP) routing lookups results in a search engine providing better performance and scalability than TCAM-based approaches. The key feature of our technique is that the performance, as determined by the number of dependent memory accesses per lookup, can be held constant for longer address lengths or additional unique address prefix lengths in the forwarding table given that memory resources scale linearly with the number of prefixes in the forwarding table.Our approach is equally attractive for Internet Protocol Version 6 (IPv6) which uses 128-bit destination addresses, four times longer than IPv4. We present a basic version of our approach along with optimizations leveraging previous advances in LPM algorithms. We also report results of performance simulations of our system using snapshots of IPv4 BGP tables and extend the results to IPv6. Using less than 2Mb of embedded RAM and a commodity SRAM device, our technique achieves average performance of one hash probe per lookup and a worst case of two hash probes and one array access per lookup.
E1A and E1B proteins inhibit inflammation induced by adenovirus (2004)

Replication-defective human adenovirus (Ad) group C transducing vectors, most of which have the E1A, E1B, and E3 genes deleted, are highly inflammatory despite the fact that the parental viruses typically cause subclinical or mild infections. To investigate this paradox, the roles that the E1A, E1B, and E3 genes play in inflammation were tested by using replication-incompetent viruses carrying a deletion of the preterminal protein gene. The viruses were injected into BALB/c mouse ears, and edema was monitored as a sensitive surrogate marker of inflammation. A virus deleted for the E1A 289R (transcription activating) protein was noninflammatory, and inhibited edema induced by empty virus particles. The E1A 243R and E1B 55-kDa (p53 binding) proteins play the most important roles in inhibition of inflammation by the noninflammatory virus. The E1B 19-kDa antiapoptotic protein inhibited edema when both the E1A 243R and E1B 55-kDa proteins were expressed but strongly induced edema when only one was expressed. E3 proteins had their greatest effect on the inhibition of edema induced by the E1A 289R protein. The results support a model in which inflammation is countered through a mechanism that involves complex genetic interactions between Ad early region proteins and offer promise for the design and construction of noninflammatory Ad gene therapy vectors that are relatively easy to grow and purify.
Multiview Video Coding Using View Interpolation and Color Correction (2007)

Neighboring views must be highly correlated in multiview video systems. We should therefore use various neighboring views to efficiently compress videos. There are many approaches to doing this. However, most of these treat pictures of other views in the same way as they treat pictures of the current view, i.e., pictures of other views are used as reference pictures (inter-view prediction). We introduce two approaches to improving compression efficiency in this paper. The first is by synthesizing pictures at a given time and a given position by using view interpolation and using them as reference pictures (view-interpolation prediction). In other words, we tried to compensate for geometry to obtain precise predictions. The second approach is to correct the luminance and chrominance of other views by using lookup tables to compensate for photoelectric variations in individual cameras. We implemented these ideas in H.264/AVC with inter-view prediction and confirmed that they worked well. The experimental results revealed that these ideas can reduce the number of generated bits by approximately 15% without loss of PSNR.
Molecular genetic characterization of the RD-114 gene family of endogenous feline retroviral sequences (1984)

RD-114 is a replication-competent, xenotropic retrovirus which is homologous to a family of moderately repetitive DNA sequences present at ca. 20 copies in the normal cellular genome of domestic cats. To examine the extent and character of genomic divergence of the RD-114 gene family as well as to assess their positional association within the cat genome, we have prepared a series of molecular clones of endogenous RD-114 DNA segments from a genomic library of cat cellular DNA. Their restriction endonuclease maps were compared with each other as well as to that of the prototype-inducible RD-114 which was molecularly cloned from a chronically infected human cell line. The endogenous sequences analyzed were similar to each other in that they were colinear with RD-114 proviral DNA, were bounded by long terminal redundancies, and conserved many restriction sites in the gag and pol regions. However, the env regions of many of the sequences examined were substantially deleted. Several of the endogenous RD-114 genomes contained a novel envelope sequence which was unrelated to the env gene of the prototype RD-114 env gene but which, like RD-114 and endogenous feline leukemia virus provirus, was found only in species of the genus Felis, and not in other closely related Felidae genera. The endogenous RD-114 sequences each had a distinct cellular flank which indicates that these sequences are not tandem but dispersed nonspecifically throughout the genome. Southern analysis of cat cellular DNA confirmed the conclusions about conserved restriction sites in endogenous sequences and indicated that a single locus may be responsible for the production of the major inducible form of RD-114.
Maturation‐specific translational enhancement mediated by the 5′‐UTR of a late pollen transcript (1996)

The tomato lat52 gene encodes an abundant protein specifically expressed in the vegetative cell of the pollen grain during pollen maturation which is essential for normal pollen tube growth. Multiple upstream cis-regulatory elements controlling the level and specificity of lat52 transcription have previously been identified. This research investigated the role of the 5'-untranslated region (5'-UTR) in controlling lat52 expression. In transient expression assays, gene fusion constructs containing the lat52 5'-UTR were expressed in pollen at levels 13- to 60-fold above those in which synthetic polylinker sequences replaced the lat52 5'-UTR. This enhancement was shown to be independent of both the promoter sequences, the linked reporter gene and the 3'-UTR. Analysis of RNA and protein levels in transgenic plants containing such gene fusions demonstrated that the lat52 5'-UTR conferred a dramatically increased translational yield to heterologous transcripts in a pollen-specific and strictly developmentally regulated manner during the final stages of pollen maturation. These results represent a novel example of translational enhancement in plants in that translational yield is regulated developmentally in a cell-specific manner via sequences located within the 5'-UTR.
Intracellular and extracellular enzymatic deacylation of bacterial endotoxin during localized inflammation induced by Escherichia coli (1991)

Acyloxyacyl hydrolase (AOAH), an enzyme that removes the secondary acyl chains of gram-negative bacterial lipid A (endotoxin), has been identified previously in human neutrophils and mouse macrophages. We report here that bovine leukocytes also contain AOAH activity. Although bovine AOAH deacylates bacterial lipopolysaccharide in a manner similar to human AOAH, it is active in vitro over a broader pH range, from 4.0 to 7.0. By using Escherichia coli infection of the bovine mammary gland as a model of localized gram-negative bacterial disease and associated tissue inflammation, AOAH activity per leukocyte increased. In addition, AOAH activity increased in the cell-free portion of infected mammary secretions. These data indicate that AOAH activity increases in leukocytes associated with inflammation induced by gram-negative bacteria and provide additional evidence of its potential involvement in the defense against the effects of bacterial endotoxin.
Isolation and Characterization of a Sulfoxide and a Desamido Derivative of Biosynthetic Human Growth Hormone (1988)

Two derivatives of biosynthetic human growth hormone, a sulfoxide and a mixture of two monodesamido isomers, have been isolated and characterized. The sulfoxide derivative arises from an oxidation of Met-14. The major site of deamidation is at Asn-149 with a minor site at Asn-152. In addition, a fraction has been isolated from a sample of human growth hormone that was maintained at 40 degrees C for 2 weeks. This fraction, the isolated impurities fraction, contains the sulfoxide and the desamido forms, thereby demonstrating that these derivatives are the primary degradation products of biosynthetic human growth hormone. The sulfoxide, the desamido, and the isolated impurities fraction exhibit full biological activity.
Secretion of prostaglandins and progesterone by cells from corpora lutea of mares (1990)

Corpora lutea (CL) were collected from mares during early (Day 4-5), mid- (Day 8-9), and late (Day 12-13) dioestrus. Dispersed cell suspensions were obtained by enzymic digestion of tissue. Two distinct luteal cell populations (large and small) were observed. The proportion of small luteal cells significantly increased as age of CL advanced. Cells (2 x 10(6)) from CL which were incubated for 24 h secreted prostaglandin (PG) F, PGE-2 and 6-keto-PGF-1 alpha (the stable metabolite of prostacyclin). Higher concentrations of all PGs were produced by cells from CL at early dioestrus than from those at mid- or late dioestrus. The ratio of PGF:PGE-2 increased from 0.33 in CL of early dioestrus to 1.34 in CL of mid-dioestrus, whereas ratios of PGF:6-keto-PGF-1 alpha remained relatively constant (approximately 0.6). The ratio of PGE-2:6-keto-PGF-1 alpha from CL decreased between early (3.27) and mid-dioestrus (0.43). Addition of LH, dbcAMP, or ionophore to cell cultures did not consistently affect secretion of progesterone or PGs by luteal cells. It is suggested that prostaglandins produced by luteal cells of mares may contribute to control of luteal function and that the changing ratios of prostaglandins may be more important in controlling the lifespan of the CL than absolute concentrations of each.
Common factors among Alzheimer’s disease, Parkinson’s disease, and epilepsy: Possible role of the noradrenergic nervous system (2012)

The neurodegenerative disorders Alzheimer's disease (AD) and Parkinson's disease (PD) share in common the neuropathologic loss of locus coeruleus (LC) noradrenergic neurons. In addition, these two neurodegenerative disorders share two symptoms that define these disorders: cognitive impairment and depression. The hippocampus is a region that is known to play a role in cognition and depression, and the hippocampus receives sole noradrenergic innervation from LC neurons. However, it is unclear how the loss of LC noradrenergic neurons contributes to these common symptoms in these two disorders. Epilepsy is not considered a neurodegenerative disorder, but the hippocampus is severely affected in temporal lobe epilepsy. Of interest, cognitive impairment and depression are also common comorbid disorders in temporal lobe epilepsy. This article describes common symptoms among these three neurologic disorders and a possible role of the noradrenergic nervous system.
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation (2002)

Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal.
Interaction of a bivalent ligand with IgM anti-lactose antibody (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteraction of a bivalent ligand with IgM anti-lactose antibodyFred Karush, Ming-Ming Chua, and John D. RodwellCite this: Biochemistry 1979, 18, 11, 2226–2232Publication Date (Print):May 1, 1979Publication History Published online1 May 2002Published inissue 1 May 1979https://pubs.acs.org/doi/10.1021/bi00578a014https://doi.org/10.1021/bi00578a014research-articleACS PublicationsRequest reuse permissionsArticle Views53Altmetric-Citations10LEARN 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
Studies on Anti-inflammatory Agents. IV. Synthesis and Pharmacological Properties of 1,5-Diarylpyrazoles and Related Derivatives. (1997)

A series of novel 1,5-diarylpyrazole derivatives was synthesized and tested for anti-inflammatory and analgesic activities to develop anti-inflammatory agents with fewer side effects than existing nonsteroidal anti-inflammatory drugs. The structure-activity relationships in this series were extensively studied. Electron-withdrawing substituents such as CN and CF3 were optimal at the 3-position of the pyrazole ring. Replacement of these substituents with bulky ones gave less active compounds. The 4-(methylsulfonyl)phenyl group seemed to be the optimal group at the 5-position of the pyrazole ring. The most potent compound was 1-(4-fluorophenyl)-5-[4-(methylsulfonyl)phenyl]-pyrazole-3-carbonitrile (19a), with oral ED50 value of 0.030 and 0.47 mg/kg on adjuvant-induced arthritis and collagen-induced arthritis, respectively, and an ED30 value of 7.4 mg/kg in the yeast-induced hyperalgesia (Randall-Selitto) assay. Compound 19a also showed potent inducible cyclooxygenase (COX-2)-inhibitory activity (IC50 = 0.24 microM) with no COX-1 inhibition even at 100 microM.
Prevalence and clinical correlates of JAK2 mutations in Down syndrome acute lymphoblastic leukaemia (2008)

Recurrent, prognostically significant chromosomal abnormalities occur in approximately 75% of paediatric acute lymphoblastic leukaemia (ALL), but only infrequently in children with Down syndrome (DS) and ALL. Recently, novel somatic activating mutations in the gene Janus kinase 2 (JAK2) were reported in 18% of DS ALL. Here we report identification and clinical correlates of JAK2 mutations in an independent cohort. JAK2 activating mutations occurred in 10/53 DS ALL cases (18.9%). Mutations were overrepresented in males (P < 0.03), occurred once in association with high hyperdiploidy and were not significantly correlated with age, initial white blood count, or event-free survival. Our results confirm the significance of JAK-STAT pathway activation in DS ALL.
Molecular Imaging of the Kinetics of Vascular Endothelial Growth Factor Gene Expression in Ischemic Myocardium (2004)

Taken together, these findings establish the feasibility of molecular imaging for monitoring angiogenic gene expression with a PET reporter gene and probe noninvasively, quantitatively, and repetitively. The principles demonstrated here can be used to evaluate other therapeutic genes of interest in animal models before future clinical trials are initiated.
Molecular species-sensitive optical coherence tomography using coherent anti-stokes Raman scattering spectroscopy (2003)

We present our progress in developing a novel technique and instrument that images specific molecular species in biological tissues using Optical Coherence Tomography (OCT). Standard OCT instruments measure only the scattering from structural features, such as refractive index changes. We utilize Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopy, a nonlinear optics technique that can selectively stimulate molecular groups, to gather compositional information from the sample. Being a coherent process, our instrument will produce interference between the nonlinear anti-Stokes signal produced in the sample and a reference molecular sample to both exclude background and nonresonant signals and range features in the tissue. Because of this, we will also gain the benefits of sensitivity that interferometry can provide. By utilizing the tunability of an optical parametric oscillator, we can address a range of molecular resonances from 1500 cm<sup>-1</sup> to 3500 cm<sup>-1</sup>. This frequency range offers the possibility of measuring the distributions and densities of proteins, lipids, and nuclear material that we believe will be useful for determining the early presence of epithelial carcinomas. We demonstrate the principle of this imaging method by producing interference between two separately produced CARS signals from the same probe and Stokes beams.
Perk Tutor: An Open-Source Training Platform for Ultrasound-Guided Needle Insertions (2012)

Image-guided needle placement, including ultrasound (US)-guided techniques, have become commonplace in modern medical diagnosis and therapy. To ensure that the next generations of physicians are competent using this technology, efficient and effective educational programs need to be developed. This paper presents the Perk Tutor: a configurable, open-source training platform for US-guided needle insertions. The Perk Tutor was successfully tested in three different configurations to demonstrate its adaptability to different procedures and learning objectives. 1) The Targeting Tutor, designed to develop US-guided needle targeting skills, 2) the Lumbar Tutor, designed for practicing US-guided lumbar spinal procedures, and (3) the Prostate Biopsy Tutor, configured for US-guided prostate biopsies. The Perk Tutor provides the trainee with quantitative feedback on progress toward the specific learning objectives of each configuration. Configurations were implemented through simple rearrangement of hardware and software components, attesting to the modularity and ease of configuration. The Perk Tutor is provided as a free resource to enable research and development of educational programs for US-guided intervention.
Flow cytometry in impression cytology specimens. A new method for evaluation of conjunctival inflammation. (1997)

Results of this preliminary study confirm that conjunctival epithelial cells may abnormally express inflammatory markers in chronic ocular surface disorders. Development of flow cytometry in analysis of cytologic specimens provides a new, sensitive, and objective tool for exploring conjunctival pathology.
Central Roles of α 5 β 1 Integrin and Fibronectin in Vascular Development in Mouse Embryos and Embryoid Bodies (2002)

Vascular development and maturation are dependent on the interactions of endothelial cell integrins with surrounding extracellular matrix. Previous investigations of the primacy of certain integrins in vascular development have not addressed whether this could also be a secondary effect due to poor embryonic nutrition. Here, we show that the alpha5 integrin subunit and fibronectin have critical roles in blood vessel development in mouse embryos and in embryoid bodies (EBs) differentiated from embryonic stem cells (a situation in which there is no nutritional deficit caused by the mutations). In contrast, vascular development in vivo and in vitro is not strongly dependent on alpha(v) or beta3 integrin subunits. In mouse embryos lacking alpha5 integrin, greatly distended blood vessels are seen in the vitelline yolk sac and in the embryo itself. Additionally, overall blood vessel pattern complexity is reduced in alpha5-null tissues. This defective vascular phenotype is correlated with a decrease in the ligand for alpha5 integrin, fibronectin (FN), in the endothelial basement membranes. A striking and significant reduction in early capillary plexus formation and maturation was apparent in EBs formed from embryonic stem cells lacking alpha5 integrin or FN compared with wild-type EBs or EBs lacking alpha(v) or beta3 integrin subunits. Vessel phenotype could be partially restored to FN-null EBs by the addition of whole FN to the culture system. These findings confirm a clear role for alpha5 and FN in early blood vessel development not dependent on embryo nutrition or alpha(v) or beta3 integrin subunits. Thus, successful early vasculogenesis and angiogenesis require alpha5-FN interactions.