gebhart/patrepeval huggingface dataset:
The 2-5A (pppA2'p5'A2'p5'A) and protein kinase systems in interferon-treated and control cells. (1981)

With respect to interferon action in general: multisite models and analogies with hormone action are in vogue. More particularly, concerning the 2-5A system, the structure of 2-5A has been confirmed. We know that in the cell-free system and intact cell it is unstable and in the absence of a regenerating system transiently activates a nuclease. This nuclease shows some specificity; preferentially cleaving RNA on the 3'-side of UN doublets (UA and UU are preferred). When introduced into the intact cell 2-5A can inhibit protein and DNA synthesis and virus growth. In addition, both 2-5A and core occur naturally in amounts sufficient for them to play a part in the antiviral and antigrowth activities of interferon. Finally, it is possible that the 2-5A system may have a significance beyond its role in interferon action in the control of cell growth or development.
Enhanced-bandwidth PIFA with T-shaped ground plane (2004)

A planar inverted-F antenna (PIFA) with a T-shaped ground plane is presented. The measured results of the proposed antenna show that by using a T-shaped ground plane, the bandwidth of a PIFA can be broadened and the operation frequency of the PIFA can be reduced. The relative measured bandwidth of the proposed antenna operating at 2.05 GHz band is 16.6%.
Synthesis and characterization of PLGA nanoparticles (2006)

Poly(lactide-co-glycolide) (PLGA) nanoparticles of different physical characteristics (size, size distribution, morphology, zeta potential) can be synthesized by controlling the parameters specific to the synthesis method employed. The aim of this review is to clearly, quantitatively and comprehensively describe the top-down synthesis techniques available for PLGA nanoparticle formation, as well as the techniques commonly used for nanoparticle characterization. Many examples are discussed in detail to provide the reader with an extensive knowledge base on the important parameters specific to the synthesis method described and ways in which these parameters can be manipulated to control the nanoparticle physical characteristics.
Scanning probe-enabled nanocombinatorics define the relationship between fibronectin feature size and stem cell fate (2012)

We report the development of a powerful analytical method that utilizes a tilted elastomeric pyramidal pen array in the context of a scanning probe lithography experiment to rapidly prepare libraries having as many as 25 million features over large areas with a range of feature sizes from the nano- to microscale. This technique can be used to probe important chemical and biological processes, opening up the field of nanocombinatorics. In a proof-of-concept investigation of mesenchymal stem cell (MSC) differentiation, combinatorial patterns first enabled a rapid and systematic screening of MSC adhesion, as a function of feature size, while uniform patterns were used to study differentiation with statistically significant sample sizes. Without media containing osteogenic-inducing chemical cues, cells cultured on nanopatterned fibronectin substrates direct MSC differentiation towards osteogenic fates when compared to nonpatterned fibronectin substrates. This powerful and versatile approach enables studies of many systems spanning biology, chemistry, and engineering areas.
Retrograde Viral Delivery of IGF-1 Prolongs Survival in a Mouse ALS Model (2003)

Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neuromuscular disease that is associated with the degeneration of spinal and brainstem motor neurons, leading to atrophy of limb, axial, and respiratory muscles. The cause of ALS is unknown, and there is no effective therapy. Neurotrophic factors are candidates for therapeutic evaluation in ALS. Although chronic delivery of molecules to the central nervous system has proven difficult, we recently discovered that adeno-associated virus can be retrogradely transported efficiently from muscle to motor neurons of the spinal cord. We report that insulin-like growth factor 1 prolongs life and delays disease progression, even when delivered at the time of overt disease symptoms.
Non‐muscle myosin heavy chain (MYH9): A new partner fused to ALK in anaplastic large cell lymphoma (2003)

In anaplastic large cell lymphoma, the ALK gene at 2p23 is known to be fused to NPM, TPM3, TPM4, TFG, ATIC, CLTC, MSN, and ALO17. All of these translocations result in the expression of chimeric ALK transcripts that are translated into fusion proteins with tyrosine kinase activity and oncogenic properties. We report a case showing a restricted cytoplasmic staining pattern of ALK and a novel chromosomal abnormality, t(2;22)(p23;q11.2), demonstrated by fluorescence in situ hybridization analysis. The result of 5' RACE analysis showed that the ALK gene was fused in-frame to a portion of the non-muscle myosin heavy chain gene, MYH9. Nucleotide sequence of the MYH9-ALK chimeric cDNA revealed that the ALK breakpoint was different from all those previously reported. It is localized in the same exonic sequence as MSN-ALK, but 6 bp downstream, resulting in an in-frame fusion of the two partner proteins. In contrast to the previously reported ALK fusion proteins, MYH9-ALK may lack a functional oligomerization domain. However, biochemical analysis showed that the new fusion protein is tyrosine phosphorylated in vivo but seems to lack tyrosine kinase activity in vitro. If further investigations confirm this latter result, the in vivo tyrosine phosphorylation of MYH9-ALK protein could involve mechanisms different from those described in the other ALK hybrid proteins.
AVA: A Video Dataset of Spatio-Temporally Localized Atomic Visual Actions (2018)

This paper introduces a video dataset of spatio-temporally localized Atomic Visual Actions (AVA). The AVA dataset densely annotates 80 atomic visual actions in 437 15-minute video clips, where actions are localized in space and time, resulting in 1.59M action labels with multiple labels per person occurring frequently. The key characteristics of our dataset are: (1) the definition of atomic visual actions, rather than composite actions; (2) precise spatio-temporal annotations with possibly multiple annotations for each person; (3) exhaustive annotation of these atomic actions over 15-minute video clips; (4) people temporally linked across consecutive segments; and (5) using movies to gather a varied set of action representations. This departs from existing datasets for spatio-temporal action recognition, which typically provide sparse annotations for composite actions in short video clips. AVA, with its realistic scene and action complexity, exposes the intrinsic difficulty of action recognition. To benchmark this, we present a novel approach for action localization that builds upon the current state-of-the-art methods, and demonstrates better performance on JHMDB and UCF101-24 categories. While setting a new state of the art on existing datasets, the overall results on AVA are low at 15.8% mAP, underscoring the need for developing new approaches for video understanding.
Trigger-based language models: a maximum entropy approach (1993)

Ongoing efforts at adaptive statistical language modeling are described. To extract information from the document history, trigger pairs are used as the basic information-bearing elements. To combine statistical evidence from multiple triggers, the principle of maximum entropy (ME) is used. To combine the trigger-based model with the static model, the latter is absorbed into the ME formalism. Given consistent statistical evidence, a unique ME solution is guaranteed to exist, and an iterative algorithm exists which is guaranteed to converge to it. Among the advantages of this approach are its simplicity, generality, and incremental nature. Among its disadvantages are its computational requirements. The model described here was trained on five million words of Wall Street Journal text. It used some 40000 unigram constraints, 200000 bigram constraints, 200000 trigram constraints, and 60000 trigger constraints. After 13 iterations, it produced a language model whose perplexity was 12% lower than that of a conventional trigram, as measured on independent data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of melatonin on cancer: studies on MCF-7 human breast cancer cells in culture. (1986)

There is some evidence to suggest that the pineal gland influences neoplastic growth. Either crude or partially-purified pineal extracts have been used to treat malignant neoplasms in humans. More compelling evidence indicates that the pineal hormone melatonin, in addition to its well known antireproductive effects, may also exert oncostatic effects particularly in animal models of human breast cancer. However, it is not clear whether melatonin inhibits mammary cancer growth via an indirect neuroendocrine mechanism or via an action directly on the cancer cells themselves. Studies are described in which physiological concentrations of melatonin are shown to have marked inhibitory effects directly on MCF-7 human breast cancer cell growth in culture. Supra- or subphysiological levels of melatonin are completely ineffective in retarding breast cancer cell proliferation. Precursors and metabolites of melatonin such as serotonin, N-acetylserotonin and 6-hydroxymelatonin do not inhibit MCF-7 cell growth. Similarly, neither 5-methoxytryptophol nor 5-methoxytryptamine, regarded by some to be putative pineal hormones, exhibit antimitogenic properties. Melatonin completely blocks the estradiol-induced stimulation of MCF-7 cell proliferation. In defined, serum-free medium, melatonin loses its antimitogenic capabilities unless cells are also simultaneously exposed to either estradiol or prolactin. Therefore, the antiproliferative effect of melatonin may be dependent on the presence of serum and a complex interaction with hormones such as estradiol and/or prolactin.
A DNA biochip for on-the-spot multiplexed pathogen identification (2006)

Miniaturized integrated DNA analysis systems have largely been based on a multi-chamber design with microfluidic control to process the sample sequentially from one module to another. This microchip design in connection with optics involved hinders the deployment of this technology for point-of-care applications. In this work, we demonstrate the implementation of sample preparation, DNA amplification, and electrochemical detection in a single silicon and glass-based microchamber and its application for the multiplexed detection of Escherichia coli and Bacillus subtilis cells. The microdevice has a thin-film heater and temperature sensor patterned on the silicon substrate. An array of indium tin oxide (ITO) electrodes was constructed within the microchamber as the transduction element. Oligonucleotide probes specific to the target amplicons are individually positioned at each ITO surface by electrochemical copolymerization of pyrrole and pyrrole-probe conjugate. These immobilized probes were stable to the thermal cycling process and were highly selective. The DNA-based identification of the two model pathogens involved a number of steps including a thermal lysis step, magnetic particle-based isolation of the target genomes, asymmetric PCR, and electrochemical sequence-specific detection using silver-enhanced gold nanoparticles. The microchamber platform described here offers a cost-effective and sample-to-answer technology for on-site monitoring of multiple pathogens.
Multiscale Quantization for Fast Similarity Search (2017)

We propose a multiscale quantization approach for fast similarity search on large, high-dimensional datasets. The key insight of the approach is that quantization methods, in particular product quantization, perform poorly when there is large variance in the norms of the data points. This is a common scenario for real- world datasets, especially when doing product quantization of residuals obtained from coarse vector quantization. To address this issue, we propose a multiscale formulation where we learn a separate scalar quantizer of the residual norm scales. All parameters are learned jointly in a stochastic gradient descent framework to minimize the overall quantization error. We provide theoretical motivation for the proposed technique and conduct comprehensive experiments on two large-scale public datasets, demonstrating substantial improvements in recall over existing state-of-the-art methods.
Comparative Genomic Characterization of Three Streptococcus parauberis Strains in Fish Pathogen, as Assessed by Wide-Genome Analyses (2013)

Streptococcus parauberis, which is the main causative agent of streptococcosis among olive flounder (Paralichthys olivaceus) in northeast Asia, can be distinctly divided into two groups (type I and type II) by an agglutination test. Here, the whole genome sequences of two Japanese strains (KRS-02083 and KRS-02109) were determined and compared with the previously determined genome of a Korean strain (KCTC 11537). The genomes of S. parauberis are intermediate in size and have lower GC contents than those of other streptococci. We annotated 2,236 and 2,048 genes in KRS-02083 and KRS-02109, respectively. Our results revealed that the three S. parauberis strains contain different genomic insertions and deletions. In particular, the genomes of Korean and Japanese strains encode different factors for sugar utilization; the former encodes the phosphotransferase system (PTS) for sorbose, whereas the latter encodes proteins for lactose hydrolysis, respectively. And the KRS-02109 strain, specifically, was the type II strain found to be able to resist phage infection through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system and which might contribute valuably to serologically distribution. Thus, our genome-wide association study shows that polymorphisms can affect pathogen responses, providing insight into biological/biochemical pathways and phylogenetic diversity.
The expression of the ubiquitin ligase SIAH2 (seven in absentia homolog 2) is mediated through gene copy number in breast cancer and is associated with a basal-like phenotype and p53 expression (2011)

SIAH2 expression is upregulated in basal-like breast cancers via copy number changes and/or transcriptional activation by p53 and is likely to be partly responsible for the enhanced hypoxic drive through abrogation of the prolyl hydroxylases.
The isolation and structure of a remarkable marine animal antineoplastic constituent: dolastatin 10 (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe isolation and structure of a remarkable marine animal antineoplastic constituent: dolastatin 10George R. Pettit, Yoshiaki Kamano, Cherry L. Herald, Albert A. Tuinman, Fred E. Boettner, Haruhisa Kizu, Jean M. Schmidt, Lubomir Baczynskyj, Kenneth B. Tomer, and Roger J. BontemsCite this: J. Am. Chem. Soc. 1987, 109, 22, 6883–6885Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://doi.org/10.1021/ja00256a070RIGHTS & PERMISSIONSArticle Views1741Altmetric-Citations434LEARN 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 InReddit PDF (380 KB) Get e-Alerts Get e-Alerts
Turbo and trellis-based constructions for source coding with side information (2003)

The problem of rate-distortion efficient constructions is studied for the problem of source coding with side information (SCSI), which has assumed heightened interest. While the Wyner-Ziv theorem from information theory has prescribed rate-distortion performance bounds for the SCSI problem, the gap between theory and practice has remained large. To reduce this gap, two different frameworks are proposed based on a trellis construction and a turbo-based construction respectively. Simulation results on the Gaussian SCSI problem reveal the promise of the proposed approaches: at 1 bit per sample, 0.5 bits/sample, 0.25 bits/sample and 0.125 bits/sample, these constructions attain performance within 1.3 dB, 1.1 dB, 0.85 dB and 0.5 dB respectively of the theoretical Wyner-Ziv rate-distortion bound.
Myogenic Tone and Reactivity of the Rat Ophthalmic Artery (2003)

This study provides the first direct evidence for myogenic autoregulatory properties and pharmacological heterogeneity in the rat ophthalmic artery.
Immunization of Malignant Melanoma Patients with Full-Length NY-ESO-1 Protein Using TLR7 Agonist Imiquimod as Vaccine Adjuvant (2008)

T cell-mediated immunity to microbes and to cancer can be enhanced by the activation of dendritic cells (DCs) via TLRs. In this study, we evaluated the safety and feasibility of topical imiquimod, a TLR7 agonist, in a series of vaccinations against the cancer/testis Ag NY-ESO-1 in patients with malignant melanoma. Recombinant, full-length NY-ESO-1 protein was administered intradermally into imiquimod preconditioned sites followed by additional topical applications of imiquimod. The regimen was very well tolerated with only mild and transient local reactions and constitutional symptoms. Secondarily, we examined the systemic immune response induced by the imiquimod/NY-ESO-1 combination, and show that it elicited both humoral and cellular responses in a significant fraction of patients. Skin biopsies were assessed for imiquimod's in situ immunomodulatory effects. Compared with untreated skin, topical imiquimod induced dermal mononuclear cell infiltrates in all patients composed primarily of T cells, monocytes, macrophages, myeloid DCs, NK cells, and, to a lesser extent, plasmacytoid DCs. DC activation was evident. This study demonstrates the feasibility and excellent safety profile of a topically applied TLR7 agonist used as a vaccine adjuvant in cancer patients. Imiquimod's adjuvant effects require further evaluation and likely need optimization of parameters such as formulation, dose, and timing relative to Ag exposure for maximal immunogenicity.
Genetic requirements and mutational specificity of the Escherichia coli SOS mutator activity (1997)

To better understand the mechanisms of SOS mutagenesis in the bacterium Escherichia coli, we have undertaken a genetic analysis of the SOS mutator activity. The SOS mutator activity results from constitutive expression of the SOS system in strains carrying a constitutively activated RecA protein (RecA730). We show that the SOS mutator activity is not enhanced in strains containing deficiencies in the uvrABC nucleotide excision-repair system or the xth and nfo base excision-repair systems. Further, recA730-induced errors are shown to be corrected by the MutHLS-dependent mismatch-repair system as efficiently as the corresponding errors in the rec+ background. These results suggest that the SOS mutator activity does not reflect mutagenesis at so-called cryptic lesions but instead represents an amplification of normally occurring DNA polymerase errors. Analysis of the base-pair-substitution mutations induced by recA730 in a mismatch repair-deficient background shows that both transition and transversion errors are amplified, although the effect is much larger for transversions than for transitions. Analysis of the mutator effect in various dnaE strains, including dnaE antimutators, as well as in proofreading-deficient dnaQ (mutD) strains suggests that in recA730 strains, two types of replication errors occur in parallel: (i) normal replication errors that are subject to both exonucleolytic proofreading and dnaE antimutator effects and (ii) recA730-specific errors that are not susceptible to either proofreading or dnaE antimutator effects. The combined data are consistent with a model suggesting that in recA730 cells error-prone replication complexes are assembled at sites where DNA polymerization is temporarily stalled, most likely when a normal polymerase insertion error has created a poorly extendable terminal mismatch. The modified complex forces extension of the mismatch largely at the exclusion of proofreading and polymerase dissociation pathways. SOS mutagenesis targeted at replication-blocking DNA lesions likely proceeds in the same manner.
Unsupervised Word Sense Disambiguation Using The WWW (2006)

This paper presents a novel unsupervised methodology for automatic disambiguation of nouns found in unrestricted corpora. The proposed method is based on extending the context of a target word by querying the web, and then measuring the overlap of the extended context with the topic signatures of the different senses by using Bayes rule. The algorithm is evaluated on Semcor 2.0. The evaluation showed that the web-based extension of the target word’s local context increases the amount of contextual information to perform semantic interpretation, in effect producing a disambiguation methodology, which achieves a result comparable to the performance of the best system in SENSEVAL 3.
Peak power reduction of space-time coded OFDM signals (2005)

Peak power reduction in space-time coded orthogonal frequency division multiplexing (OFDM) systems is a challenging task. Most of the current peak power reduction schemes reduce the peak power by manipulating the signal at the final IDFT process. However, in the case of space-time coded OFDM, any processing at this stage would violate the space-time code structure, making its detection at the receiver impossible. The paper shows that selected mapping (SLM) reduces the peak power of space-time coded OFDM signals without violating the space-time code. Reduced peak power of the OFDM signal relaxes the strict dynamic range requirements of the transmitter.