gebhart/patrepeval huggingface dataset:
Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis (2004)

Jasmonates (JA) are important regulators of plant defense responses that activate expression of many wound-induced genes including the tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes. Elements required for JA induction of the LAP gene are all present in the -317 to -78 proximal promoter region. Using yeast one-hybrid screening, we have identified the bHLH-leu zipper JAMYC2 and JAMYC10 proteins, specifically recognizing a T/G-box AACGTG motif in this promoter fragment. Mutation of the G-box element decreases JA-responsive LAP promoter expression. Expression of JAMYC2 and JAMYC10 is induced by JA, with a kinetics that precedes that of the LAP or pin2 transcripts. JAMYC overexpression enhanced JA-induced expression of these defense genes in potato, but did not result in constitutive transcript accumulation. Using footprinting assays, an additional protected element was identified, located directly adjacent to the T/G-box motif. Mutation of this element abolishes JA response, showing that recognition of this duplicated element is also required for gene expression. Knockout mutants in the AtMYC2 homolog gene of Arabidopsis are insensitive to JA and exhibit a decreased activation of the JA-responsive genes AtVSP and JR1. Activation of the PDF1.2 and b-CHI, ethylene/JA-responsive genes, is, however, increased in these mutants. These results show that the JAMYC/AtMYC2 transcription factors function as members of a MYC-based regulatory system conserved in dicotyledonous plants with a key role in JA-induced defense gene activation.
Time and frequency offset estimation in OFDM systems employing pulse shaping (2002)

Time and frequency offset estimation is addressed in an OFDM system that uses a cyclic prefix and pulse shaping. Earlier work has presented a method that avoids the use of pilots by exploiting the inherent correlation in the cyclically extended OFDM symbol. In this paper this technique is extended to include systems with pulse shaping. The joint maximum likelihood estimator of time and frequency offsets for such systems is presented and evaluated. An implementable structure of the extended estimator is given. Simulations show that it is possible to maintain the performance when introducing pulse shaping into an OFDM system.
Restoration of normal morphology and estrogen responsiveness in cultured vaginal and uterine epithelia transplanted with stroma. (1986)

We have investigated the capacity of vaginal and uterine epithelia (VE and UE) to reexpress normal morphology and hormone responsiveness following cell culture. VE and UE from adult ovariectomized mice were grown in a collagen gel matrix with serum-free medium for 7-10 days. Proliferation of these cells occurs in the absence of 17 beta-estradiol and is not stimulated by 17 beta-estradiol; the VE usually does not keratinize or stratify in vitro. Cultured VE and UE were recombined with homologous vaginal or uterine stroma (VS and US, respectively) and these recombinants were grown under the renal capsule of female hosts for 4 weeks. The epithelium of the VS + VE recombinants cycled, proliferated and stratified in response to estrogen and mucified normally in response to progesterone. The UE that was grown in vivo with cultured US also showed normal morphology and estrogen responsiveness. These changes in the UE and VE were not simply a result of return to the in vivo environment, as epithelia alone in collagen gels transplanted under the renal capsule did not survive. These results indicate that both VE and UE, which are not estrogen-dependent in vitro, reexpress their estrogen dependency and normal morphology when recombined with homologous stroma and grown in vivo. Thus, the changes these cells show when grown in culture are the result of altered conditions in vitro rather than an irreversible alteration in the cells themselves or the selection of specific subpopulations that are not mitogenically or morphologically responsive to estrogen under any condition.
Mixture Model-based Minimum Bayes Risk Decoding using Multiple Machine Translation Systems (2010)

We present Mixture Model-based Minimum Bayes Risk (MMMBR) decoding, an approach that makes use of multiple SMT systems to improve translation accuracy. Unlike existing MBR decoding methods defined on the basis of single SMT systems, an MMMBR decoder reranks translation outputs in the combined search space of multiple systems using the MBR decision rule and a mixture distribution of component SMT models for translation hypotheses. MMMBR decoding is a general method that is independent of specific SMT models and can be applied to various commonly used search spaces. Experimental results on the NIST Chinese-to-English MT evaluation tasks show that our approach brings significant improvements to single system-based MBR decoding and outperforms a state-of-the-art system combination method.
Advances in interactive digital multimedia systems (1991)

This paper introduces basic concepts in digital multimedia systems and surveys recent literature. Background is provided regarding developments in interactive videodiscs, which first made images and video accessible through computer systems. Digital storage media, including optical, magnetic, and network options, are addressed. The characteristics of audio and video and their digital representations are discussed. Because these media are so demanding of space and channel bandwidth, compression methods are reviewed. Standards for digital multimedia are considered. Current multimedia systems are described, and future prospects are indicated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Intrinsic fluorescence spectroscopy in turbid media: disentangling effects of scattering and absorption (2001)

The fluorescence from a turbid medium such as biologic tissue contains information about scattering and absorption, as well as the intrinsic fluorescence, i.e., the fluorescence from an optically thin sample of pure fluorophores. The interplay of scattering and absorption can result in severe distortion of the intrinsic spectral features. These distortions can be removed by use of a photon-migration-based picture and information from simultaneously acquired fluorescence and reflectance spectra. We present experimental evidence demonstrating the validity of such an approach for extracting the intrinsic fluorescence for a wide range of scatterer and absorber concentrations in tissue models, ex vivo and in vivo tissues. We show that variations in line shape and intensity in intrinsic tissue fluorescence are significantly reduced compared with the corresponding measured fluorescence.
Polyphosphazenes with etheric side groups: prospective biomedical and solid electrolyte polymers (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolyphosphazenes with etheric side groups: prospective biomedical and solid electrolyte polymersHarry R. Allcock, Paul E. Austin, Thomas X. Neenan, John T. Sisko, Peter M. Blonsky, and Duward F. ShriverCite this: Macromolecules 1986, 19, 6, 1508–1512Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://pubs.acs.org/doi/10.1021/ma00160a003https://doi.org/10.1021/ma00160a003research-articleACS PublicationsRequest reuse permissionsArticle Views656Altmetric-Citations126LEARN 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
Divalent metal ion catalysis in the hydrolysis of esters of picolinic acid. Metal ion promoted hydroxide ion and water catalyzed reactions (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDivalent metal ion catalysis in the hydrolysis of esters of picolinic acid. Metal ion promoted hydroxide ion and water catalyzed reactionsThomas H. Fife and Theodore J. PrzystasCite this: J. Am. Chem. Soc. 1985, 107, 4, 1041–1047Publication Date (Print):February 1, 1985Publication History Published online1 May 2002Published inissue 1 February 1985https://pubs.acs.org/doi/10.1021/ja00290a048https://doi.org/10.1021/ja00290a048research-articleACS PublicationsRequest reuse permissionsArticle Views1265Altmetric-Citations82LEARN 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
Antifungal Steroid Saponins fromDioscorea cayenensis (2004)

From the rhizomes of Dioscorea cayenensis Lam.-Holl (Dioscoreaceae), the new 26- O- beta- D-glucopyranosyl-22-methoxy-3 beta,26-dihydroxy-25( R)-furost-5-en-3- O- alpha- L-rhamnopyranosyl-(1-->4)- alpha- L-rhamnopyranosyl-(1-->4)-[ alpha- L-rhamnopyranosyl-(1-->2)]- beta- D-glucopyranoside ( 1) was isolated together with the known dioscin ( 2) and diosgenin 3- O- alpha- L-rhamnopyranosyl-(1-->4)- alpha- L-rhamnopyranosyl-(1-->4)-[ alpha- L-rhamnopyranosyl-(1-->2)]- beta- D-glucopyranoside ( 3). Their structures were established on the basis of spectral data. Compound 2 exhibited antifungal activity against the human pathogenic yeasts Candida albicans, C. glabrata and C. tropicalis (MICs of 12.5, 12.5 and 25 micro g/mL, respectively) whereas 3 showed weak activity and 1 was inactive.
Software Techniques for Scratchpad Memory Management (2015)

Scratchpad memory is commonly encountered in embedded systems as an alternative or supplement to caches [3], however, cache-containing architectures continue to be preferred in many applications due to their general ease of programmability. A language-agnostic software management system is envisioned that improves portability to scratchpad architectures and significantly lowers power consumption of ported applications. We review a selection of existing techniques, discuss their applicability to various memory systems, and identify opportunities for applying new methods and optimizations to improve memory management on relevant architectures.
Packet Transactions: A Programming Model for Data-Plane Algorithms at Hardware Speed (2015)

Data-plane algorithms execute on every packet traversing a network switch; they encompass many schemes for congestion control, network measurement, active-queue management, and load balancing. Because these algorithms are implemented in hardware today, they cannot be changed after being built. To address this problem, recent work has proposed designs for programmable line-rate switches. However, the languages to program them closely resemble the underlying hardware, rendering them inconvenient for this purpose. 
This paper presents Domino, a C-like imperative language to express data-plane algorithms. Domino introduces the notion of a packet transaction, defined as a sequential code block that is atomic and isolated from other such code blocks. The Domino compiler compiles Domino code to PISA, a family of abstract machines based on emerging programmable switch chipsets. We show how Domino enables several data-plane algorithms written in C syntax to run at hardware line rates.
Medullary carcinoma of the breast. An unusual cytologic finding in cyst fluid aspirates (1990)

Cystic medullary carcinoma of the breast is unusual. This report describes five patients with medullary carcinoma who presented clinically with a breast cyst. Fine-needle aspiration biopsy (NAB) was performed as part of the initial physical examination and the retrieved cyst fluid was examined cytologically. Four of the five patients were premenopausal, more typical of benign cystic disease and significantly younger than the average (60+ years) for other forms of cystic breast carcinoma. Only three of the five patients demonstrated suspicious findings of hemorrhagic cyst fluid, a residual mass after NAB, or refilling of the cyst. Due to the relatively young age of most patients, the innocuous clinical presentation, and the abundant inflammatory component noted in the aspiration biopsy cytologic study (ABC), misinterpretation as an inflamed cyst is possible. The ABC of cystic medullary carcinoma is presented with histologic correlation.
In vitro construction and characterization of phoA-lacZ gene fusions in Escherichia coli (1983)

Using recombinant DNA techniques, we have constructed phoA-lacZ gene fusions. Two of the fusions encode hybrid proteins containing approximately half of alkaline phosphatase at the amino terminus joined to beta-galactosidase. For the one fusion strain analyzed in detail, it was shown that the hybrid protein is found in the membrane fraction of cells. In its membrane location, the beta-galactosidase activity of the hybrid is not sufficient to support cell growth on lactose. Unexpectedly, fusions containing phoA and lacZ joined in the wrong translational reading frame were also obtained. These fusions direct the phosphate-regulated synthesis of beta-galactosidase, apparently via a translation restart mechanism. Thus, when gene fusions are constructed, the presence of properly regulated beta-galactosidase activity does not necessarily indicate that a hybrid protein is being produced.
Netrins Promote Developmental and Therapeutic Angiogenesis (2006)

Axonal guidance and vascular patterning share several guidance cues, including proteins in the netrin family. We demonstrate that netrins stimulate proliferation, migration, and tube formation of human endothelial cells in vitro and that this stimulation is independent of known netrin receptors. Suppression of netrin1a messenger RNA in zebrafish inhibits vascular sprouting, implying a proangiogenic role for netrins during vertebrate development. We also show that netrins accelerate neovascularization in an in vivo model of ischemia and that they reverse neuropathy and vasculopathy in a diabetic murine model. We propose that the attractive vascular and neural guidance functions of netrins offer a unique therapeutic potential.
Channel codes classical and modern (2009)

Channel coding lies at the heart of digital communication and data storage, and this detailed introduction describes the core theory as well as decoding algorithms, implementation details, and performance analyses. In this book, Professors Ryan and Lin provide clear information on modern channel codes, including turbo and low-density parity-check (LDPC) codes. They also present detailed coverage of BCH codes, Reed-Solomon codes, convolutional codes, finite geometry codes, and product codes, providing a one-stop resource for both classical and modern coding techniques. Assuming no prior knowledge in the field of channel coding, the opening chapters begin with basic theory to introduce newcomers to the subject. Later chapters then extend to advanced topics such as code ensemble performance analyses and algebraic code design. 250 varied and stimulating end-of-chapter problems are also included to test and enhance learning, making this an essential resource for students and practitioners alike
Inhibiting the Evolution of Antibiotic Resistance (2018)

Efforts to battle antimicrobial resistance (AMR) are generally focused on developing novel antibiotics. However, history shows that resistance arises regardless of the nature or potency of new drugs. Here, we propose and provide evidence for an alternate strategy to resolve this problem: inhibiting evolution. We determined that the DNA translocase Mfd is an "evolvability factor" that promotes mutagenesis and is required for rapid resistance development to all antibiotics tested across highly divergent bacterial species. Importantly, hypermutator alleles that accelerate AMR development did not arise without Mfd, at least during evolution of trimethoprim resistance. We also show that Mfd's role in AMR development depends on its interactions with the RNA polymerase subunit RpoB and the nucleotide excision repair protein UvrA. Our findings suggest that AMR development can be inhibited through inactivation of evolvability factors (potentially with "anti-evolution" drugs)-in particular, Mfd-providing an unexplored route toward battling the AMR crisis.
A cell surface antigen (BAL) defined by a mouse monoclonal antibody inducing apoptosis in a human lymphocytic leukemia cell line (1994)

The lack of apoptosis or programmed cell death in human tumor cells has been suggested to be one factor allowing uncontrolled growth of neoplasms. We have developed a mouse monoclonal antibody (MAb) that induces programmed cell death in a human acute leukemia cell line (KM-3) of the pre B-cell type. Stable, antibody-producing hybridomas were produced by fusing mouse myeloma cells to spleen cells from mice immunized with viable KM-3 cells. Incubation of KM-3 cells with the MAb (designated anti-BAL) resulted in growth inhibition and subsequent cell death within 2-3 days. Anti-BAL required cross-linking with a rabbit anti-mouse antibody to induce DNA fragmentation typical of apoptosis. Immunoblotting experiments with anti-BAL identified a 37-kDa protein, apparently different from any previously described apoptosis-related surface antigen. Strongest expression of the antigen was generally found on cells of lymphoid or myeloid origin. However, several other cell types such as fibroblasts and endothelial cells were also stained by anti-BAL in flow cytometry but less intensively. Despite the apparent presence of this cell surface-bound 37-kDa antigen on several normal and malignant cell types, anti-BAL induced cell death only in human malignant cell lines expressing a more immature phenotype.
Genotypic and Antimicrobial Characterisation ofPropionibacterium acnesIsolates from Surgically Excised Lumbar Disc Herniations (2013)

The anaerobic skin commensal Propionibacterium acnes is an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised from each of 64 patients with lumbar disc herniation. P. acnes and other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence of P. acnes in their excised herniated disc tissue. Using recA and mAb typing methods, 52% of the isolates were type II (50% of culture-positive patients), while type IA strains accounted for 28% of isolates (42% patients). Type III (11% isolates; 21% patients) and type IB strains (9% isolates; 17% patients) were detected less frequently. The MIC values for all isolates were lowest for amoxicillin, ciprofloxacin, erythromycin, rifampicin, tetracycline, and vancomycin (≤1 mg/L). The MIC for fusidic acid was 1-2 mg/L. The MIC for trimethoprim and gentamicin was 2 to ≥4 mg/L. The demonstration that type II and III strains, which are not frequently recovered from skin, predominated within our isolate collection (63%) suggests that the role of P. acnes in lumbar disc herniation should not be readily dismissed.
Identification of Distinct Sequences in Human Blood Coagulation Factor Xa and Prothrombin Essential for Substrate and Cofactor Recognition in the Prothrombinase Complex (2003)

To identify amino acid sequences in factor Xa (fXa) and prothrombin (fII) that may be involved in prothrombinase complex (fXa.factor Va.fII.phospholipids) assembly, synthetic peptides based on fXa and fII sequences were prepared and screened for their ability to inhibit fXa-induced clotting of normal plasma. One fII peptide (PT557-571 homologous to chymotrypsin (CHT) residues 225-239) and two fXa peptides (X404-418, CHT231-244, and X415-429, CHT241-252C) potently inhibited plasma clotting and prothrombinase activity with 50% inhibition between 41 and 115 microM peptide. Inhibition of prothrombinase by PT557-571 and X415-429 was fVa-independent, whereas the inhibition by X404-418 was fVa-dependent. X404-418 inhibited the binding of fVa to fluorescein-labeled, inhibited fXai in the presence of phosphatidylcholine/phosphatidylserine vesicles, whereas X415-429 inhibited binding of fII to phospholipid-bound fluorescein-labeled, inhibited fXai. PT557-571 altered the fluorescence emission of fluorescein-labeled fXai, showing that PT557-571 binds to fXai. These data suggest that residues 404-418 in fXa provide fVa binding sites, whereas residues 557-571 in fII and 415-429 in fXa mediate interactions between fXa and fII in the prothrombinase complex.
Three-dimensional computer vision: a geometric viewpoint (1994)

Projective geometry modelling and calibrating cameras edge detection representing geometric primitives and their uncertainty stereo vision determining discrete motion from points and lines tracking tokens over time motion fields of curves interpolating and approximating three-dimensional data recognizing and locating objects and places answers to problems. Appendices: constrained optimization some results from algebraic geometry differential geometry.
Animal models of polycystic kidney disease (1995)

Polycystic kidney disease (PKD) is one of the most prevalent causes of heritable renal failure. The disease is characterized by the occurrence of numerous fluid-filled cysts within the parenchyma of kidney. The cysts are epithelial in origin and expand in size, leading to crowding of normal kidney tissue. Ultimately, there is gross enlargement of the kidneys with loss of normal functions, and death usually occurs because of complications related to renal failure. Animal models of polycystic kidney disease are proving to be extremely useful for studying the molecular basis of renal cyst formation and for the isolation of genes carrying the mutations. This article describes the various animal models of polycystic kidney disease, spontaneously and experimentally derived, that have recently been identified.