gebhart/patrepeval huggingface dataset:
Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries (2004)

Comprehensive identification of sequences that regulate transcription is one of the major goals of genome biology. Focal alteration in chromatin structure in vivo, detectable through hypersensitivity to DNaseI and other nucleases, is the sine qua non of a diverse cast of transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions. We developed an approach for genome-scale identification of DNaseI hypersensitive sites (HSs) via isolation and cloning of in vivo DNaseI cleavage sites to create libraries of active chromatin sequences (ACSs). Here, we describe analysis of >61,000 ACSs derived from erythroid cells. We observed peaks in the density of ACSs at the transcriptional start sites of known genes at non-gene-associated CpG islands, and, to a lesser degree, at evolutionarily conserved noncoding sequences. Peaks in ACS density paralleled the distribution of DNaseI HSs. ACSs and DNaseI HSs were distributed between both expressed and nonexpressed genes, suggesting that a large proportion of genes reside within open chromatin domains. The results permit a quantitative approximation of the distribution of HSs and classical cis-regulatory sequences in the human genome.
War1p, a Novel Transcription Factor Controlling Weak Acid Stress Response in Yeast (2003)

The Saccharomyces cerevisiae ATP-binding cassette (ABC) transporter Pdr12p effluxes weak acids such as sorbate and benzoate, thus mediating stress adaptation. In this study, we identify a novel transcription factor, War1p, as the regulator of this stress adaptation through transcriptional induction of PDR12. Cells lacking War1p are weak acid hypersensitive, since they fail to induce Pdr12p. The nuclear Zn2Cys6 transcriptional regulator War1p forms homodimers and is rapidly phosphorylated upon sorbate stress. The appearance of phosphorylated War1p isoforms coincides with transcriptional activation of PDR12. Promoter deletion analysis identified a novel cis-acting weak acid response element (WARE) in the PDR12 promoter required for PDR12 induction. War1p recognizes and decorates the WARE both in vitro and in vivo, as demonstrated by band shift assays and in vivo footprinting. Importantly, War1p occupies the WARE in the presence and absence of stress, demonstrating constitutive DNA binding in vivo. Our results suggest that weak acid stress triggers phosphorylation and perhaps activation of War1p. In turn, War1p activation is necessary for the induction of PDR12 through a novel signal transduction event that elicits weak organic acid stress adaptation.
QoS measurement of Real Time Multimedia services on the Internet (1999)

Real-time applications such as IP telephony, Internet radio stations and video conferencing tools require certain levels of QoS (Quality of Service). Because the Internet is still a best-effort network, the QoS of these applications must be measured and monitored in order to provide feedbacks to applications for rate and/or error control, and to both end-users and service providers. A standardized objective measurement technology makes it possible to compare between service providers in a fair way. We address the problems of packet delay and loss measurement, since they are the major determining factor of multimedia quality. We first describe the problems and techniques in obtaining good measurement results. Then, we discuss the modeling and analysis of delay and loss. Our goal is to establish feasible metrics that can reliably predict perceived quality. We find that the extended Gilbert model (2-state being a special case) is a suitable loss model,and the inter-loss distance metric is useful in capturing the burstiness between loss runs. For delay, besides the autocorrelation metric, a conditional cumulative distribution function may be useful. We apply these models to some of our Internet packet traces,and find that losses are generally bursty, and that delays usually have a strong temporal dependency component. We also find that the final loss pattern after applying playout delay adjustment (and FEC if used) still corresponds well to the extended Gilbert model.
Sphingosine-1-Phosphate Receptor-1 Selective Agonist Enhances Collateral Growth and Protects against Subsequent Stroke (2015)

These results suggest that S1PR1 is one of the principal regulators of leptomeningeal collateral recruitment at the site of increased shear stress and provide evidence that an S1PR1 selective agonist has a role in promoting collateral growth and preventing of ischemic damage and neurological dysfunction after subsequent stroke in patients with intracranial major artery stenosis or occlusion.
CW-laser-pumped telecom-band polarization-entangled photon-pair source with a fidelity of 97.8% (2011)

Quantum entanglement is one of the most important resources for quantum communication, information and computing. Since active polarization stabilization methods could alleviate the polarization-drift problem over optical fibre, telecom-band polarization-entangled photon-pairs can be well distributed and shared. Spontaneous four-wave mixing in a dispersion-shifted fibre (DSF) can be used to realize a source of telecom-band polarization-entangled photon pairs, but DSF is often cooled to suppress noise photons generated by spontaneous Raman-scattering. Second-order nonlinear crystals or waveguides such as periodically-poled lithium niobate (PPLN) waveguides are also available and generation has been reported on the conditions of careful selection of two nearly identical nonlinear crystals or accurate temperature-control of waveguides.
The Glutamine-Rich Activation Domains of Human Sp1 Do Not Stimulate Transcription in <i>Saccharomyces cerevisiae</i> (1995)

Eukaryotic transcriptional activators have been classified on the basis of the characteristics of their activation domains. Acidic activation domains, such as those in the yeast GAL4 or GNC4 proteins and the herpes simplex virus activator VP16, stimulate RNA polymerase II transcription when introduced into a variety of eukaryotic cells. This species interchangeability demonstrates that the mechanism by which acidic activation domains function is highly conserved in the eukaryotic kingdom. To determine whether such a conservation of function exists for a different class of activation domain, we have tested whether the glutamine-rich activation domains of the human transcriptional activator Sp1 function in the yeast Saccharomyces cerevisiae. We report here that the glutamine-rich domains of Sp1 do not stimulate transcription in S. cerevisiae, even when accompanied by human TATA-box binding protein (TBP) or human-yeast TATA-box binding protein hybrids. Thus, in contrast to the case for acidic activation domains, the mechanism by which glutamine-rich domains stimulate transcription is not conserved between S. cerevisiae and humans.
Non-uniform residual stresses for parallel assembly of out-of-plane surface-micromachined structures (2006)

This note describes a method for the parallel self-assembly of out-of-plane surface-micromachined structures that uses non-uniform residual stresses, inherent in many surface-micromachining processes. The residual stresses are used to achieve a one-time only actuation capable of lifting and assembling raised structures. Theory is provided to calculate the deflection and stiffness of bi-layer cantilevers. Devices for amplifying the vertical deflection are demonstrated and used to assemble large arrays of devices.
Multiple Electrophoretic Zones Arising from Protein-Buffer Interaction<sup>*</sup> (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiple Electrophoretic Zones Arising from Protein-Buffer Interaction*John R. CannCite this: Biochemistry 1966, 5, 3, 1108–1112Publication Date (Print):March 1, 1966Publication History Published online1 May 2002Published inissue 1 March 1966https://doi.org/10.1021/bi00867a042Request reuse permissionsArticle Views78Altmetric-Citations52LEARN 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 (2 MB) Get e-Alertsclose Get e-Alerts
Limitations of a QRS scoring system to assess left ventricular function and prognosis at hospital discharge after myocardial infarction. (1985)

The value of a QRS scoring system derived from 12 lead electrocardiograms to estimate left ventricular ejection fraction was assessed in a prospective study of 285 hospital survivors of myocardial infarction. In these patients both the QRS score and ejection fraction were measured by radionuclide ventriculography at discharge. The correlation between ejection fraction and QRS score was weak. In 22 patients who died during six to 12 months follow up the ability of the ejection fraction and QRS score to predict mortality was assessed in terms of sensitivity, specificity, predictive value of a positive and negative test, and efficiency. For ejection fraction less than 40% and a QRS score greater than or equal to 6 sensitivity was respectively 73% and 64%, specificity 73% and 56%, predictive value of a positive test 18% and 11%, predictive value of a negative test 97% and 95%, and efficiency 73% and 56%. Both ejection fraction and QRS score may be used to identify patients at low and high risk during one year follow up, but, contrary to initial expectations, the QRS score appears to be of little value in estimating ejection fraction and is less accurate than ejection fraction in predicting late survival in hospital survivors of myocardial infarction.
VIISta 810 dosimetry performance (2003)

Details of the dosimetry system for the Varian VIISta 810 medium current implanter are described. The system design provides improvements to the VSEA E-series implanters. The wafer scan velocity is variable, allowing a better match of the dose to the number of wafer scans, which in turn enables higher wafer throughput. Detailed vertical uniformity information is uploaded to the control system host computer enabling interrupted implants to be completed at another time, even on a different VIISta 810. Data is presented demonstrating the dosimetry performance for top off, glitched and high-tilt implants.
A rapid synthesis of high aspect ratio copper nanowires for high-performance transparent conducting films (2013)

This communication presents a way to produce copper nanowires with aspect ratios as high as 5700 in 30 min, and describes the growth processes responsible for their formation. These nanowires were used to make transparent conducting films with a transmittance >95% at a sheet resistance <100 Ω sq(-1).
Overexpression of p53 and HER-2/neu Proteins as Prognostic Markers in Early Stage Breast Cancer (1994)

The p53 and HER-2/neu oncogenes have proven but limited prognostic value. An approach that combines several molecular genetic markers with established pathologic criteria may help physicians to make more accurate predictions of prognosis in patients with early stage breast cancer.
Copolymerization parameters (1961)

Abstract Copolymerization parameters, Q and e , have been calculated for several monomers whose relative reactivity ratios, r 1 and r 2 , are available. The ratios and parameters are tabulated in an effort to bring the various data in the literature to a single source of reference.
Crown Gall Disease and Hairy Root Disease (1990)

The neoplastic diseases crown gall and hairy root are incited by the phytopathogenic bacteria Agrobacterium tumefaciens and Agrobacterium rhizogenes, respectively. Although the molecular mechanism of T-DNA transfer to the plant most likely is the same for both species, the physiological basis of tumorigenesis is fundamentally different. Crown gall tumors result from the over-production of the phytohormones auxin and cytokinin specified by A. tumefaciens T-DNA genes. Although the T-DNA of some Riplasmids of A. rhizogenes contains auxin biosynthetic genes, these loci are not always necessary for hairy root formation. Recent experiments suggest that hairy root tumors result from the increased sensitivity of transformed cells to endogenous auxin levels. An understanding of hairy root tumorigenesis will likely result in an increased knowledge of plant developmental processes.
Integrating databases with publish/subscribe (2005)

Publish/subscribe is emerging as an appropriate communication paradigm for large-scale, widely-distributed systems. In this paper, we describe our work on integrating active databases with publish/subscribe, using PostgreSQL and Hermes as the experimental context. In the proposed architecture, each database manager defines and advertises change events, in contrast with a continuous query model. Advertised events, which may span a number of physical relations, correspond to the virtual relations of a security view. Clients subscribe to events of interest, and can refine their subscriptions through content-based filter expressions. An event is published whenever a database change, detected via a dynamic triggering layer, matches some active subscription. Security and routing of database events are handled in the same way as for conventional Hermes events.
A Framework for Appraising Educational Reforms (1996)

Transaction-cost economics provides a framework for appraising educational reforms, i.e., deciding whether these reforms are likely to succeed in the “real life” of schools. This framework conceives of reform as a contract between reformers and stake-holders (teachers, students, parents), and these transactions are marked by bounded rationality, opportunism, and the protection of specific assets (e.g., accumulated knowledge and skills) on the part of participants. Not acknowledging these attributes turns reforms into unproductive planning exercises—mere promises without results—or stakeholders struggling to protect their assets, resulting in the failure of the reform. Several current educational reforms are judged on the basis of their transaction costs and consequent prospects for success.
Signature recognition state-of-the-art (2005)

A summarization of one of the most successful behavioral biometric recognition methods: signature recognition. Probably this is one of the oldest biometric recognition methods, with high legal acceptance. Technological advances have made possible new perspectives for signature recognition, by means of capturing devices which provide more than the simple signature image: pressure, acceleration, etc., making it even more difficult to forge a signature.
A decision support system for the optimal planning of a weather radar network: a case study (2002)

A methodology that allows defining the optimal planning of a weather radar network (WRN) is presented. This methodology allows defining the optimal siting of a WRN selecting up to W optimal sites out of N eligible sites according to the optimization of a planning cost function. Several aspects affecting the planning decision, including ter- rain blockage, the need to measure with two Doppler weather radars in some regions, and the environmental impact of their installation, are taken into account using a proper mathemati- cal formulation. The decisional problem takes on a form that closely resembles a well-known combinatorial optimization problem, i.e., the weighted set-covering problem. The pro- posed mathematical approach can serve as a methodological basis of a decision support system, whose function is to as- sist decision makers in the selection of optimal sites for the installation of weather radars in a given region. In this paper, the methodology is presented and an application to the case study of the planning of the forthcoming Italian WRN is pre- sented.
Two-frequency secondary radar incorporating passive transponders (1973)

A radar technique incorporating a simultaneous transmission on different frequencies is described. It is used with passive transponders employing nonlinear diodes that mix the two carrier frequencies and use one of the intermodulation frequencies to generate a reply from the transponder.
The chondrogenic transcription factor Sox9 is a target of signaling by the parathyroid hormone-related peptide in the growth plate of endochondral bones (2000)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The Catabolic Fate of Hyaluronic Acid (1986)

Part of the hyaluronic acid (HA) synthesized in peripheral tissues enters the blood circulation through the lymph. It is rapidly taken up by the endothelial cells in the liver (half-life in blood is 2.5-5.5 minutes) and degraded. Pure primary cultures of liver endothelial cells were obtained by a newly developed technique and used to follow the metabolism of the polysaccharide on the cell surface. At 37 degrees C the HA is effectively endocytosed and degraded to acetate and lactate. A radioassay specific for HA and sensitive in the nanogram range has been developed to follow the concentration of HA in serum. The normal level in man is 10 to 100 micrograms/l. Elevated serum levels of HA are seen in liver cirrhosis, rheumatoid arthritis and scleroderma indicating that both an impaired catabolism in the liver and an increased synthesis in the peripheral tissues can modify the HA level.
Domain adaptive training BERT for response selection (2019)

We focus on multi-turn response selection in a retrieval-based dialog system. In this paper, we utilize the powerful pre-trained language model Bi-directional Encoder Representations from Transformer (BERT) for a multi-turn dialog system and propose a highly effective post-training method on domain-specific corpus. Although BERT is easily adopted to various NLP tasks and outperforms previous baselines of each task, it still has limitations if a task corpus is too focused on a certain domain. Post-training on domain-specific corpus (e.g., Ubuntu Corpus) helps the model to train contextualized representations and words that do not appear in general corpus (e.g.,English Wikipedia). Experiment results show that our approach achieves new state-of-the-art on two response selection benchmark datasets (i.e.,Ubuntu Corpus V1, Advising Corpus) performance improvement by 5.9% and 6% on Recall@1.
Reverse DRC channel performance analysis for 1xEV-Do: third generation high-speed wireless data systems (2003)

In systems based on the 1xEV-Do standard (also known as IS-856), the access terminal (AT) measures the channel condition and reports it through the reverse-link data rate control (DRC) channel to accommodate asymmetric high-speed forward-link data traffic. Although a high DRC rate can provide better forward-link channel estimation, resulting in a more accurate channel assignment, the rise in generated noise on the reverse link degrades the reverse-link capacity. To understand the impact on forward-link and reverse-link capacity, link-level simulations were performed to determine the required E/sub b//N/sub 0/ for a given slot-error-rate criterion in the DRC channel. The tradeoff between the erasure rate and the required E/sub b//N/sub 0/ in the DRC channel was also determined based on a simple DRC threshold setting mechanism. For different DRC lengths, the impact on the forward-link and the reverse-link throughputs is discussed.
Base-Catalyzed Cleavage of 1,3-Diols<sup>1,2</sup> (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBase-Catalyzed Cleavage of 1,3-Diols1,2SCOTT SEARLES Jr., EDWIN K. IVES, and SHOGO NUKINACite this: J. Org. Chem. 1959, 24, 11, 1770–1775Publication Date (Print):November 1, 1959Publication History Published online1 May 2002Published inissue 1 November 1959https://pubs.acs.org/doi/10.1021/jo01093a041https://doi.org/10.1021/jo01093a041research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations8LEARN 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
Binary software components in the undergraduate computer science curriculum (2001)

At one time, commercial software applications were released as single binary executable files. Discussions of the notion of a "software component" were almost always limited to the context of source code. However, with the proliferation of numerous new technologies, applications are now more typically released as collections of cooperating binary components. While there is significant industrial emphasis on binary component technologies, computer science curricula have not yet standardized upon a corpus of fundamentally sound concepts to support education within this paradigm. In this paper, we describe our efforts to define a fundamental core set of concepts to support this important programming paradigm, as well as our efforts to integrate these concepts into a typical undergraduate computer science curriculum.
Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients (2017)

These data confirm K. pneumoniae colonization is a significant risk factor for infection in ICU, and indicate ~50% of K. pneumoniae infections result from patients' own microbiota. Screening for colonization on admission could limit risk of infection in the colonized patient and others.
Two-phase deadlock detection algorithm (1988)

A deadlock detection algorithm utilizing a transaction-wait-for (TWF) graph is presented. It is a fully distributed algorithm which allows multiple outstanding requests. The proposed algorithm can achieve improved overall performance, using multiple disjoint controllers coupled with the two-phase property, while maintaining the simplicity of centralized schemes. The detection step is divided into two phases. Phase 1 analyzes the conditions of the system of interacting transactions, involving phase 2 only if conditions are possible for deadlocks to occur. Phase 2 performs the actual cycle detection. The proposed algorithm can be used in transaction-based distributed processing systems. Some results on the complexity of the algorithm are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>