gebhart/patrepeval huggingface dataset:
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator (2008)

Thermus thermophilus SdrP is one of four cyclic AMP receptor protein (CRP)/fumarate and nitrate reduction regulator (FNR) family proteins from the extremely thermophilic bacterium T. thermophilus HB8. Expression of sdrP mRNA increased in the stationary phase during cultivation at 70 degrees C. Although the sdrP gene was non-essential, an sdrP-deficient strain showed growth defects, particularly when grown in a synthetic medium, and increased sensitivity to disulphide stress. The expression of several genes was altered in the sdrP disruptant. Among them, we found eight SdrP-dependent promoters using in vitro transcription assays. A predicted SdrP binding site similar to that recognized by Escherichia coli CRP was found upstream of each SdrP-dependent promoter. In the wild-type strain, expression of these eight genes tended to increase upon entry into the stationary phase. Transcriptional activation in vitro was independent of any added effector molecule. The hypothesis that apo-SdrP is the active form of the protein was supported by the observation that the three-dimensional structure of apo-SdrP is similar to that of the DNA-binding form of E. coli CRP. Based on the properties of the SdrP-regulated genes found in this study, it is speculated that SdrP is involved in nutrient and energy supply, redox control, and polyadenylation of mRNA.
Data from Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Abnormal alternative splicing has been associated with cancer. Genome-wide microarrays can be used to detect differential splicing events. In this study, we have developed ExonPointer, an algorithm that uses data from exon and junction probes to identify annotated cassette exons. We used the algorithm to profile differential splicing events in lung adenocarcinoma A549 cells after downregulation of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1). Data were generated using two different microarray platforms. The PCR-based validation rate of the top 20 ranked genes was 60% and 100%. Functional enrichment analyses found a substantial number of splicing events in genes related to RNA metabolism. These analyses also identified genes associated with cancer and developmental and hereditary disorders, as well as biologic processes such as cell division, apoptosis, and proliferation. Most of the top 20 ranked genes were validated in other adenocarcinoma and squamous cell lung cancer cells, with validation rates of 80% to 95% and 70% to 75%, respectively. Moreover, the analysis allowed us to identify four genes, &lt;i&gt;ATP11C&lt;/i&gt;, &lt;i&gt;IQCB1&lt;/i&gt;, &lt;i&gt;TUBD1&lt;/i&gt;, and proline-rich coiled-coil 2C (&lt;i&gt;PRRC2C&lt;/i&gt;), with a significantly different pattern of alternative splicing in primary non–small cell lung tumors compared with normal lung tissue. In the case of &lt;i&gt;PRRC2C&lt;/i&gt;, SRSF1 downregulation led to the skipping of an exon overexpressed in primary lung tumors. Specific siRNA downregulation of the exon-containing variant significantly reduced cell growth. In conclusion, using a novel analytical tool, we have identified new splicing events regulated by the oncogenic splicing factor SRSF1 in lung cancer. &lt;i&gt;Cancer Res; 74(4); 1105–15. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
On the Global Output SNR of the Parameterized Frequency-Domain Multichannel Noise Reduction Wiener Filter (2010)

The parameterized multichannel Wiener filter (PMWF) is known to allow for a flexible tuning of speech distortion and noise reduction. In addition, the output signal-to-noise ratio (SNR) is a natural metric that shows the true effect of such a filter on both residual noise and filtered speech. Earlier contributions have only shown that the output SNR of the Wiener filter is larger than the input SNR (as a proof of its effectiveness). However, the effect of the tuning parameter (denoted as ß following the notation of [1]) on this metric is not yet understood. In this paper, we prove that the global (fullband) output SNR of the PMWF is an increasing function of ß but remains below an asymptotic value. As a byproduct, a very simplified proof of the global output SNR improvement is provided.
Reaching Approximate Agreement in the Presence of Faults. (1985)

This paper considers a variant of the Byzantine Generals problem, in which processes start with arbitrary real values rather than Boolean values or values from some bounded range, and in which approximate, rather than exact, agreement is the desired goal. Algorithms are presented to reach approximate agreement in asynchronous, as well as synchronous systems. The asynchronous agreement algorithm is an interesting contrast to a result of Fischer et al, who show that exact agreement with guaranteed termination is not attainable in an asynchronous system with as few as one faulty process. The algorithms work by successive approximation, with a provable convergence rate that depends on the ratio between the number of faulty processes and the total number of processes. Lower bounds on the convergence rate for algorithms of this form are proved, and the algorithms presented are shown to be optimal.
Markov paging (1992)

This paper considers the problem of paging under the assumption that the sequence of pages accessed is generated by a Markov chain. The authors use this model to study the fault-rate of paging algorithms, a quantity of interest to practitioners. They first draw on the theory of Markov decision processes to characterize the paging algorithm that achieves optimal fault-rate on any Markov chain. They address the problem of efficiently devising a paging strategy with low fault-rate for a given Markov chain. They show that a number of intuitively good approaches fail. Their main result is an efficient procedure that, on any Markov chain, will give a paging algorithm with fault-rate at most a constant times optimal. Their techniques also show that some algorithms that do poorly in practice fail in the Markov setting, despite known (good) performance guarantees when the requests are generated independently from a probability distribution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Contrasting responses within a single neuron class enable sex-specific attraction in (2016)

Animals find mates and food, and avoid predators, by navigating to regions within a favorable range of available sensory cues. How are these ranges set and recognized? Here we show that male Caenorhabditis elegans exhibit strong concentration preferences for sex-specific small molecule cues secreted by hermaphrodites, and that these preferences emerge from the collective dynamics of a single male-specific class of neurons, the cephalic sensory neurons (CEMs). Within a single worm, CEM responses are dissimilar, not determined by anatomical classification and can be excitatory or inhibitory. Response kinetics vary by concentration, suggesting a mechanism for establishing preferences. CEM responses are enhanced in the absence of synaptic transmission, and worms with only one intact CEM show nonpreferential attraction to all concentrations of ascaroside for which CEM is the primary sensor, suggesting that synaptic modulation of CEM responses is necessary for establishing preferences. A heterogeneous concentration-dependent sensory representation thus appears to allow a single neural class to set behavioral preferences and recognize ranges of sensory cues.
Characterization of chlorins within a natural chlorin mixture using electrospray/ion trap mass spectrometry (1994)

Abstract Chlorins in a sedimentary mixture were characterized, without prior isolation of individual components, using electrospray ionization combined with ion trap mass spectrometry. Collision‐induced dissociation in the atmospheric sampling interface and multi‐step mass spectrometry (i.e. MS n where n ⩾ 2) were used in order to obtain structural information about the macrocycle. Fragmentation pathways are proposed for different macrocycle types based on data from model chlorins. Three unknown chlorins (RMM = 888, 844 and 790) are assigned as having bacteriochlorophyll macrocycle types esterifled to unusual side‐chains (i.e. dihydrophytol for the unknown with a bacteriopheophorbide a structure, phytol and an alcohol with a molecular mass of 242 u for the two unknowns with a proposed bacteriopyropheophorbide d structure).
Inhibition of exchange proteins directly activated by cAMP as a strategy for broad-spectrum antiviral development (2023)

The recent SARS-CoV-2 and mpox outbreaks have highlighted the need to expand our arsenal of broad-spectrum antiviral agents for future pandemic preparedness. Host-directed antivirals are an important tool to accomplish this as they typically offer protection against a broader range of viruses than direct-acting antivirals and have a lower susceptibility to viral mutations that cause drug resistance. In this study, we investigate the exchange protein activated by cAMP (EPAC) as a target for broad-spectrum antiviral therapy. We find that the EPAC-selective inhibitor, ESI-09, provides robust protection against a variety of viruses, including SARS-CoV-2 and Vaccinia (VACV)-an orthopox virus from the same family as mpox. We show, using a series of immunofluorescence experiments, that ESI-09 remodels the actin cytoskeleton through Rac1/Cdc42 GTPases and the Arp2/3 complex, impairing internalization of viruses that use clathrin-mediated endocytosis (e.g. VSV) or micropinocytosis (e.g. VACV). Additionally, we find that ESI-09 disrupts syncytia formation and inhibits cell-to-cell transmission of viruses such as measles and VACV. When administered to immune-deficient mice in an intranasal challenge model, ESI-09 protects mice from lethal doses of VACV and prevents formation of pox lesions. Altogether, our finding shows that EPAC antagonists such as ESI-09 are promising candidates for broad-spectrum antiviral therapy that can aid in the fight against ongoing and future viral outbreaks.
Common genetic predisposition for heart failure and cancer (2020)

Cardiovascular diseases and cancer are major causes of mortality in industrialized societies. They share common risk factors (e.g., genetics, lifestyle, age, infection, toxins, and pollution) and might also mutually promote the onset of the respective other disease. Cancer can affect cardiac function directly while antitumor therapies may have acute- and/or late-onset cardiotoxic effects. Recent studies suggest that heart failure might promote tumorigenesis and tumor progression. In both cancer and cardiovascular diseases, genetic predisposition is implicated in the disease onset and development. In this regard, genetic variants classically associated with cardiomyopathies increase the risk for toxic side effects on the cardiovascular system. Genetic variants associated with increased cancer risk are frequent in patients with peripartum cardiomyopathy complicated by cancer, pointing to a common genetic predisposition for both diseases. Common risk factors, cardiotoxic antitumor treatment, genetic variants (associated with cardiomyopathies and/or cancer), and increased cardiac stress lead us to propose the "multi-hit hypothesis" linking cancer and cardiovascular diseases. In the present review, we summarize the current knowledge on potential connecting factors between cancer and cardiovascular diseases with a major focus on the role of genetic predisposition and its implication for individual therapeutic strategies and risk assessment in the novel field of oncocardiology.
High-Accuracy Defect-Free X-Ray Mask Technology (1994)

There are many material and processing options for building highly accurate defect-free X-ray masks that meet the 0.25-µ m and smaller lithography groundrules. IBM's path and rationale for reducing the key mask parameters of image size, image placement and defects is covered. For image size resolution and control, high voltage e-beam lithography (greater then 50 kV) is the preferred technique for X-ray masks. For tighter image placement control, special writing schemes that reduce the e-beam lithography systematic and random placement errors must be used. Special absorber electroplating conditions and thermal controls were implemented to control process-induced distortion. For tight defect control, identifying and eliminating sources of defect is key. Clearly, for IBM, most of the defect sources were process rather than foreign material related. Our defect reduction work has resulted in the fabrication of a fully functional 64-Mb DRAM (single chip) mask.
Merging the best of both worlds: hybrid lipid-enveloped matrix nanocomposites in drug delivery (2013)

The advent of nanotechnology has revolutionized drug delivery in terms of improving drug efficacy and safety. Both polymer-based and lipid-based drug-loaded nanocarriers have demonstrated clinical benefit to date. However, to address the multifaceted drug delivery challenges ahead and further expand the spectrum of therapeutic applications, hybrid lipid-polymer nanocomposites have been designed to merge the beneficial features of both polymeric drug delivery systems and liposomes in a single nanocarrier. This review focuses on different classes of nanohybrids characterized by a drug-loaded polymeric matrix core enclosed in a lipid shell. Various nanoengineering approaches to obtain lipid-polymer nanocomposites with a core-shell nanoarchitecture will be discussed as well as their predominant applications in drug delivery.
XML data management (panel session) (2001)

XML data is likely to be widely used as a data exchange format but users also need to store and query XML data. The purpose of this panel is to explore whether and how to best provide this functionality.
Precision metrology for studying optical surfaces (1991)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Jean M. Bennett, Virgil Elings, and Kevin Kjoller, "Precision metrology for studying optical surfaces," Optics & Photonics News 2(5), 14-18 (1991) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Fabrication of self-cleaning textiles by TiO2-carbon nanotube treatment (2013)

The purpose of this study is to fabricate self-cleaning textiles with photocatalyst excited by sunlight irradiation. Self-cleaning textiles were realized by coating carbon nanotube (CNT)-TiO 2 -acrylate copolymer on cotton and nylon fabrics using the dip-pad-dry process. The effect of CNT addition to TiO 2 was observed on the self-cleaning performance and tensile stress of the treated fabrics. The morphology, chemical structure and particle size of acrylate copolymer with CNT-TiO 2 and treated fabrics were analyzed using transmission electron microscopy, field emission scanning electron microscopy, Fourier transform infrared spectroscopy and a dynamic particle-size analyzer. The self-cleaning efficiency of the treated samples was examined by decomposition rates of methylene blue in aqueous solution and that of a wine stain under sunlight irradiation. It was found that the decomposition rates both for methylene blue and the wine stain were improved by CNT addition to TiO 2 treatment on fabrics. When tensile degradation by photocatalytic reaction was monitored for TiO 2 and CNT-TiO 2 -treated fabrics, the tensile deterioration after 48 hours of irradiation appeared to be mitigated by CNT addition to TiO 2 treatment.
High Antibody-Dependent Cellular Cytotoxicity Responses Are Correlated with Strong CD8 T Cell Viral Suppressive Activity but Not with B57 Status in HIV-1 Elite Controllers (2013)

The role of Antibody-dependent cellular cytotoxicity (ADCC) responses in HIV-1 controllers is still unclear due to the heterogeneity of these patients. We analyzed 67 HIV-1 controllers and found significantly higher levels of ADCC antibodies in controllers versus viremic subjects (p = 0.017). Moreover, multivariate analysis revealed significantly higher ADCC titers in HLA B57- controllers compared to HLA-B57+ ones (p = 0.0086). These data suggest a role for ADCC in immune control of HIV, especially in HLA B57 negative controllers.
Novel design of inherently gain-flattened discrete highly nonlinear photonic crystal fiber Raman amplifier and dispersion compensation using a single pump in C-band (2005)

In this paper, we report, for the first time, an inherently gain-flattened discrete highly nonlinear photonic crystal fiber (HNPCF) Raman amplifier (HNPCF-RA) design which shows 13.7 dB of net gain (with +/-0.85-dB gain ripple) over 28-nm bandwidth. The wavelength dependent leakage loss property of HNPCF is used to flatten the Raman gain of the amplifier module. The PCF structural design is based on W-shaped refractive index profile where the fiber parameters are well optimized by homely developed genetic algorithm optimization tool integrated with an efficient vectorial finite element method (V-FEM). The proposed fiber design has a high Raman gain efficiency of 4.88 W(-1) . km(-1) at a frequency shift of 13.1 THz, which is precisely evaluated through V-FEM. Additionally, the designed module, which shows ultra-wide single mode operation, has a slowly varying negative dispersion coefficient (-107.5 ps/nm/km at 1550 nm) over the operating range of wavelengths. Therefore, our proposed HNPCF-RA module acts as a composite amplifier with dispersion compensator functionality in a single component using a single pump.
Metabolic Characterization of Escherichia coli Strains Adapted to Growth on Lactate (2007)

ABSTRACT In comparison with intensive studies of genetic mechanisms related to biological evolutionary systems, much less analysis has been conducted on metabolic network responses to adaptive evolution that are directly associated with evolved metabolic phenotypes. Metabolic mechanisms involved in laboratory evolution of Escherichia coli on gluconeogenic carbon sources, such as lactate, were studied based on intracellular flux states determined from 13 C tracer experiments and 13 C-constrained flux analysis. At the end point of laboratory evolution, strains exhibited a more than doubling of the average growth rate and a 50% increase in the average biomass yield. Despite different evolutionary trajectories among parallel evolved populations, most improvements were obtained within the first 250 generations of evolution and were generally characterized by a significant increase in pathway capacity. Partitioning between gluconeogenic and pyruvate catabolic flux at the pyruvate node remained almost unchanged, while flux distributions around the key metabolites phosphoenolpyruvate, oxaloacetate, and acetyl-coenzyme A were relatively flexible over the course of evolution on lactate to meet energetic and anabolic demands during rapid growth on this gluconeogenic carbon substrate. There were no clear qualitative correlations between most transcriptional expression and metabolic flux changes, suggesting complex regulatory mechanisms at multiple levels of genetics and molecular biology. Moreover, higher fitness gains for cell growth on both evolutionary and alternative carbon sources were found for strains that adaptively evolved on gluconeogenic carbon sources compared to those that evolved on glucose. These results provide a novel systematic view of the mechanisms underlying microbial adaptation to growth on a gluconeogenic substrate.
Novel alkaloids from the tropical plant Ancistrocladus abbreviatus inhibit cell killing by HIV-1 and HIV-2 (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel alkaloids from the tropical plant Ancistrocladus abbreviatus inhibit cell killing by HIV-1 and HIV-2Kirk P. Manfredi, John W. Blunt, John H. Cardellina II, James B. McMahon, Lewis L. Pannell, Gordon M. Cragg, and Michael R. BoydCite this: J. Med. Chem. 1991, 34, 12, 3402–3405Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/jm00116a011https://doi.org/10.1021/jm00116a011research-articleACS PublicationsRequest reuse permissionsArticle Views438Altmetric-Citations138LEARN 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
Investigation of the Effect of Spatial Filtering for Detecting Auditory Steady-State Responses Recorded from Ear-EEG (2022)

Auditory steady-state responses (ASSRs) enable hearing threshold estimation based on electrophysiological measurements and are widely used in clinical practice. Traditionally, ASSRs are recorded from a few electroencephalography (EEG) electrodes placed on the scalp. Ear-EEG is a method in which the EEG is recorded from electrodes placed within or around the ear and is thus more suitable for use in everyday life. Ear-EEG is typically recorded from multiple electrodes in order to enhance redundancy and robustness, but a pair of electrodes (so-called "best pair") is usually chosen for the further analysis. Spatial filtering uses an optimized weighted combination of the electrodes, and is thus in general a better method for analysis of multichannel EEG. In this study we propose a new spatial filtering method based on solving a constrained optimization problem. Empirical evaluation based on ear-EEG recorded from nine subjects shows that the proposed spatial filtering method provides a significant increase in ASSR SNR as compared to the conventional "best pair" method. Clinical Relevance - ASSR can be estimated from ear-EEG recordings. Integrating ear-EEG into hearing aids would allow hearing aids to characterize hearing loss and thereby adjust the audio processing accordingly.