gebhart/patrepeval huggingface dataset:
Transcription Termination and Regulation in Bacteriophages P22 and Lambda (1976)

INTRODUCTION Evidence is accumulating indicating that control of the termination of transcription by specific protein effectors is an important mechanism of genetic regulation in bacteria and bacteriophages. The N -gene product of bacteriophage λ appears to stimulate expression of the “early” phage genes by preventing termination of transcription at sites that occur beyond the first gene of each of the early phage operons (Roberts 1969; Adhya, Gottesman and de Crombrugghe 1974; Franklin 1974). It has been suggested that the mechanism by which the Q -gene product of λ exerts its positive regulatory effect on the late genes also involves interference with termination of transcription (Roberts 1975; Sklar, Yot and Weissman 1975; Blattner and Dahlberg 1972). Finally, a similar control mechanism appears to regulate the expression of the tryptophan operon of E. coli : most transcription initiated at the trp promoter appears to be aborted at a site prior to the first structural gene unless termination is prevented through intervention of a control system that somehow senses starvation for tryptophan (Bertrand et al. 1975). In the case of the bacteriophages, and presumably in the case of the trp operon as well, protein regulators are implicated that are thought to interact with target sequences (in DNA or RNA) near a specific promoter to make transcription therefrom privileged against termination (Adhya, Gottesman and de Crombrugghe 1974; Franklin 1974). Control by “antitermination” in phage λ was inferred primarily from the observation that the phage promoters are in most cases followed quite closely by transcription termination sites: transcription...
Molecular dosimetry of O4-ethyldeoxythymidine in rats continuously exposed to diethylnitrosamine. (1987)

There is considerable interest in incorporating mechanistically based biological data into the process of quantitative risk assessment. Presently, no adequate data bases for internal dosimeters, such as DNA adducts, exist for humans or experimental animals. Therefore, the major promutagenic ethyl adduct, O4-ethyldeoxythymidine (O4-EtdT), has been quantitated in liver DNA after continuous exposure of rats to drinking water containing 0.4, 1, 4, 10, 40, or 100 ppm diethylnitrosamine (DEN) for 1, 4, 7, 14, 28, 49, or 70 days. The rate of O4-EtdT accumulation was modeled as the difference between a DEN-dependent rate of formation and an O4-EtdT concentration-dependent rate of loss. In general, O4-EtdT concentrations increased rapidly during the first 7 days of exposure and by 7-28 days O4-EtdT had accumulated to apparent steady-state concentrations that were DEN concentration-dependent over the entire dose range. The concentration of the adduct increased with DEN concentration over the entire dose range for exposures of 28 days or less and for doses of 0.4 to 40 ppm DEN the adduct level increased with DEN concentration for exposures of 70 days or less. Although the dose response of O4-EtdT was relatively linear, with increasing DEN concentration a trend toward a less than linear relationship was observed. This suggests that there was a lower efficiency of formation and/or greater loss of O4-EtdT during high-dose exposures. This study provides a data base that can be used to qualitatively and quantitatively examine the relationship between external dose and O4-EtdT over a DEN dose range covering several orders of magnitude.
The Virtualization Solution (2010)

Is virtualization the solution to computing security? A brief look at the history of computer security salvation might provide some insight. A basic concept underlying OS protection is separation. The OS provides separation of files, directories, processes, users, and devices from each other, even though the hardware lets them interact arbitrarily. In the OS's role as mediator, it prevents user processes from subverting the OS and each other by limiting where they can read from and write to; dominating input, output, storage, and processing resources; and intermediating for the hardware mechanism so that only the OS has direct access.
Effect of a novel load-bearing trabecular Nitinol scaffold on rabbit radius bone regeneration (2015)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Irena Gotman, Asaph Zaretzky, Sergey G. Psakhie, Elazar Y. Gutmanas; Effect of a novel load-bearing trabecular Nitinol scaffold on rabbit radius bone regeneration. AIP Conference Proceedings 27 October 2015; 1683 (1): 020243. https://doi.org/10.1063/1.4932933 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
The minor ecdysteroids from Ajuga turkestanica (2015)

Ajuga turkestanica ecdysteroids are characterised by the abundance of 11α-hydroxylated compounds and by the simultaneous presence of 24C, 27C, 28C and 29C ecdysteroids. It is expected that even more ecdysteroids are to be found in this plant since the starting material for this study lacked the less polar ecdysteroids. The simultaneous presence of 20-hydroxyecdysone and turkesterone (its 11α-hydroxy analogue) as the two major ecdysteroids suggests that every ecdysteroid is probably present in both 11α-hydroxy and 11-deoxy forms.
Optimizing Chemotherapy Scheduling Using Local Search Heuristics (2006)

We develop a method for computing efficient patient-specific drug protocols. Using this method, we identify two general categories of anticancer drug protocols, depending on the temporal cycle parameters of the host and cancer cells: a one-time intensive treatment, or a series of nonintensive treatments. Our method is based on a theoretical and experimental work showing that treatment efficacy can be improved by determining the dosing frequency on the drug-susceptible target and host cell-cycle parameters. Simulating the patient's pharmaco-dynamics in a simple model for cell population growth, we calculate the number of drug susceptible cells at every moment of therapy. Local search heuristics are then used to conduct a search for the desired solution, as defined by our criteria. These criteria include the patient's state at the end of a predetermined time period, the number of cancer and host cells at the end of treatment, and the time to the patient's cure. The process suggested here does not depend on the exact biological assumptions of the model, thus enabling its use in a more complex description of the system. We test three solution methods. Simulated annealing is compared to threshold acceptance and old bachelor acceptance, which are less known variants to this method. The conclusions concerning the three approximation methods are that good results can be achieved by choosing the proper parameters for each of the methods, but the computational effort required for achieving good results is much greater in simulated annealing than in the other methods. Also, a large number of iterations does not guarantee better solution quality, and resources would be better used in several short searches with different parameter values than in one long search.
Circadian Health and Light: A Report on the National Heart, Lung, and Blood Institute’s Workshop (2018)

Despite the omnipresence of artificial and natural light exposure, there exists little guidance in the United States and elsewhere on light exposure in terms of timing, intensity, spectrum, and other light characteristics known to affect human health, performance, and well-being; in parallel, there is little information regarding the quantity and characteristics of light exposure that people receive. To address this, the National Center on Sleep Disorders Research, in the Division of Lung Diseases, National Heart, Lung, and Blood Institute, held a workshop in August 2016 on circadian health and light. Workshop participants discussed scientific research advances on the effects of light on human physiology, identified remaining knowledge gaps in these research areas, and articulated opportunities to use appropriate lighting to protect and improve circadian-dependent health. Based on this workshop, participants put forth the following strategic intent, objectives, and strategies to guide discovery, measurement, education, and implementation of the appropriate use of light to achieve, promote, and maintain circadian health in modern society.
Unusual reactions of guaiazulene with N-bromosuccinimide and synthesis of variously functionalized azulenes using these reactions (1991)

Treatment of guaiazulene ( Ia ) with NBS in benzene gives various, side-chain-brominated compounds, but in hexane it affords exclusively 3-bromoguaiazulene ( Id ). Compound Id is stable in hexane at 5°C in the absence of oxygen, whereas in benzene it changes very rapidly to a mixture of similar compounds as those directly obtained from Ia and NBS in benzene. Possible pathways for the formation of these compounds are briefly discussed. By utilizing these reactions, various kinds of side-chain functionalized azulenes that are otherwise not available by conventional methods can be readily prepared from Ia .
Performance comparison of Yb:YAG ceramics and crystal gain material in a large-area, high-energy, high average–power diode-pumped laser (2020)

We compare for the first time the influence of different Yb:YAG gain media on the performance of a large-area, high average-power laser system with an output energy of up to 6 J. Monocrystalline slabs grown by a new technique without central growth defect are compared with ceramics. Small signal gain, maximum output energy and thermal lensing are compared for ceramic slabs with co-sintered amplified spontaneous emission (ASE) absorber cladding, monocrystalline slab with and without optically bonded ASE absorber cladding, and surface structured monocrystalline slabs. We show that these large monocrystals with optically bonded absorber cladding have similar performance to cladded ceramics, so far the only material for high-energy Yb:YAG lasers.
Discrimination of the binary coherent signal: Gaussian-operation limit and simple non-Gaussian near-optimal receivers (2008)

We address the limit of the Gaussian operations and classical communication in the problem of quantum state discrimination. We show that the optimal Gaussian strategy for the discrimination of the binary phase shift keyed (BPSK) coherent signal is a simple homodyne detection. We also propose practical near-optimal quantum receivers that beat the BPSK homodyne limit in all areas of the signal power. Our scheme is simple and does not require realtime electrical feedback.
Design and Analysis of Observational Studies (2014)

ABSTRACT Appropriate study design forms the basis of any successful organized research. Irrespective of the underlying rationale of the research question, inappropriate design of an experiment or execution of a study may not give a valid result. As defined, the research should have the following characteristics: it should be undertaken within the framework of a set of philosophies, should have an unbiased objective and a design comprising of methods and techniques that have been tested for their validity and reliability. These principles of research clearly emphasize the need for an appropriate study design. The current review focuses on the planning and analysis of an observational study to obtain significant and accurate findings. How to cite this article Suresh KP, Gajendragad MR, Rahman H. Design and Analysis of Observational Studies. Int J Infertil Fetal Med 2014;5(2):33-39.
Novel aberration monitor for optical lithography (1999)

The aberration monitor allows independent determination of spherical, coma, astigmatism and three point in a single experiment using existing equipment. The monitor consists of a circular phase object, with a diameter of approximately (lambda) /NA and a phase depth of (lambda) /2. Due to the relative large diameter, the image prints as a narrow ring into the resist. Without aberrations its contours are concentric circles. Aberrations deform the ring in a characteristic way. A detailed analysis of the ring shape through focus identifies the aberrations of the projection lens. A linear aberration model is compared with simulations. Experimental results of various aberrations are shown and ar correlated to line width measurements and interferometric lens data.
The role of hypoxia-inducible factor-2 in digestive system cancers (2015)

Hypoxia is an all but ubiquitous phenomenon in cancers. Two known hypoxia-inducible factors (HIFs), HIF-1α and HIF-2α, primarily mediate the transcriptional response to hypoxia. Despite the high homology between HIF-1α and HIF-2α, emerging evidence suggests differences between both molecules in terms of transcriptional targets as well as impact on multiple physiological pathways and tumorigenesis. To date, much progress has been made toward understanding the roles of HIF-2α in digestive system cancers. Indeed, HIF-2α has been shown to regulate multiple aspects of digestive system cancers, including cell proliferation, angiogenesis and apoptosis, metabolism, metastasis and resistance to chemotherapy. These findings make HIF-2α a critical regulator of this malignant phenotype. Here we summarize the function of HIF-2 during cancer development as well as its contribution to tumorigenesis in digestive system malignancies.
A Microfluidic Device with an Integrated Waveguide Beam Splitter for Velocity Measurements of Flowing Particles by Fourier Transformation (2003)

A microfabricated capillary electrophoresis device for velocity measurements of flowing particles is presented. It consists of a 1 x 128 planar waveguide beam splitter monolithically integrated with an electrically insulated fluidic channel network for fluorescence excitation at multiple points. Stray light rejection structures are included in order to suppress unwanted light between the detection regions. The emission pattern of particles passing the detection region was collected by a photomultiplier tube that was placed in close proximity to the channel, thereby avoiding the use of transfer optics. The integrated planar waveguide beam splitter was, furthermore, permanently connected to the light source by a glued-on optical fiber, to achieve a robust and alignment-free operation of the system. The velocity was measured using a Fourier transformation with a Shah function, since the response of the light array was designed to approximate a square profile. Deviations from this response were observed as a result of the multimode nature of the integrated waveguides.
Synthesis of dl-sirenin (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of dl-sireninJacob J. Plattner, Uday T. Bhalerao, and Henry RapoportCite this: J. Am. Chem. Soc. 1969, 91, 17, 4933–4934Publication Date (Print):August 1, 1969Publication History Published online1 May 2002Published inissue 1 August 1969https://doi.org/10.1021/ja01045a066RIGHTS & PERMISSIONSArticle Views305Altmetric-Citations33LEARN 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 (257 KB) Get e-Alerts Get e-Alerts
A Ghost Target Suppression Technique using Interference Replica for Automotive FMCW Radars (2020)

As an automotive FMCW (Frequency Modulated Continuous Wave) radar used for automated driving or ADAS (Advanced Driver Assistance System) will be widely deployed, miss-detection and/or false detection due to inter-radar interference can be a serious problem in near future. In order to mitigate narrowband interference resulting in false detection or so-called ghost target detection, this paper proposes a novel ghost target suppression technique using interference replica for automotive FMCW radars where the narrowband interference replicas is generated by performing carrier sense before initiating radar signal transmission and suppresses the ghost target from the received beat signals by subtracting the generated interference replica from the received signals in the frequency spectrum. Computer simulations confirm the proposed ghost target suppression scheme is feasible.
Enhanced Vertical Perception through Head-Related Impulse Response Customization Based on Pinna Response Tuning in the Median Plane (2008)

Human's ability to perceive elevation of a sound and distinguish whether a sound is coming from the front or rear strongly depends on the monaural spectral features of the pinnae. In order to realize an effective virtual auditory display by HRTF (head-related transfer function) customization, the pinna responses were isolated from the median HRIRs (head-related impulse responses) of 45 individual HRIRs in the CIPIC HRTF database and modeled as linear combinations of 4 or 5 basic temporal shapes (basis functions) per each elevation on the median plane by PCA (principal components analysis) in the time domain. By tuning the weight of each basis function computed for a specific height to replace the pinna response in the KEMAR HRIR at the same height with the resulting customized pinna response and listening to the filtered stimuli over headphones, 4 individuals with normal hearing sensitivity were able to create a set of HRIRs that outperformed the KEMAR HRIRs in producing vertical effects with reduced front/back ambiguity in the median plane. Since the monaural spectral features of the pinnae are almost independent of azimuthal variation of the source direction, similar vertical effects could also be generated at different azimuthal directions simply by varying the ITD (interaural time difference) according to the direction as well as the size of each individual's own head.
Unified platform for genetic and serological detection of COVID-19 with single-molecule technology (2021)

The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.
Real‐Time Subspace Integration for Example‐Based Elastic Material (2015)

Abstract Example‐based material allows simulating complex material behaviors in an art‐directed way. This paper presents a method for fast subspace integration for example‐based elastic material, which is suitable for real‐time simulation in computer graphics. At the core of the method is the formulation of a new potential using example‐based Green strain tensors. By using this potential, the deformation can be attracted towards the example‐based deformation feature space, the example weights can be explicitly obtained and the internal force can be decomposed into the conventional one and an additional one induced by the examples. The real‐time subspace integration is then developed with subspace integration costs independent of geometric complexity, and both the reduced conventional internal force and additional one being cubic polynomials in reduced coordinates. Experiments demonstrate that our method can achieve real‐time simulation while providing comparable quality with the prior art.
Correlation of Thrombosis With Increased Platelet Turnover in Thrombocytosis (1998)

There are no readily applicable methods to routinely assess thrombosis risk and treatment response in thrombocytosis. Reticulated platelets (RP) define the most recently released platelets in the circulation, and the RP% has been shown to estimate platelet turnover in thrombocytopenic states. We examined whether increased RP values were associated with thrombotic complications in thrombocytosis. Platelet count, RP%, and absolute RP count were measured at presentation in 83 patients with chronic or transient thrombocytosis, 46 patients with deep vein (DVT) or arterial (ART) thrombosis and normal platelet counts, and 83 healthy controls with normal platelet counts. Chronic thrombocytosis patients presenting with thrombosis (n = 14) had significantly higher RP% (14.7% +/- 10. 1%, mean +/- SD) than asymptomatic chronic thrombocytosis patients (n = 23, RP% = 3.4% +/- 1.8%), healthy controls (3.4% +/- 1.3%), DVT patients (n = 21, 3.8% +/- 2.1%), or ART patients (n = 25, 4.5% +/- 4.1%, P < .05 for all comparisons). Chronic thrombocytosis patients with thrombosis also had significantly higher absolute RP counts than asymptomatic chronic thrombocytosis patients (98 +/- 64 x 10(9)/L [range, 54 to 249 x 10(9)/L] v 30 +/- 13 x 10(9)/L [range, 11 to 51 x 10(9)/L]; P = .0004), whereas healthy controls, DVT, and ART patients had similarly low absolute RP counts (6 +/- 6 x 10(9)/L, 9 +/- 7 x 10(9)/L, and 11 +/- 7 x 10(9)/L, respectively; P > .49). The RP% and absolute RP counts remained significantly higher in chronic thrombocytosis patients with thrombosis when patients were further subdivided into primary myeloproliferative disorders versus secondary thrombocytosis. Similarly elevated RP percentages and absolute counts were also noted in transient thrombocytosis patients with thrombosis (n = 6, 11.5% +/- 4.4% and 90 +/- 46 x 10(9)/L, respectively) when compared with asymptomatic transient thrombocytosis patients (n = 40, 4.5% +/- 2.7% and 35 +/- 16 x 10(9)/L, respectively) and to all control groups (P < .05 for all comparisons). In addition, 7 of 8 thrombocytosis patients who were studied before developing symptoms of thrombosis had elevated absolute RP counts compared with only 1 of 63 thrombocytosis patients who remained asymptomatic. Follow-up studies in seven chronic thrombocytosis patients showed that successful aspirin treatment of symptomatic recurrent thrombosis significantly reduced the RP% from 17.1% +/- 10.9% before therapy to 4.8% +/- 2.0% after therapy; absolute RP counts decreased from 102 +/- 67 x 10(9)/L to 26 +/- 10 x 10(9)/L (P < .01 for both). We conclude that thrombosis in the setting of an elevated platelet count is associated with increased platelet turnover, which is reversed by aspirin therapy. Measurement of reticulated platelets to assess platelet turnover may be useful in evaluating both treatment response and thrombotic risk in thrombocytosis.