gebhart/patrepeval huggingface dataset:
Unique and Highly Selective Anticytomegalovirus Activities of Artemisinin-Derived Dimer Diphenyl Phosphate Stem from Combination of Dimer Unit and a Diphenyl Phosphate Moiety (2013)

We report that the artemisinin-derived dimer diphenyl phosphate (DPP; dimer 838) is the most selective inhibitor of human cytomegalovirus (CMV) replication among a series of artemisinin-derived monomers and dimers. Dimer 838 was also unique in being an irreversible CMV inhibitor. The peroxide unit within artemisinins' chemical structures is critical to their activities, and its absence results in loss of anti-CMV activities. Surprisingly, the deoxy dimer of 838 retained modest anti-CMV activity, suggesting that the DPP moiety of dimer 838 contributes to its anti-CMV activities. DPP alone did not inhibit CMV replication, but triphenyl phosphate (TPP) had modest CMV inhibition, although its selectivity index was low. Artemisinin DPP derivatives dimer 838 and monomer diphenyl phosphate (compound 558) showed stronger CMV inhibition and a higher selectivity index than their analogs lacking the DPP unit. An add-on and removal assay revealed that removing DPP derivatives (compounds 558 and 838) but not the non-DPP backbones (artesunate and compound 606) at 24 h postinfection (hpi) already resulted in dominant CMV inhibition. CMV inhibition was fully irreversible with 838 and partially irreversible with 558, while non-DPP artemisinins were reversible inhibitors. While all artemisinin derivatives and TPP reduced the expression of the CMV immediate early 2 (IE2), UL44, and pp65 proteins at or after 48 hpi, only TPP inhibited the expression of both IE1 and IE2. Combination of a non-DPP dimer (compound 606) with TPP was synergistic in CMV inhibition, while ganciclovir and TPP were additive. Although TPP shared structural similarity with monomer DPP (compound 558) and dimer DPP (compound 838), its pattern of CMV inhibition was significantly different from the patterns of the artemisinins. These findings demonstrate that the DPP group contributes to the unique activities of compound 838.
Uncorrelated Interference in 79 GHz FMCW and PMCW Automotive Radar (2019)

An extensive comparison on radar-to-radar interference in frequency-modulated continuous wave (FMCW) and binary phase-modulated continuous wave (PMCW) radars is performed. The noise-plus-interference power for FMCW-to-FMCW and PMCW-to-PMCW interference in a single victim and single interferer environment is compared for generalized waveform-based scenarios. It is proven that the interference suppression is equal in FMCW and PMCW radars in case the time-bandwidth product in both systems is equal.
A fixed point method for homotopic ℓ 0 -minimization with application to MR image recovery (2008)

A novel method for highly-undersampled Magnetic Resonance Image (MRI) reconstruction is presented. One of the principal challenges faced in clinical MR imaging is the fundamental linear relation between net exam duration and admissible spatial resolution. Increased scan duration diminishes patient comfort while increasing the risk of susceptibility to motion artifact and limits the ability to depict many physiological events at high temporal rates. With the recent development of Compressive Sampling theory, several authors have successfully demonstrated that clinical MR images possessing a sparse representation in some transform domain can be accurately reconstructed even when sampled at rates well below the Nyquist limit by casting the recovery as a convex ℓ<sub>1</sub>-minimization problem. While ℓ<sub>1</sub>-based techniques offer a sizeable advantage over Nyquist-limited methods, they nonetheless require a modest degree of over-sampling above the true theoretical minimum sampling rate in order to guarantee the achievability of exact reconstruction. In this work, we present a reconstruction model based on homotopic approximation of the ℓ<sub>0</sub> quasi-norm and discuss the ability of this technique to reconstruct undersampled MR images at rates even lower than are achievable than with ℓ<sub>1</sub>-minimization and arbitrarily close to the true minimum sampling rate. A semi-implicit numerical solver is presented for efficient numerical computation of the reconstruction process and several examples depicting the capability for accurate MRI reconstructions from highly-undersampled K-space data are presented.
1. Boolean Networks (2010)

Boolean networks are a class of discrete dynamical systems that can be characterized by the interactions over a set of Boolean variables. Random Boolean networks (RBNs), which are ensembles of random network structures, were first introduced by Stuart Kauffman in 1969 as a simple model class for studying dynamical properties of gene regulatory networks at a time when the structure of such networks was largely unknown. The idea behind such an approach is to define an ensemble of Boolean networks such that it fulfills certain known features of biological networks and then study random instances of these networks to learn more about general properties of such networks. This iterative and highly interdisciplinary process depends, on the one hand, on the input of new biological findings and might guide, on the other hand, the research of the experimentalist. For example, the now classical Kauffman ensembles in which every gene takes its inputs from exactly 2 other genes turned out to be “critical,” lying at a phase transition between an ordered and a chaotic phase, in regard to the propagation of perturbations, and contributed to the hypothesis that living systems may be poised at the “edge of chaos”—a hypothesis for which experimental evidence has been mounting (Ramö et al., 2006; Shmulevich et al., 2005; Nykter et al., 2008). There have been hundreds of publications, primarily in the physics, mathematics, and theoretical biology literature, that have focused on the ensemble approach for studying genetic networks in which the center of attention lies not in the entities comprising a system but qualities possessed by the system as a whole—much like the concept of entropy in physics. We will not attempt to review or even summarize the numerous results and insights gained from such studies as the vast amount of material deserves an entire book on this subject, and we limit ourselves only to mentioning that such approaches have shed light on fundamental principles of complex living systems at all scales of organization, including adaptability and evolvability, robustness, coordination of complex behaviors, storage of information, and the relationships between the structure of such complex systems and their dynamical behavior. Further, we refer the reader to several excellent review articles that cover the ensemble properties of Boolean networks (Aldana et al., 2002; Drossel, 2007), as well as Kauffman's book (Kauffman, 1993), which covers a much broader range of topics but contains much material, albeit somewhat dated, on Boolean networks. Our aim in this chapter is to give only the necessary definitions and concepts pertaining to Boolean networks to the extent that they are necessary for studying probabilistic Boolean networks. We will also review several examples of genetic networks using the Boolean network formalism.
Hierarchical Compression of Color Look Up Tables (2007)

Color lookup tables (CLUTs) that are embedded in printer firmware consume precious flash memory. In order to conserve memory and thereby reduce cost, it is desirable to compress CLUTs prior to storage and restore tables as required. In this paper, we investigate methods for lossless compression of CLUTs. We demonstrate that, through suitable pre-processing of data, significant improvements in compression performance can be obtained as compared to a direct application of lossless data compression methods. In particular, the gains in performance with the proposed methods are accomplished by exploiting the characteristics of CLUT data and utilizing a combination of hierarchical differential encoding and re-ordering for the pre-processing. Experimental results over a representative data set indicate that the proposed methods can result in a 26% reduction in memory requirements in comparison to direct compression. As compared to uncompressed tables this corresponds to a memory saving of 68%.
A novel plied yarn structure with negative Poisson’s ratio (2015)

This article presents an experimental and geometrical study of a novel kind of plied yarn structure with negative Poisson’s ratio (NPR). The deformation mechanism of the yarn structure formed with two stiff yarns and two soft yarns to achieve NPR behavior was firstly introduced. Based on the proposed yarn structure, four kinds of yarn samples were then fabricated with two kinds of stiff yarns and two types of soft yarns and tested under the axial extension to verify their auxetic or NPR effect. A geometric analysis was finally conducted to theoretically calculate the Poisson’s ratio of the yarn structure and compared with the experimental results. The study shows that the proposed yarn structure has obvious NPR effect and the geometrical analysis can well predict its Poisson’s ratio in the higher axial strain range. It is expected that this study could promote further development of auxetic textiles with unusual behavior.
Precise Wet Gas Measurement Using Venturi Meters (2017)

Abstract This paper presents the methodology of correcting the erroneous reading of the venturi meters for measuring the gas rate when high amounts of liquids, including condensate and water, are being produced from the gas wells. The proposed system takes advantage of existing infrastructure in proximity of the venturi meters and is designed to be retrofitted to the existing meters to knock out the liquid before the meter and recombines it after. This method eliminates the need for an additional flow line to carry out the liquid or a compressor to reinject the separated liquid back into the pressurized gas line.
Anthelmintic Avermectins Kill Mycobacterium tuberculosis, Including Multidrug-Resistant Clinical Strains (2012)

Avermectins are a family of macrolides known for their anthelmintic activities and traditionally believed to be inactive against all bacteria. Here we report that members of the family, ivermectin, selamectin, and moxidectin, are bactericidal against mycobacterial species, including multidrug-resistant and extensively drug-resistant clinical strains of Mycobacterium tuberculosis. Avermectins are approved for clinical and veterinary uses and have documented pharmacokinetic and safety profiles. We suggest that avermectins could be repurposed for tuberculosis treatment.
Arterial elasticity imaging: comparison of finite-element analysis models with high-resolution ultrasound speckle tracking (2010)

Since pressure equalization may increase the dynamic range of strain imaging, the effect of the surrounding tissue on strain should be incorporated into models of arterial strain, particularly when the pressure equalization technique is used.
An efficient binary system for gene expression in the silkworm, <i>Bombyx mori</i>, using GAL4 variants (2011)

A binary gene expression system using the yeast GAL4 DNA-binding protein and the upstream activating sequence (UAS) of galactose-driven yeast genes is an established and powerful tool for the analysis of gene function. However, in the domesticated silkworm, Bombyx mori, this system has been limited in its utility by the relatively low transcriptional activation activity of GAL4 and by its toxicity. In this study, we investigated the potential of several established GAL4 variants (GAL4Δ, GAL4VP16, GAL4VPmad2, GAL4VPmad3, and GAL4NFκB) and of two new GAL4 variants, GAL4Rel and GAL4Relish, which contain the transcription-activating regions of the BmRel and BmRelish genes, respectively, to improve the utility of the GAL4/UAS system in B. mori. We generated constructs containing these GAL4 variants under the control of constitutive or inducible promoters and investigated their transcription-activating activity in cultured B. mori cells and embryos and in transgenic silkworms. GAL4VP16 and GAL4NFκB exhibited high transactivation activity but appeared to be toxic when used as transgenes under the control of a constitutive promoter. Similarly, GAL4VPmad2 and GAL4VPmad3 exhibited higher transactivation activity than GAL4, combined with strong toxicity. The transcription-activating activity of GAL4Δ was about twice that of GAL4. The two new GAL4 variants, GAL4Rel and GAL4Relish, were less active than GAL4. Using GAL4VP16 and GAL4NFκB constructs, we have developed a very efficient GAL4/UAS binary gene expression system for use in cultured B. mori cells and embryos and in transgenic silkworms.
Direct diode-pumped Kerr Lens 13 fs Ti:sapphire ultrafast oscillator using a single blue laser diode (2017)

We demonstrate a direct diode-pumped Kerr Lens Modelocked Ti:sapphire laser producing 13 fs pulses with 1.85 nJ energy at 78 MHz (145 mW) using a single laser diode pump. We also present a similar laser using three spectrally combined diodes, generating >300 mW output power with >50 nm bandwidth. We discuss the use of far-from TEM<sub>00</sub> pump laser sources, and their effect on the Kerr lens modelocking process.
CspA, the major cold shock protein of Escherichia coli, negatively regulates its own gene expression (1997)

When the gene for CspA, the major cold shock protein of Escherichia coli, was disrupted by a novel positive/negative selection method, the deltacspA cells did not show any discernible growth defect at either 37 or 15 degrees C. By two-dimensional gel electrophoresis, total protein synthesis was analyzed after temperature downshift in the deltacspA strain. The production of the CspA homologs CspB and CspG increased, and the duration of their expression was prolonged, suggesting that both CspB and CspG compensate for the function of CspA in the absence of CspA during cold shock adaptation. Interestingly, the production of the 159-base 5'-untranslated region (5'-UTR) of cspA from the chromosomal cspA::cat gene, detected by primer extension, failed to be repressed after cold shock. When an independent system to produce CspA was added to the deltacspA strain, the 5'-UTR production for the cspA::cat gene was significantly reduced compared to that of the deltacspA strain. By examining the expression of translationally fused cspA and cspB genes to lacZ in the deltacspA strain, it was found that cspA is more strongly regulated by CspA than cspB is. We showed that the increased expression of the 5'-UTR of the cspA mRNA in the deltacspA strain occurred mainly at the level of transcription and, to a certain extent, at the level of mRNA stabilization. The mRNA stabilization in the deltacspA strain was observed for other mRNAs, supporting the notion that CspA functions as an mRNA chaperone to destabilize secondary structures in mRNAs.
Fluid coupled metallic micromachined needle arrays (2002)

Fluid coupled metallic micromachined needle arrays are designed, fabricated, and characterized. The described hollow metallic needle arrays include design features such as dual structural supports and needle coupling channels. The supports and needle walls are formed by micro-electroformed metal to provide increased structural integrity. The needle coupling channels are used to fluidically interconnect the needles and allow pressure equalization and balance of fluid flow between needles. In addition, the needle coupling channels minimize the effects of restricted needle passages by providing a redistribution point for fluid flow between them. The optimum design for the needle coupling channels is investigated using an ANSYS finite element numerical model. The significance of this work includes the development of hollow, metallic micromachined needle arrays for biomedical applications. The authors also discuss structural, fluidic, and biological design considerations.
Spectral Detection of Micro-Metastases and Individual Metastatic Cells in Lymph Node Histology (2011)

The detection of micro-metastases and individual metastatic cells in lymph node tissue by spectral methods is summarized. These methods are based on instrument-based acquisition of thousands of infrared spectra of individual tissue pixels from the tissue section, and analysis of the resulting spectral hypercube by multivariate algorithms. The method of infrared image acquisition, followed by multivariate analysis, is henceforth referred to as Spectral Histopathology (SHP). SHP produces pseudo-color images of tissue sections which reveal details that compare very favorably with images collected from hematoxylin/eosin (H and E) stained tissues in that the same tissue structures are detected. However, the infrared results are based on objective and reproducible measurements and do not depend on subjective interpretation. One of the major topics of this paper is the comparison of spectral patterns observed for the same cancer type from different patients. While this is easy in some tissue types, we found it to be difficult in tissues of very different cellularity, or tissue sections that exhibit high levels of inflammatory response. In both cases, spectral quality will be compromised due to confounding effects resulting from scattering effects. The correction of these effects now permits the direct comparison of different patient samples, and paves the way for diagnostic algorithms for cancer detection to be developed.
A Rapid Screening Approach to Identify Resistance to Basil Downy Mildew (Peronospora belbahrii) (2014)

Sweet basil ( Ocimum basilicum L.) is among the most widely popular and economically important culinary herbs. Worldwide production of sweet basil has been threatened by a newly emerging disease, downy mildew ( Peronospora belbahrii ). Although tolerance and resistance have been identified in other Ocimum species, the traditional sweet basils all have been reported to be highly susceptible. There is an urgent need for evaluation of basil germplasm to identify sources of host resistance to P. belbahrii within Ocimum spp. and especially among O. basilicum species. In searching for genetic resistance, we developed a rapid approach to screen and evaluate downy mildew response at the cotyledon and true leaf growth stages under controlled environmental conditions. To confirm the reliability and reproducibility of this screening method, an experiment was conducted in which three basil species ( Ocimum basilicum , sensitive; O. xcitriodorum , tolerant; and O. americanum , resistant to basil downy mildew) were evaluated for response to downy mildew inoculations at three growth stages. Disease incidence (DI) at the cotyledon growth stage was equal to or greater than true leaf growth stages for all species indicating that cotyledon response to downy mildew inoculations is a viable marker for predicting true leaf stage resistance. This approach was then used to screen 36 USDA-NPGS O. basilicum accessions at cotyledon and first true leaf growth stages to identify promising downy mildew-resistant breeding lines. Thirty accessions were susceptible at both growth stages (DI = 1.0). Four accessions exhibited little or no sporulation at either growth stage (DI less than 0.06), three of which showed other symptoms including chlorosis and necrosis. One accession, PI 652053, demonstrated no signs or symptoms but differed greatly from other accessions in regard to leaf morphology and habit. Results show that a resistant, mature plant can be identified at the cotyledon growth stage, providing a robust, low-input approach to identify promising downy mildew-resistant breeding material. Field evaluations of basils under high downy mildew pressure confirmed the applicability of this new screening approach to identify resistance to basil downy mildew.
NIR-Emitting Erbium/Oxygen-Doped Silicon by Self-Assembled Techniques (2019)

Self-assembled monolayer (SAM) techniques have been developed to dope silicon surfaces with use of erbium radiation sources. After rapid thermal annealing at 1050 oC, surface monolayer structure and dopant concentration distribution were characterized by X-ray photoelectron spectroscopy and secondary ion mass spectroscopy measurements, respectively. A distinctive 4I13/2 → 4I15/2 transition of erbium ion (4f) glowing at 1.54 μm has been observed at room temperature for these Er/O-doped Si samples. With these preliminary results, it is promising to develop room-temperature silicon-based light-emitting devices and lasers on the basis of these bottom-up SAM techniques.
In vivo characterization of a porous hydrogel material for use as a tissue bulking agent (2001)

Tissue engineered biomaterial constructs are needed for plastic and reconstructive applications. To successfully form a space-filling tissue, the construct should induce a minimal inflammatory response, create minimal or no fibrotic capsule, and establish a vascular bed within the first few days after implantation to ensure survival of the implanted cells. In addition, the biomaterial should support cellular adhesion and induce tissue ingrowth. A macroporous hydrogel bead using sodium alginate covalently coupled with an arginine, glycine, and aspartic acid-containing peptide was created. A 6-month subcutaneous rat model study was performed to determine if the implanted material induced tissue ingrowth throughout the implantation area and maintained a three-dimensional vascular bed. The implanted materials produced a vascular bed, minimal inflammation and capsule formation, and good tissue ingrowth throughout the experiment. The material retained its bulking capacity by demonstration of no significant change of the cross-sectional area as measured from the center of the implants after the 2-week time point. In addition, the granulation tissue formed around the implant was loosely organized, and the surrounding tissue had integrated well with the implant. These results indicate that this material has the desired properties for the development of soft-tissue-engineering constructs.
Speculative Parallel Threading Architecture and Compilation (2005)

Thread-level speculation is a technique that brings thread-level parallelism beyond the data-flow limit by executing a piece of code ahead of time speculatively before all its input data are ready. This technique appears particularly appealing for speeding up hard-to-parallelize applications. Although various thread-level speculation architectures and compilation techniques have been proposed by the research community, scalar applications remain difficult to be parallelized. It has not yet shown how well these applications can actually be benefited from thread-level speculation and if the performance gain is significant enough to justify the required hardware support. In an attempt to understand and realize the potential gain with thread-level speculation especially for scalar applications, we proposed an SPT (speculative parallel threading) architecture and developed an SPT compiler to generate optimal speculatively parallelized code. Our evaluation showed that with our SPT approach 10 SPECint2000 programs can achieve an average of 15.6% speedup on a two-core SPT processor by exploiting only loop parallelism. This paper describes the SPT architecture and the SPT compiler which performs aggressive cost-driven loop selection and transformation, and presents our performance evaluation results.