gebhart/patrepeval huggingface dataset:
Butane-1,2,3,4-tetraol-based amphiphilic stereoisomers for membrane protein study: importance of chirality in the linker region (2016)

Amphiphile selection is a crucial step in membrane protein structural and functional study. As conventional detergents have limited scope and utility, novel agents with enhanced efficacy need to be developed. Although a large number of novel agents have been reported, so far there has been no systematically designed comparative study of the protein stabilization efficacy of stereo-isomeric amphiphiles. Here we designed and prepared a novel class of stereo-isomeric amphiphiles, designated butane-1,2,3,4-tetraol-based maltosides (BTMs). These stereoisomers showed markedly different behaviour for most of the targeted membrane proteins depending on the chirality of the linker region. These findings indicate an important role for detergent stereochemistry in membrane protein stabilization. In addition, we generally observed enhanced detergent efficacy with increasing alkyl chain length, reinforcing the importance of the balance between hydrophobicity and hydrophilicity in detergent design. The stereo-isomeric difference in detergent efficacy observed provides an important design principle for the development of novel amphiphiles for membrane protein manipulation.
Double-sided liquid cooling for power semiconductor devices using embedded power packaging (2005)

This paper presents double-sided liquid thermal management schemes for MOSFETs using embedded power technology. Physics based RC lumped thermal models were developed for embedded power with double-sided forced liquid convection and a wire bond package with single-sided forced liquid convection. Embedded power with double-sided liquid cooling is expected to produce up to a 40% reduction in thermal resistance compared to a wire bond package with single-sided liquid cooling. A liquid module test bed has been created based on the convection modeled and is used with MOSFET based samples to explore the validity of the modeling results. Temperature measurements from experimental results are comparable to the modeling results for single-side cooled wire bond packaging for a loss between 10 to 100 W and 0.15 to 5 GPM water flow rate. Pulse loss results also mimic transient heat transfer trends depicted in modeling. Experiments for double-sided cooling with embedded power are in progress.
Improved Packaging System for Generation of High-Level Noncytotoxic HSV-1 Amplicon Vectors Using Cre-loxP Site-Specific Recombination to Delete the Packaging Signals of Defective Helper Genomes (2003)

Amplicons are promising helper-dependent HSV-1-derived vectors that allow the transfer and expression of very large foreigner DNA into dividing and quiescent cells. We had already described an approach to prepare large amounts of high-titer amplicon vectors, using Cre-loxP site-specific recombination system to delete the packaging ("a") signals of an HSV-1 recombinant helper virus (HSV-1 LaL). Amplicon vectors prepared using such a system showed a level of contamination with helper particles lower than 1%. The residual helper particles generated by this system are, however, replication-competent, thus precluding their use in gene therapy. To avoid such potential spread of residual particles, we present here the development of a defective Cre-loxP-based helper virus (HSV-1 LaL Delta J), deleted of the genes encoding ICP4 and ICP34.5 proteins from the helper genome, in addition to the native "a" signals. HSV-1 LaL Delta J carries a single floxed "a" signal in gC locus. To produce HSV-1 LaL Delta J and to prepare the amplicon vectors, we have constructed two novel cell lines expressing the essential ICP4 protein, either alone or in combination with Cre recombinase. These cell lines were conceived to complement ICP4 while minimizing the probability of generating replication-competent particles. In this paper we present results demonstrating that the novel helper system allows ready production of large amounts of high-titer amplicon vectors. Residual helper particles generated still do not exceed 0.5% of the viral population and can grow only in cells expressing ICP4. Amplicon vectors produced with this method showed no cytotoxicty for infected cells.
Polymer‐immobilized cyclodextrin trapping of model organic pollutants in flowing water streams (2003)

Abstract Epichlorohydrin‐crosslinked β‐cyclodextrin polymers (BCDPs) were prepared and characterized by Fourier transform infrared. Beads of the BCDPs were used to pack a column for trapping organic contaminants in flowing water (flow rate = 5–32 mL/min). The contaminants were naphthalene (a model for polyaromatic hydrocarbons), naproxen (a model for pollutants of pharmaceutical origin), and 2‐naphthol (a model for pesticides with pH‐dependent ionization states). The trapping efficiencies were determined with fluorescence spectroscopy as the analytical technique. The best trapping efficiencies were obtained for BCDPs with a nominal cyclodextrin/epichlorohydrin ratio of 1:29. Trapping was highly efficient for naphthalene (98%) and 2‐naphthol (70%), but it was much less efficient for naproxen (18%). Possible causes for these differences were examined. The trapped organics could be flushed from the column with an ethanol wash. The recovery of the organics with this approach was very good (>95%). This simple column design, made of inexpensive and reusable materials, has potential applications in water remediation and water sampling. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 2103–2110, 2003
Application of Natural Receptors in Sensors and Assays (2002)

Biosensors are analytical devices that use a biological or biologically derived material immobilized at a physicochemical transducer to measure one or more analytes. Although there are a large number of reviews on biosensors in general, there has been little systematic information presented on the application of natural receptors in sensor technology. This perspective discusses broadly the fundamental properties of natural receptors, which make them an attractive option for use as biorecognition elements in sensor technology. It analyses the current situation by reference to typical examples, such as the application of nicotinic acetylcholine receptor and G protein-linked receptors in affinity sensors and analyses the problems that need to be resolved prior to any commercialization of such devices.
Stable expression in yeast of the mature form of human telomerase RNA depends on its association with the box H/ACA small nucleolar RNP proteins Cbf5p, Nhp2p and Nop10p (2001)

Telomerase is a ribonucleoprotein (RNP) particle required for the replication of telomeres. The RNA component, termed hTR, of human telomerase contains a domain structurally and functionally related to box H/ACA small nucleolar RNAs (snoRNAs). Furthermore, hTR is known to be associated with two core components of H/ACA snoRNPs, hGar1p and Dyskerin (the human counterpart of yeast Cbf5p). To assess the functional importance of the association of hTR with H/ACA snoRNP core proteins, we have attempted to express hTR in a genetically tractable system, Saccharomyces cerevisiae. Both mature non-polyadenylated and polyadenylated forms of hTR accumulate in yeast. The former is associated with all yeast H/ACA snoRNP core proteins, unlike TLC1 RNA, the endogenous RNA component of yeast telomerase. We show that the presence of the H/ACA snoRNP proteins Cbf5p, Nhp2p and Nop10p, but not Gar1p, is required for the accumulation of mature non-polyadenylated hTR in yeast, while accumulation of TLC1 RNA is not affected by the absence of any of these proteins. Our results demonstrate that yeast telomerase is unrelated to H/ACA snoRNPs. In addition, they show that the accumulation in yeast of the mature RNA component of human telomerase depends on its association with three of the four core H/ACA snoRNP proteins. It is likely that this is the case in human cells as well.
Computational complexity of controllability/observability problems for combinational circuits (2003)

The computational complexity of fault detection problems and various controllability and observability problems for combinational logic circuits are analyzed. It is shown that the fault detection problem is still NP-complete even for monotone circuits limited in fanout, i.e. the number of signal lines which fanouts from a signal line is limited to three. It is also shown that the observability problem for unate circuits is NP-complete, but that the controllability problem for unate circuits can be solved in time complexity O(m), where m is the number of lines in a circuit. Furthermore, two classes of circuits, called k-binate-bounded circuits and k-bounded circuits, are introduced. For k-binate-bounded circuits, the controllability problem is solvable in polynomial time, and for k-bounded circuits, the fault detection problem is solvable in polynomial time, when k<or=log p(m) for some polynomial p(m). The class of k-bounded circuits includes many practical circuits such as decoders, adders, one-dimensional cellular arrays, two-dimensional cellular arrays, etc.<<ETX>>
Synthesis and solution structure of 3,5-dioxopimelic acid diesters—stable 1,3,5,7-tetracarbonyl derivatives (2008)

A variety of 3,5-dioxopimelic acid diesters, stable 1,3,5,7-tetracarbonyl derivatives, were prepared by catalytic condensation of 1,3-bis(trimethylsilyloxy)-1,3-butadienes with methyl malonyl chloride. The keto-enol tautomerization of these compounds has been investigated by NMR spectroscopy. One keto and up to four enolic tautomers could be detected in chloroform solution and the influence of the substituents on the tautomeric equilibria has been studied.
Identification of Phosphocholine‐Containing Glycoglycerolipids Purified from <i>Mycoplasma fermentans</i>‐Infected Human Helper T‐Cell Culture as Components of <i>M. fermentans</i> (1995)

Previously, we have reported the occurrence of novel phosphocholine-containing glycoglycerolipids (GGPLs: GGPL-I and GGPL-III) in human helper T-cell (MT-4 cell line) (Mustuda et al, Glycoconjugate J. 10:340). However, the GGPLs disappeared from the MT-4 after treatment with an antimycoplasma agent. This disappearance suggested the involvement of microorganisms in the GGPL expression. In this paper, we show that the novel lipids are components of Mycoplasma fermentans itself. The supernatant fluid of the antimycoplasma agent-untreated Mt-4 cell culture produced mycoplasma-like colonies on PPLO agar plates, and PCR and immunological methods revealed the presence of M. fermentans. GGPLs were expressed again in the treated Mt-4 cells after infection with the isolated M. fermentans. The isolated M. fermentans had glycoglycerolipids corresponding to GGPL-I and GGPL-III. Thin-layer chromatography-mass spectrometry and immunological analyses showed that these glycoglycerolipid which were derived from the isolated M. fermentans were identical with GGPL-I and GGPL-III previously obtained. This is the first report that shows mycoplasma has phosphocholine-containing glycoglycerolipids.
Synthesis of trans-2,5-dimethylpyrrolidine by intramolecular amidomercuration (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of trans-2,5-dimethylpyrrolidine by intramolecular amidomercurationKenn E. Harding and Stephen R. BurksCite this: J. Org. Chem. 1981, 46, 19, 3920–3922Publication Date (Print):September 1, 1981Publication History Published online1 May 2002Published inissue 1 September 1981https://pubs.acs.org/doi/10.1021/jo00332a036https://doi.org/10.1021/jo00332a036research-articleACS PublicationsRequest reuse permissionsArticle Views456Altmetric-Citations71LEARN 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
A Study and Comparison of Human and Deep Learning Recognition Performance under Visual Distortions (2017)

Deep neural networks (DNNs) achieve excellent performance on standard classification tasks. However, under image quality distortions such as blur and noise, classification accuracy becomes poor. In this work, we compare the performance of DNNs with human subjects on distorted images. We show that, although DNNs perform better than or on par with humans on good quality images, DNN performance is still much lower than human performance on distorted images. We additionally find that there is little correlation in errors between DNNs and human subjects. This could be an indication that the internal representation of images are different between DNNs and the human visual system. These comparisons with human performance could be used to guide future development of more robust DNNs.
Rifamycins do not function by allosteric modulation of binding of Mg <sup>2+</sup> to the RNA polymerase active center (2008)

Rifamycin antibacterial agents inhibit bacterial RNA polymerase (RNAP) by binding to a site adjacent to the RNAP active center and preventing synthesis of RNA products >2-3 nt in length. Recently, Artsimovitch et al. [(2005) Cell 122:351-363] proposed that rifamycins function by allosteric modulation of binding of Mg(2+) to the RNAP active center and presented three lines of biochemical evidence consistent with this proposal. Here, we show that rifamycins do not affect the affinity of binding of Mg(2+) to the RNAP active center, and we reassess the three lines of biochemical evidence, obtaining results not supportive of the proposal. We conclude that rifamycins do not function by allosteric modulation of binding of Mg(2+) to the RNAP active center.
A Procedure for the Preparation of Pure 1,4-Cyclohexadiene from Benzene (1990)

Abstract Pure 1,4-cyclohexadiene can be obtained by reaction of benzene with an excess of lithium in a mixture of t-butyl alcohol and liquid ammonia.
1 kW cw Yb-fiber-amplifier with <0.5GHz linewidth and near-diffraction limited beam-quality for coherent combining application (2011)

In this paper, we present results on a master-oscillator Yb-doped fiber amplifier with 1 kW cw output power (at 1064nm), and near-diffraction limited beam quality (M2<1.4), with internal quantum efficiency >83%. The final amplifier stage uses a very high Yb-doped 35-um core LMA fiber, using a new process recipe that virtually eliminates photo-darkening. As a result, high efficiency, SBS-free operation to 1 kW cw power level is obtained, with a phase modulation bandwidth of only 450MHz, well below other reported results. To enable single-frequency cw power scaling to kW levels, we investigate LMA fiber waveguide designs exploiting gain-discrimination, using partially Yb-doped LMA fiber cores, with various diameters up to 80-um. SBS-free, singlefrequency (few kHz) operation is demonstrated up to 0.9kW cw power. At the lower cw powers (<200W) neardiffraction limited beam-quality is obtained, but is observed to deteriorate at higher cw powers. We discuss potential causes, and present a detailed simulation model of kW large-core fiber-amplifiers, that includes all guided modes, fiber bend, transverse spatial hole burning, gain-tailoring, mode-scattering, SBS nonlinearity, and various thermal effects. This model shows good agreement with the observed single-frequency power scaling and beam-quality characteristics.
Solvent Directed Morphogenesis and Electrical Properties of a Peptide–Perylenediimide Conjugate (2018)

Molecular organization of electron-deficient aromatic systems like perylenediimides (PDI) is extremely appealing, as they are potential candidates for organic electronics. The performance of these molecules in such applications primarily depends on the self-organization of the molecules. However, any correlation between the morphology of these self-assembled semiconducting molecules and their electrical performances has not yet been formulated. Herein, for the first time, we have made an effort to find such a correlation by studying the self-assembly, morphology, and their conducting properties for a peptide-PDI conjugate. The PDI conjugate formed fiber-like morphology in relatively nonpolar solvents (THF and CHCl<sub>3</sub>) while in more polar solvents (HFIP, MeOH, ACN, and acetone), spherical morphology could be found. Interestingly, the self-assembly and the morphologies showed a clear dependence on the solvent polarity. In polar solvents, the conjugate aggregates more efficiently than in the nonpolar solvents, and with decrease in solvent polarity, the dimension of the nanostructures increased. However, in all the tested solvents, irrespective of their polarity, the PDI-peptide conjugate adopts a right-handed helicity. To find a correlation between the morphologies with the conducting property, detailed electrical characterization of these nanostructures was carried out. While no significant change could be observed for the dc conductivities of these nanostructures, the ac conductivities show prominent difference at the low-frequency region. A dispersion of conductivity was observed for the nanospheres due to the polarization effect. A critical correlation between the nanostructures and the activation energy was observed as with decrease in radii of curvature of the aggregates the activation energy increases with an exception in the case of MeOH. The observed results suggest that the long-range transport of charge carriers is less favorable when the aggregates are small and closely packed.
Effect of Perfluorochemicals on BCNU Chemotherapy in a 9L Rat Brain Tumor Model (1982)

Perfluorochemicals are characterized by their small size and high propensity for carrying oxygen and carbon dioxide. This study was undertaken to identify the combined effect of a perfluorochemical (Fluosol-43, 20 ml/kg) and a chemotherapeutic agent (BCNU, LD10 dose: 13.3 mg/kg) in a 9L rat brain tumor model. Brain tumor was induced by intracerebral implantation of 9L rat glioma cells (7×105 cells) into male CD Fisher 344 rats weighing about 100 g. The tumor growth curve of this model was exponential, and at 7 days after implantation, the control animals had a macrotumor weighing about 51 mg. The tumor-bearing rats on day 7 after implantation were randomly divided into 5 groups: control; BCNU alone; Fluosol-43 with oxygen; Fluosol-43 plus BCNU; and Fluosol-43 plus BCNU with oxygen. High oxygen was produced in an oxygen chamber with 95% oxygen and 5% carbon dioxide, and the PaO2 was maintained between 300 and 400 mmHg. Control animals had a mean survival time of 15.23 ± 2.84 (S.D.) days, and the Fluosol-43 with oxygen group showed no prolongation of the mean survival time (p>0.2). BCNU treatment alone prolonged the mean survival time to 20.90 ± 3.80 days (p<0.05), whereas the Fluosol-43 plus BCNU group had no further prolongation of the mean survival time: The Fluosol-43 plus BCNU with oxygen showed a mean survival time of 32.27 ± 4.80 days, which was significantly longer than that of the BCNU treatment alone (p < 0.005). Perfluorochemicals (Fluosol-43) with oxygen may have a synergistic effect on BCNU chemotherapy for malignant brain tumor. Fluosol-43 with oxygen might have oxygenated the hypoxic cells so that they became sensitized to BCNU. Also, the transport of BCNU into hypoxic and hypovascular areas might have been enhanced by Fluosol-43 and oxygen.
Person Reidentification via Discrepancy Matrix and Matrix Metric (2017)

Person reidentification (re-id), as an important task in video surveillance and forensics applications, has been widely studied. Previous research efforts toward solving the person re-id problem have primarily focused on constructing robust vector description by exploiting appearance’s characteristic, or learning discriminative distance metric by labeled vectors. Based on the cognition and identification process of human, we propose a new pattern, which transforms the feature description from characteristic vector to discrepancy matrix. In particular, in order to well identify a person, it converts the distance metric from vector metric to matrix metric, which consists of the intradiscrepancy projection and interdiscrepancy projection parts. We introduce a consistent term and a discriminative term to form the objective function. To solve it efficiently, we utilize a simple gradient-descent method under the alternating optimization process with respect to the two projections. Experimental results on public datasets demonstrate the effectiveness of the proposed pattern as compared with the state-of-the-art approaches.
Rapid Screening Method for the Total Petroleum Hydrocarbons in Water Samples by Solid-Phase Microextraction and GC-MS (2012)

Determination of total petroleum hydrocarbons (TPH) in water is an important tool for monitoring of contamination due to oil spills or leaking storage tanks. In this study, a screening method for the quantification of total petroleum hydrocarbons in water based on solid phase microextraction (SPME) in combination with gas chromatography - mass spectrometry (GC-MS) is presented. Extraction of hydrocarbons from water samples were conducted by SPME fiber coating placed into the headspace above water. Petroleum hydrocarbons were desorbed from the fiber coating in the injection port of gas chromatograph. The effect of the following parameters affecting the distribution of the analytes between three phases on the response of TPH were studied: SPME fiber coating type and dimensions, extraction temperature, extraction time and pH. The optimized method uses 100 Ојm polydimethylsiloxane fiber coating, extraction time 600 s, extraction temperature 80 °C, without addition of salt at basic pH. The developed method was successfully applied for detection of total petroleum hydrocarbons in water taken from Koschagyl oil fields and Koschagyl village.