gebhart/patrepeval huggingface dataset:
Ketone homologation to produce α-methoxyketones: application to conduritol synthesis (1997)

The scope of Trost’s sulfone homologation procedure for the conversion of ketones into their α-methoxylated higher homologues has been dramatically expanded. The use of zirconium (or hafnium) tetrachloride in the hydroxy sulfone rearrangement step gives good yields with the adducts of aryl alkyl ketones, dialkyl ketones and cycloalkanones, and the rearrangement occurs with total regioselectivity. Mechanistic observations are presented which account for the formation of α-hydroxy aldehydes as by-products and which indicate an efficient method for their preparation. Application of the homologation methodology to the stereoselective synthesis of dihydroconduritols is described.
Cells Lacking the PolQ Polymerase Are Moderately Sensitive to Ionizing Radiation and the Oxidant Induced Toxicity of Paraquat and Bleomycin. (2007)

Abstract The DNA polymerase POLQ (pol theta) can bypass abasic sites in DNA and thymine glycol, a common product of reactive oxygen species damage to DNA. POLQ may also have a back-up role in base excision repair. To explore the role of POLQ in tolerance of DNA damage following irradiation, and exposure to agents that induce oxidative stress we established bone marrow stromal cell lines from the PolQ+/+ and PolQ−/− mice. Irradiation survival curves were obtained for PolQ +/+, and 2 clones of PolQ −/− cells. Dose-response experiments using the free radical generators paraquat, hydrogen peroxide and bleomycin were done on 2 clones each of PolQ +/+ and PolQ −/− cells. There was no significant difference over 23 weeks in cumulative granulopoiesis in LTBMCs from PolQ +/+ and PolQ −/− mice. PolQ+/+ cells and 2 independent clones of PolQ−/− cells were exposed to 0 – 8 Gy of gamma radiation, and colony forming ability was measured. PolQ −/− cells were more sensitive to irradiation as shown by decreased Do from 1.38 + 0.06 Gy for PolQ +/+ cells compared to 1.27 + 0.16 and 0.98 + 0.10 (p = 0.0316) Gy for PolQ −/− clones 1 and 3 respectively. Micronucleated reticulocytes were measured in peripheral blood of PolQ+/+, +/− or −/− mice after irradiation with 75 cGy or 700 cGy. Before irradiation, PolQ−/− mice had a higher fraction of MN- reticulocytes compared to PolQ+/+. Forty hr after irradiation, MN reticulocytes in PolQ−/− mice increased to 8.53 ± 1.48%, compared to 2.35 ± 0.12% and 2.55 ± 0.17% in PolQ+/+ mice (p = 0.0032). PolQ +/+ and PolQ −/− cells were exposed to paraquat (0–20 mM), hydrogen peroxide (0–40 uM) and bleomycin (0–5 ug/ml) for 1 hr prior to plating. After 7 days, the cells were stained and colonies of 50 cells or greater were counted. Statistical analysis was done using ANCOVA. PolQ −/− cells were modestly more sensitive to paraquat (p&lt; 0.0001) and bleomycin (p&lt; 0.0001) than PolQ +/+ cells. When the cells were treated with hydrogen peroxide, there was no significant difference in surviving fraction (p=0.7327) between the PolQ +/+ and the −/− cells. The moderate but significant sensitivity of POLQ-defective cells to bleomycin, ionizing radiation and paraquat supports the hypothesis that POLQ normally participates in helping cells tolerate DNA damage. The increased frequencies of spontaneous and radiation-induced micronuclei in peripheral blood red cells indicate that POLQ has a role in maintaining genomic integrity via limiting double-strand DNA breaks.
Synchronisation of Feed Axes with Differing Bandwidths Using Set Point Delay (2017)

This paper presents an effective method for the synchronisation of multiple feed axes with differing controller bandwidths by delaying the set point trajectories of those axes with higher bandwidths. First, a simplified model of a cascade-controlled feed axis is defined, which allows the problem to be treated analytically. The problem of synchronisation of the feed axes is then analysed mathematically, leading to the hypothesis of synchronisation through a delay of the set points of the more dynamic axes. Subsequently, the dynamic error behaviour and boundaries of a feed axis are calculated. The optimal damping factor for a feed axis is shown to be 1/√2 and the dynamic error can be formulated in terms of the bandwidth and acceleration or jerk limit. The proposed method is proven through a simulation and verified based on experimental results. In addition, the stated error bounds are verified, and the limits of the applicability are determined.
Security primitives and protocols for ultra low power sensor systems (2011)

Security requirements in sensor systems include resiliency against physical and side-channel attacks, low energy for communication, storage, and computation, and the ability to realize a variety of public-key protocols. Furthermore, primitives and protocols that enable trusted remote operation in terms of data, time, and location are essential to guarantee secure sensing. By integrating physically unclonable functions (PUFs) directly into sensor hardware and using device aging to securely match groups of sensors, we enable a variety of ultra low power security protocols for trusted remote sensing, including authentication and public key communication.
Visually Determining Gamma for Softcopy Display (2005)

We propose estimating the gamma value for the blue channel of a softcopy display via a grey-balancing task. A &#x201C;near-neutral&#x201D; patch is displayed along with a neutral reference pattern made from black and white pixels. The red and green values for this near-neutral patch are derived from a separate calibration of these 2 channels. The user then adjusts the blue value until the near-neutral patch appears neutral with respect to the surrounding reference. Gamma for the blue channel is estimated from the selected value. Implementations include interactive adjustment with mouse and/or keyboard, or selecting from a fixed set of patches the one that appears most neutral. When compared with the standard technique, inter- and intra-observer variation in the settings for blue were substantially reduced.
A Study on Risk Assessment of Structure Failure for Fixed Platforms Based on the Importance Sampling Procedure (2006)

Risk assessment of platform structure failure caused by combined effects of typhoon induced extreme sea conditions is one of the most important problems in the establishment of quantitative risk analysis systems for offshore oil engineering projects.In this paper,in order to establish a practical and reliable risk assessing system of platform structures,a stochastic simulation technique based on the importance sampling procedure is used to estimate the structure failure probability for CB12-C platform in the Bohai Sea and consequent analysis is also made.The method presents a new technique for quantitative risk assessment of fixed platforms,in which the uncertainty in the risk assessing procedure is considered,so the quantitative result of risk assessment is more reliable.
SPECT- CT study of directed drug delivery using /sup 111/In-labeled liposomes in a murine mammary carci-noma model (2006)

Liposomal drugs offer the promise of an improved therapeutic index due to improvements in the specific delivery of anti-cancer agents to tumors. The presented work concentrates on imaging the tumor uptake of /sup 111/In-labeled liposomes noninvasively as a specific tumor drug delivery carrier in a murine cancer model. The tumor uptake of liposomes has been imaged using a microSPECT/microCT small animal dedicated scanner prototype constructed at our laboratory. The imaging system consists of a high resolution SPECT (700 /spl mu/m) and high resolution CT (70 /spl mu/m). The SPECT subsystem consists in specially designed CZT gamma cameras shielded for energies up to 250 keV. The mice were injected with liposomes and scanned at the time of maximum tumor uptake (24 h). The total activity of the mouse samples was of the order of 250 uCi, and with tumor sizes of 1000-1500 mm/sup 3/. The imaging geometries in the CT and SPECT acquisitions were selected to obtain high magnification and high efficiency to image the tumor located within the torso. The SPECT and CT projections were taken sequentially. The acquired images show that necrotic tumors can de imaged with high resolution to observe liposome inhomogeneous uptake.
Synthesis and bioactivity of a new class of rigid glutamate analogs. Modulators of the N-methyl-D-aspartate receptor (1990)

A variety of derivatives of azetidine-2,4-dicarboxylic acid were synthesized and examined for their ability to stimulate 45Ca2+ uptake in cultures of cerebellar granule cells. Of the compounds tested, the cis-azetidine-2,4-dicarboxylic acid (10f) was found to be the most potent agent in potentiating glutamate, aspartate, or N-methyl-D-aspartate (NMDA) stimulated 45Ca2+ uptake at the NMDA receptor. The mechanism of action of 10f was further investigated in [3H]MK-801 binding assays and [3H]GABA release from cultured embryonic rat forebrain neurons. All of the results from the functional studies of azetidine 10f are consistent with a selectivity of action at the NMDA receptor. Moreover, azetidine 10f appears to exhibit a dual type of action, behaving as a glutamate-like agonist at higher concentrations and as a positive modulator at concentrations below 50 microM.
Selective Small Molecule Probes for the Hypoxia Inducible Factor (HIF) Prolyl Hydroxylases (2013)

The hypoxia inducible factor (HIF) system is central to the signaling of low oxygen (hypoxia) in animals. The levels of HIF-α isoforms are regulated in an oxygen-dependent manner by the activity of the HIF prolyl-hydroxylases (PHD or EGLN enzymes), which are Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. Here, we describe biochemical, crystallographic, cellular profiling, and animal studies on PHD inhibitors including selectivity studies using a representative set of human 2OG oxygenases. We identify suitable probe compounds for use in studies on the functional effects of PHD inhibition in cells and in animals.
ortho‐Quinones and Analogues Thereof: Highly Reactive Intermediates for Fast and Selective Biofunctionalization (2017)

Fast, selective and facile functionalization of biologically relevant molecules is a pursuit of ever-growing importance. A promising approach in this regard employs the high reactivity of quinone and quinone analogues for fast conjugation chemistry by nucleophilic addition or cycloadditions. Combined with in situ generation of these compounds, selective conjugation on proteins and surfaces can be uniquely induced in a time and spatially resolved manner: generation of a quinone can often be achieved by simple addition of an enzyme or stoichiometric amounts of chemoselective oxidant, or by exposure to light. In this Minireview, we discuss the generation and subsequent functionalization of quinones, iminoquinones, and quinone methides. We also discuss practical applications regarding these conjugation strategies.
European Union and NIH Collaborate (2008)

The National Institutes of Health (NIH) and the European Commission (EC) recently decided to reinforce our mutual interest in scientific collaboration. We believe that greater trans-Atlantic cooperation and smarter competition in science will lead to faster breakthroughs in health research and ultimately to a better quality of life for the citizens of the world.

![Figure][1] 

Partners. 
Former NIH Director Elias Zerhouni (left) and European Commissioner for Science and Research Janez Potocnik (right) make their new collaboration official.

CREDIT: MICHAEL SPENCER/NIH

The NIH has a long tradition of funding collaborations between U.S. and European scientists. To this end, the NIH recently clarified its policies for funding global collaborations ([1][2]). And on 3 September 2008, the European Commission published a new call for proposals within the health theme of its Seventh Framework Programme for Research and Development ([2][3]). For the first time, the EC has announced that researchers working in U.S. institutions are eligible not only to participate in EC-supported research projects but also to receive funds from the EC if they are part of a consortium with European Union (EU) investigators.

We live at a time of great scientific opportunity, where global collaborations are essential for facilitating scientific discoveries aimed at improving public health. As science has become more complex, so has the need for both specialization and multidisciplinary approaches to problem-solving. While discovery increasingly depends on a new level of collaboration, it also depends on expertise, which may not reside within one country or even within one continent. A prime example of global collaboration is the tremendously successful Human Genome Project, which reached its goals ahead of time and under budget. Similarly, global collaboration is essential to the conduct of clinical trials and genetic research, where disease prevalence in a given region enables research that could otherwise not be conducted in the confines of a single country.

We hope that our initiative, aimed at opening our research programs, will serve as a launch pad for wider and more intense U.S.-EU cooperation in health as well as in other areas of research. This is a historic step for our institutions today, and we are confident that it will also prove to be a significant step for the future of science.

1. 1.[↵][4] Updates and Reminders on NIH Policy Pertaining to Grants to Foreign Institutions, International Organizations and Domestic Grants with Foreign Components ( ).
 

2. 2.[↵][5] Seventh Research Framework Programme ( ).

 [1]: pending:yes
 [2]: #ref-1
 [3]: #ref-2
 [4]: #xref-ref-1-1 View reference 1. in text
 [5]: #xref-ref-2-1 View reference 2. in text
Search for diphoton events with large missing transverse momentum in 7 TeV proton–proton collision data with the ATLAS detector (2012)

A search for diphoton events with large missing transverse momentum has been performed using proton–&#13;\nproton collision data at&#13;\n√&#13;\ns = 7 TeV recorded with the ATLAS detector, corresponding to an integrated&#13;\nluminosity of 4.8 fb−1. No excess of events was observed above the Standard Model prediction and&#13;\nmodel-dependent 95% confidence level exclusion limits are set. In the context of a generalised model&#13;\nof gauge-mediated supersymmetry breaking with a bino-like lightest neutralino of mass above 50 GeV,&#13;\ngluinos (squarks) below 1.07 TeV (0.87 TeV) are excluded, while a breaking scale Λ below 196 TeV is&#13;\nexcluded for a minimal model of gauge-mediated supersymmetry breaking. For a specific model with&#13;\none universal extra dimension, compactification scales 1/R &lt; 1.40 TeV are excluded. These limits provide&#13;\nthe most stringent tests of these models to date.
Simple Interface Modification of Electroactive Polymer Film Electrodes (2019)

Understanding the role of interface properties is crucial in the search for alternative design strategies to optimize the efficiency, performance, and lifetime of both solid-state and redox active organic semiconductor devices. Recent advances have focused on controlling and tailoring interfacial effects on the morphology and molecular structure of the active film in multilayer devices triggering new developments in the area of interface engineering. Here, we demonstrate that an inorganic electrode/organic semiconductor interface modification using PEDOT:PSS as an interfacial material influences the charge and ion transport, capacitive, morphological, and color switching properties of a solution processed purple-to-clear switching electrochromic PProDOT-(CH<sub>2</sub>OEtHx)<sub>2</sub> polymer film. We find that the barrier to charge transport from electrode to active material is lowered when adding this PEDOT:PSS film, allowing us to present a fully roll-to-roll compatible, simple, and versatile battery-type electrochromic device (ECD) design without the need for oxidizing the charge storage film, in combination with improved processing reproducibility. In addition to producing ECDs with minimal color differences compared to devices prepared in the more traditional and complicated manner, this new ECD design strategy provides competitive performance showing a consistent optical contrast of 50-55% and switching times of 2-4 s.
Optimal reference genes for normalization of qPCR gene expression data from proton and photon irradiated dermal fibroblasts (2018)

The transcriptional response of cells exposed to proton radiation is not equivalent to the response induced by traditional photon beams. Changes in cellular signalling is most commonly studied using the method Quantitative polymerase chain reaction (qPCR). Stable reference genes must be used to accurately quantify target transcript expression. The study aim was to identify suitable reference genes for normalisation of gene expression levels in normal dermal fibroblasts irradiated with either proton or photon beams. The online tool RefFinder was used to analyse and identify the most stably expressed genes from a panel of 22 gene candidates. To assess the reliability of the identified reference genes, a selection of the most and least stable reference genes was used to normalise target transcripts of interest. Fold change levels varied considerably depending on the used reference gene. The top ranked genes IPO8, PUM1, MRPL19 and PSMC4 produced highly similar target gene expression, while expression using the worst ranked genes, TFRC and HPRT1, was clearly modified due to reference gene instability.
Immunocytochemical ultrastructural analysis of chromatophore membrane formation in Rhodospirillum rubrum (1986)

An immunocytochemical ultrastructural study of Rhodospirillum rubrum cultured under semiaerobic conditions was conducted to correlate the localization of functional components with membrane formation. R. rubrum is a facultatively phototrophic organism. Under reduced oxygen, this bacterium forms an intracytoplasmic chromatophore membrane that is the site of the photosynthetic apparatus. Immunogold techniques were used to localize intracellular protein antigens associated with the photosynthetic apparatus. Antibody, demonstrated by immunoblotting to be specific for the reaction center and light-harvesting photochemical components, was conjugated to colloidal gold particles and used for direct immunolabeling of fixed, sectioned specimens. Membrane invaginations appeared by 4 h after transition to induction conditions, and mature chromatophore membrane was abundant by 22 h. The occurrence of chromatophore membrane was correlated with bacteriochlorophyll a content and the density of the immunolabel. In uninduced (aerobic) cells and those obtained from cultures 0.5 h posttransition, the immunogold preferentially labeled the peripheral area of the cell. In contrast, in cells obtained after 22 h of induction, the central region of the cell was preferentially immunolabeled. These findings provided immunocytochemical evidence supporting the hypothesis that the chromatophore membrane is formed by invagination of the cytoplasmic membrane.
Perceptual Consequences of Curved Screens (2015)

When looking at a picture from the center of projection (CoP), the image on the retina is identical to the retinal image produced by the original scene. But pictures are usually not viewed from the CoP, so the retinal image differs from what would have occurred when viewing the original scene. Nonetheless, pictures seen from the wrong place continue to look largely veridical. Vishwanath et al. (2005) showed that the visual system compensates for off-to-the-side viewing by estimating the orientation of the picture surface at each point of interest (based on binocular disparity and frame perspective) and uses this estimate to in effect adjust the dimensions of the retinal image. Interestingly, when the eye is actually at the CoP, this compensation mechanism creates visible distortions in eccentric regions of the picture; the distortions are most obvious in pictures with large fields of view. We examined whether these wide-angle distortions can be reduced by (1) curving the projection plane used to create images, and (2) curving the display screen. Curving the projection plane decreases its slant from the CoP thereby reducing the stretching of the image of a depicted object, which should reduce perceived distortion. By curving the screen, the local slant of the display surface is minimized, which should also reduce distortion. We tested these predictions by measuring perceptual distortions on flat and curved (curvature radius = 418 cm) screens from 30 different viewing angles ranging from 0-50º and 6 viewing distances. We found that the local slant of the display surface was the sole predictor of perceptual distortions: i.e., distortions were reduced when pictures were presented on the curved screen. We derive a set of software and hardware guidelines to create natural-looking images based on focal length, projection plane curvature, and screen curvature. Meeting abstract presented at VSS 2015
Chemistry in Interphases—A New Approach to Organometallic Syntheses and Catalysis (1999)

Combining the advantages of homogeneous and heterogeneous catalysis is still a problem that has not been satisfactorily solved. Chemistry in interphases offers a new approach for overcoming the difficulties, as is described in this article. Owing to the swellable or porous matrix, an interphase represents a state which in the most favorable case is similar to that of a solution. Moreover the proper choice of a mobile hybrid copolymer enables the control of the density and accessibility of the reactive centers, which results in a distinct improvement of the activity of the catalysts (two examples are shown schematically).
Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey (2017)

To study the molecular basis for predator-prey coevolution, we investigated how <i>Caenorhabditis elegans</i> responds to the predatory fungus <i>Arthrobotrys oligospora</i>. <i>C. elegans</i> and other nematodes were attracted to volatile compounds produced by <i>A. oligospora</i>. Gas-chromatographic mass-spectral analyses of <i>A. oligospora</i>-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several <i>Caenorhabditis</i> species. Furthermore, when MMB is present, it interferes with nematode mating, suggesting that MMB might mimic sex pheromone in <i>Caenorhabditis</i> species. Forward genetic screening suggests that multiple receptors are involved in sensing MMB. Response to fungal odors involves the olfactory neuron AWCs. Single-cell RNA-seq revealed the GPCRs expressed in AWC. We propose that <i>A. oligospora</i> likely evolved the means to use olfactory mimicry to attract its nematode prey through the olfactory neurons in <i>C. elegans</i> and related species.