gebhart/patrepeval huggingface dataset:
Synthesis of 1,3,4-Oxadiazoles Using Polymer-supported Reagents (2001)

The preparation of a novel polystyrene-supported dehydrating agent and its application to the synthesis of 1,3,4-oxadiazoles under thermal and microwave conditions is described. An alternative procedure using tosyl chloride and P-BEMP is also presented.
Resistance acquisition to MDM2 inhibitors (2014)

Various experimental strategies aim to (re)activate p53 signalling in cancer cells. The most advanced clinically are small-molecule inhibitors of the autoregulatory interaction between p53 and MDM2 (murine double minute 2). Different MDM2 inhibitors are currently under investigation in clinical trials. As for other targeted anti-cancer therapy approaches, relatively rapid resistance acquisition may limit the clinical efficacy of MDM2 inhibitors. In particular, MDM2 inhibitors were shown to induce p53 mutations in experimental systems. In the present article, we summarize what is known about MDM2 inhibitors as anti-cancer drugs with a focus on the acquisition of resistance to these compounds.
Forest canopy closure from classification and spectral mixing of scene components: multi-sensor evaluation of application to an open canopy (2002)

Three types of remote sensing data, colour infrared aerial photograph (CIR), compact airborne spectrographic imager (CASI) images and airborne visible/infrared imaging spectrometer (AVIRIS) image, have been used in estimating forest canopy closure for an open-canopy forest environment. The high spatial resolution CIR and CASI images were classified to generate forest canopy closure estimates. These estimates were used to validate the forest canopy closure estimation accuracies obtained using the AVIRIS image. Reflectance spectra extracted from the spectral-mode CASI image were used to atmospherically calibrate the raw AVIRIS image and converted it into a reflectance image. Classification and spectral unmixing methods have been applied to the AVIRIS image. Results indicate that both the classification and the spectral unmixing methods can produce reasonably accurate estimates of forest canopy closure (within 3% agreement) when relatively pure reflectance spectra and related statistics are extracted from the image. However, it is more challenging to use the spectral unmixing technique to derive subpixel-scale scene components whose reflectance spectra cannot be directly extracted from the AVIRIS image.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Using Bayesian Optimization to Guide Probing of a Flexible Environment\n for Simultaneous Registration and Stiffness Mapping (2015)

One of the goals of computer-aided surgery is to match intraoperative data to\npreoperative images of the anatomy and add complementary information that can\nfacilitate the task of surgical navigation. In this context, mechanical\npalpation can reveal critical anatomical features such as arteries and\ncancerous lumps which are stiffer that the surrounding tissue. This work uses\nposition and force measurements obtained during mechanical palpation for\nregistration and stiffness mapping. Prior approaches, including our own,\nexhaustively palpated the entire organ to achieve this goal. To overcome the\ncostly palpation of the entire organ, a Bayesian optimization framework is\nintroduced to guide the end effector to palpate stiff regions while\nsimultaneously updating the registration of the end effector to an a priori\ngeometric model of the organ, hence enabling the fusion of ntraoperative data\ninto the a priori model obtained through imaging. This new framework uses\nGaussian processes to model the stiffness distribution and Bayesian\noptimization to direct where to sample next for maximum information gain. The\nproposed method was evaluated with experimental data obtained using a Cartesian\nrobot interacting with a silicone organ model and an ex vivo porcine liver.\n
Evaluation of epidermal growth factor-related growth factors and receptors and of neoangiogenesis in completely resected stage I-IIIA non-small-cell lung cancer: amphiregulin and microvessel count are independent prognostic indicators of survival. (1998)

We have determined the expression of transforming growth factor alpha (TGF alpha), amphiregulin (AR), CRIPTO, the epidermal growth factor receptor (EGFR), erbB-2, erbB-3, and tumor angiogenesis in a series of 195 patients with stage I-IIIA non-small cell lung cancer (NSCLC) treated with radical surgery to define their usefulness as prognostic indicators of survival. A variable degree of specific staining in cancer cells was observed for the three growth factors and for the three growth factor receptors in the majority of NSCLC patients. A statistically significant association between overexpression of TGF alpha, AR, and CRIPTO was observed. Enhanced expression of AR was significantly correlated with enhanced expression of erbB-2 and advanced T-stage. A direct association was also detected for overexpression of TGF alpha and of erbB-2 or erbB-3, respectively. Sex, tumor size, nodal status, stage, microvessel count, as a measure of neovascularization, and AR overexpression significantly correlated with overall survival at univariate analysis. In a Cox multivariate analysis, the only characteristics with an independent prognostic effect on OAS were microvessel count [relative hazard (RH), 6.61; P < 0.00001), nodal status (RH, 1.59; P = 0.0013), and AR overexpression (RH, 1.72; P = 0.02). These results suggest that evaluation of neoangiogenesis and of certain growth factors, such as AR, can be useful in addition to conventional pathological staging to select high-risk NSCLC patients who may benefit from post-surgical systemic therapies.
1056 (2015)

Nakamura, Yoshihiko; Kiyomi, Fumiaki; Hoshino, Kota; Ichiki, Reiko; Kawano, Yasumasa; Mizunima, Mariko; Ishikura, Hiroyasu
CANEs: an execution environment for composable services (2003)

Active networks represent a change in network paradigm from a static, one-size-fits-all packet-transport service to a flexible platform capable of being programmed to provide new services. Active networks will allow rapid deployment of new and complex network services. An important property of an active network API is the support it provides for composing complex services out of components. An efficient and robust composition mechanism is essential for incremental development of useful services. We describe the CANEs Active Networking Environment. CANEs is an EE (Execution Environment) specifically built for composing services within the network. We discuss the design philosophy behind CANEs, describe the formal model which the composition mechanism is based upon, and detail the current CANEs implementation.
VAR, SVAR and SVEC Models: Implementation WithinRPackagevars (2008)

The structure of the package vars and its implementation of vector autoregressive, structural vector autoregressive and structural vector error correction models are explained in this paper. In addition to the three cornerstone functions VAR(), SVAR() and SVEC() for estimating such models, functions for diagnostic testing, estimation of a restricted models, prediction, causality analysis, impulse response analysis and forecast error variance decomposition are provided too. It is further possible to convert vector error correction models into their level VAR representation. The different methods and functions are elucidated by employing a macroeconomic data set for Canada. However, the focus in this writing is on the implementation part rather than the usage of the tools at hand.
Anomalies in near-threshold photoabsorption: Resonances, ''white-lines'' and other enhancements (1987)

Synchrotron measurements of near-threshold and broad-range (80 to 1000 eV) absolute photoabsorption cross sections were taken at Brookhaven using the plane grating monochromator at the VuV storage ring beam line U14A of the NSLS facility. Transmission data for well characterized multilayer foils of C, Ti, Cr, Ni, Cu, Th and U provided absolute cross sections with 10% overall uncertainties and better than 2 eV resolution.
Nitrogen limitation differentially affects acclimation by two contrasting Betula species to low and high growth temperatures and decreases the advantage of fast growth strategy under warming climates (2017)

Increasing atmospheric CO2 and other greenhouse gasses coupled to the accelerated rate of global warming puts plants and ecosystems under the strain of a rapidly changing abiotic environment. Understanding the impacts of changing global climate is a strong focus of plant science and the establishment of more resilient crop variants is an important goal for breeding programs. Our understanding of plant responses and acclimation to abiotic conditions has improved substantially over the last decades but the combination of a complex abiotic environment and high biological diversity, both on molecular as well as on species level, leaves us still with a lot of uncertainties. The aim of this doctoral thesis was to establish a link between plant thermal responses and the carbon-nitrogen balance of plants. The work in this thesis focused on ecologically significant species of the boreal region: Picea abies, Pinus sylvestris and Betula pendula; and Betula utilis, which is one of the prominent tree species in the high altitudes of the Himalayas. The results presented demonstrate that sub-optimal temperatures combined with other abiotic factors can have additive effects that are not easily deducible from the effect of the two factors separately. Low nitrogen availability enhanced the negative effect of low temperature, while elevated CO2 enhanced plant growth under moderate increases in temperatures but under a more extreme temperature increase it exacerbated the negative effect of heat. I also show evidence that species, despite being grouped into the same functional group or inhabiting the same biome can have different thresholds to temperature and to shifts in the C/N balance of their environment and that these differences can, to some extent, be explained by their differential growth strategies. Furthermore, I demonstrate results supporting the hypothesis that the C-N fluxes between mycorrhizal fungi and tree are strongly dependent on the C and N in the environment, highlighting the significance of the tree-mycorrhiza associations in the C sequestration capacity of the boreal region. In this thesis I also present a generalised empirically based mathematical model that can describe the respiration-temperature response of plant functional types or biomes with high precision, giving a more accurate estimate of NPP when implemented in global climate models, and has the potential to incorporate the thermal acclimation of respiration, further increasing the precision of estimating carbon fluxes under future warming temperatures. My results provide novel insights into the interactive temperature-carbon-nitrogen responses of plants, taking a step towards better understanding the response of plants and forests to future climates.
Maternal or Paternal Suicide and Offspring's Psychiatric and Suicide-Attempt Hospitalization Risk (2010)

Maternal suicide is associated with increased risk of suicide-attempt hospitalization for offspring, beyond the risk associated with maternal accidental death. However, paternal suicide is not associated with suicide-attempt hospitalization. Future studies should examine factors that might differ between offspring who experience maternal versus paternal suicide, including genetic or early environmental determinants.
Optimization with Genetic Algorithms of a Gas Turbine Cycle with H2-Separating Membrane Reactor for CO2Capture (2005)

A gas turbine power process with CO2 capture through precombustion decarbonization, which employs a H2-separating membrane reactor is presented. Optimization with the process thermal efficiency as objective function is made through the use of genetic algorithms. The use of genetic algorithms enabled a division of the optimization parameters into two groups; one group where the values are at their optimum at the limit of the investigated parameter range, and one group where there actually is an optimum within the investigated range. It was found that the process has a severe efficiency penalty caused by the use of heat from hydrogen combustion for the reforming process. The process is a zero CO2 emission power process and also NOx emissions should be low, due to the inherent mixing of hydrogen with steam.
Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure (2018)

Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite pharmacological interest in IDLs, their three-dimensional (3D) structure is still undetermined due to their variation in size, composition, and dynamic structure. To explore the 3D structure of IDLs, we reconstructed 3D density maps from individual IDL particles using cryo-electron microscopy (cryo-EM) and individual-particle electron tomography (IPET, without averaging from different molecules). 3D reconstructions of IDLs revealed an unexpected polyhedral structure that deviates from the generally assumed spherical shape model (Frias et al., 2007; Olson, 1998; Shen et al., 1977). The polyhedral-shaped IDL contains a high-density shell formed by flat surfaces that are similar to those of very-low-density lipoproteins but have sharper dihedral angles between nearby surfaces. These flat surfaces would be less hydrophobic than the curved surface of mature spherical high-density lipoprotein (HDL), leading to a lower binding affinity of IDL to hydrophobic proteins (such as cholesteryl ester transfer protein) than HDL. This is the first visualization of the IDL 3D structure, which could provide fundamental clues for delineating the role of IDL in lipid metabolism and cardiovascular disease.
Biomarker development for external CO2 injury prediction in apples through exploration of both transcriptome and DNA methylation changes (2013)

Several apple cultivars are susceptible to CO2 injury, a physiological disorder that can be expressed either externally or internally, and which can cause major losses of fruit during controlled atmosphere (CA) storage. Disorder development can also be enhanced using SmartFresh™ technology, based on the inhibition of ethylene perception by 1-methylcyclopropene (1-MCP). Injury development is associated with less mature fruit with lower ethylene production, but the aetiology of the disorder is poorly understood. Here we report on the progress made using mRNAseq approaches to explore the transcriptome during the development of external CO2 injury. Next-generation sequencing was used to mine the apple transcriptome for gene expression changes that are associated with the development of external CO2 injury. 'Empire' apples from a single orchard were treated with either 1 µL L(-1) 1-MCP or 1 g L(-1) diphenylamine or left untreated, and then stored in a CA of 5 kPa CO2 and 2 kPa O2. In addition, susceptibility to the disorder in the 'Empire' apples from five different orchards was investigated and the methylation state of the ACS1 promoter investigated using McrBC endonuclease digestion and real-time quantitative polymerase chain reaction. Expression of over 30 000 genes, aligned to the apple genome, was monitored, with clear divergence of expression among treatments after 1 day of CA storage. Symptom development, internal ethylene concentrations (IECs) and methylation state of the ACS1 promoter were different for each of five orchards. With transcriptomic changes affected by treatment, this dataset will be useful in discovering biomarkers that assess disorder susceptibility. An inverse correlation between the frequency of this disorder and the IEC was detected in a multiple orchard trial. Differential methylation state of the ACS1 promoter correlated with both IEC and injury occurrence, indicating epigenetic regulation of ethylene biosynthesis and possibly events leading to disorder development.
In Situ Detection of Phosphorylated Platelet-derived Growth Factor Receptor β Using a Generalized Proximity Ligation Method (2007)

Improved methods are needed for in situ characterization of post-translational modifications in cell lines and tissues. For example, it is desirable to monitor the phosphorylation status of individual receptor tyrosine kinases in samples from human tumors treated with inhibitors to evaluate therapeutic responses. Unfortunately the leading methods for observing the dynamics of tissue post-translational modifications in situ, immunohistochemistry and immunofluorescence, exhibit limited sensitivity and selectivity. Proximity ligation assay is a novel method that offers improved selectivity through the requirement of dual recognition and increased sensitivity by including DNA amplification as a component of detection of the target molecule. Here we therefore established a generalized in situ proximity ligation assay to investigate phosphorylation of platelet-derived growth factor receptor beta (PDGFRbeta) in cells stimulated with platelet-derived growth factor BB. Antibodies specific for immunoglobulins from different species, modified by attachment of DNA strands, were used as secondary proximity probes together with a pair of primary antibodies from the corresponding species. Dual recognition of receptors and phosphorylated sites by the primary antibodies in combination with the secondary proximity probes was used to generate circular DNA strands; this was followed by signal amplification by replicating the DNA circles via rolling circle amplification. We detected tyrosine phosphorylated PDGFRbeta in human embryonic kidney cells stably overexpressing human influenza hemagglutinin-tagged human PDGFRbeta in porcine aortic endothelial cells transfected with the beta-receptor, but not in cells transfected with the alpha-receptor, and also in immortalized human foreskin fibroblasts, BJ hTert, endogenously expressing the PDGFRbeta. We furthermore visualized tyrosine phosphorylated PDGFRbeta in tissue sections from fresh frozen human scar tissue undergoing wound healing. The method should be of great value to study signal transduction, screen for effects of pharmacological agents, and enhance the diagnostic potential in histopathology.
The influence of serpentinite and other rocks on the stability of concretes in the Middle East (1980)

Summary It has been suggested that the expansive serpentinization of olivine can occur in concretes which contain ultrabasic aggregates. This process could lead to the deterioration of concretes and has been blamed for the poor performance of some concretes in the Middle East. This paper reviews the petrology of serpentinite-bearing concretes and mortars made with aggregates collected in the United Arab Emirates. It shows that most, if not all, of the deleterious changes observed in the field can be explained by other mechanisms involving contaminant lithologies and factors not connected with the aggregates; and that olivine has remained unaltered in concretes of up to 40 years in age.
Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase. 1. Ligand-Induced Coordination Changes Probed by X-ray Crystallography:  Inhibition, Ordering Effect, and Mechanistic Insights (2002)

The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at 1.70 and 2.15 A resolution, respectively. Both inhibitors asymmetrically chelate the metal center and assume a common orientation in the active site cleft. Their molecular plane blocks access to the inner portion of the cavity which is lined by the side chains of residues Met51, Thr53, Phe75, Phe114, and Met123 and which is believed to bind the flavonol B-ring of the natural substrate. The binding of the inhibitors brings order into the mixed coordination observed in the native enzyme. DDC and KOJ induce a single conformation of the Glu73 side chain, although in different ways. In the presence of DDC, Glu73 is detached from the copper ion with its carboxylate moiety pointing away from the active site cavity. In contrast, when KOJ is bound, Glu73 ligates the Cu ion through its O(epsilon)(1) atom with a monodentate geometry. Compared to the native coordinating conformation, this conformation is approximately 90 degrees rotated about the chi(3) angle. This latter Glu73 conformation is compatible with the presence of a bound substrate.
Kerr-lens mode-locked Yb 3+ :Lu 2 O 3 thin-disk laser (2016)

We present the first Kerr-lens mode-locked Yb3+:Lu 2 O 3 thin-disk laser in clean modelocking operation. We obtained 165 fs with 0.1 μJ pulse energy and 60 MHz repetition rate.
Autonomous and adaptive oceanographic feature tracking on board autonomous underwater vehicles (2015)

The capabilities of autonomous underwater vehicles (AUVs) and their ability to perform tasks both autonomously and adaptively are rapidly improving, and the desire to quickly and efficiently sample the ocean environment as Earth's climate changes and natural disasters occur has increased significantly in the last decade. As such, this thesis proposes to develop a method for single and multiple AUVs to collaborate autonomously underwater while autonomously adapting their motion to changes in their local environments, allowing them to sample and track various features of interest with greater efficiency and synopticity than previously possible with preplanned AUV or ship-based surveys. This concept is demonstrated to work in field testing on multiple occasions: with a single AUV autonomously and adaptively tracking the depth range of a thermocline or acousticline, and with two AUVs coordinating their motion to collect a data set in which internal waves could be detected. This research is then taken to the next level by exploring the problem of adaptively and autonomously tracking spatiotemporally dynamic underwater fronts and plumes using individual and autonomously collaborating AUVs.