gebhart/patrepeval huggingface dataset:
Coordination Chemistry in Water of a Free and a Lipase-Embedded Cationic NCN-Pincer Platinum Center with Neutral and Ionic Triarylphosphines (2012)

The coordination chemistry in aqueous media was studied for the platinum center of low-molecular-weight cationic NCN-pincer platinum complexes [RC6H2(CH2NMe2)2-3,5-Pt(H2O)-4]+ (R = −(CH2)3P(═O)(OEt)(OC6H4NO2-4) (1(OH2)), H (2(OH2))) as well as of the platinum center of the NCN-pincer platinum cation embedded in the lipase cutinase (cut-1; molecular weight 20 619.3) with various anionic, neutral, and cationic triarylphosphines. A 31P NMR study of the coordination of triarylphosphines to the cationic NCN-pincer platinum center in low-molecular-weight [2(OH2)][OTf] in both D2O and Tris buffer (Tris = tris(hydroxylmethyl)aminomethane) showed that the phosphine–platinum coordination is strongly affected by Tris buffer molecules. Two crystal structures of a NCN-pincer platinum–phosphine and a NCN-pincer platinum–ethanolamine coordination complex with ethanolamine as a functional model of Tris with hydrogen bridges, provoking a dimeric supramolecular structure, confirmed that the coordination observed in solution occurred in the solid state as well. A 31P NMR and ESI-MS study of the lipase cut-1 showed that the coordination of various triarylphosphines to the enzyme-embedded platinum center is affected by the surrounding protein backbone, discriminating between phosphines on the basis of their size and charge. By using 31P NMR spectroscopy and ESI-MS spectrometry, study of the coordination of triarylphosphines to cut-1 was possible, thereby avoiding the need for the application of laborious biochemical procedures. To the best of our knowledge, this is the first example of a study involving the selective binding of organic ligands to the metal center of a semisynthetic metalloprotein, unequivocally demonstrating that the well-established coordination chemistry for small-molecule complexes can be transferred to biological molecules. This initial study allows future explorations in the field of selective protein targeting and identification, as in protein profiling or screening studies.
Beyond execution time: expanding the use of performance models (1994)

Improved performance is a major motivation for using parallel computation. However, performance models are frequently used only to predict an algorithm's execution time, not to accurately evaluate how the choices of architecture, operating system, interprocessor communication protocol, and programming language also dramatically affect parallel performance. We have developed an analytic model for synchronous iterative algorithms running on distributed-memory MIMD machines, and refined it for disrete-event simulation. The model describes the execution time of a single run in terms of application parameters such as the number of iterations and the required computation in each, and architectural parameters such as the number of processors, processor speed, and communication time. Our experience has shown us that an analytic model can not only accurately predict an algorithm's performance but can also match the algorithm to an appropriate architecture, identify ways to improve the algorithm's performance, quantify the performance effects of algorithmic or architectural changes, and provide a better understanding of how the algorithm works.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data from Bcl9/Bcl9l Are Critical for Wnt-Mediated Regulation of Stem Cell Traits in Colon Epithelium and Adenocarcinomas (2023)

&lt;div&gt;Abstract&lt;p&gt;Canonical Wnt signaling plays a critical role in stem cell maintenance in epithelial homeostasis and carcinogenesis. Here, we show that in the mouse this role is critically mediated by Bcl9/Bcl9l, the mammalian homologues of Legless, which in &lt;i&gt;Drosophila&lt;/i&gt; is required for Armadillo/β-catenin signaling. Conditional ablation of Bcl9/Bcl9l in the intestinal epithelium, where the essential role of Wnt signaling in epithelial homeostasis and stem cell maintenance is well documented, resulted in decreased expression of intestinal stem cell markers and impaired regeneration of ulcerated colon epithelium. Adenocarcinomas with aberrant Wnt signaling arose with similar incidence in wild-type and mutant mice. However, transcriptional profiles were vastly different: Whereas wild-type tumors displayed characteristics of epithelial-mesenchymal transition (EMT) and stem cell–like properties, these properties were largely abrogated in mutant tumors. These findings reveal an essential role for Bcl9/Bcl9l in regulating a subset of Wnt target genes involved in controlling EMT and stem cell–related features and suggest that targeting the Bcl9/Bcl9l arm of Wnt signaling in Wnt-activated cancers might attenuate these traits, which are associated with tumor invasion, metastasis, and resistance to therapy. Cancer Res; 70(16); 6619–28. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
A Study of Atmospheric Reactions of Neutral Sodium Species and Other Metals of Meteoric Origin (1986)

Abstract : The reactions of metallic species introduced into the atmosphere by meteor ablation may play a significant role in mesospheric and stratospheric chemistry. Rate constants for the recombination reactions of alkali atoms with molecular oxygen, K + O2 + M yields KO2 + M and Na + O2 + M yields NaO2 + M, have been measured as a function of temperature from to 300 to 700 K using a fast flow reactor. Laser induced fluorescence is used to monitor the disappearance of Na or K as a function of O2 and M. The reactions are studied in their low pressure third order limit from 1 to 7 torr total pressure with N2, He, and Ar as third bodies. The rate constants are found to have the expected negative temperature dependence. The results are compared with other recent measurements from flame and flash photolysis studies and with theoretical expectations based on an energy transfer RRKM mechanism for the NaO2 activated complex. It has been suggested that the reaction of NaOH with HCl might affect the concentration of odd chlorine, thus having an impact on the ozone balance. This report also describes the first measurement of this reaction rate constant. We have also determined estimates of the same room temperature rate constants.
Laser-Induced Damage And The Role Of Self-Focusing (1989)

We review the influence of self-focusing on the measurement of bulk laser-induced-damage (LID) thresholds in normally transparent optical mate-rials. This role is experimentally determined by measuring the spot size and polarization dependence of LID and by observing beam distortion in the far field. Utilizing these techniques, we find that by using a tight focusing geometry in which the breakdown power is below P2, the effects of self-focusing can be practically eliminated in an LID experiment. P2 is the so-called second critical power for self-focusing, and P2 = 3.77P1, where P1 = cX2/327r2n2, where c is the speed of light in vacuum, X is the laser wavelength and n2 is the nonlinear index of refraction. This is in accordance with numerical calculations by J. H. Marburger [in Progress in Quantum Electronics, J. H. Sanders and S. Sten-holm, eds., Vol. 4, Part 1, pp. 35-110, Pergamon, Oxford (1975)]. With this knowledge we determine that damage is only partially explained by avalanche ionization and that the initiation of damage is strongly influenced by extrinsic processes. We therefore conclude that we are measuring extrinsic LID.
The effect of deep AR suppression with enzalutamide or apalutamide on endogenous glucocorticoids: Implications for adverse effects and development of combination therapies. (2020)

17 Background: Metabolic consequences of potent AR suppression with enzalutamide and apalutamide are unresolved. Endocrine perturbations induced by potent AR antagonists may promote adverse effects and impinge on the potential efficacy of combination therapies, including for example, immunotherapies. We hypothesized that enzalutamide and apalutamide will block 11β-HSD2, the major enzyme that inactivates cortisol in peripheral tissues and results in increased systemic exposure to endogenous active glucocorticoids. We further hypothesized that AR is co-expressed with 11β-HSD2, suggesting a mechanism of suppression. Methods: Cortisol and cortisol/cortisone ratio (substrate/product of 11β-HSD2) were measured in serum using mass spectrometry before and on-treatment in 3 clinical trials: 1) neoadjuvant apalutamide + leuprolide 2) enzalutamide +/- PROSTVAC for metastatic castration-resistant prostate cancer 3) enzalutamide +/- PROSTVAC for non-metastatic castration-sensitive prostate cancer. AR and 11β-HSD2 expression were assessed in kidneys of 13 men and 9 women. Results: A rise in cortisol concentration and cortisol/cortisone ratio occurs uniformly across all 3 trials of potent AR antagonists. For example, a rise in cortisol/cortisone ratio occurred in 23/25 (92%) patients (p&lt;0.001), 30/38 (79%) patients (p=0.051), and 36/64 (67%) patients (p&lt;0.001), in the 3 respective trials. AR is only expressed alongside 11β-HSD2 in the kidneys of men but not women. Conclusions: Treatment with enzalutamide or apalutamide increases systemic exposure to active glucocorticoids. This effect is likely mediated by AR suppression of 11β-HSD2 in the kidney. These findings have potential consequences for immune suppression, the efficacy of treatment combinations using next-generation AR antagonists, and adverse effects of these drugs.
Development of ytterbium doped Sr5(PO4)3F for the Mercury Laser Project (2001)

No abstract prepared.
Flame retardancy and mechanical properties of polyamide 6 with melamine polyphosphate and ionic liquid surfactant‐treated montmorillonite (2014)

ABSTRACT The mechanical properties and inflammability of polyamide 6 (PA6) nanocomposites incorporated with Montmorillonite organoclay (MMT) modified with thermal stable ionic liquid surfactants were investigated. The compatibility between ionic liquid‐treated MMT and PA6 matrix was improved and the intercalation morphology was achieved, which resulted in the increaseof tensile modulus. However, the addition of organo‐MMTs alone did not improve the inflammability of the PA6 nanocomposite, because of strong melt‐dripping behavior of PA6 matrix. Addition of auxiliary melamine polyphosphate (MPP) intumescent flame retardant to the nanocomposite prevented the melt dripping and enhanced inflammability performance. The enhanced inflammability of PA6/organoclay/MPP nanocomposites was attributed to the synergistic effect between imidazolium or phosphonium organo‐MMTs and intumescent flame retardant MPP. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40648.
Room‐Temperature Carbide‐Derived Carbon Synthesis by Electrochemical Etching of MAX Phases (2014)

Abstract Porous carbons are widely used in energy storage and gas separation applications, but their synthesis always involves high temperatures. Herein we electrochemically selectively extract, at ambient temperature, the metal atoms from the ternary layered carbides, Ti 3 AlC 2 , Ti 2 AlC and Ti 3 SiC 2 (MAX phases). The result is a predominantly amorphous carbide‐derived carbon, with a narrow distribution of micropores. The latter is produced by placing the carbides in HF, HCl or NaCl solutions and applying anodic potentials. The pores that form when Ti 3 AlC 2 is etched in dilute HF are around 0.5 nm in diameter. This approach forgoes energy‐intensive thermal treatments and presents a novel method for developing carbons with finely tuned pores for a variety of applications, such as supercapacitor, battery electrodes or CO 2 capture.
Accurate quantitation of salivary and pancreatic amylase activities in human plasma by microchip electrophoretic separation of the substrates and hydrolysates coupled with immunoinhibition (2008)

A high-performance determination system for alpha-amylase isoenzyme activities in human plasma involving microchip electrophoresis with a plastic chip was developed. The combination of microchip electrophoresis for substrate and hydrolysate separation and an immunoinhibition method for the differentiation of isoenzyme activities using antihuman salivary amylase (S-AMY) mAb allowed the highly selective determination of amylase isoenzyme (S-AMY and pancreatic amylase (P-AMY)) activities even in a complex matrix such as a crude plasma sample. We used 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled maltohexaose (G6) as a substrate. Amylase in a human plasma sample hydrolyzed APTS-G6 into APTS-maltotriose (G3) and G3, which was measured as the fluorescence intensity of APTS-G3 on microchip electrophoresis. A double logarithm plot revealed a linear relationship between amylase activity and fluorescence intensity in the range of 5-500 U/L of amylase activity (r2=0.9995, p<0.01), and the LOD was 4.38 U/L. Amylase activities in 13 subjects determined by the present method were compared with the results obtained by conventional methods with nitrophenylated oligosaccharides as substrates, respectively. Good correlations were observed for each method on simple linear regression analysis (both p<0.01). The reproducibilities of within-days for total amylase and P-AMY were 2.98-6.27 and 3.83-6.39%, respectively, and these between-days were 2.88-5.66 and 3.64-5.63%, respectively. This system enables us to determine amylase isoenzyme activities in human plasma with high sensitivity and accuracy, and thus will be applicable to clinical diagnosis.
Phylum-Wide Analysis of SSU rDNA Reveals Deep Phylogenetic Relationships among Nematodes and Accelerated Evolution toward Crown Clades (2006)

Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.
Correction: Corrigendum: Pharmacological characterisation of the highly NaV1.7 selective spider venom peptide Pn3a (2017)

Scientific Reports 7: Article number: 40883; published online: 20 January 2017; updated: 26 May 2017 In this Article, Affiliation 6 is incorrectly listed as ‘Venomtech, Sophie-Antipolis, 06560, Valbonne, France’. The correct affiliation is listed below: VenomeTech, Sophie-Antipolis, 06560, Valbonne,France.
Oleuropein as a bioactive constituent of functional milk and yogurt (2008)

In recent years, interest in antioxidants isolated from plants has arisen due to their vital role in the protection of cell damage caused by the excess of free radicals (oxidative stress) [1]. Moreover, antioxidants are also used by food industries, as additives for the improvement of several properties of foods (biofunctional foods). One of the most important and developing category in this area is the dairy products, which are natural sources of high nutritional value [2]. Oleuropein is an important constituent of olive fruits. According to in vivo and in vitro studies, oleuropein exhibits anti-ischemic, antioxidative, and hypolipidemic effects [2]. In the present study, two functional dairy products were prepared by addition of oleuropein. An analytical method for the measurement of oleuropein in milk and yogurt was developed and validated. The new products were examined about the stability of oleuropein during their treatment. The results showed that oleuropein was resistant during heating of milk at 90oC for 5min. Furthermore, during coagulation of milk, oleuropein was not hydrolysed by the produced acids, it was not metabolized by lactic acid bacteria and it did not stop their growth. Also its stability during the maintenance of milk and yogurt for 35 days at 4 oC was proven. The functional milk and yogurt production was performed in laboratory and semi-industrial scale. Oleuropein was completely soluble in the selected concentration (0.1mg/ml) and it did not give any peculiar taste, as the products had the same taste and flavor with the conventional ones [4]. The selection of the concentration was based on the oleuropein quantity corresponding to consumption of 15 olive drupes per day. All the above results show that oleuropein can be added as active ingredient in milk and yogurt and two new biofunctional products can be produced, whose properties remain constant, during the overall process.
Shape Model Segmentation of Long-Axis Contrast Enhanced Echocardiography (2006)

We segment long-axis, four-chamber contrast enhanced echocardiography imagery using active shape models. The active shape model algorithm uses principal component analysis to model the shape variability found in a database of training shapes. Accurate segmentation from this model is accomplished by applying a specialized gradient vector flow field to guide the contours to the myocardial borders. The success of the proposed algorithm was verified by application to 65 patient myocardial contrast echocardiography (MCE) studies and through comparison with manually drawn contours. This approach improved accuracy over previously reported data, providing an average accuracy of 0.98, sensitivity of 0.84, specificity of 0.99, and RMSE of 3.3 pixels, when compared to ground truth. Error and variability from automatic segmentation were found to be less than those among multiple human observers. The approach also compares favorably against a standard active contour solution
Negotiation as a Foundational Skill (2011)

This article argues that a course in Negotiation should be required or strongly suggested at all law schools, and should be offered earlier in the curriculum and to more students than is the norm. It then suggests how to deliver the course in a more cost-effective manner, using adjuncts along with full-time faculty.
Angular weighted hybrid cone-beam CT reconstruction for circular trajectories (2001)

Hybrid reconstruction techniques have been introduced for the volume reconstruction of axially truncated cone-beam computed tomography projection data acquired along a circular source-detector trajectory. The introduction of weighted half-scan techniques into this framework is described in this paper. Due to the cone-beam geometry it is not possible to perform the weighting on the projections as is typically done in conventional single-line computed tomography. Hence, in this paper we present an efficient way to incorporate angular weighting functions, depending on the object point position, into the framework of hybrid cone-beam reconstruction. Four different angular weighting functions are introduced and discussed with respect to their cone-beam artefact behaviour and their influence on the signal-to-noise ratio. As a result, the most effective angular weighting function for hybrid circular cone-beam reconstruction is determined by means of a simulation study based on mathematical phantoms and clinical data sets. This distance-weighted angular weighting scheme yields the best results in terms of high image quality, low computational complexity and signal-to-noise variations in the reconstruction volume.
Human hair shape is programmed from the bulb (2005)

Background Few biological data on curly hair follicles have been reported in the literature. Objectives To investigate the growth and morphology of curly hair follicles. Methods Follicles were dissected from scalp skin samples from African, Guyanese and caucasian volunteers and were observed macroscopically, in culture in William's E medium, and by immunohistochemistry. Results Macroscopic study of scalp biopsies obtained from African volunteers showed that the dermal implantation of follicles was curved with a retrocurvature at the level of the bulb, as opposed to a straight shape in caucasian follicles. The bulb itself was bent, in the shape of a golf club, while both the outer root sheath (ORS) and the connective tissue sheath were dissymmetrical along the follicle. In vitro growth of curly hair follicles was slightly slower than that of caucasian follicles but, more importantly, the curvature was maintained in the hair shaft produced in vitro. As shown by immunohistochemistry, the proliferative matrix compartment of curly hair follicles was asymmetrical, Ki‐67‐labelled cells being more numerous on the convex side and extending above the Auber line. On the convex part of the follicle, the ORS was thinner and the differentiation programmes of the inner root sheath and hair shaft were delayed. Furthermore, some ORS cells expressed α‐smooth muscle actin protein on the concave side of the curvature, reflecting a mechanical stress. Conclusions Hair curliness is programmed from the bulb and is linked to asymmetry in differentiation programmes.
3D Tracking in Industrial Scenarios: A Case Study at the ISMAR Tracking Competition (2013)

One of the more challenging tasks in augmented reality is to develop a tracking system for the industrial scenario. It is due the fact that this environment has characteristics that defy most of the techniques available, such as texture less objects that in some case are too large and in others are very small. This work proposes the combination of established techniques for 3D reconstruction and tracking, as well as a calibration routine, that is suitable for this type of scenario. This complete tracking system was evaluated in the ISMAR Tracking Competition, a contest that simulates industrial scenarios and is promoted to test state of the art trackers. The system presented good results in the competition and a discussion regarding its performance is lodged, aiming to introduce an analysis that could help others during the development of their own tracking system for industrial scenario.