gebhart/patrepeval huggingface dataset:
Ground-state properties of Fe, Co, Ni, and their monoxides: Results of the generalized gradient approximation (1991)

The lattice parameter, bulk modulus, cohesive energy, and magnetization of Fe, Co, and Ni are calculated using the generalized gradient approximation (GGA) of Perdew and co-workers. The GGA results agree better with experimental data than the corresponding results calculated with the local-spin-density approximation (LSDA). In particular, the overestimation of the cohesive energies are reduced and the GGA correctly predicts the bcc ferromagnetic phase to be the ground state of Fe, while the LSDA fails to do so. We have also studied the electronic and magnetic properties of the insulating antiferromagnetic transition-metal compounds FeO, CoO, and NiO with the GGA. For these oxides it is found that the results are very similar to the results calculated with use of the LSDA.
Vergleich der Verbesserungsverfahren (2004)

Analog zu den Auswertungen der numerischen Experimente bei den Eröffnungsverfahren werden in den folgenden Abschnitten die durch die Verbesserungsverfahren erzielten Ergebnisse anhand der Beurteilungskriterien Lösungsqualität, Rechenzeitaufwand sowie Robustheit untersucht und miteinander verglichen. Um die Einflüsse unterschiedlicher Parametereinstellungen, Nachbarschaften, Auswahlkriterien und Ausgangslösungen besser analysieren zu können, erfolgen die Untersuchungen ebenfalls in mehreren Auswertungsphasen, die in Abschnitt 10.1 näher erläutert werden. Die Ergebnisse der einzelnen Auswertungsphasen werden in den Abschnitten 10.2 bis 10.4 dargestellt und die wichtigsten Schlußfolgerungen in Abschnitt 10.5 zusammengefaßt. Die den Abbildungen zugrundeliegenden sowie ergänzende Daten befinden sich in den Tabellen D im Anhang D, der unter http://www.uni-magdeburg.de/mansci/rm/multproc/_veröffentlicht_ist.
On Reverse Engineering-Based Hardware Trojan Detection (2015)

Due to design and fabrication outsourcing to foundries, the problem of malicious modifications to integrated circuits (ICs), also known as hardware Trojans (HTs), has attracted attention in academia as well as industry. To reduce the risks associated with Trojans, researchers have proposed different approaches to detect them. Among these approaches, test-time detection approaches have drawn the greatest attention. Many test-time approaches assume the existence of a Trojan-free (TF) chip/model also known as “golden model.” Prior works suggest using reverse engineering (RE) to identify such TF ICs for the golden model. However, they did not state how to do this efficiently. In fact, RE is a very costly process which consumes lots of time and intensive manual effort. It is also very error prone. In this paper, we propose an innovative and robust RE scheme to identify the TF ICs. We reformulate the Trojan-detection problem as clustering problem. We then adapt a widely used machine learning method, ${K}$ -means clustering, to solve our problem. Simulation results using state-of-the-art tools on several publicly available circuits show that the proposed approach can detect HTs with high accuracy rate. A comparison of this approach with our previously proposed approach [1] is also conducted. Both the limitations and application scenarios of the two methods are discussed in detail.
Routing Bridges (RBridges): Adjacency (2011)

The IETF TRILL (TRansparent Interconnection of Lots of Links) protocol
provides optimal pair-wise data forwarding without configuration, safe
forwarding even during periods of temporary loops, and support for
multipathing of both unicast and multicast traffic. TRILL accomplishes
this by using IS-IS (Intermediate System to Intermediate System) link
state routing and by encapsulating traffic using a header that
includes a hop count. Devices that implement TRILL are called Routing
Bridges (RBridges). TRILL supports multi-access LAN (Local Area
Network) links that can have multiple end stations and RBridges
attached. This document describes four aspects of the TRILL LAN Hello
protocol used on such links, particularly adjacency, designated
RBridge selection, and MTU (Maximum Transmission Unit) and pseudonode
procedures, with state machines. There is no change for IS-IS point-
to-point Hellos used on links configured as point-to-point in TRILL.
[STANDARDS-TRACK]
SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains (2012)

ABSTRACT: The synthetic biology toolkit contains a growing number of parts for regulating transcription and translation, but very few that can be used to control protein association. Here we report characterization of 22 previously published heterospecific synthetic coiled-coil peptides called SYNZIPs. We present biophysical analysis of the oligomeriza-tion states, helix orientations, and affinities of 27 SYNZIP pairs. SYNZIP pairs were also tested for interaction in two cell-based assays. In a yeast two-hybrid screen,&amp;gt;85 % of 253 comparable interactions were consistent with prior in vitro measurements made using coiled-coil microarrays. In a yeast-signaling assay controlled by coiled-coil mediated scaffolding, 12 SYNZIP pairs were successfully used to down-regulate the expression of a reporter gene following treatment with α-factor. Characterization of these interaction modules dramatically increases the number of available protein interaction parts for synthetic biology and should facilitate a wide range of molecular engineering applications. Summary characteristics of 27 SYNZIP peptide pairs are reported in specification sheets available in the Supporting Information and at the SYNZIP Web site
CYP2C9 involvement in ACT‐453859 metabolism (2015)

We thank Dr Srinivas for reading our paper carefully, for his positive general comments, and for raising some interesting discussion points. He indicated that the data described in our paper suggested a reduced metabolism after an 800-mg single dose of ACT-453859. The metabolite-to-parent exposure ratios in the Multiple Ascending Dose (MAD) part are 0.48, 0.36, and 0.41 for the 10-, 100-, and 800-mg once daily dosing regimen, respectively, and, therefore, independent of dose. In the Single Ascending Dose (SAD) part, this ratio for the highest dose of 800 mg is 0.38, which is within the range observed in the MAD part. Therefore, no apparent saturation of metabolism after single- or multiple-dose administration of ACT-453859 up to high dose levels was observed in this study. We acknowledge that the pharmacodynamics (PD) contribution of M1 is substantial, especially at trough (predose), at which M1 might be responsible for up to one-fourth of the overall PD effect. However, we respectfully disagree with Dr Srinivas that removing the PD contribution of M1 from the overall PD profile would transform ACT-453859 into a compound similar to setipiprant. In vitro, ACT-453859 is 15-fold more effective in blocking PGD2-mediated internalization of CRTH2 on eosinophils (IC50 = 45 nM)1 than setipiprant (IC50 = 684 nM).2 As deduced by Dr Srinivas, preliminary in vitro experiments suggested that ACT-453859 is metabolized by a CYP enzyme. CYP2C9 is thought to be the primary driver of M1 formation. In the SAD/MAD study, the enrolled subjects were genotyped for cyp2c9. All of them had at least one wild-type cyp2c9 allele which resulted in apparent normal cyp2c9 gene activity. The impact of cyp2c9 slow metabolizer phenotypes on M1 formation will need to be further assessed in a dedicated study. As mentioned above, we agree that M1 contributes in vivo to ACT-453859 PD, but an interaction with a CYP2C9 inhibitor would not be of concern in terms of PD activity, as it would lead to a more pronounced presence of the parent compound, which is 4.5-fold more potent than M1 (IC50 = 205 nM).1 However, the relevance and extent of drug-drug interactions should be further assessed during the clinical development of ACT-453859.
High Al Composition AlGaN-Channel High-Electron-Mobility Transistor on AlN Substrate (2010)

AlGaN-channel high-electron-mobility transistor (HEMT) with high Al composition of 0.51 has been developed. The epitaxial layers were grown on a free-standing AlN substrate to improve crystalline quality. The fabricated device exhibited a maximum drain current (Idsmax) of 25.2 mA/mm with a maximum transconductance (gmmax) of 4.7 mS/mm. The characteristic features of the device were a high source-to-drain breakdown voltage of 1800 V and a high applicable gate-to-source voltage of 4 V in the forward direction. Temperature dependence of DC characteristics demonstrated that the drain current degradation at elevated temperatures for the AlGaN-channel HEMT was appreciably small as compared with the conventional AlGaN/GaN HEMT. This is the first report showing successful DC operation of AlGaN-channel HEMT with high Al composition of over 0.5.
Photothermal Effect: Large Photothermal Effect in Sub‐40 nm h‐BN Nanostructures Patterned Via High‐Resolution Ion Beam (Small 22/2018) (2018)

In article number 1800072, Josué J. López and co-workers use photothermal microscopy to measure the near-field absorption of nanostructured hexagonal boron nitride (h-BN) and reveal a large photothermal expansion in the nanostructures. This effect is attributed to the anisotropy of the thermal expansion coefficients of h-BN and the nanostructuring implemented. The photothermal expansion should be present in other van der Waals materials and may lead to nanomechanical switches driven by light.
Derivado enzimático basado en enzima inmovilizada sobre óxido de grafeno (2019)

La presente invención se refiere a un derivado enzimático que comprende una enzima hidrolítica, preferentemente la naringinasa, inmovilizada a través de enlaces covalentes sobre óxido de grafeno, así como a su procedimiento de obtención y sus usos, preferentemente como biocatalizador. La inmovilización de la naringinasa mediante el procedimiento descrito es capaz de incrementar su estabilidad térmica, su estabilidad a diferentes pHs, su actividad catalítica y su afinidad por el sustrato, respecto de la enzima libre sin inmovilizar. Además, el derivado enzimático de la invención es capaz de reutilizarse en más de ciclos consecutivos sin disminuir su actividad catalítica, mostrando una estabilidad catalítica superior a la observada al utilizar otros soportes diferentes
Augmented Sparse Reconstruction of Protein Signaling Networks (2007)

The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of the most well-studied and clinically important signaling networks in biology today, the epidermal growth factor receptor (EGFR) driven signaling cascade. More specifically, we suggest a method, augmented sparse reconstruction, for the identification of links among nodes of ordinary differential equation (ODE) networks from a small set of trajectories with different initial conditions. Our method builds a system of representation by using a collection of integrals of all given trajectories and by attenuating block of terms in the representation itself. The system of representation is then augmented with random vectors, and minimization of the 1-norm is used to find sparse representations for the dynamical interactions of each node. Augmentation by random vectors is crucial, since sparsity alone is not able to handle the large error-in-variables in the representation. Augmented sparse reconstruction allows to consider potentially very large spaces of models and it is able to detect with high accuracy the few relevant links among nodes, even when moderate noise is added to the measured trajectories. After showing the performance of our method on a model of the EGFR protein network, we sketch briefly the potential future therapeutic applications of this approach.
Total Syntheses of Nominal and Actual Prorocentin (2023)

The dinoflagellate-derived polyether prorocentin is a co-metabolite of the archetypical serine/threonine phosphatase inhibitor okadaic acid. Whereas a structural relationship cannot be missed and a biosynthetic link was proposed, it is currently unknown whether there is any parallel in the bioactivity profile of these natural products. However, it was insinuated in the past that the structure assigned to prorocentin might need to be revised. Indeed, re-examination of the published spectra cast doubts as to the constitution of the fused/spirotricyclic BCD-ring system in the core. To clarify this issue, a flexible synthesis blueprint was devised that allowed us to obtain the originally proposed structure as well as the most plausible amended structure. The key to success was late-stage gold-catalyzed spirocyclization reactions that furnished the isomeric central segments with excellent selectivity. The lexicon of catalytic transformations used to make the required cyclization precursors comprised a titanium-mediated ester methylenation/metathesis cascade, a rare example of a gold-catalyzed allylic substitution, and chain extensions via organocatalytic asymmetric aldehyde propargylation. A wing sector to be attached to the isomeric cores was obtained by Krische allylation, followed by a superbly selective cobalt-catalyzed oxidative cyclization of the resulting di-unsaturated alcohol with the formation of a 2,5-<i>trans</i>-disubstituted tetrahydrofuran; the remaining terminal alkene was elaborated into an appropriate handle for fragment coupling by platinum-catalyzed asymmetric diboration/oxidation. The assembly of the different building blocks to the envisaged isomeric target compounds proved that the structure of prorocentin needs to be revised as disclosed herein.
Modifying the American Society for Therapeutic Radiology and Oncology Definition of Biochemical Failure to Minimize the Influence of Backdating in Patients With Prostate Cancer Treated With 3-dimensional Conformal Radiation Therapy Alone (2003)

Adoption of the ASTRO consensus definition has been crucial for evaluating outcome in the radiation oncology community. However, the date of failure should be moved from the current point to one closer to the point at which failure is declared. Additional analysis with large numbers of patients from multiple institutions is necessary to determine the point.
Condensation and evaporation of water on ice surfaces (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCondensation and evaporation of water on ice surfacesD. R. Haynes, N. J. Tro, and S. M. GeorgeCite this: J. Phys. Chem. 1992, 96, 21, 8502–8509Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/j100200a055https://doi.org/10.1021/j100200a055research-articleACS PublicationsRequest reuse permissionsArticle Views1255Altmetric-Citations219LEARN 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 options Get e-Alerts
Rare event counting of CD59− red cells in human blood: A 47‐month experience using PNH consensus guidelines for WBC and RBC testing in a reference lab (2015)

PNH RBC testing is a good example of rare event analysis applied to clinical cytometry—only 2.5 min are required to collect 1 million RBCs. With an established normal range of CD59- RBCs, the correlation between total cell count and sensitivity for detecting an abnormal population can be calculated using Poisson statistics.
Recovering 3D Structure of Multilayer Transparent Objects from Multi-view Ray Tracing (2017)

3D reconstruction of object shape is one of the most important problems in the field of computer vision.
Although many methods have been proposed up to now, the 3D reconstruction of transparent objects is still
a very difficult unsolved problem. In particular, if the transparent objects have multiple layers with different
refraction properties, the recovery of the 3D structure of transparent objects is quite difficult. In this paper,
we propose a method for recovering the 3D structure of multilayer transparent objects. For this objective we
introduce a new representation of 3D space by using a boxel with refraction properties, and recovering the
refraction properties of each boxel by using the ray tracing. The efficiency of the proposed method is shown
by some preliminary experiments.
Arithmetic and trellis coded quantization (2002)

This paper presents realizations of entropy-constrained trellis coded quantisation as arithmetic coded trellis coded quantisation. The block diagram of the arithmetic and trellis coded quantisation (ATCQ) is shown. The decoder, encoder and the performance of the ATCQ system are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of an ultra-high-temperature process for the enzymatic hydrolysis of lactose. I. The properties of two thermostable ?-glycosidases (1999)

Recombinant beta-glycosidases from hyperthermophilic Sulfolobus solfataricus (SsbetaGly) and Pyrococcus furiosus (CelB) have been characterized with regard to their potential use in lactose hydrolysis at about 70 degrees C or greater. Compared with SsbetaGly, CelB is approximately 15 times more stable against irreversible denaturation by heat, its operational half-life time at 80 degrees C and pH 5.5 being 22 days. The stability of CelB but not that of SsbetaGly is decreased 4-fold in the presence of 200 mM lactose at 80 degrees C. CelB displays a broader pH/activity profile than SsbetaGly, retaining at least 60% enzyme activity between pH 4 and 7. Both enzymes have a similar activation energy for lactose hydrolysis of approximately 75 kJ/mol (pH 5.5), and this is constant between 30 and 95 degrees C. D-Galactose is a weak competitive inhibitor against the release of D-glucose from lactose (Ki approximately 0.3 M), and at 80 degrees C the ratio of Ki, D-galactose to Km,lactose is 2.5 and 4.0 for CelB and SsbetaGly, respectively. SsbetaGly is activated up to 2-fold in the presence of D-glucose with respect to the maximum rate of glycosidic bond cleavage, measured with o-nitrophenyl beta-D-galactoside as the substrate. By contrast, CelB is competitively inhibited by D-glucose and has a Ki of 76 mM. The transfer of the galactosyl group from lactose to acceptors such as lactose or D-glucose rather than water is significant for both enzymes and depends on the initial lactose concentration as well as the time-dependent substrate/product ratio during batchwise lactose conversion. It is approximately 1.8 times higher for SsbetaGly, compared with CelB. Overall, CelB and SsbetaGly share their catalytic properties with much less thermostable beta-glycosidases and thus seem very suitable for lactose hydrolysis at >/=70 degrees C.
Nanoarchitectonics for Controlling the Number of Dopant Atoms in Solid Electrolyte Nanodots (2018)

Controlling movements of electrons and holes is the key task in developing today's highly sophisticated information society. As transistors reach their physical limits, the semiconductor industry is seeking the next alternative to sustain its economy and to unfold a new era of human civilization. In this context, a completely new information token, i.e., ions instead of electrons, is promising. The current trend in solid-state nanoionics for applications in energy storage, sensing, and brain-type information processing, requires the ability to control the properties of matter at the ultimate atomic scale. Here, a conceptually novel nanoarchitectonic strategy is proposed for controlling the number of dopant atoms in a solid electrolyte to obtain discrete electrical properties. Using α-Ag<sub>2+</sub><sub>δ</sub> S nanodots with a finite number of nonstoichiometry excess dopants as a model system, a theory matched with experiments is presented that reveals the role of physical parameters, namely, the separation between electrochemical energy levels and the cohesive energy, underlying atomic-scale manipulation of dopants in nanodots. This strategy can be applied to different nanoscale materials as their properties strongly depend on the number of doping atoms/ions, and has the potential to create a new paradigm based on controlled single atom/ion transfer.
ChemInform Abstract: Protein Folding Triggered by Electron Transfer (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Simplified Modified Compression Field Theory for Calculating Shear Strength of Reinforced Concrete Elements (2006)

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Abstract 3452: Conversion of abiraterone to D4A drives antitumor activity in castration-resistant prostate cancer (2015)

Abstract Castration resistant prostate cancer (CRPC) still relies on androgens for progression. Abiraterone, an FDA approved CYP17A inhibitor, blocks androgen synthesis and prolongs survival. Abiraterone metabolites are generally thought to be inactive. We have identified a novel abiraterone metabolite, D4A, which inhibits three steroidogenic enzymes and androgen receptor (AR) itself. After abiraterone acetate administration, plasma from mice and patients were analyzed with liquid chromatography-mass spectrometry (LC-MS). The LC-MS results indicate that abiraterone is converted to D4A at detectable concentrations in both mice and patients. To test the function of D4A, the androgen synthesis pathway was analyzed in cell lines and xenografts. After incubation with [3H] labeled androgens, metabolites from cell lines and xenografts were analyzed by HPLC. We found that D4A inhibits activity of the steroidogenic enzymes CYP17A, 3β-hydroxysteroid dehydrogenase (3[[Unsupported Character - Symbol Font ]]HSD) and 5α-reductase. Furthermore D4A competes with the AR agonist R1881 and binds to AR directly. D4A inhibits DHT-induced AR occupancy on the PSA enhancer as detected by chromatin immunoprecipitation and reduces PSA expression. Our findings suggest that D4A is an abiraterone metabolite and a potent inhibitor of the androgen pathway. Citation Format: Zhenfei Li, Nima Sharifi. Conversion of abiraterone to D4A drives antitumor activity in castration-resistant prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3452. doi:10.1158/1538-7445.AM2015-3452
Partial arsenic pressure and crystal orientation during the molecular beam epitaxy of GaAs on SrTiO3(001) (2010)

A study of epitaxial growth of GaAs islands on (2×1) reconstructed SrTiO3(001) surface is presented. Under low arsenic partial pressures (PAs), GaAs islands are (001)-oriented, and increasing PAs leads to the progressive formation of (111)-oriented GaAs islands. This results from the competition between the formation of Ga–O and Ga–As bonds at the early stages of the growth, as supported by the analysis of the evolution of the island density with respect to PAs.