gebhart/patrepeval huggingface dataset:
Abstract 3346: Development of a multiplex screening panel for Akt signaling pathway biomarkers in cell and tissue lysate models (2014)

Abstract Major challenges face the large-scale implementation of intracellular tumor biomarkers for clinical diagnosis and therapeutic development. These challenges include non-quantitative results, insufficient assay sensitivity, and lack of multiplexing capability. For many studies, sample volumes are limited (e.g., tumor lysates); however, it is essential to extract as much biomarker information as possible from a given sample while maintaining the quality and consistency necessary to sustain ongoing studies. To address these challenges, MSD® has developed multiplex panels for assaying cell signaling biomarkers using fit-for-purpose methods that emphasize optimal multiplex combinations and rigorous development of critical reagents. Here we report the development and verification of a multiplex screening panel of immunoassays for simultaneous measurement of total and phosphorylated analytes of the Akt signalling pathway using MSD technology. Markers in the panel include phosphorylated and total forms of GSK3B, p70S6K, FOXO3a, PTEN, Akt, S6RP, PRAS40, and ERK1. We demonstrate the ability of these assays to measure analyte levels in multiple tumor-derived cell lines and human tissue samples (normal and tumor) with excellent sensitivity and performance. Most analytes can be quantified using no more than 10 µg of sample. By using recombinant proteins to calibrate some of the assays, we were able to quantify analytes in cultured cell lysates, including MCF-7 and Jurkat T-cells. Lack of analyte specificity is a well-known issue when multiplexing intracellular signaling analytes, especially those in a common signaling pathway such as the Akt pathway. Through rigorous optimization, we achieved non-specific binding less than or equal to 1% for all analytes in this panel. Spike recovery and dilution linearity were characterized to demonstrate matrix tolerance in tumor cell line and tissue lysates as well as dynamic ranges between 3 and 4 logs, allowing quantification of analytes at different abundance levels without using multiple dilutions. In conclusion, MSD MULTI-SPOT® Akt signaling assay panels have been developed and verified for measurement of intracellular tumor biomarkers of relevance to clinical diagnosis, therapeutic development, and treatment of various cancers. The accuracy, reliability, ease of use, and high-throughput features of these multiplex assays make them ideally suited for use in large-scale clinical studies. Citation Format: Thomas W. Miller, Karen Tressler, Jill Dunty, Paula Eason, Leonid Dzantiev, Sripriya Ranganathan, Laura Schaefer, David Stewart, Pankaj Oberoi, Jacob Wohlstadter. Development of a multiplex screening panel for Akt signaling pathway biomarkers in cell and tissue lysate models. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3346. doi:10.1158/1538-7445.AM2014-3346
Certolizumab pegol has a different profile from other anti-TNFs, including golimumab, in a variety of in vitro assays (2010)

Differences in structure and in vitro properties of anti-TNF agents may account for different modes of action and clinical outcomes. The activities of certolizumab pegol (CZP), etanercept (ETA), infliximab (IFX) and adalimumab (ADA) have been compared using in vitro assays. [1] However, golimumab (GLM) has not previously been evaluated.
A Biomechanical Study of Odontoid Fractures and Fracture Fixation (1993)

The purpose of this study was to measure the stability of the odontoid process after fracture and subsequent screw fixation. To accomplish this, we mechanically reproduced Type II and Type III odontoid fractures on isolated C2 vertebrae by varying the direction of load. These fractures were subsequently stabilized with a single 3.5 mm screw and retested for multidirectional stability and load to failure. Reduced and instrumented specimens were found to have a stiffness equivalent to one half of that of the unfractured odontoid. Load to failure was also slightly less than one half of the original fracture force (average 160 lb). Screw failure was by a cut-out mechanism in all Type III fractures and by bending of the screw in all Type III fractures. Our findings, in conjunction with the existing literature, strongly suggest that Type III fractures result from extension forces, whereas Type II fractures result from lateral or oblique loading forces. Single screw fixation of an odontoid fracture will provide stability equal to approximately one half that of the unfractured bone.
Catalytic Coupling of Arene C–H Bonds and Alkynes for the Synthesis of Coumarins: Substrate Scope and Application to the Development of Neuroimaging Agents (2012)

C-H bond functionalization offers strategically novel approaches to complex organic compounds. However, many C-H functionalization reactions suffer from poor compatibility with Lewis basic functional groups, especially amines, which are often essential for biological activity. This study describes a systematic examination of the substrate scope of catalytic hydroarylation in the context of complex amino coumarin synthesis. The choice of substrates was guided by the design and development of the next generation of fluorescent false neurotransmitters (FFNs), neuroimaging probes we recently introduced for optical imaging of neurotransmission in the brain. Comparison of two mild protocols using catalytic PtCl(4) or Au(PPh(3))Cl/AgSbF(6)revealed that each method has a broad and mutually complementary substrate scope. The relatively less active platinum system out-performed the gold catalyst with indole substrates lacking substitution at the C-3 position and provided higher regioselectivity in the case of carbazole-based substrates. On the other hand, the more active gold catalyst demonstrated excellent functional group tolerance, and the ability to catalyze the formation of strained, helical products. The development of these two protocols offers enhanced substrate scope and provides versatile synthetic tools required for the structure-activity examination of FFN neuroimaging probes as well as for the synthesis of complex coumarins in general.
On Rényi Differential Privacy in Statistics-Based Synthetic Data Generation (2023)

Privacy protection with synthetic data generation often uses differentially private statistics and model parameters to quantitatively express theoretical security. However, these methods do not take into account privacy protection due to the randomness of data generation. In this paper, we theoretically evaluate Rényi differential privacy of the randomness in data generation of a synthetic data generation method that uses the mean vector and the covariance matrix of an original dataset. Specifically, for a fixed $α&gt; 1$, we show the condition of $\varepsilon$ such that the synthetic data generation satisfies $(α, \varepsilon)$-Rényi differential privacy under a bounded neighboring condition and an unbounded neighboring condition, respectively. In particular, under the unbounded condition, when the size of the original dataset and synthetic datase is 10 million, the mechanism satisfies $(4, 0.576)$-Rényi differential privacy. We also show that when we translate it into the traditional $(\varepsilon, δ)$-differential privacy, the mechanism satisfies $(4.00, 10^{-10})$-differential privacy.
Neuroconductor: an R platform for medical imaging analysis (2017)

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience.
Strain-driven formation of epitaxial nanostructures in brownmillerite strontium cobaltite thin films (2023)

Nanostructured materials can display unique physical properties and are of particular interest for their new functionalities. Epitaxial growth is a promising approach for the controlled synthesis of nanostructures with desired structures and crystallinity. SrCoO<sub>x</sub> is a particularly intriguing material owing to a topotactic phase transition between an antiferromagnetic insulating brownmillerite SrCoO<sub>2.5</sub> (BM-SCO) phase and a ferromagnetic metallic perovskite SrCoO<sub>3-δ</sub> (P-SCO) phase depending on the oxygen concentration. Here, we present the formation and control of epitaxial BM-SCO nanostructures by substrate-induced anisotropic strain. Perovskite substrates with a (110)-orientation and which allow for compressive strain result in the creation of BM-SCO nanobars, while (111)-oriented substrates give rise to the formation of BM-SCO nanoislands. We have found that substrate-induced anisotropic strain coupled with the orientation of crystalline domains determines the shape and facet of the nanostructures, while their size can be tuned by the degree of strain. Moreover, the nanostructures can be transformed between antiferromagnetic BM-SCO and ferromagnetic P-SCO via ionic liquid gating. Thus, this study provides insights into the design of epitaxial nanostructures whose structure and physical properties can be readily controlled.
Aspect-oriented Data and Safety Modeling for Cyber-Physical Systems in Process Automation (2016)

Cyber-physical systems (CPS) integrate computation with physical processes, enabling the dynamic adaption of systems based on economic and environmental conditions. The adoption of CPS in industrial process automation is impeded by legacy systems with severe functional safety constraints and the need for highly configurable devices. To transfer the benefits of CPS to process automation, the inherent conflict between CPS safety and configurability must be explicitly considered during system design and operation. This paper proposes aspect-oriented modeling of safety and data for CPS in process automation as a baseline for formal consistency monitoring.
A five component land seismic sensor for measuring lateral gradients of the wavefield (2018)

ABSTRACT We built a five‐component (5C) land seismic sensor that measures both the three‐component (3C) particle acceleration and two vertical gradients of the horizontal wavefield through a pair of 3C microelectromechanical accelerometers. The sensor is a small cylindrical device planted vertically just below the earth's surface. We show that seismic acquisition and processing 5C sensor data has the potential to replace conventional seismic acquisition with analogue geophone groups by single 5C sensors placed at the same station interval when combined with a suitable aliased ground roll attenuation algorithm. The 5C sensor, therefore, allows for sparser, more efficient, data acquisition. The accuracy of the 5C sensor wavefield gradients depends on the 3C accelerometers, their sensitivity, self‐noise and their separation. These sensor component specifications are derived from various modelling studies. The design principles of the 5C sensor are validated using test data from purpose‐built prototypes. The final prototype was constructed with a pair of 3C accelerometers separated by 20 cm and with a self‐noise of 35 ng Hz −1/2 . Results from a two‐dimensional seismic line show that the seismic image of 5C sensor data with ground roll attenuated using 5C sensor gradient data was comparable to simulated analogue group data as is the standard in the industry. This field example shows that up to three times aliased ground roll was attenuated. The 5C sensor also allows for correcting vertical component accelerometer data for sensor tilt. It is shown that a vertical component sensor that is misaligned with the vertical direction by 10° introduces an error in the seismic data of around –20 dB with respect to the seismic signal, which can be fully corrected. Advances in sensor specifications and processing algorithms are expected to lead to even more effective ground roll attenuation, enabling a reduction in the receiver density resulting in a smaller number of sensors that must be deployed and, therefore, improving the operational efficiency while maintaining image quality.
Contraction and Expansion of Stimuli-Responsive DNA Bonds in Flexible Colloidal Crystals (2016)

DNA surface ligands can be used as programmable "bonds" to control the arrangement of nanoparticles into crystalline superlattices. Here, we study the intrinsic responsiveness of these DNA bonds to changes in local dielectric constant (εr) as a new approach to dynamically modulate superlattice structure. Remarkably, ethanol (EtOH) addition can be used to controllably tune DNA bond length from 16 to 3 nm and to increase bond stability by >40 °C, while retaining long-range order and crystal habit. Interestingly, we find that these structural changes, which involve the expansion and contraction of crystals by up to 75% in volume, occur in a cooperative fashion once a critical percentage of EtOH is reached. These results provide a facile and robust approach to create stimuli-responsive lattices, to access high volume fractions, and to improve thermal stability.
Ultraviolet integrated photonic circuits (Conference Presentation) (2016)

Quantum information processing relies on the fundamental property of quantum interference, where the quality of the interference directly correlates to the indistinguishability of the interacting particles. The creation of these indistinguishable particles, photons in this case, has conventionally been accomplished with nonlinear crystals and optical filters to remove spectral distinguishability, albeit sacrificing the number of photons. This research describes the use of an integrated aluminum nitride microring resonator circuit to selectively generate photon pairs at the narrow cavity transmissions, thereby producing spectrally indistinguishable photons. These spectrally indistinguishable photons can then be routed through optical waveguide circuitry, concatenated interferometers, to manipulate and entangle the photons into the desired quantum states. Photon sources and circuitry are only two of the three required pieces of the puzzle. The final piece which this research is aimed at interfacing with are trapped ion quantum memories, based on trapped Ytterbium ions. These ions serve as very long lived and stable quantum memories with storage times on the order of 10’s of minutes, compared with photonic quantum memories which are limited to 10-6 to 10-3 seconds. The caveat with trapped ions is the interaction wavelength of the photons is 369.5nm and therefore the goal of this research is to develop entangled photon sources and circuitry in that wavelength regime to interact directly with the trapped ions and bypass the need for frequency conversion.
Personalized Assessment of Arousal and Valence from Videos (2020)

Human behavior is influenced by numerous subjective factors such as the environment, culture, hormones, genes etc. This makes the development of a one-size-fits-all behavioral model for emotion recognition challenging, especially in the domain of affect recognition. In this paper we present a method to classify and assess arousal and valence from video in a personalized way. We represent the inherent information in the video independently through three semantically different types of signals, namely motion, appearance and physiology. We use a single- and multi-stream LSTM model for data fusion and classification, and compare our results against published values on a publicly available dataset consisting of 40 subjects. We further demonstrate that the personalized approach reaches better performance (Arousal: 78.16% avg. acc.; Valence 89.22% avg. acc.), while providing more insight into the role of each signal group. For arousal classification we can distinguish between subjects that show dominance of motion-related expressions against others that exhibit more static expressions. Fusion of all three signal types gave an advantage on very few subjects, a challenge that might be related to the video recordings being too short.
Object Recognition with Less Requirements (2011)

In recent years remarkable results have been achieved in the field of object recognition. Recognition performance of more than 90% are not rare anymore leading to the conclusion of an application beyond scientific fields. However, such a high performance is often a result of unrealistic constraints of the images to be recognized and the use-cases which are only applicable in controlled laboratory environments. In this paper we propose a system working even under difficult conditions and achieving higher recognition performance as compared to other state-of-the-art systems.
Growth and etching characteristics of (001)β-Ga2O3by plasma-assisted molecular beam epitaxy (2017)

We investigated the homoepitaxial growth and etching characteristics of (001) β-Ga2O3 by plasma-assisted molecular beam epitaxy. The growth rate of β-Ga2O3 increased with increasing Ga-flux, reaching a clear plateau of 56 nm h−1, and then decreased at higher Ga-flux. The growth rate decreased from 56 to 42 nm h−1 when the substrate temperature was increased from 750 °C to 800 °C. The growth rate was negative (net etching) when only Ga-flux was supplied. The etching rate proportionally increased with increasing the Ga-flux, reaching 84 nm h−1. The etching was enhanced at higher temperatures. It was found that Ga-etching of (001) β-Ga2O3 substrates prior to the homoepitaxial growth markedly improved the surface roughness of the film.
Prevalence of Propionibacterium acnes in Intervertebral Discs of Patients Undergoing Lumbar Microdiscectomy: A Prospective Cross-Sectional Study (2016)

In a large series of patients, the prevalence of discs with abundant P. acnes was 11%. We believe, disc tissue homogenization releases P. acnes from the biofilm so that they can then potentially be cultured, reducing the rate of false-negative cultures. Further, quantification study revealing significant bioburden based on both culture and real-time PCR minimize the likelihood that observed findings are due to contamination and supports the hypothesis P. acnes acts as a pathogen in these cases of degenerative disc disease.
Excited state Raman spectroscopy of tetracarbonyl(.alpha.-diimine)tungsten complexes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExcited state Raman spectroscopy of tetracarbonyl(.alpha.-diimine)tungsten complexesJing Huei Perng and Jeffrey I. ZinkCite this: Inorg. Chem. 1990, 29, 6, 1158–1161Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/ic00331a010https://doi.org/10.1021/ic00331a010research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ChemInform Abstract: New Aryl/Heteroaryl C—N Bond Cross‐Coupling Reactions via Arylboronic Acid/Cupric Acetate Arylation. (1998)

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.
Microwave image reconstruction utilizing log-magnitude and unwrapped phase to improve high-contrast object recovery (2001)

Reconstructing images of large high-contrast objects with microwave methods has proved difficult. Successful images have generally been obtained by using a priori information to constrain the image reconstruction to recover the correct electromagnetic property distribution. In these situations, the measured electric field phases as a function of receiver position around the periphery of the imaging field-of-view vary rapidly often undergoing changes of greater than pi radians especially when the object contrast and illumination frequency increase. In this paper, we introduce a modified form of a Maxwell equation model-based image reconstruction algorithm which directly incorporates log-magnitude and phase of the measured electric field data. By doing so, measured phase variation can be unwrapped and distributed over more than one Rieman sheet in the complex plane. Simulation studies and microwave imaging experiments demonstrate that significant image quality enhancements occur with this approach for large high-contrast objects. Simple strategies for visualizing and unwrapping phase values as a function of the transmitter and receiver positions within our microwave imaging array are described. Metrics of the degree of phase variation expressed in terms of the amount and extent of phase wrapping are defined and found to be figures-of-merit which estimate when it is critical to deploy the new image reconstruction approach. In these cases, the new algorithm recovers high-quality images without resorting to the use of a priori information on object contrast and/or size as previously required.
Mechanistic Aspects of Radiation-Induced Free Radical Formation in Frozen Aqueous Solutions of DNA Constituents: Consequences for DNA? (1992)

Frozen aqueous solutions of 1 M thymidine-5'-monophosphate were X-irradiated 77 K. The free radicals formed were analyzed by electron spin resonance spectroscopy between 77 K and about 260 K and were shown to result nearly exclusively from electron reaction at 77 K forming the thymine base anion, which converts into the well known 5-thymyl radical upon annealing. Primary oxidation of the substrate was not detectable. A minority species denoted TOH., which appeared at about 200 K, was suggested to result from OH. addition to carbon C6 of the base, perhaps via intermediate oxidation involving H2O2 or from direct reaction of OH. with the base. Another minority species at 77 K up to about 150 K, which was strongly enhanced by H2O2, was shown to be the allyl radical formed by reaction of the OH. with the methyl group. Support for this was given from experiments using BeF2 glasses. The possible spectral features for the cation of dTMP were extracted from aqueous pastes of the Ca2+ salt at 77 K. The mechanistic aspects derived from the results are in conflict with previous assumptions and are discussed for DNA model compounds and DNA.