gebhart/patrepeval huggingface dataset:
Abstract 761: The development of cell permeable Shp2 PTP inhibitors (2010)

Abstract Protein tyrosine phosphorylation affects cellular activities that control tumor growth and progression. Protein tyrosine phosphorylation, a key regulatory process of signal transduction pathways, is controlled by the action protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Kinases are now a clinically proven anticancer drug target. The development of PTP inhibitors is, by comparison, a relatively new field. Since PTPs do not require a small molecule cofactor they generally show a low propensity to bind a small molecule inhibitor. Nevertheless there are now examples of highly potent PTP inhibitors that provide promising proof-of-principle that PTPs are druggable. Most PTP inhibitors have a charged or highly polar functional group that mimics the phosphotyrosine residue, that often leads to poor ADME and cell permeability properties. We will report our efforts to address the problems of cell permeability we have encountered in our Shp2 PTP inhibitor program. We have previously reported a series of isatin based Shp2 inhibitors based on a compound (NSC-117199) identified from screen of the NCI Diversity Set. We synthesized &gt;100 analogs of NSC-117199 in our lead optimization effort, which yielded several compounds with approximately 50-fold increase in potency and &gt; 10-fold increase in selectivity (Shp2 versus Shp1). However, these Shp2 PTP inhibitors have either a polar nitro or carboxyl group and have no detectable cellular activity. We will report three approaches to address this problem. The first approach was to prepare neutral ester prodrugs. Several compounds have clearly demonstrable activity against Shp2 in cells. A series of esters has also been designed to also improve the water solubility of the PTP inhibitor. A second approach taken was to further modify the isatin scaffold that does not necessitate the use of a prodrug strategy. We will report the discovery of new isatins related to NSC-117199 that have new modifications that result in cell active Shp2 inhibitors. Finally we will report the discovery and preliminary optimization of new classes of cell active Shp2 inhibitors based on alternative scaffolds. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 761.
Electroactive Mesoporous Yttria Stabilized Zirconia Containing Platinum or Nickel Oxide Nanoclusters: A New Class of Solid Oxide Fuel Cell Electrode Materials (2001)

The electroactivity of surfactant-templated mesoporous yttria stabilized zirconia, containing nanoclusters of platinum or nickel oxide, is explored by alternating current (AC) complex impedance spectroscopy. The observed oxygen ion and mixed oxygen ion–electron charge-transport behavior for these materials, compared to the sintered-densified non-porous crystalline versions, is ascribed to the unique integration of mesoporosity and nanocrystallinity within the binary and ternary solid solution microstructure. These attributes inspire interest in this new class of materials as candidates for the development of improved performance solid oxide fuel cell electrodes.
Echinocandin resistance among Candida isolates at an academic medical centre 2005–15: analysis of trends and outcomes (2018)

Echinocandin resistance in C. glabrata has been increasingly reported but rates at our institution remain very low. We hypothesize that a focus on antifungal stewardship may have led to these observations. Knowledge of local resistance patterns is key to appropriate empirical treatment strategies.
Identifying authoritative sources of multimedia content (2011)

We present a framework for identifying authoritative sources (such as web sites or individual users) that are likely to produce high-quality or interesting images. We construct a directed graph across sources based on the propensity of one source to "cite" the content from another. A graph-centrality measure scores the authority for each source, which could then be applied for retrieval purposes. We apply this method to web image retrieval, where web sites are the sources, and citations are found via copy detection; and on a photo sharing site, where individuals are the sources and citations are users' favorites. We are able to identify primary or influential sources of media while avoiding the computational cost of other approaches.
Breakthrough instruments and products: An integrated instrument for enhanced, highly precise Hall effect measurement and analysis of electronic materials (2021)

This report highlights the use of a measurement controller with patented technology that enables rapid Hall effect measurement of electronic materials, with examples demonstrating its utility for characterization of various materials.
Chemical probes for molecular imaging and detection of hydrogen sulfide and reactive sulfur species in biological systems (2014)

Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploits the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems.
Auto-Scaling Mechanism in the ICT Converged Cross Stratum Orchestration Architecture for Zero-Touch Service and Network Management (2018)

This paper is aimed to provide a novel approach for an auto-scaling mechanism that are applied in the ICT converged cross stratum orchestration (CSO) architecture. CSO refers to an end-to-end orchestration across Application orchestration, Data Center SDN orchestration, and WAN SDN orchestration so that applications can be created seamlessly and optimally for operators and their customers. The auto-scaling mechanism presented in this paper is built on active monitoring of both DC compute/storage/network resources and DCI Transport network resources and then provides dynamically configurable auto-scaling and resource re-allocation. This mechanism will help tremendously the operators to control and manage their networks in an automated fashion.
Objective Speech Quality Measurement Using Statistical Data Mining (2005)

Measuring speech quality by machines overcomes two major drawbacks of subjective listening tests, their low speed and high cost. Real-time, accurate, and economical objective measurement of speech quality opens up a wide range of applications that cannot be supported with subjective listening tests. In this paper, we propose a statistical data mining approach to design objective speech quality measurement algorithms. A large pool of perceptual distortion features is extracted from the speech signal. We examine using classification and regression trees (CART) and multivariate adaptive regression splines (MARS), separately and jointly, to select the most salient features from the pool, and to construct good estimators of subjective listening quality based on the selected features. We show designs that use perceptually significant features and outperform the state-of-the-art objective measurement algorithm. The designed algorithms are computationally simple, making them suitable for real-time implementation. The proposed design method is scalable with the amount of learning data; thus, performance can be improved with more offline or online training.
Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development (2018)

The discovery of somatic cell nuclear transfer proved that somatic cells can carry the same genetic code as the zygote, and that activating parts of this code are sufficient to reprogram the cell to an early developmental state. The discovery of induced pluripotent stem cells (iPSCs) nearly half a century later provided a molecular mechanism for the reprogramming. The initial creation of iPSCs was accomplished by the ectopic expression of four specific genes (OCT4, KLF4, SOX2, and c-Myc; OSKM). iPSCs have since been acquired from a wide range of cell types and a wide range of species, suggesting a universal molecular mechanism. Furthermore, cells have been reprogrammed to iPSCs using a myriad of methods, although OSKM remains the gold standard. The sources for iPSCs are abundant compared with those for other pluripotent stem cells; thus the use of iPSCs to model the development of tissues, organs, and other systems of the body is increasing. iPSCs also, through the reprogramming of patient samples, are being used to model diseases. Moreover, in the 10 years since the first report, human iPSCs are already the basis for new cell therapies and drug discovery that have reached clinical application. In this review, we examine the generation of iPSCs and their application to disease and development.
Exceptional Electronic Modulation of Porphyrins through <i>meso</i>-Arylethynyl Groups. Electronic Spectroscopy, Electronic Structure, and Electrochemistry of [5,15-Bis[(aryl)ethynyl]- 10,20-diphenylporphinato]zinc(II) Complexes. X-ray Crystal Structures of [5,15-Bis[(4‘-fluorophenyl)ethynyl]- 10,20-diphenylporphinato]zinc(II) and 5,15-Bis[(4‘-methoxyphenyl)ethynyl]-10,20-diphenylporphyrin (1996)

A new class of porphyrins in which intervening ethynyl moieties connect aryl groups to the porphyrin 5- and 15-positions is described. The synthesis and optical spectroscopy of five new compounds are reported: [5,15-bis[(4‘-dimethylaminophenyl)ethynyl]-10,20-diphenylporphinato]zinc(II), [5,15-bis[(4‘-methoxyphenyl)ethynyl]-10,20-diphenylporphinato]zinc(II), [5,15-bis[(phenyl)ethynyl]-10,20-diphenylporphinato]zinc(II), [5,15-bis[(4‘-fluorophenyl)ethynyl]-10,20-diphenylporphinato]zinc(II), and [5,15-bis[(4‘-nitrophenyl)ethynyl]-10,20-diphenylporphinato]zinc(II). The X-ray structure of one of these complexes, [5,15-bis[(4‘-fluorophenyl)ethynyl]-10,20-diphenylporphinato]zinc(II), is unusual in that it shows the arylethynyl-phenyl rings to be coplanar with the porphyrin macrocycle. This arrangement of aryl rings with respect to the porphyrin macrocycle underscores the fact that the steric barrier to rotation between the porphyrin and arylethynyl-phenyl aromatic systems has been removed and highlights the enhanced π-conjugative interactions responsible for the unusual electronic characteristics of these molecules. Electronic spectroscopy and electrochemistry of these systems evince the ability of this new porphyrin structural motif to modulate extensively chromophore electronic structure. ZINDO-determined (INDO-1 semiempirical parameters; CI level = 20) frontier orbital energies for the [5,15-bis[(aryl)ethynyl]-10,20-diphenylporphinato]zinc(II) complexes demonstrate that these properties derive from energetic differences between the porphyrin HOMO and HOMO-1 and a substantial splitting of the formerly degenerate porphyrin LUMO; these significant electronic perturbations (relative to simple (porphinato)zinc(II) complexes) are manifest in the fact that the low lying singlet excited states of these compounds are highly polarized.
High frequency permeability and permittivity spectra of BiFeO3/(CoTi)-BaM ferrite composites (2015)

Low magnetic loss ferrite composites consisting of Ba(CoTi)1.2Fe9.6O19 and BiFeO3 (BFO) ferrite were investigated for permeability, permittivity, and high frequency losses at 10 MHz–1 GHz. The phase fraction of BiFeO3 was quantitatively analyzed by X-ray diffraction measurements. An effective medium approach was employed to predict the effective permeability and permittivity for the ferrite composites, which was found to be in good agreement with experimental data. The experiment demonstrated low magnetic losses (&lt;0.128), modified by BFO phase fraction, while retaining high permeability (∼10.86) at 300 MHz. More importantly, the BFO phase resulted in a reduction of magnetic loss by 32%, as BFO phase increased from 2.7 vol. % to 12.6 vol. %. The effect of BFO phase on magnetic and dielectric properties revealed great potential for use in the miniaturization of high efficiency antennas.
WE‐D‐304A‐09: Characterization of Multi‐Beam Field Emission X‐Ray Source for Stationary Digital Breast Tomosynthesis (2009)

Purpose : The current prototype digital breast tomosynthesis (DBT) scanners are based on the regular full‐field digital mammography systems and require partial isocentric motion of a mammography x‐ray tube over certain angular range to record the projection views needed for reconstruction. This prolongs the scanning time and in turn degrades the imaging quality due to motion blur. We are developing a stationary DBT (s‐DBT) scanner to mitigate the above limitations. Method and Materials : The proposed s‐DBT system is based on the carbon nanotube multi‐pixel field emission x‐ray (MBFEX) technology demonstrated by our group. The pixilated and spatially distributed MBFEX source can generate x‐ray radiation from multiple views without any mechanical motion of the source, detector, or object. This enables the design of tomography systems with great flexibility in source configuration and imaging sequence. It further enables multiplexing imaging — simultaneously collection of multiple images using one detector. Results and Conclusions : To demonstrate the feasibility of the s‐DBT scanner, we have designed and constructed a proof‐of‐concept full‐field s‐DBT system. The configuration of the system, in terms of angular coverage, number of views, and dose, etc., closely resembles the Siemens DBT scanner for a more realistic comparison. In the Siemens DBT scanner, the x‐ray tube moves along an arc with the exposure points evenly distributed along the rotation route. Our s‐DBT scanner is designed with the MBFEX pixels positioned in a straight line parallel to the detector plane. We will report a detailed study on the design and the performance characteristics of the MBFEX source. In particular evaluation on key parameters including the x‐ray flux, the lifetime of the x‐ray source, effective x‐ray focal spot size, variation between different source, system spatial resolution, and x‐ray energy spectrum will be reported. These preliminary results demonstrate the feasibility of the proposed s‐DBT scanner.
Continuous cuff-less blood pressure monitoring based on the pulse arrival time approach: The impact of posture (2008)

There is an unmet need for cuff-less blood pressure (BP) monitoring especially, in personal healthcare applications. The pulse arrival time (PAT) approach might offer a suitable solution to enable comfortable BP monitoring even at beat-level. However, the methodology is based on hemodynamic surrogate measures, which are sensitive to patient activities such as posture changes, not necessarily related to blood pressure variations. In this paper, we analyze the impact of posture on the PAT measure and related hemodynamic parameters such as the pre-ejection period in well-defined procedures. Additionally, the PAT of a monitored subject is investigated in an unsupervised scenario illustrating the complexity of such a measurement. Our results show the failure of blood pressure inference based on simple calibration strategies using the PAT measure only. We discuss opportunities to compensate for the observed effects towards the realization of wearable cuff-less blood pressure monitoring. These findings emphasize the importance of accessing context information in personal healthcare applications, where vital sign monitoring is typically unsupervised.
Link aware HTTP Adaptive Streaming for enhanced quality of experience (2013)

We propose a physical link-aware video rate adaptation approach for HTTP Adaptive Streaming (HAS) systems. This approach is especially suited for wireless links, whose characteristics fluctuate with time depending on the physical environment as well as load on the system. Our novel strategy relies on estimating the available link bandwidth from physical layer goodput information and using it as a complement to higher layer estimates. We develop simple novel video rate-adaptation enhancements that use physical layer goodput information to - i) improve startup video quality under tolerable startup delay and ii) reduce re-buffering during video playback. Simulation results on an LTE (Long Term Evolution) system level simulator indicate improved video quality and lower re-buffering percentage using our approach.
Stabilization of Liquid Foams through the Synergistic Action of Particles and an Immiscible Liquid (2014)

Abstract Liquid foams are familiar from beer, frothed milk, or bubble baths; foams in general also play important roles in oil recovery, lightweight packaging, and insulation. Here a new class of foams is reported, obtained by frothing a suspension of colloidal particles in the presence of a small amount of an immiscible secondary liquid. A unique aspect of these foams, termed capillary foams, is the particle‐mediated spreading of the minority liquid around the gas bubbles. The resulting mixed particle/liquid coating can stabilize bubbles against coalescence even when the particles alone cannot. The coated bubbles are further immobilized by entrapment in a network of excess particles connected by bridges of the minority liquid. Capillary foams were prepared with a diverse set of particle/liquid combinations to demonstrate the generality of the phenomenon. The observed foam stability correlates with the particle affinity for the liquid interface formed by spreading the minority liquid at the bubble surface.
Studies on mechanical properties of thermoelectric materials by nanoindentation (2015)

In order to fabricate durable and efficient thermoelectric generators (TEG) for applications like automobile waste heat recovery, where thermal stress is a major concern, one needs to assess the mechanical performance of the TE materials. This work reports the hardness and elastic modulus of the moderate temperature range (200–1000 °C) TE materials, including half‐Heusler, skutterudites, bismuth telluride, silicon germanium alloys, and lead selenide, using nanoindentation and atomic force microscopy (AFM). The p‐type half‐Heusler exhibits considerably higher hardness and modulus values, and lower brittleness as compared with other materials, which may be indicative of its more robust mechanical performance.
Fungal transformation of ferulic acid from sugar beet pulp to natural vanillin (1999)

Ferulic acid, derived from sugar beet pulp, was used as precursor in a biotechnological two-step process to produce‘natural’ vanillin. This process combined the biotransformation of sugar beet pulp ferulic acid to vanillic acid by a micromycete, Aspergillus niger and the biotransformation of recovered vanillic acid into vanillin by a basidiomycete, Pycnoporus cinnabarinus. The system produced more than 100 mg litre−1 natural vanillin. The sensorial analysis of this new natural vanillin revealed, besides a predominant vanillin flavour, a slight odour of chocolate as a secondary organoleptic sensation. © 1999 Society of Chemical Industry
Use of NIR and pyrolysis-MBMS coupled with multivariate analysis for detecting the chemical changes associated with brown-rot biodegradation of spruce wood (2002)

Near infrared (NIR) spectroscopy and pyrolysis-molecular beam mass spectrometry (py-MBMS) analysis can be used in conjunction with multivariate regression and principal components analysis to differentiate brown-rot-degraded wood from non-degraded spruce and to follow the temporal changes in wood undergoing brown-rot degradation. Regression of NIR test results vs. percent weight loss for Postia placenta- and Gloeophyllum trabeum-infected spruce wood blocks yielded a correlation coefficient of 0.96. Regression of MBMS test results for the same samples yielded a correlation coefficient of 0.96. Principle components analysis was used to differentiate non-infected wood and P. placenta- and G. trabeum-infected wood. These techniques may be used to detect different types of biodegradation and to develop a better understanding of the chemical changes that the wood undergoes when it is subjected to brown-rot biodegradation.
Electrical microfluidic pressure gauge for elastomer microelectromechanical systems (2007)

We report on an electrical microfluidic pressure gauge. A polydimethylsiloxane microvalve closes at a characteristic applied pressure determined by the material's properties and the valve's dimensions. Hence, when the same pressure is applied to all valves of a heterogeneous valve array, some valves close while others remain open. The state of the array is combined with knowledge of the respective characteristic closing pressures of the individual valves to yield an estimate of the applied pressure. The state of each valve is obtained by electrical measurements, since the electrical resistance of the respective underlying fluid-filled channel increases by at least two orders of magnitude as the valve closes and its insulating elastomer material interrupts the electrical circuit. The overall system functions as a pressure gauge with electrical readout. This device would be a critical component in active pressure-regulation loops in future integrated microfluidic systems.
Randomized distributed space-time coding for cooperative communication in self organized networks (2005)

We consider a wireless network in which a single source transmits its message with the help of multiple cooperative relays to a far away destination. In our model the source broadcasts the message and only the relays that are able to produce an inference of acceptable quality retransmit the message by using orthogonal space-time codes. The novelty of our transmission protocol is that, unlike other works on cooperative space-time coding, the code assignment is performed in a completely distributed way by having each node pick one column of the space-time code matrix at random. The interesting result of our analysis is that this simple method achieves the maximum possible diversity order for signal-to-noise ratio (SNR) below a threshold SNR/sub t/, which increases with node density. Hence depending on the SNR range of a given system, one can achieve the maximum diversity order by increasing the number of relay nodes. In addition, for any SNR, the average error probability of the scheme decreases proportional to L/sup N/, where L is the number of columns in the space-time code matrix, and N is the number of active relay nodes.