gebhart/patrepeval huggingface dataset:
PerDREP (2019)

In contrast to the one-size-fits-all approach to medicine, precision medicine will allow targeted prescriptions based on the specific profile of the patient thereby avoiding adverse reactions and ineffective but expensive treatments. Longitudinal observational data such as Electronic Health Records (EHRs) have become an emerging data source for personalized medicine. In this paper, we propose a unified computational framework, called PerDREP, to predict the unique response patterns of each individual patient from EHR data. PerDREP models individual responses of each patient to the drug exposure by introducing a linear system to account for patients' heterogeneity, and incorporates a patient similarity graph as a network regularization. We formulate PerDREP as a convex optimization problem and develop an iterative gradient descent method to solve it. In the experiments, we identify the effect of drugs on Glycated hemoglobin test results. The experimental results provide evidence that the proposed method is not only more accurate than state-of-the-art methods, but is also able to automatically cluster patients into multiple coherent groups, thus paving the way for personalized medicine.
LiteGreen: saving energy in networked desktops using virtualization (2010)

To reduce energy wastage by idle desktop computers in enterprise environments, the typical approach is to put a computer to sleep during long idle periods (e.g., overnight), with a proxy employed to reduce user disruption by maintaining the computer’s network presence at some minimal level. However, the Achilles ’ heel of the proxy-based approach is the inherent trade-off between the functionality of maintaining network presence and the complexity of application-specific customization. We present LiteGreen, a system to save desktop energy by virtualizing the user’s desktop computing environment as a virtual machine (VM) and then migrating it between the user’s physical desktop machine and a VM server, depending on whether the desktop computing environment is being actively used or is idle. Thus, the user’s desktop environment is “always on”, maintaining its network presence fully even when the user’s physical desktop machine is switched off and thereby saving energy. This seamless operation allows LiteGreen to save energy during short idle periods as well (e.g., coffee breaks), which is shown to be significant according to our analysis of over 65,000 hours of data gathered from 120 desktop machines. We have prototyped LiteGreen on the Microsoft Hyper-V hypervisor. Our findings from a small-scale deployment comprising over 3200 user-hours of the system as well as from laboratory experiments and simulation analysis are very promising, with energy savings of 72-74 % with LiteGreen compared to 32 % with existing Windows and manual power management. 1
Cover Picture: NMR Hyperpolarization Techniques of Gases (Chem. Eur. J. 4/2017) (2016)

Nuclear spin polarization can be significantly increased through the process of hyperpolarization, leading to an increase in the sensitivity of nuclear magnetic resonance experiments by 4–8 orders of magnitude. Hyperpolarized gases can be more readily separated from the compounds used to mediate the hyperpolarization processes. These pure hyperpolarized gases enabled many novel MRI applications including the visualization of void spaces, imaging of lung function, remote detection, etc. This article covers the fundamentals of the preparation of hyperpolarized gases and focuses on selected applications of interest to biomedicine and materials science. More information can be found in the Minireview by E. Y. Chekmenev et al. on page 725 ff. Nuclear spin polarization can be significantly increased through the process of hyperpolarization, leading to an increase in the sensitivity of nuclear magnetic resonance experiments by 4–8 orders of magnitude. Hyperpolarized gases can be more readily separated from the compounds used to mediate the hyperpolarization processes. These pure hyperpolarized gases enabled many novel MRI applications including the visualization of void spaces, imaging of lung function, remote detection, etc. This article covers the fundamentals of the preparation of hyperpolarized gases and focuses on selected applications of interest to biomedicine and materials science. More information can be found in the Minireview by E. Y. Chekmenev et al. on page 725 ff.
Scanning near-field optical microscopy in Basel, Ruschlikon, and Zurich (1995)

The concepts of near-field optical microscopy and experimental and theoretical work carried out in Switzerland over the last 10 years are reviewed. After a description of the pioneering experiments of the mid-1980s, we focus on the recent efforts of the three Swiss laboratories currently working in the field in close collaboration. This newly refreshed initiative in near-field optics is supported by the Swiss Priority Program Optique.
Proteolytic <sup>18</sup>O Labeling by Peptidyl-Lys Metalloendopeptidase for Comparative Proteomics (2005)

The potential capabilities of a new proteolytic 18O labeling method employing peptidyl-Lys metalloendopeptidase (Lys-N) have been demonstrated for use in comparative proteomics. Conditions (pH>or=9.5) have been found such that Lys-N incorporates only a single 18O atom into the carboxyl terminus of each proteolytically generated peptide. This 18O labeling method has a major advantage over current protelytic 18O labeling methods that generate a mixture of isotopic isoforms resulting from the incorporation of one or two 18O atoms into each peptide species by the proteases (trypsin, Lys-C, or Glu-C) used. We demonstrate that the single 18O atom incorporation property of Lys-N overcomes the major problem of the current proteolytic 18O labeling methods and provides accurate quantification results for isotopically labeled peptides.
Post‐treatment‐Free Solution‐Processed Non‐stoichiometric NiO<i><sub>x</sub></i> Nanoparticles for Efficient Hole‐Transport Layers of Organic Optoelectronic Devices (2015)

High-quality non-stoichiometric NiOx nanoparticles are synthesized by a facile chemical precipitation method. The NiOx film can function as an effective hole-transport layer (HTL) without any post-treatments, while offering wide temperature applicability from room temperature to 150 °C. A high efficiency of 9.16% is achieved in organic solar cells using the NiOx HTL. A better performance in a NiOx-based organic light-emitting diode is observed, compared with a device using PEDOT:PSS.
Modeling of Shale-Swelling Behavior in Aqueous Drilling Fluids (2013)

Abstract Shale swelling is a serious issue in water-based muds (WBM) as it may lead to stuck pipe, shale sloughing and decreased rate of penetration. Linear Swell Meter (LSM) testing is one of well-known laboratory tests used to characterize shale swelling. This paper describes how the time-dependent swelling response from LSM is modeled to extract characteristic parameters of swelling behavior. The study was performed for different shales with appreciable variation in smectite, illite and Cation Exchange Capacity (CEC). Swelling of these shales in WBM was investigated using different salt concentrations, mud weights and viscosities of the fluids. Shale swelling as a function of time was modeled in a novel way as %S(t) = A *[f(B*t)+C*g(t)] where %S(t) represents swelling at time t. The equation was derived after combining first order kinetics term as f(B*t) with filtration loss term based as C*g(t). Thus, A represents saturation swelling volume, B represents first-order rate of swelling and C is filtrate loss rate parameter. The model fits well to experimental data with R2 &gt; 0.97 for all shale-fluid combinations investigated which was used to extract the characteristic parameters. Saturation swelling volume, A, increased with an increase in CEC of the shale. In addition, A decreased linearly till a critical salt concentration in fluid was reached and then flattened out with further increase in salt concentration. Such behavior conforms to osmotic transport of water through shale. It was observed that A was independent of mud weight and fluid viscosity; however B was observed to increase with a decrease in viscosity which may be interpreted as result of diffusion phenomena governing swelling rate. Filtrate loss rate parameter C was estimated to be between 0 and 1 in most of shale-fluid combinations studied. Information obtained from parameters A, B and C can allow us to optimize WBM formulations for shale that can save cost and time.
High power density supercapacitors using locally aligned carbon nanotube electrodes (2005)

A new form of thin films formed by multi-walled carbon nanotubes exhibiting high packing density and local alignment were fabricated using a highly concentrated colloidal suspension of carbon nanotubes. Electrical double layer capacitors built from these film electrodes exhibited a close to rectangular cyclic voltammogram even at a high scan rate of 1000 mV s−1, and produced very high specific power density of about 30 kW kg−1, ideal for surge-power delivery applications. The preparation procedure is very simple, and does not require any binders. It has potential for highly efficient manufacturing of high power density supercapacitors and other similar electronic devices.
Two-Dimensional Optical Storage (2004)

Two-dimensional optical storage aims at increasing the data capacity and data rate for a given physical read-out system. It uses parallel read-out in combination with advanced signal-processing. Experimental results results on read only memory (ROM) discs are presented that proof the concept. Laser beam recorded discs proof the concept, and electron beam recorded disc show the feasibility at real physical parameters for a density at 35 GB with ample tilt margins.
Characterization of Aloeride, a New High-Molecular-Weight Polysaccharide from <i>Aloe vera</i> with Potent Immunostimulatory Activity (2000)

We have characterized a new immunostimulatory polysaccharide called Aloeride from commercial aloe vera (Aloe barbadensis) juice. Aloeride is between 4 and 7 million Da, and its glycosyl components include glucose (37.2%), galactose (23.9%), mannose (19.5%), and arabinose (10.3%). At 0.5 microg/mL Aloeride increased NF-kappa B directed luciferase expression in THP-1 human monocytic cells to levels 50% of those achieved by maximal concentrations (10 microg/mL) of LPS. Aloeride induced the expression of the mRNAs encoding IL-1beta and TNF-alpha to levels equal to those observed in cells maximally activated by LPS. Acemannan, the major carbohydrate component from aloe, used at 200 microg/mL in the macrophage assay resulted in negligible NF-kappa B activation. Analysis of acemannan and Aloeride using size-exclusion chromatography suggests that the low activity of acemannan is due to trace amounts of Aloeride. Although Aloeride comprises only 0.015% of the aloe juice dry weight, its potency for macrophage activation accounts fully for the activity of the crude juice.
A New Optical Communication Architecture for Delivering Extremely Large Volumes of Data from Space to Ground (2015)

Space-based laser communication has been demonstrated at rates ranging from 10’s of Mbps to a few Gbps for near-Earth crosslinks and for direct-to-Earth downlinks from ranges as far as the Moon. We describe a novel space-to-Earth communication architecture that can deliver many terabytes of data regularly, if the user is willing to accept certain amounts of delay. With careful design of space and ground terminals, and by tapping the recent advances in integrated extremely high rate modems developed by the fiber telecommunications industry, we believe that space terminal cost, ground terminal cost, and operations costs can be kept much lower than present day radio-frequency or proposed optical systems while increasing the amount of data delivery by orders of magnitude.
A 15-nW per Sensor Interference-Immune Readout IC for Capacitive Touch Sensors (2019)

This paper presents a readout IC that uses an asynchronous capacitance-to-digital-converter (CDC) to digitize the capacitance of a touch sensor. A power-efficient tracking algorithm ensures that the CDC consumes negligible power consumption in the absence of touch events. To facilitate its use in wake-on-touch applications, the CDC can be periodically triggered by a co-integrated ultra-low-power relaxation oscillator. At a 38-Hz scan rate, the readout IC consumes 15 nW per touch sensor, which is the lowest reported to date.
Retinoic acid analogs with ring modifications. Synthesis and pharmacological activity (1981)

Analogues of retinoic acid that have their major modifications in the 5,6 double bond and 4-methylene group regions of the beta-cyclogeranylidene ring have been synthesized as potential agents for the treatment and prevention of epithelial cancer. These modifications were intended to reduce retinoid toxicity by lowering the effective treatment dose because the major metabolic deactivation pathway would be inhibited. Ethyl (E)-3,7-dimethyl-9-(exo-2-bicyclo[2.2.1]-heptyl)-2,4,6,8-nonatetraenoate (7), ethyl (E)-3,7-dimethyl-9-(2,2,6-trimethylbicyclo[4.1.0]hept-1-yl)-2,4,6,8-nonatetraen oate (18), (E)-1-(4-carbethoxyphenyl)-2-methyl-4-(2,2,6-trimethylbicyclo[4.1.0]hept-1-yl)- 1,3-butadiene (28), (E)-retinoic acid-4,4,18,18,18-d5 (39), and ethyl (E)-3,7-dimethyl-9-(3,3-ethano-2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate (47) displayed moderate to excellent activity in an assay for the inhibition of tumor promoter-induced mouse epidermal ornithine decarboxylase.
Evidence for Ionic Liquid Gate-Induced Metallization of Vanadium Dioxide Bars over Micron Length Scales (2017)

It has recently been shown that the metal-insulator transition in vanadium dioxide epitaxial films can be suppressed and the material made metallic to low temperatures by ionic liquid gating due to migration of oxygen. The gating is only possible on certain crystal facets where volume channels along the VO<sub>2</sub>'s rutile c-axis intersect the surface. Here, we fabricate bars with the c-axis in plane and oriented parallel to or perpendicular to the length of the bars. We show that only bars with the c-axis perpendicular to the bars, for which the volume channels are accessible from the sides of the bar, can be metallized by ionic liquid gating. Moreover, we find that bars up to at least 0.5 μm wide can be fully gated, demonstrating the possibility of the electric field induced migration of oxygen over very long distances, ∼5 times longer than previously observed.
Nodal fragility of intracranial EEG networks: Towards an EEG fingerprint for the epileptogenic zone (2019)

Epilepsy is a global epidemic and 30% of the 60 million patients do not respond to medication treatment. The only treatment options for patients with medically refractory epilepsy are surgical removal or electrical stimulation of the epileptogenic zone (EZ) i.e. the source of their seizures. Despite extensive evaluations with neuroimaging, visual EEG analysis and clinical testing, surgical success rates vary between 30-70%. Currently, no computational methods have been translated into the clinic to assist in localizing the EZ. Here, we applied a dynamical network model that quantifies the fragility of nodes within a patient9s intracranial EEG (iEEG) brain network. Fragility is quantified as the minimal amount of perturbation that must to be applied to a node9s influence on a network to cause imbalance. Here, a balanced network is one in which the connectivity between excitatory and inhibitory nodes render a stable system, and an imbalanced network is unstable and hence can generate seizures. Using iEEG data from 91 patients treated across 5 epilepsy centers (44 successes, 47 failures), we demonstrated that nodal fragility is greater in electrodes within the EZ. In addition, we compared fragility of iEEG nodes to 7 frequency-based and 14 graph theoretic features of the EZ in both seizure (n=91) and non-seizure data (n=54). We calculated a confidence statistic, defined as the ratio of the value of a given feature averaged across electrodes in the clinically annotated seizure onset zone to its average across all other electrodes. Fragility has a significantly greater effect size difference between surgical outcomes when compared to other features. This novel feature, outperformed the most popular iEEG features when comparing across surgical outcomes, possibly defining a superior network-based EEG fingerprint for the EZ.
Abstract 5242: Effect of total saponins of Gynostemma pentaphyllum on melanogenesis and anti-melanoma effect in B16 cells. (2013)

Abstract Melanogenesis is a physiological process of melanin production in response to UV exposure, which is modulated through multi-signaling pathways including cAMP/PKA, Wnt/β-catenin and MAPK signaling cascades. In this study, we investigated both the melanogenesis and anti-melanoma effects of total saponins of Gynostemma pentaphyllum (GpS). Our results showed that non-toxic dosages of GpS stimulated tyrosinase activity and increased melanin content in a dose-dependent manner. Western blot analysis showed that GpS treatment significantly up-regulated the expression levels of the melanogenic proteins, tyrosinase (TYR) and microphthalmia-associated transcription factor (MITF) in a dose-dependent manner. The p-CREB, which is the down-stream target of PKA is also elevated upon GpS treatment. We further observed that H89, a PKA inhibitor, attenuated the GpS induced tyrosinase activity, melanin content, and the protein expression of p-CREB and the nuclear β-catenin. To identify the active saponins, GpS was fractionated in the MCI-CHP 20P column and eluted with methanol in a gradient of 50 to 100% . The resulting ten fractions were tested for their melanogensis activities. We found that Fractions 5 to 9 showed the strongest effect in melanin synthesis in B16 cultures, while up-regulated the expression levels of TYR and MITF, while Fractions 7 to 9 increased nucleus β-catenin protein expression. Further purification of GpS is under way. Our early works showed that GpS exhibits strong anti-cancer effects in both in cellular and animal model. We were wonder whether GpS would exert anti-cancer effect against melanoma. To address this question, we tested and showed that GpS inhibited B16 cells migration in a dose-dependent manner. Meanwhile, GpS also increased G1/S ratio of the GpS-treated B16 cells, suggesting that GpS may act as G1 inhibitor. Our study seems to be in line with the recent reports that stimulation of melanogenesis might be associated with the anti-melanoma effect by decreasing proliferation and invasiveness of melanoma (Chien, et al.,2009). Based on the above results, we proposed that GpS might exert the anti-melanoma effect by stimulating the melanogenesis through the activation of cAMP/PKA and Wnt/β-catenin signaling pathways. Citation Format: Ting Fung Tsang, William Chi Shing Tai, Wendy Wen Luan Hsiao. Effect of total saponins of Gynostemma pentaphyllum on melanogenesis and anti-melanoma effect in B16 cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5242. doi:10.1158/1538-7445.AM2013-5242
Catalytic Ethylene Dimerization and Oligomerization: Recent Developments with Nickel Complexes Containing P,N‐Chelating Ligands (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access the actual ChemInform Abstract, please click on HTML or PDF.
A Modified <i>Saccharomyces cerevisiae</i> Strain That Consumes <scp>l</scp> -Arabinose and Produces Ethanol (2003)

Metabolic engineering is a powerful method to improve, redirect, or generate new metabolic reactions or whole pathways in microorganisms. Here we describe the engineering of a Saccharomyces cerevisiae strain able to utilize the pentose sugar L-arabinose for growth and to ferment it to ethanol. Expanding the substrate fermentation range of S. cerevisiae to include pentoses is important for the utilization of this yeast in economically feasible biomass-to-ethanol fermentation processes. After overexpression of a bacterial L-arabinose utilization pathway consisting of Bacillus subtilis AraA and Escherichia coli AraB and AraD and simultaneous overexpression of the L-arabinose-transporting yeast galactose permease, we were able to select an L-arabinose-utilizing yeast strain by sequential transfer in L-arabinose media. Molecular analysis of this strain, including DNA microarrays, revealed that the crucial prerequisite for efficient utilization of L-arabinose is a lowered activity of L-ribulokinase. Moreover, high L-arabinose uptake rates and enhanced transaldolase activities favor utilization of L-arabinose. With a doubling time of about 7.9 h in a medium with L-arabinose as the sole carbon source, an ethanol production rate of 0.06 to 0.08 g of ethanol per g (dry weight). h(-1) under oxygen-limiting conditions, and high ethanol yields, this yeast strain should be useful for efficient fermentation of hexoses and pentoses in cellulosic biomass hydrolysates.
Management and protection of digital content with the flexible IPMP scheme: MPEG-21 IPMP (2005)

To ensure secure digital content delivery, MPEG has dedicated significant effort to DRM (Digital Rights Management) issues. The IPMP (Intellectual Property Management and Protection) components, the fourth part of the new MPEG standard project-MPEG-21 (Multimedia Framework) is one of the most important parts of this standardization activity. It defines an interoperable framework for IPMP. Fairly soon after MPEG-4, with its IPMP hooks became an International Standard, MPEG decided to start a new project named "MPEG-4 IPMP Extensions" on more interoperable IPMP systems and tools. The project includes standardized ways of retrieving IPMP tools from remote locations, standardized messages exchanged among IPMP tools and the terminal. It also addresses authentication of IPMP tools, and has provisions for integrating Rights Expressions according to the Rights Data Dictionary and the Rights Expression Language. After MPEG-2/4 IPMP standardization work is finished, efforts are currently ongoing to define the similar mechanism for the management and protection of intellectual property in the various parts of the MPEG-21 standard currently under development. The present paper describes the technologies that are now included in MPEG-21 IPMP Components Committee Draft to effectively manage and protect the digital content with the flexible IPMP scheme, which specifies how protection is applied to Digital Items and facilitates the exchange of governed content declared by a standard constructor MPEG-21 DID (Digital Item Declaration) between MPEG-21 Peers.
Neurophysics-inspired parallel architecture with resistive crosspoint array for dictionary learning (2014)

This paper proposes a parallel architecture with resistive crosspoint array. The design of its two essential operations, Read and Write, is inspired by the biophysical behavior of a neural system, such as integrate-and-fire and time-dependent synaptic plasticity. The proposed hardware consists of an array with resistive random access memory (RRAM) and CMOS peripheral circuits, which perform matrix product and dictionary update in a fully parallel fashion, at the speed that is independent of the matrix dimension. The entire system is implemented in 65nm CMOS technology with RRAM to realize high-speed unsupervised dictionary learning. As compared to state-of-the-art software approach, it achieves more than 3000X speedup, enabling real-time feature extraction on a single chip.
Parallel Multi-Color Fluorescence Lifetime Tomography in Deep Tissue (2013)

We present a deep tissue multi-color fluorescence lifetime imaging method based on scanning laser optical tomography and Fourier fluorescence lifetime excitation-emission matrix spectroscopy. We demonstrate FRET sensor measurements in live transgenic zebrafish embryo.