gebhart/patrepeval huggingface dataset:
Clinical and Preclinical Studies with Huperzine (1991)

One of the pharmacological approaches currently employed in the treatment of symptoms of dementia in Alzheimer’s disease (AD) is the administration of acetylcholinesterase (AChE) inhibitors. This strategy is used with the goal of inhibiting acetylcholine degradation in vivo, and hence alleviating the cholinergic deficiency which has been shown to occur in patients with AD.
An Open-Source Framework for FPGA Emulation of Analog/Mixed-Signal Integrated Circuit Designs (2021)

This article presents an open-source framework for emulating mixed-signal chip designs on a field-programmable gate array (FPGA). It includes a Python-based synthesizable model generator for mixed-signal blocks (msdsl), a fixed-point and floating-point synthesizable SystemVerilog library for representing real numbers (svreal), and a Python-based tool that generates emulator control infrastructure and automates the FPGA build process (anasymod). The framework includes features for efficiently modeling analog dynamics, nonlinearity, and noise, often making use of compile-time caching to reduce the required computational resources of the FPGA. We demonstrate the framework’s generality by discussing three applications: 1) a high-speed link receiver (DragonPHY); 2) a firmware-controlled flyback converter; and 3) an NFC-powered chip. Our framework makes it easy to emulate these systems, while providing runtimes 2–3 orders of magnitude faster than CPU simulations with real-number functional models.
Improving the Accuracy of Protein‐Ligand Binding Mode Prediction Using a Molecular Dynamics‐Based Pocket Generation Approach (2018)

Protein-drug binding mode prediction from the apo-protein structure is challenging because drug binding often induces significant protein conformational changes. Here, the authors report a computational workflow that incorporates a novel pocket generation method. First, the closed protein pocket is expanded by repeatedly filling virtual atoms during molecular dynamics (MD) simulations. Second, after ligand docking toward the prepared pocket structures, binding mode candidates are ranked by MD/Molecular Mechanics Poisson-Boltzmann Surface Area. The authors validated our workflow using CDK2 kinase, which has an especially-closed ATP-binding pocket in the apo-form, and several inhibitors. The crystallographic pose coincided with the top-ranked docking pose for 59% (34/58) of the compounds and was within the top five-ranked ones for 88% (51/58), while those estimated by a conventional prediction protocol were 9% (5/58) and 50% (29/58), respectively. Our study demonstrates that the prediction accuracy is significantly improved by preceding pocket expansion, leading to generation of conformationally-diverse binding mode candidates. © 2018 Wiley Periodicals, Inc.
ChemInform Abstract: Achieving Synthetic Efficiency Through New Method Development (2010)

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.
Spectroscopic elucidation of ionic motion processes in tunnel oxide-based memristive devices (2018)

Resistive switching oxides are highly attractive candidates to emulate synaptic behaviour in artificial neural networks. Whilst the most widely employed systems exhibit filamentary resistive switching, interface-type switching systems based on a tunable tunnel barrier are of increasing interest, since their gradual SET and RESET processes provide an analogue-type of switching required to take over synaptic functionality. Interface-type switching devices often consist of bilayers of one highly mixed-conductive oxide layer and one highly insulating tunnel oxide layer. However, most tunnel oxides used for interface-type switching are also prone to form conducting filaments above a certain voltage bias threshold. We investigated two different tunnel oxide devices, namely, Pr1-xCaxMnO3 (PCMO) with yttria-stabilized ZrO2 (YSZ) tunnel barrier and substoichiometric TaOx with HfO2 tunnel barrier by interface-sensitive, hard X-ray photoelectron spectroscopy (HAXPES) in order to gain insights into the chemical changes during filamentary and interface-type switching. The measurements suggest an exchange of oxygen ions between the mixed conducting oxide layer and the tunnel barrier, that causes an electrostatic modulation of the effective height of the tunnel barrier, as the underlying switching mechanism for the interface-type switching. Moreover, we observe by in operando HAXPES analysis that this field-driven ionic motion across the whole area is sustained even if a filament is formed in the tunnel barrier and the device is transformed into a filamentary-type switching mode.
The liquid fraction from hydrothermal pretreatment of wheat straw provides lytic polysaccharide monooxygenases with both electrons and H2O2 co-substrate (2019)

Our results support the growing understanding that fine-tuned control over the rates of H<sub>2</sub>O<sub>2</sub> production and consumption in different, enzymatic and non-enzymatic reactions is essential for harnessing the full catalytic potential of LPMOs in lignocellulose valorization.
Quantification of fat in the liver by MRI (2012)

Poster: ECR 2012 / C-1935 / Quantification of fat in the liver by MRI by: I. Zbinden1, X. Deligianni1, C. Bernsmeier1, O. Bieri1, G. M. Bongartz1, U. Zingg2, S. Potthast2; 1Basel/CH, 2Schlieren/CH
Supporting media workflows on an advanced cloud object store platform (2016)

The media industry faces daily challenges storing, managing and facilitating collaboration for vast amounts of video, photos, text, audio, and social media. This, together with increasing quality factors like high frame rates and Ultra-High resolution, drives the need for more dependable storage and scalable computation. As a solution to tackle these challenges, we describe the Active Media Store (AMS), which extends OpenStack Swift with storlets and content-centric access. Computation units called "Storlets" run typical media workflow functions, such as transcoding, metadata extraction and quality checks, close to the stored data, thereby reducing data transfer bandwidth and latency typically associated with cloud storage. Powerful search capabilities over rich user-defined metadata enable content-centric access, the ability to find stored media objects based on their content and relationships. Media workflows are easily implemented and managed through the Media Bridge, middleware running over the AMS and adapting its low level APIs. We describe an example workflow for file staging over this infrastructure in order to illustrate its power.
Electroluminescence Properties of Dye-Dispersed Poly-Imide Multilayer Light Emitting Diode (Led): (I) Absorption, Photoluminescence, and Structures (1996)

Abstract In this article, the absorption and photoluminescence spectra of Alq3/ poly(ether imide)(PEI) blend films are discussed, in order to get insights on the electroluminescence properties of the Alq3-dispersed PEI multilayer LED. The structure of the Alq3-dispersed PEI films was also investigated by optical microscopy with image processor.
Ultraviolet‐C Light for Treatment ofCandida albicansBurn Infection in Mice (2011)

Burn patients are at high risk of invasive fungal infections, which are a leading cause of morbidity, mortality, and related expense exacerbated by the emergence of drug resistant fungal strains. In this study, we investigated the use of UVC light (254 nm) for the treatment of yeast Candida albicans infection in mouse third degree burns. In vitro studies demonstrated that UVC could selectively kill the pathogenic C. albicans compared with a normal mouse keratinocyte cell line in a light exposure dependent manner. A mouse model of chronic C. albicans infection in non-lethal third degree burns was developed. The C. albicans strain was stably transformed with a version of the Gaussia princeps luciferase gene that allowed real-time bioluminescence imaging of the progression of C. albicans infection. UVC treatment with a single exposure carried out on day 0 (30 min postinfection) gave an average 2.16-log(10)-unit (99.2%) loss of fungal luminescence when 2.92 J cm(-2) UVC had been delivered, while UVC 24 h postinfection gave 1.94-log(10)-unit (95.8%) reduction of fungal luminescence after 6.48 J cm(-2). Statistical analysis demonstrated that UVC treatment carried out on both day 0 and day 1 significantly reduced the fungal bioburden of infected burns. UVC was found to be superior to a topical antifungal drug, nystatin cream. UVC was tested on normal mouse skin and no gross damage was observed 24 h after 6.48 J cm(-2). DNA lesions (cyclobutane pyrimidine dimers) were observed by immunofluorescence in normal mouse skin immediately after a 6.48 J cm(-2) UVC exposure, but the lesions were extensively repaired at 24 h after UVC exposure.
SmartReality: Integrating the Web into Augmented Reality (2012)

This poster and accompanying demo shows how Semantic Web and Linked Data technologies are incorporated into an Augmented Reality platform in the SmartReality project and form the basis for enhanced Augmented Reality mobile applications in which information and content in the user's surroundings can be presented in a more meaningful and useful manner. We describe how things of interest are described semantically and linked into the Linked Open Data cloud. Relevant metadata about things is collected and processed in order to identify and retrieve related content and services on the Web. Finally, the us- er sees this information intuitively in their Smart Reality view of the reality around them.
Argininosuccinate Synthetase' Reactions by Fast Atom Bombardment Mass Spectrometry: Application to (1985)

Fast atom bombardment mass spectrometry (FAB-MS) has been used to measure positional isotope exchange rates in enzyme-catalyzed reactions. The technique has been applied to the reactions catalyzed by acetyl-coA synthetase and argininosuccinate synthetase. The FAB technique is also able to quantitatively determine the oxygen-18 or oxygen-17 content of nucleotides on as little as 10 nmol of material with no prior derivatization. Acetyl-coA synthetase has been shown by FAB-MS to catalyze the positional exchange of an oxygen-18 of ATP from the 0-nonbridge position to the &bridge position in the presence of acetate. These results are consistent with acetyl adenylate as a reactive intermediate in this reaction. Argininosuccinate synthetase was shown not to catalyze a positional isotope exchange reaction designed to test for the formation of citrulline adenylate as a reactive intermediate. Argininosuccinate synthetase was also found not to catalyze the transfer of oxygen-18 from (ureido-'80)citrulline to the a-phosphorus of ATP in the absence of added aspartate. This experiment was designed to test for the transient formation of a carbodiimide as a reactive intermediate. These results suggest that either argininosuccinate synthetase does not catalyze the formation of citrulline adenylate or the enzyme is able to completely suppress the rotation of the phosphoryl groups of PPi.
Shaping Amorphous Calcium Carbonate Films into 2D Model Substrates for Bone Cell Culture (2006)

Knochen offengelegt: Bei der Herstellung gemusterter Calciumcarbonatfilme (200–400 μm) kamen die photolithographischen Eigenschaften des Polysilan-ABA-Blockcopolymers PHEMA-PMPS-PHEMA zum Einsatz. Die Muster könnten als 2D-Modellsysteme für CaCO3-Biomaterialien dienen, an denen die Resorption von CaCO3 durch Osteoklasten und die Calciumphosphatabscheidung durch Osteoblasten unter dem optischen Mikroskop untersucht werden kann.
Mammostrat®as a tool to stratify breast cancer patients at risk of recurrence during endocrine therapy (2010)

This is the fifth independent study providing evidence that Mammostrat can act as an independent prognostic tool for ER-positive, tamoxifen-treated breast cancer. In addition, this study revealed for the first time a possible association with outcome regardless of node status and ER-negative tumors. When viewed in the context of previous results, these data provide further support for this antibody panel as an aid to patient management in early-stage breast cancer.
Native Oxide Growth on Silicon Surface in Ultrapure Water and Hydrogen Peroxide (1990)

The effects of n-type dopant (P, As) concentration in silicon (100), temperature, and oxidizing species on native oxide growth in liquid water are described. The oxide growth on phosphorus (P)- and arsenic (As)-doped n + -Si surfaces (10 20 cm -3 ) in ultrapure water exhibits saturation of oxide thickness, suggesting a field-assisted mechanism. Oxide thickness saturation was also found on n-Si in hydrogen peroxide (H 2 O 2 ) solution or in H 2 O 2 solution in the presence of a platinum (Pt) mesh that creates oxidizing radicals or ions. The oxide growth rate in ultrapure water increases with an increase of temperature.
Mediterranean Diet, Brain and Muscle: Olive Polyphenols and Resveratrol Protection in Neurodegenerative and Neuromuscular Disorders (2021)

The Mediterranean diet is worldwide recognized as a good prototype of nutrition due to the conspicuous intake of olive oil, nuts, red wine, legumes, fruit, and vegetables, all fundamental elements rich in antioxidant substances and polyphenols. Polyphenols are a wide range of phytochemicals and/or synthetic chemical compounds with proven beneficial properties for human health. In the present review, we critically summarize the wellcharacterized antioxidant and anti-inflammatory properties of polyphenols contained in the olives and extra virgin olive oil and of resveratrol, a non-flavonoid phenolic compound. We discuss the potential use of these polyphenols as pharmaceutical formulations for the treatment of human diseases. We also show the emerging importance of their consumption in the prevention and management of crucial neurodegenerative conditions (alcohol-related brain disorders and aging) and in neuromuscular disorders (Spinal Muscular Atrophy and Amyotrophic Lateral Sclerosis and Duchenne Muscular Dystrophy), where oxidative stress plays a predominant role.
Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice (2003)

KinI kinesins are important in regulating the complex dynamics of the microtubule cytoskeleton. They are unusual in that they depolymerize, rather than move along microtubules. To determine the attributes of KinIs that distinguish them from translocating kinesins, we examined the ATPase activity, microtubule affinity, and three-dimensional microtubule-bound structure of a minimal KinI motor domain. Together, the kinetic, affinity, and structural data lead to the conclusion that on binding to the microtubule lattice, KinIs release ADP and enter a stable, low-affinity, regulated state, from which they do not readily progress through the ATPase cycle. This state may favor detachment, or diffusion of the KinI to its site of action, the microtubule ends. Unlike conventional translocating kinesins, which are microtubule lattice-stimulated ATPases, it seems that with KinIs, nucleotide-mediated modulation of tubulin affinity is only possible when it is coupled to protofilament deformation. This provides an elegant mechanistic basis for their unique depolymerizing activity.
The Major Brain Cholesterol Metabolite 24(S)-Hydroxycholesterol Is a Potent Allosteric Modulator ofN-Methyl-d-Aspartate Receptors (2013)

N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels that are critical to the regulation of excitatory synaptic function in the CNS. NMDARs govern experience-dependent synaptic plasticity and have been implicated in the pathophysiology of various neuropsychiatric disorders including the cognitive deficits of schizophrenia and certain forms of autism. Certain neurosteroids modulate NMDARs experimentally but their low potency, poor selectivity, and very low brain concentrations make them poor candidates as endogenous ligands or therapeutic agents. Here we show that the major brain-derived cholesterol metabolite 24(S)-hydroxycholesterol (24(S)-HC) is a very potent, direct, and selective positive allosteric modulator of NMDARs with a mechanism that does not overlap that of other allosteric modulators. At submicromolar concentrations 24(S)-HC potentiates NMDAR-mediated EPSCs in rat hippocampal neurons but fails to affect AMPAR or GABAA receptors (GABA(A)Rs)-mediated responses. Cholesterol itself and other naturally occurring oxysterols present in brain do not modulate NMDARs at concentrations ≤10 μM. In hippocampal slices, 24(S)-HC enhances the ability of subthreshold stimuli to induce long-term potentiation (LTP). 24(S)-HC also reverses hippocampal LTP deficits induced by the NMDAR channel blocker ketamine. Finally, we show that synthetic drug-like derivatives of 24(S)-HC, which potently enhance NMDAR-mediated EPSCs and LTP, restore behavioral and cognitive deficits in rodents treated with NMDAR channel blockers. Thus, 24(S)-HC may function as an endogenous modulator of NMDARs acting at a novel oxysterol modulatory site that also represents a target for therapeutic drug development.
Spec2Fab (2013)

Multi-material 3D printing allows objects to be composed of complex, heterogenous arrangements of materials. It is often more natural to define a functional goal than to define the material composition of an object. Translating these functional requirements to fabri-cable 3D prints is still an open research problem. Recently, several specific instances of this problem have been explored (e.g., appearance or elastic deformation), but they exist as isolated, monolithic algorithms. In this paper, we propose an abstraction mechanism that simplifies the design, development, implementation, and reuse of these algorithms. Our solution relies on two new data structures: a reducer tree that efficiently parameterizes the space of material assignments and a tuner network that describes the optimization process used to compute material arrangement. We provide an application programming interface for specifying the desired object and for defining parameters for the reducer tree and tuner network . We illustrate the utility of our framework by implementing several fabrication algorithms as well as demonstrating the manufactured results.
A Facile Radiolabeling of [18F]FDPA via Spirocyclic Iodonium Ylides: Preliminary PET Imaging Studies in Preclinical Models of Neuroinflammation (2017)

A suitable TSPO PET ligand may visualize and quantify neuroinflammation in a living brain. Herein we report a <sup>18</sup>F-ligand, [<sup>18</sup>F]2 ([<sup>18</sup>F]FDPA), is radiolabeled in high yield and high specific activity based on our spirocyclic iodonium ylide (SCIDY) strategy. [<sup>18</sup>F]2 demonstrated saturable specific binding to TSPO, substantially elevated brain uptake, and slow washout of bound PET signal in the preclinical models of brain neuroinflammation (cerebral ischemia and Alzheimer's disease).
Viscosity sensing in heated alkaline zeolite synthesis media (2008)

A quartz disc resonator operating in thickness shear mode was used for the in situ monitoring of the viscosity during zeolite crystal formation.
Thermal management of telecommunication optical module in forced convection mode (2003)

Thermal management plays an important role in the design of optical modules. The main objective in the thermal design of an optical module is to minimize its size in order to have very dense packaging in the card level. This can lead to a significant increase in its heat flux. Most optical components should be maintained at a fixed temperature, therefore a thermal electrical cooler, TEC, is used to provide this feature. As a result, a detailed thermal analysis is required to define the thermal performance of these modules. In this study, a thermal model for an optical module was investigated numerically in a velocity range of 1 m/s to 4 m/s. Both laminar and turbulent models were applied to determine the temperature rise of the optical module in the transition regime. Furthermore, the present study proposed a thermal compact model. This thermal compact model can be integrated in the board level analysis to represent the detailed thermal structure of the optical module. It is concluded that the resistance network model allows faster simulations at an accuracy of 14% thereby validating the resistance network model.
Practically Deployable and Effectively Single Mode All-Solid Photonic Bandgap Fiber with Large Effective Area (2011)

We have designed and fabricated a practically deployable large effective area all-solid photonic bandgap fiber. Effectively single mode operation and 440 μm2 effective area were achieved at a 7.5 cm-bending radius.
WASP-mediated regulation of anti-inflammatory macrophages is IL-10 dependent and is critical for intestinal homeostasis (2018)

Mutations in Wiskott-Aldrich syndrome protein (WASP) cause autoimmune sequelae including colitis. Yet, how WASP mediates mucosal homeostasis is not fully understood. Here we show that WASP-mediated regulation of anti-inflammatory macrophages is critical for mucosal homeostasis and immune tolerance. The generation and function of anti-inflammatory macrophages are defective in both human and mice in the absence of WASP. Expression of WASP specifically in macrophages, but not in dendritic cells, is critical for regulation of colitis development. Importantly, transfer of WT anti-inflammatory macrophages prevents the development of colitis. DOCK8-deficient macrophages phenocopy the altered macrophage properties associated with WASP deficiency. Mechanistically, we show that both WASP and DOCK8 regulates macrophage function by modulating IL-10-dependent STAT3 phosphorylation. Overall, our study indicates that anti-inflammatory macrophage function and mucosal immune tolerance require both WASP and DOCK8, and that IL-10 signalling modulates a WASP-DOCK8 complex.
Eliminating Periodic Flush Overhead of File I/O with Non-Volatile Buffer Cache (2014)

File I/O buffer caching plays an important role to narrow the wide speed gap between main memory and secondary storage. However, data loss or inconsistency may occur if the system crashes before updated data in the buffer cache is flushed to storage. Thus, most operating systems adopt a daemon that periodically flushes dirty data to secondary storage. This periodic flush degrades the caching efficiency seriously because most write requests lead to direct storage accesses. We show that periodic flush accounts for 30-70 percent of the total write traffic to storage. To remove this inefficiency, this paper presents a new buffer cache architecture that adopts a small amount of non-volatile memory to maintain modified data. This novel buffer cache architecture removes almost all storage accesses due to periodic flush operations without any loss of reliability. It also improves the buffer cache performance through space-efficient management techniques, such as delta-write and fragment-grouping. Our experimental results show that the proposed buffer cache reduces the storage write traffic by 44.3 percent and also improves the throughput by 23.6 percent on average.
Sol-gel chemistry for nonlinear optics (1992)

Nonlinear optical materials have been synthesized via the sol-gel route. A chemical control of the reactivity of molecular precursors toward hydrolysis and condensation allows the deposition of transparent thin or thick films. Potassium titanyl phosphate (KTP) can be better synthesized from phosphoester precursors [PO(OH)<SUB>3-x</SUB>(OR)<SUB>x</SUB>] rather than phosphoric acid [PO(OH)<SUB>3</SUB>] or phosphate esters [PO(OR)<SUB>3</SUB>]. These precursors lead to crystalline transparent KTP thin films around 600 degree(s)C. Organic molecules for nonlinear optics can be embedded into an oxide sol-gel matrix. Second harmonic generation has been obtained after poling with thick films in which organic chromophores are chemically bonded to the oxide backbone via the use of functionalized silicon alkoxide precursors.