gebhart/patrepeval huggingface dataset:
Morpholine Derivatives Greatly Enhance the Selectivity of Mammalian Target of Rapamycin (mTOR) Inhibitors (2009)

Dramatic improvements in mTOR-targeting selectivity were achieved by replacing morpholine in pyrazolopyrimidine inhibitors with bridged morpholines. Analogues with subnanomolar mTOR IC(50) values and up to 26000-fold selectivity versus PI3Kalpha were prepared. Chiral morpholines gave inhibitors whose enantiomers had different selectivity and potency profiles. Molecular modeling suggests that a single amino acid difference between PI3K and mTOR (Phe961Leu) accounts for the profound selectivity seen by creating a deeper pocket in mTOR that can accommodate bridged morpholines.
Nomenclature of Natural Orifice Translumenal Endoscopic Surgery (NOTES ™ ) and Laparoendoscopic Single-Site Surgery (LESS) Procedures in Urology (2008)

Standardization of the nomenclature applied to natural orifice transluminal endoscopic surgery (NOTES) and laparo-endoscopic single-site surgery (LESS) is essential as the body of literature continues to grow in order to allow clear and precise scientific communication. As the techniques continue to evolve, we propose that NOTES and LESS be designated as the common terms to define these new procedures in urology.
Crystal Structure of the Intermediate Na2V2(PO4)3 Phase and Electrochemical Reaction Mechanisms in NaxV2(PO4)3 (1 ≤ x ≤ 4) System (2021)

The Na-superionic-conductor (NASICON) Na3V2(PO4)3 is an important positive electrode material for Na-ion batteries. Here, we investigate the mechanisms of phase transition in NaxV2(PO4)3 (1 ≤ x ≤ 4) upon a non-equilibrium battery cycling. Unlike the widely believed two-phase reaction in Na3V2(PO4)3 – Na1V2(PO4)3 system, we determine a new intermediate Na2V2(PO4)3 phase using operando synchrotron X-ray diffraction. Density functional theory calculations further support the existence of the Na2V2(PO4)3 phase. We propose for the first time two possible crystal structures of Na2V2(PO4)3 analyzed by Rietveld refinement. The two structure models with the space groups P21/c or P2/c for the new intermediate Na2V2(PO4)3 phase show similar unit cell parameters but different atomic arrangements, including a vanadium charge ordering. As the appearance of the intermediate Na2V2(PO4)3 phase is accompanied by symmetry reduction, Na(1) and Na(2) sites split into several positions in Na2V2(PO4)3, in which one of the splitting Na(2) position is found to be a vacancy whereas the Na(1) positions are almost fully filled. The intermediate Na2V2(PO4)3 phase reduces the lattice mismatch between Na3V2(PO4)3 and Na1V2(PO4)3 phases facilitating a fast phase transition. This work paves the way for a better understanding of great rate capabilities of Na3V2(PO4)3.
The pursuit of tens of gigabits per second wireless systems [Industry Perspectives] (2013)

More than any time ever before, today technology has a significant impact on people's lives. The proliferation of slim, mobile, and portable devices such as notebooks, ultrabooks, tablets, and smartphones is a clear testament to the importance of computing and communication in modern society. In the particular case of wireless systems, this explosive growth has led to an insatiable need to constantly boost capacity so that innovative uses can be offered to consumers. This vicious cycle has brought to market many innovative wireless solutions including the IEEE 802.11 family of standards, third generation (3G), and fourth generation (4G), to name a few. When it comes to wireless systems with data rates greater than 1 Gb/s at a few meters, the most notable examples include the IEEE 802.11ac and IEEE 802.11ad amendments to the base IEEE 802.11 standard [2], with key parameters summarized in Table 1. Several companies have announced products implementing these technologies, with a few of those products already available, or soon to be available, to consumers. The data rates offered by IEEE 802.11ac and IEEE 802.11ad can meet the needs of many applications, with replacement of wired digital interface (WDI) cables arguably the most prominent new use of these technologies. This includes replacing WDI cables used between a notebook/tablet/smartphone and certain display (e.g., HDMI, DisplayPort) and IO (e.g., USB) devices, thereby enabling a fully wireless user experience [4].
Profit-Driven User Association and Smart Grid Energy Transfer in Green Cellular Networks (2019)

On-grid brown energy consumption of cellular infrastructure is contributing to the detrimental impact on the environment, among which base stations (BSs) are guzzling the largest amount of energy in powering the cellular infrastructure. Leveraging green (renewable) energy to power cellular BSs is a radical energy solution. However, in order to minimize the consumption of on-grid brown energy, most related researches focus on maximizing the utilization of green energy in cellular BSs while compromising the user quality of service (QoS). In this paper, we jointly consider the network QoS and green energy utilization in the dual-battery architecture enabled green cellular network. The profit-driven user association and smart grid green energy transfer scheme is proposed to benefit the network providers, in which, some heuristics are further developed to reduce the computational complexity, as the profit-driven user association problem is NP-hard. Extensive simulations have been conducted to validate the proposed scheme. The systematic analysis of this work can serve as a benchmark for greening other information and communication technology infrastructures.
A new Vegetation Integrity metric for trading losses and gains in terrestrial biodiversity value (2021)

The Vegetation Integrity metric has been designed within a clear management and decision-making context: to quantify losses and predict gains in terrestrial biodiversity value at development and offset sites. The metric incorporates a number of key developments that differentiate it from others. Firstly, the intent is explicitly defined and therefore falsifiable: scores have a positive relationship with the species richness and/or abundance of native plants and animals at sites within the same vegetation type. This relationship is posited because the metric is constructed from a practical set of habitat attributes representative of biodiversity composition, structure and function with known relationships with species occurrence. Secondly, the quantitative features of the metric improve both its practical and theoretical properties. These features include: normalisation of attribute scores by reference to best-on-offer benchmarks that account for inherent differences in attribute abundance among vegetation types; dynamic weighting of attributes to accommodate differences in relative abundance of attributes within vegetation types; attribute scoring using a non-linear continuous function to better represent metric intent and avoid exacerbation of measurement error; and aggregation of composition, structure and function scores using the geometric mean to reduce substitution effects. Thirdly, the prediction of gain in biodiversity value at offset sites is explicit with: attribute-specific probabilistic estimates of reaching best-on-offer benchmark status over 20 years with the management of threats and pressures (assisted natural regeneration); modification of these estimates based on expected site resilience, competition from invasive non-native plants and connectivity to the surrounding landscape; and where appropriate, additional risk-adjusted estimates of gain arising from the reintroduction of missing plant species or other habitat attributes (active restoration). In the absence of active restoration, the design of the Vegetation Integrity metric favours biodiversity offset sites with moderate Vegetation Integrity scores. Early evaluation of sites assessed under the Biodiversity Conservation Act 2016 suggest that offset sites are dominated by areas with moderate scores which is consistent with the intent of improving biodiversity value rather than averting future losses. Although developed within the Australian context, the new Vegetation Integrity metric has general appeal to robust, transparent and practical quantification of terrestrial biodiversity value elsewhere.
A Delay-Locked Loop Synchronization Scheme for High-Frequency Multiphase Hysteretic DC-DC Converters (2009)

This paper reports a delay-locked loop (DLL) based hysteretic controller for high-frequency multiphase dc-dc buck converters. The DLL control loop employs the switching frequency of a hysteretic comparator as reference to automatically synchronize the remaining phases and eliminate the need for external synchronization. A dedicated duty cycle control loop is used to enable current sharing and ripple cancellation. We demonstrate a four-phase high-frequency buck converter that operates at 25-70 MHz with fast hysteretic control and output conversion range of 17.5%-80%. The converter achieves an efficiency of 83% at 2 W and 80% at 3.3 W. The circuit has been implemented in standard 0.5 mum 5 V CMOS process.
Microstructures and Magnetic Properties of FePt Thin Films on TiON Intermediate Layer (2014)

The microstructures and magnetic properties of FePt(-SiOx-C) thin films grown on TiON and TiON/TiN intermediate layers were studied. TiON possessed smaller surface energy and smaller lattice constant than TiN. With increasing TiOx doping concentration, FePt grain shape changed from semi-spherical to square and grain size was significantly reduced. Meanwhile, good perpendicular magnetic anisotropy was retained, indicating that TiON intermediate layer could achieve a good balance between island growth and epitaxial growth. Furthermore, using TiON/TiN combined intermediate layer, FePt grain size was further reduced and the opening-up of in-plane M-H loop diminished. With 45 vol.% SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> -25 vol.% C doping, well-isolated FePt grains with an average size as small as 5.7 nm and the grain size distribution of 0.9 nm were achieved. It also exhibited good perpendicular magnetic anisotropy with an out-of-plane coercivity of 18 kOe.
Metabolic alterations associated with the antidiabetic effect of beta 3-adrenergic receptor agonists in obese mice (1995)

Treatment of obese (ob/ob) mice with the beta 3-adrenergic receptor (beta 3-AR) agonist BRL-35135 (1 mg.kg body wt-1.day-1 for 20 days) normalized plasma glucose levels and significantly decreased plasma insulin and nonesterified fatty acid levels. The time frame for the hypoglycemic effect, which reached a maximum after 10 days of treatment, paralleled an increase in brown adipose tissue DNA and protein content. The basal level of mRNA for the beta 3-AR and mitochondrial uncoupling protein was found to be markedly decreased in the ob/ob animals relative to the lean group. Chronic treatment of ob/ob mice for 20 days resulted in a twofold increase in beta 3-AR mRNA and a fivefold increase in uncoupling protein mRNA in brown adipose tissue relative to the placebo group. These findings indicate that chronic treatment of ob/ob animals with a beta 3-AR agonist results in proliferation of brown adipose tissue, with an upregulation of the beta 3-AR, which is associated with a decrease in plasma glucose, insulin, and nonesterified fatty acid levels.
Per-channel regularization for regression-based spectral reconstruction (2020)

Spectral reconstruction algorithms seek to recover spectra from RGB images. This estimation problem is often formulated as least-squares regression, and a Tikhonov regularization is generally incorporated, both to support stable estimation in the presence of noise and to prevent over-fitting. The degree of regularization is controlled by a single penalty-term parameter, which is often selected using the cross validation experimental methodology. In this paper, we generalize the simple regularization approach to admit a per-spectral-channel optimization setting, and a modified cross-validation procedure is developed. Experiments validate our method. Compared to the conventional regularization, our per-channel approach significantly improves the reconstruction accuracy at multiple spectral channels, by up to 17% increments for all the considered models.
Macro- to nanoscale wear prevention via molecular adsorption. (2007)

As the size of mechanical systems shrinks from macro- to nanoscales, surface phenomena such as adhesion, friction, and wear become increasingly significant. This paper demonstrates the use of alcohol adsorption as a means of continuously replenishing the lubricating layer on the working device surfaces and elucidates the tribochemical reaction products formed in the sliding contact region. Friction and wear of native silicon oxide were studied over a wide range of length scales from macro- to nanoscales using a ball-on-flat tribometer (millimeter scale), sidewall microelectromechanical system (MEMS) tribometer (micrometer scale), and atomic force microscopy (nanometer scale). In all cases, the alcohol vapor adsorption successfully lubricated and prevented wear. Imaging time-of-flight secondary ion mass spectrometry analysis of the sliding contact region revealed that high molecular weight oligomeric species were formed via tribochemical reactions of the adsorbed linear alcohol molecules. These tribochemical products seemed to enhance the lubrication and wear prevention. In the case of sidewall MEMS tests, the lifetime of the MEMS device was radically increased via vapor-phase lubrication with alcohol.
Short-term Result of Revision Total Hip Arthroplasty (2004)

The purpose of present study is to report the short-term results of revision total hip arthroplasty (revision THA) without cement. Thirty-four hips of 33 patients who underwent revision THA from September 1998 to August 2002 and who could be followed up for one year or more were enrolled in the study. There were six men seven hips and 27 female 27 hips, and mean age was 73 years. In AAOS classification, Type 2 was eight hips and Type 3 was 26 hips. The average full weight bearing time was 8 days. Only one hip was movement of acetabular component and required re-operation. Initial fixation in acetabular enabled early full weight bearing and early social rehabilitation.
Electrodeposition Fueled by Newman and Tobias (2010)

In 1962, Newman and Tobias described the current distribution in a porous electrode, presenting equations in a general form with Butler-Volmer kinetics, the three modes of transport: diffusion, migration, and convection, and the equation of conservation of charge (J. Newman and C. W. Tobias, J. Electrochem. Soc., 109, 1183 (1962); doi: 10.1149/1.2425269). The paper itself and the impact of this work in the following years are reviewed. To date, many of the electrodeposition current distribution models are based on the themes presented by Newman and Tobias and those fundamentals will help the electrodeposition community in its future growth.
Double‐Side Co‐Catalytic Activation of Anodic TiO2 Nanotube Membranes with Sputter‐Coated Pt for Photocatalytic H2 Generation from Water/Methanol Mixtures (2016)

Self-standing TiO<sub>2</sub> nanotube layers in the form of membranes are fabricated by self-organizing anodization of Ti metal and a potential shock technique. The membranes are then decorated by sputtering different Pt amounts i) only at the top, ii) only at the bottom or iii) at both top and bottom of the tube layers. The Pt-decorated membranes are transferred either in tube top-up or in tube top-down configuration onto FTO slides and are investigated, after crystallization, as photocatalysts for H<sub>2</sub> generation using either front or back-side light irradiation. Double-side Pt-decoration of the tube membranes leads to higher H<sub>2</sub> generation rates (independently of tube and light-irradiation configuration) compared to membranes decorated at only one side with similar overall Pt amounts. The results suggest that this effect cannot be only ascribed to the overall amount of Pt co-catalyst as such but also to its distribution at both tube extremities. This leads to optimized light absorption and electron diffusion/transfer dynamics: the central part of the membranes acts as light-harvesting zone and electrons therein generated can diffuse towards the Pt/TiO<sub>2</sub> active zones (tube extremities) where they can react with the environment and generate H<sub>2</sub> .
ViKY Robotic Scope Holder: Initial Clinical Experience and Preliminary Results Using Instrument Tracking (2010)

Robotic endoscope holders constitute an alternative to complete telesurgery systems, by offering a “third hand” to the surgeon during a laparoscopic procedure. ViKY robotic scope holder (Endocontrol, Grenoble, France) is a lightweight, sterilizable body-mounted robot with 3 DOF. In this paper, we present the specifics of this robot, the newly developed XL version dedicated to single-port surgery and the initial clinical experience. We have proposed a method to control the robot, based on the detection and tracking of surgical instrument from image analysis and shape priors, to enrich the interaction between the surgeon and the robot. We present here, our work in progress toward its integration into a probabilistic framework, with the aim of improving the method's speed and robustness. We also present the surgeons’ viewpoints on the feasibility of its integration into the operating theater.
Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia (2009)

Epigenetic alterations, including gain or loss of DNA methylation, are a hallmark of nearly every malignancy. Changes in DNA methylation can impact expression of cancer-related genes including apoptosis regulators and tumor suppressors. Because such epigenetic changes are reversible, they are being aggressively investigated as potential therapeutic targets. Here we use the Emu-TCL1 transgenic mouse model of chronic lymphocytic leukemia (CLL) to determine the timing and patterns of aberrant DNA methylation, and to investigate the mechanisms that lead to aberrant DNA methylation. We show that CLL cells from Emu-TCL1 mice at various stages recapitulate epigenetic alterations seen in human CLL. Aberrant methylation of promoter sequences is observed as early as 3 months of age in these animals, well before disease onset. Abnormally methylated promoter regions include binding sites for the transcription factor FOXD3. We show that loss of Foxd3 expression due to an NF-kappaB p50/p50:HDAC1 repressor complex occurs in TCL1-positive B cells before methylation. Therefore, specific transcriptional repression is an early event leading to epigenetic silencing of target genes in murine and human CLL. These results provide strong rationale for the development of strategies to target NF-kappaB components in CLL and potentially other B-cell malignancies.
Delivery of Active Collagenase to Skin Using a Lorentz-Force Actuated Needle-Free Injector (2006)

The development of new therapeutics and the desire to reduce the frequency of needle stick injuries, overcome the improper reuse of needles, improve compliance, and reduce the prohibitive cost of disposal have fueled resurgent efforts to develop alternative drug delivery methods. This report discusses the use of a controllable Lorentz-force actuated needle-free injector to deliver a blend of bacterial collagenases to the skin. Drug ejected/injected using a preprogrammed pressure vs time profile through a 100 or 200 microm orifice showed activity comparable to that observed following ejection/injection using a conventional syringe as determined by a solution based fluorescence assay and zymography. In a live animal trial, necrosis, hair loss, and minimal bruising were observed at drug injected sites regardless of the delivery mode as were changes in tissue morphology.
306 IN VITRO CARDIOMYOGENIC AND NEUROGENIC DIFFERENTIATION OF MINIPIG BONE MARROW MESENCHYMAL STEM CELLS (2010)

Differentiation of mesenchymal stem cells (MSC) into specialised cells in vitro before transplantation may improve the engraftment efficiency of the transplanted cells as well as the safety and efficacy of treatment. To understand the differentiation process and the functional identities of cells in an animal model, we examined the in vitro differentiation capacity of porcine MSC (3–6 passage) into cardiomyocyte-like and neuron-like cells. The MSC isolated from the bone marrow of postnatal miniature piglets [T-type, PWG Micro-pig (R), PWG Genetics, Korea] exhibited a typical fibroblast-like morphology and expressed the specific markers, such as CD29, CD44, and CD90. After 21 days of culture in induction media, MSC revealed the appropriate phenotype of osteocytes (von Kossa and Alizarin red), adipocytes (Oil red O), and chondrocytes (Alcian blue). Ther MSC were further induced into cardiomyogenic and neurogenic differentiation following the protocols described earlier (Tomita et al. 2002 J. Thorac. Cardiovasc. Surg. 123, 1132–1140) and (Woodbury et al. 2002 J. Neurosci. Res. 96, 908–917), respectively, with minor modifications. Expression of lineage-specific markers was evaluated by immunocytochemistry, and RT-PCR and quantitative PCR (RT-qPCR). For cardiomyogenic differentiation, MSC were stimulated with 10 µM 5-azacytidine for 24 h, 3 days, or 7 days, and the cells were maintained in culture for 21 days. Upon induction, MSC exhibited elongated and stick-like morphology with extended cytoplasmic processes, and toward the end of culture, cells formed aggregates and myotube-like structures. Immunostaining was positive for the markers of cardiomyocyte-like cells, such as a-smooth muscle actin, cardiac troponin T, desmin, and a-cardiac actin. The RT-PCR and RT-qPCR analysis showed the expression and a time dependent up-regulation of cardiac troponin T, desmin, a-cardiac actin, and ß-myosin heavy chain genes. Following induction with neuronal-specific media for 3 days, above 80% of MSC acquired the morphology of neuron-like cells with bi- or multipolar cell processes forming a network-like structure. Induced cells with neuronal phenotype were positively stained for nestin, neuronal nuclei (NeuN), glial fibrillary acidic protein (GFAP), and neurofilament-M (NF-M). The expression of neural transcripts, such as nestin, GFAP, and NF-M, was further confirmed by RT-PCR and RT-qPCR. In conclusion, our results showed the potential of porcine MSC to differentiate in vitro into cardiomyocyte-like and neuron-like cells, thus offering a useful model for studying their functional and molecular properties before transplantation. This work was supported by Basic Science Research Program through the National Research Foundation (NRF) funded by the Ministry of Education, Science and Technology (2010-0010528) and BioGreen 21 (20070301034040), Republic of Korea.
High-Confidence Interactome for RNF41 Built on Multiple Orthogonal Assays (2018)

Ring finger protein 41 (RNF41) is an E3 ubiquitin ligase involved in the ubiquitination and degradation of many proteins including ErbB3 receptors, BIRC6, and parkin. Next to this, RNF41 regulates the intracellular trafficking of certain JAK2-associated cytokine receptors by ubiquitinating and suppressing USP8, which, in turn, destabilizes the ESCRT-0 complex. To further elucidate the function of RNF41 we used different orthogonal approaches to reveal the RNF41 protein complex: affinity purification-mass spectrometry, BioID, and Virotrap. We combined these results with known data sets for RNF41 obtained with microarray MAPPIT and Y2H screens. This way, we establish a comprehensive high-resolution interactome network comprising 175 candidate protein partners. To remove potential methodological artifacts from this network, we distilled the data into a high-confidence interactome map by retaining a total of 19 protein hits identified in two or more of the orthogonal methods. AP2S1, a novel RNF41 interaction partner, was selected from this high-confidence interactome for further functional validation. We reveal a role for AP2S1 in leptin and LIF receptor signaling and show that RNF41 stabilizes and relocates AP2S1.