gebhart/patrepeval huggingface dataset:
Phase Discrimination through Oxidant Selection in Low-Temperature Atomic Layer Deposition of Crystalline Iron Oxides (2013)

Control over the oxidation state and crystalline phase of thin-film iron oxides was achieved by low-temperature atomic layer deposition (ALD), utilizing a novel iron precursor, bis(2,4-methylpentadienyl)iron. This low-temperature (T = 120 °C) route to conformal deposition of crystalline Fe3O4 or α-Fe2O3 thin films is determined by the choice of oxygen source selected for the second surface half-reaction. The approach employs ozone to produce fully oxidized α-Fe2O3 or a milder oxidant, H2O2, to generate the Fe(2+)/Fe(3+) spinel, Fe3O4. Both processes show self-limiting surface reactions and deposition rates of at least 0.6 Å/cycle, a significantly high growth rate at such mild conditions. We utilized this process to prepare conformal iron oxide thin films on a porous framework, for which α-Fe2O3 is active for photocatalytic water splitting.
A class of throughput optimal routing policies (2010)

This paper considers the problem of routing packets across a multi-hop wireless network while ensuring throughput optimality. One of the main challenges in the design of throughput optimal routing policies is identifying an appropriate Lyapunov function with negative expected drift. The only known throughput optimal routing policies in the literature, most notably backpressure routing, are constructed using simple node-based quadratic or exponential Lyapunov functions of the queue backlogs and as such exhibit poor delay performance under many network topologies and traffic conditions. By constructing a class of continuous, differentiable, and piece-wise quadratic Lyapunov functions, this paper provides a large class of throughput optimal routing policies. The nature of the proposed Lyapunov functions is such that, under a “sufficiently unbalanced” backlog state, the traffic must be routed away from nodes with significantly large backlogs (consistent with backpressure) in order to ensure a negative expected drift. In contrast, under all other backlog states, any non-idling policy can ensure a negative expected drift in the proposed Lyapunov function, providing tremendous flexibility in controlling routing decisions for most of the state-space.
A Multiprotein Complex That Mediates Translational Enhancement in Drosophila (2007)

Modulating the efficiency of translation plays an important role in a wide variety of cellular processes and is often mediated by trans-acting factors that interact with cis-acting sequences within the mRNA. Here we show that a cis-acting element, the Hsp83 degradation element (HDE), within the 3'-untranslated region of the Drosophila Hsp83 mRNA functions as a translational enhancer. We show that this element is bound by a multiprotein complex, and we identify components using a novel affinity-based method called tandem RNA affinity purification tagging. Three proteins (DDP1, Hrp48, and poly(A)-binding protein) are components of the HDE-binding complex and function in translational enhancement. Our data support a model whereby the HDE is composed of several cis-acting subelements that represent binding sites for trans-acting factors, and the combined action of these trans-acting factors underlies the ability of the HDE to stimulate translation.
Novel Structure Elucidation of AAL Toxin TA Backbone (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel Structure Elucidation of AAL Toxin TA BackboneCraig D. Boyle, Jean-Christophe Harmange, and Yoshito KishiCite this: J. Am. Chem. Soc. 1994, 116, 11, 4995–4996Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/ja00090a058https://doi.org/10.1021/ja00090a058research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations50LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Noisy Blackbox Optimization with Multi-Fidelity Queries: A Tree Search Approach (2018)

We study the problem of black-box optimization of a noisy function in the presence of low-cost approximations or fidelities, which is motivated by problems like hyper-parameter tuning. In hyper-parameter tuning evaluating the black-box function at a point involves training a learning algorithm on a large data-set at a particular hyper-parameter and evaluating the validation error. Even a single such evaluation can be prohibitively expensive. Therefore, it is beneficial to use low-cost approximations, like training the learning algorithm on a sub-sampled version of the whole data-set. These low-cost approximations/fidelities can however provide a biased and noisy estimate of the function value. In this work, we incorporate the multi-fidelity setup in the powerful framework of noisy black-box optimization through tree-like hierarchical partitions. We propose a multi-fidelity bandit based tree-search algorithm for the problem and provide simple regret bounds for our algorithm. Finally, we validate the performance of our algorithm on real and synthetic datasets, where it outperforms several benchmarks.
Activation of MAPK Signaling by CXCR7 Leads to Enzalutamide Resistance in Prostate Cancer (2019)

Castration-resistant prostate cancer (CRPC) that has developed resistance to the new-generation androgen receptor (AR) antagonist enzalutamide is a lethal disease. Transcriptome analysis of multiple prostate cancer models identified CXCR7, an atypical chemokine receptor, as one of the most upregulated genes in enzalutamide-resistant cells. AR directly repressed <i>CXCR7</i> by binding to an enhancer 110 kb downstream of the gene and expression was restored upon androgen deprivation. We demonstrate that CXCR7 is a critical regulator of prostate cancer sensitivity to enzalutamide and is required for CRPC growth <i>in vitro</i> and <i>in vivo</i>. Elevated CXCR7 activated MAPK/ERK signaling through ligand-independent, but β-arrestin 2-dependent mechanisms. Examination of patient specimens showed that CXCR7 and pERK levels increased significantly from localized prostate cancer to CRPC and further upon enzalutamide resistance. Preclinical studies revealed remarkable efficacies of MAPK/ERK inhibitors in suppressing enzalutamide-resistant prostate cancer. Overall, these results indicate that CXCR7 may serve as a biomarker of resistant disease in patients with prostate cancer and that disruption of CXCR7 signaling may be an effective strategy to overcome resistance. SIGNIFICANCE: These findings identify CXCR7-mediated MAPK activation as a mechanism of resistance to second-generation antiandrogen therapy, highlighting the therapeutic potential of MAPK/ERK inhibitors in CRPC.
Identification of missed pulmonary nodules on low-dose CT lung cancer screening studies using an automatic detection system (2003)

Multi-slice CT (MSCT) scanners allow nodules as small as 3mm to be identified during screening. However the associated large data sets make it challenging for radiologists to identify all small nodules in a reasonable amount of time. Computer-aided detection may play a critical role in identifying missed nodules. 13 MSCT screening studies, initially interpreted as "non-actionable" by a radiologist, were selected from participants in a lung cancer screening study. The study protocol defines "actionable" studies as those containing at least 1 solid non-calcified nodule larger than 3mm, for which follow-up studies are recommended to exclude interval growth. An automatic detection algorithm was applied to the 13 studies to determine whether it might detect missed nodules, and whether any of these were of sufficient size to be considered "actionable". There were a total of 138 automatically detected candidate nodules, an average of 10.6 per patient. 83 candidates were characterized as true positives, yielding a positive predictive value of 60.1%. 10 automatically detected candidates were judged to be actionable nodules greater than 3mm in diameter. 6 of 13 (46%) patients had at least one "actionable" finding detected by the computer that had been overlooked in the initial exam.
Total Hip Arthroplasty Dislocation after Cardioversion: A Case Report. (2017)

New onset postoperative atrial fibrillation (AF) is the most common perioperative arrhythmia in the elderly. The incidence after total joint arthroplasty is much lower than other non-cardiac surgeries. Since postoperative atrial fibrillation can cause increased length of hospital stay, mortality, and healthcare costs, it is critical to focus on prevention and prompt management. New onset atrial fibrillation is treated with rhythm control for patients who demonstrate hemodynamic instability or refractory to rate control measures. Electrical cardioversion is an effective option for unstable patients with known complications. However, there is limited data on orthopedic problems after cardioversion. A unique case is reported presenting postoperative total hip arthroplasty (THA) dislocation after electrical cardioversion for new onset atrial fibrillation in the postanesthesia care unit (PACU).
Two members of a distinct subfamily of 5-hydroxytryptamine receptors differentially expressed in rat brain. (1993)

We report two serotonin (5-hydroxytryptamine, 5-HT) receptors, MR22 and REC17, that belong to the G-protein-associated receptor superfamily. MR22 and REC17 are 371 and 357 amino acids long, respectively, as deduced from nucleotide sequence and share 68% mutual amino acid identity and 30-35% identity with known catecholamine and 5-HT receptors. Saturable binding of 125I-labeled (+)-lysergic acid diethylamide to transiently expressed MR22 in COS-M6 cells was inhibited by ergotamine > methiothepin > 5-carboxamidotryptamine > 5-HT. For REC17, the rank of potency was ergotamine > 5-carboxamidotryptamine > methiothepin > methysergide > 5-HT. Both were insensitive to 5-HT1A, 5-HT1D or 5-HT2 serotonergic ligands [8-hydroxy-2-(di-n-propylamino)tetralin, sumatriptan, and 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane]. The mRNAs encoding MR22 were detected in the CA1 region of hippocampus, the medial habenula, and raphe nuclei. In contrast, mRNAs encoding REC17 were found throughout the rat central nervous system. We propose that REC17 and MR22, designated as 5-HT5 alpha and 5-HT5 beta, represent a distinct subfamily of 5-HT receptors.
Avian Bursal Lymphocytes Apoptosis is prevented by HIV-1 Tat gene expression (1994)

International audience
On changing the shape of ASIC based fully balanced analog system design (2002)

Two new and general methods of a fully balanced (FB) analog system design, which contribute towards achieving both a great reduction of the design time and a high performance system "implementation" are presented. It is shown that a single-ended system based on any type of op amps (rail-to-rail, constant g/sub m/, etc.), realized in any technology (CMOS, bilpolar, BiCMOS, GaAs), can be easily and effectively converted to its FB counterpart in a very practical way. Using the proposed rules, any FB system implementation with op amps (data converter, modulator, filter, etc.) requires only a single-ended system version design and the drawbacks related to a conventional FB system design are avoided. A final schematic/layout of a FB system can be achieved by pattern modification only of double single-ended system schematics/layouts, which are now available in the ASIC libraries of many companies.
Power Optimized PA Clipping for MIMO-OFDM Systems (2011)

For a multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) system that is being pushed into power amplifier (PA) saturation, this letter investigates power-optimized PA clipping. Our goal is to identify the optimum clipping level for a MIMO-OFDM system that delivers the desired bit error rate (BER) with minimum power consumption in the PA. We present a complete theoretical framework resulting in an analytical expression for the BER of a MIMO-OFDM system subject to PA clipping. PA power saving is addressed by the total degradation metric, which shows that as much as 6dB power reduction can be achieved by proper choice of the clipping level.
Prism adaptation and spatial neglect: the need for dose-finding studies (2015)

Spatial neglect is a devastating disorder in 50-70% of right-brain stroke survivors, who have problems attending to, or making movements towards, left-sided stimuli, and experience a high risk of chronic dependence. Prism adaptation is a promising treatment for neglect that involves brief, daily visuo-motor training sessions while wearing optical prisms. Its benefits extend to functional behaviors such as dressing, with effects lasting 6 months or longer. Because one to two sessions of prism adaptation induce adaptive changes in both spatial-motor behavior (Fortis et al., 2011) and brain function (Saj et al., 2013), it is possible stroke patients may benefit from treatment periods shorter than the standard, intensive protocol of ten sessions over two weeks-a protocol that is impractical for either US inpatient or outpatient rehabilitation. Demonstrating the effectiveness of a lower dose will maximize the availability of neglect treatment. We present preliminary data suggesting that four to six sessions of prism treatment may induce a large treatment effect, maintained three to four weeks post-treatment. We call for a systematic, randomized clinical trial to establish the minimal effective dose suitable for stroke intervention.
Feasibility of simultaneous temperature and tissue stiffness detection by MRE (2006)

Temperature and tissue stiffness are two indices that can be used to monitor MRI-guided focused ultrasound thermal therapy. It would be beneficial to have both measures available to monitor treatment progression during thermal therapy. MR Elastography (MRE) has already been shown to provide tissue stiffness information; the purpose of this work is to demonstrate how temperature can be derived from the same MRE data acquisition. MRE data were acquired from 1.5% agarose phantoms and ex vivo porcine muscle tissue (from a grocery store) while they were heated slowly. The temperatures were measured using a fluorescent thermometer. The phase average from the MRE acquisition was used to calculate the phase shift induced by the proton resonance frequency shift associated with the temperature change. The results show that the phase shift due to temperature extracted from MRE data correlate well with the temperature change recorded by thermometer, yielding a temperature coefficient of -0.0096 ppm/ degrees C for the agarose phantom, and -0.0103 ppm/ degrees C for the ex vivo porcine tissue. These results indicate that it is possible to simultaneously measure both temperature and tissue shear stiffness using a new method of MRE data reconstruction.
Cladding pumped Yb-doped HOM power amplifier with high gain (2018)

Higher-order mode (HOM) fibers have been engineered to allow propagation of linearly polarized symmetric modes LP<sub>0,N</sub> in a robust way. Compared with the fundamental mode LP(0,1), HOMs exhibits an effective area that can be larger by over two order magnitude, and thus propagating light in these modes could greatly suppress the effect of nonlinear effects. HOM fibers could also be doped with rare earth ions in order to amplify light propagating in these modes, which offers the enormous potential for generating high-intensity pulses. Excitation of HOM gain fiber using cladding pumping with multimode pump source is attractive for ytterbium based amplifiers, because of the availability of low-cost multimode pump diodes in the 975nm wavelength range. One problem associated with cladding pumping which leads to excitation of the large doped core (over 100 &mu;m diameter) is that it could result in a large amount of amplifiedspontaneous- emission (ASE) noise, particularly when the input signal is weak. Optimization of amplifier design is critical in order to suppress ASE and achieve high gain and pump-to-signal conversion efficiency. We conducted numerical modeling of a cladding pumped HOM-amplifier, which revealed that this problem could be mitigated by using a relatively long gain-fiber that allowed reabsorption of the forward propagating ASE resulting in a further amplification of the signal. We demonstrate efficient amplification of a LP<sub>0,10</sub> mode with an effective area 3140&mu;m<sup>2</sup> in an Yb-doped HOM amplifier cladding pumped at 975nm. We have successfully obtained a 20.2dB gain for 0.95 W 1064 nm input seed signal to more than 105W.
Localization of the Insulin-like Growth Factor I Receptor Binding Sites for the SH2 Domain Proteins p85, Syp, and GTPase Activating Protein (1995)

Potential signaling substrates for the insulin-like growth factor I (IGF-I) receptor are SH2 domain proteins including the p85 subunit of phosphatidylinositol 3-kinase, the tyrosine phosphatase Syp, GTPase activating protein (GAP), and phospholipase C-gamma (PLC-gamma). In this study, we demonstrate an association between the IGF-I receptor and p85, Syp, and GAP, but not with PLC-gamma in lysates of cells overexpressing the human IGF-I receptor. We further investigated these interactions using glutathione S-transferase (GST) fusion proteins containing the amino-terminal SH2 domains of p85 or GAP, or both SH2 domains of Syp or PLC-gamma to precipitate the IGF-I receptor from purified receptor preparations and from whole cell lysates. p85-, Syp-, and GAP-GSTs precipitated the IGF-I receptor, whereas the PLC-gamma-GST did not. Using phosphopeptides corresponding to IGF-I receptor phosphorylation sites, we determined that the p85- and Syp-GST association with the IGF-I receptor could be inhibited by a carboxyl-terminal peptide containing pY1316 and that the GAP-GST association could be inhibited by a NPXY domain peptide. The GAP-GST binding site was confirmed by showing that a mutant IGF-I receptor with a deletion of the NPXY domain including tyrosine 950 was poorly precipitated by the GAP-GST. We conclude that p85 and Syp may bind directly to the IGF-I receptor at tyrosine 1316, and that GAP may bind to the IGF-I receptor at and PLC-gamma was not evident. p85, Syp, and GAP are potential modulators of IGF-I receptor signal transduction.
Preclinical Studies in the mdx Mouse Model of Duchenne Muscular Dystrophy with the Histone Deacetylase Inhibitor Givinostat (2013)

Previous work has established the existence of dystrophin-nitric oxide (NO) signaling to histone deacetylases (HDACs) that is deregulated in dystrophic muscles. As such, pharmacological interventions that target HDACs (that is, HDAC inhibitors) are of potential therapeutic interest for the treatment of muscular dystrophies. In this study, we explored the effectiveness of long-term treatment with different doses of the HDAC inhibitor givinostat in mdx mice--the mouse model of Duchenne muscular dystrophy (DMD). This study identified an efficacy for recovering functional and histological parameters within a window between 5 and 10 mg/kg/d of givinostat, with evident reduction of the beneficial effects with 1 mg/kg/d dosage. The long-term (3.5 months) exposure of 1.5-month-old mdx mice to optimal concentrations of givinostat promoted the formation of muscles with increased cross-sectional area and reduced fibrotic scars and fatty infiltration, leading to an overall improvement of endurance performance in treadmill tests and increased membrane stability. Interestingly, a reduced inflammatory infiltrate was observed in muscles of mdx mice exposed to 5 and 10 mg/kg/d of givinostat. A parallel pharmacokinetic/pharmacodynamic analysis confirmed the relationship between the effective doses of givinostat and the drug distribution in muscles and blood of treated mice. These findings provide the preclinical basis for an immediate translation of givinostat into clinical studies with DMD patients.
Impact of negative sequence current injection by wind power plants (2013)

This paper presents an analysis of the impact from negative sequence current injection by wind power plants in power systems under steady-state and short-term unbalanced conditions, including faults. The separate positive and negative sequence current control capability of the grid-side converters of full scale converter type wind turbines may be utilized to alter voltage imbalance at the point of connection and further into the grid, in turn changing the resultant negative sequence current flow in the grid. The effects of such control actions have been analyzed and discussed through theoretical as well as simulation studies.
Application of double negative metamaterials for improving the performance of maritime antennas (2007)

Recent interest in a new class of materials known collectively as metamaterials has sparked great interest in the antenna research community. Metamaterials are materials whose electrical properties go beyond those which can be achieved with conventional materials science. Some examples of metamaterials are electronic bandgap materials, artificial magnetic conductors, and artificial chiral materials. This work shall focus on the sub-group of metamaterials known as double negative metamaterials—materials with negative relative permittivity and permeability—and what benefits they can bring to improving the performance of antennas designed to operate using the ocean as a ground plane. ^ Two specific cases shall be considered. The first is the vertical electric dipole antenna surrounded by a double negative metamaterial shell operating over the ocean's surface. The second is the horizontal electric dipole antenna with a double negative metamaterial coating operating at or just below the ocean's surface. In both cases, the Sommerfeld integral representation of the fields shall be derived and predictions on the antenna performance made. Should significant improvement be predicted, genetic algorithms shall be used to optimize the antenna's performance. Where possible and practical, experimental measurements shall be used to validate the theoretical treatment presented. ^
A Concise Route to MK-4482 (EIDD-2801) from Cytidine: Part 2 (2020)

A new route to MK-4482 (&lt;b&gt;1&lt;/b&gt;) was developed. The route replaces uridine with the more available and less expensive cytidine. Low cost, simple reagents are used for the chemical transformations and the yield is improved from 17% to 44%. A step is removed from the longest linear sequence, and these advancements are expected to expand access to MK-4482 should it become a viable drug substance.