gebhart/patrepeval huggingface dataset:
Study of epitaxial graphene on non-polar 6H-SiC faces (2012)

We present epitaxial graphene (EG) growth on non-polar a-plane and m-plane 6H-SiC faces where material characterization is compared with that known for EG grown on polar faces. Atomic force microscopy (AFM) surface morphology exhibits nanocrystalline graphite like features for non-polar faces, while the polar silicon face shows step like features. This differing behavior is attributed to the lack of a hexagonal template on the non-polar faces. Non-polar faces also exhibit greater disorder and red shift of all Raman peaks (D, G and 2D) with increasing temperature. This is attributed to decreasing stress with increasing temperature. These variations provide evidence of different EG growth mechanisms on non-polar and polar faces, likely due to differences in surface free energy. We also present differences between a-plane EG and m-plane EG in terms of morphology, thickness and Raman characteristics
Clinicopathological and prognostic correlations of HER3 expression and its degradation regulators, NEDD4–1 and NRDP1, in primary breast cancer (2018)

Low HER3 expression is suggested to be a valuable prognostic biomarker to predict recurrence in HER2-amplified breast cancer. Neither NEDD4-1 nor NRDP1 demonstrated relevance in prognostics or in the subclassification of HER2-amplified breast carcinomas.
Sulfur‐Containing Glycomimetics (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Photoluminescence enhancement of colloidal quantum dots embedded in a monolithic microcavity (2003)

We demonstrate an enhancement of the spontaneous emission from colloidal CdSe quantum dots embedded in a half-wavelength one-dimensional cavity. When embedded in the cavity, the emission of the quantum dots is enhanced by a factor of 2.7. We also show a strong amplification by one order of magnitude in the absorption of the CdSe quantum dots due to the cavity effect.
Caching in Dynamic IoT Networks by Deep Reinforcement Learning (2020)

The sensing service of Internet-of-Things (IoT) networks enables IoT sensors to sense the environment information (e.g., temperature and traffic conditions) and send them through the IoT gateway to the users who request those information. The explosive growth of IoT users and sensors injects massive traffic into IoT networks and easily depletes the battery of IoT sensors. Caching at the IoT gateway is hence a promising solution to mitigate this problem by storing popular IoT data at the IoT gateway and sending them directly to the users instead of activating IoT sensors to transmit the data. In our work, we investigate the content placement problem, which determines data to be cached at each time epoch in dynamic IoT networks with the objective to minimize the average data transmission delay constrained by the cache storage capacity and IoT data freshness. We formulate our problem as an integer linear programming (ILP) problem and then model it as a Markov decision process (MDP). A deep reinforcement learning algorithm is proposed to solve this problem and its performances are demonstrated via extensive simulations.
Building customizable auto-luminescent luciferase-based reporters in plants (2020)

Bioluminescence is a powerful biological signal that scientists have repurposed as a reporter for gene expression in plants and animals. However, there are downsides associated with the need to provide a substrate to these reporters, including its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) <i>in planta</i> using a composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP <i>in planta</i> to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for future construction of programmable auto-luminescent plant traits, such as light driven plant-pollinator interactions or light emitting plant-based sensors.
Membrane disruption and cytotoxicity of hydrophobic N-alkylated imino sugars is independent of the inhibition of protein and lipid glycosylation (2003)

The N-alkyl moiety of N-alkylated imino sugars is crucial for therapeutic activities of these compounds as inhibitors of glycosphingolipid (GSL) biosynthesis and as antivirals. The improved potency afforded by a long N-alkyl moiety is coincident with increased compound-induced cytotoxicity. Therefore, in the present study, we examined the mechanism of this cytotoxicity in detail. Despite N-butyl-deoxynojirimycin and N-butyl-deoxygalactonojirimycin inhibiting the glycosylation of ceramide to glucosylceramide, ceramide levels did not increase in HL60 cells treated with these compounds. Long-chain N-alkylated imino sugars were toxic to cells at concentrations considerably lower than the critical micellar concentrations for these compounds and consequently did not solubilize radioactively labelled cellular proteins and lipids. However, membrane disruption and cell fragmentation did increase in a concentration- and chain-length-dependent manner. These results are consistent with previously proposed interactions between surface-active amphiphiles and protein-containing lipid membranes when drug concentrations are below the critical micellar concentration. Taken together, these results demonstrate that the cellular toxicity of hydrophobic N-alkylated imino sugars is due to cell lysis and cell fragmentation and, most importantly, is not related to the beneficial therapeutic effects of these compounds on protein and in lipid glycosylation. This information will aid in the future development of more selective imino sugar therapeutics for the treatment of human disease.
Lentivirus Transduction of Hematopoietic Cells: Figure 1. (2007)

INTRODUCTIONEfficient transfer and sustained expression of transgenes are among the most important issues in gene delivery. The majority of hematopoietic cells are nondividing or slowly self-renewing. Thus, they are refractory to most nonviral or retroviral delivery methods. Lentiviral vectors are capable of transducing nondividing cells and maintaining long-term and sustained expression of the transgenes. They are becoming useful for many delivery protocols, such as long-term expression of short hairpin RNA (shRNA) and functional genetics. They may also have great potential in gene therapy. This protocol describes lentivirus-vector-based delivery of foreign genes to hematopoietic cells. The method is applicable to various cell types in experiments that require long-term transgene expression.
Modelling the vascular response to sympathetic postganglionic nerve activity (2015)

This paper explores the influence of burst properties of the sympathetic nervous system on arterial contractility. Specifically, a mathematical model is constructed of the pathway from action potential generation in a sympathetic postganglionic neurone to contraction of an arterial smooth muscle cell. The differential equation model is a synthesis of models of the individual physiological processes, and is shown to be consistent with physiological data. The model is found to be unresponsive to tonic (regular) stimulation at typical frequencies recorded in sympathetic efferents. However, when stimulated at the same average frequency, but with repetitive respiratory-modulated burst patterns, it produces marked contractions. Moreover, the contractile force produced is found to be highly dependent on the number of spikes in each burst. In particular, when the model is driven by preganglionic spike trains recorded from wild-type and spontaneously hypertensive rats (which have increased spiking during each burst) the contractile force was found to be 10-fold greater in the hypertensive case. An explanation is provided in terms of the summative increased release of noradrenaline. Furthermore, the results suggest the marked effect that hypertensive spike trains had on smooth muscle cell tone can provide a significant contribution to the pathology of hypertension.
Quantum Computation (2018)

The remarkable developments in theoretical and experimental quantum computation that have been inspired by Feynman’s seminal papers on the subject are reviewed. Following an introduction to quantum computation, the implications for cryptography of quantum factoring are discussed. The requirements and challenges for practical quantum computational hardware are illustrated with an overview of the ion trap quantum computation project at Los Alamos. The physical limitations to quantum computation with trapped ions are analyzed and an assessment of the computational potential of the technology is made. … it seems that the laws of physics present no barrier to reducing the size of computers until bits are the size of atoms, and quantum behavior holds dominant sway.” R. P. Feynman, 1985 [1]. “I think I can safely say that nobody understands quantum mechanics.” R. P. Feynman, 1965 [2].
Design of compact BPF with controllable multiple transmission zeros for WIMAX applications (2013)

This paper proposes novel design for a compact LTCC BPF with high rejection over a wide stopband operating in the 3.4-3.6 GHz WIMAX band. The presented BPF has feedback paths for a grounding inductor and a coupling capacitor to provide controllable multiple transmission zeros at 2.4/5 GHz stopband, which enhances the desired stopband rejection.
Super‐resolution of sodium images from simultaneous 1H MRF/23Na MRI acquisition (2023)

In this work, we introduce a super-resolution method that generates a high-resolution (HR) sodium (<sup>23</sup> Na) image from simultaneously acquired low-resolution (LR) <sup>23</sup> Na density-weighted MRI and HR proton density, T<sub>1</sub> , and T<sub>2</sub> maps from proton (<sup>1</sup> H) MR fingerprinting in the brain at 7 T. The core of our method is a partial least squares regression between the HR (<sup>1</sup> H) images and the LR (<sup>23</sup> Na) image. An iterative loop and deconvolution with the point spread function of each acquired image were included in the algorithm to generate a final HR <sup>23</sup> Na image without losing features from the LR <sup>23</sup> Na image. The method was applied to simultaneously acquired HR proton and LR sodium data with in-plane resolution ratios between sodium and proton data of 3.8 and 1.9 and the same slice thickness. Four volunteers were scanned to evaluate the method's performance. For the data with a resolution ratio of 3.8, the mean absolute difference between the generated and ground truth HR <sup>23</sup> Na images was in the range of 1.5%-7.2% of the ground truth with a multiscale structural similarity index (M-SSIM) of 0.93 ± 0.03. For the data with a resolution ratio of 1.9, the mean absolute difference was in the range of 4.8%-6.3% with an M-SSIM of 0.95 ± 0.01.
PTU-055 Comparative cost-effectiveness of gastroesophageal reflux disease (GORD) centric and population based barrett’s oesophagus (BO) screening (2019)

<h3>Introduction</h3> With the development of minimally invasive tests for BO, the prospect of population screening (all adults age ≥50) instead of targeted screening (white, male, age ≥50, GORD) has arisen. We aimed to evaluate the comparative cost effectiveness of current tests utilising recently published data on prevalence, accuracy, screening uptake, and costs. <h3>Methods</h3> Decision analytic methods were conducted using Markov Modeling. The simulation compared six screening strategies to no screening: sedated OGD (sOGD, Cytosponge with TFF3 biomarker, Sponge on String (SoS) with methylated DNA markers, breath testing (E-Nose), hospital-based transnasal endoscopy (hTNE), and mobile unit-based transnasal endoscopy (mTNE). The model simulated a hypothetical cohort of 100,000 individuals aged ≥50 followed up for 40 years. sOGD was used as a confirmatory test of positive findings for all other diagnostic tests. Mean costs (direct as well as indirect costs resulting from missed or false positive diagnoses and low test uptake) were calculated for each strategy. Quality of life outcomes were based on quality adjusted life years (QALYs). <h3>Results</h3> Screening (GORD centric and population) was associated with small gains in QALYs compared to no screening (table 1). Under the general population analysis, mean costs ranged from $120 (mTNE) to $554 (E-Nose). While mTNE was the dominant strategy, both the Cytosponge and SoS tests had the lowest incremental cost effectiveness ratios (ICERs) (table 1). Under the GORD centric screening analysis, mean costs ranged from $212 (mTNE) to $768 (E-Nose). Cytosponge, SoS, hTNE, and mTNE were all dominant strategies compared to no screening. Out of those, mTNE was the least costly and most effective strategy. The E Nose test had the highest ICER primarily due to lower accuracy estimates. <h3>Conclusions</h3> While mTNE was the dominant strategy for both screening scenarios, this technique is not widely utilised and has been only evaluated in one centre. The Cytosponge and SoS strategies had very favourable ICERs in both strategies and may make population based BO screening regardless of GORD status feasible.
169-08: Electrical drivers of hemodynamic response to cardiac resynchronization therapy (2016)

Introduction: The drivers of cardiac resynchronization therapy (CRT) response remain unclear. We combined clinical electrocardiographic imaging (ECGi) data with cardiovascular model simulations (CircAdapt) to investigate how inter- and intra-ventricular dispersion of activation influences acute hemodynamic CRT response. Results: Computed changes of LVdP/dtmax based on both VEU and DISP data showed good agreement with measurements (FIG.A). High baseline VEU appeared to be both essential and sufficient for acute CRT response (FIG.A&B). When the VEU substrate was absent, response to CRT varied from worsening to slight improvement of hemodynamic function, depending on DISP. Consequently, including DISP as an input parameter in CircAdapt improved response prediction for the NICD and NARROW patient groups (FIG.A). Conclusion: Combining electrical activation from ECGi with computer simulations predicts hemodynamic improvement following CRT. VEU, representing interventricular dispersion of activation, is the dominant driver of CRT response. In patients with low baseline values for VEU, intraventricular dispersion of activation, characterized by DISP, is a strong determinant of baseline hemodynamic function and thereby additive as a predictor of response to CRT.
Hepatic Peroxisome Proliferator-Activated Receptor γ Coactivator 1α and Hepcidin Are Coregulated in Fasted/Refed States in Mice (2012)

To the Editor:

Hepcidin plays a central role in iron homeostasis and contributes to the pathogenesis of several disorders. Consequently, development of a clear understanding of hepcidin regulation in various pathophysiological conditions has been the subject of intensive research. Technical limitations, however, have limited the wide availability of assays for measuring this iron-regulatory hormone in human serum. Recently, Troutt et al. developed a specific and robust sandwich immunoassay for hepcidin-25 and measured it in the serum of healthy volunteers. They reported diurnal variation in its concentrations in the circulation (1). In particular, the authors demonstrated that hepcidin-25 concentrations were significantly increased after 3 days of fasting, an intriguing result considering the hyposideremic effect of hepcidin. The authors hypothesized that this increase in hepcidin could be caused by suppressed erythropoiesis to maintain tissue iron concentrations.

To investigate the molecular mechanisms responsible for hepcidin regulation by fasting, we fasted C57BL/6J mice for 24 h and then separated them into 2 groups. The first group was fasted for an additional 12-h period (“fasted” conditions); the second …
Supplementary Figure 1 from The TGFβ–miR200–MIG6 Pathway Orchestrates the EMT-Associated Kinase Switch That Induces Resistance to EGFR Inhibitors (2023)

&lt;p&gt;PDF file - 2120KB, FAK activity is significantly higher in erlotinib-resistant cells from lung and H and N origin. Total cell lysates were extracted from two pairs of lung (H358/H1703 and Calu3/Calu6) and two pairs of H and N (SCC-S/SCC-R and JHU011/JHU028) cancer cell lines and were subjected to immunoblot analysis with antibodies specific for phosphorylated and total FAK. Beta-actin was used a loading control.&lt;/p&gt;
Co-migration and internalization of transferrin and its receptor on K562 cells. (1983)

The incorporation of iron into human cells involves the binding of diferric transferrin to a specific cell surface receptor. We studied the process of endocytosis in K562, a human erythroid cell line, by using tetramethylrhodamine isothiocyanate-labeled transferrin (TRITC-transferrin) and fluorescein isothiocyanate-labeled Fab fragments of goat antireceptor IgG preparation (FITC-Fab-antitransferrin receptor antibody). Because the antireceptor antibody and transferrin bind to different sites on the transferrin receptor molecule it was possible to simultaneously and independently follow ligand and receptor. At 4 degrees C, the binding of TRITC-transferrin or FITC-Fab antitransferrin receptor antibody exhibited diffuse membrane fluorescence. At 20 degrees C, the binding of TRITC-transferrin was followed by the rapid formation of aggregates. However, the FITC-Fab antitransferrin receptor did not show similar aggregation at 20 degrees C unless transferrin was present. In the presence of transferrin, the FITC-Fab antitransferrin receptor antibody formed aggregates at the same sites and within the same time period as TRITC transferrin, indicating co-migration. Although the diffuse surface staining of either label was removed by proteolysis, the larger aggregates were not susceptible to enzyme degradation, indicating that they were intracellular. The internal location of the aggregates was also demonstrated using permeabilized cells that had been preincubated with transferrin and fixed with 4% paraformaldehyde. These cells showed aggregated receptor in the interior of the cell when reacted with fluorescein-labeled antibody to the receptor. This indicated that the transferrin and the transferrin receptor co-internalize and migrate to the same structures within the cell.
Far-Lateral Approach Without Drilling the Occipital Condyle for Vertebral Artery–Posterior Inferior Cerebellar Artery Aneurysms (2017)

A far-lateral approach that leaves the occipital condyle intact is adequate for treating most patients with VA-PICA aneurysms.
Carbon Nanofiber Supported Nickel Catalysts for the reductive splitting of Cellulose (2013)

status: Published
Treatment for patients with relapsed/refractory mantle cell lymphoma: European-based recommendations (2017)

Patients with mantle cell lymphoma (MCL) usually respond to initial combination chemotherapy, but the disease inevitably relapses and often follows an aggressive course. Here, clinical study results published since 2008 for patients with relapsed/refractory MCL were reviewed to compare available evidence for treatment guidance. Most trials identified were non-randomized, phase II studies performed at a limited number of sites, and many evaluated MCL as one of multiple non-Hodgkin lymphoma subtypes. Additional randomized, comparative trials are needed. Treatment selection generally depends on patient need, age and fitness, time of relapse, and line of therapy. Combination regimens typically produce higher response rates than single agents, and adding rituximab generally improves outcomes. The inclusion of ibrutinib, lenalidomide, temsirolimus, and bortezomib, represents an important advance for patients ineligible for, unable to tolerate, or failing high-intensity combination chemotherapy. A high need for effective treatments in relapsed/refractory MCL remains, particularly for elderly and frail patients.
Selective Epimerization of Rapamycin via a Retroaldol/Aldol Mechanism Mediated by Titanium Tetraisopropoxide (1999)

We describe the efficient and selective epimerization of the immunosuppressant rapamycin to 28-epirapamycin under mild conditions. The mechanism of epimerization involves an equilibrium of the four C28/C29 diastereomers through a two-step retroaldol/aldol (macrocycle ring-opening/ring-closing) sequence. This retroaldol/aldol equilibration is not restricted to rapamycin but is also applicable to acyclic beta-hydroxyketones. A potentially useful extension of the method--the use of beta-hydroxyketones as enolate synthons for effecting inter- or intramolecular aldol reactions under neutral conditions--is demonstrated.
Data from CD20-TCB with Obinutuzumab Pretreatment as Next-Generation Treatment of Hematologic Malignancies (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Despite promising clinical activity, T-cell–engaging therapies including T-cell bispecific antibodies (TCB) are associated with severe side effects requiring the use of step-up-dosing (SUD) regimens to mitigate safety. Here, we present a next-generation CD20-targeting TCB (CD20-TCB) with significantly higher potency and a novel approach enabling safer administration of such potent drug.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We developed CD20-TCB based on the 2:1 TCB molecular format and characterized its activity preclinically. We also applied a single administration of obinutuzumab (Gazyva pretreatment, Gpt; Genentech/Roche) prior to the first infusion of CD20-TCB as a way to safely administer such a potent drug.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; CD20-TCB is associated with a long half-life and high potency enabled by high-avidity bivalent binding to CD20 and head-to-tail orientation of B- and T-cell–binding domains in a 2:1 molecular format. CD20-TCB displays considerably higher potency than other CD20-TCB antibodies in clinical development and is efficacious on tumor cells expressing low levels of CD20. CD20-TCB also displays potent activity in primary tumor samples with low effector:target ratios. &lt;i&gt;In vivo&lt;/i&gt;, CD20-TCB regresses established tumors of aggressive lymphoma models. Gpt enables profound B-cell depletion in peripheral blood and secondary lymphoid organs and reduces T-cell activation and cytokine release in the peripheral blood, thus increasing the safety of CD20-TCB administration. Gpt is more efficacious and safer than SUD.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; CD20-TCB and Gpt represent a potent and safer approach for treatment of lymphoma patients and are currently being evaluated in phase I, multicenter study in patients with relapsed/refractory non-Hodgkin lymphoma (NCT03075696). &lt;i&gt;Clin Cancer Res; 24(19); 4785–97. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Prakash and Diefenbach, p. 4631&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
X-ray exposures of electrodeposited photoresist for conformal lithography on corrugated surfaces (1998)

Proximity printing using synchrotron x-ray lithography provides high resolution pattern transfer with large depth of field, low diffraction effects and no reflection form the substrate. Electro-plating of photo-resist allows deposition of thin, uniform films over geometrically complex and topographically diverse, electrically conductive surfaces. Two electro-deposited photoresists produced by Shipley, EAGLE 2100 ED negative tone and PEPR 2400 positive tone resist, have been tested with x-rays demonstrating micron pattern transfer over depths-of-field in fractions of millimeters.