gebhart/patrepeval huggingface dataset:
Compositional, structural, and electrical characterization of plasma oxidized thin aluminum layers for spin-tunnel junctions (2000)

In this paper we present results on how the plasma oxidation of a thin (1.5 nm) Al layer proceeds. Transmission electron microscopy of a Co/Al–oxide multilayer was used to determine the thickness of the oxides and Rutherford backscattering spectrometry and elastic recoil detection were utilized in order to determine the oxygen content. The oxide was also characterized via ac impedance measurements. These measurements indicated that the oxidation of Al on Co occurs in three discrete steps.
Dual Surface‐Functionalized Janus Nanocomposites of Polystyrene/Fe3O4@SiO2 for Simultaneous Tumor Cell Targeting and Stimulus‐Induced Drug Release (2013)

Folic acid (FA) and doxorubicin (DOX) are coupled separately onto Fe3O4@SiO2 and polystyrene surfaces of a unique polystyrene/Fe3O4@SiO2 Janus structure. This super-paramagnetic, dual-functionalized Janus nanocomposite enables effective tumor cell targeting and internalization via the folate receptor, and induces significant cancer cell death by controlled, stimulus-induced drug release under acidic conditions in endosomal compartments. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Thymic involution produced by diesel exhaust particles and their constituents in mice (2006)

Epidemiological studies suggest that diesel exhaust particles (DEP) contribute to an increase in allergic diseases. To assess the effects of DEP on the central immune system, mice were exposed to DEP by intraperitoneal (IP) administration. Exposure to DEP resulted in severe thymic involution accompanied by a reduction in the number of thymocytes, especially in cortical CD4+CD8+ double positive and double negative subsets. Core carbon particles associated with a mixture of chemical compounds in DEP did not appear to be responsible for the DEP-induced thymic involution because carbon graphite does not affect neither the number nor the CD4/CD8 profile of thymocytes. Extraction of DEP by ether, acidic and basic solvents showed that several independent fractions including the neutral ether fraction, which contains polycyclic aromatic hydrocarbons (PAH), induced thymic involution. Among major PAH components of DEP, benzo[b]fluoranthene (BbF), benzo[a]pyrene (BaP), and benzo[k]fluoranthene (BkF) were very potent inducers of thymic involution at an ED50 of less than 100 ng per mouse body. Nonetheless, DEP treatment of mice with targeted disruption of genes encoding the aryl hydrocarbon receptor (AHR), AHR nuclear translocator (ARNT), or microsomal epoxide hydolase (mEH) indicated that DEP produced thymic involution even in the absence of PAH-induced AHR/ARNT signal transduction or mEH-mediated PAH catabolism. On the other hand, BaP-mediated thymic involution was completely dependent on AHR, partially dependent on ARNT in T cells, and independent of mEH. These results indicate that DEP-induced thymic involution is mediated both by PAH-AHR/ARNT-dependent and -independent mechanisms.
Supplementary Data from Ethnic Differences and Functional Analysis of MET Mutations in Lung Cancer (2023)

Supplementary Data from Ethnic Differences and Functional Analysis of MET Mutations in Lung Cancer
Trimethyl-p-benzoquinone Provides Excellent Structural, Spectroscopic, and Thermochemical Models for Plastoquinone-1 and Its Radical Anion (1997)

Trimethyl-p-benzoquinone (TMQ) has been proposed to furnish an accurate thermochemical model for plastoquinones, key electron acceptors in oxygenic photosynthetic electron transfer. Free energy perturbation/molecular dynamics simulations combined with hybrid Hartree−Fock/density functional (HF/DF) calculations confirm that TMQ and plastoquinone-1 have approximately equal aqueous one-electron reduction potentials, within the accuracy of the calculations. HF/DF calculations using the B3LYP/6-31G(d) method also show that TMQ and its radical anion have (1) structures almost identical to those of PQa model for plastoquinone-1 without the isoprenoid chain's methyl groupsand its radical anion, respectively, have (2) spin densities for TMQ•- and PQ•- which differ by 0.01 electrons at most, and have (3) key CO and CC stretching frequencies for the TMQ/PQ and TMQ•-/PQ•- pairs differing by only 1−8 cm-1. Thus, TMQ and TMQ•- are excellent models for the structures, spin densities, and vibrational frequencies of plastoquinones and their radical anions, respectively.
Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses by potentiating glucocorticoid receptor activity (2021)

In macrophages, homeostatic and immune signals induce distinct sets of transcriptional responses, defining cellular identity and functional states. The activity of lineage-specific and signal-induced transcription factors are regulated by chromatin accessibility and other epigenetic modulators. Glucocorticoids are potent antiinflammatory drugs; however, the mechanisms by which they selectively attenuate inflammatory genes are not yet understood. Acting through the glucocorticoid receptor (GR), glucocorticoids directly repress inflammatory responses at transcriptional and epigenetic levels in macrophages. A major unanswered question relates to the sequence of events that result in the formation of repressive regions. In this study, we identify bromodomain containing 9 (BRD9), a component of SWI/SNF chromatin remodeling complex, as a modulator of glucocorticoid responses in macrophages. Inhibition, degradation, or genetic depletion of BRD9 in bone marrow-derived macrophages significantly attenuated their responses to both liposaccharides and interferon inflammatory stimuli. Notably, BRD9-regulated genes extensively overlap with those regulated by the synthetic glucocorticoid dexamethasone. Pharmacologic inhibition of BRD9 potentiated the antiinflammatory responses of dexamethasone, while the genetic deletion of BRD9 in macrophages reduced high-fat diet-induced adipose inflammation. Mechanistically, BRD9 colocalized at a subset of GR genomic binding sites, and depletion of BRD9 enhanced GR occupancy primarily at inflammatory-related genes to potentiate GR-induced repression. Collectively, these findings establish BRD9 as a genomic antagonist of GR at inflammatory-related genes in macrophages, and reveal a potential for BRD9 inhibitors to increase the therapeutic efficacies of glucocorticoids.
Introduction (2015)

This issue of Birth Defects Research Part C. Embryo Today: Reviews spotlights the role of the microbiome in infant development. The term "microbiome" refers to the trillions of organisms we harbor, on our skin and within our respiratory and gastrointestinal tracts.
Nonparametric Inverse-Probability-Weighted Estimators Based on the Highly Adaptive Lasso (2022)

Inverse-probability-weighted estimators are the oldest and potentially most commonly used class of procedures for the estimation of causal effects. By adjusting for selection biases via a weighting mechanism, these procedures estimate an effect of interest by constructing a pseudopopulation in which selection biases are eliminated. Despite their ease of use, these estimators require the correct specification of a model for the weighting mechanism, are known to be inefficient, and suffer from the curse of dimensionality. We propose a class of nonparametric inverse-probability-weighted estimators in which the weighting mechanism is estimated via undersmoothing of the highly adaptive lasso, a nonparametric regression function proven to converge at nearly <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:msup><mml:mi>n</mml:mi> <mml:mrow><mml:mo>-</mml:mo> <mml:mn>1</mml:mn> <mml:mo>/</mml:mo> <mml:mn>3</mml:mn></mml:mrow> </mml:msup> <mml:annotation>$ n^{-1/3}$</mml:annotation></mml:semantics> </mml:math> -rate to the true weighting mechanism. We demonstrate that our estimators are asymptotically linear with variance converging to the nonparametric efficiency bound. Unlike doubly robust estimators, our procedures require neither derivation of the efficient influence function nor specification of the conditional outcome model. Our theoretical developments have broad implications for the construction of efficient inverse-probability-weighted estimators in large statistical models and a variety of problem settings. We assess the practical performance of our estimators in simulation studies and demonstrate use of our proposed methodology with data from a large-scale epidemiologic study.
Expression, secretion and surface display of a human alkaline phosphatase by the ciliate Tetrahymena thermophila (2011)

With the expression of hiAP, not only a protein of commercial interest could be produced, but also a reporter enzyme that offers the possibility to analyze T. thermophila genes that play a role in the regulation of protein secretion. Additionally, the fact that ciliates do not secrete an endogenous alkaline phosphatase provides the possibility to use the truncated hiAP as a reporter enzyme, allowing the quantification of measures that will be necessary for further optimization of the host strains and the fermentation processes.
Monitoring longitudinal changes in irradiated head and neck cancer xenografts using diffuse reflectance spectroscopy (2016)

Radiation therapy is often used as the preferred clinical treatment for control of localized head and neck cancer. However, during the course of treatment (6-8 weeks), feedback about functional and/or physiological changes within impacted tissue are not obtained, given the onerous financial and/or logistical burdens of scheduling MRI, PET or CT scans. Diffuse optical sensing is well suited to address this problem since the instrumentation can be made low-cost and portable while still being able to non-invasively provide information about vascular oxygenation in vivo. Here we report results from studies that employed an optical fiber-based portable diffuse reflectance spectroscopy (DRS) system to longitudinally monitor changes in tumor vasculature within two head and neck cancer cell lines (SCC-15 and FaDu) xenografted in the flanks of nude mice, in two separate experiments. Once the tumor volumes were 100mm<sup>3</sup>, 67% of animals received localized (electron beam) radiation therapy in five fractions (8Gy/day, for 5 days) while 33% of the animals served as controls. DRS measurements were obtained from each animal on each day of treatment and then for two weeks post-treatment. Reflectance spectra were parametrized to extract total hemoglobin concentration and blood oxygen-saturation and the resulting time-trends of optical parameters appear to be dissimilar for the two cell-lines. These findings are also compared to previous animal experiments (using the FaDu line) that were irradiated using a photon beam radiotherapy protocol. These results and implications for the use of fiber-based DRS measurements made at local (irradiated) tumor site as a basis for identifying early radiotherapy-response are presented and discussed.
Hardware demonstration on an efficient radio access for massive machine-type communication (mMTC) (2017)

A rapid increase of uplink traffic is predicted with the spread of IoT (Internet of Things) devices. The 5G (5th generation mobile communications systems) requires that base stations effectively receive small-size packets but massive uplink signals transmitted by the IoT devices. To solve this problem, we have researched and developed techniques to increase number of devices that one base station can accumulate and to decrease delay time. We have evaluated channel estimation techniques and interference suppression and cancellation techniques by computer simulation. However, we have not evaluated the techniques on real machine yet. In this paper, we use software defined radio (SDR) on wired environment and evaluate accuracy of the proposed channel estimation techniques and signal separation performance of successive interference cancellation techniques.
FUSION OF A KEMPTIDE-DERIVATIVE TO THE FAB' FRAGMENT OF AN ANTI-CEA, HUMANIZED MN14 ANTIBODY, FACILITATES KINASE-MEDIATED 32P LABELING (1994)

s: Fifth Conference on Radioimmunodetection and Radioimmunotherapy of Cancer: Poster Session: PDF Only
Automated hyperspectral vegetation index derivation using a hyperparameter optimisation framework for high‐throughput plant phenotyping (2022)

Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple two-band indices that limit the net performance and often do not generalise well for traits other than those for which they were originally designed. We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel two- to six-band trait-specific indices in a streamlined process covering model selection, optimisation and evaluation, driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat. Results showed that AutoVI can rapidly generate complex novel VIs (at least a four-band index) that correlated strongly (R<sup>2</sup> > 0.8) with measured chlorophyll and sugar contents in wheat. Automated hyperspectral vegetation index-derived indices were used as features in simple and stepwise multiple linear regressions for chlorophyll and sugar content estimation, and outperformed the results achieved with the existing 47 VIs and those provided using partial least squares regression. The AutoVI system can deliver novel trait-specific VIs readily adoptable to high-throughput plant phenotyping platforms and should appeal to plant scientists and breeders. A graphical user interface for the AutoVI is provided here.
In utero exposure to endogenous maternal polyclonal anti-Caspr2 antibody leads to an autism-like phenotype in male mice (2020)

Abstract Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a complex etiology. A strong sex bias has been observed in ASD with boys being four times more likely to be diagnosed than girls. The maternal immune system has been repeatedly implicated in the etiology of ASD. Maternal infection with fever during pregnancy has been linked to ASD. Increased levels of maternal cytokines and chemokines during gestation, including interleukin 6, have been associated with ASD in children with intellectual disabilities. Studies, including our own, have consistently supported the hypothesis that maternal brain-reactive antibodies can predispose to ASD by affecting the developing brain during a critical period. We have previously demonstrated that antibodies targeting the neuronal protein Caspr2 are present at high frequency in mothers with brain-reactive serology and a ASD child. Furthermore, male mice but not female mice exposed in utero to a monoclonal anti-Caspr2 antibody cloned from a mother of a child with ASD, develop an ASD -like phenotype. In the present study we use a new model in which female mice are immunized with the extracellular portion of Caspr2, and therefore harbor anti-Caspr2 antibodies throughout gestation to mimic the human condition. Male mice born to dams harboring polyclonal anti-Caspr2 antibodies exhibit abnormal cortical development, decreased dendritic complexity of excitatory neurons and reduced numbers of inhibitory neurons in the hippocampus, as well as repetitive behaviors and impairments in social interactions as adults. These studies will increase our understanding of the triggers of neurodevelopmental impairment and possibly suggest novel approaches to protecting the fetal brain.
Constitutive Equation for Gas Sensitivity of Nanocrystalline Tin Oxide Sensor (2004)

A new constitutive equation for the gas sensitivity of nanocrystalline tin oxide (SnO2) thin film sensor is proposed in this investigation. The experimentally observed variation in the gas sensitivity as a function of operating temperature and the amount of reducing gas, as reported in the literature, is shown to be satisfactorily explained by the proposed theoretical model. © 2004 American Scientific Publishers. All rights reserved.
Bcl-2 Sustains Increased Mucous and Epithelial Cell Numbers in Metaplastic Airway Epithelium (2004)

Bcl-2, an inhibitor of apoptosis, is expressed in LPS-induced metaplastic goblet cells of rat airways. The present study investigated expression of Bcl-2 in airway mucous cells of persons with cystic fibrosis and tested in rats and mice whether its expression is responsible for sustaining metaplastic mucous cells. A significantly higher percentage of mucous cells expressed Bcl-2 in humans with cystic fibrosis compared with control subjects with no disease or subjects with other diseases. In LPS-instilled F344/N rats, the percentage of Bcl-2-positive mucous cells was decreased to background levels before the resolution of goblet cell metaplasia. Furthermore, intraperitoneal injection of rats with antisense oligonucleotides significantly reduced Bcl-2 expression and goblet cell metaplasia in nasal and pulmonary airway epithelia in rats. In contrast, sustained expression of Bcl-2 in transgenic mice by a metallothionein promoter caused increased LPS-induced goblet cell metaplasia over 8 days compared with wild-type mice. These studies demonstrate that Bcl-2 expression sustains goblet cell metaplasia in various species, that epithelial cell numbers are directly linked to the regulation of the numbers of goblet cells, and that downregulating Bcl-2 expression reduces goblet cell metaplasia.
REBL DPG lenslet structure: design for charging prevention (2014)

KLA-Tencor is currently developing Reflective Electron Beam Lithography (REBL), targeted as a production worthy multiple electron beam tool for next generation high volume lithography. The Digital Pattern Generator (DPG) integrated with CMOS and MEMS lenslets is a critical part of REBL. Previously, KLA-Tencor reported on progress towards a REBL tool for maskless lithography below the 10 nm technology node. However, the MEMS lenslet structure suffered from charging up during writing, requiring the usage of a charge drain coating. Since then, the TSMC multiple e-beam team and the KLA-Tencor REBL team have worked together to further develop the DPG for direct write lithography. In this paper, we introduce a hollow-structure MEMS lenslet array that inherently prevents charging during writing, and preliminary verification results are also presented.
Delivering object-based audio visual services (2003)

Delivery of audio-visual objects differs from the traditional video on demand systems in the characteristics of the presentations delivered. Video on demand has mainly been about delivering MPEG-2 audio and video. In the case of object based presentations such as MPEG-4 presentations, the media data and the media composition data are transmitted to a client as separate streams, typically with different QoS requirements, in the same session. Furthermore, as the number of objects in a presentation can be quite large, the overhead required to manage the session is large. Interactivity makes this problem more complex as the resources required for a session will now depend on the user behavior, especially when user interaction with objects changes the number of objects in the scene either by adding or deleting objects. In this paper, we present our recent work on delivering audio-visual services based on MPEG-4. The issues covered include object-based audio-visual (MPEG-4) servers, object scheduling, object-to-object communications, and content creation.
Delay-Optimized Network Coding for Video Streaming over Wireless Networks (2010)

In this paper, we study delay-optimized network coding for video streaming over wireless networks with network coding capabilities. It has been demonstrated that network coding can increase throughput in wireless networks, by mixing packets from different flows into a single packet, thus increasing the information content per transmission. However, network coding potential is not always fully exploited in this setting, because there may not be enough packets at intermediate nodes to do network coding due to bursty nature of transport protocols, packet losses, and difference in path delays. One way to deal with this problem is to delay packets at intermediate nodes in order to create more network coding opportunities. However, introducing large or varying delays eventually hurts video traffic, which requires low delay and delay jitter. In this paper, we study this tradeoff in coded wireless networks, and we propose a packet delaying scheme at intermediate nodes to maximize video quality.
Industry Perspectives (2017)

Driven by the data requirements envisioned for the fifth generation (5G) of wireless services, the mobile community is focusing on breaking the spectrum gridlock that characterizes cellular technology. In this context, researchers and industries have identified millimeter-wave (mmWave) communications as a key enabler for providing unprecedented radio access capacity. Nevertheless, due to the specific differences between this technology and microwave systems, there are multiple research challenges spanning from the hardware to the overall system architecture. The goal of this column is to provide an overview of these challenges and discuss the most promising solutions to make 5G mmWave communications a reality.
Electrophile, Substrate Functionality, and Catalyst Effects in the Synthesis of α‐Mono and Di‐Substituted Benzylamines via Visible‐Light Photoredox Catalysis in Flow (2018)

Abstract We report herein the facile and one‐pot synthesis of α‐mono‐ and di‐substituted benzylamines from cheap and readily available α‐amino acids, via photocatalytic decarboxylative arylation in flow. This enables to access intermediates and building blocks that are difficult to obtain via other synthetic routes, but are key for the manufacture of pharmaceuticals, agrochemicals, and fine chemicals. The optimal decarboxylative conditions were identified through a high‐throughput evaluation of catalysts, organic or inorganic bases, ligands, and reaction parameters (i. e., contact time, temperatures, and photoelectron power). The reaction turned out to be electronically controlled as the yields increased with increasing electron‐density on the aryl moiety. The results were correlated with the redox properties of the photocatalysts, deriving catalyst structure‐performance relationships which can facilitate the future identification of even better materials. In addition, compared to traditional batch chemistry, the use of a flow protocol led to quicker reactions (30 min instead of 12–72 h) and ensured more predictable reaction scale‐ups.