gebhart/patrepeval huggingface dataset:
Allylic Oxidations of Terminal Olefins Using a Palladium Thioether Catalyst (2010)

A palladium catalyst that converts terminal olefins to linear allylic acetates at lower catalyst loadings and faster reaction times than current systems is reported. This reaction can be conducted using benzoquinone as the oxidizing agent or catalytic amounts of copper and hydroquinone under one atmosphere of oxygen. Preliminary reactivity studies of pi-allylpalladium complexes under our reaction conditions do not provide results similar to those obtained in the catalytic reaction, which may suggest an alternative reaction pathway. The palladium catalyst is ligated by an aryloxyalkyl aryl sulfide, which is identified as a new ligand for homogeneous catalysis.
Low Temperature Formation of Silicon Oxide Thin Films by Atomic Layer Deposition Using NH3/O2 Plasma (2013)

High-quality silicon oxide (SiO2) thin films are deposited by plasma-enhanced atomic layer deposition (PEALD) using bis(diethylamino)silane as a Si precursor and ammonia/oxygen plasmas at a substrate temperature of 150°C. The SiO2 films are formed at a growth rate of ∼0.137 nm/cycle in high purity. The overall quality of the PEALD-SiO2 films are assessed by infrared spectroscopy, wet etch rate in 0.5% hydrofluoric solution, Auger electron spectroscopy, and current-voltage analysis. The quality of the films formed at low temperature using the combination of ammonia/oxygen plasmas compares well with deposition at higher temperatures (350°C) using oxygen plasma only.
Carbon Nanotube Linear Bearing Nanoswitches (2006)

We exploit the remarkable low-friction bearing capabilities of multiwalled carbon nanotubes (MWNTs) to realize nanoelectromechanical switches. Our switches consist of two open-ended MWNT segments separated by a nanometer-scale gap. Switching occurs through electrostatically actuated sliding of the inner nanotube shells to close the gap, producing a conducting ON state. For double-walled nanotubes in particular, a gate voltage can restore the insulating OFF state. Acting as a nonvolatile memory element capable of several switching cycles, our devices are straightforward to implement, self-aligned, and do not require complex fabrication or geometries, allowing for convenient scalability.
Selective leptin resistance: a new concept in leptin physiology with cardiovascular implications (2002)

Leptin, an adipocyte secreted hormone, acts in the hypothalamus to inhibit appetite and promote thermogenic metabolism, thereby reducing adiposity and body weight. Leptin has multiple autonomic and cardiovascular actions, including sympathetic activation, increases in endothelium derived nitric oxide (NO), and angiogenesis. The predominant cardiovascular effect of chronic hyperleptinemia is a pressor effect mediated by increased sympathetic activity. The sympathetic and cardiovascular actions of leptin are discussed and evidence derived from studies of obese mice for the novel concept of selective leptin resistance is reviewed. This concept holds that in some obese states, there is preservation of the sympathoexcitatory actions of leptin despite resistance to the satiety and weight-reducing actions of the hormone. Selective leptin resistance might explain how hyperleptinemia could contribute to increases in sympathetic activity and arterial pressure in obese states where there is resistance to the metabolic (satiety and weight-reducing) actions of leptin. It is speculated here, that this concept may have potential implications for human obesity, which is often associated with elevated plasma leptin and partial resistance to the satiety effects of leptin. If selective leptin resistance occurs in obese humans, then leptin could contribute to the sympathetic overactivity and hypertension despite resistance to its metabolic actions.
Altering the Thermodynamics of Phase Separation in Inverted Bulk‐Heterojunction Organic Solar Cells (2009)

Organic solar cells: By incorporating nonvolatile additives into blends of P3HT:PCBM, the efficiencies of inverted bulk-heterojunction solar cells are improved almost twofold (see figure). These additives selectively partition into the P3HT phase, effectively increasing phase separation between the P3HT and PCBM. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by 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.
Allylglucosinolate and Herbivorous Caterpillars: A Contrast in Toxicity and Tolerance (1978)

Allylglucosinolate, found in many cruciferous plants, is acutely toxic to Papilio polyxenes larvae, which do not normally attack crucifers. By contrast, larval growth of Pieris rapae, a crucifer specialist, is not affected even by artificially high concentrations of allylglucosinolate. Larval growth of Spodoptera eridania, a generalist feeder, is inhibited by high but not by low concentrations of the compound.
Systematical Study of the Basic Properties of Surface Acoustic Wave Devices Based on ZnO and GaN Multilayers (2020)

Recently, surface acoustic wave (SAW) devices based on layered structures are a popular area of research. Multilayered structures, including ZnO and GaN, have shown great performance and can be applied in diverse fields. Meanwhile, thin films, such as AlGaN and n-ZnO, can be added to these structures to form a 2-D electron gas (2DEG) which makes the devices tunable. This work systematically studies the basic properties of SAW devices based on ZnO and GaN multilayers via COMSOL Multiphysics. The sorts of structures with different crystal orientations are simulated, and various acoustic modes are considered. Results show that a range of phase velocity from about 2700 m/s to 6500 m/s can be achieved, and devices based on ZnO and GaN multilayers can meet the requirements of the electromechanical coupling coefficient from about 0 to 7%. Every structure’s unique properties are valuable for diverse applications. For example, c-ZnO/c-GaN/c-sapphire structure can be used for high-frequency and large-bandwidth SAW devices, while SAW devices based on a-ZnO/a-GaN/r-sapphire and 2DEG are suitable for programmable SAW sensors. This work has great reference value for future research into SAW devices.
Cloning of a Putative Ligand for the T1/ST2 Receptor (1996)

T1/ST2 is a receptor-like molecule homologous to the type I interleukin-1 receptor. Despite this sequence similarity, we have been unable to demonstrate binding of T1/ST2 to any of the three interleukin-1 species. In searching for a ligand for T1/ST2, we have cloned a cell surface protein to which it binds. This protein is unable to initiate signal transduction by the T1/ST2 receptor in several in vitro assays.
Naturally occurring human lymphocyte antigen-A2 restricted CD8+ T-cell response to the cancer testis antigen NY-ESO-1 in melanoma patients. (2000)

Cancer testis (CT) antigens are particularly interesting candidates for cancer vaccines. However, T-cell reactivity to CT antigens has been detected only occasionally in cancer patients, even after vaccination. A new group of CT antigens has been recently identified using the SEREX technique based on immunoscreening of tumor cDNA expression libraries with autologous sera. We have used fluorescent HLA-A2/peptide tetramers containing an optimized antigenic peptide to directly identify HLA-A2-restricted CD8+ T cells specific for the SEREX-defined CT antigen NY-ESO-1 in melanoma patients. High frequencies of NY-ESO-1-specific CD8+ T cells were readily detected in peptide-stimulated peripheral blood mononuclear cells as well as in lymphocytes infiltrating melanoma lesions from patients with measurable antibody responses to NY-ESO-1. NY-ESO-1-specific CD8+ T cells were also detectable in peptide-stimulated peripheral blood mononuclear cells from some seronegative patients. Whereas the frequencies of NY-ESO-1-specific CD8+ T cells in circulating lymphocytes were usually below the limit of detection by tetramer staining, the presence of NY-ESO-1 CD8+ T cells displaying a memory phenotype was clearly detectable ex vivo in blood from a seropositive patient over an extended period of time. These results indicate that sustained CD8+ T-cell responses to CT antigens can naturally occur both locally and systemically in melanoma patients.
Compression Artifacts in Perceptual Audio Coding (2008)

Perceptual audio coding achieves a high compression ratio by exploiting the perceptual irrelevance and data redundancies. By using advanced and sophisticated signal processing methods, perceptual coding has generated artifacts that are quite different from the traditional distortions. A new audio technology becomes mature through the successful modeling, measuring, and control on the artifacts incurred from the technology. With the advance of new coding modules in advanced audio coding (AAC), spectral band replication (SBR), and parametric coding, the incurred artifacts are far more difficult to model, measure, and control than those caused by previous encoding systems like pulse code modulation. This paper models the audible artifacts through the time-frequency diagrams, considers the artifacts-susceptible music types, and analyzes the critical encoding technologies incurring these artifacts.
Lung metastases detection in CT images using 3D template matching (2007)

The aim of this study is to demonstrate a novel, fully automatic computer detection method applicable to metastatic tumors to the lung with a diameter of 4-20 mm in high-risk patients using typical computed tomography (CT) scans of the chest. Three-dimensional (3D) spherical tumor appearance models (templates) of various sizes were created to match representative CT imaging parameters and to incorporate partial volume effects. Taking into account the variability in the location of CT sampling planes cut through the spherical models, three offsetting template models were created for each appearance model size. Lung volumes were automatically extracted from computed tomography images and the correlation coefficients between the subregions around each voxel in the lung volume and the set of appearance models were calculated using a fast frequency domain algorithm. To determine optimal parameters for the templates, simulated tumors of varying sizes and eccentricities were generated and superposed onto a representative human chest image dataset. The method was applied to real image sets from 12 patients with known metastatic disease to the lung. A total of 752 slices and 47 identifiable tumors were studied. Spherical templates of three sizes (6, 8, and 10 mm in diameter) were used on the patient image sets; all 47 true tumors were detected with the inclusion of only 21 false positives. This study demonstrates that an automatic and straightforward 3D template-matching method, without any complex training or postprocessing, can be used to detect small lung metastases quickly and reliably in the clinical setting.
The Relationship of Depression to Cardiovascular Disease (1998)

This article reviews the burgeoning literature on the relationship of mood disorders and heart disease. Major depression and depressive symptoms, although commonly encountered in medical populations, are frequently underdiagnosed and undertreated in patients with cardiovascular disease (CVD). This is of particular importance because several studies have shown depression and its associated symptoms to be a major risk factor for both the development of CVD and death after an index myocardial infarction. This review of the extant literature is derived from MEDLINE searches (1966-1997) using the search terms "major depression," "psychiatry," "cardiovascular disease," and "pathophysiology." Studies investigating pathophysiological alterations related to CVD in depressed patients are reviewed. The few studies on treatment of depression in patients with CVD are also described. Treatment of depression in patients with CVD improves their dysphoria and other signs and symptoms of depression, improves quality of life, and perhaps even increases longevity. Recommendations for future research are proposed.
c-Ski Acts as a Transcriptional Co-repressor in Transforming Growth Factor-β Signaling through Interaction with Smads (1999)

Smads are intracellular signaling mediators of the transforming growth factor-beta (TGF-beta) superfamily that regulates a wide variety of biological processes. Among them, Smads 2 and 3 are activated specifically by TGF-beta. We identified c-Ski as a Smad2 interacting protein. c-Ski is the cellular homologue of the v-ski oncogene product and has been shown to repress transcription by recruiting histone deacetylase (HDAC). Smad2/3 interacts with c-Ski through its C-terminal MH2 domain in a TGF-beta-dependent manner. c-Ski contains two distinct Smad-binding sites with different binding properties. c-Ski strongly inhibits transactivation of various reporter genes by TGF-beta. c-Ski is incorporated in the Smad DNA binding complex, interferes with the interaction of Smad3 with a transcriptional co-activator, p300, and in turn recruits HDAC. c-Ski is thus a transcriptional co-repressor that links Smads to HDAC in TGF-beta signaling.
The Global Signal and Observed Anticorrelated Resting State Brain Networks (2009)

Resting state studies of spontaneous fluctuations in the functional MRI (fMRI) blood oxygen level dependent (BOLD) signal have shown great promise in mapping the brain's intrinsic, large-scale functional architecture. An important data preprocessing step used to enhance the quality of these observations has been removal of spontaneous BOLD fluctuations common to the whole brain (the so-called global signal). One reproducible consequence of global signal removal has been the finding that spontaneous BOLD fluctuations in the default mode network and an extended dorsal attention system are consistently anticorrelated, a relationship that these two systems exhibit during task performance. The dependence of these resting-state anticorrelations on global signal removal has raised important questions regarding the nature of the global signal, the validity of global signal removal, and the appropriate interpretation of observed anticorrelated brain networks. In this study, we investigate several properties of the global signal and find that it is, indeed, global, not residing preferentially in systems exhibiting anticorrelations. We detail the influence of global signal removal on resting state correlation maps both mathematically and empirically, showing an enhancement in detection of system-specific correlations and improvement in the correspondence between resting-state correlations and anatomy. Finally, we show that several characteristics of anticorrelated networks including their spatial distribution, cross-subject consistency, presence with modified whole brain masks, and existence before global regression are not attributable to global signal removal and therefore suggest a biological basis.
The MKK7 Gene Encodes a Group of c-Jun NH 2 -Terminal Kinase Kinases (1999)

The c-Jun NH2-terminal protein kinase (JNK) is a member of the mitogen-activated protein kinase (MAPK) group and is an essential component of a signaling cascade that is activated by exposure of cells to environmental stress. JNK activation is regulated by phosphorylation on both Thr and Tyr residues by a dual-specificity MAPK kinase (MAPKK). Two MAPKKs, MKK4 and MKK7, have been identified as JNK activators. Genetic studies demonstrate that MKK4 and MKK7 serve nonredundant functions as activators of JNK in vivo. We report here the molecular cloning of the gene that encodes MKK7 and demonstrate that six isoforms are created by alternative splicing to generate a group of protein kinases with three different NH2 termini (alpha, beta, and gamma isoforms) and two different COOH termini (1 and 2 isoforms). The MKK7alpha isoforms lack an NH2-terminal extension that is present in the other MKK7 isoforms. This NH2-terminal extension binds directly to the MKK7 substrate JNK. Comparison of the activities of the MKK7 isoforms demonstrates that the MKK7alpha isoforms exhibit lower activity, but a higher level of inducible fold activation, than the corresponding MKK7beta and MKK7gamma isoforms. Immunofluorescence analysis demonstrates that these MKK7 isoforms are detected in both cytoplasmic and nuclear compartments of cultured cells. The presence of MKK7 in the nucleus was not, however, required for JNK activation in vivo. These data establish that the MKK4 and MKK7 genes encode a group of protein kinases with different biochemical properties that mediate activation of JNK in response to extracellular stimuli.
Expression of the ErbB-neuregulin signaling network during human cerebellar development: implications for the biology of medulloblastoma. (1998)

The four receptor tyrosine kinase I receptors, ErbB-1, ErbB-2, ErbB-3, and ErbB-4, which have been implicated in the development of a variety of normal and malignant tissues, are activated through ligand mediated homo- and heterodimerization. We have previously reported the frequent coexpression, heterodimerzation, and prognostic significance of ErbB-2 and ErbB-4 in childhood medulloblastoma, an embryonal tumor of the cerebellar external granule cell layer (EGL). In the present study, we have used immunohistochemistry and Western blotting analysis to analyze the expression of the ErbB receptors and neuregulin (NRG) 1-alpha and NRG1-beta ligands during normal human cerebellar development. We demonstrate that ErbB-1, ErbB-3, ErbB-4, and NRG1-beta display specific temporal and topographical distribution in the cerebellum during intrauterine and postnatal life, and that normal ErbB-NRG signaling in the EGL multiplying zone is likely to be mediated by ErbB-4 and NRG1-beta. In contrast, ErbB-2, which is expressed in 86% of medulloblastomas, could not be detected at any stage of cerebellar development. Therefore, we propose that positive deregulation of ErbB-2 expression in the cerebellar EGL, leading to the formation of a NRG41-beta-driven ErbB-2/ErbB-4 autocrine loop, is an important factor in medulloblastoma tumorigenesis. In further support of this hypothesis, we provide evidence using reverse transcription-PCR analysis that expression of the ErbB-2 and ErbB-4 receptors, but not ErbB-1 or ErbB-3, is deregulated in medulloblastoma compared with normal developing cerebellum. We also demonstrate NRG1-beta expression in 87% (n = 46 of 48) of medulloblastoma primary tumors, with the greatest expression levels occurring in tumors with high ErbB-2 and ErbB-4 receptor coexpression. Furthermore, the expression of all three components of the proposed autocrine loop (ie., ErbB-2, ErbB-4, and NRG1-beta) was significantly related to the presence of metastases at diagnosis (P < 0.05).
Cloning and expression of apoptosis inhibitory protein homologs that function to inhibit apoptosis and/or bind tumor necrosis factor receptor-associated factors. (1996)

Baculovirus inhibitors of apoptosis (IAPs) act in insect cells to prevent cell death. Here we describe three mammalian homologs of IAP, MIHA, MIHB, and MIHC, and a Drosophila IAP homolog, DIHA. Each protein bears three baculovirus IAP repeats and an N-terminal ring finger motif. Apoptosis mediated by interleukin 1beta converting enzyme (ICE), which can be inhibited by Orgyia pseudotsugata nuclear polyhedrosis virus IAP (OpIAP) and cowpox virus crmA, was also inhibited by MIHA and MIHB. As MIHB and MIHC were able to bind to the tumor necrosis factor receptor-associated factors TRAF1 and TRAF2 in yeast two-hybrid assays, these results suggest that IAP proteins that inhibit apoptosis may do so by regulating signals required for activation of ICE-like proteases.
Indicators Based on Fluorescence Resonance Energy Transfer (FRET): Figure 1. (2009)

One of the major new trends in the design of indicators for optically imaging biochemical and physiological functions of living cells has been the exploitation of fluorescence resonance energy transfer (FRET). FRET is a well-known spectroscopic technique for monitoring changes in the proximity and mutual orientation of pairs of chromophores. It has long been used in biochemistry and cell biology to assess distances and orientations between specific labeling sites within a single macromolecule or between two separate molecules. More recently, macromolecules or molecular pairs have been engineered to change their FRET in response to biochemical and physiological signals such as membrane potential, cyclic AMP (cAMP), protease activity, free Ca(2+) and Ca(2+)-calmodulin (CaM) concentrations, protein-protein heterodimerization, phosphorylation, and reporter-gene expression. Because FRET is general, nondestructive, and easily imaged, it has proven to be one of the most versatile spectroscopic readouts available to the designer of new probes. FRET is particularly amenable to emission ratioing, which is more reliably quantifiable than single-wavelength monitoring and better suited than excitation ratioing to high-speed and laser-excited imaging. This article summarizes the photophysical principles of FRET and the types of indicators used.
Early lymphocyte recovery predicts superior survival after autologous hematopoietic stem cell transplantation in multiple myeloma or non-Hodgkin lymphoma (2001)

Autologous stem cell transplantation (ASCT) improves survival in patients with previously untreated multiple myeloma (MM) and relapsed, chemotherapy-sensitive, aggressive non-Hodgkin lymphoma (NHL). Lower relapse rates seen in allogeneic stem cell transplantation have been related to early absolute lymphocyte count (ALC) recovery as a manifestation of early graft-verus-tumor effect. In ASCT, the relation between ALC recovery and clinical outcomes in MM and NHL was not previously described. This is a retrospective study of patients with MM and NHL who underwent ASCT at the Mayo Clinic between 1987 and 1999. The ALC threshold was determined at 500 cells/microL on day 15 after ASCT. The study identified 126 patients with MM and 104 patients with NHL. The median overall survival (OS) and progression-free survival (PFS) times for patients with MM were significantly longer in patients with an ALC of 500 cells/microL or more than patients with an ALC of fewer than 500 cells/microL (33 vs 12 months, P <.0001; 16 vs 8 months, P <.0003, respectively). For patients with NHL, the median OS and PFS times were significantly longer in patients with an ALC of 500 cells/microL or more versus those with fewer than 500 cells/microL (not reached vs 6 months, P <.0001; not reached vs 4 months, P <.0001, respectively). Multivariate analysis demonstrated day 15 ALC to be an independent prognostic indicator for OS and PFS rates for both groups of patients. In conclusion, ALC is correlated with clinical outcome and requires further study. (Blood. 2001;98:579-585)