gebhart/patrepeval huggingface dataset:
Abstract 2219: Inhibitor of differentiation-1 is a novel prognostic factor among NSCLC patients with adenocarcinoma histology and contributes to therapy resistance (2011)

Abstract High Id1 levels have been found in some tumor types, particularly in advance stages. We aimed to study Id1 levels and their prognostic value in a large series of different histologies of stage I-IV NSCLC patients and to test Id1 function in cell lines and cells derived from malignant pleural effusions (MPE) from patients (pts). Id1 expression was analyzed in NSCLC samples from 311 pts and 65 normal lung tissues by immunohistochemistry. Id1 mRNA expression was also studied in 111 pts using publicly available microarrays. Significantly higher Id1 protein expression levels were found in tumors compared to normal tissue (p&amp;lt;0.001) and in adenocarcinomas (AC) compared so squamous histology (p&amp;lt;0.001). Among the localized NSCLC pts undergoing surgery, higher Id1 expression levels were associated with a shorter overall survival (OS) for AC histology (p=0.017). In the surgery+adjuvant chemo-radiotherapy pts, the same correlation was found between Id1 levels and OS among AC samples (p=0.038). Consistently, in stage IV pts receiving palliative chemotherapy, Id1 maintained its prognostic value (shorter OS in pts with higher levels) for AC (p=0.003). Id1 was also correlated with time-to-progression (TTP) after chemotherapy (lower levels, prolonged TTP) in AC pts (p=0.008). The in silico analysis confirmed this association. High expression of Id1 was also found by western blots in squamous cell lines (H520, HCC15, H157 and H58) and in lesser extent in AC cell lines (SKLU-1, LXF-289, H322, H23) and MPE-derived AC cells. Id1 knockdown resulted in a significant reduction of the clonogenic activity of squamous and AC cells. Id1 silencing on radiotherapy and chemotherapy-resistant MPE-derived cells restored sensitivity to both therapies. We conclude that Id1 protein and mRNA expression is an independent prognostic factor among pts with AC but no other histologies, regardless of the stage or treatment received. In cell lines derived from MPE pts, Id1 downregulation decreases NSCLC cell proliferation and sensitizes cells to radiotherapy and chemotherapy, in vitro. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2219. doi:10.1158/1538-7445.AM2011-2219
Rho3 ofSaccharomyces cerevisiae, Which Regulates the Actin Cytoskeleton and Exocytosis, Is a GTPase Which Interacts with Myo2 and Exo70 (1999)

The Rho3 protein plays a critical role in the budding yeast Saccharomyces cerevisiae by directing proper cell growth. Rho3 appears to influence cell growth by regulating polarized secretion and the actin cytoskeleton, since rho3 mutants exhibit large rounded cells with an aberrant actin cytoskeleton. To gain insights into how Rho3 influences these events, we have carried out a yeast two-hybrid screen using an S. cerevisiae cDNA library to identify proteins interacting with Rho3. Two proteins, Exo70 and Myo2, were identified in this screen. Interactions with these two proteins are greatly reduced or abolished when mutations are introduced into the Rho3 effector domain. In addition, a type of mutation known to produce dominant negative mutants of Rho proteins abolished the interaction with both of these proteins. In contrast, Rho3 did not interact with protein kinase C (Pkc1), an effector of another Rho family protein, Rho1, nor did Rho1 interact with Exo70 or Myo2. Rho3 did interact with Bni1, another effector of Rho1, but less efficiently than with Rho1. The interaction between Rho3 and Exo70 and between Rho3 and Myo2 was also demonstrated with purified proteins. The interaction between Exo70 and Rho3 in vitro was dependent on the presence of GTP, since Rho3 complexed with guanosine 5'-O-(3-thiotriphosphate) interacted more efficiently with Exo70 than Rho3 complexed with guanosine 5'-O-(3-thiodiphosphate). Overlapping subcellular localization of the Rho3 and Exo70 proteins was demonstrated by indirect immunofluorescence. In addition, patterns of localization of both Exo70 and Rho3 were altered when a dominant active allele of RHO3, RHO3(E129,A131), which causes a morphological abnormality, was expressed. These results provide a direct molecular basis for the action of Rho3 on exocytosis and the actin cytoskeleton.
Charge Transport in Self-Organized π-Stacks of p-Phenylene Vinylene Oligomers (2005)

We have studied the mobility of charge carriers along self-organizing pi-stacks of hydrogen-bonded phenylene vinylene oligomers in solution, by time-resolved microwave conductivity measurements. The value deduced for the mobility along the stacks is 3 x 10(-3) and 9 x 10(-3) cm2/(V s) for holes and electrons, respectively. Additionally, we have calculated the mobility along the pi-stacks using a hopping model based on parameters from density functional theory. The mobility values obtained from these calculations are in good agreement with the experimental values if it is assumed that there are relatively large twist angles between neighboring molecules in the stack. It is shown that a significantly higher mobility can be attained if the twist angle between neighboring oligomers is reduced.
Impact of gate materials on positive charge formation in HfO2∕SiO2 stacks (2006)

The use of metal gates removes gate depletion and allows aggressive downscaling of equivalent oxide thickness. The impact of changing gate from poly-Si to metal on device reliability has not been fully addressed. This work focuses on how TaN gate affects the positive charge formation in HfO2∕SiO2 stacks. Under positive gate bias stresses, the results show that positive charge formation in metal-gated samples is significantly higher than in poly-Si gated samples. However, positive charge formation is similar in these two types of samples, when stressed under negative gate bias. The results are explained by assuming that there are more hydrogenous species at the metal/dielectric interface and the hydrogen release from the anode dominates the positive charge formation. The behavior of positive charges in the stack is also compared with that in a single SiO2 layer.
Cryophotoclustering techniques for synthesizing very small, naked silver clusters Agn of known size (where n = 2-5). The molecular metal cluster-bulk metal particle interface (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCryophotoclustering techniques for synthesizing very small, naked silver clusters Agn of known size (where n = 2-5). The molecular metal cluster-bulk metal particle interfaceGeoffrey A. Ozin and Helmut HuberCite this: Inorg. Chem. 1978, 17, 1, 155–163Publication Date (Print):January 1, 1978Publication History Published online1 May 2002Published inissue 1 January 1978https://pubs.acs.org/doi/10.1021/ic50179a029https://doi.org/10.1021/ic50179a029research-articleACS PublicationsRequest reuse permissionsArticle Views461Altmetric-Citations167LEARN 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-Alertsclose Get e-Alerts
An inward‐rectifying K+ current in clonal rat pituitary cells and its modulation by thyrotrophin‐releasing hormone. (1990)

1. Voltage-dependent K+ currents were recorded in cultured tumour-derived anterior pituitary cells of the rat (GH3 cells) with the patch clamp technique. An inward-rectifying current is described which is found to be carried by K+. 2. In isotonic KCl, whole-cell inward K+ currents were elicited by hyperpolarizing pulses from a holding potential of -40 mV. These inward K+ currents showed time- and voltage-dependent inactivation at potentials more negative than -60 mV. Inactivation was faster and more complete at larger hyperpolarizations. Recovery from inactivation was also time- and voltage-dependent. It was faster and more complete with more positive potentials. Time course of inactivation and of recovery from inactivation could be fitted by single exponentials. 3. Two results showed that a steady inward K+ current is present at -40 mV. The holding current at -40 mV was reduced following complete inactivation of the inward K+ current during strong hyperpolarizing pulses, and the amplitude of maximum inward K+ current elicited by hyperpolarization increased after depolarizing pre-pulses of 5 s. The resting conductance was estimated to be 20-30% of the maximum inward-rectifying conductance. 4. The inward K+ current was drastically reduced by Cs+ and Ba2+, but not by Ni2+ and Co2+. Quinidine, 4-aminopyridine and tetraethylammonium chloride blocked the current. In contrast, dendrotoxin was without effect. 5. Thyrotrophin-releasing hormone (TRH) which induces biphasic secretion of prolactin in GH3 cells consistently reduced the inward K+ current in the presence of internal Ca2+. This reduction was abolished if the pipette solution contained guanosine 5'-O-(2-thiodiphosphate) (GDP beta S; 400 microM), confirming the involvement of G-proteins in the signal transduction pathway. 6. TRH shifted the voltage-dependence of inward K+ current inactivation to less negative potentials resulting in pronounced K+ current inactivation in the range of the resting potential of these cells (-40 to -60 mV). 7. In intact cells, closing of K+ channels would result in a depolarization. The existence of an inward-rectifying K+ current in GH3 cells which is able to be reduced by TRH could readily explain the TRH-induced increase in action potential firing underlying the sustained second phase of secretion.
Protein phosphorylation and the control of glycogen metabolism in skeletal muscle (1983)

Abstract Glycogen metabolism in mammalian skeletal muscle is controlled by a regulatory network in which six protein kinases, four protein phosphatases and several thermostable regulatory proteins determine the activation state of glycogen phosphorylase and glycogen synthase, the rate-limiting enzymes of this process. Thirteen phosphorylation sites are involved, twelve of which have been isolated and sequenced and shown to be phosphorylated in vivo. The effects of adrenalin and insulin on the state of phosphorylation of each site have been determined. The neural control of glycogen metabolism is mediated by calcium ions and involves phosphorylase kinase, and a specific calmodulin-dependent glycogen synthase kinase. The β-adrenergic control of the system is mediated by cyclic AMP, and involves the phosphorylation of phosphorylase kinase, glycogen synthase and inhibitor 1 by cyclic-AMP-dependent protein kinase. Inhibitor 1 is a specific inhibitor of protein phosphatase 1, the major phosphatase involved in the control of glycogen metabolism. The stimulation of glycogen synthesis by insulin results from the dephosphorylation of glycogen synthase at sites (3a + 3b + 3c), which are introduced by the enzyme glycogen synthase kinase 3. The structure, regulation and substrate specificities of the protein phosphatases involved in glycogen metabolism are reviewed. Protein phosphatase 1 can exist in an inactive form termed the Mg-ATP-dependent protein phosphatase, which consists of a complex between the catalytic subunit and a thermostable protein termed inhibitor 2. Activation of this complex is catalysed by glycogen synthase kinase 3. It involves the phosphorylation of inhibitor 2 and its dissociation from the catalytic subunit. Protein phosphatase 2A can be resolved into three forms by ion exchange chromatography. These species contain the same catalytic subunit and other subunits that may have a regulatory function. Protein phosphatase 2B is a Ca2+-dependent enzyme composed of two subunits, A and B. Its activity is increased tenfold by calmodulin, which interacts with the A-subunit. The B-subunit is a Ca2+-binding protein that is homologous with calmodulin. Its N-terminus contains the unusual myristyl blocking group, only found previously in the catalytic subunit of cyclic-AMP-dependent protein kinase. Protein phosphatase 2C is a Mg2+-dependent enzyme that accounts for a very small proportion of the glycogen synthase phosphatase activity in skeletal muscle. It is likely to be involved in the regulation of other metabolic processes in vivo such as cholesterol synthesis. Recent evidence suggests that many of the proteins involved in the control of glycogen metabolism have much wider roles, and that they participate in the neural and hormonal regulation of a variety of intracellular processes.
Where Are the GaPs? A Rational Approach to Monomer Acquisition and Selection (2000)

Gridding and partitioning (GaP) is a computational method for the classification and selection of monomers for combinatorial libraries. The molecules are described in terms of the pharmacophoric groups they contain and where those pharmacophoric groups can be located in three-dimensional space. The approach involves a detailed conformational analysis of each molecule. This conformational analysis is done within a common coordinate frame, thus enabling the monomers to be compared. The use of a partitioned space is central to this particular application as it facilitates the identification of regions of space which are not well represented by existing compounds. Several ways to extend the use of partitioned pharmacophore spaces are described. Applications of the approach in monomer acquisition and in library design are outlined.
Optimising a 3D convolutional neural network for head and neck computed tomography segmentation with limited training data (2022)

Through careful tuning and customisation we trained a 3D CNN with a small dataset to produce segmentations of HN OARs with an accuracy that is comparable with inter-clinician deviations. Our proposed model performed competitively with current SOTA methods.
ChemInform Abstract: Hydrothermal Synthesis and Crystal and Molecular Structure of a Three‐ Dimensional Vanado‐Arsonate (NH4)3((VO)(V2O3)(AsO4)2(HAsO4)), Exhibiting Both (V‐O‐V)∞ Chains and Isolated (V2O3) Units. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Suppressing artificial equilibrium states caused by spurious currents in droplet spreading simulations with dynamic contact angle model (2020)

Accurate methods for numerical simulation of dynamic wetting and spreading phenomena are a valuable tool to support the advancement of related technological processes such as inkjet-printing. Here, it is demonstrated that numerical methods employing dynamic contact angle models are prone to artificial equilibrium states caused by spurious (parasitic) currents. The capability of different approaches in reducing spurious currents for sessile and spreading droplets with low equilibrium contact angle is evaluated. To minimise the influence of spurious currents on dynamic contact angle models, a smoothing step in the evaluation of the contact line velocity is introduced in this paper. The benefit and performance of this new approach is demonstrated by algebraic volume-of-fluid simulations of spreading and receding droplets with the Kistler dynamic contact angle model.
Antinociception mediated by the periaqueductal gray is attenuated by orphanin FQ (1997)

Orphanin FQ or nociceptin (OFQ/N(1-17)) is a recently discovered peptide which, upon intracerebroventricular administration, reverses opioid-mediated analgesias. OFQ/N(1-17) terminals are located in the periaqueductal gray (PAG), a structure known to be involved in pain modulation, suggesting that the functional anti-opioid effects of OFQ/N(1-17) are mediated by PAG neurons. To test this, subsequent microinjections of morphine or kainic acid and OFQ/N(1-17) were made into the PAG of awake rats. Administration of OFQ/N(1-17) attenuated the tail flick inhibition produced by both morphine and kainic acid microinjection. OFQ/N(1-17) attenuation of antinociception produced by a neuroexcitant indicates that OFQ/N(1-17) reverses opioid antinociception by inhibiting PAG output neurons.
Molten salt considerations for accelerator-driven subcritical fission to close the nuclear fuel cycle (2013)

The host salt selection, molecular modeling, physical chemistry, and processing chemistry are presented here for an accelerator-driven subcritical fission in a molten salt core (ADSMS). The core is fueled solely with the transuranics (TRU) and long-lived fission products (LFP) from used nuclear fuel. The neutronics and salt composition are optimized to destroy the transuranics by fission and the long-lived fission products by transmutation. The cores are driven by proton beams from a strong-focusing cyclotron stack. One such ADSMS system can destroy the transuranics in the used nuclear fuel produced by a 1GWe conventional reactor. It uniquely provides a method to close the nuclear fuel cycle for green nuclear energy.
Use of Solvent Mapping for Characterizing the Binding Site and for Predicting the Inhibition of the Human Ether-á-Go-Go-Related K+ Channel (2022)

Molecular dynamics was used to optimize the droperidol-hERG complex obtained from docking. To accommodate the inhibitor, residues T623, S624, V625, G648, Y652, and F656 did not move significantly during the simulation, while F627 moved significantly. Binding sites in cryo-EM structures and in structures obtained from molecular dynamics simulations were characterized using solvent mapping and Atlas ligands, which were negative images of the binding site, were generated. Atlas ligands were found to be useful for identifying human ether-á-go-go-related potassium channel (hERG) inhibitors by aligning compounds to them or by guiding the docking of compounds in the binding site. A molecular dynamics optimized structure of hERG led to improved predictions using either compound alignment to the Atlas ligand or docking. The structure was also found to be suitable to define a strategy for lowering inhibition based on the proposed binding mode of compounds in the channel.
Architecture design of an H.264/AVC decoder for real-time FPGA implementation (2006)

This paper discusses hardware development of a real-lime H.264/AVC video decoder. Synthesis results are presented for example implementations of the inverse quantization, inverse transform, and deblocking filter stages. A hardware architecture is also proposed for FPGA implementations of a complete video decoder
Polyurethanes from Direct Organocatalytic Copolymerization of p‐Tosyl Isocyanate with Epoxides (2020)

Abstract The direct copolymerization of p ‐tosyl isocyanate (TSI) with epoxides, initiated by onium salts in the presence of trialkylborane, to produce polyurethanes is reported. The rate of copolymerization and the (regio)selectivity were investigated in relation to the trialkylborane and the initiator used. Under optimized conditions such copolymerizations have been successfully performed for a wide range of epoxides, including ethylene oxide, propylene oxide, 1‐octene oxide, cyclohexene oxide, and allyl glycidyl ether. These copolymerizations afford a new category of polyurethanes, clear of side products such as cyclic oxazolidinone, isocyanurate, and poly(isocyanate) linkages. The experimental conditions used in this work are compatible with those for the organocatalytic (co)polymerization of other oxygenated monomers and CO 2 , holding the potential for their terpolymerization with p ‐tosyl isocyanate and the development of new materials with unprecedented properties.
Photoelectrochemical Investigation of Ultrathin Film Iron Oxide Solar Cells Prepared by Atomic Layer Deposition (2010)

Atomic layer deposition was used to grow conformal thin films of hematite with controlled thickness on transparent conductive oxide substrates. The hematite films were incorporated as photoelectrodes in regenerative photoelectrochemical cells employing an aqueous [Fe(CN)(6)](3-/4-) electrolyte. Steady state current density versus applied potential measurements under monochromatic and simulated solar illumination were used to probe the photoelectrochemical properties of the hematite electrodes as a function of film thickness. Combining the photoelectrochemical results with careful optical measurements allowed us to determine an optimal thickness for a hematite electrode of ∼20 nm. Mott-Schottky analysis of differential capacitance measurements indicated a depletion region of ∼17 nm. Thus, only charge carriers generated in the depletion region were found to contribute to the photocurrent.
Separating the wheat from the chaff (2015)

Performance-analysis tools are indispensable for understanding and optimizing the behavior of parallel programs running on increasingly powerful supercomputers. However, with size and complexity of hardware and software on the rise, performance data sets are becoming so voluminous that their analysis poses serious challenges. In particular, the search space that must be traversed and the number of individual performance views that must be explored to identify phenomena of interest becomes too large. To mitigate this problem, we use visual analytics. Specifically, we accelerate the analysis of performance profiles by automatically identifying (1) relevant and (2) similar data subsets and their performance views. We focus on views of the virtual-process topology, showing that their relevance can be well captured with visual-quality metrics and that they can be further assigned to topical groups according to their visual features. A case study demonstrates that our approach helps reduce the search space by up to 80%.
Epidermal growth factor receptor cytoplasmic domain mutations trigger ligand-independent transformation. (1990)

The transforming gene product of avian erythroblastosis virus, v-erbB, is derived from the epidermal growth factor (EGF) receptor but has lost its extracellular ligand-binding domain and was mutated in its cytoplasmic portion, which is thought to be responsible for biological signal generation. We have repaired the deletion of extracellular EGF-binding sequences and investigated the functional consequences of cytoplasmic erbB mutations. Within the resulting EGF receptors, the autophosphorylation activities of the cytoplasmic domains of v-erbB-H and v-erbB-ES4 were fully ligand dependent in intact cells. However, the mitogenic and transforming signaling activities of an EGF receptor carrying v-erbB-ES4 (but not v-erbB-H) cytoplasmic sequences remained ligand independent, whereas those of a receptor with a v-erbB-H cytoplasmic domain were regulated by EGF or transforming growth factor alpha. Thus, structural alterations in the cytoplasmic domain of growth factor receptor tyrosine kinases may induce constitutive signaling activity without autophosphorylation. These findings provide new insight into the mechanism of receptor-mediated signal transduction and suggest a novel alternative for subversion of cellular control mechanisms and proto-oncogene activation.