gebhart/patrepeval huggingface dataset:
A combined genetic and biochemical approach to mammalian signal transduction (1995)

The last five years have seen a rapid increase in interest and understanding of signal transduction pathways. While the description of such pathways has become more detailed and complex, a number of consistent findings have emerged. Modular domains, such as SH2 and SH3 domains, are present on a wide variety of proteins and mediate specific protein-protein interactions. By defining the interaction mediated by such domains, a 'language' of interaction between proteins in signalling pathways is emerging. As more signalling proteins are identified it has become apparent that most oncogenes and tumour suppressor genes are components of major signalling pathways. Therefore, studies on the basic biology of signal transduction are having a direct impact on our understanding of cell transformation. With the characterisation of signalling pathways in a range of organisms, it has also become obvious that signalling pathways are ancient and have been highly conserved over the last billion years of evolution. A practical result of this finding has been the ability to exploit results obtained in genetically tractable invertebrate species such as C. elegans and Drosophila melanogaster to investigate signal transduction in mammals. This is an approach we have emphasized in our investigation of signal transduction by tyrosine kinase receptors in human and mouse cells. Results obtained in these studies with the Sos and Siah proteins are reviewed.
Fronto‐Parietal gray matter and white matter efficiency differentially predict intelligence in males and females (2016)

While there are minimal sex differences in overall intelligence, males, on average, have larger total brain volume and corresponding regional brain volumes compared to females, measures that are consistently related to intelligence. Limited research has examined which other brain characteristics may differentially contribute to intelligence in females to facilitate equal performance on intelligence measures. Recent reports of sex differences in the neural characteristics of the brain further highlight the need to differentiate how the structural neural characteristics relate to intellectual ability in males and females. The current study utilized a graph network approach in conjunction with structural equation modeling to examine potential sex differences in the relationship between white matter efficiency, fronto-parietal gray matter volume, and general cognitive ability (GCA). Participants were healthy adults (n = 244) who completed a battery of cognitive testing and underwent structural neuroimaging. Results indicated that in males, a latent factor of fronto-parietal gray matter was significantly related to GCA when controlling for total gray matter volume. In females, white matter efficiency and total gray matter volume were significantly related to GCA, with no specificity of the fronto-parietal gray matter factor over and above total gray matter volume. This work highlights that different neural characteristics across males and females may contribute to performance on intelligence measures. Hum Brain Mapp 37:4006-4016, 2016. © 2016 Wiley Periodicals, Inc.
The Role of Insulin in Human Brain Glucose Metabolism (2002)

The effect of basal insulin on global and regional brain glucose uptake and metabolism in humans was studied using 18-fluorodeoxyglucose and positron emission tomography (FDG-PET). Eight healthy male volunteers aged 49.3 +/- 5.1 years were studied twice in random order. On each occasion, they received an infusion of 0.1 mg. kg(-1). min(-1) somatostatin to suppress endogenous insulin production. In one study 0.3 mU. kg(-1). min(-1) insulin was infused to replace basal circulating insulin levels, and in the other study a saline infusion was used as control. We sought stimulatory effects of basal insulin on brain glucose metabolism particularly in regions with deficiencies in the blood-brain barrier and high density of insulin receptors. Insulin levels were 27.07 +/- 1.3 mU/l with insulin replacement and 3.51 +/- 0.4 mU/l without (P = 0.001). Mean global rate of brain glucose utilization was 0.215 +/- 0.030 mmol. kg(-1). min(-1) without insulin and 0.245 +/- 0.021 mmol. kg(-1). min(-1) with insulin (P = 0.008, an average difference of 15.3 +/- 12.5%). Regional analysis using statistical parametric mapping showed that the effect of basal insulin was significantly less in the cerebellum (Z = 5.53, corrected P = 0.031). We conclude that basal insulin has a role in regulating global brain glucose uptake in humans, mostly marked in cortical areas.
Cadherin exits the junction by switching its adhesive bond (2011)

The plasticity of cell–cell adhesive structures is crucial to all normal and pathological morphogenetic processes. The molecular principles of this plasticity remain unknown. Here we study the roles of two dimerization interfaces, the so-called strand-swap and X dimer interfaces of E-cadherin, in the dynamic remodeling of adherens junctions using photoactivation, calcium switch, and coimmunoprecipitation assays. We show that the targeted inactivation of the X dimer interface blocks the turnover of catenin-uncoupled cadherin mutants in the junctions of A-431 cells. In contrast, the junctions formed by strand-swap dimer interface mutants exhibit high instability. Collectively, our data demonstrate that the strand-swap interaction is a principal cadherin adhesive bond that keeps cells in firm contact. However, to leave the adherens junction, cadherin reconfigures its adhesive bond from the strand swap to the X dimer type. Such a structural transition, controlled by intercellular traction forces or by lateral cadherin alignment, may be the key event regulating adherens junction dynamics.
Age-dependent decrease of hepatic geranylgeranoic acid and its oral supplementation prevents spontaneous hepatoma in C3H/HeN mice (2021)

Abstract Aim Geranylgeranoic acid (GGA) has been developed as a preventive agent against second primary hepatoma. Recently, GGA was reported to induce cell death in human hepatoma cells via TLR4-mediated pyroptosis. We have reported that GGA is enzymatically biosynthesized from mevalonic acid in human hepatoma-derived cells and that endogenous GGA is found in most organs of rats. In addition, we found that upregulation of endogenous GGA levels by zaragozic acid A (ZAA) induced cell death in human hepatoma-derived cells. Therefore, we investigated the age-related changes of hepatic GGA and the possibility of suppressing hepatocarcinogenesis by GGA supplementation using male C3H/HeN mice that spontaneously develop hepatoma. Methods We measured endogenous GGA and mRNA of MAOB, a key enzyme of GGA biosynthesis, in the liver of male C3H/HeN mice aged 6–93 weeks. We also tried suppressing spontaneous hepatocarcinogenesis by a single administration of GGA to C3H/HeN mice. Results Hepatic GGA content and Maob mRNA expression level age-dependently decreased in male C3H/HeN mice, some of which produced spontaneous hepatoma in 2 years. A single oral administration of GGA at 11 months of age significantly prevented hepatoma in terms of the number and weight of tumors per mouse at 23 months. Oral supplementation with GGA or geranylgeraniol significantly increased endogenous hepatic GGA contents dose-dependently, and ZAA dramatically upregulated hepatic GGA. Conclusion In this study, we found an age-dependent decrease in hepatic endogenous GGA in male C3H/HeN mice and efficient prevention of spontaneous hepatoma by a single administration of GGA at 11 months of age.
Slimming Neural Networks using Adaptive Connectivity Scores (2020)

In general, deep neural network (DNN) pruning methods fall into two categories: 1) Weight-based deterministic constraints, and 2) Probabilistic frameworks. While each approach has its merits and limitations there are a set of common practical issues such as, trial-and-error to analyze sensitivity and hyper-parameters to prune DNNs, which plague them both. In this work, we propose a new single-shot, fully automated pruning algorithm called Slimming Neural networks using Adaptive Connectivity Scores (SNACS). Our proposed approach combines a probabilistic pruning framework with constraints on the underlying weight matrices, via a novel connectivity measure, at multiple levels to capitalize on the strengths of both approaches while solving their deficiencies. In \alg{}, we propose a fast hash-based estimator of Adaptive Conditional Mutual Information (ACMI), that uses a weight-based scaling criterion, to evaluate the connectivity between filters and prune unimportant ones. To automatically determine the limit up to which a layer can be pruned, we propose a set of operating constraints that jointly define the upper pruning percentage limits across all the layers in a deep network. Finally, we define a novel sensitivity criterion for filters that measures the strength of their contributions to the succeeding layer and highlights critical filters that need to be completely protected from pruning. Through our experimental validation we show that SNACS is faster by over 17x the nearest comparable method and is the state of the art single-shot pruning method across three standard Dataset-DNN pruning benchmarks: CIFAR10-VGG16, CIFAR10-ResNet56 and ILSVRC2012-ResNet50.
Ytterbium-doped fibre laser with a Bragg grating reflector written in a multimode fibre (2005)

An efficient cladding-pumped Yb-doped fibre laser with a Bragg grating written in a multimode graded-index fibre is fabricated for the first time. The laser emits one transverse mode with a slope efficiency of 60%. The resonator design proposed in the paper can be used for the development of high-power fibre lasers with an increased fibre core diameter.
Immunolocalization of Fascin, an Actin‐Bundling Protein and Glial Fibrillary Acidic Protein in Human Astrocytoma Cells (2009)

Fascin is a 55-kDa globular protein that functions to organize filamentous-actin into parallel bundles. A role for fascin in cell migration has led to its study in many tumor types. In this report, we investigate fascin in astrocytomas. We show that fascin is expressed in astrocytes and in a panel of human astrocytoma cell lines. Immunofluorescence analysis demonstrates that fascin and the intermediate filament protein, glial fibrillary acidic protein (GFAP), are both expressed in the perinuclear region and within cytoplasmic processes of astrocytes and astrocytoma cells. Amino acid residues within the NH2 terminus of GFAP can undergo phosphorylation; these modifications regulate intermediate filament disassembly and occur during cytokinesis. We show that fascin and specific phosphorylated species of GFAP colocalize within dividing cells. Finally, we demonstrate that fascin co-immunoprecipitates with GFAP and that immunocomplex formation is preferential for GFAP phosphorylated at serine residues 8 and 13. These data show that fascin and GFAP are immunolocalized regionally within cells and tumors of astrocytic origin and suggest that their binding may occur during dynamic reorganization of intermediate filaments.
Ion-networks: a sparse data format capturing full data integrity of data independent acquisition mass spectrometry (2019)

Data-independent acquisition (DIA) mass spectrometry (MS) has introduced deter-ministic, periodic and simultaneous acquisition of all fragment ions. Despite the chimeric side-effects associated with this unprecedented data integrity, DIA data analysis approaches still use conventional spectra and extracted ion chromatograms (XICs) that represent individual precursors and fragments. Here, we introduce ion-networks, an alternative data format wherein nodes correspond to reproducible fragment ions from multiple runs and edges correspond to consistent co-elution. Each ion-network represents a complete experiment and computationally eliminates chimericy based on reproducibility without sacrificing data integrity.
Study of Cetane Properties of ATJ Blends Based on World Survey of Jet Fuels (2016)

Abstract : The cetane properties of a fuel blend containing highly iso-paraffinic ATJ fuel and Jet fuel were studied. Literature review was conducted to obtain cetane properties from PQIS database, CRC report and Tri-Services report. Based on data collected from Task 2.4 of WD0024, on cetane properties of ATJ blends, correlation equations were developed to determine cetane properties as a function of volume percentage of ATJ in the fuel, which was used to determine cetane properties of maximum ATJ blends (50/50 ATJ/Jet fuel). The overall conclusion is that maximum ATJ blends from any jet fuel (Jet A, Jet A-1, and JP-8) had an increase in CI from 7% to 8% using the four variable, D4737 method, while the increase in CI was approximately 3% using D976 method. Based on the extensive decrease in CN and DCN values much below 40, maximum ATJ blends (50/50 ATJ/Jet fuel blends) were deemed not fit-for-use. It was concluded that the amount of ATJ that must be blended with Jet A or JP-8 to obtain 40 DCN, was less than 50% for all the PADD.
Dynamic Contract Trading in Spectrum Markets (2014)

We propose a structured spectrum market and consider two basic types of spectrum contracts that can help attain desired flexibilities and trade-offs in terms of service quality, spectrum usage efficiency and pricing: long-term guaranteed-bandwidth contracts, and short-term opportunistic-access contracts. A primary provider (seller) and a secondary provider (buyer) creates and maintains a portfolio composed of an appropriate mix of these two types of contracts. We address the question of how the spectrum contract portfolio of a seller (buyer) in the spectrum market should be dynamically adjusted, so as to maximize return (minimize cost) subject to meeting the bandwidth demands of its own subscribers. We formulate the above question as a stochastic dynamic programming problem, and obtain structural properties of the optimal dynamic trading strategy that takes into account the current market prices of the contracts and the subscriber demand process in the decision-making.
Metal binding and activation of the ribonuclease H domain from Moloney murine leukemia virus (1999)

The RNase H family of enzymes degrades RNA in RNA.DNA hybrids in a divalent cation-dependent manner. RNases H from diverse sources such as Escherichia coli and human immunodeficiency virus (HIV) share homologous metal-binding active sites, and the activity of the RNase H domain of reverse transcriptase (RT) is required for retroviral replication. The isolated RNase H domain from HIV RT, however, is inactive. In contrast, the RNase H domain of Moloney murine leukemia virus (MMLV) is active, enabling functional studies. Unlike both E. coli RNase HI and HIV RT, the RNase H activity of MMLV RT shows greater activity in Mn(2+) than Mg(2+). We investigated the effect of mutations in five conserved active-site residues of the isolated MMLV RNase H domain. Mutations in two carboxylates eliminate metal binding while mutations in other active-site residues allow retention of metal ion affinity. Mutations that inactivate E.coli RNase HI in Mg(2+) have similar effects on the Mn(2+)-dependent activity of MMLV RNase H. These results suggest a similar one-metal catalytic mechanism for the Mn(2+)- and Mg(2+)-dependent activities of both prokaryotic and retroviral ribonucleases H.
Lasing from high-quality lead halide perovskite single-crystal microparticles (2018)

We have synthesized CsPbBr3 and CH3NH3PbBr3 single-crystal microplates with improved surface quality and obtained whispering-gallery-mode lasing from a size of 2 µm. The method can produce high-quality perovskite microlasers in large quantity within minutes.
Glucocorticoid effects on extracellular matrix proteins and integrins in bovine trabecular meshwork cells in relation to glaucoma. (1998)

The trabecular meshwork (TM) is a specialized eye tissue essential for regulation of the aqueous humor outflow and control of the intraocular pressure. Disturbances of TM cells may lead to elevated intraocular pressure and glaucoma. This study assessed the dexamethasone effects on levels of extracellular matrix proteins and their integrin receptors in bovine TM cells. Instillation of glucocorticoids such as dexamethasone is known to result in ocular hypertension. The histologic changes induced resemble those seen in glaucoma. Examination of the effects of glucocorticoid therefore may provide insights into the pathogenesis of glaucoma. TM cells in either tissue culture or organ cultures were treated with 0 (control), 0.1, or 1 microM of dexamethasone for 72 h. Immunostaining, Western, Northern and dot blot analyses showed that dexamethasone caused an increase in levels of fibronectin and collagen type IV in tissue-cultured TM cells. Increased focal contacts were also observed but the levels of laminin and collagen type I were unaffected. The dexamethasone effect was similarly demonstrated in organ cultures, with the exception that collagen type I also was enhanced. These results suggest that dexamethasone modulates extracellular matrices in the TM. Glucocorticoid may exert its effect through such a modulation in the development of steroid glaucoma.
Diamond as a quantum sensor for space exploration (2018)

Sensing devices used in (aero)space are constrained by energy consumption, mass, volume and environmental&#13;\ncompatibility. Although quantum sensors offer potentially better sensitivity than classical sensors, they are bulky and&#13;\noften require cooling to cryogenic temperatures or operation in vacuum. Here we propose a technical realization of a&#13;\nquantum sensor for magnetic field detection based on nitrogen-vacancy (NV) centers in diamond, which is compatible&#13;\nwith miniaturization and offers potential sub-picotesla sensitivity. The miniaturization is based on recently developed&#13;\nelectric readout of the NV center electron spin resonance. Our engineering platform allows to use diamond chip as a&#13;\nportable magnetic field sensor. We have designed and tested a miniaturized prototype and describe all key components&#13;\nfor technical miniaturization. We achieved a power consumption down to 3.5 W, a weight of the fully integrated sensor&#13;\nof only 27g and small dimensions of 45 x 25 x 25 mm including all driving and readout components. We have proved&#13;\nthe chip functionality in vacuum and explored its thermal behavior. The system will be further used for on-board&#13;\nstratospheric balloon experiment. The miniaturized sensor we developed has potential applications in a wide range of&#13;\nfields including navigation, bio-signal measurement, material analysis or space weather monitoring and planetary&#13;\nobservation.
Por un mundo más sostenible: 2015: Año internacional de la luz y las tecnologías basadas en la luz y año internacional del suelo (2015)

La proclamacion del ano 2015 como Ano Internacional de la Luz y las Tecnologias Basadas en la 
Luz, pretende comunicar a la sociedad la importancia de la luz, y sus tecnologias asociadas, en el 
mundo actual en areas tan importantes como la energia, la educacion, la salud, la comunicacion, etc. 
Cuenta con el copatrocinio de 35 paises entre los que se encuentra Espana. 
Al mismo tiempo, el suelo es importante para asegurar la alimentacion de la poblacion , la 
seguridad alimentaria y los ecosistemas estables. La gestion sostenible del suelo es fundamental 
para el mantenimiento de la calidad de vida
The Reaction of Cyclopentadiene and Ketene (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reaction of Cyclopentadiene and KeteneBenjamin T. Brooks and Godfrey WilbertCite this: J. Am. Chem. Soc. 1941, 63, 3, 870–871Publication Date (Print):March 1, 1941Publication History Published online1 May 2002Published inissue 1 March 1941https://pubs.acs.org/doi/10.1021/ja01848a503https://doi.org/10.1021/ja01848a503research-articleACS PublicationsRequest reuse permissionsArticle Views208Altmetric-Citations24LEARN 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
Abstract 1924: miR-142-3p is a candidate mediator of chloride intracellular channel 4 (CLIC4) loss during squamous cancer progression (2016)

Abstract Chloride intracellular channel 4 (CLIC4) is a broadly expressed protein that has been implicated in multiple cellular processes, including cellular differentiation and apoptosis. As a soluble factor, CLIC4 translocates to the nucleus following exposure to a variety of stimuli, including TGF-β, TNF-α, and etoposide. Nuclear CLIC4 potentiates TGF-β signaling by preventing the dephosphorylation of phospho-SMAD2 and 3 and promotes growth arrest. Although its primary function is as a tumor suppressor, CLIC4 expression is progressively diminished during cancer progression and CLIC4 protein is excluded from the nucleus of many human epithelial neoplasms and squamous cell carcinoma (SCC) cell lines. To date, no gene deletions or mutations have been identified to account for this phenomenon; thus, identifying the mechanism of CLIC4 loss is our primary focus. To determine if epigenetic gene silencing is responsible, we evaluated the methylation status of the CLIC4 promoter in a progression panel (normal, papilloma, SCC) of epithelial cell lines by performing bisulfite sequencing. No differential promoter methylation was found between the cell lines, suggesting that the regulation may be post-transcriptional or post-translational. Because microRNAs (miRNAs) are known to regulate gene expression by mediating the degradation or translational repression of target mRNAs, we performed a bioinformatic analysis of the CLIC4 3’ UTR, which revealed a large number of putative targeting miRNAs. One such miRNA, miR-142-3p, has been predicted to target CLIC4 by multiple algorithms and has been shown to interact with the CLIC4 3’ UTR by high-throughput sequencing and crosslinking immunoprecipitation. We confirmed the functional activity of miR-142-3p against the CLIC4 3’ UTR by using a 3’ UTR luciferase reporter assay and a miR-142-3p mimic. miR-142-3p is high in the tumor tissue and plasma of patients with head and neck SCC and is correlated with worse prognosis, where CLIC4 expression is known to be low. Thus, miR-142-3p may be responsible for mediating CLIC4 loss in squamous lesions and warrants further investigation. Citation Format: Brandi L. Carofino, Stuart H. Yuspa. miR-142-3p is a candidate mediator of chloride intracellular channel 4 (CLIC4) loss during squamous cancer progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1924.