gebhart/patrepeval huggingface dataset:
Epigenetic Inactivation of the Secreted Frizzled-Related Protein Gene Family in Multiple Myeloma. (2007)

Abstract Multiple myeloma (MM) is a B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. Previous molecular studies have largely focused on acquired genetic aberrations in MM. There is increasing evidence that in addition to genetic aberrations epigenetic processes play a major role in carcinogenesis. Aberrant methylation of CpG islands near gene promoter regions is the most widely studied epigenetic abnormality in human malignancies and is associated with loss of gene function. This epigenetic event acts as an alternative to mutations and deletions to disrupt tumor suppressor gene function. The Wnt pathway has been recognized to be essential for normal organ development, and a role for Wnt signal transduction at several stages of lymphocyte differentiation and in the self-renewal of hematopoietic stem cells could be demonstrated. Alterations in the Wnt pathway have been shown to contribute to the pathogenesis of various human malignancies. Epigenetic silencing of the family of secreted frizzled-related proteins (SFRPs), which act as Wnt antagonists, was recently reported in several solid tumors and in acute lymphoblastic leukemia. In order to investigate the potential role of abnormal Wnt signaling in MM, we determined the methylation status of the promoter-associated CpG islands of SFRP-1, 2, 4 and 5 in the MM cell lines U266, LP-1, RPMI-8226 and OPM-2. Methylation-specific polymerase chain reaction (MSP) analysis revealed that promoter hypermethylation of the SFRP genes was a frequent event in MM cell lines (SFRP-1: 2/4, SFRP-2: 2/4, SFRP-4: 1/4 and SFRP-5: 3/4). Aberrant methylation of SFRP-1 and SFRP-2 in MM cell lines was associated with transcriptional silencing, as determined by real-time reverse transcriptase polymerase chain reaction. Treatment of cell lines that carry a hypermethylated SFRP-1 and SFRP-2 gene, respectively, with the demethylating agent 5-aza-2′-deoxycytidine resulted in gene reexpression. We then analyzed by MSP the methylation status of SFRP-1, 2, 4 and 5 in 76 specimens obtained from MM patients. The frequency of aberrant methylation among the primary patient samples was 38.2% (29/76) for SFRP-1, 59.2% (45/76) for SFRP-2, 2.6% (2/76) for SFRP-4 and 7.6% (6/76) for SFRP-5. There was a high incidence of concomitant hypermethylation of SFRP-1 and SRFP-2. We conclude that promoter hypermethylation of the SFRP genes is a novel epigenetic event in MM that may contribute to aberrant activation of the Wnt pathway. Further studies are warranted to elucidate the functional consequences of aberrant Wnt signaling by downregulation of the SFRP genes in the pathogenesis of MM. Additionally, the increasing evidence for the important role of DNA methylation changes in malignant plasma cell disorders may serve as a basis for the use of epigenetically targeted therapeutic approaches in MM in the future.
Enzymology of l-Tyrosine Biosynthesis in Mung Bean (Vigna radiata [L.] Wilczek) (1979)

The enzymes of the 4-hydroxyphenylpyruvate (prephenate dehydrogenase and 4-hydroxyphenylpyruvate aminotransferase) and pretyrosine (prephenate aminotransferase and pretyrosine dehydrogenase) pathways of l-tyrosine biosynthesis were partially purified from mung bean (Vigna radiata [L.] Wilczek) seedlings. NADP-dependent prephenate dehydrogenase and pretyrosine dehydrogenase activities coeluted from ion exchange, adsorption, and gel-filtration columns, suggesting that a single protein (52,000 daltons) catalyzes both reactions. The ratio of the activities of partially purified prephenate to pretyrosine dehydrogenase was constant during all purification steps as well as after partial inactivation caused by p-hydroxymercuribenzoic acid or heat. The activity of prephenate dehydrogenase, but not of pretyrosine dehydrogenase, was inhibited by l-tyrosine at nonsaturating levels of substrate. The K(m) values for prephenate and pretyrosine were similar, but the specific activity with prephenate was 2.9 times greater than with pretyrosine.Two peaks of aromatic aminotransferase activity utilizing l-glutamate or l-aspartate as amino donors and 4-hydroxyphenylpyruvate, phenylpyruvate, and/or prephenate as keto acid substrates were eluted from DEAE-cellulose. Of the three keto acid substrates, 4-hydroxyphenylpyruvate was preferentially utilized by 4-hydroxyphenylpyruvate aminotransferase whereas prephenate was best utilized by prephenate aminotransferase. The identity of a product of prephenate aminotransferase as pretyrosine following reaction with prephenate was established by thin layer chromatography of the dansyl-derivative.
SIMPLIFIED PREDICTIVE MODELS FOR CO₂ SEQUESTRATION PERFORMANCE ASSESSMENT RESEARCH TOPICAL REPORT ON TASK #3 STATISTICAL LEARNING BASED MODELS (2014)

We compare two approaches for building a statistical proxy model (metamodel) for CO₂ geologic sequestration from the results of full-physics compositional simulations. The first approach involves a classical Box-Behnken or Augmented Pairs experimental design with a quadratic polynomial response surface. The second approach used a space-filling maxmin Latin Hypercube sampling or maximum entropy design with the choice of five different meta-modeling techniques: quadratic polynomial, kriging with constant and quadratic trend terms, multivariate adaptive regression spline (MARS) and additivity and variance stabilization (AVAS). Simulations results for CO₂ injection into a reservoir-caprock system with 9 design variables (and 97 samples) were used to generate the data for developing the proxy models. The fitted models were validated with using an independent data set and a cross-validation approach for three different performance metrics: total storage efficiency, CO₂ plume radius and average reservoir pressure. The Box-Behnken–quadratic polynomial metamodel performed the best, followed closely by the maximin LHS–kriging metamodel.
Molecular Characterization of the Highest Risk Adult Patients with Acute Myeloid Leukemia (AML) through Multi-omics Clustering (2021)

Abstract Background : Acute myeloid leukemia (AML) is a clinically heterogeneous group of diseases with poor outcomes that are partly due to its complex and poorly understood heterogeneity. Methods : Here, we use a multi-omics approach to identify a molecular subgroup with the worst response to chemotherapy, and to identify promising drug targets specifically for this AML subgroup. Results : Multi-omics clustering analysis using RNA and CNA expression data resulted in the three primary clusters of 166 AML adult TCGA cancer cases. One of these clusters, which we label as the high-risk molecular subgroup (HRMS), consisted of cases that responded very poorly to standard chemotherapy, with only about 10% survival to two years. The gene TP53 was mutated in most cases in the HRMS, but not in other cases. The top 6 genes over-expressed in the HRMS included E2F4, CD34, CD109, MN1, MMLT3, and CD200. Multi-omics pathway analysis using RNA and CNA expression data identified in the HRMS subgroup over-expressed pathways related to immune function, cell proliferation, and DNA damage. Conclusion : Some AML patients are not successfully treated with the current standard of care chemotherapy, and urgently need targeted therapeutics. Potential drug targets include over-expressed genes E2F4, and MN1, as well as mutations in TP53, and several molecular pathways.
Thermal Conductivity of Graphene and Graphite: Collective Excitations and Mean Free Paths (2014)

We characterize the thermal conductivity of graphite, monolayer graphene, graphane, fluorographane, and bilayer graphene, solving exactly the Boltzmann transport equation for phonons, with phonon-phonon collision rates obtained from density functional perturbation theory. For graphite, the results are found to be in excellent agreement with experiments; notably, the thermal conductivity is 1 order of magnitude larger than what found by solving the Boltzmann equation in the single mode approximation, commonly used to describe heat transport. For graphene, we point out that a meaningful value of intrinsic thermal conductivity at room temperature can be obtained only for sample sizes of the order of 1 mm, something not considered previously. This unusual requirement is because collective phonon excitations, and not single phonons, are the main heat carriers in these materials; these excitations are characterized by mean free paths of the order of hundreds of micrometers. As a result, even Fourier's law becomes questionable in typical sample sizes, because its statistical nature makes it applicable only in the thermodynamic limit to systems larger than a few mean free paths. Finally, we discuss the effects of isotopic disorder, strain, and chemical functionalization on thermal performance. Only chemical functionalization is found to play an important role, decreasing the conductivity by a factor of 2 in hydrogenated graphene, and by 1 order of magnitude in fluorogenated graphene.
Learning Neural Templates for Text Generation (2018)

While neural, encoder-decoder models have had significant empirical success in text generation, there remain several unaddressed problems with this style of generation. Encoderdecoder models are largely (a) uninterpretable, and (b) difficult to control in terms of their phrasing or content. This work proposes a neural generation system using a hidden semimarkov model (HSMM) decoder, which learns latent, discrete templates jointly with learning to generate. We show that this model learns useful templates, and that these templates make generation both more interpretable and controllable. Furthermore, we show that this approach scales to real data sets and achieves strong performance nearing that of encoderdecoder text generation models.
DEVELOPMENT OF RETROFIT RAILINGS FOR THROUGH TRUSS BRIDGES (1983)

The design and development of bridge railing systems for through truss structures are described in this paper. The unique design of these structures makes rigid railings mandatory to exclude the errant vehicles from the truss members located behind the railing. The two systems were designed to meet different performance conditions. The high-performance system contained and redirected a 20,000-lb (9000-kg) bus impacting at 55 mph (90 km/h) and a 15-degree angle. The low-service-level system contained and redirected a 4,500-lb (2000-kg) car impacting at 60 mph (95 km/h) and a 15-degree angle. In addition, 2,250-lb (1000-kg) and 1,800-lb (800-kg) cars were used to evaluate the systems, including the bridge approach railing, for the high-performance system. The two systems meet the design criteria and are recommended for immediate implementation.
Modeling of Single Photon Avalanche Diode Array Detectors for PET Applications (2014)

We developed a configurable model of single photon avalanche diodes (SPAD) array photodetectors with intelligent control and active quenching. In this model individual components can be simulated independently and subsequently linked to provide the overall detector response. The model enables the simulation of the entire detector and analysis of performance, including photon detection efficiency, timing and energy resolution. It can be used to optimize detector performance for specific applications, such as positron emission tomography (PET). The simulator consists of multiple configurable and interchangeable modules to model the array geometry as well as physical and optical characteristics based on physical models and statistical equations. Readout electronics are also simulated in an algorithmic form. Monte Carlo simulations are used to model the 511 keV annihilation photon interactions and the optical photon transport in the scintillator, as well as carrier random walk in the silicon. Different methods to extract information from the digital output signal can be investigated. The simulator paves the way to the developement of new algorithms to extract relevant information in PET, but also for other applications such as Cerenkov radiation and fluorescence microscopy. Simulation results for photon detection efficiency, energy resolution and timing resolution are reported, showing the functionality of the simulator.
Supplementary Figure S4 from Radioresistant Cancer Cells Can Be Conditioned to Enter Senescence by mTOR Inhibition (2023)

&lt;p&gt;Supplementary Figure S4 - PDF file 302K, Suppression of autophagic flux decreases survival of radioresistant AMC-HN-9 cells&lt;/p&gt;
Cross-Coupling Hydrogen Evolution Reaction in Homogeneous Solution without Noble Metals (2014)

A highly efficient noble-metal-free homogeneous system for a cross-coupling hydrogen evolution (CCHE) reaction is developed. With cheap, earth-abundant eosin Y and molecular catalyst Co(dmgH)2Cl2, good to excellent yields for coupling reactions with a variety of isoquinolines and indole substrates and H2 have been achieved without any sacrificial oxidants. Mechanistic insights provide rich information on the effective, clean, and economic CCHE reaction.
Analysis of Polymeric Methylaluminoxane (MAO) via Small Angle Neutron Scattering (2007)

Since its discovery as a crucial cocatalyst in metallocene and post-metallocene olefin polymerizations methylaluminoxane (MAO) has retained commercial and academic status. In spite of continued interest the MAO structure remains ambiguously defined. Because of limited alkane solubility toluene emerged as the MAO solvent of necessity. With time these toluene solutions can develop a gel fraction. The MAO structures proposed include linear, ring, ladder, and cyclic with the latter involving fused four and six membered rings along with cage and drumlike architectures. The linear and ring structures have aluminum and oxygen valences of three and two respectively while the other structures require Al/O co-ordination numbers of four and three. MAO structural information has been gathered from colligative property measurements, various NMR formats and quantum chemical calculations. We have used small-angle neutron scattering (SANS)fortified with static and dynamic light scattering (SLS/DLS)as the primary analysis tool for dilute MAO solutions (φ/φ* ≤ 0.6). The main structure assayed is a linear polymer chain consisting of [−Al(CH3)−O−] monomer units with an Mw of 20 kg/mol and a negative second virial coefficient. The latter fortifies the recognized state of play that toluene is a poor MAO solvent. About 0.8 wt % of MAO was captured as large-scale three-dimensional aggregates. Elemental analysis results show that in these large-scale aggregates the ratio of O/Al is significantly larger than for the smaller polymer chains. Additionally the large-scale aggregates contain only a small fraction of CH3 units. Those structures may be the precursor aggregates to the previously observed macroscopic gel fraction reported to form over time at room temperature. The solutions studied in this work did not show gel formation over an 8-month period at ∼0 °C.
X-ray diffraction (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTX-ray diffractionC. E. PflugerCite this: Anal. Chem. 1978, 50, 5, 161–166Publication Date (Print):April 1, 1978Publication History Published online1 May 2002Published inissue 1 April 1978https://doi.org/10.1021/ac50028a019RIGHTS & PERMISSIONSArticle Views165Altmetric-Citations1LEARN 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 InReddit PDF (1002 KB) Get e-Alerts Get e-Alerts
The 35th Sir Frederick Bartlett Lecture: Eye movements and attention in reading, scene perception, and visual search (2009)

Eye movements are now widely used to investigate cognitive processes during reading, scene perception, and visual search. In this article, research on the following topics is reviewed with respect to reading: (a) the perceptual span (or span of effective vision), (b) preview benefit, (c) eye movement control, and (d) models of eye movements. Related issues with respect to eye movements during scene perception and visual search are also reviewed. It is argued that research on eye movements during reading has been somewhat advanced over research on eye movements in scene perception and visual search and that some of the paradigms developed to study reading should be more widely adopted in the study of scene perception and visual search. Research dealing with "real-world" tasks and research utilizing the visual-world paradigm are also briefly discussed.
MM&T: Testing of Electro-Optic Components (1981)

Abstract : Current optical component testing methods were reviewed. Suggested optical testing procedures and standards related to production testing were presented. Optical transfer functions and related applications were reviewed. New approach to production testing of optical components including an analog OFT measurement was laboratory demonstrated.
Feeling and seeing: issues in force display (1990)

This paper is about using the sense of touch, the hapti c system, as part of our everyday interface wit h computationally created worlds .
Nanotubes in Microwave Fields:  Light Emission, Intense Heat, Outgassing, and Reconstruction (2003)

SWNTs, produced via the HiPco process, display strong microwave absorption (1.01 × 10-5 eV microwave field) with subsequent dramatic light emission, intense heat release (2000 °C), outgassing, mechanical extension, and nanotube reconstruction (welding and loop formation).
Entitled to Learn Together? (2018)

This chapter provides the interconnected British studies that investigated young 'normal' children's interactions with classmates with Severe Learning Difficulties (SLD). Various types of child-child learning were discussed as possible models for interaction. Different types of shared learning including buddy systems, peer tutoring, cooperative learning and collaborative learning were reviewed. The SLD school staff hoped that the same work would cultivate their pupil’s independence and abilities to communicate with others. The interviews probed the ordinary school children's understanding of SLD as well as their feelings towards the children with SLD. One child believed that if his friend with SLD was given a Disprin he would be well again and would then resemble children from the ordinary school. Several striking findings emerged from analyses of whether and how ordinary school children interacted with children with SLD. Interaction between ordinary and SLD school children occurred about one quarter of the time.
The economic impact of wasted prescription medication in an outpatient population of older adults. (2001)

The causes and costs of outpatient medication waste are not known. We report the results of a cross-sectional pilot survey of medication waste in a convenience sample of 73 New Hampshire retirement community residents aged 65 years or older. We used questionnaires and in-home pill counts to determine the annual occurrence of medication waste, defined as no intention to take leftover medicines prescribed within the past year. Mean individual annual cost of wasted medication was $30.47 (range = $0-$131.56). Waste represented 2.3% of total medication costs. The main causes for waste included: resolution of the condition for which the medication was prescribed (37.4%), patient-perceived ineffectiveness (22.6%), prescription change by the physician (15.8%), and patient-perceived adverse effects (14.4%). Individual costs were modest, but if $30 per person represents a low estimate of average annual waste, the US national cost for adults older than 65 years would top $1 billion per year.
Development of a Deep Image Retrieval Network Using Hierarchical and Multi-scale Spatial Features (2023)

Image retrieval aims to find similar images to a given query by matching features extracted directly from the images of a database. Deep convolutional neural networks provide an excellent framework for obtaining highly representative feature vectors from images to improve an image retrieval method. Deep residual networks perform better than existing deep networks, as they can incorporate useful information into the feature vectors through residual learning by designing appropriate operations in the employed residual block. One type of such information is spatial information obtained at different scales and levels of abstraction. In this paper, a novel residual block is proposed to generate a rich set of features for the task of image retrieval. The development of the residual block consists of three modules: a hierarchical spatial feature extraction module focusing on spatial information at different abstraction levels, a multi-scale feature extraction module that generates features at three different scales, and a feature fusion module. The results of experiments on various datasets and an ablation study show that the proposed residual block noticeably improves the representational capacity of the network, which, in turn, significantly enhances the retrieval performance of the deep image retrieval network.
Anion control as a strategy to achieve high-mobility and high-stability oxide thin-film transistors (2013)

Ultra-definition, large-area displays with three-dimensional visual effects represent megatrend in the current/future display industry. On the hardware level, such a "dream" display requires faster pixel switching and higher driving current, which in turn necessitate thin-film transistors (TFTs) with high mobility. Amorphous oxide semiconductors (AOS) such as In-Ga-Zn-O are poised to enable such TFTs, but the trade-off between device performance and stability under illumination critically limits their usability, which is related to the hampered electron-hole recombination caused by the oxygen vacancies. Here we have improved the illumination stability by substituting oxygen with nitrogen in ZnO, which may deactivate oxygen vacancies by raising valence bands above the defect levels. Indeed, the stability under illumination and electrical bias is superior to that of previous AOS-based TFTs. By achieving both mobility and stability, it is highly expected that the present ZnON TFTs will be extensively deployed in next-generation flat-panel displays.
Applications of Correlation to the Communication of Information (2005)

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