gebhart/patrepeval huggingface dataset:
A unique role for the Rb protein in controlling E2F accumulation during cell growth and differentiation. (1996)

Examination of the interactions involving transcription factor E2F activity during cell growth and terminal differentiation suggests distinct roles for Rb family members in the regulation of E2F accumulation. The major species of E2F in quiescent cells is a complex containing the E2F4 product in association with the Rb-related p130 protein. As cells enter the cell cycle, this complex disappears, and there is a concomitant accumulation of free E2F activity of which E2F4 is a major component. E2F4 then associates with the Rb-related p107 protein as cells enter S phase. Rb can be found in interactions with each E2F species, including E2F4, during G1, but there appears to be a limited amount of Rb with respect to E2F, likely due to the maintenance of most Rb protein in an inactive state by phosphorylation. A contrasting circumstance can be found during the induction of HL60 cell differentiation. As these cells exit the cell cycle, active Rb protein appears to exceed E2F, as there is a marked accumulation of E2F-Rb interactions, involving all E2F species, including E2F4, which is paralleled by the conversion of Rb from a hyperphosphorylated state to a hypophosphorylated state. These results suggest that the specific ability of Rb protein to interact with each E2F species, dependent on concentration of active Rb relative to accumulation of E2F, may be critical in cell-growth decisions.
Exon-mediated activation of transcription starts (2019)

Summary The processing of transcripts from mammalian genes often occurs near in time and space to their transcription. Here we describe a phenomenon we call exon-mediated activation of transcription starts (EMATS) that affects thousands of mammalian genes in which the splicing of internal exons impacts the spectrum of promoters used and expression level of the host gene. We observed that evolutionary gain of new internal exons is associated with gain of new TSSs nearby and increased gene expression. Inhibiting exon splicing reduced transcription from nearby promoters. Conversely, creation of new splice sites and enable splicing of new exons activated transcription from cryptic promoters. The strongest effects were associated with weak promoters located proximal and upstream of efficiently spliced exons. Together, our findings support a model in which splicing factors recruit transcription machinery locally to influence TSS choice, and identify exon gain, loss and regulatory change as major contributors to the evolution of alternative promoters and altered gene expression in mammals.
Transit Applications of Vehicle-to-Vehicle and Vehicle-to-Infrastructure Technology (2015)

Advances in mobile devices, wired and wireless information connectivity, and computing power make possible new forms of traffic management and control. In a near-term future where vehicles, signals, and central traffic control servers are all connected, what would be the implications for public transit? What role would transit play? In this paper, the authors describe some ways in which vehicle-to-infrastructure (V2I) and vehicle-to-vehicle (V2V) communications can be applied to public transit, focusing on changes in transit stations and service typically controlled by public agencies. The authors review some novel and emerging applications of such technology that could improve transit service and operational efficiency. These include: real-time communications via display devices at transit stations and stops, anti-bunching feedback protocols, crash prevention sensors, dynamic routing in response to nonrecurring congestion, and dynamically managed lanes which enable transit priority. Each of these promises unique benefits, and offers unique implementation challenges. Taken as a whole, they give a sense of the potential of connected transit systems. The authors conclude by discussing the path to implementation and the questions that remain.
<title>Hydrosiloxane-modified styrene-diene block copolymer resists</title> (1993)

Block copolymers are a class of polymers deserving of more investigation by the resist community. We are investigating styrene-hydrosiloxane modified diene block copolymers which have good properties for use as negative tone, electron sensitive resists. Resolution better than 0.1 micrometers , sensitivity of 30 (mu) C/cm<SUP>2</SUP> and contrast of 2.8 have been demonstrated using a poly(styrene)-pentamethyldisiloxane modified poly(isoprene) block copolymer (PS-b-PDPI). Used in a bilayer resist scheme, PS-b-PDPI has an oxygen RIE selectivity ratio of 42 with respect to poly(imide). A poly(styrene)-heptamethyltrisiloxane modified poly(butadiene) block copolymer (PS-b-HTPB) has an oxygen RIE selectivity ratio of 54 with respect to poly(imide). In a bilayer resist system, using PS-b-PDPI as the imageable layer, patterns of 0.3 micrometers wide lines and 1.5 micrometers wide spaces have been transferred through a 1.2 micrometers thick poly(imide) planarizing layer.
Step-Twist Waveguide Components (1955)

The step twist is a number of adjoining sections of straight rectangular waveguide, twisted about their common axis at their junction faces. The technique of designing the step twist resides in the proportioning of the section dimensions and the angles at the twist faces. The resulting design is much shorter than the usual twisted waveguide; it offers further advantages in ease of specifying shape and dimensions, and in their reproducibility in construction. A series of fixed 90-degree step twists has been designed for the rated 40 per cent frequency bandwidths in the standard waveguide sizes for 1 to 40 kmc. The total angle is divided equally among seven faces spaced about 1/8 wavelength in the guide. Each step twist is matched within 0.3 db swr with plain flanges or 0.5 db swr with choke flanges at both ends. Rotary step twists for operation at all angles out to +-90 degrees have been designed for the same bandwidths. The total angle is divided unequally among four faces (choke flanges) spaced about 1/4 wavelength in the guide. The entire unit at maximum rotation is matched within 1.2 db swr with choke flanges at both ends; the matching is closer at lesser rotation.
An Inexpensive Pump for Liquid Sodium (1971)

An inexpensive, commercially available linear actuator has been modified into a small annular linear induction pump for sodium. Sodium temperatures <300°C may be conveniently pumped at pressures up to 2 psi. The total cost, including a cooling fan, is less than $100.
BASNet: Boundary-Aware Salient Object Detection (2019)

Deep Convolutional Neural Networks have been adopted for salient object detection and achieved the state-of-the-art performance. Most of the previous works however focus on region accuracy but not on the boundary quality. In this paper, we propose a predict-refine architecture, BASNet, and a new hybrid loss for Boundary-Aware Salient object detection. Specifically, the architecture is composed of a densely supervised Encoder-Decoder network and a residual refinement module, which are respectively in charge of saliency prediction and saliency map refinement. The hybrid loss guides the network to learn the transformation between the input image and the ground truth in a three-level hierarchy -- pixel-, patch- and map- level -- by fusing Binary Cross Entropy (BCE), Structural SIMilarity (SSIM) and Intersection-over-Union (IoU) losses. Equipped with the hybrid loss, the proposed predict-refine architecture is able to effectively segment the salient object regions and accurately predict the fine structures with clear boundaries. Experimental results on six public datasets show that our method outperforms the state-of-the-art methods both in terms of regional and boundary evaluation measures. Our method runs at over 25 fps on a single GPU. The code is available at: https://github.com/NathanUA/BASNet.
Induced decision trees for case-based reasoning (2002)

The paper examines application of a machine learning technique, decision tree induction, to the development of CBR systems. The decision tree generated by the induction algorithm is generally used to create a set of rules for a traditional rule based system; however, it may be used to determine the weight (i.e., importance) of features for classification. This approach combines the flexibility of CBR systems with the machine learning ability to automatically derive decision criteria. We experimentally assess the tolerance of rule induction to noise and missing values and find it surprisingly resilient to poor quality training data. This bodes well for use of rule induction to allow the process of CBR system development to be more independent of expert judgement.
Insight into the mode of action of the LRRK2 Y1699C pathogenic mutant (2010)

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most prevalent known cause of autosomal dominant Parkinson's disease. The LRRK2 gene encodes a Roco protein featuring a Ras of complex proteins (ROC) GTPase and a kinase domain linked by the C-terminal of ROC (COR) domain. Here, we explored the effects of the Y1699C pathogenic LRRK2 mutation in the COR domain on GTPase activity and interactions within the catalytic core of LRRK2. We observed a decrease in GTPase activity for LRRK2 Y1699C comparable to the decrease observed for the R1441C pathogenic mutant and the T1348N dysfunctional mutant. To study the underlying mechanism, we explored the dimerization in the catalytic core of LRRK2. ROC-COR dimerization was significantly weakened by the Y1699C or R1441C/G mutation. Using a competition assay, we demonstrated that the intra-molecular ROC : COR interaction is favoured over ROC : ROC dimerization. Interestingly, the intra-molecular ROC : COR interaction was strengthened by the Y1699C mutation. This is supported by a 3D homology model of the ROC-COR tandem of LRRK2, showing that Y1699 is positioned at the intra-molecular ROC : COR interface. In conclusion, our data provides mechanistic insight into the mode of action of the Y1699C LRRK2 mutant: the Y1699C substitution, situated at the intra-molecular ROC : COR interface, strengthens the intra-molecular ROC : COR interaction, thereby locally weakening the dimerization of LRRK2 at the ROC-COR tandem domain resulting in decreased GTPase activity.
Chiral recognition in adrenergic receptor binding mimics prepared by molecular imprinting (1996)

Molecularly imprinted polymers were prepared against the adrenomimetic agents ephedrine and pseudoephedrine. These compounds each incorporate two chiral centres. The polymers were evaluated with respect to enantiodiscrimination of various adrenergic ligands. The selectivity of the polymeric binding sites for the imprinted molecules was very high, and it was found that binding of both the enantiomeric and diastereomeric isomers of the imprint species were effectively obstructed, it was found that these polymers could selectively recognize the enantiomers of the endogenous adrenergic ligand epinephrine as well as several beta-adrenergic blockers. These observations suggest that these polymers effectively mimic the recognition patterns exhibited by natural adrenergic receptors.
A Systematic Approach to Instruction: Innovative and Sensitive (1970)

An approach of this nature is by definition innovative if only because of its prior absence. In order for this kind of instruction to take root and survive, a high degree of sensitivity must be demonstrated by the architect and implementors of the instruction.
Molecular recognition through intercalation chemistry: immobilization of organoclays on piezoelectric devices (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular recognition through intercalation chemistry: immobilization of organoclays on piezoelectric devicesYongan Yan and Thomas BeinCite this: Chem. Mater. 1993, 5, 7, 905–907Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://doi.org/10.1021/cm00031a003RIGHTS & PERMISSIONSArticle Views168Altmetric-Citations52LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
Modular MEMS design and fabrication for an 80 x 80 transparent optical cross-connect switch (2004)

The ability to transparently switch optical signals from one fiber to another without conversion to the electrical domain is a basic functionality that has a wide range of applications within the fiber optic industry. The so-called 3D-MEMS architecture has emerged as the preferred approach for building transparent, scalable systems with port-counts ranging from 16x16 to 1024x1024. The primary components of the 3D-MEMS architecture are fiber array, lens array, and MEMS mirror array. While a central theme in the MEMS industry is integration, we adopted a strategy of modularization. The key MEMS components, which include mirror array, ceramic substrate, and high-voltage drivers, were manufactured separately and then combined to yield a working product. Central to our modular approach was critical design parameter tolerancing to ensure manufacturability. Results from a large sampling of MEMS components and MEMS assemblies are presented to highlight manufacturability and performance.
Machine Learning Approaches for Mood Classification of Songs toward Music Search Engine (2009)

Human often wants to listen to music that fits best his current emotion. A grasp of emotions in songs might be a great help for us to effectively discover music. In this paper, we aimed at automatically classifying moods of songs based on lyrics and metadata, and proposed several methods for supervised learning of classifiers. In future, we plan to use automatically identified moods of songs as metadata in our music search engine. Mood categories in a famous contest about Audio Music Mood Classification (MIREX 2007) are applied for our system. The training data is collected from a LiveJournal blog site in which each blog entry is tagged with a mood and a song. Then three kinds of machine learning algorithms are applied for training classifiers: SVM, Naive Bayes and Graph-based methods. The experiments showed that artist, sentiment words, putting more weight for words in chorus and title parts are effective for mood classification. Graph-based method promises a good improvement if we have rich relationship information among songs.
Mass accommodation coefficient for HO<sub>2</sub> radicals on aqueous particles (1987)

The rate of reaction of gas phase HO 2 radicals with a monodisperse, submicrometer aerosol was measured in a flow tube reactor at atmospheric pressure. At the relative humidity of the experiments (75%), the aerosol consisted of concentrated solution droplets of either LiNO 3 or NH 4 HSO 4 . When the aerosol contained a sufficient amount of Cu(II) ions, reaction of HO 2 with the aerosol was observed. The mass accommodation coefficient for HO 2 on aqueous particles was determined to be greater than 0.2. This implies that in clouds HO 2 mass transport will be limited by gas‐phase diffusion and HO 2 will be in equilibrium at the gas‐liquid interface. Reactions of HO 2 with Cu(I) and Cu(II) ions in submicrometer aerosols may have a significant role in converting atmospheric odd hydrogen radicals into H 2 O 2 .
Effects of okadaic acid, a protein phosphatase inhibitor, on glucocorticoid receptor-mediated enhancement. (1992)

The effects of okadaic acid (OA), a protein phosphatase inhibitor, on transcriptional enhancement activity of rat glucocorticoid receptor (GR) were examined in transiently transfected cells. In the absence of hormone, GRs expressed in CV-1 and COS-1 fibroblasts were capable of enhancing transcription from cotransfected chloramphenicol acetyltransferase reporter plasmids in response to OA treatment. Synergistic enhancement resulted from combined hormone and OA treatment. The effects of OA on GR-mediated enhancement required the presence of linked glucocorticoid response elements and were observed with reporter plasmids that contained different promoters and glucocorticoid response elements. Since OA did not affect nuclear translocation of the receptor, enhancement mediated by unliganded GR was most likely accounted for by the accumulation of some unliganded GRs within nuclei of transfected CV-1 and COS-1 cells. Deletion of individual GR transactivation domains and point mutations within DNA- and hormone-binding domains severely reduced the response of receptors to OA, although some mutant receptors retained the capacity to elicit a synergistic response when exposed to OA and hormone. The effects of OA on transcriptional enhancement did not appear to correlate with major changes in GR phosphorylation, as visualized by two-dimensional tryptic mapping of in vivo 32P-labeled GRs. Thus, phosphorylation of various components of the GR signal transduction pathway, and not necessarily the receptor itself, may influence its transcriptional enhancement activity.
Microfluidic characterization of cilia-driven fluid flow using optical coherence tomography-based particle tracking velocimetry (2011)

Motile cilia are cellular organelles that generate directional fluid flow across various epithelial surfaces including the embryonic node and respiratory mucosa. The proper functioning of cilia is necessary for normal embryo development and, for the respiratory system, the clearance of mucus and potentially harmful particulate matter. Here we show that optical coherence tomography (OCT) is well-suited for quantitatively characterizing the microfluidic-scale flow generated by motile cilia. Our imaging focuses on the ciliated epithelium of Xenopus tropicalis embryos, a genetically manipulable and experimentally tractable animal model of human disease. We show qualitative flow profile characterization using OCT-based particle pathline imaging. We show quantitative, two-dimensional, two-component flow velocity field characterization using OCT-based particle tracking velocimetry. Quantitative imaging and phenotyping of cilia-driven fluid flow using OCT will enable more detailed research in ciliary biology and in respiratory medicine.
An Introduction to the Analysis of Single-Cell RNA-Sequencing Data (2018)

The recent development of single-cell RNA sequencing has deepened our understanding of the cell as a functional unit, providing new insights based on gene expression profiles of hundreds to hundreds of thousands of individual cells, and revealing new populations of cells with distinct gene expression profiles previously hidden within analyses of gene expression performed on bulk cell populations. However, appropriate analysis and utilization of the massive amounts of data generated from single-cell RNA sequencing experiments are challenging and require an understanding of the experimental and computational pathways taken between preparation of input cells and output of interpretable data. In this review, we will discuss the basic principles of these new technologies, focusing on concepts important in the analysis of single-cell RNA-sequencing data. Specifically, we summarize approaches to quality-control measures for determination of which single cells to include for further examination, methods of data normalization and scaling to overcome the relatively inefficient capture rate of mRNA from each cell, and clustering and visualization algorithms used for dimensional reduction of the data to a two-dimensional plot.
Automatic Constraint Based Test Generation for Behavioral HDL Models (2008)

With the emergence of complex high-performance microprocessors, functional test generation has become a crucial design step. Constraint-based test generation is a well-studied directed behavioral level functional test generation paradigm. The paradigm involves conversion of a given circuit model into a set of constraints and employing constraint solvers to generate tests for it. However, automatic extraction of constraints from a given behavioral hardware design language (HDL) model remained a challenging open problem. This paper proposes an approach for automatic extraction of word-level model constraints from the behavioral verilog HDL description. The scenarios to be tested are also expressed as constraints. The model and the scenario constraints are solved together using an integer solver to arrive at the necessary functional test. The effectiveness of the approach is demonstrated by automatically generating the constraint models for: 1) an exclusive-shared-invalid multiprocessor cache coherency model and 2) the 16-bit DLX-architecture, from their respective Verilog-based behavioral models. Experimental results that generate test vectors for high level scenarios like pipeline hazards, cache miss, etc., spanning over multiple time-frames are presented.
CD-ROM: The pros and cons (1997)

The carcinogenicity of gardenia blue colour was examined in Fischer 344 (F344) rats. Groups of 50 males and 50 females were given the material at dietary doses of 0 (control), 2.5 or 5% for 104 weeks and then sacrificed. The doses were selected on the basis of results from a 13-week subchronic toxicity study. A slight increase in relative organ weights of the left lung was observed in male rats of the 5% group. However, no significant differences between the control and treated groups were noted with regard to clinical signs, mortality and haematological findings. A variety of tumours developed in all groups, including the controls, but all were histologically similar to those known to occur spontaneously in F344 rats, and no statistically significant increase in the incidence of any type of neoplastic lesion was found for either sex in the treated groups. Thus, it was concluded that, under the present experimental conditions, gardenia blue colour is not carcinogenic in F344 rats.
Copolymerization of butadiene and styrene by initiation with alkyllithium and alkali metal <i>tert</i>‐butoxides (1969)

Abstract Combinations of the various alkali metal tert ‐butoxides with organolithium initiators give homogeneous copolymers of butadiene and styrene. The unprecedented flexibility of this initiator system allowed preparation of random copolymers with various amounts of vinyl unsaturation and various degrees of randomness. The butyllithium–potassium tert ‐butoxide initiator system was more efficient than phenylpotassium.