gebhart/patrepeval huggingface dataset:
Pioneer transcription factors: establishing competence for gene expression (2011)

Transcription factors are adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression. Yet much of the DNA in the eukaryotic cell is in nucleosomes and thereby occluded by histones, and can be further occluded by higher-order chromatin structures and repressor complexes. Indeed, genome-wide location analyses have revealed that, for all transcription factors tested, the vast majority of potential DNA-binding sites are unoccupied, demonstrating the inaccessibility of most of the nuclear DNA. This raises the question of how target sites at silent genes become bound de novo by transcription factors, thereby initiating regulatory events in chromatin. Binding cooperativity can be sufficient for many kinds of factors to simultaneously engage a target site in chromatin and activate gene expression. However, in cases in which the binding of a series of factors is sequential in time and thus not initially cooperative, special "pioneer transcription factors" can be the first to engage target sites in chromatin. Such initial binding can passively enhance transcription by reducing the number of additional factors that are needed to bind the DNA, culminating in activation. In addition, pioneer factor binding can actively open up the local chromatin and directly make it competent for other factors to bind. Passive and active roles for the pioneer factor FoxA occur in embryonic development, steroid hormone induction, and human cancers. Herein we review the field and describe how pioneer factors may enable cellular reprogramming.
Differences in the Large Extracellular Loop between the K+-Cl− Cotransporters KCC2 and KCC4 (2010)

K(+)Cl(-) cotransporters (KCCs) play fundamental physiological roles in processes such as inhibitory neurotransmission and cell volume regulation. Mammalian genomes encode four distinct KCC paralogs, which share basic transport characteristics but differ significantly in ion affinity, pharmacology, and relative sensitivity to cell volume. Studies to identify divergence in functional characteristics have thus far focused on the cytoplasmic termini. Here, we investigated sequence requirements of the large extracellular loop (LEL) for function in KCC2 and KCC4. Mutation of all four evolutionarily conserved cysteines abolished KCC2 transport activity. This behavior differs from that of its closest relative, KCC4, which is insensitive to this mutation. Chimeras supported the differences in the LEL of the two cotransporters, because swapping wild-type LEL resulted in functional KCC2 but rendered KCC4 inactive. Insertion of the quadruple cysteine substitution mutant of the KCC4 loop, which was functional in the parental isoform, abolished transport activity in KCC2. Dose-response curves of wild-type and chimeric KCCs revealed that the LEL contributes to the different sensitivity to loop diuretics; a KCC2 chimera containing the KCC4 LEL displayed an IC(50) of 396.5 mum for furosemide, which was closer to KCC4 (548.8 mum) than to KCC2 (184.4 mum). Cell surface labeling and immunocytochemistry indicated that mutations do not affect trafficking to the plasma membrane. Taken together, our results show a dramatic and unexpected difference in the sequence requirements of the LEL between the closely related KCC2 and KCC4. Furthermore, they demonstrate that evolutionarily highly conserved amino acids can have different functions within KCC members.
Optimized linear contactless power transmission systems for different applications (2002)

Linear contactless power transmission systems are proposed as alternative power supplies to mobile loads used in harsh environments. Such systems comprise a core with a secondary winding sliding along an extended primary winding. In long applications the transformer primary winding is the most limiting component in the system whereas in short applications the transformer core size is usually the detrimental factor. Formulas to optimize and design sliding transformers for different applications are given. The implementation of these formulas are then illustrated by designs for three different applications. Experimental waveforms for a 5 m, 15 kVA sliding transformer are presented.
Layered screen video coding leveraging hardware video codec (2013)

In this paper, we propose a layered screen video coding scheme based on existing video codecs to leverage hardware video codec for efficient screen video compression. In this scheme, the screen video compression is performed as two-layer coding: base layer coding and enhancement layer coding. The screen video is first analyzed in both frame and block levels for useful temporal and spatial information extraction to assist coding content selection in each layer. The non-skip screen frames are directly compressed by the conventional video codec in the base layer, while the screen contents sensitive to the video quality degradation are selected for improved coding in the enhancement layer. For contents to be enhanced, two intra coding modes are designed to improve the quality of the compressed text/graphics contents and suppress the artifacts introduced by chroma downsampling. The experimental results demonstrate that the screen video quality is improved objectively and subjectively by the proposed scheme with low cost on bitrate and computation complexity. Moreover, an average of 2.95dB coding gain is achieved in high bitrate.
Hydrothermal synthesis and characterization of a series of luminescent Zn(ii) and Cd(ii) coordination polymers with the new versatile multidentate ligand 1,3-di-(1,2,4-triazol-4-yl)benzene (2013)

Used a newly designed multidentate benzene-based bis-triazole ligand 1,3-di-(1,2,4-triazol-4-yl)benzene (L), a series of luminescent Zn(II) and Cd(II) coordination polymers, namely, {[Zn(μ2-L)2(H2O)2]·(SiF6)·H2O}n (1), {[Cd(μ2-L)2(H2O)2]·(SiF6)·2H2O}n (2), {[Zn(μ2-L)Br2]·H2O}n (3), {[Cd(μ2-L)2(NCS)2]·2H2O}n (4), {[Cd(μ2-L)(μ4-L)](BF4)2}n (5), {[Cd(μ2-L)(μ4-L)](ClO4)2}n (6) and {[Cd3(μ3-L)6](NO3)6}n (7) have been isolated under hydrothermal conditions. Both 1 and 2 present 1D double chain structures, which contain two kinds of different supramolecular channels. For 3, zinc(II) ions are linked by L ligands and arranged into infinite right- or left-handed helical chains. 4 presents a 2D framework in which 1D right-handed and left-handed helical structures are interlinked via Cd(II) centers as hinges. 5 and 6 respectively contain μ2- and μ4-L ligands in triazole–metal complexes. These μ4-L ligands link neighboring Cd(II) centers forming a 2D network containing infinite {Cd-(trz)2-Cd}n chains, which is quite different from the 2D arrangement in 4. 7 presents a novel 3D porous MOF (porous metal–organic framework) containing triangular nano-porous channels with edges of 13.622 Å, in which free NO3− anions are located. Anion exchange experiments based on 7 also indicate that NO3− anions are able to be exchanged with ClO4− anions in the solid state. Both the dihedral angles (between two triazole rings or between triazole and aromatic benzene rings) for L are flexible and ultimately tune the coordination geometries in constructing various different coordination polymers. For 1–7 the comparison between powder X-ray diffraction (PXRD) and a simulated analysis from crystal data confirmed the pure crystal phases. Solid-state luminescent properties and thermal stabilities of 1–7 also have been determined.
An Innovative Approach for Adaptation of Generic Rate Control Algorithms for Target Video Standards (2007)

This paper discusses an innovative approach to make a generic rate control algorithm adaptable to a specific targeted video standard, by incorporating the `Adaptation layer'. The proposed Adaptation Layer utilizes the technique of statistical regression to provide a mechanism using which the rate control algorithm can be acclimatized to any video standard. Experimental results, on applying the proposed technique on a constant bitrate control algorithm for VC1 show that a maximum deviation of 1.5% from the target bitrate is obtained with desired quality. Furthermore, the proposed technique drastically reduces the design complexity required in adapting a rate control algorithm to a particular video standard with a marginal increase in computational complexity.
Creating efficient codebooks for visual recognition (2005)

Visual codebook based quantization of robust appearance descriptors extracted from local image patches is an effective means of capturing image statistics for texture analysis and scene classification. Codebooks are usually constructed by using a method such as k-means to cluster the descriptor vectors of patches sampled either densely ('textons') or sparsely ('bags of features' based on key-points or salience measures) from a set of training images. This works well for texture analysis in homogeneous images, but the images that arise in natural object recognition tasks have far less uniform statistics. We show that for dense sampling, k-means over-adapts to this, clustering centres almost exclusively around the densest few regions in descriptor space and thus failing to code other informative regions. This gives suboptimal codes that are no better than using randomly selected centres. We describe a scalable acceptance-radius based clusterer that generates better codebooks and study its performance on several image classification tasks. We also show that dense representations outperform equivalent keypoint based ones on these tasks and that SVM or mutual information based feature selection starting from a dense codebook further improves the performance.
Human Multidrug-Resistant Cell Lines: Increased <i>mdr</i> 1 Expression Can Precede Gene Amplification (1986)

The development of simultaneous resistance to multiple structurally unrelated drugs is a major impediment to cancer chemotherapy. Multidrug resistance in human KB carcinoma cells selected in colchicine, vinblastine, or Adriamycin is associated with amplification of specific DNA sequences (the multidrug resistance locus, mdr1). During colchicine selection resistance is initially accompanied by elevated expression of a 4.5-kilobase mdr1 messenger RNA (mRNA) without amplification of the corresponding genomic sequences. During selection for increased levels of resistance, expression of this mRNA is increased simultaneously with amplification of mdr1 DNA. Increased expression and amplification of mdr1 sequences were also found in multidrug-resistant sublines of human leukemia and ovarian carcinoma cells. These results suggest that increased expression of mdr1 mRNA is a common mechanism for multidrug resistance in human cells. Activation of the mdr1 gene by mutations or epigenetic changes may precede its amplification during the development of resistance.
Locality-Sensitive Hashing of Curves (2017)

We study data structures for storing a set of polygonal curves in R^d such that, given a query curve, we can efficiently retrieve similar curves from the set, where similarity is measured using the discrete Fréchet distance or the dynamic time warping distance. To this end we devise the first locality-sensitive hashing schemes for these distance measures. A major challenge is posed by the fact that these distance measures internally optimize the alignment between the curves. We give solutions for different types of alignments including constrained and unconstrained versions. For unconstrained alignments, we improve over a result by Indyk [SoCG 2002] for short curves. Let n be the number of input curves and let m be the maximum complexity of a curve in the input. In the particular case where m <= (a/(4d)) log n, for some fixed a>0, our solutions imply an approximate near-neighbor data structure for the discrete Fréchet distance that uses space in O(n^(1+a) log n) and achieves query time in O(n^a log^2 n) and constant approximation factor. Furthermore, our solutions provide a trade-off between approximation quality and computational performance: for any parameter k in [m], we can give a data structure that uses space in O(2^(2k) m^(k-1) n log n + nm), answers queries in O( 2^(2k) m^(k) log n) time and achieves approximation factor in O(m/k).
Stability, repeatability, and the expression of signal magnitude in functional magnetic resonance imaging (1999)

In 23 fMRI studies on six subjects, we examined activation in visual and motor tasks. We modeled the expected activation time course by convolving a temporal description of the behavioral task with an empirically determined impulse response function. We evaluated the signal activation intensity as both the number of activated voxels over arbitrary correlation thresholds and as the slope of the regression line between our modeled time course and the actual data. Whereas the voxel counting was strikingly unstable (standard deviation 74% in visual trials at a correlation of 0.5), the slope was relatively constant across trials and subjects (standard deviation <14%). Using Monte Carlo methods, we determined that the measured slope was largely independent of the contrast-to-noise ratio. Voxel counting is a poor proxy for activation intensity, with greatly increased scatter, much reduced statistical power, and increased type II error. The data support an alternative approach to functional magnetic resonance imaging (fMRI) that allows for quantitative comparisons of fMRI response magnitudes across trials and laboratories.
Organotellurium compounds of biological interest-unique properties of the N-chlorosuccinimide oxidation product of 9-telluraheptadecanoic acid (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganotellurium compounds of biological interest-unique properties of the N-chlorosuccinimide oxidation product of 9-telluraheptadecanoic acidG. Kirsch, M. M. Goodman, and F. F. Knapp Jr.Cite this: Organometallics 1983, 2, 3, 357–363Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://pubs.acs.org/doi/10.1021/om00075a001https://doi.org/10.1021/om00075a001research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations23LEARN 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
What is Cooperativity? (2009)

The lamprey holds the clue to the link between supramolecular self-assembly and allosteric ligand binding. Chelate cooperativity in self-assembled structures results in denaturation behavior that is indistinguishable from allosteric ligand binding. The chelate effect is the most common origin of positive cooperativity, yet its significance has been widely overlooked. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Cerebral endothelial nitric oxide synthase expression after focal cerebral ischemia in rats. (1993)

The rapid and intense differential expression of the endothelial NOS in the core and peripheral areas of the lesion indicates a role for endothelial NOS in ischemic cell damage and suggests that the increased expression of NOS may mediate changes in the cerebral blood flow.
Image Denoising via CNNs: An Adversarial Approach (2017)

Is it possible to recover an image from its noisy version using convolutional neural networks? This is an interesting problem as convolutional layers are generally used as feature detectors for tasks like classification, segmentation and object detection. We present a new CNN architecture for blind image denoising which synergically combines three architecture components, a multi-scale feature extraction layer which helps in reducing the effect of noise on feature maps, an ℓp regularizer which helps in selecting only the appropriate feature maps for the task of reconstruction, and finally a three step training approach which leverages adversarial training to give the final performance boost to the model. The proposed model shows competitive denoising performance when compared to the state-of-the-art approaches.
Advanced Reactor Design, Operation and Economy (1986)

Of the high rate anaerobic wastewater treatment systems the UASB (Upflow Anaerobic Sludge Blanket) reactor has found the widest application. Therefore the attention with respect to design, operation and economy will be focussed on this reactor type. In designing a UASB reactor specific attention is needed for the GSS (Gas-Solids Separator) device and the feed inlet system. For soluble wastewater generally no phase separation is required. Only for wastewaters high in suspended solids pre-acidification in a separate acidification reactor can be beneficial. Increasing attention is given to the development of modified UASB systems, such as a combination of a sludge bed reactor and an anaerobic filter. Other possible modified UASB systems may be found in a FS (Floating Settling) UASB reactor, the EGSB (Expanded Granular Sludge Bed) reactor and the UASB IC (Internal Circulation) reactor. As many factors are involved in the costs of a UASB reactor, only some rough data on reactor costs are presented.
The enzymatic Baeyer-Villiger oxidation: enantioselective synthesis of lactones from mesomeric cyclohexanones (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe enzymatic Baeyer-Villiger oxidation: enantioselective synthesis of lactones from mesomeric cyclohexanonesMichael J. Taschner and Donald J. BlackCite this: J. Am. Chem. Soc. 1988, 110, 20, 6892–6893Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://pubs.acs.org/doi/10.1021/ja00228a053https://doi.org/10.1021/ja00228a053research-articleACS PublicationsRequest reuse permissionsArticle Views922Altmetric-Citations136LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
microRNA: A Master Regulator of Cellular Processes for Bioengineering Systems (2010)

microRNAs (miRNAs) are small RNAs 18 to 24 nucleotides in length that serve the pivotal function of regulating gene expression. Instead of being translated into proteins, the mature single-stranded miRNA binds to messenger RNAs (mRNAs) to interfere with the translational process. It is estimated that whereas only 1% of the genomic transcripts in mammalian cells encode miRNA, nearly one-third of the encoded genes are regulated by miRNA. Various bioinformatics databases, tools, and algorithms have been developed to predict the sequences of miRNAs and their target genes. In combination with the in silico approaches in systems biology, experimental studies on miRNA provide a new bioengineering approach for understanding the mechanism of fine-tuning gene regulation. This review aims to provide state-of-the-art information on this important mechanism of gene regulation for researchers working in biomedical engineering and related fields. Particular emphases are placed on summarizing the current tools and strategies for miRNA study from a bioengineering perspective and the possible applications of miRNAs (such as antagomirs and miRNA sponges) in biomedical engineering research.
Charge localization in the carbonium ions of methylbenzanthracenes (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharge localization in the carbonium ions of methylbenzanthracenesErcole Cavalieri and Melvin CalvinCite this: J. Org. Chem. 1976, 41, 16, 2676–2679Publication Date (Print):August 1, 1976Publication History Published online1 May 2002Published inissue 1 August 1976https://pubs.acs.org/doi/10.1021/jo00878a003https://doi.org/10.1021/jo00878a003research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations3LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Photoreflectance on wide bandgap nitride semiconductors (2005)

Abstract Extensive research has been reported on the wide band gap nitride materials system in the past few years. Despite the development of many well‐working GaN based opto‐ and electronic devices, theoretical and experimental understanding of many fundamental properties remains still incomplete. In this paper, we show the unique benefits that can be drawn from optical modulation spectroscopy as applied to nitride materials, despite the difficulties in working in the UV spectral range, that is required for the photoreflectance measurements of wide band gap semiconductors. By performing PR spectroscopy at low temperature in cubic phase GaN layers grown on c‐SiC pseudo‐substrates, the different valence band excitons are measured and compared with theoretical calculations, allowing the determination of residual strain inside the epitaxial layer. The second part of the paper is devoted to emphasize the unique interest of PR spectroscopy in the Franz Keldysh oscillations regime, especially in the case of wurtzite phase GaN/AlGaN quantum structures, in order to extract the piezoelectric field in a non‐destructive all‐optical experiment. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)