gebhart/patrepeval huggingface dataset:
Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins (2012)

Alternative splicing plays a major role in increasing proteome complexity and regulating gene expression. Here, we developed a new fluorescent protein-based approach to quantitatively analyze the alternative splicing of a target cassette exon (skipping or inclusion), which results in an open-reading frame shift. A fragment of a gene of interest is cloned between red and green fluorescent protein (RFP and GFP)-encoding sequences in such a way that translation of the normally spliced full-length transcript results in expression of both RFP and GFP. In contrast, alternative exon skipping results in the synthesis of RFP only. Green and red fluorescence intensities can be used to estimate the proportions of normal and alternative transcripts in each cell. The new method was successfully tested for human PIG3 (p53-inducible gene 3) cassette exon 4. Expected pattern of alternative splicing of PIG3 minigene was observed, including previously characterized effects of UV light irradiation and specific mutations. Interestingly, we observed a broad distribution of normal to alternative transcript ratio in individual cells with at least two distinct populations with ∼45% and >95% alternative transcript. We believe that this method is useful for fluorescence-based quantitative analysis of alternative splicing of target genes in a variety of biological models.
Ecological, morphological and allozymic differentiation between diploid and tetraploid knapweeds (Centaurea jacea) from a contact zone in the Belgian Ardennes (2000)

In the northeastern part of Belgium, the Centaurea jacea complex shows extensive morphological variation and is represented by a diploid (2n = 22) and a tetraploid (2n = 44) cytotype. Polysomic inheritance of allozyme markers in the tetraploids, suggesting autopolyploidy, is here demonstrated for the first time. In order to test whether the two cytotypes occupy distinct habitats and possess different gene pools, patterns of allozymic and morphological variation were investigated in relation to ploidy level and site characteristics in 26 populations from the Belgian Ardennes. The two cytotypes showed a parapatric distribution, the diploids occurring at higher elevations (mostly above 500 m) than the tetraploids (mostly below 500 m). Three mixed populations were found near the contact zone of the two cytotypes. Within the mixed populations no triploid plant and no evidence for gene flow between cytotypes were found, despite widely overlapping flowering periods. The two cytotypes can be distinguished on the basis of morphological traits and enzymatic gene pools. The congruence of morphological and allozymic variation with chromosome numbers suggests a secondary contact between the two cytotypes with limited gene flow between them. The origin and persistence of the parapatric distribution are discussed.
Scan registration using segmented region growing NDT (2014)

The Normal Distributions Transform (NDT) scan registration algorithm divides a point cloud using rectilinear voxel cells, then models the points within each cell as a set of Gaussian distributions. A nonlinear optimization is performed in order to register the scans, however the voxel-based approach results in ill-defined cost function derivatives as points cross cell boundaries. In this work, a Segmented Region Growing NDT (SRG-NDT) variant is proposed, which first removes the ground points from the scan, then uses natural features in the environment to generate Gaussian clusters for the NDT algorithm. The removal of the ground points is shown to significantly speed up the scan registration process with negligible effect on the registration accuracy. By clustering the remaining points, the SRG-NDT approach is able to model the environment with fewer Gaussian distributions compared with the voxel-based NDT methods, which allows for a smooth and continuous cost function that guarantees that the optimization will converge. Furthermore, the use of a relatively small number of Gaussian distributions allows for a significant improvement in run-time. Experiments in both urban and forested environments demonstrate that the SRG-NDT approach is able to achieve comparable accuracy to existing methods, but with an average decrease in computation time over ICP, G-ICP, and NDT, of 90.1%, 95.3%, and 94.5%, respectively.
Detection of Polycyclic Aromatic Hydrocarbons Using Quartz Crystal Microbalances (2003)

A chemically coated piezoelectric sensor has been developed for the determination of PAHs in the liquid phase. An organic monolayer attached to the surface of a gold electrode of a quartz crystal microbalance (QCM) via a covalent thiol-gold link complete with an ionically bound recognition element has been produced. This study has employed the PAH derivative 9-anthracene carboxylic acid which, once bound to the alkane thiol, functions as the recognition element. Binding of anthracene via pi-pi interaction has been observed as a frequency shift in the QCM with a detectability of the target analyte of 2 ppb and a response range of 0-50 ppb. The relative response of the sensor altered for different PAHs despite pi-pi interaction being the sole communication between recognition element and analyte. It is envisaged that such a sensor could be employed in the identification of key marker compounds and, as such, give an indication of total PAH flux in the environment.
Follow and Facilitate (2013)

The educational practices of the municipality of Reggio Emilia, Italy, are celebrated as among the best in the world. Inspired by this educational system, schools across America have adapted the Reggio Emilia approach. Yet, music educators may be unaware of its principles as the approach is not often discussed in music education literature. The purpose of this article is to describe the major tenets of the Reggio Emilia approach and to suggest how its principles might be incorporated into American music classroom contexts. Suggestions include creating a constructivist classroom, documenting student learning, and using the physical classroom environment to entice musicking.
An infrared study of hot dust in quasars using prism spectrophotometry (1993)

Low-resolution near-infrared spectra were obtained for 14 quasars with redshift z &lt; 0.3. The observed continua from 0.95 to 2.5 microns were reproduced remarkably well with a combination of two radiation components, i.e., the power law and the blackbody radiation which are, respectively, dominated at shorter than ~1.2 microns and longer than ~1.5 microns. The longer part of the spectra fit a single-temperature blackbody of 1470+/-90 K which is attributable to the thermal emission from hot dust grains heated by the central power source. The flux ratio of the blackbody of the power-law component ranges by a factor of 6. It was found that an IRAS color selected sample tended to have a larger flux ratio as compared to non-IRAS quasars.
Interacting with networked devices (2006)

Networking technology has become applicable in domains beyond the conventional computer. One such domain currently receiving a significant amount of research attention is networking arbitrary devices such as TVs, refrigerators, and sensors. In this dissertation, we focus on the following question: how does an infrastructure deploy a user-interface for a single device or a composition of several ones? 
We identify and evaluate several deployment approaches. The evaluation shows the approach of automatically generating device user-interfaces 'on the fly' as particularly promising since it offers low programming/maintenance costs and high reliability. The approach, however, has the important limitation of taking a long time to create a user-interface. It is our thesis that it is possible to overcome this limitation and build graphical and speech user-interface generators with deployment times that are as low as the inherently fastest approach of locally loading predefined code. Our approach is based on user-interface retargeting and history-based generation. User-interface retargeting involves dynamically mapping a previously generated user-interface of one device to another (target) device that can share the user-interface. History-based generation predicts and presents just the content a user needs in a device's user-interface based on the user's past behavior. By filtering out unneeded content from a screen, it our thesis that history-based generation can also be used to address the issue of limited screen space on mobile computers. 
The above ideas apply to both single and multiple device user-interfaces. The multi-device case also raises the additional issue of how devices are composed. Current infrastructures for composing devices are unsuccessful in simultaneously providing high-level and flexible support of all existing composition semantics. It is our thesis that it is possible to build an infrastructure that: (1) includes the semantics of existing high-level infrastructures and (2) provides higher-level support than all other infrastructures that can support all of these semantics. Such an infrastructure requires a composition framework that is both data and operation oriented. Our approach is based on the idea of pattern-based composition, which uses programming patterns to extract data and operation information from device objects. This idea is used to implement several abstract algorithms covering the specific semantics of existing systems.
Candidate genes and pathways downstream of PAX8 involved in ovarian high-grade serous carcinoma (2016)

Understanding the biology and molecular pathogenesis of ovarian epithelial cancer (EOC) is key to developing improved diagnostic and prognostic indicators and effective therapies. Although research has traditionally focused on the hypothesis that high-grade serous carcinoma (HGSC) arises from the ovarian surface epithelium (OSE), recent studies suggest that additional sites of origin exist and a substantial proportion of cases may arise from precursor lesions located in the Fallopian tubal epithelium (FTE). In FTE cells, the transcription factor PAX8 is a marker of the secretory cell lineage and its expression is retained in 96% of EOC. We have recently reported that PAX8 is involved in the tumorigenic phenotype of ovarian cancer cells. In this study, to uncover genes and pathways downstream of PAX8 involved in ovarian carcinoma we have determined the molecular profiles of ovarian cancer cells and in parallel of Fallopian tube epithelial cells by means of a silencing approach followed by an RNA-seq analysis. Interestingly, we highlighted the involvement of pathways like WNT signaling, epithelial-mesenchymal transition, p53 and apoptosis. We believe that our analysis has led to the identification of candidate genes and pathways regulated by PAX8 that could be additional targets for the therapy of ovarian carcinoma.
Hybrid concatenated codes and iterative decoding (2002)

A hybrid concatenated code is a combination of parallel and serial concatenated codes. Here we consider an example with three codes and two interleavers. An upper bound to the bit error rate (BER) of the hybrid code is obtained. Design rules for the three component codes that maximize the interleavers gain and the asymptotic slope of the BER curves are discussed. A low-complexity iterative decoding algorithm with near maximum-likelihood performance is proposed. Comparisons with "turbo codes" and with serially concatenated codes show that the hybrid scheme offers better performance at very low BER.
Green and Inexpensive Choline‐Derived Solvents for Cellulose Decrystallization (2011)

A new generation of cheap and sustainable choline-derived ionic solvents is reported. These solvents are capable of rapidly dissolving and decrystallizing microcrystalline cellulose (MCC) in only a few minutes, thus offering an eco-efficient alternative to the traditional use of imidazolium-based ionic liquids (see scheme). 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.
A standard system phantom for magnetic resonance imaging (2021)

A standard system phantom is useful for characterization of scanner performance, monitoring a scanner over time, and to compare different scanners. This type of calibration structure is useful for quality assurance, benchmarking quantitative MRI protocols, and to transition MRI from a qualitative imaging technique to a precise metrology with documented accuracy and uncertainty.
iProprio: a Smartphone-based system to measure and improve proprioceptive function (2016)

International audience
Kineziterapijos poveikio įvertinimas po klubo sąnario endoprotezavimo dėl koksartrozės (2008)

Skapaitė L. Kineziterapijos poveikio įvertinimas po klubo sąnario endoprotezavimo dėl koksartrozės; magistro baigiamasis darbas / mokslinis vadovas doc. A. Kimtys; Kauno medicinos universitetas, Slaugos fakultetas, Reabilitacijos klinika. – Kaunas, 2008.\nDarbo tikslas buvo įvertinti kineziterapijos poveikį asmenims po klubo sąnario endoprotezavimo dėl koksartrozės antrame reabilitacijos etape.\nReabilitacijos kurso trukmė buvo 30 dienų.\nTyrime dalyvavo 21 vienos ligoninės Fizinės medicinos ir reabilitacijos skyriaus pacientas po klubo sąnario endoprotezavimo dėl koksartrozės. Tiriamąją grupę sudarė 2 vyrai (9%) ir 19 moterų (91%), kurių amžius 50-70 metų.\nPacientai buvo suskirstyti į dvi grupes pagal amžių. Pirmojoje grupėje – 7 pacientai, kurių amžius 50-65 metai (33%), antrojoje grupėje – 14 pacientų, kurių amžius 66-70 metų (67%). Tiriamųjų amžiaus vidurkis buvo 65,9 ± 6,09 metai. Pirmosios grupės pacientų amžiaus vidurkis 58,9 ± 5,96 metai, antrosios grupės pacientų amžiaus vidurkis 69,4 ± 1,01 metai. \nPacientai buvo tiriamai du kartus: pirmąjį – tik atvykus į Fizinės medicinos ir reabilitacijos skyrių, antrąjį kartą – prieš išvykstant pacientui iš šio skyriaus. \nKineziterapijos poveikiui vertinti buvo atliekami šie tyrimai ir testai: šlaunies raumenų jėga vertinama naudojant Oxford skalę, judesių amplitudės klubo sąnaryje – goniometriniu metodu, paciento mobilumas – pagal modifikuotą Keitel indeksą, skausmas - naudojant vizualinės analogijos skausmo skalę... [toliau žr. visą tekstą]
Wavelength dependence of birefringence in highly birefringent fibers (1982)

A simple technique is used to measure the wavelength dependence of the birefringence in highly birefringent fibers. In stress-induced fibers, the stress and shape birefringences reinforce each other, whereas in elliptical-core fibers the stress and shape birefringences can either reinforce each other or partially cancel, depending on the wavelength.
Evaluation of a transient, simultaneous, arbitrary Lagrange–Euler based multi-physics method for simulating the mitral heart valve (2012)

A transient multi-physics model of the mitral heart valve has been developed, which allows simultaneous calculation of fluid flow and structural deformation. A recently developed contact method has been applied to enable simulation of systole (the stage when blood pressure is elevated within the heart to pump blood to the body). The geometry was simplified to represent the mitral valve within the heart walls in two dimensions. Only the mitral valve undergoes deformation. A moving arbitrary Lagrange-Euler mesh is used to allow true fluid-structure interaction (FSI). The FSI model requires blood flow to induce valve closure by inducing strains in the region of 10-20%. Model predictions were found to be consistent with existing literature and will undergo further development.
Sources of Nonlinear van’t Hoff Temperature Dependence in High-Performance Liquid Chromatography (2019)

In HPLC, the nonlinear behavior of the retention factor <i>k</i>' with temperature (dependence of ln <i>k</i>' on 1/<i>T</i>) can be attributed to the multiple interactions of a unique analyte in the separation process and/or to the existence in solution of multiple forms of the analyte (also leading to different free enthalpies of interaction). In this study, several examples of nonlinear retention-temperature dependence are evaluated for both reversed-phase (RP) and hydrophilic interaction chromatography (HILIC) separations. The potential explanation for nonlinear retention-temperature behavior is evaluated for each example, some caused by multiple interactions in the separation system of a unique analyte and others by multiple forms of the analyte. In cases where the analyte does not have more forms and the separation is based predominantly on one type of interaction (e.g., hydrophobic interaction in RP-HPLC), the dependence is linear, as expected. By studying the changes in the chemical structure of a compound as a function of pH it is possible to decide, in many cases, if a unique form or multiple forms of a compound are present in the solution. The use of this information allows us to determine when the lack of linearity (when present) is caused by multiple interactions in the separation system (for one form of the compound) and when more forms are causing the lack of linearity. The approximation with a quadratic form for the nonlinear dependence has been verified in most cases to be good, and only minor improvements were obtained when using higher polynomial dependencies.
tmRDB (tmRNA database) (2000)

The tmRNA database (tmRDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and is accessible on the WWW at URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.++ +html. A tmRDB mirror site is located on the campus of Auburn University, Auburn, Alabama, reachable at the URL http://www.ag.auburn.edu/mirror/tmRDB/. Since April 1997, the tmRDB has provided sequences of tmRNA (previously called 10Sa RNA), a molecule present in most bacteria and some organelles. This release adds 17 new sequences for a total of 60 tmRNAs. Sequences and corresponding tmRNA-encoded tag peptides are tabulated in alphabetical and phylo-genetic order. The updated tmRNA alignment improves the secondary structures of known tmRNAs on the level of individual basepairs. tmRDB also provides an introduction to tmRNA function in trans-translation (with links to relevant literature), a limited number of tmRNA secondary structure diagrams, and numerous three-dimensional models generated interactively with the program ERNA-3D.
The Structures of Two Alkaloids from Patchouli Oil (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Structures of Two Alkaloids from Patchouli OilG. Büchi, I. M. Goldman, and Dana W. MayoCite this: J. Am. Chem. Soc. 1966, 88, 13, 3109–3113Publication Date (Print):July 1, 1966Publication History Published online1 May 2002Published inissue 1 July 1966https://pubs.acs.org/doi/10.1021/ja00965a040https://doi.org/10.1021/ja00965a040research-articleACS PublicationsRequest reuse permissionsArticle Views261Altmetric-Citations36LEARN 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
Security visualization: Cyber security storm map and event correlation (2011)

Efficient visualization of cyber incidents is the key in securing increasingly complex information infrastructure. Extrapolating security-related information from data from multiple sources can be a daunting task for organizations to maintain safe and secure operating environment. However, meaningful visualizations can significantly improve decision-making quality and help security administrators in taking rapid response. The purpose of this work is to explore this possibility by building on previously gained knowledge and understanding of weather maps used in meteorology, assessing the gaps, and applying various techniques and matrices to quantify the impacts of cyber incidences in an efficient way.
On Viscous Fluid Flow Down an Inclined Plane and the Development of Roll Waves (1977)

We develop a tractable, and mathematically rigorous, asymptotic theory for the development of instability in viscous fluid flow down an inclined plane, at supercritical Reynolds numbers. Our theory involves consideration of an ill posed problem, and provides a new example of the way such problems come up in applied mathematics. We show how one may use additional information, inherent in the problem one really wishes to solve, in order to regularize this improperly posed problem. We discuss several numerical experiments and compare the results with experimental observations of “roll waves” and “slug flows” in inclined channels, at similar slopes and Reynolds numbers.
The Effective Free Fraction of Estradiol and Xenoestrogens in Human Serum Measured by Whole Cell Uptake Assays: Physiology of Delivery Modifies Estrogenic Activity (1998)

The biological activity of natural estrogens is influenced by the degree to which they bind to serum proteins. To determine directly how serum affected the uptake of estradiol, we compared the whole cell uptake of [3H]estradiol in intact MCF-7 human breast cancer cells from serum-free medium with the uptake from 100% serum from adult men. In estrogen receptor saturation assays, 28.9 times more estradiol was required in serum to occupy the same number of estrogen receptors as was required in serum-free medium (SFM), suggesting that the effective free fraction of estradiol in adult male serum was 3.46% (1/28.9). Since most xenoestrogens are not available in tritium-labeled form, the cell uptake of unlabeled xenoestrogens could not be measured directly with saturation analysis. Therefore, we developed the relative binding affinity-serum modified access (RBA-SMA) assay to determine the effect of serum on the access of nonradioactive xenoestrogens to estrogen receptors within intact MCF-7 cells. Serum modified access (SMA) was calculated by dividing the relative binding affinity (RBA, relative to estradiol) measured in 100% serum, by the RBA measured in serum-free medium. An SMA > 1 indicated that the xenoestrogen had greater access to estrogen receptors than estradiol from serum. In contrast, an SMA < 1 indicated that the xenoestrogen had less access to estrogen receptors from serum than did estradiol. The synthetic estrogen diethylstilbestrol (DES) binds poorly to sex hormone binding globulin (SHBG), and DES showed enhanced access in serum, SMA = 6.2. Additional calculations through the Ki (inhibition constant) indicated that this corresponded to an effective free fraction of 26.9% for DES in serum. The phytoestrogens, coumestrol, genistein, and equol, showed substantial enhanced access in serum, over 10-fold relative to estradiol (SMA = 12.1, 10.3, and 11.3, respectively), and effective free fractions in serum of 47.8, 45.8, and 49.7%, respectively. Since most in vitro assays of xenoestrogens do not address how serum influences their bioactivity, the estrogenic activity of these phytoestrogens would be underestimated. Conversely, biochanin A showed decreased access from serum (SMA = 0.44) and had an effective free fraction of 2.4%; its estrogenic activity would be overestimated in serum-free assays.