gebhart/patrepeval huggingface dataset:
Selection of Alternative 5′ Splice Sites: Role of U1 snRNP and Models for the Antagonistic Effects of SF2/ASF and hnRNP A1 (2000)

The first component known to recognize and discriminate among potential 5' splice sites (5'SSs) in pre-mRNA is the U1 snRNP. However, the relative levels of U1 snRNP binding to alternative 5'SSs do not necessarily determine the splicing outcome. Strikingly, SF2/ASF, one of the essential SR protein-splicing factors, causes a dose-dependent shift in splicing to a downstream (intron-proximal) site, and yet it increases U1 snRNP binding at upstream and downstream sites simultaneously. We show here that hnRNP A1, which shifts splicing towards an upstream 5'SS, causes reduced U1 snRNP binding at both sites. Nonetheless, the importance of U1 snRNP binding is shown by proportionality between the level of U1 snRNP binding to the downstream site and its use in splicing. With purified components, hnRNP A1 reduces U1 snRNP binding to 5'SSs by binding cooperatively and indiscriminately to the pre-mRNA. Mutations in hnRNP A1 and SF2/ASF show that the opposite effects of the proteins on 5'SS choice are correlated with their effects on U1 snRNP binding. Cross-linking experiments show that SF2/ASF and hnRNP A1 compete to bind pre-mRNA, and we conclude that this competition is the basis of their functional antagonism; SF2/ASF enhances U1 snRNP binding at all 5'SSs, the rise in simultaneous occupancy causing a shift in splicing towards the downstream site, whereas hnRNP A1 interferes with U1 snRNP binding such that 5'SS occupancy is lower and the affinities of U1 snRNP for the individual sites determine the site of splicing.
Near‐field nano‐ellipsometer for ultrathin film characterization (2003)

We describe a near-field ellipsometer for accurate characterization of ultrathin dielectric films. Optical tunnelling mimics the absorption in metallic films, enabling accurate measurement of the refractive index of ultrathin dielectric film. A regression model shows that a refractive index resolution of 0.001 for films as thin as 1 nm is possible. A solid-immersion nano-ellipsometer that incorporates this near-field ellipsometric technique with a solid-immersion lens is constructed to demonstrate the viability of this technique. Such a nano-ellipsometer can accurately characterize thin films ranging in thickness from subnanometre to micrometres with potential transverse resolution of the order of 100 nm.
Renal tissue Po2sensing during acute hemodilution is dependent on the diluent (2020)

Sensing changes in blood oxygen content ([Formula: see text]) is an important physiological role of the kidney; however, the mechanism(s) by which the kidneys sense and respond to changes in [Formula: see text] are incompletely understood. Accurate measurements of kidney tissue oxygen tension ([Formula: see text]) may increase our understanding of renal oxygen-sensing mechanisms and could inform decisions regarding the optimal fluid for intravascular volume resuscitation to maintain renal perfusion. In some clinical settings, starch solution may be nephrotoxic, possibly due to inadequacy of tissue oxygen delivery. We hypothesized that hemodilution with starch colloid solutions would reduce [Formula: see text] to a more severe degree than other diluents. Anesthetized Sprague-Dawley rats (<i>n</i> = 77) were randomized to undergo hemodilution with either colloid (6% hydroxyethyl starch or 5% albumin), crystalloid (0.9% saline), or a sham procedure (control) (<i>n</i> = 13-18 rats/group). Data were analyzed by ANOVA with significance assigned at <i>P</i> < 0.05. After hemodilution, mean arterial pressure (MAP) decreased marginally in all groups, while hemoglobin (Hb) and [Formula: see text] decreased in proportion to the degree of hemodilution. Cardiac output was maintained in all groups after hemodilution. [Formula: see text] decreased in proportion to the reduction in Hb in all treatment groups. At comparably reduced Hb, and maintained arterial oxygen values, hemodilution with starch resulted in larger decreases in [Formula: see text] relative to animals hemodiluted with albumin or saline (<i>P</i> < 0.008). Renal medullary erythropoietin (EPO) mRNA levels increased more prominently, relative to other hypoxia-regulated molecules (GLUT-1, GAPDH, and VEGF). Our data demonstrate that the kidney acts as a biosensor of reduced [Formula: see text] following hemodilution and that [Formula: see text] may provide a quantitative signal for renal cellular responsiveness to acute anemia. Evidence of a more severe reduction in [Formula: see text] following hemodilution with starch colloid solution suggests that tissue hypoxia may contribute to starch induced renal toxicity.
Session details: Paper session 1 (ranking and recommendations) (2012)

No abstract available.
Autonomous Flexible Sensors for Health Monitoring (2018)

A concise, although admittedly non-exhaustive, didactic summary is given of some of the main concepts and approaches related to recent advances and developments to enable autonomous detection and monitoring of the likelihood or existence of a health risk state in continuous and real-time modes. To give a comprehensive statement, different aspects of these advanced materials and related devices are presented and discussed, such as: flexible sensors used for non-invasive detection of health-related physiological markers; self-powered materials to enable extended usage periods by harvesting energy from body movement and temperature; and self-healing properties of the materials used on the wearable devices to enable extended usage periods if scratched or cut. The linkage of these advanced materials and technologies together is particularly specified. Some of the strong and weak points in the development of each wearable material/device are clearly highlighted and criticized. Several ideas regarding further improvement of skin-based wearable devices are also discussed.
Electrocrystallization of Metallophthalocyanines: Effects of Substituents on the Oxidation Potential and Crystallization (1988)

Abstract A series of oxidation potentials of substituted metallophthalocyanines are examined with cyclic voltammetry. Relation between oxidation potential and the Hammett's constant of substituents is found to be linear for both octa- and tetrasubstituted derivatives. The oxidation potential shift is found to be calculated by electron-withdrawing or donating ability of substituents. Electrocrystallization of these compounds gives crystals which are composed of only cyanometallophthalocyanine. Crystals of substituted derivatives are analyzed to have different molecular arrangements from unsubstituted one because of steric effect of the substituents. Crystals of unsubstituted derivatives show highly inherent conductivity, but substituted ones show less conductivity due to the different molecular arrangements.
Cost-Effectiveness of Referring Patients to Centers of Excellence for Mitral Valve Surgery (2015)

BACKGROUND The 2014 American Heart Association/American College of Cardiology Valvular Heart Disease Guidelines state that mitral valve diseases should be repaired at a Center of Excellence (CoE). We evaluate the cost-effectiveness of such referrals. METHODS We estimate patients’ life expectancy based on projected survival of patients after mitral valve surgery and develop a cost model to calculate short- and long-term benefits and costs to both patients and payers. Benefits include increased life expectancy and avoidance of medical complications for patients. Short-term costs include all upfront payments by patients and payers at the time of discharge. Long-term costs include all payments associated with the condition that prompted the surgical procedure incurred during the remainder of a patient’s life. We assess cost-effectiveness of treating patients with various ages and major comorbidities at CoEs vs non-CoEs. RESULTS Full implementation of the guidelines would result in an increase in the percentage of patients obtaining mitral valve repair instead of valve replacement from 58% to 72%. Depending on the patient’s age and comorbidities, it would also result in a 6.64% to 12.47% reduction in mortality, 7.85% to 9.97% reduction in reoperation, 9.97% to 17.16% reduction in stroke, and an average gain of 3.77 to 9.88 months of life expectancy. Finally, greater reliance on CoEs results in financial savings to payers, due to avoidance of the costs of future complications. CONCLUSION Patients benefit from mitral valve surgery at a CoE regardless of their age or comorbidities. Payers may incur additional short-term costs when patients are referred to a CoE, but these are fully offset by long-term savings at the current repair rate gap of 24% between CoEs and non-CoEs in New York State. Redesigning co-pay structures and/or refining the set of patients who are referred to CoEs could further align the incentives of patients and payers on a case-by-case basis and achieve an even more desirable social outcome.
Scalability of InGaAs gate-all-around FET integrated on 300mm Si platform: Demonstration of channel width down to 7nm and L<inf>g</inf> down to 36nm (2016)

We report In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> GaAs-channel gate-all-around FETs with channel width down to 7nm and L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> down to 36nm, the smallest dimensions reported to date for IIIV devices fabricated on 300mm Si wafer. Furthermore, we systematically study the device scalability. InGaAs S/D improves the peak g <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> by 25% compared to InAs S/D. A g <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> of 1310 µS/µm with an SS <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</inf> of 82mV/dec is achieved for an L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> =46nm device. At this L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> , a record I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</inf> above 200µA/µm is obtained at I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</inf> of 100nA/µm and V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ds</inf> =0.5V on a 300mm Si platform.
A Size-Selective Intracellular Delivery Platform (2016)

Identifying and separating a subpopulation of cells from a heterogeneous mixture are essential elements of biological research. Current approaches require detailed knowledge of unique cell surface properties of the target cell population. A method is described that exploits size differences of cells to facilitate selective intracellular delivery using a high throughput microfluidic device. Cells traversing a constriction within this device undergo a transient disruption of the cell membrane that allows for cytoplasmic delivery of cargo. Unique constriction widths allow for optimization of delivery to cells of different sizes. For example, a 4 μm wide constriction is effective for delivery of cargo to primary human T-cells that have an average diameter of 6.7 μm. In contrast, a 6 or 7 μm wide constriction is best for large pancreatic cancer cell lines BxPc3 (10.8 μm) and PANC-1 (12.3 μm). These small differences in cell diameter are sufficient to allow for selective delivery of cargo to pancreatic cancer cells within a heterogeneous mixture containing T-cells. The application of this approach is demonstrated by selectively delivering dextran-conjugated fluorophores to circulating tumor cells in patient blood allowing for their subsequent isolation and genomic characterization.
Rapid search for spherical objects in aerial photographs (2003)

A methodology is presented for designing detectors which locate specific features in an image. The method is applied to the detection and segmentation of spherical features. A vital part of the detection and segmentation is the use of the gradient angle transform. An analysis of the gradient angle for ideal spheres is presented, with a discussion of how this may be used to locate the boundaries of the sphere. The algorithms used by a program which detects and segments spherical features are then presented. The results of applying the program to images with man-made spherical features are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
T cell receptor selection by and recognition of two class I major histocompatibility complex-restricted antigenic peptides that differ at a single position. (1993)

Peptides derived from HLA-Cw3 and HLA-A24 within region 170-179 differ by a single substitution, at position 173, and are both presented by the class I major histocompatibility complex molecule H-2Kd for recognition by murine cytolytic T lymphocytes (CTLs). As a first approach to understand the way T cell receptors (TCRs) intact with the HLA peptides, we have analyzed the TCR selection by, and recognition of, the two HLA antigenic sites. First, we have compared the TCR repertoires selected by HLA-Cw3 and HLA-A24, not only by sequencing the TCRs carried by CTL clones isolated and grown in vitro, but also by analyzing the TCRs expressed in vivo by peritoneal exudate lymphocytes from immune animals. Second, we have compared the TCR crossrecognition of HLA-A24 by CTLs selected by HLA-Cw3 with that of HLA-Cw3 by CTLs selected by HLA-A24. The combined analysis of TCR selection by and recognition of these two related HLA antigenic sites provides evidence that the TCR beta junctional regions interact with the amino-terminal part of the HLA peptides.
Dendritic and Axonal Propagation Delays May Shape Neuronal Networks With Plastic Synapses (2018)

Biological neuronal networks are highly adaptive and plastic. For instance, spike-timing-dependent plasticity (STDP) is a core mechanism which adapts the synaptic strengths based on the relative timing of pre- and postsynaptic spikes. In various fields of physiology, time delays cause a plethora of biologically relevant dynamical phenomena. However, time delays increase the complexity of model systems together with the computational and theoretical analysis burden. Accordingly, in computational neuronal network studies propagation delays were often neglected. As a downside, a classic STDP rule in oscillatory neurons without propagation delays is unable to give rise to bidirectional synaptic couplings, i.e., loops or uncoupled states. This is at variance with basic experimental results. In this mini review, we focus on recent theoretical studies focusing on how things change in the presence of propagation delays. Realistic propagation delays may lead to the emergence of neuronal activity and synaptic connectivity patterns, which cannot be captured by classic STDP models. In fact, propagation delays determine the inventory of attractor states and shape their basins of attractions. The results reviewed here enable to overcome fundamental discrepancies between theory and experiments. Furthermore, these findings are relevant for the development of therapeutic brain stimulation techniques aiming at shifting the diseased brain to more favorable attractor states.
Duplex RNAs and ss-siRNAs Block RNA Foci Associated with Fuchs' Endothelial Corneal Dystrophy (2019)

Fuchs' endothelial corneal dystrophy (FECD) leads to vision loss and is one of the most common inherited eye diseases. Corneal transplants are the only curative treatment available, and there is a major unmet need for treatments that are less invasive and independent of donor tissue. Most cases of FECD are associated with an expanded CUG repeat within the intronic region of TCF4 and the mutant RNA has been implicated as the cause of the disease. We previously presented preliminary data suggesting that single-stranded antisense oligonucleotides (ASOs) can inhibit CUG RNA foci in patient-derived cells and tissue. We now show that duplex RNAs and single-stranded silencing RNAs (ss-siRNAs) reduce the number of cells with foci and the number of foci per cells. Potencies are similar to those that are achieved with chemically modified ASOs designed to block foci. These data widen the potential for synthetic nucleic acids to be used to treat a widely prevalent and debilitating disease.
Concise Radiometric Calibration Using The Power of Ranking (2017)

Compared with raw images, the more common JPEG images are less useful for machine vision algorithms and professional photographers because JPEG-sRGB does not preserve a linear relation between pixel values and the light measured from the scene. A camera is said to be radiometrically calibrated if there is a computational model which can predict how the raw linear sensor image is mapped to the corresponding rendered image (e.g. JPEGs) and vice versa. This paper begins with the observation that the rank order of pixel values are mostly preserved post colour correction. We show that this observation is the key to solving for the whole camera pipeline (colour correction, tone and gamut mapping). Our rank-based calibration method is simpler than the prior art and so is parametrised by fewer variables which, concomitantly, can be solved for using less calibration data. Another advantage is that we can derive the camera pipeline from a single pair of raw-JPEG images. Experiments demonstrate that our method delivers state-of-the-art results (especially for the most interesting case of JPEG to raw).
Electrically conductive metallomacrocyclic assemblies. High-resolution solid-state NMR spectroscopy as a probe of local architecture and electronic structure in phthalocyanine molecular and macromolecular "metals" (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrically conductive metallomacrocyclic assemblies. High-resolution solid-state NMR spectroscopy as a probe of local architecture and electronic structure in phthalocyanine molecular and macromolecular "metals"Paul J. Toscano and Tobin J. MarksCite this: J. Am. Chem. Soc. 1986, 108, 3, 437–444Publication Date (Print):February 1, 1986Publication History Published online1 May 2002Published inissue 1 February 1986https://pubs.acs.org/doi/10.1021/ja00263a013https://doi.org/10.1021/ja00263a013research-articleACS PublicationsRequest reuse permissionsArticle Views345Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Incorporation of a Novel CD4+ Helper Epitope Identified from Aquifex aeolicus Enhances Humoral Responses Induced by DNA and Protein Vaccinations (2020)

CD4+ T cells play an important role in the maturation of the antibody responses. Conjugation of identified CD4+ T cell helper epitope to the target antigen has been developed as a strategy to enhance vaccine-induced humoral immunity. In this work, we reported the identification of a novel HLA-IAb helper epitope LS-3 from Aquifex aeolicus. In silico analysis predicted this epitope to have high binding affinity to common human HLA alleles and have complementary binding coverage to the established PADRE epitope. Introduction of HLA-IAb knockout mutations to the LS-3 epitope significantly attenuated humoral responses induced by a vaccine containing this epitope. Finally, engineered fusion of the epitope to a model antigen, influenza hemagglutinin, significantly improved both binding and hemagglutination inhibition antibody responses in mice receiving DNA or protein vaccines. In summary, LS-3 and additional identified CD4+ helper epitopes may be further explored to improve vaccine responses in translational studies.
Inhibition of cell growth and telomerase activity of breast cancer cells in vitro by retinoic acids. (2000)

The effects of retinoic acid (RA) and its analogs, all-trans RA, 9-cis RA and 13-cis RA, were investigated in human breast cancer MCF-7 cells and immortalized breast epithelial cell line MCF-10A. RA inhibited the telomerase activity of MCF-7 cells in a wide range of concentrations. RA at 10 microM also inhibited the growth of MCF-7 cells in a time-dependent manner. However, no significant growth inhibition was found between untreated control and RA-treated MCF-10A cells. Moreover, a marked inhibition of telomerase activity by RA was detected early in MCF-7 cells (after 24 h of RA treatment), which was preceded by a reduction of hTERT mRNA expression (after 12 h of RA treatment). However, MCF-10A cells showed a reduction of telomerase activity and down-regulation of hTERT after 4 days of RA treatment. Simultaneous changes in hTERT mRNA expression and telomerase activity were found for MCF-10A cells. The expressions of hTR and hTEP1 telomerase component genes were not changed after RA treatment. These results indicate that the anti-breast cancer activity of RA could be mediated by its ability to down-regulate the expression of hTERT telomerase gene.