gebhart/patrepeval huggingface dataset:
Efficient inhibition of RNA self-primed extension by addition of competing 3′-capture DNA-improved RNA synthesis by T7 RNA polymerase (2019)

In vitro synthesized RNA is used widely in studies of RNA biology, biotechnology and RNA therapeutics. However, in vitro synthesized RNA often contains impurities, such as RNAs with lengths shorter and longer than the expected runoff RNA. We have recently confirmed that longer RNA products are formed predominantly via cis self-primed extension, in which released runoff RNA folds back on itself to prime its own RNA-templated extension. In the current work, we demonstrate that addition of a DNA oligonucleotide (capture DNA) that is complementary to the 3' end of the expected runoff RNA effectively prevents self-primed extension, even under conditions commonly used for high RNA yields. Moreover, the presence of this competing capture DNA during 'high yield' transcription, leads to an increase in the yield of expected runoff RNA by suppressing the formation of undesired longer RNA byproducts.
Right-cyclic Hadamard coding schemes and fast Fourier transforms for use in computing spectrum estimates in Hadamard-transform spectrometry (1996)

Two computationally efficient spectrum-recovery schemes were recently developed for use by Hadamard-transform spectrometers that have static and dynamic nonidealities in their encoding masks. These methods make use of a left-cyclic Hadamard encodement scheme and the ability to express the left-cyclic W/sub D/ matrix in factored form as W/sub D/=ST/sub D/. The matrix W/sub D/ describes the dynamic characteristics of and the encodement scheme for the mask. This paper focuses on the use of a right-cyclic Hadamard pattern to encode the mask and computationally efficient methods that can be used to obtain the spectrum-estimate. The major advantage of right-cyclic over left-cyclic encodement schemes is due to the resulting right-cyclic nature of both W/sub D/ and W/sub D//sup -1/. Fast algorithms, such as a fast Fourier transform (FFT) or a Trench algorithm, that take advantage of the right-cyclic nature of W/sub D/ can be used to obtain W/sub D//sup -1/ directly. In general, the number of mask elements is not an integer power of two, and non-radix-2 FFT's must be used to compute W/sub D//sup -1/. Since W/sub D//sup -1/ is right-cyclic, the vector-matrix product of W/sub D//sup -1/ and the measurement vector can be expressed as a circular correlation and implemented indirectly via FFT's. With appropriate zero-padding of the vectors, radix-2 FFT's can be used for this computation. Various algorithms were used at each step in the overall computation of the spectrum-estimate, and the total computation times are presented and compared. The size of the mask is important in determining which algorithms are the most efficient in recovering the spectrum-estimate.
Knock-out Mice Reveal the Contributions of P2Y and P2X Receptors to Nucleotide-induced Ca2+ Signaling in Macrophages (2006)

Immune cell function is modulated by changes in extracellular nucleotide levels. Here we used reverse transcription-PCR analyses, single cell Ca2+ imaging, and knock-out mice to define the receptors mediating nucleotide-induced Ca2+ signaling in resident peritoneal macrophages. In Ca2+-free buffer, the potent (K0.5<1 microm) stimulatory effect of UTP (or ATP) on endoplasmic reticulum (ER) Ca2+ release was abolished in cells isolated from P2Y2/P2Y4 double knock-out mice. Moreover, P2Y4(0/-), but not P2Y2-/-, macrophages responded to UTP. In P2Y2-/- macrophages, we could elicit Ca2+ responses to "pure" P2X receptor activation by applying ATP in buffer containing Ca2+. Purified UDP and ADP were ineffective agonists, although modest UDP-induced Ca2+ responses could be elicited in macrophages after "activation" with lipopolysaccharide and interferon-gamma. Notably, in Ca2+-free buffer, UTP-induced Ca2+ transients decayed within 1 min, and there was no response to repeated agonist challenge. Measurements of ER [Ca2+] with mag-fluo-4 showed that ER Ca2+ stores were depleted under these conditions. When extracellular Ca2+ was available, ER Ca2+ stores refilled, but Ca2+ increased to only approximately 40% of the initial value upon repeated UTP challenge. This apparent receptor desensitization persisted in GRK2+/- and GRK6-/- macrophages and after inhibition of candidate kinases protein kinase C and calmodulin-dependent kinase II. Initial challenge with UTP also reduced Ca2+ mobilization by complement component C5a (and vice versa). In conclusion, homologous receptor desensitization is not the major mechanism that rapidly dampens Ca2+ signaling mediated by P2Y2, the sole Gq-coupled receptor for UTP or ATP in macrophages. UDP responsiveness (P2Y6 receptor expression) increases following macrophage activation.
Optimum broadcasting and personalized communication in hypercubes (1989)

Four different communication problems are addressed in Boolean n-cube configured multiprocessors: (1) one-to-all broadcasting: distribution of common data from a single source to all other nodes; (2) one-to-all personalized communication: a single node sending unique data to all other nodes; (3) all-to-all broadcasting: distribution of common data from each node to all other nodes; and (4) all-to-all personalized communication: each node sending a unique piece of information to every other node. Three communication graphs (spanning trees) for the Boolean n-cube are proposed for the routing, and scheduling disciplines provably optimum within a small constant factor are proposed. With appropriate scheduling and concurrent communication on all ports of every processor, routings based on these two communication graphs offer a speedup of up to n/2, and O( square root n) over the routings based on the spanning binomial tree for cases (2)-(4) respectively. All three spanning trees offer optimal communication times for cases (2)-(4) and concurrent communication on all ports of every processor. Timing models and complexity analysis are verified by experiments on a Boolean-cube-configured multiprocessor.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A flexible three-dimensional electrode mesh: An enabling technology for wireless brain–computer interface prostheses (2016)

The neural interface is a key component in wireless brain-computer prostheses. In this study, we demonstrate that a unique three-dimensional (3D) microneedle electrode on a flexible mesh substrate, which can be fabricated without complicated micromachining techniques, is conformal to the tissues with minimal invasiveness. Furthermore, we demonstrate that it can be applied to different functional layers in the nervous system without length limitation. The microneedle electrode is fabricated using drawing lithography technology from biocompatible materials. In this approach, the profile of a 3D microneedle electrode array is determined by the design of a two-dimensional (2D) pattern on the mask, which can be used to access different functional layers in different locations of the brain. Due to the sufficient stiffness of the electrode and the excellent flexibility of the mesh substrate, the electrode can penetrate into the tissue with its bottom layer fully conformal to the curved brain surface. Then, the exposed contact at the end of the microneedle electrode can successfully acquire neural signals from the brain.
Gold Nanoparticles: An Efficient Antimicrobial Agent against Enteric Bacterial Human Pathogen (2016)

Enteric bacterial human pathogens, <i>i.e.</i>, Escherichia coli, Staphylococcus aureus, Bacillus subtilis and Klebsiella pneumoniae, are the major cause of diarrheal infections in children and adults. Their structure badly affects the human immune system. It is important to explore new antibacterial agents instead of antibiotics for treatment. This project is an attempt to explain how gold nanoparticles affect these bacteria. We investigated the important role of the mean particle size, and the inhibition of a bacterium is dose-dependent. Ultra Violet (UV)-visible spectroscopy revealed the size of chemically synthesized gold nanoparticle as 6-40 nm. Atomic force microscopy (AFM) analysis confirmed the size and X-ray diffractometry (XRD) analysis determined the polycrystalline nature of gold nanoparticles. The present findings explained how gold nanoparticles lyse Gram-negative and Gram-positive bacteria.
Porous shape memory polymers: Design and applications (2016)

ABSTRACT Porous shape memory polymers (SMPs) exhibit geometric and volumetric shape change when actuated by an external stimulus and can be fabricated as foams, scaffolds, meshes, and other polymeric substrates that possess porous three‐dimensional macrostructures. These materials have applications in multiple industries such as textiles, biomedical devices, tissue engineering, and aerospace. This review article examines recent developments in porous SMPs, with a focus on fabrication methods, methods of characterization, modes of actuation, and applications. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54 , 1300–1318
Systematic Chemistry of C Beginning To Emerge (1991)

RETURN TO ISSUEPREVNewsNEXTSystematic Chemistry of C Beginning To EmergeBuckminsterfullerene, C, in contrast to its physical stability, is quite reactive chemically—a feature chemists are exploitingRUBY M. BAUMView Author Information C&EN San FranciscoCite this: Chem. Eng. News 1991, 69, 50, 17–20Publication Date (Print):December 16, 1991Publication History Published online10 November 2010Published inissue 16 December 1991https://pubs.acs.org/doi/10.1021/cen-v069n050.p017https://doi.org/10.1021/cen-v069n050.p017newsACS PublicationsCopyright © 1991 AMERICAN CHEMICAL SOCIETYArticle Views142Altmetric-Citations5LEARN 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 options SUBJECTS:Carbon,Molecules Get e-Alerts
Notch‐associated gene expression in embryonic and adult taste papillae and taste buds suggests a role in taste cell lineage decisions (2003)

The Notch signaling pathway is involved in cell fate decisions during development. To explore the role of this signaling cascade in the taste system, we investigated the expression patterns of Notch signaling genes in fetal and adult mouse tongues using in situ hybridization. Three of the four murine Notch receptors, their ligands, Delta-like 1 (Dll-1), Jagged1, and Jagged2, as well as three transcription factors, Hes1, Hes6, and Mash1, are expressed in the embryonic taste epithelium. Expression is first detected in the circumvallate papilla at embryonic day E14.5, when Notch1, Jagged1, and Jagged2 are expressed broadly in the papilla and general lingual epithelium. In contrast, Mash1 and Hes6 are restricted to only a few epithelial cells in the apical region of the developing papilla. By E18.5, many of the genes now exhibit a bimodal expression pattern in the papillary epithelium: apically and dorsally they are expressed in sparse clusters of cells, while more ventrally expression typically occurs throughout the lower regions of the trenches. The extent of papilla innervation was compared with Mash1 and Hes6 expression. At E14.5, when Hes6 and Mash1 are already expressed in small numbers of epithelial cells, PGP9.5 immunoreactive fibers have not yet invaded the epithelium, consistent with the specification of taste bud primordia prior to nerve contact. All of the genes examined (except Notch2) are also expressed in subsets of cells within circumvallate taste buds in adult mice, although Notch1 is restricted to basal cells adjacent to taste buds. The onset of embryonic Notch associated gene expression after the morphological differentiation of the circumvallate papilla argues that this signaling cascade may specify taste receptor cell lineages within an already specified taste papilla. Similarly, Notch gene expression in adult taste buds suggests continued roles in cell lineage determination and cell turnover.
Minimally invasive mitral valve repair via right mini-thoracotomy in patient with myelodysplastic syndrome (2018)

A MICS-mitral procedure may be an effective option for MR patients with MDS who require a mitral valve repair to avoid postoperative infection and reduce the incidence of perioperative transfusion.
<i>In Vivo</i> Demonstration of Load-Induced Fluid Flow in the Rat Tibia and Its Potential Implications For Processes Associated With Functional Adaptation (2000)

Load-induced extravascular fluid flow has been postulated to play a role in mechanotransduction of physiological loads at the cellular level. Furthermore, the displaced fluid serves as a carrier for metabolites, nutrients, mineral precursors and osteotropic agents important for cellular activity. We hypothesise that load-induced fluid flow enhances the transport of these key substances, thus helping to regulate cellular activity associated with processes of functional adaptation and remodelling. To test this hypothesis, molecular tracer methods developed previously by our group were applied in vivo to observe and quantify the effects of load-induced fluid flow under four-point-bending loads. Preterminal tracer transport studies were carried out on 24 skeletally mature Sprague Dawley rats. Mechanical loading enhanced the transport of both small- and larger-molecular-mass tracers within the bony tissue of the tibial mid-diaphysis. Mechanical loading showed a highly significant effect on the number of periosteocytic spaces exhibiting tracer within the cross section of each bone. For all loading rates studied, the concentration of Procion Red tracer was consistently higher in the tibia subjected to pure bending loads than in the unloaded, contralateral tibia. Furthermore, the enhancement of transport was highly site-specific. In bones subjected to pure bending loads, a greater number of periosteocytic spaces exhibited the presence of tracer in the tension band of the cross section than in the compression band; this may reflect the higher strains induced in the tension band compared with the compression band within the mid-diaphysis of the rat tibia. Regardless of loading mode, the mean difference between the loaded side and the unloaded contralateral control side decreased with increasing loading frequency. Whether this reflects the length of exposure to the tracer or specific frequency effects cannot be determined by this set of experiments. These in vivo experimental results corroborate those of previous ex vivo and in vitro studies. Strain-related differences in tracer distribution provide support for the hypothesis that load-induced fluid flow plays a regulatory role in processes associated with functional adaptation.
Bixin and norbixin protect against DNA‐damage and alterations of redox status induced by methylmercury exposure in vivo (2012)

Populations in the Amazon are exposed to organic mercury via consumption of contaminated foods. These ethnic groups consume a specific plant seed "annatto" which contains certain carotenoids. The aim of this study was to find out if these compounds (bixin, BIX and norbixin, NOR), protect against DNA-damage caused by the metal. Therefore, rats were treated orally with methylmercury (MeHg) and with the carotenoids under conditions that are relevant to humans. The animals were treated either with MeHg (30 μg/kg/bw/day), BIX (0.1-10 mg/kg/bw/day), NOR (0.01-1.0 mg/kg/bw/day) or combinations of the metal compound and the carotenoids consecutively for 45 days. Subsequently, the glutathione levels (GSH) and the activity of catalase were determined, and DNA-damage was measured in hepatocytes and leukocytes using single cell gel electrophoresis assays. Treatment with the metal alone caused a decrease in the GSH levels (35%) and induced DNA damage, which resulted in increased DNA migration after electrophoresis in liver and blood cells, whereas no effects were seen with the carotenoids alone. When BIX or NOR were given in combination with organic mercury, the intermediate and the highest concentrations of the carotenoids (1.0 and 10.0 mg/kg/bw/day BIX and 0.1 and 1.0 mg/kg/bw/day NOR) protected against DNA-damage. Furthermore, we found with both carotenoids, a moderate increase in the GSH levels in both metal-treated and untreated animals, while the activities of catalase remained unchanged. Our results indicate that consumption of BIX and NOR may protect humans against the adverse health effects caused by exposure to organic mercury.
Early lesions of Kaposi's sarcoma in homosexual men. An ultrastructural comparison with other vascular proliferations in skin. (1983)

An aggressive variant of Kaposi's sarcoma (KS) has appeared in young homosexual men with evidence of systemic immunosuppression. The ultrastructure in biopsy specimens from 8 KS cases in young homosexual men has been compared with that in biopsy specimens from 4 KS cases in elderly heterosexuals and with that in biopsy specimens from 23 cases of benign vascular disorders of skin. In all cases of KS the small blood vessels lacked a prominent investment of pericytes and their processes, had a fragmented and often absent basal lamina, had frequent discontinuities in the endothelial lining, and had only a few small junctional densities between endothelial cells. Some clinically aggressive cases of KS also had necrosis of individual endothelial cells and had prominent cytoplasmic processes entrapping individual collagen fibers. The benign disorders lacked these features. These differences in the structure of the small vessels may be of diagnostic value in some early cases of KS. The loss of dendritic pericytes in blood capillaries in KS might relate to the telangiectasia which is a prominent feature of the early lesions of KS.
Depth Sensor-Based Realtime Tumor Tracking for Accurate Radiation Therapy (2014)

We present an image guided radiation therapy (IGRT) system for tracking tumors in realtime based on continuous structured light imaging. While an accurate positioning of the radiation isocenter to pre-imaged cancer cells is critical to minimize the risk of damaging healthy tissues, patients undergo involuntary motions such as breathing or unpredictable gestures during treatment. Moreover, multiple sessions are typically necessary and repositioning the patient accurately can be difficult. Our approach consists of determining the tumor position by densely tracking the deformation of a stream of 3D scans using a realtime variant of a state-of-the-art non-rigid registration algorithm and an FEM simulation on the interior body. We use interactive reprojection for visual guidance to adjust the posture of the patient and couch position, depending on the tumor location. Compared to existing techniques, our method uniquely estimates tumor deviations under body deformations. Our pipeline has been successfully commercialized as part of the C-RAD AB CatalystTM product line and is already deployed in a number of hospitals.
Distributed economic model predictive control for large-scale building temperature regulation (2016)

Although recent research has suggested model predictive control as a promising solution for minimizing energy costs of commercial buildings, advanced control systems have not been widely deployed in practice. Large-scale implementations, including industrial complexes and university campuses, may contain thousands of air handler regions each with tens of zones. A single centralized control system for these applications is not desirable. In this paper, we propose a distributed control system to economically optimize temperature regulation for large-scale commercial building applications. Since there is no clear time-scale separation, we propose a decomposition strategy that considers the complexities of thermal energy storage, zone interactions, and chiller plant equipment while remaining computationally tractable. One of the primary benefits of the proposed formulation is that the low-level airside problem can be decoupled and solved in a distributed manner; hence, it can be easily extended to handle large applications. Peak demand charges, a major source of coupling, are included. Iterations and communication between the low-level subsystems are not required. Since the time scale of regulatory controllers is significant, their dynamics are modeled. The interactions of the airside system with the waterside system are also considered, including discrete decisions, such as turning chillers on and off. Previously, heuristics have been used to make these decisions. We demonstrate the effectiveness of this control system architecture via a simulation study. In the presence of sufficient active thermal energy storage, we provide a simplification of the proposed control strategy that remains economically optimal.
Progesterone Receptor Antagonists – A Novel Treatment for Severe Hyponatremia from the Endocrine Paraneoplastic Syndrome (2021)

Hyponatremia related to ectopic secretion of cancer cells of argininevasopressin (AVP) or atrial natriuretic peptide (ANP) is most commonlycaused by small cell lung cancer. The ideal treatment would be one thatnot only corrects the hyponatremia, especially if it is life threatening, butat the same time causes regression of the cancer, and thus improves bothquality and length of life. As one is waiting for chemotherapy, surgery,or radiotherapy to decrease the cancer burden, tolvaptan has been usedto correct the hyponatremia to improve symptoms or prevent death.Mifepristone, a progesterone receptor modulator/antagonist has been usedto treat various cancers. The oral 200mg tablet was given to an 80-year-oldwoman who developed sudden extensive lung cancer with a serum sodiumof 118 mmol/L. She refused chemotherapy but agreed to take mifepristone.The hyponatremia was completely corrected (145 mmol/L) within onemonth of treatment. She was in complete remission for 5 years and diednot from lung cancer, but an acute myocardial infarction. Mifepristonemay serve the purpose to not only quickly correct hyponatremia when itis related to an endocrine paraneoplastic syndrome, but also to provideimproved quality and length of life.