gebhart/patrepeval huggingface dataset:
Detection and analysis of spliced chimeric mRNAs in sequence databanks (2003)

We have developed a databank screening procedure, the In Silico Trans-splicing Retrieval System (ISTReS), to identify heterologous, spliced mRNAs with potential origin from chromosomal translocations, mRNA trans-splicing and multi-locus transcription. A parsing algorithm to screen cDNA versus genome Blast outputs was implemented. Key filtering criteria were Blast scores of > or =300, match lengths of > or =95% of the query sequences, junction of the two partners at exon-exon borders and concordant 'sense/sense' reading orientation. ISTReS was validated by the successful identification of bona fide chromosomal translocation-derived fusion transcripts in the HGI and RefSeq databanks. The performance of ISTReS was verified against recently identified chimeric antisense transcripts, where it revealed essentially no independent proof of antisense transcription and absence of exon-exon borders at the chimeric join, consistent with an artefactual origin. Analysis of the UNIGENE database revealed 21 742 chimeric sequences overall that correspond to approximately 1% of the database transcripts. Novel FOP-Rho GAP and methionyl tRNA synthetase-advillin chimeric mRNAs with the canonical features of heterologous-genes spliced-transcripts were identified among 246 chimeras from the RefSeq databank. This suggests a frequency of canonically-spliced chimeras of approximately 1% of all the hybrid sequences in current databanks. These findings demonstrate the efficiency of ISTReS and the overall feasibility of sequence/structure-based strategies to search for chimeric mRNAs candidate to derive from the splicing of heterologous transcripts.
The pulse protocol: sensor network routing and power saving (2005)

We present a performance evaluation of the pulse protocol operating in a sensor network. In this work, a number of modifications are made to the original pulse protocol to provide efficient operation in a sensor network environment. The pulse protocol utilizes a periodic flood (the pulse) initiated by a single node (the pulse source) to provide both routing and synchronization to the network. This periodic pulse forms a pro-actively updated spanning tree rooted at the pulse source. Nodes communicate by forwarding packets through this tree. In addition, nodes are able to synchronize with the periodic pulse, allowing idle nodes to power off their radios a large percentage of the time when they are not required for packet forwarding. This results in substantial energy savings. A new mechanism called intermediate wake-up periods is introduced in this work in order to reduce the energy costs of low delay applications. Through simulation we explore the performance of both the protocol and the modifications with respect to energy efficiency and delay.
Improved Techniques for the Fabrication of Frisch Collar CdZnTe Gamma Ray Spectrometers (2009)

New methods, designed for the commercial-scale production of Frisch collar CdZnTe gamma ray spectrometers, are described in detail in the following work. Past methods required considerable skilled labor, were not readily automatable, and batch processing was only supported through a portion of the fabrication process. Advances in dielectric materials technology allow for new processes that readily apply the required dielectric film between the CdZnTe crystal and the conductive collar. The processes use spray or chemical vapor deposition methods to accurately achieve a specific thickness. Furthermore, application of the conductive collar was improved to facilitate commercial manufacturing. Comparisons in device performance are presented between the previous and new methods to illustrate the effectiveness and robustness of the new fabrication method. Parylene N performed well as the dielectric layer, while nickel-based paint, high-purity silver-based paint, and a silver-suspension Electrodag all performed well as the conductive layer, each maintaining spectral performance.
Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field (2007)

1999年に北浦らにより提唱されたフラグメント分子軌道(FMO)法は、分子系をフラグメントに分割し、フラグメントのモノマー、ダイマー・・・の計算から系全体を計算する方法であり、タンパク質やDNAのような巨大分子系全体を量子論的に扱う計算方法として、近年注目を集めている。本稿では、FMO法の概要と、多層FMO(MLFMO)法に基づいたタンパク質の励起状態計算、及びFMO法に基づいたconfiguration analysis for fragment interaction (CAFI)やvisualized cluster analysis of protein-ligand interaction (VISCANA)といった解析方法について報告し、FMO法の今後について展望する。
Calibration method of the specific characteristic of an electronic system of a rotating-analyzer ellipsometer (1997)

In photometric ellipsometry the optical signal is transformed into an electrical signal by a photodetector, and it passes an electronic system to reduce the noise and to amplify the signal. But inherently it will induce a phase shift and an amplitude attenuation of the output signal. Such a specific characteristic of an electronic system depends on the angular frequency of the signal and gives systematic errors to the results of the measurement of rotating-analyzer ellipsometry. We propose a modified method of measurement that enables us to calibrate the electronic system in the ellipsometric measurement configuration.
Loss of spr1 Expression Measurable by Quantitative RT-PCR in Human Bronchogenic Carcinoma Cell Lines (1998)

Expression of the small, proline-rich protein (spr1) squamous differentiation marker was measured in five cultured normal and 12 malignant human bronchial epithelial cell (BEC) populations by quantitative reverse transcriptase polymerase chain reaction (RT-PCR). Whereas spr1 expression was quantifiable and inducible in all five cultured normal cell populations, in all 12 carcinoma cell lines evaluated it was neither quantifiable nor inducible. Primers spanning the entire spr1 coding sequence amplified full-length PCR product from genomic DNA; therefore, large deletions in the coding region were not responsible for the loss of expression measurable by RT-PCR. This is the first molecular genetic marker reported that distinguishes all normal from all carcinoma cell populations evaluated. Because the spr1 protein is a component of the crosslinked envelope that forms during the squamous differentiation process, we hypothesize that the apparent loss of spr1 gene expression disrupts mechanisms for terminal squamous differentiation in the bronchial epithelium, thereby contributing to malignant transformation.
Modeling local coherence (2005)

This paper considers the problem of automatic assessment of local coherence.We present a novel entity-based representation of discourse which is inspired by Centering Theory and can be computed automatically from raw text.We view coherence assessment as a ranking learning problem and show that the proposed discourse representation supports the effective learning of a ranking function.Our experiments demonstrate that the induced model achieves significantly higher accuracy than a state-of-the-art coherence model.
Mass Spectrometry: Applications in the Analysis of Nucleosides, Nucleotides and Oligonucleotides (1990)

Abstract The past ten years have been an exciting time in mass spectrometry as a number of important instrumental developments have revolutionized the field, including the analysis of nucleic acid components.1,2 The focus of this talk will be on the impact that new ionization methods, e.g., plasma desorption(PD) and fast atom bombardment(FAB), and new magnet technology (expanded mass range and scan speed capability) have had on the analysis of nucleosides and nucleotides. Results from the speaker's laboratory will be used to illustrate the significance of capillary GC/MS techniques for the separation and analysis of complex mixtures of nucleosides derived from a biological source. In addition, some approaches being developed to overcome current limitations in the FAB analysis of nucleosides and nucleotides will be described. Unfortunately, time does not permit a discussion of other new areas of interest, i.e., LC/MS3 and MS/MS.4
Nucleophilic Aromatic Substitution for Heteroatoms:  An Oxidative Electrochemical Approach (2002)

The nucleophilic aromatic substitution for heteroatom through electrochemical oxidation of the intermediate sigma-complexes (Meisenheimer complexes) in simple nitroaromatic compounds is reported for the first time (NASX process). The studies have been carried out with hydride, cyanide, fluoride, methoxy, and ethanethiolate anions and n-butylamine as a nucleophile, at the cyclic voltammetry (CV) and preparative electrolysis level. The cyclic voltammetry experiments allow for detection and characterization of the sigma-complexes and they have led us to a proposal for the mechanism of the oxidation step. Furthermore, the power of the CV technique in the analysis of the reaction mixture throughout the whole chemical and electrochemical process is described.
Assessing the influence of different cation chemistries on ionic conductivity and alkaline stability of anion exchange membranes (2012)

Polysulfone (PSF) backbones were functionalized with reactive chloromethyl groups for preparing thin film anion exchange membranes (AEMs) with fixed benzyl quaternary cations. Three different cation chemistries of varying basicity were evaluated: 1,4-dimethylpiperazinium (DMP+), trimethylammonium (TMA+), and trimethylphosphonium (TMP+). The water uptake, ionic conductivity, and stability in alkaline media of these AEMs were assessed with both chloride and hydroxide counteranions. The results obtained revealed that the basicity value of the free base conjugate of the functionalized quaternary cations correlated well with gains in ionic conductivity. Cation basicity also correlated well with the alkaline stability of cations with the same inorganic atom, but was not an appropriate heuristic for comparing alkaline stability across cations with different inorganic atoms. The alkaline stability studies indicated that the primal degradation pathway of the TMA+ cation differed from that of the TMP+ cation (direct nucleophilic attack versus ylide formation). PSF with TMA+ and DMP+ cations were demonstrated to show alkaline fuel cell performance that reflected their respective ionic conductivity values.
Introduction to Coronary Artery Disease (CAD) and Biochemical Markers (1998)

Cardiovascular disease (CVD) (of which CAD is a subset) is the leading cause of morbidity and mortality in the Western world. In the US, there are approx 70 million people who suffer from one form of this disease or another (Fig. 1) (1). Each year, 500,000 suffer from stroke (cerebrovascular accident, CVA). The annual mortality rate of CVA is about 150,000 and individually ranks third overall behind acute myocardial infarction (AMI) (discussed in Chapter 3) and cancer. Approximately six million Americans are admitted to hospitals with a diagnosis of chest pain. Of those 70 million individuals with CVD, roughly 5% (three million) have silent ischemia. The incidence of AMI from the combination of patients with symptomatic and asymptomatic (silent) CAD is 1.5 million patients/yr. The mortality rate is 500,000/yr. Half of these deaths occur before they reach the hospital for treatment. Unstable angina (discussed in Chapter 2) and congestive heart failure (CHF) account for a large fraction of non-AMI patients who are admitted to a hospital with chest pain. A large number of chest pain patients are also inappropriately admitted for noncardiac causes. The remainder are discharged to home. From this group, there is roughly 30,000 who are inappropriately discharged from the emergency department. Chapter 4 discusses the impact that cardiac markers have on the discharge of patients from the emergency department.
A chemistry exhibit (1932)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA chemistry exhibitH. W. Baker and L. I. Phares Cite this: J. Chem. Educ. 1932, 9, 3, 500Publication Date (Print):March 1, 1932Publication History Received3 August 2009Published online1 March 1932Published inissue 1 March 1932https://doi.org/10.1021/ed009p500RIGHTS & PERMISSIONSArticle Views35Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (4 MB) Get e-Alerts Get e-Alerts
Cytoplasmic Free [Ca2+] is Increased in the Platelets of Spontaneously Hypertensive Rats and Essential Hypertensive Patients (1985)

The cytoplasmic free calcium concentration [( Ca2+]i) was assessed with the fluorescent dye Quin 2 in platelets and lymphocytes of spontaneously hypertensive rats (SHR), normotensive Wistar-Kyoto rats (WKY), essential hypertensive patients (EHP) and normotensive human control subjects (NCS). [Ca2+]i was significantly higher in the platelets of 8- and 20-week-old SHR in comparison with WKY. However, no difference was evident after weaning. Changes of cellular calcium in hypertensive rats apparently evolved simultaneously with the development of high arterial pressure. [Ca2+]i was significantly higher in platelets of EHP than in NCS. In lymphocytes of SHR, [Ca2+]i was not different from WKY at 4 and 8 weeks, but was increased at 14 weeks and at older ages. In EHP, intralymphocytic [Ca2+] was only modestly higher than in controls. On the whole, the results suggest that control of cytoplasmic calcium in these blood cells is similarly affected in human and animal models of primary hypertension.
PP.LB02.08 (2015)

Objective: Scientific societies and manufacturers recommend that arm cuff for blood pressure (BP) should be placed with the bladder centred above brachial artery for correct measurement. Although cuff malpositioning may be common it is not clear whether the related error is relevant. This study is aimed to address this issue and to evaluate the usefulness of a novel arm cuff to overcome the problem of incorrect cuff positioning. Design and method: An interim analysis in 28 (out of 50 planned) subjects was performed (age 51.2 ± 16.9, 11 M/17F, BMI 29.4 ± 5.2 kg/m2, arm circumference 31.4 ± 3.1 cm). Two sequences of BP measurements on both arms were performed in each participant: 1) with two mercury sphygmomanometers (device A, always correctly placed, Device B either in correct position, rotated by 90° medially, by 90° laterally and by 180°); 2) with a mercury sphygmomanometer (Device A always in correct position) and an Omron M6-Comfort (HEM-7321-E) validated oscillometric device coupled with IntelliWrap cuff (device B, in correct position, rotated by 90° laterally and by 180°). Results: Mean differences are shown in Table, respectively for sequence 1 (two mercury devices, as above) and sequence 2 (BP with Omron M6-Comfort with cuff in different positions minus BP obtained with a reference mercury device having cuff correctly positioned).Conclusions: Interim results show that incorrect conventional cuff positioning significantly affects BP measurement results, with BP overestimation when the bladder centre is displaced by 90° laterally or by 180° compared to correct position. No effect of cuff position was observed when IntelliWrap cuff was used, although BP values obtained with oscillometric device tended to be lower than those obtained by reference method (possibly because of relative undercuffing with mercury device in subjects with large arm circumference).
All-Or-Nothing Transforms Using Quasigroups (2008)

Abstract. In this paper we suggest a new transformation scheme for All-Or-Nothing encryption, originally suggested by Rivest. The new transform concerns the use of quasigroups for the preprocessing of the data before any ordinary encryption method. We describe a method of constructing random quasigroups and we propose a way of using the advantages of quasigroup in Rivest&apos;s method. This combination makes the method faster and maintains the advantages against brute-force attacks. 1
Enhancing Photochemical Activity of Semiconductor Nanoparticles with Optically Active Ag Nanostructures: Photochemistry Mediated by Ag Surface Plasmons (2010)

Composite materials composed of optically active Ag nanostructures and TiO2 photocatalysts show enhanced photoactivity compared to the pure TiO2 in the decomposition of methylene blue. The enhanced photochemical activity is attributed to radiative transfer of energy, mediated by surface plasmons, from Ag particles to the semiconductor leading to higher concentrations of charge carriers (e−/h+ pairs) in the semiconductor and therefore to higher photochemical activity. We demonstrate that the performance of the composite photocatalysts is a strong function of the size and shape of Ag nanostructures. This can be explained by the size- and shape-specific optical activity of Ag nanostructures. We show that by rationally changing the size and shape of Ag nanostructures it is possible to maximize photochemical activity of a semiconductor at a given excitation wavelength.
Regulation of expression and function of TLR4 in macrophages by human cord blood serum (2005)

Objective To investigate the regulation of expression and function of TLR4 in murine macrophage cell line RAW264. 7 by human cord blood serum. Methods Cord blood serum and peripheral blood serum were obtained from term pregnant women. The toxicity of human serum to RAW264. 7 cell was evaluated by electron microscopy and MTT assay. RT-PCR and flow cytometry were used to detect the expression of TLR4 in RAW264. 7 cells. The activation of TLR4 signal pathway was detected by the intracellular level of 1 kBα: by immunofluoresence technique and the expression of COX-2 by RT-PCR. Results Compared with the peripheral blood serum, the human cord blood serun did not destroy the murine macrophage cells. And the human cord blood serum could down-regulate the expression of TLR4 in RAW264.7 cells. The activation of NF-kB and expression of COX-2 induced by LPS in RAW264.7 cells were inhibited by pretreatment with human cord blood serum. Conclusion Human cord blood serum can down-regulate the expression of TLR4 and inhibit the TLR4 signal transduction in RAW264.7 cells. These results provides a new experimental clue to the research on the mechanism of the immune regulation by cord blood cells.
Pairing of single mutations yields obligate Cre-type site-specific recombinases (2021)

Tyrosine site-specific recombinases (SSRs) represent a versatile genome editing tool with considerable therapeutic potential. Recent developments to engineer and evolve SSRs into heterotetramers to improve target site flexibility signified a critical step towards their broad utility in genome editing. However, SSR monomers can form combinations of different homo- and heterotetramers in cells, increasing their off-target potential. Here, we discover that two paired mutations targeting residues implicated in catalysis lead to simple obligate tyrosine SSR systems, where the presence of all distinct subunits to bind as a heterotetramer is obligatory for catalysis. Therefore, only when the paired mutations are applied as single mutations on each recombinase subunit, the engineered SSRs can efficiently recombine the intended target sequence, while the subunits carrying the point mutations expressed in isolation are inactive. We demonstrate the utility of the obligate SSR system to improve recombination specificity of a designer-recombinase for a therapeutic target in human cells. Furthermore, we show that the mutations render the naturally occurring SSRs, Cre and Vika, obligately heteromeric for catalytic proficiency, providing a straight-forward approach to improve their applied properties. These results facilitate the development of safe and effective therapeutic designer-recombinases and advance our mechanistic understanding of SSR catalysis.
GENETIC ANALYSIS OF A "DOUBLE MALE" STRAIN OF ESCHERICHIA COLI K-12 (1963)

The behavior of a double male strain of Escherichia coli K12 has been compared to that of its parents and a primary F' strain carrying F14 in order to determine whether the genome of the double male, responsible for the double origin mode of gene transmission, is composed of one or two linkage groups. F-prime plasmids carrying leu and pyrB and argG and metC have been detected following mating an F(-)recA(-) recipient with the double male. Their existence strongly supports the contention that the double male is composed of a single linkage group with two integrated sex factors. Data from acridine orange curing experiments places the frequency of double male cells in the population of growing cells in the two-chromosome configuration as less than one percent. Evidence for a unique origin and terminus of DNA replication deduced by the density labelling and transduction of double male DNA supports the contention that the double male is best considered a cell with a single chromosome carrying two integrated F plasmids.
Rectangular convolution for fast filtering of characters (1987)

While the race towards higher-resolution bitmap displays is still on, many grayscale displays have appeared on the scene. To fully utilize their capabilities, grayscale fonts are needed, and these can be produced by filtering bi-level masters. Most of the efficient filtering techniques cannot directly be applied. For example, prefiltering is impractical, due to the number of character masters and the requirement of sub-pixel positioning. Furthermore, we would like to impose as few restrictions as possible on the characteristics of the filter, in order to facilitate exploration into the quality of various filters.We describe a fast filtering technique especially adapted to this task. The characters are decomposed into rectangles, and a summed-area representation of the filter is efficiently convolved with each individual rectangle to construct the grayscale character. For a given filter, the number of operations is O (linear size of the grayscale character), which is optimal.We give an analysis of the efficiency of this technique, and examples of its implementation applied to various families of fonts and point sizes. The performance of the implementation is such that filtering characters for grayscale displays is feasible in realtime on personal workstations.
<title>Hybrid scheme for color dithering</title> (1990)

This paper presents a hybrid color dithering scheme suitable for rendering continuous tone color images on a CRT display with a small number (on the order of 16-256) of distinct colors. Monochrome (especially bi-level) dithering techniques are well studied. Which of these techniques extend naturally to color? We look at four classes of monochrome dithering techniques and attempt to generalize each one, first to multiple gray-level (but still monochrome) inks and then to a multiple color pallette. In the monochrome case, we discover that texture introduced by the dithering process can significantly affect the appearance of the image. We develop a scheme by which the user can control these texture effects. The primary tradeoff is between very fine grained textures which depend critically on the local gray level and relatively coarser, more obvious, textures which appear uniform across the entire image. In the color case, we have the further complication of choosing a color pallette. We deal primarily with the case where there are a small number of available colors, and where the color pallette is not optimized separately for each image.