gebhart/patrepeval huggingface dataset:
Removal of a Single α-Tubulin Gene Intron Suppresses Cell Cycle Arrest Phenotypes of Splicing Factor Mutations in <i>Saccharomyces cerevisiae</i> (2002)

Genetic and biochemical studies of Schizosaccharomyces pombe and Saccharomyces cerevisiae have identified gene products that play essential functions in both pre-mRNA splicing and cell cycle control. Among these are the conserved, Myb-related CDC5 (also known as Cef1p in S. cerevisiae) proteins. The mechanism by which loss of CDC5/Cef1p function causes both splicing and cell cycle defects has been unclear. Here we provide evidence that cell cycle arrest in a new temperature-sensitive CEF1 mutant, cef1-13, is an indirect consequence of defects in pre-mRNA splicing. Although cef1-13 cells harbor global defects in pre-mRNA splicing discovered through intron microarray analysis, inefficient splicing of the alpha-tubulin-encoding TUB1 mRNA was considered as a potential cause of the cef1-13 cell cycle arrest because cef1-13 cells arrest uniformly at G(2)/M with many hallmarks of a defective microtubule cytoskeleton. Consistent with this possibility, cef1-13 cells possess reduced levels of total TUB1 mRNA and alpha-tubulin protein. Removing the intron from TUB1 in cef1-13 cells boosts TUB1 mRNA and alpha-tubulin expression to near wild-type levels and restores microtubule stability in the cef1-13 mutant. As a result, cef1-13 tub1Deltai cells progress through mitosis and their cell cycle arrest phenotype is alleviated. Removing the TUB1 intron from two other splicing mutants that arrest at G(2)/M, prp17Delta and prp22-1 strains, permits nuclear division, but suppression of the cell cycle block is less efficient. Our data raise the possibility that although cell cycle arrest phenotypes in prp mutants can be explained by defects in pre-mRNA splicing, the transcript(s) whose inefficient splicing contributes to cell cycle arrest is likely to be prp mutant dependent.
Salt bridges: Geometrically specific, designable interactions (2010)

Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms.
Layout of an Automobile Transmission Using Three-Dimensional Shapeable Components (1999)

Abstract An extended pattern search algorithm is presented for the placement of shapeable components within a product layout. The algorithm is applied to an automobile transmission layout taking into account the shapeability of the components. Overlap between components is allowed and penalized during the optimization process. Shapeable octrees are used to evaluate the amount of overlap between pairs of components. The algorithm minimizes the connection cost in addition to optimizing the position and size of the components. A shapeable component has a defined geometry, but its size may vary within limits. The size of clutches in a transmission is determined by the torque capacity requirement, thermal requirement, and gain requirement. Under a given load, the size of a clutch satisfying a set of functional requirements is related to its location in the transmission assembly, making it necessary to design the clutches on the fly while laying out the components.
A three transistor MOS memory cell with internal refresh (1972)

A 1024-bit N-channel read/write memory has been fabricated using a memory call composed of three minimum geometry transistors. Each cell includes refresh circuitry within its 6.7 mil <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> area.
Minimizing the bottom reflection in Ultrasonic CMUT Transducer backing using low profile structuring (2009)

Capacitive Micro-machined Ultrasonic Transducer (CMUT) transducers need an acoustic backing to ensure that any acoustic signal which propagates from the transducer into the substrate is absorbed in the backing. The backing should be made such that it does not give a false echo in the signal received by or transmitted from the transducer. Ideally, this backing material should provide high attenuation and it should match the acoustic impedance of the CMUT supporting structure (usually silicon). To avoid the echoes described above, a thick backing layer is required. But in many cases, there is little space available under the transducer so that it is difficult to accommodate a sufficiently thick layer of material with realistic propagation losses, to ensure that no signal is reflected back to the transducer. In this paper, we discuss irregular structures at the bottom surface that are used to scatter the waves. The proposed structure scatters the waves into waves with significantly changed propagation directions, giving long propagation paths back to the transducer. The structure is analyzed using FEM simulations for a simple 2D case. Different ways of implementing the structure is also discussed.
Magnetic susceptibility of semimagnetic semiconductors: The high-temperature regime and the role of superexchange (1986)

We present a systematic experimental study of the high-temperature susceptibility of diluted magnetic (semimagnetic) semiconductors ${\mathrm{Cd}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Mn}}_{\mathrm{x}}$Se, ${\mathrm{Cd}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Mn}}_{\mathrm{x}}$Te, and ${\mathrm{Hg}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Mn}}_{\mathrm{x}}$Se, and we analyze these together with the previously published results for ${\mathrm{Hg}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Mn}}_{\mathrm{x}}$Te and ${\mathrm{Zn}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Mn}}_{\mathrm{x}}$Te. Despite their variety, all these materials reveal a common and very systematic pattern of behavior, which displays several interesting features. We formulate a theoretical model for the magnetic susceptibility in these systems in terms of the theory of a randomly dilute Heisenberg magnet, and we determine the dominant exchange integrals for each of the alloys by analyzing the available data according to this theory. The spin of ${\mathrm{Mn}}^{2+}$ ion in the first three compounds is also obtained and is found to be close to the atomic value of S=(5/2). We find quantitative correlations between the exchange integrals for the three tellurides, and similarity for both selenides, and on the basis of these observations we argue that superexchange is the dominant mechanism determining the magnetic behavior of all those systems. Within this mechanism of exchange the p-d (anion-${\mathrm{Mn}}^{2+}$) and the d-d (${\mathrm{Mn}}^{2+}$-${\mathrm{Mn}}^{2+}$) exchange integrals can be related. Since in semimagnetic semiconductors both integrals can be obtained from independent measurements, these materials provide a unique opportunity for detailed experimental testing of superexchange.
Regio- and Stereoselective Synthesis of Isoindolin-1-ones via Electrophilic Cyclization (2005)

[reaction: see text] A variety of substituted isoindolin-1-ones are readily prepared in good to excellent yields under very mild reaction conditions by the reaction of o-(1-alkynyl)benzamides with ICl, I(2), and NBS. In a few cases, substituted isoquinolin-1-ones were obtained as the major product instead. This methodology accommodates various alkynyl amides and functional groups and has been successfully extended to heterocyclic starting materials. This chemistry has been successfully applied to the synthesis of a biologically interesting alkaloid, cepharanone B.
Quorum Sensing Controls Biofilm Formation in <i>Vibrio cholerae</i> through Modulation of Cyclic Di-GMP Levels and Repression of <i>vpsT</i> (2008)

Two chemical signaling systems, quorum sensing (QS) and 3',5'-cyclic diguanylic acid (c-di-GMP), reciprocally control biofilm formation in Vibrio cholerae. QS is the process by which bacteria communicate via the secretion and detection of autoinducers, and in V. cholerae, QS represses biofilm formation. c-di-GMP is an intracellular second messenger that contains information regarding local environmental conditions, and in V. cholerae, c-di-GMP activates biofilm formation. Here we show that HapR, a major regulator of QS, represses biofilm formation in V. cholerae through two distinct mechanisms. HapR controls the transcription of 14 genes encoding a group of proteins that synthesize and degrade c-di-GMP. The net effect of this transcriptional program is a reduction in cellular c-di-GMP levels at high cell density and, consequently, a decrease in biofilm formation. Increasing the c-di-GMP concentration at high cell density to the level present in the low-cell-density QS state restores biofilm formation, showing that c-di-GMP is epistatic to QS in the control of biofilm formation in V. cholerae. In addition, HapR binds to and directly represses the expression of the biofilm transcriptional activator, vpsT. Together, our results suggest that V. cholerae integrates information about the vicinal bacterial community contained in extracellular QS autoinducers with the intracellular environmental information encoded in c-di-GMP to control biofilm formation.
Conduction failure and nerve conduction slowing in experimental allergic neuritis induced by P<sub>2</sub>‐specific T‐cell lines (1986)

P2-specific T cells (LiP2/A) mediate experimental allergic neuritis (EAN) in the Lewis rat after adoptive transfer to naive recipients. After a latent period of 4 days, injection of 2 X 10(6) line cells induced fulminant paraplegia and complete conduction failure in the peripheral nerves and roots, resembling acute axonal breakdown. Injection with 10(6) cells caused milder clinical signs, nerve conduction failure, and conduction slowing. Clinical and electrophysiological recovery from adoptively transferred EAN was nearly complete and its time course was inversely correlated to the initial severity of EAN. These findings suggest that EAN induced by the P2-specific T-cell line can lead to a profound and rapidly evolving nerve dysfunction in a dose-dependent fashion.
Nano-particulate pressed powder tablets for LA-ICP-MS (2014)

A new method produces undiluted pressed powder tablets for LA-ICP-MS opening prospects for manufacturing mineral standards for isotopic and geochemical analysis.
Acute leukemia (1997)

The acute leukemias continue to present a formidable challenge for which there is not yet a reliably curative 'standard approach' for the majority of adults with this family of diseases. In order to make progress in terms of curing these devastating diseases, we must understand leukemia biology on the clinical, cellular and molecular levels, with exploitation of the leukemia-associated molecular targets in designing strategies aimed at eradicating the leukemic clone. In this review, we will discuss a few key mechanisms of leukemogenesis that represent convergent pathways of malignant transformation and, as such, present pivotal molecular targets for therapy. Specifically, we focus on normal and leukemic hematopoietic cell cycle regulation, issues surrounding DNA damage and repair, programmed cell death (apoptosis) and drug responsiveness, and multidrug resistance as a marker for stem cell involvement and as a novel target for intervention. When functioning normally, such mechanisms determine a cell's ability to respond to DNA damage, traverse the cell cycle and maintain genomic integrity. And in addition to the target cell itself, there are crucial extracellular determinants of hematopoietic cell proliferation and differentiation that modulate net signalling activity and gene expression, cell-cell contact and growth-modulating factors for instance. The molecular dissection of these intersecting pathways, from the extracellular milieu to the genes themselves, in both the normal and transformed states will elucidate the means by which cells escape treatment-induced death. Such understanding should, in turn, lead to the development of targeted therapeutic strategies that exploit differences between normal and malignant cells, overcome the mechanisms by which leukemic cells acquire drug resistance, and enhance the curability of these devastating diseases.
Basic circuit theory (1972)

1. Introduction. 2. Resistors, Sourses, and Simple Circuits. 3. Resistance Networks. 4. Capacitors and Inductors. 5. First-Order Circuits. 6. Second-Order aqnd Higher-Order Circuits. 7. Sinusoidal Steady-State Analysis-I. 8. Sinusoidal Steady-State Analysis-II. 9. The Laplace Transform-I. 10. The Laplace Transform-II. 11. Two-Port Network Parameters. 12. The Fourier Series. A. Matrices and Determinants. B. Complex Numbers. C. Use of Spice in Circuit Analysis. Answers to Review Questions. Answers to Selected Problems. Index.
Schottky contacts on a highly doped organic semiconductor (1995)

Schottky-diode action in thiophene oligomer is investigated by current-density--voltage (J-V) and capacitance-voltage (C-V) measurements. An energy-band diagram is deduced that explains the diode characteristics for both unintentionally and highly doped thiophene oligomers. We conclude that the diode consists of a thin layer of low ionizable acceptor density (${\mathit{p}}^{\mathrm{\ensuremath{-}}}$) at the metal-oligomer interface and a semiconductor bulk layer that has a higher dopant concentration (${\mathit{p}}^{+}$). The presence of the lower doped ${\mathit{p}}^{\mathrm{\ensuremath{-}}}$ layer leads to a built-in voltage of 0.5 V, which is both experimentally observed and predicted using standard Schottky theory. Differences in J-V characteristics upon doping the thiophene semiconductor are explained by the Schottky-barrier lowering effect for the reverse current density, and by a higher conductivity of the bulk for the forward current density.
Interference between cellular telephones and implantable rhythm devices: a review on recent papers. (2006)

Cellular phones are likely to interfere with implantable rhythm devices if operated in close proximity or during programming of the device. Patients with implanted devices can safely use cellular phones if they are not carried close to the implanted devices or operated near them. Carrying the cellular phones in the belt position, receiving calls in the ear opposite to the side of the implanted device and keeping the phone as far away as possible while dialing can be considered a safe practice. Interrogation of the devices should take place exclusively in areas where utilization of cellular phones is strictly prohibited. Studies on pacemakers published in the current decade have shown much lesser rates of interference, possibly due to improvement in device technology.
Presence of IgE antibodies to staphylococcal exotoxins on the skin of patients with atopic dermatitis. Evidence for a new group of allergens. (1993)

In the current study, we investigated whether Staphylococcus aureus grown from affected skin of atopic dermatitis (AD) patients secreted identifiable toxins that could act as allergens to induce IgE-mediated basophil histamine release. The secreted toxins of S. aureus grown from AD patients were identified by ELISA using antibodies specific for staphylococcal enterotoxin (SE) exfoliative toxin (ET), or toxic shock syndrome toxin (TSST-1). S. aureus isolates from 24 of 42 AD patients secreted identifiable toxins with SEA, SEB, and TSST accounting for 92% of the isolates. 32 of 56 AD sera (57%) tested contained significant levels of IgE primarily to SEA, SEB, and/or TSST. In contrast, although SEA, SEB, or TSST secreting S. aureus could be recovered from the skin of psoriasis patients, their sera did not contain IgE antitoxins. Freshly isolated basophils from 10 AD patients released 5-59% of total histamine in response to SEA, SEB, or TSST-1 but only with toxins to which patients had specific IgE. Basophils from eight other AD patients and six normal controls who had no IgE antitoxin failed to demonstrate toxin-induced basophil histamine release. Stripped basophils sensitized with three AD sera containing IgE to toxin released 15-41% of total basophil histamine only when exposed to the relevant toxin, but not to other toxins. Sensitization of basophils with AD sera lacking IgE antitoxin did not result in release of histamine to any of the toxins tested. These data indicate that a subset of patients with AD mount an IgE response to SEs that can be grown from their skin. These toxins may exacerbate AD by activating mast cells, basophils, and/or other Fc epsilon-receptor bearing cells armed with the relevant IgE antitoxin.
First Application of Concentric Nitrogen Injection Technique for a Managed Pressure Drilling Depleted Well in Southern Mexico (2009)

Abstract Samaria field in southern Mexico is one of the oldest light oil producers. Reservoir pressures can be classified as highly depleted in cretaceous, the use of nitrogen injection thru the drill pipe to lighten the mud column is a common practice to reach low equivalent circulating densities and avoid massive loss circulation and related hole cleaning problems. Large amounts of nitrogen injection rates are also a common scenario in this specific field many times reaching the technical limit of a multiphase Managed Pressure Drilling application avoiding the friction dominated side of pressure curves. Natural tendency to achieve more production is to drill horizontal wells as demonstrated by the production results of a number of attempts made in the past. However, the presence of high N2 injection rates thru the drill pipe represents a serious challenge for measuring and logging while drilling pulse type downhole tools frustrating the possibility of achieving a full directional control in the reservoir section. Dowhole temperatures are also higher than conventional drilling because of the presence of high gas vs liquid ratios, reaching very fast the technology limits. This document presents the engineering process, planning and design for the drilling with concentric casing nitrogen injection technique in a horizontal well with directional control in real time, into a low pressure reservoir. The technique allowed building up and correcting the well trajectory successfully reaching the proposed targets. (Horizontal length, Drain Area) The steady stable and transient simulations to validate stabilization are also presented along with the final results in terms of production and skin damage.
Alumina-catalyzed reactions of hydroxyarenes and hydroaromatic ketones. 9. Reaction of phenol with 1-propanol (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlumina-catalyzed reactions of hydroxyarenes and hydroaromatic ketones. 9. Reaction of phenol with 1-propanolLeRoy H. Klemm and Dennis R. TaylorCite this: J. Org. Chem. 1980, 45, 22, 4320–4326Publication Date (Print):October 1, 1980Publication History Published online1 May 2002Published inissue 1 October 1980https://pubs.acs.org/doi/10.1021/jo01310a012https://doi.org/10.1021/jo01310a012research-articleACS PublicationsRequest reuse permissionsArticle Views621Altmetric-Citations21LEARN 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
Fault diagnoses for the Dc filters of power electronic converters (2012)

DC filters are responsible for more than half of the failures in electric power converters. One approach to improving the reliability, performance and maintainability is to include failure diagnosis logic within the power converter. DC bus capacitor failures may be classified as gradual faults caused by capacitor aging and sudden faults which may take the form of breakdown faults resulting from a blown capacitor fuse, and open circuit O-C faults. This paper presents new methods to detect and isolate failures in the DC filters of power converters caused by capacitor aging and O-C faults.
Structural evaluation of sugar cane bagasse steam pretreated in the presence of CO2 and SO2 (2012)

The SEM, TEM, XRD and FTIR spectroscopy techniques used in this work contributed to structural and chemical analysis of the untreated and pretreated bagasse. The images from SEM and TEM can be related to the severity of SO2 pretreatment, which is almost twice higher. The crystallinity index values obtained from XRD showed that pretreated materials have higher values when compared with untreated material, due to the partial removal of hemicellulose after pretreatment. FTIR spectroscopy supported SEM, TEM and XRD results. CO2 can actually be used as impregnating agent for steam pretreatment, although the present study confirmed a more extensive action of SO2.
Swimming upstream (1997)

A major report from the King’s Fund has highlighted shortfalls in health promotion and education. Maura McNally summarises some of its main points and Rod Thomson gives a community nursing perspective on its conclusions