cssi/SciSciGPT-SciSciNet huggingface dataset:
Structural and functional analysis of the first intron of the human α2(I) collagen-encoding gene

Abstract The nucleotide (nt) sequence of the first intron of the human α2(I) collagen-encoding gene ( COLIA2 ) has been determined from its 5′ terminus (nt 207) to nt 2045 with respect to the transcription start point. Although the first intron contains elements known to function in transcriptional regulation of other genes (two AP1-binding sites and an alternating GT stretch), comparison of this sequence with that of the mouse COLIA2 first intron revealed a low degree of nt sequence identity and very few common DNA-protein binding motifs. In keeping with this structural analysis, the human intron was found to inhibit COLIA2 promoter activity in transfection experiments, whereas a strong enhancer was reported to be present in the first intron of mouse COLIA2 [Rossi and deCrombrugghe, Proc. Natl. Acad. Sci. USA 84 (1987) 5590–5594]. We conclude that the high degree of nt sequence conservation existing in the promoter and first exons of human, mouse and chicken COLIA2 does not extend to the first introns of these genes but that the promoter activity of COLIA2 is strongly influenced by the presence of the first intron.
Popular Criticism of Jean-François Millet in Nineteenth-Century America

During the later 19th century, the popularity of Jean-Francois Millet (1814-1875) and his genre paintings reached phenomenal proportions in the United States. In large part, this was a situation created by contemporary American critics, both amateur and professional, who, writing skillfully evocative descriptions of the artist, created an enduring image of Millet that instantly captivated the imaginations and sympathies of their readers through the three routes of nostalgia, religious reference, and political inference.The introduction of newly discovered American criticism of Millet and the placement of this body of literature within the post-bellum context demonstrate that Millet's paintings were used to assist in the rebuilding of a national self-image of superior wealth, moral rectitude, artistic connoisseurship, and political tolerance.
Image quality of an analog radiation therapy simulator-based tomographic scanner

The spatial resolution and noise level of images produced by a commercial analog tomographic scanner have been measured and compared to those of imagesreconstructed digitally from projections from the same detector. The full width at half maximum of the line spread function was 3.6 mm for images from the analog scanner and 1.1 mm for the digitally reconstructed images. The standard deviation of the CT numbers over a 10‐cm2 circular area at the center of a large water phantom, calculated as a percentage of the linear attenuation coefficient of water, was 3.5% for the analog images, 15.4% for high‐resolution digital images, and 3.2% for digital imagesreconstructed using a convolution filter which reduced the resolution to that of the analog images. The data contributing to each digital image were fewer than those contributing to each analog image by a factor of 10. The noise level did not depend on tube current in either the analog or the digital images. The utility of this analog device in radiation therapy planning will depend upon whether errors in contour localization resulting from transferring data from diagnostic CTscanners exceed the errors due to its poorer image quality.
Composition and annealing effects on the mechanical properties of superelastic thin film nickel titanium

ABSTRACT This work examines the influence of annealing temperature on the transformation temperatures, stress necessary to induce martensite ( AM ), and the Youngs modulus of superelastic NiTi of two different compositions--47.5 at.% Ni and 50.5 at.% Ni. The films were sputter deposited, crystallized, and annealed for two hours at three different temperatures of 400 C, 500 C, and 600 C. Isothermal tensile tests at the austenite finish temperature (A f ) were performed for evaluating the mechanical response. For the 47.5 at.% Ni film, increasing the annealing temperature from 400 C to 500 C decreased AM by 55 MPa, while the film annealed at 600 C failed to demonstrate complete superelastic behavior. For the 50.5 at.% Ni film, increasing the annealing temperature from 400 C to 600 C decreased AM by 138 MPa. Results were explained using the transformation temperatures and the Clausius-Clapeyron relationship. Keywords: Shape memory, superelastic, nickel, titanium, NiTi, annealing, mechanical properties, sputter deposition
On Chip Plasmonic Monopole Nano-Antennas and Circuits

Analogues of many radio frequency (RF) antenna designs such as the half-wave dipole and Yagi-Uda have been successfully adapted to the optical frequency regime, opening the door for important advances in biosensing, photodetection, and emitter control. Examples of monopole antennas, however, are conspicuously rare given the element's extensive use in RF applications. Monopole antennas are attractive as they represent an easy to engineer, compact geometry and are well isolated from interference due the ground plane. Typically, however, the need to orient the antenna element perpendicular to a semi-infinite ground plane requires a three-dimensional structure and is incompatible with chip-based fabrication techniques. We propose and demonstrate here for the first time that monopole antenna elements can be fashioned out of single element nanoparticles fabricated in conventional planar geometries by using a small nanorod as a wire reflector. The structure offers a compact geometry and the reflector element provides a measure of isolation analogous to the RF counterpart. This isolation persists in the conductive coupling regime, allowing multiple monopoles to be combined into a single nanoparticle, yet still operate independently. This contrasts with several previous studies that observed dramatic variations in the spectral response of conductively coupled particles. We are able to account for these effects by modeling the system using circuit equations from standard RF antenna theory. Our model accurately describes this behavior as well as the detailed resonance tuning of the structure. As a specific practical application, the monopole resonances are precisely tuned to desired protein absorption bands, thereby enhancing their spectroscopic signatures. Furthermore, the accurate modeling of conductive coupling and demonstrated electronic isolation should be of general interest to the design of complex plasmonic circuits incorporating multiple antennas and other current carrying elements.
Effects of linear alkylbenzene sulfonate on the sorption of Brij 30 and Brij 35 onto aquifer sand.

Surfactant sorption is of considerable importance to environmental applications, including surfactant flushing to mobilize hydrophobic contaminants; effects of surfactants on the transport of dissolved contaminants, microorganisms, and colloids through porous media; and bioremediation of hydrophobic organic compounds, as well as understanding the fate and transport of surfactants as environmental contaminants themselves. Although most sorption studies consider pure surfactants, commercial detergent formulations typically consist of mixtures of nonionic and anionic surfactants. In this study, the effects of varying concentrations of the anionic surfactant linear alkylbenzene sulfonate (LAS) on micelle formation and sorption behavior of the two commonly used nonionic surfactants Brij 30 and Brij 35 onto aquifer sand were examined. A strong linear relationship was observed between the critical micelle concentration (CMC) of the Brij surfactants and the concentration of LAS in the mixture, with the CMC decrea...
Biosynthesis of Surfactant Protein D CONTRIBUTIONS OF CONSERVED NH2-TERMINAL CYSTEINE RESIDUES AND COLLAGEN HELIX FORMATION TO ASSEMBLY AND SECRETION

Surfactant protein D (SP-D) is preferentially secreted as dodecamers consisting of four collagenous trimers cross-linked by disulfide bonds. In these studies, we examined the biosynthesis of wild-type rat SP-D (RrSP-D) and selected mutants by stably transfected CHO-K1 cells to determine the roles of a conserved N-linked oligosaccharide, the collagen helix, and interchain disulfide bonds in SP-D assembly and secretion. The major intracellular form of RrSP-D accumulated in the RER as complexes containing up to four trimeric subunits. Disulfide cross-link formation and RrSP-D secretion were selectively inhibited by 2,2'-dipyridyl, an inhibitor of prolyl and lysyl hydroxylase, and by 2 mM dithiothreitol, but unaffected by tunicamycin or elimination of the consensus sequence for glycosylation at Asn70. Although mutants with serine substituted for Cys15 and Cys20 (RrSP-Dser15/20) are secreted as trimeric subunits, proteins with single cysteine substitutions were retained in the cell. Surprisingly, the secretion of RrSP-Dser15/20 was unaffected by 2,2'-dipyridyl. These studies strongly suggest that the most important and rate-limiting step for the secretion of SP-D involves the association of cross-linked trimeric subunits to form dodecamers stabilized by specific inter-subunit disulfide cross-links. Interference with collagen helix formation prevents secretion by interfering with efficient disulfide cross-linking of the NH2-terminal domain.
A Four-planet System Orbiting The K0V Star HD?141399

We present precision radial velocity (RV) data sets from Keck-HIRES and from Lick Observatory's new Automated Planet Finder Telescope and Levy Spectrometer on Mt. Hamilton that reveal a multiple-planet system orbiting the nearby, slightly evolved, K-type star HD 141399. Our 91 observations over 10.5 yr suggest the presence of four planets with orbital periods of 94.35, 202.08, 1070.35, and 3717.35 days and minimum masses of 0.46, 1.36, 1.22, and 0.69 MJ , respectively. The orbital eccentricities of the three inner planets are small, and the phase curves are well sampled. The inner two planets lie just outside the 2:1 resonance, suggesting that the system may have experienced dissipative evolution during the protoplanetary disk phase. The fourth companion is a Jupiter-like planet with a Jupiter-like orbital period. Its orbital eccentricity is consistent with zero, but more data will be required for an accurate eccentricity determination.
Small and large deformation of thick and thin-film multi-layers: Effects of layer geometry, plasticity and compositional gradients

The thermomechanical response of multi-layered materials subjected to small and large deformation during temperature excursions is examined in this paper. General bilayer and trilayer plates with comparable layer thicknesses, as well as the limiting cases of thin films on thicker substrates with and without compositionally graded interfaces are examined, all within the context of the classical Kirchoff theory for thin plates. Closed-form analytical formulations for small elastic deformation are presented whereby explicit expressions for stress/curvature relations are obtained for any general bilayer or graded trilayer with isotropic elastic properties, but anisotropic strains. The effects of the variation of Poisson ratio through the thickness of layered and compositionally graded materials on the evolution of multiple curvatures are analyzed. New theoretical results are presented on the effects of layer geometry, plastic flow and compositional gradation on large deformation (small strains and small rotations) in bilayer and trilayer systems comprising thick or thin-film layers. It is shown that the small deformation theory predictions for the generalized plane strain state provide an upper bound for curvature evolution among all the cases considered. By recourse to analytical methods and three-dimensional finite element modeling involving shell elements, particular attention is devoted to the occurrence of bifurcation in the solution for curvature evolution and the associated geometry changes in the thermoelastoplastic response of layered materials during thermal excursions. The model systems chosen for analyses include NiAl2O3 layers with a sharp or compositionally graded interfaces, AlSi thin-film bilayers and a compositionally graded interlayer sandwiched between layers in In0.12Ga0.88As and GaAs for applications in microelectronics and optoelectronics, and a carbon/ epoxy laminated composite.
Speeding up stochastic reconstructions of binary images from limited projection directions

Abstract In earlier work, a stochastic method for reconstructing certain classes of two-dimensional binary images from limited projection directions was presented. In the present study, we experiment with different implementations of this method to minimize the running time. Our fastest implementation is based on a look-up table and pre-generated arrays of random integers. This is more than 40 times faster than the implementation used in the earlier work. This speedup makes it practical to conduct extensive searches to find the optimal values of the method's parameters for each class of images to be reconstructed.
Effect of gas flow rates and Boudouard reactions on the performance of Ni/YSZ anode supported solid oxide fuel cells with solid carbon fuels

Abstract The effects of carrier gas flow rates and Boudouard reaction on the performance of Ni/YSZ anode-supported solid oxide fuel cells (SOFCs) have been studied with coconut coke fuels at 800 °C. Decreasing flow rates of carrier gas from 1000 to 50 ml min −1 increased open circuit voltages and current densities from 0.71 to 0.87 V and from 0.12 to 0.34 A cm −2 , respectively. The increased cell performance was attributed to the increasing extent of electrochemical oxidation of CO, a product of Boudouard reaction. The contribution of CO oxidation to current generation was estimated to 66% in flowing inert carrier gas at 50 ml min −1 . The pulse transient studies confirmed the effect of flow rates on cell performance and also revealed that CO and CO 2 can displace adsorbed hydrogen on carbon fuels. Flowing CO 2 over coconut coke fuel produced CO via Boudouard reaction. The presence of CO led to a highest power density of 95 mW cm −2 , followed by a concurrent decline of power density and CO concentration. The declined power density along with decreasing CO concentration further verified contribution of gaseous CO to the power generation of C-SOFC; the decreasing CO concentration showed a typical kinetics behavior of Boudouard reaction, suggesting the loss of active sites on carbon surface for the reaction.
Transferable embryo recovery rates following different insemination schedules in superovulated beef cattle.

The objective of this study was to evaluate the transferable embryo recovery rates from superovulated donor cattle after different artificial insemination (AI) schedules. Sixty mixed-breed crossbred females were administered follicle stimulating hormone (FSH) and prostaglandin F2α (PGF2α) to induce a superovulatory response. At standing estrus, donor females were randomly allotted to one of five treatment groups for AI. Donors were inseminated with two units of high-quality or low-quality frozen semen at 12, 24, 36, or 48 h after the onset of estrus in treatment Groups I, II, III, and IV, respectively, or inseminated with two units at 12, 24, 36, and 48 h (eight units/donor) in control Group V. Donor females inseminated once at either 12 or 24 h after the onset of estrus did not differ from donors inseminated in Group V in overall fertilization and transferable embryo recovery rates. The highest fertilization rate (89.5%) and transferable embryo recovery rate (74.9%) per donor resulted when AI was performed with high-quality semen at 24 h after the onset of estrus. These findings indicate that repeated insemination of superovulated beef cattle is not necessary to attain optimal fertilization rates and production of transferable quality embryos in beef cattle.
The Old English “Life of Malchus” and Two Vernacular Tales from the Vitas Patrum in MS Cotton Otho C.i: A Translation (Part 1)

The Old English translation of Jerome's Vita Malchi and of two tales from the Vitas Patrum cycle survives in only a single manuscript, MS British Library, Cotton Otho C.i, volume 2 (eleventh centur...
A treat and extend regimen using ranibizumab for neovascular age-related macular degeneration clinical and economic impact.

Purpose To evaluate the visual outcome, number of injections, and direct medical cost of a "treat and extend" regimen (TER) in managing neovascular age-related macular degeneration (nAMD) with intravitreal ranibizumab. Design Retrospective, interventional, consecutive case series. Participants Ninety-two eyes of 92 patients met the entry criteria from May 2006 to May 2008. Methods All patients with treatment-naive nAMD were treated monthly until no intraretinal or subretinal fluid was observed on optical coherence tomography (OCT). The treatment intervals were then sequentially lengthened by 2 weeks until signs of exudation recurred. The interval was individualized for each patient in an attempt to maintain an exudation-free macula. Main Outcome Measures Change from baseline visual acuity, proportion of eyes losing Results The mean follow-up was 1.52 years. Mean Snellen visual acuity improved from 20/135 at baseline to 20/77 at 1 year follow-up ( P P = 0.002). The proportion of eyes that lost P Conclusions Eyes with nAMD experienced significant visual improvement when managed with intravitreal ranibizumab using a TER. This treatment approach also was associated with significantly fewer patient visits, injections, and direct annual medical cost compared with monthly injections such as in the phase III clinical trials. Financial Disclosure(s) Proprietary or commercial disclosure may be found after the references.
Are there generational differences?: social media use and perceived shared reality

Are there generational differences in how social media influences our perceived reality of the world? Based on the survey results of 1,060 adults in the U.S., this article examines generational differences between so-called "digital natives" --- millennial students who have grown up using information communication technologies --- and earlier generations, who have adopted social media tools later in life. We examined both traditional and social media usage patterns to see if social media use plays a role in perceived shared reality---how people are influenced by their network. The results suggest that the two generations differ in terms of how different facets of social media use are correlated with their perception of shared reality. However, certain uses of social media, such as clicking links provided by social media contacts, contribute to perceived shared reality both for younger and older people.
Cancer of the posterior hypopharyngeal wall

Abstract Thirty-five patients with cancer of the posterior pharyngeal wall treated at the University of Virginia Hospital since 1956 have been reviewed. A minimum follow-up of five years was available in all patients. These have been analyzed by stage and treatment modality, and the crude and determinate three and five year survival figures presented. In contradistinction to results reported for other hypopharyngeal sites, radiotherapy alone has proved the most effective treatment in the posterior wall, particularly for T1 and T2, NO lesions, where the crude and determinate survival after 5 years were 45 and 50 % respectively. For advanced lesions no treatment approach has approved efficacious, although 2 of 10 (20%) patients treated initially by radiotherapy alone survived disease free for 3 years with subsequent surgical removal of residual nodal disease.
Covariance of weibull order statistics

Let X1 0. Formulae for computing Cov (Xi, Xj) are well known, but they are difficult to use in practice. A simple approximation to Cov(Xi, Xj) is presented here, and its accuracy is discussed.
Structural refinements of Yb2BaCuO5 and Lu2BaCuO5 by powder neutron diffraction

Abstract The structure of the “211” or “green phases,” Yb 2 BaCuO 5 and Lu 2 BaCuO 5 , have been refined from time-of-flight powder neutron diffraction data. Both crystallize in the orthorhombic system, space group Pnma , with lattice parameters a = 12.0588(1), A, b = 5.6123(1), A, c = 7.0535(1), A, and a = 12.0314(1), A, b = 5.5989(1), A, c = 7.0380(1), A, respectively. The phases are isostructural with Y 2 BaCuO 5 , consisting of a three-dimensional framework of M O 7 units ( M = Yb, Lu) enclosing cavities occupied by the Ba and Cu atoms. Ba is 11-coordinate and Cu 5-coordinate, in a distored squarepyramidal environment.
The Human Rap1 Protein Complex and Modulation of Telomere Length

Proper maintenance of telomere length and structure is necessary for normal proliferation of mammalian cells. Mammalian telomere length is regulated by a number of proteins including human repressor activator protein (hRap1), a known association factor of TRF2. To further delineate hRap1 function and its associated proteins, we affinity-purified and identified the hRap1 protein complex through mass spectrometry analysis. In addition to TRF2, we found DNA repair proteins Rad50, Mre11, PARP1 (poly(ADP-ribose) polymerase), and Ku86/Ku70 to be in this telomeric complex. We demonstrated by deletional analysis that Rad-50/Mre-11 and Ku86 were recruited to hRap1 independent of TRF2. PARP1, however, most likely interacted with hRap1 through TRF2. Interestingly, knockdown of endogenous hRap1 expression by small hairpin interference RNA resulted in longer telomeres. In addition, overexpression of full-length and mutant hRap1 that lacked the BRCA1 C-terminal domain functioned as dominant negatives and extended telomeres. Deletion of a novel linker domain of hRap1 (residues 199–223), however, abolished the dominant negative effect of hRap1 overexpression. These results indicate that hRap1 negatively regulates telomere length in vivo and suggest that the linker region of hRap1 may modulate the recruitment of negative regulators of telomere length.
A methodology to model the dynamic structure of an organization

Abstract The Integrated Computer Aided Manufacturing (ICAM) program of the U.S. Air Force identified a need to better communicate and analyze manufacturing for the people involved in improving productivity. To satisfy that need, the ICAM program developed the IDEF (ICAM Definition) method to address particular characteristics of manufacturing. This IDEF Method is equally applicable in analyzing other types of organizations. IDEF comprises of three modeling methodologies: function model methodology (IDEF 0 ), information model methodology (IDEF 1 ) and dynamics model methodology (IDEF 2 ). This paper reports on the dynamics model methodology only. This methodology is used to construct models which help in understanding the Dynamic (time-varying behavior) structure which the functions of an organization exhibit.
Translation as a language testing procedure: does it work?:

This article looks at translation from L2 to L1 as a language testing procedure. Two studies are presented. The first examines the reliability and validity of a translation reading test under condi...
Long-range photoinduced electron transfer through a DNA helix

Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)2dppz2+ (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)2phen3+ (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10(9) per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)3(2+) and Rh(phen)3(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae

We thank Anna Panchenko for performing the threading analysis and Vishva Dixit, Robert King and Natalia Mal’ceva for useful discussions.
Hydrogen-induced low temperature CO displacement from the Pt(111) surface

Abstract A new low temperature displacement mechanism for CO on the Pt(111) surface has been observed in the presence of high pressures of hydrogen (0.001 to 0.1 Torr H 2 ). Temperature-programmed fluorescence yield near-edge spectroscopy (TP FYNES) was used to continuously monitor the CO coverage as a function of temperature both with and without hydrogen. For hydrogen pressures above 0.01 Torr, removal of CO begins at 130 K ( E d = 10.6 kcal / mol ) instead of near the desorption temperature of 400 K ( E d = 26 kcal / mol ). The large decrease in CO desorption energy appears to be caused by substantial repulsive interactions in the compressed monolayer induced by coadsorbed hydrogen. The new low temperature CO desorption channel appears to be caused by displacement of the compressed CO adlayer by coadsorbed hydrogen. In addition, the desorption activation energy for the main desorption channel of CO near 400 K is lowered by ~ 1 kcal/mol for hydrogen pressures in the 0.001 to 0.1 Torr range. These new results clearly emphasize the importance of in-situ methods capable of performing kinetic experiments at high pressures on well characterized adsorbed monolayers on single crystal surfaces. High coverages of coadsorbed hydrogen resulting from substantial overpressures may substantially modify desorption activation energies and thus coverages and kinetic pathways available even for strongly chemisorbed species. These phenomena may play an important role in surface reactions which occur at high pressure.
The osteoarthritis knee model: Psychophysical characteristics and putative outcomes

Abstract The knee osteoarthritis (KOA) model is a convenient and coherent archetype that is frequently used in pharmaceutical trials of drugs with analgesic and/or anti-inflammatory properties; yet, little is known about its specific pathophysiology. The presumed chronic inflammatory etiology of osteoarthritis suggests that nociceptive processes and neurogenic inflammation predominate in this condition. However, most chronic pain conditions are associated with changes in peripheral and central processing. Recent data corroborate this as an important mechanism in KOA. We compared psychophysical characteristics (including thermal Quantitative Sensory Testing); thermal, mechanical, and functional wind-up; thermal and mechanical aftersensations; and pressure algometry of 37 subjects with KOA with 35 age- and sex-matched controls. A third of the KOA subjects demonstrated hypoesthesia to vibration and the 4.56 von Frey fiber, yet few showed allodynia in their worse knee. The majority of subjects had abnormalities to pinprick (41% were hyperalgesic and 27% were hypoesthetic). Compared to controls, the more painful knee was hypoesthetic to cold detection and had greater thermal wind-up, lower pressure-pain thresholds, thermal and mechanical aftersensations, and twice the pain ratings of controls after stair climb. Substantial intraindividual differences were found in KOA subjects and controls for mechanical wind-up and algometric thresholds. Perspective These results develop the KOA model and suggest mechanistic hypotheses. Certain of these tests may ultimately prove to be responsive, quasi-objective, and quantitative outcomes for research and lend empirical support to the notion of measurable sensitization in osteoarthritis.
Developing patient-specific anatomic models for validation of cardiac ablation guidance procedures

Image-guided cardiac ablation has the potential to decrease procedure times and improve clinical outcome for patients with cardiac arrhythmias. There are several proposed methods for integrating patient-specific anatomy into the cardiac ablation procedure; however, these methods require thorough validation. One of the primary challenges in validation is determining ground truth as a standard for comparison. Some validation protocols have been developed for animals models and even in patients; however, these methods can be costly to implement and may increase the risk to patients. We have developed an approach to building realistic patient-specific anatomic models at a low-cost in order to validate the guidance procedure without introducing additional risk to the patients. Using a pre-procedural cardiac computed tomography scan, the blood pool of the left and right atria of a patient are segmented semi-manually. In addition, several anatomical landmarks are identified in the image data. The segmented atria and landmarks are converted into a polygonalized model which is used to build a thin-walled patient-specific blood pool model in a stereo-lithography system. Thumbscrews are inserted into the model at the landmarks. The entire model is embedded in a platinum silicone material which has been shown to have tissue-mimicking properties relative to ultrasound. Once the pliable mold has set, the blood pool model is extracted by dissolving the rigid material. The resulting physical model correctly mimics a specific patient anatomy with embedded fiducals which can be used for validation experiments. The patient-specific anatomic model approach may also be used for pre-surgical practice and training of new interventionalists.
Detection of internal exon deletion with exon Del

Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons. Internal exon deletions are the absence of consecutive exons in a gene. Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation. Therefore, to the need for efficient detection of such deletions using exome sequencing data exists. We present ExonDel, a tool specially designed to detect homozygous exon deletions efficiently. We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs. Subsequently, we verified our findings using RNAseq and PCR technologies. Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools. ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data. ExonDel and its source code can be downloaded freely at https://github.com/slzhao/ExonDel .
Investigation of cationic organic dyes used as molecular probes by liquid secondary ion mass spectrometry

The positive-ion mass spectra of twelve organic dyes used as molecular probes were measured using liquid secondary ion mass spectrometry (LSIMS). Nine of the twelve dyes were singly charged cations and the other three were doubly charged cations. The mass spectra of each of the dyes in m-nitrobenzyl alcohol contain abundant signals for the intact cation, C+ (singly charged cation dyes), or for singly-charged forms of the doubly charged cation formed by proton loss, [C2+ H+]+, or halogen counter ion attachment, [C2+ + X−]+. Fragmentation is usually minimal under the conditions used. However, the cations of five of the singly charged compounds appear to undergo charge-remote fragmentation. Collision-induced dissociation experiments on a hybrid mass spectrometer of EBqQ geometry at collision energies up to 300 eV failed to access this fragmentation pathway. In contrast to the LSIMS of many other doubly charged organic compounds, two of the dicationic dyes produced a doubly charged ion of reasonable abundance (2–20%) in the mass spectrum. When glycerol was used as a matrix solvent, the addition of the matrix modifier trifluoroacetic acid increased the abundance of C2+.
Attachment Style and Memory for Attachment-Related Events:

Previous research has demonstrated attachment-schematic processing of attachment-related stories when attachment-related memories are activated before exposure to a story. This study investigated the possibility of obtaining attachment-schematic processing without the activation of attachment-related memories. Undergraduate participants provided attachment style self-ratings and several weeks later read either a positive or negative version of a friendship story. After a distractor task, they took a recall test about the story. Secure and fearful attachment ratings were positively associated with recall of focal story events, relative to peripheral story details, when participants read the negative story. However, secure attachment was associated with recall of focal events involving the friends' joint activities, whereas fearful attachment was associated with recall of those involving their separate activities. These and other results are discussed in terms of attachment-related models of self and other.
ON THE SOURCES OF AGGREGATE FLUCTUATIONS IN EMERGING ECONOMIES

Recent research on macroeconomic fluctuations in emerging economies has advocated introducing a stochastic productivity trend or allowing for interest rate shocks and financial frictions. We estimate a model that encompasses these two approaches, shedding light on their relative merits and on how financial frictions affect the transmission of shocks. The model accounts for aggregate fluctuations by assigning a dominant role to financial frictions in amplifying conventional (temporary) productivity shocks, whereas trend shocks play a minor role. A link between spreads and expected future productivity emerges as essential for a reasonable approximation to the data.
Application of the Preece-Baines growth model to cross-sectional data: Problems of validity and interpretation.

The Preece-Baines growth model (PBGM) is a family of curves that conform to the shape of the human growth curve. It is most often used to analyze longitudinal records on individuals, but it can be applied to cross-sectional data from population surveys. The purpose of this study was to determine empirically the validity of applying the PBGM to cross-sectional data to make inferences about the timing and nature of the adolescent growth spurt. Longitudinal records (n = 339) from the Third Harvard Growth Study were analyzed individually using the PBGM. Results for each sex were pooled to characterize longitudinal growth in this population. Ten independent random cross-sectional samples were generated from the same data set. These were divided by sex and the age means for height were analyzed using the PBGM. Comparisons between the pooled longitudinal estimates and those from the random cross-sectional samples indicated that the PBGM can accurately estimate the age at peak height velocity in males, as well as other characteristics of the adolescent growth spurt when using cross-sectional data. In females, spurious results were obtained when cross-sectional data are used. Possible sources of bias are discussed. © 1994 Wiley-Liss, Inc.
Power management in external memory using PA-CDRAM

Main memory is one of the major energy consumers in computing systems. In this paper, we propose a new memory organisation, called Power-Aware Cached-DRAM (PA-CDRAM) that integrates a moderately sized cache directly into a memory device. We use this cache to turn memory banks off immediately after memory accesses to reduce energy consumption. We modify CDRAM (originally optimised for performance) to reduce energy consumption. We describe our memory organisation, the challenges for achieving low energy consumption and how to address them. Results show that PA-CDRAM achieves 28% average improvement in energy-delay when compared to traditional memory employing time-out power management.
Becoming the Parent of a Child With Life-Threatening Food Allergies

Food induced anaphylaxis (FIA) is a serious medical event and managing it can place tremendous mental, emotional and financial burdens on parents of children with FIA. Using grounded theory methods, the experiences of parents caring for a child with FIA and the adjustments and strategies used to effectively manage a child's diagnosis were examined. Findings revealed once a child is diagnosed with FIA, parental competency is often severely challenged, calling into question parents' ability to succeed in the parenting role. To regain parental competency, parents engage in a 3 phase process to learn how to parent a child with FIA.
A local approach to the stabilization of linear systems defined over non-commutative normed *-algebras

We define below a notion of local stabilizability for systems whose coefficients lie in a C*-algebra, and we show that such a system is stabilizable if and only if it is locally stabilizable. The C*-algebra is not assumed to be commutative. Since B(H) is a C*- algebra, the results of this paper apply in particular to any system whose coefficients can be represented as bounded linear operators on some Hilbert space H.
Burned out binge eaters: a preliminary investigation

Objective The purpose of this study was to compare individuals who meet all the diagnostic criteria for binge eating disorder (BED), except loss of control, to individuals with BED and eating disorder not otherwise specified (EDNOS) on weight history variables. Method Subjects were solicited among new participants in weight loss programs, with 35 meeting BED criteria, 47 meeting criteria for EDNOS, and 6 meeting criteria for BED without loss of control. Results Groups were not found to differ on age of onset of overweight or dieting, age of first binge, rate of largest weight loss, or number of times of losing 10 + lb. Groups did differ on highest weight ever and current body mass index (BMI). Subjects with BED without loss of control had a significantly higher highest weight and current BMI than both BED and EDNOS subjects. Discussion The results suggest that individuals reporting all the symptoms of BED except loss of control may be "former" BEDs who have "given up" on efforts to control their binge eating.
Endotracheal epinephrine in a canine anaphylactic shock model

This study was undertaken to determine if epinephrine administered endotracheally is as effective in treating anaphylactic shock as is intravenously administered epinephrine. An animal model of anaphylactic shock was produced in anesthetized dogs by the intravenous administration of histamine phosphate. Both the endotracheal and intravenous routes of epinephrine administration resulted in efficient and effective reversal of histamine-induced hypotension. At the doses employed, the intravenous administration of epinephrine resulted in the production of significantly (p
Working Out: Managerialism in Workplace Health Promotion

This article examines workplace health promotion (WHP) from a critical perspective. Based on a 2-year ethnographic case study of the development of the Associate Recreation Center (ARC) at an autom...
Emergency department-initiated palliative care for advanced cancer patients: protocol for a pilot randomized controlled trial

For patients with advanced cancer, visits to the emergency department (ED) are common. Such patients present to the ED with a specific profile of palliative care needs, including burdensome symptoms such as pain, dyspnea, or vomiting that cannot be controlled in other settings and a lack of well-defined goals of care. The goals of this study are: i) to test the feasibility of recruiting, enrolling, and randomizing patients with serious illness in the ED; and ii) to evaluate the impact of ED-initiated palliative care on health care utilization, quality of life, and survival. This is a protocol for a single center parallel, two-arm randomized controlled trial in ED patients with metastatic solid tumors comparing ED-initiated palliative care referral to a control group receiving usual care. We plan to enroll 125 to 150 ED-advanced cancer patients at Mount Sinai Hospital in New York, USA, who meet the following criteria: i) pass a brief cognitive screen; ii) speak fluent English or Spanish; and iii) have never been seen by palliative care. We will use balanced block randomization in groups of 50 to assign patients to the intervention or control group after completion of a baseline questionnaire. All research staff performing assessment or analysis will be blinded to patient assignment. We will measure the impact of the palliative care intervention on the following outcomes: i) timing and rate of palliative care consultation; ii) quality of life and depression at 12 weeks, measured using the FACT-G and PHQ-9; iii) health care utilization; and iv) length of survival. The primary analysis will be based on intention-to-treat. This pilot randomized controlled trial will test the feasibility of recruiting, enrolling, and randomizing patients with advanced cancer in the ED, and provide a preliminary estimate of the impact of palliative care referral on health care utilization, quality of life, and survival. Clinical Trials.gov identifier: NCT01358110 (Entered 5/19/2011).
Management and Governance Processes in Community Health Coalitions: A Procedural Justice Perspective

Community-based coalitions are a popular strategy for promoting community health despite the fact that coalitions often fail to achieve measurable results. Using a procedural justice framework, this study seeks to advance knowledge about the relationship between coalition governance and management processes and indicators of coalition functioning. Member survey data from 25 coalitions participating in the Community Care Network Demonstration Program were analyzed using two-stage least squares regression. Results show that personal influence in decision making, decision process clarity, and collaborative conflict resolution were significantly associated with procedural fairness perceptions. Procedural fairness perceptions, in turn, were positively associated with member satisfaction with coalition decisions, but not personal engagement in the coalition or organizational integration of coalition goals and activities. Personal influence in decision making and collaborative conflict resolution also exhibited ...
Reactions to Threat by Defensive and Congruent Internals and Externals: A Self-Esteem Analysis.

Abstract The hypothesis that vulnerable self-esteem internals and externals would react more defensively to negative intellectual and personality feedback than congruent (more secure self-esteem) internals and externals was investigated in two experiments. The defensive (DE)-congruent (CE) external distinction was strongly confirmed in both cases. In Experiment 1, DEs assumed less personal responsibility for failure than for success, while CEs assumed little personal responsibility for either outcome. Defensive externals performed more poorly than CEs on a task described as an IQ test, suggesting greater anxiety in the face of possible failure. In Experiment 2, DEs rated themselves more favorably and derogated evaluator's competence more than CEs following receipt of negative information regarding their interpersonal skills. Congruent internals (CI) performed more poorly than defensive internals (DI) on the “IQ” task, while male DIs attributed responsibility for outcomes more defensively. It was suggested that a consistently internal view of causation may increase stress in evaluative situations. Implications of these findings for better understanding the relationship between locus of control and maladjustment were discussed, and suggestions for future research were presented.
Nuclear Enzymes, Fragile Sites, and Cancer

The finding of a large number of recurrent fragile sites on human chromosomes provides suggestive evidence for the origin of recurrent chromosomal rearrangements that are a common feature in most neoplasias. These fragile sites can be induced by a wide variety of mutagens and carcinogens that are known to act through different molecular mechanisms. They correlate with two-thirds of the recurrent cancer chromosomal breakpoints known thus far and with the location of most mapped oncogenes and growth factors. Because we have now found that a large number of fragile sites can also be induced by agents such as DNase I and benzo[a]pyrene diol-epoxide (BPDE), which are known to induce hypersensitive chromatin sites, it is possible that a class of fragile sites represents regulatory regions of active genes. We have also introduced restriction enzymes into cultured lymphocytes and found that fragile sites are expressed in a pattern similar to that produced by DNase I and BPDE. Because fragile sites have a higher expression with advancing age, cigarette smoking, and deficiency of folic acid and B12 vitamins, they may represent active genomic sites that are vulnerable to physiological and environmental disturbance.
Association Between Quantity of Liver Fat and Cardiovascular Risk in Patients With Nonalcoholic Fatty Liver Disease Independent of Nonalcoholic Steatohepatitis

Background & Aims The association between quantity of liver fat and the presence of metabolic syndrome needs to be assessed systematically. We aimed to determine the association between the quantity of liver fat and the presence of the metabolic syndrome in patients with biopsy-proven nonalcoholic fatty liver disease (NAFLD), independent of nonalcoholic steatohepatitis (NASH). Methods We recruited 146 patients with well-characterized biopsy-proven NAFLD and 50 individuals without NAFLD (controls) to participate in a case–control study at the NAFLD Translational Research Unit at the University of California San Diego. Liver fat was quantified in patients with NAFLD and controls using an advanced magnetic resonance imaging–based biomarker, the proton-density-fat-fraction (MRI-PDFF). Patients with NAFLD were divided into groups based on whether they were above or below the median MRI-PDFF value (15.4% in patients with NAFLD); the MRI-PDFF value for controls was less than 5%. The primary outcome was the presence of the metabolic syndrome using Adult Treatment Panel III criteria without and with adjustment for the presence of NASH. Results Compared with NAFLD patients with MRI-PDFF values below the median, and compared with controls, NAFLD patients with MRI-PDFF values above the median were more likely to have abdominal obesity ( P P P P P Conclusions Increased liver fat content in patients with NAFLD is associated with increased rates of the metabolic syndrome, independent of NASH. There appears to be an association between the quantity of liver fat and the risk for cardiovascular disease in patients with NAFLD.
Optical Recording of Single-Channel TRPV1 Activity and Mobility in Isolated Dorsal Root Ganglion (DRG) Neurons and Cultured Mammalian Cells

TRPV1 is a calcium-permeable non-selective cation channel recognized for its sensitivity to heat, low pH, oxidation and numerous endogenous agonists. To date there is very little known about the activity of the individual channel in the intact cell. In order to explore TRPV1 in this context we employed total internal reflection fluorescence (TIRF) microscopy to observe the open states of the channel as a fluorescent “sparklet” at the site where calcium influx occurs. Preliminary investigations into the sparklet activity elicited by capsaicin in DRG neurons indicate that TRPV1 is free to move laterally in the plasma membrane while conducting calcium into the cytosol. Importantly, two-state fluorescent sparklets indicate that channels function independently in vivo. In HEK293T/17 cells transiently transfected with TRPV1-eGFP we simultaneously imaged mobile channels by their eGFP label and their capsaicin-activated sparklets. We implemented both the eGFP photobleaching subunit counting strategy as well as sparklet intensity analysis of TRPV1 sites. Consistent with results in DRG neurons, we found that individual channels, rather than assemblies of channels, were present and functional in the plasma membrane. Further analysis of the subset of mobile sparklets revealed that the mobility of TRPV1 sparklets steadily decreased with its open duration. Activity dependence of TRPV1 mobility may represent a new form of channel regulation in which its function becomes spatially compartmentalized.