bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation
Authors: Moonsamy P. V. , Williams T. , Bonella P. , Holcomb C. L. , Höglund B. N. , Hillman G. , Goodridge D. , Turenchalk G. S. , Blake L. A. , Daigle D. A. , Simen B. B. , Hamilton A. , May A. P. , Erlich H. A. 
Published: February 2013

AbstractThe human leukocyte antigen (HLA) class I and class II loci are the most polymorphic genes in the human genome; distinguishing the thousands of HLA alleles is challenging. Next generation sequencing of exonic amplicons with the 454 genome sequence (GS) FLX System and Conexio Assign ATF 454 software provides high resolution, high throughput HLA genotyping for eight class I and class II loci. HLA typing of potential donors for unrelated bone marrow donor registries typically uses a subset of these loci at high sample throughput and low cost per sample. The Fluidigm Access Array System enables the incorporation of 48 different multiplex identifiers (MIDs) corresponding to 48 genomic DNA samples with up to 48 different primer pairs in a microfluidic device generating 2304 parallel polymerase chain reactions (PCRs). Minimal volumes of reagents are used. During genomic PCR, in this 4‐primer system, the outer set of primers containing the MID and the 454 adaptor sequences are incorporated into an amplicon generated by the inner HLA target‐specific primers each containing a common sequence tag at the 5′ end of the forward and reverse primers. Pools of the resulting amplicons are used for emulsion PCR and clonal sequencing on the 454 Life Sciences GS FLX System, followed by genotyping with Conexio software. We have genotyped 192 samples with 100% concordance to known genotypes using 8 primer pairs (covering exons 2 and 3 of HLA‐A, B and C, and exon 2 of DRB1, 3/4/5 and DQB1) and 96 MIDs in a single GS FLX run. An average of 166 reads per amplicon was obtained. We have also genotyped 96 samples at high resolution (14 primer pairs covering exons 2, 3, and 4 of the class I loci and exons 2 of DRB1, 3/4/5, DQA1, DQB1, DPB1, and exon 3 of DQB1), recovering an average of 173 sequence reads per amplicon.
Foreign Equity Trading and Average Stock‐return Volatility
Authors: Umutlu Mehmet , Akdeniz Levent , Altay‐Salih Aslihan 
Published: February 2013

AbstractWe examine whether there is a relationship between foreign equity trading and average total volatility, measured as the value‐weighted average of stock‐return variance in the Istanbul Stock Exchange. We employ foreign equity purchase and sale data to track changes in foreign equity trading, which not only enable us to capture effective foreign investor participation but also to observe the potential asymmetric effects of incoming and outgoing funds on the average total volatility. Consistent with the implications of the asymmetric information hypothesis, we find that net equity flow is positively associated with average total volatility. Furthermore, we show that net equity flow affects the average total volatility through the local and idiosyncratic volatilities, suggesting that foreign investors engage in the production of firm specific and market wide information.
Foreign Exchange Intervention in Emerging Markets: A Survey of Empirical Studies
Authors: Menkhoff Lukas 
Published: February 2013

AbstractNowadays foreign exchange interventions occur in emerging market economies, whereas empirical studies on interventions mainly refer to advanced economies. However, interventions in emerging markets are different from those in advanced economies: they occur ‘regularly’ and central banks have considerable leverage, derived from relatively high reserves, some non‐sterilisation, the central bank’s information advantage and capital controls. Consequently, these interventions often successfully impact the level and volatility of exchange rates. Nevertheless, more research on interventions in emerging markets is needed analysing the influence of heterogeneous institutional circumstances, examining the role of central bank communication and using high‐frequency data.
Number One Country, Number One Currency?1
Authors: Eichengreen Barry 
Published: February 2013

AbstractThis paper assesses the prospects for renminbi internationalisation, arguing that the process will encounter significant challenges. Some of these are familiar: the Chinese economy, while large, remains poor; China’s financial markets lack depth and liquidity; encouraging international use of the renminbi will require substantial capital account liberalisation, in the course of which things can go wrong. In addition, I highlight a less familiar challenge: China’s political system may be an obstacle to renminbi internationalisation. Since the early nineteenth century, the leading international currency or currencies have been those of countries with democratic political systems where there are constraints on the executive, which have built durable alliances, and where creditors are well represented. This is not a prediction that China must have a Democratic Spring before the renminbi becomes a leading international and reserve currency. But it does suggest that the country will have to contemplate significant political reform.
Does filaggrin expression correlate with severity of clinical signs in dogs with atopic dermatitis?
Authors: Marsella Rosanna 
Published: February 2013

BackgroundFilaggrin expression is decreased in subsets of humans and dogs with atopic dermatitis (AD). Filaggrin expression is modulated by inflammation, but it is unknown whether expression is inversely correlated with clinical signs.Hypothesis/ObjectivesTo investigate the correlation between filaggrin expression and the severity of clinical signs in an experimental model of canine AD.AnimalsEighteen atopic research beagle dogs sensitized to house dust mite allergens.MethodsDogs were challenged with house dust mites for 3 days consecutively (days 1–3) and skin biopsies collected on days 1 (before allergen challenge), 3 (peak of challenge) and 10 (at resolution of lesions). Clinical signs were scored using a modified version of CADESI‐03, the Canine Atopic Dermatitis Extent and Severity Index. Immunohistochemical staining was measured subjectively by three investigators who graded filaggrin staining for continuity, granularity and intensity. For objective evaluation of staining, the stratum granulosum and epidermis were traced, and the percentage of filaggrin per unit stratum granulosum and epidermal area were calculated. Correlations were investigated using Pearson's product–moment correlation (for linear correlations) and Spearman's rank correlation (for nonlinear correlations), pooling all days together and then separately on each day, using total clinical scores and either subjective or objective filaggrin scores.ResultsThe only significant correlation was found between the subjective filaggrin scores and total clinical scores on day 1.Conclusions and clinical importanceNo inverse correlation exists between the severity of clinical signs and filaggrin expression; the clinical relevance of filaggrin in canine AD is unknown.
Objective models of compressed breast shapes undergoing mammography
Authors: Feng Steve Si Jia , Patel Bhavika , Sechopoulos Ioannis 
Published: February 2013

Purpose:To develop models of compressed breasts undergoing mammography based on objective analysis, that are capable of accurately representing breast shapes in acquired clinical images and generating new, clinically realistic shapes.Methods:An automated edge detection algorithm was used to catalogue the breast shapes of clinically acquired cranio‐caudal (CC) and medio‐lateral oblique (MLO) view mammograms from a large database of digital mammography images. Principal component analysis (PCA) was performed on these shapes to reduce the information contained within the shapes to a small number of linearly independent variables. The breast shape models, one of each view, were developed from the identified principal components, and their ability to reproduce the shape of breasts from an independent set of mammograms not used in the PCA, was assessed both visually and quantitatively by calculating the average distance error (ADE).Results:The PCA breast shape models of the CC and MLO mammographic views based on six principal components, in which 99.2% and 98.0%, respectively, of the total variance of the dataset is contained, were found to be able to reproduce breast shapes with strong fidelity (CC view mean ADE = 0.90 mm, MLO view mean ADE = 1.43 mm) and to generate new clinically realistic shapes. The PCA models based on fewer principal components were also successful, but to a lesser degree, as the two‐component model exhibited a mean ADE = 2.99 mm for the CC view, and a mean ADE = 4.63 mm for the MLO view. The four‐component models exhibited a mean ADE = 1.47 mm for the CC view and a mean ADE = 2.14 mm for the MLO view. Paired t‐tests of the ADE values of each image between models showed that these differences were statistically significant (max p‐value = 0.0247). Visual examination of modeled breast shapes confirmed these results. Histograms of the PCA parameters associated with the six principal components were fitted with Gaussian distributions. The six‐component model was also used to generate CC and MLO view mammogram breast shapes, using the mean PCA parameter values of these distributions and randomly generated values based on the fitted Gaussian distributions, which resemble clinically encountered breasts. A spreadsheet with the data necessary to apply this model is provided as the supplementary material.Conclusions:Our PCA models of breast shapes in both mammographic views successfully reproduce analyzed breast shapes and generate new clinically relevant shapes. This work can aid in research applications which incorporate breast shape modeling, such as x‐ray scatter correction, dosimetry, and image registration.
Is lack of suitable housing a barrier to home-based dialysis therapy for patients with end-stage renal disease? A cohort study
Authors: Forbes Suzanne H , McCafferty Kieran , Lawson Trevor , Stoby-Fields Meagan , Raftery Martin , Yaqoob Muhammad Magdi 
Published: February 2013

ObjectiveTo determine whether inadequate housing is the main barrier to the provision of home dialysis treatment.DesignProspective observational study.ParticipantsAll patients attending a predialysis clinic between 2006 and 2009 deemed medically suitable for home dialysis and not active on the preemptive transplant list.SettingA predialysis clinic in a London teaching hospital.Main outcome measureAssessment of patient's accommodation for suitability for home-based dialysis using departmental guidelines and the Government's Housing Health and Safety Rating System regulations 2005.ResultsA lack of adequate housing prohibited the provision of home haemodialysis to all but one of these patients. Moreover, only 29% of homes assessed were suitable for peritoneal dialysis, despite the lower spatial demands of this form of renal replacement therapy. In addition to the specific requirements of dialysis, we also found that only 33% of the homes visited fulfilled the minimum standard of housing as defined in the Government's Decent Homes Standard, with multiple specific hazards identified across the properties.ConclusionsThis study illustrates that the lack of suitable housing is a major barrier to the provision of home-based dialysis and underscores the need for this to be addressed urgently at both the central government and local authority levels. We suggest that it should be considered as a major priority to rehouse medically suitable patients with a view to enabling home-based therapy.
Maximizing the Benefits of Off-Target Kinase Inhibitor Activity
Authors: Brewer Monica Red , Pao William 
Published: February 2013

Abstract
Summary: Investigators report the identification of novel mutant-specific inhibition of EGF receptor (EGFR) T790M by bis-indole–based inhibitors of protein kinase C using a small-molecule cancer cell line–based screening platform. This study shows the power of high-throughput drug screening in cancer cell lines and provides new lead scaffolds for optimization against resistant EGFR mutants in lung cancer. Cancer Discov; 3(2); 138–40. ©2012 AACR.
See related article by Lee et al., p. 168
Surface and Atmospheric Controls on the Onset of Moist Convection over Land
Authors: Gentine Pierre , Holtslag Albert A. M. , D'Andrea Fabio , Ek Michael 
Published: February 2013

Abstract
The onset of moist convection over land is investigated using a conceptual approach with a slab boundary layer model. The authors determine the essential factors for the onset of boundary layer clouds over land and study their relative importance. They are 1) the ratio of the temperature to the moisture lapse rates of the free troposphere, that is, the inversion Bowen ratio; 2) the mean daily surface temperature; 3) the relative humidity of the free troposphere; and 4) the surface evaporative fraction. A clear transition is observed between two regimes of moistening of the boundary layer as assessed by the relative humidity at the boundary layer top. In the first so-called wet soil advantage regime, the moistening results from the increase of the mixed-layer specific humidity, which linearly depends on the surface evaporative fraction and inversion Bowen ratio through a dynamic boundary layer factor. In the second so-called dry soil advantage regime, the relative humidity tendency at the boundary layer top is controlled by the thermodynamics and changes in the moist adiabatic induced by the decreased temperature at the boundary layer top and consequent reduction in saturation water vapor pressure. This regime pertains to very deep boundary layers under weakly stratified free troposphere over hot surface conditions. In the context of the conceptual model, a rise in free-tropospheric temperature (global warming) increases the occurrence of deep convection and reduces the cloud cover over moist surfaces. This study provides new intuition and predictive capacity on the mechanism controlling the occurrence of moist convection over land.
Improvement of AERI T/q Retrievals and Their Validation at Anmyeon-Do, South Korea
Authors: Kang Shin-Hoo , Goo Tae-Young , Ou Mi-Lim 
Published: February 2013

Abstract
An Atmospheric Emitted Radiance Interferometer (AERI), which measures downwelling radiances, has been in operation at Anmyeon-do, South Korea, since June 2010. Temperature and moisture (T/q) profiles with high temporal and vertical resolution can be retrieved from the measured AERI spectrum through the retrieval algorithm AERIPROF. In this work, AERIPROF has been optimized to improve the retrieval performance: 1) a bias spectrum was computed from the coincident radiosondes during the field experiments at Anmyeon-do and 2) regression coefficients were obtained from local radiosondes and associated simulated spectral radiances. An evaluation was performed in the lower troposphere (&lt;700 hPa) with the radiosondes on clear-sky days during the field experiments at Anmyeon-do. The optimized statistical regression results in an improvement of ~0.6 K for temperature and ~0.6 g kg−1 for the mixing ratio on average, in comparison to the original statistical regression. In addition, the optimized AERI T/q retrievals are compared with the satellite [Aqua/Atmospheric Infrared Sounder (AIRS), Meteorological Operation (MetOp)/Infrared Atmospheric Sounding Interferometer (IASI)] T/q retrievals as well as with T/q profiles analyzed from the regional NWP model, the Korea Local Analysis and Prediction System (KLAPS) analysis. The RMS errors of the AERI retrievals are smaller than those of the satellite retrievals (the KLAPS analysis) by ~1.3 K (~0.2 K) for temperature and ~0.3 g kg−1 (~0.2 g kg−1) for the mixing ratio on average. Significant differences could be found between the AERI retrievals with the KLAPS and the satellite retrievals. The local climatic condition seems to be an important factor to bring about this improvement. Considering the training dataset made with spatially distant radiosondes, this is a significant finding. The AERI could bring new information about the lower troposphere.
Design and Application of an Unattended Multifunctional H-TDMA System
Authors: Tan Haobo , Xu Hanbing , Wan Qilin , Li Fei , Deng Xuejiao , Chan P. W. , Xia Dong , Yin Yan 
Published: February 2013

Abstract
The hygroscopic properties of aerosols have a significant impact on aerosol particle number size distributions (PNSD), formation of cloud condensation nuclei, climate forcing, and atmospheric visibility, as well as human health. To allow for the observation of the hygroscopic growth of aerosols with long-term accuracy, an unattended multifunctional hygroscopicity-tandem differential mobility analyzer (H-TDMA) system was designed and built by the Institute of Tropical and Marine Meteorology (ITMM), China Meteorological Administration (CMA), in Guangzhou, China. The system is capable of measuring dry and wet PNSD, hygroscopic growth factor by particle size, and mixing states. This article describes in detail the working principles, components, and calibration methods of the system. Standard polystyrene latex (PSL) spheres with five different diameters were chosen to test the system’s precision and accuracy of particle size measurement. Ammonium sulfate was used to test the hygroscopic response of the system for accurate growth factor measurement. The test results show that the deviation of the growth factor measured by the system is within a scope of −0.01 to −0.03 compared to Köhler theoretical curves. Results of temperature and humidity control performance tests indicate that the system is robust. An internal temperature gradient of less than 0.2 K for a second differential mobility analyzer (DMA2) makes it possible to reach a set-point relative humidity (RH) value of 90% and with a standard deviation of ±0.44%, sufficient for unattended field observation.
Observations of Air–Sea Interaction and Intensity Change in Hurricanes
Authors: Cione Joseph J. , Kalina Evan A. , Zhang Jun A. , Uhlhorn Eric W. 
Published: February 2013

Abstract
Recent enhancements to the tropical cyclone-buoy database (TCBD) have incorporated data from the Extended Best Track (EBT) and the Statistical Hurricane Intensity Prediction Scheme (SHIPS) archive for tropical cyclones between 1975 and 2007. This information is used to analyze the relationships between large-scale atmospheric parameters, radial and shear-relative air–sea structure, and intensity change in strengthening and weakening hurricanes. Observations from this research illustrate that the direction of the large-scale vertical wind shear at mid- to low levels can impact atmospheric moisture conditions found near the surface. Drier low-level environments were associated with northerly shear conditions. In a separate analysis comparing strengthening and weakening hurricanes, drier surface conditions were also found for the intensifying sample. Since SST conditions were similar for both groups of storms, it is likely that the atmosphere was primarily responsible for modifying the near-surface thermodynamic environment (and ultimately surface moisture flux conditions) for this particular analysis.
Midfoot Fusion
Authors: Pope Ernest J. , Takemoto Richelle C. , Kummer Frederick J. , Mroczek Kenneth J. 
Published: February 2013

Background: Numerous reconstructive techniques for midfoot collapse secondary to Charcot neuroarthropathy have been described, but few have been studied biomechanically. The purpose of this study was to biomechanically compare 2 of the most common techniques. Methods: Seven paired below-knee specimens were amputated through the talonavicular and calcaneocuboid joints. The nonligamentous soft tissue was stripped proximal to the metatarsal heads and disarticulated through the tarsometatarsal (TMT) joints. For each paired specimen, the TMT joints were fused by plantar plating or intramedullary screw fixation for the contralateral side. The specimens were mounted, loaded, and cycled, and fixation stiffness was determined. Load versus displacement graphs were used to calculate overall construct stiffness, and data were analyzed by Student t tests. Results: There was no failure of hardware. All failures were at the bone-implant interface. Failure was either by screw pull-out, bone fracture, or a combination of the two. There were no notable differences between the 2 fixation techniques with respect to stiffness or loads to failure. There was a trend toward a stiffer first TMT construct using the plantar plating method. Five of the 7 screw fixations failed by pullout of the base of the first metatarsal and the other 2 by pullout of screws from all MT bases. Seven of the 7 plantar plate fixations failed by separation of the fifth to third MT bases originating at the fifth, and 3 showed fracture of the fifth metatarsal base. Conclusions: There was no notable biomechanical difference between the 2 techniques. There was a trend toward a stiffer construct at the first TMT with plantar plating. Clinical Relevance: This study biomechanically analyzes two common Charcot midfoot reconstruction techniques and highlights the need for further study of both techniques and combinations of these techniques.
Mycoplasma suis infection results endothelial cell damage and activation: new insight into the cell tropism and pathogenicity of hemotrophic mycoplasma
Authors: Sokoli Albina , Groebel Katrin , Hoelzle Katharina , Amselgruber Werner M , Mateos José M , Schneider Mårten KJ , Ziegler Urs , Felder Kathrin M , Hoelzle Ludwig E 
Published: February 2013

AbstractHemotrophic mycoplasmas (HM) are highly specialized red blood cell parasites that cause infectious anemia in a variety of mammals, including humans. To date, no in vitro cultivation systems for HM have been available, resulting in relatively little information about the pathogenesis of HM infection. In pigs,Mycoplasma suis-induced infectious anemia is associated with hemorrhagic diathesis, and coagulation dysfunction. However, intravasal coagulation and subsequent consumption coagulopathy can only partly explain the sequence of events leading to hemorrhagic diathesis manifesting as cyanosis, petechial bleeding, and ecchymosis, and to disseminated coagulation. The involvement of endothelial activation and damage inM. suis-associated pathogenesis was investigated using light and electron microscopy, immunohistochemistry, and cell sorting.M. suisinteracted directly with endothelial cells in vitro and in vivo. Endothelial activation, widespread endothelial damage, and adherence of red blood cells to the endothelium were evident inM. suis-infected pigs. These alterations of the endothelium were accompanied by hemorrhage, intravascular coagulation, vascular occlusion, and massive morphological changes within the parenchyma.M. suisbiofilm-like microcolonies formed on the surface of endothelial cells, and may represent a putative persistence mechanism ofM. suis. In vitro analysis demonstrated thatM. suisinteracted with the endothelial cytoskeletal protein actin, and induced actin condensation and activation of endothelial cells, as determined by the up-regulation of ICAM, PECAM, E-selectin, and P-selectin. These findings demonstrate an additional cell tropism of HM for endothelial cells and suggest thatM. suisinterferes with the protective function of the endothelium, resulting in hemorrhagic diathesis.