bluuebunny/crossref_metadata_2025_split huggingface dataset:
Onset of aquaporin‐4 expression in the developing mouse brain
Authors: Fallier‐Becker Petra , Vollmer Jörg P. , Bauer Hans‐C. , Noell Susan , Wolburg Hartwig , Mack Andreas F. 
Published: June 2014

AbstractThe main water channel in the brain, aquaporin‐4 (AQP4) is involved in maintaining homeostasis and water exchange in the brain. In adult mammalian brains, it is expressed in astrocytes, mainly, and in high densities in the membranes of perivascular and subpial endfeet. Here, we addressed the question how this polarized expression is established during development. We used immunocytochemistry against AQP4, zonula occludens protein‐1, glial fibrillary acidic protein, and β‐dystroglycan to follow astrocyte development in E15 to P3 NMRI mouse brains, and expression of AQP4. In addition we used freeze‐fracture electron microscopy to detect AQP4 in the form of orthogonal arrays of particles (OAPs) on the ultrastructural level.We analyzed ventral, lateral, and dorsal regions in forebrain sections and found AQP4 immunoreactivity to emerge at E16 ventrally before lateral (E17) and dorsal (E18) areas. AQP4 staining was spread over cell processes including radial glial cells in developing cortical areas and became restricted to astroglial endfeet at P1–P3. This was confirmed by double labeling with GFAP. In freeze‐fracture replicas OAPs were found with a slight time delay but with a similar ventral to dorsal gradient. Thus, AQP4 is expressed in the embryonic mouse brain starting at E16, earlier than previously reported. However a polarized expression necessary for homeostatic function and water balance emerges at later stages around and after birth.
Evolution of ventricular tachycardia ablation in structural heart disease
Authors: Tung Roderick 
Published: June 2014

AbstractThe field of catheter ablation of VT has evolved conceptually and technologically over the past three decades. From the fundamental understanding of the reentrant mechanism in scar‐mediated VT to the advent and routine implementation of electroanatomic mapping, catheter ablation has emerged from a palliative last‐resort therapy to a more preemptive strategy for patients at risk for arrhythmia recurrence. An increasing utilization of pre‐procedural imaging, high‐density mapping, epicardial access, and more extensive ablation strategies have all contributed to improved clinical success. Advances in ablation technology and randomized trials are needed to build upon the progress in this growing field as sudden cardiac death from ventricular tachyarrhythmia continues to be the one of leading causes of death throughout the world.
Catheter ablation of epicardial ventricular tachycardia
Authors: Yamada Takumi 
Published: June 2014

AbstractVentricular tachycardias (VTs) can usually be treated by endocardial catheter ablation. However, some VTs can arise from the epicardial surface, and their substrate can be altered only by epicardial catheter ablation. There are two approaches to epicardial catheter ablation: transvenous and transthoracic. The transvenous approach through the coronary venous system (CVS) has been commonly used because it is easily accessible. However, this approach may be limited by the distribution of the CVS and insufficient radiofrequency energy delivery. Transthoracic epicardial catheter ablation has been developed to overcome these limitations of the transvenous approach. It is a useful supplemental or even preferred strategy to eliminate epicardial VTs in the electrophysiology laboratory. This technique has been applied for scar‐related VTs secondary to often non‐ischemic cardiomyopathy and sometimes ischemic cardiomyopathy, and idiopathic VTs as the epicardial substrates of these VTs have become increasingly recognized. When endocardial ablation and epicardial ablation through the CVS are unsuccessful, transthoracic epicardial ablation should be the next option. Intrapericardial access is usually obtained through a subxiphoidal pericardial puncture. This approach might not be possible in patients with pericardial adhesions caused by prior cardiac surgery or pericarditis. In such cases, a hybrid procedure involving surgical access with a subxiphoid pericardial window and a limited anterior or lateral thoracotomy might be a feasible and safe method of performing an epicardial catheter ablation in the electrophysiology laboratory. Potential complications associated with this technique include bleeding and collateral damage to the coronary arteries and phrenic nerve. Although the risk of these complications is low, electrophysiologists who attempt epicardial catheter ablation should know the complications associated with this technique, how to minimize their occurrence, and how to rapidly recognize and treat the complications that they encounter. This review discusses the indications, techniques, and complications of the transvenous and transthoracic epicardial catheter ablation of VTs.
Formation of liquid crystalline phases in aqueous suspensions of platelet-like tripalmitin nanoparticles
Authors: Schmiele Martin , Gehrer Simone , Westermann Martin , Steiniger Frank , Unruh Tobias 
Published: June 2014

Suspensions of platelet-like shaped tripalmitin nanocrystals stabilized by the pure lecithin DLPC and the lecithin blend S100, respectively, have been studied by small-angle x-ray scattering (SAXS) and optical observation of their birefringence at different tripalmitin (PPP) concentrations φPPP. It could be demonstrated that the platelets of these potential drug delivery systems start to form a liquid crystalline phase already at pharmaceutically relevant concentrations φPPP of less than 10 wt. %. The details of this liquid crystalline phase are described here for the first time. As in a previous study [A. Illing et al., Pharm. Res. 21, 592 (2004)] some platelets are found to self-assemble into lamellar stacks above a critical tripalmitin concentration \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{st}$\end{document}φPPPst of 4 wt. %. In this study another critical concentration \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{lc}\approx 7$\end{document}φPPPlc≈7 wt. % for DLPC and \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{lc}\approx 9$\end{document}φPPPlc≈9 wt. % for S100 stabilized dispersions, respectively, has been observed. \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{lc}$\end{document}φPPPlc describes the transition from a phase of randomly oriented stacked lamellae and remaining non-assembled individual platelets to a phase in which the stacks and non-assembled platelets exhibit an overall preferred orientation. A careful analysis of the experimental data indicates that for concentrations above \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{lc}$\end{document}φPPPlc the stacked lamellae start to coalesce to rather small liquid crystalline domains of nematically ordered stacks. These liquid crystalline domains can be individually very differently oriented but possess an overall preferred orientation over macroscopic length scales which becomes successively more expressed when further increasing φPPP. The lower critical concentration for the formation of liquid crystalline domains of the DLPC-stabilized suspension compared to \documentclass[12pt]{minimal}\begin{document}$\varphi _{PPP}^{lc}$\end{document}φPPPlc of the S100-stabilized suspension can be explained by a larger aspect ratio of the corresponding tripalmitin platelets. A geometrical model based on the excluded volumes of individual platelets and stacked lamellae has been developed and successfully applied to reproduce the critical volume fractions for both, the onset of stack formation and the appearance of the liquid crystalline phase.
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
Authors: Parker Hilary S. , Leek Jeffrey T. , Favorov Alexander V. , Considine Michael , Xia Xiaoxin , Chavan Sameer , Chung Christine H. , Fertig Elana J. 
Published: June 2014

AbstractMotivation: Sample source, procurement process and other technical variations introduce batch effects into genomics data. Algorithms to remove these artifacts enhance differences between known biological covariates, but also carry potential concern of removing intragroup biological heterogeneity and thus any personalized genomic signatures. As a result, accurate identification of novel subtypes from batch-corrected genomics data is challenging using standard algorithms designed to remove batch effects for class comparison analyses. Nor can batch effects be corrected reliably in future applications of genomics-based clinical tests, in which the biological groups are by definition unknown a priori.Results: Therefore, we assess the extent to which various batch correction algorithms remove true biological heterogeneity. We also introduce an algorithm, permuted-SVA (pSVA), using a new statistical model that is blind to biological covariates to correct for technical artifacts while retaining biological heterogeneity in genomic data. This algorithm facilitated accurate subtype identification in head and neck cancer from gene expression data in both formalin-fixed and frozen samples. When applied to predict Human Papillomavirus (HPV) status, pSVA improved cross-study validation even if the sample batches were highly confounded with HPV status in the training set.Availability and implementation: All analyses were performed using R version 2.15.0. The code and data used to generate the results of this manuscript is available from https://sourceforge.net/projects/psva .Contact: ejfertig@jhmi.eduSupplementary information: Supplementary data are available at Bioinformatics online.
ABRA: improved coding indel detection via assembly-based realignment
Authors: Mose Lisle E. , Wilkerson Matthew D. , Hayes D. Neil , Perou Charles M. , Parker Joel S. 
Published: June 2014

AbstractMotivation: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative.Results: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation.Availability and implementation: ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra .Contact: lmose@unc.edu ; parkerjs@email.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
Authors: Kim Jihoon , Levy Eric , Ferbrache Alex , Stepanowsky Petra , Farcas Claudiu , Wang Shuang , Brunner Stefan , Bath Tyler , Wu Yuan , Ohno-Machado Lucila 
Published: June 2014

AbstractSummary: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—&gt;600% end-to-end performance improvement over state of the art. MAGI’s salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication.Availability and implementation: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu .Contact: j5kim@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Improving upon the efficiency of complete case analysis when covariates are MNAR
Authors: Bartlett Jonathan W. , Carpenter James R. , Tilling Kate , Vansteelandt Stijn 
Published: June 2014

Abstract
Missing values in covariates of regression models are a pervasive problem in empirical research. Popular approaches for analyzing partially observed datasets include complete case analysis (CCA), multiple imputation (MI), and inverse probability weighting (IPW). In the case of missing covariate values, these methods (as typically implemented) are valid under different missingness assumptions. In particular, CCA is valid under missing not at random (MNAR) mechanisms in which missingness in a covariate depends on the value of that covariate, but is conditionally independent of outcome. In this paper, we argue that in some settings such an assumption is more plausible than the missing at random assumption underpinning most implementations of MI and IPW. When the former assumption holds, although CCA gives consistent estimates, it does not make use of all observed information. We therefore propose an augmented CCA approach which makes the same conditional independence assumption for missingness as CCA, but which improves efficiency through specification of an additional model for the probability of missingness, given the fully observed variables. The new method is evaluated using simulations and illustrated through application to data on reported alcohol consumption and blood pressure from the US National Health and Nutrition Examination Survey, in which data are likely MNAR independent of outcome.
Biomass consumption by breeding seabirds in the western Indian Ocean: indirect interactions with fisheries and implications for management
Authors: Danckwerts D. K. , McQuaid C. D. , Jaeger A. , McGregor G. K. , Dwight R. , Le Corre M. , Jaquemet S. 
Published: June 2014

AbstractFisheries potentially affect seabirds both directly and indirectly. Well-documented direct effects have resulted in significant losses to seabird populations, but indirect effects are less well known. One way in which tropical seabirds may be indirectly affected is through overexploitation of large subsurface predators. Tropical seabirds must forage over wide areas to attain sufficient prey and have evolved various methods of increasing foraging efficiency. One strategy is their association with surface-feeding tunas. When feeding, these predators drive prey to the surface, making them available to seabirds feeding from above. Losses in predator biomass will reduce prey accessibility (but not necessarily prey abundance) for seabirds, contributing to declines in bird populations. To explore indirect fisheries effects, we compared estimates of the magnitude and spatial distributions of consumption by breeding seabirds with fisheries offtake in the western Indian Ocean (WIO). Data from the literature were compared with Indian Ocean Tuna Commission longline and purse seine landings of selected tuna and billfish species from between 2000 and 2009. Breeding seabird populations (adults and immature birds) were estimated at ∼19 million individuals, assuming 50% breeding success. Based on the literature, these birds will consume between 150 000 and 500 000 metric tonnes (t) of prey; values that are of the same magnitude as mean annual longline (904±632 t) and purse seine (349 861±61 820 t) landings for the region. Spatial overlap between fisheries and seabirds is high, especially around the Seychelles, suggesting that the indirect impacts of fisheries on seabird populations may be great. Sooty Tern (Onychoprion fuscatus) is by far the dominant seabird in the study area, accounting for over 80% of numbers and consumption estimates. Our results highlight the importance of seabirds within WIO marine trophic webs and emphasize the potential indirect effects of industrial tuna fisheries on their populations.
A novel mucosal vaccine targeting Peyer’s patch M cells induces protective antigen-specific IgA responses
Authors: Shima Hideaki , Watanabe Takashi , Fukuda Shinji , Fukuoka Shin-Ichi , Ohara Osamu , Ohno Hiroshi 
Published: June 2014

Abstract
Mucosal vaccines can induce mucosal immunity, including antigen-specific secretory IgA production, to protect from invasion by pathogens and to neutralize toxins at mucosal surfaces. We established an effective antigen-delivering fusion protein, anti-GP2-SA, as a mucosal vaccine. The anti-GP2-SA consists of streptavidin (SA) fused to the antigen-binding fragment region from a mAb against glycoprotein 2 (GP2), an antigen-uptake receptor specifically expressed on M cells. Anti-GP2-SA targets antigen-sampling M cells in the follicle-associated epithelium covering Peyer’s patches. Immunofluorescence showed that anti-GP2-SA specifically bound to M cells. Orally administered biotinylated ovalbumin peptide (bOVA) conjugated with anti-GP2-SA more efficiently induced OVA-specific fecal IgA secretion compared with bOVA alone or bOVA conjugated with SA. Furthermore, mice immunized by oral administration of the biotinylated Salmonella enterica serovar Typhimurium (S. Typhimurium) lysate conjugated with anti-GP2-SA were significantly better protected from subsequent infection by virulent S. Typhimurium than mice treated with the bacterial lysate alone or conjugated with SA. These results suggest that anti-GP2-SA-based M-cell-targeting vaccines are a novel strategy for inducing efficient mucosal immunity.
Dark matter–baryons separation at the lowest mass scale: the Bullet Group★
Authors: Gastaldello F. , Limousin M. , Foëx G. , Muñoz R. P. , Verdugo T. , Motta V. , More A. , Cabanac R. , Buote D. A. , Eckert D. , Ettori S. , Fritz A. , Ghizzardi S. , Humphrey P. J. , Meneghetti M. , Rossetti M. 
Published: June 2014

Abstract
We report on the X-ray observation of a strong lensing selected group, SL2S J08544-0121, with a total mass of 2.4 ± 0.6 × 1014 M⊙ which revealed a separation of 124 ± 20 kpc between the X-ray emitting collisional gas and the collisionless galaxies and dark matter (DM), traced by strong lensing. This source allows to put an order of magnitude estimate to the upper limit to the interaction cross-section of DM of 10 cm2 g−1. It is the lowest mass object found to date showing a DM–baryons separation, and it reveals that the detection of bullet-like objects is not rare and confined to mergers of massive objects opening the possibility of a statistical detection of DM–baryons separation with future surveys.
Analyzing ion distributions around DNA
Authors: Lavery Richard , Maddocks John H. , Pasi Marco , Zakrzewska Krystyna 
Published: June 2014

Abstract
We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.
Substantial Overlap Between Incarceration and Tuberculosis in Atlanta, Georgia, 2011
Authors: Haddad Maryam B. , Foote Mary K. , Ray Susan M. , Maggio David M. , Sales Rose-Marie F. , Kim Min Jung , Kempker Russell R. , Spaulding Anne C. 
Published: June 2014

Abstract
Standard tuberculosis case reporting captures incarceration at diagnosis only. This retrospective analysis of 106 US-born adults with prevalent tuberculosis in 2011 found that 46.2% had documented histories of being in jail or prison, including 16.0% during the year before diagnosis.
Disparities in CD4+ T-Lymphocyte Monitoring Among Human Immunodeficiency Virus-Positive Medicaid Beneficiaries: Evidence of Differential Treatment at the Point of Care
Authors: Davis Anna C. , Watson Greg , Pourat Nadereh , Kominski Gerald F. , Roby Dylan H. 
Published: June 2014

Abstract
Background.  Monitoring of immune function, measured by CD4+ T-lymphocyte (CD4) cell count, is an essential service for people with human immunodeficiency virus (HIV). Prescription of antiretroviral (ARV) medications is contingent on CD4 cell count; patients without regular CD4 monitoring are unlikely to receive ARVs when indicated. This study assesses disparities in CD4 monitoring among HIV-positive Medicaid beneficiaries.
Methods.  In this retrospective observational study, we examined 24 months of administrative data on 2250 HIV-positive, continuously enrolled, fee-for-service, Medicaid beneficiaries with at least 2 outpatient healthcare encounters. We used logistic regression to evaluate the association of patient demographics (age, gender, race or ethnicity, and language) with receipt of at least 1 CD4 test per year, controlling for other potentially confounding variables.
Results.  Having a history of ARV therapy was positively associated with receipt of CD4 tests. We found racial or ethnic, gender, and age disparities in CD4 testing. Among individuals with a history of ARV use, all racial or ethnic groups were significantly less likely to have CD4 tests than White non-Latinos (African Americans, odds ratio [OR] = 0.35, P &lt; .0001; Asian or Pacific Islanders, OR = 0.31, P = .0047; and Latinos, OR = 0.42, P &lt; .0001).
Conclusions.  We identified disparities in receipt of CD4 tests, a finding that may elucidate one potential pathway for previously reported disparities in ARV treatment. Further qualitative and quantitative research is needed to identify the specific factors that account for these disparities, so that appropriate interventions can be implemented.