bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Amino Acid Modification of Adeno-Associated Virus Capsid Changes Transduction and Humoral Immune Profiles
Authors: Li Chengwen , Diprimio Nina , Bowles Dawn E. , Hirsch Matthew L. , Monahan Paul E. , Asokan Aravind , Rabinowitz Joseph , Agbandje-McKenna Mavis , Samulski R. Jude 
Published: May 2012

ABSTRACTAdeno-associated virus (AAV) vectors have the potential to promote long-term gene expression. Unfortunately, humoral immunity restricts patient treatment and in addition provides an obstacle to the potential option of vector readministration. In this study, we describe a comprehensive characterization of the neutralizing antibody (NAb) response to AAV type 1 (AAV1) through AAV5 bothin vitroandin vivo. These results demonstrated that NAbs generated from one AAV type are unable to neutralize the transduction of other types. We extended this observation by demonstrating that a rationally engineered, muscle-tropic AAV2 mutant containing 5 amino acid substitutions from AAV1 displayed a NAb profile different from those of parental AAV2 and AAV1. Here we found that a single insertion of Thr from AAV1 into AAV2 capsid at residue 265 preserved high muscle transduction, while also changing the immune profile. To better understand the role of Thr insertion at position 265, we replaced all 20 amino acids and evaluated both muscle transduction and the NAb response. Of these variants, 8 mutants induced higher muscle transduction than AAV2. Additionally, three classes of capsid NAb immune profile were defined based on the ability to inhibit transduction from AAV2 or mutants. While no relationship was found between transduction, amino acid properties, and NAb titer or its cross-reactivity, these studies map a critical capsid motif involved in all steps of AAV infectivity. Our results suggest that AAV types can be utilized not only as templates to generate mutants with enhanced transduction efficiency but also as substrates for repeat administration.
Marek's Disease Virus Expresses Multiple UL44 (gC) Variants through mRNA Splicing That Are All Required for Efficient Horizontal Transmission
Authors: Jarosinski Keith W. , Osterrieder Nikolaus 
Published: May 2012

ABSTRACTMarek's disease (MD) is a devastating oncogenic viral disease of chickens caused byGallid herpesvirus 2, or MD virus (MDV). MDV glycoprotein C (gC) is encoded by the alphaherpesvirus UL44 homolog and is essential for the horizontal transmission of MDV (K. W. Jarosinski and N. Osterrieder, J. Virol. 84:7911-7916, 2010). Alphaherpesvirus gC proteins are type 1 membrane proteins and are generally anchored in cellular membranes and the virion envelope by a short transmembrane domain. However, the majority of MDV gC is secretedin vitro, although secondary-structure analyses predict a carboxy-terminal transmembrane domain. In this report, two alternative mRNA splice variants were identified by reverse transcription (RT)-PCR analyses, and the encoded proteins were predicted to specify premature stop codons that would lead to gC proteins that lack the transmembrane domain. Based on the size of the intron removed for each UL44 (gC) transcript, they were termed gC104 and gC145. Recombinant MDV viruses were generated in which only full-length viral gC (vgCfull), gC104 (vgC104), or gC145 (vgC145) was expressed. Predictably, gCfull was expressed predominantly as a membrane-associated protein, while both gC104 and gC145 were secreted, suggesting that the dominant gC variants expressedin vitroare the spliced variants. In experimentally infected chickens, the expression of each of the gC variants individually did not alter replication or disease induction. However, horizontal transmission was reduced compared to that of wild-type or revertant viruses when the expression of only a single gC was allowed, indicating that all three forms of gC are required for the efficient transmission of MDV in chickens.
The Chimeric Genome of
Sphaerochaeta
: Nonspiral Spirochetes That Break with the Prevalent Dogma in Spirochete Biology
Authors: Caro-Quintero A. , Ritalahti K. M. , Cusick K. D. , Löffler F. E. , Konstantinidis K. T. 
Published: May 2012

ABSTRACT

Spirochaetes
is one of a few bacterial phyla that are characterized by a unifying diagnostic feature, namely, the helical morphology and motility conferred by axial periplasmic flagella. Their unique morphology and mode of propulsion also represent major pathogenicity factors of clinical spirochetes. Here we describe the genome sequences of two coccoid isolates of the recently described genus
Sphaerochaeta
which are members of the phylum
Spirochaetes
based on 16S rRNA gene and whole-genome phylogenies. Interestingly, the
Sphaerochaeta
genomes completely lack the motility and associated signal transduction genes present in all sequenced spirochete genomes. Additional analyses revealed that the lack of flagella is associated with a unique, nonrigid cell wall structure hallmarked by a lack of transpeptidase and transglycosylase genes, which is also unprecedented in spirochetes. The
Sphaerochaeta
genomes are highly enriched in fermentation and carbohydrate metabolism genes relative to other spirochetes, indicating a fermentative lifestyle. Remarkably, most of the enriched genes appear to have been acquired from nonspirochetes, particularly clostridia, in several massive horizontal gene transfer events (>40% of the total number of genes in each genome). Such a high level of direct interphylum genetic exchange is extremely rare among mesophilic organisms and has important implications for the assembly of the prokaryotic tree of life.

IMPORTANCE
Spiral shape and motility historically have been the unifying hallmarks of the phylum
Spirochaetes
. These features also represent important virulence factors of highly invasive pathogenic spirochetes such as the causative agents of syphilis and Lyme disease. Through the integration of genome sequencing, microscopy, and physiological studies, we conclusively show that the spiral morphology and motility of spirochetes are not universal morphological properties. In particular, we found that the genomes of the members of the recently described genus
Sphaerochaeta
lack the genes encoding the characteristic flagellar apparatus and, in contrast to most other spirochetes, have acquired many metabolic and fermentation genes from clostridia. These findings have major implications for the isolation and study of spirochetes, the diagnosis of spirochete-caused diseases, and the reconstruction of the evolutionary history of this important bacterial phylum. The
Sphaerochaeta
sp. genomes offer new avenues to link ecophysiology with the functionality and evolution of the spirochete flagellar apparatus.
The multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a novel macrophage lactoferrin receptor1This article is part of Special Issue entitled Lactoferrin and has undergone the Journal's usual peer review process.
Authors: Rawat Pooja , Kumar Santosh , Sheokand Navdeep , Raje Chaaya Iyengar , Raje Manoj 
Published: May 2012

Several proteins with limited cell type distribution have been shown to bind lactoferrin. However, except in the case of hepatic and intestinal cells, these have not been definitively identified and characterized. Here we report that the multifunctional glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) functions as a novel receptor for lactoferrin (Lf) in macrophages. GAPDH is a well-known moonlighting protein, and previous work from our laboratory has indicated its localization on macrophage cell surfaces, wherein it functions as a transferrin (Tf) receptor. The KDvalue for GAPDH–lactoferrin interaction was determined to be 43.8 nmol/L. Utilizing co-immunoprecipitation, immunoflorescence, and immunogold labelling electron microscopy we could demonstrate the trafficking of lactoferrin to the endosomal compartment along with GAPDH. We also found that upon iron depletion the binding of lactoferrin to macrophage cell surface is enhanced. This correlated with an increased expression of surface GAPDH, while other known lactoferrin receptors CD14 and lipoprotein receptor-related protein (LRP) were found to remain unaltered in expression levels. This suggests that upon iron depletion, cells prefer to use GAPDH to acquire lactoferrin. As GAPDH is an ubiquitously expressed molecule, its function as a receptor for lactoferrin may not be limited to macrophages.
Differential Expression of 2′,3′-Cyclic-Nucleotide 3′-Phosphodiesterase and Neural Lineage Markers Correlate with Glioblastoma Xenograft Infiltration and Patient Survival
Authors: Zorniak Michael , Clark Paul A. , Leeper Heather E. , Tipping Matthew D. , Francis David M. , Kozak Kevin R. , Salamat M. Shahriar , Kuo John S. 
Published: May 2012

Abstract
Purpose: Glioblastoma multiforme (GBM) is a poorly treated human brain cancer with few established clinically useful molecular prognostic markers. We characterized glioblastoma stem–like cells (GSC) according to developmental neural lineage markers and correlated their expression with patient survival.
Experimental Design: Immunoblot array of neural lineage markers classified five independently isolated human GSC lines into three classes exhibiting differential expression of oligodendrocyte progenitor cells (OPC), astrocyte progenitor cells (APC), and neural progenitor cells (NPC) markers. Immunodeficient mice were orthotopically implanted with each cell line to evaluate tumor infiltration and recipient survival. 2′,3′-Cyclic-nucleotide 3′-phosphodiesterase (CNP) antigenic expression was used to evaluate a clinically annotated GBM tissue microarray with 115 specimens.
Results: We report that molecular classification of patient-derived GSCs using neural lineage markers show association with differential xenograft invasiveness, and also show significant correlation to survival in both the mouse model and human patients. Orthotopic implantation into immunodeficient mice showed Ki-67 proliferative index independent xenograft infiltration: class I GSCs (OPC and NPC positive) established focal lesions, class II GSCs (NPC positive) formed minimally invasive lesions, and class III GSCs (APC positive) established highly infiltrative lesions. The OPC marker, CNP also exhibited high expression in focal xenografts versus low expression in invasive xenografts. Differential CNP expression correlated with mouse model survival, and CNP immunoassay of a large GBM tissue microarray also showed significant differential patient survival.
Conclusions: GSC classification with developmental neural lineage markers revealed CNP as a novel and potentially useful clinical prognosis marker, and suggests clinical importance for patient-specific GSC analysis. Clin Cancer Res; 18(13); 3628–36. ©2012 AACR.
FES Kinase Promotes Mast Cell Recruitment to Mammary Tumors via the Stem Cell Factor/KIT Receptor Signaling Axis
Authors: Kwok Ester , Everingham Stephanie , Zhang Shengnan , Greer Peter A. , Allingham John S. , Craig Andrew W.B. 
Published: May 2012

Abstract
KIT receptor is required for mast cell development, survival, and migration toward its ligand stem cell factor (SCF). Many solid tumors express SCF and this leads to mast cell recruitment to tumors and release of mediators linked to tumor angiogenesis, growth, and metastasis. Here, we investigate whether FES protein-tyrosine kinase, a downstream effector of KIT signaling in mast cells, is required for migration of mast cells toward SCF-expressing mammary tumors. Using a novel agarose drop assay for chemotaxis of bone marrow–derived mast cells (BMMC) toward SCF, we found that defects in chemotaxis of fes-null BMMCs correlated with disorganized microtubule networks in polarized cells. FES displayed partial colocalization with microtubules in polarized BMMCs and has at least two direct microtubule binding sites within its N-terminal F-BAR and SH2 domains. An oligomerization-disrupting mutation within the Fer/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain had no effect on microtubule binding, whereas microtubule binding to the SH2 domain was dependent on the phosphotyrosine-binding pocket. FES involvement in mast cell recruitment to tumors was tested using the AC2M2 mouse mammary carcinoma model. These tumor cells expressed SCF and promoted BMMC recruitment in a KIT- and FES-dependent manner. Engraftment of AC2M2 orthotopic and subcutaneous tumors in control or fes-null mice, revealed a key role for FES in recruitment of mast cells to the tumor periphery. This may contribute to the reduced tumor growth and metastases observed in fes-null mice compared with control mice. Taken together, FES is a potential therapeutic target to limit the progression of tumors with stromal mast cell involvement. Mol Cancer Res; 10(7); 881–91. ©2012 AACR.
Dietary Energy Balance Modulates Epithelial-to-Mesenchymal Transition and Tumor Progression in Murine Claudin-Low and Basal-like Mammary Tumor Models
Authors: Dunlap Sarah M. , Chiao Lucia J. , Nogueira Leticia , Usary Jerry , Perou Charles M. , Varticovski Lyuba , Hursting Stephen D. 
Published: May 2012

Abstract
Using novel murine models of claudin-low and basal-like breast cancer, we tested the hypothesis that diet-induced obesity (DIO) and calorie restriction (CR) differentially modulate progression of these aggressive breast cancer subtypes. For model development, we characterized two cell lines, “mesenchymal (M)-Wnt” and “epithelial (E)-Wnt,” derived from MMTV-Wnt-1 transgenic mouse mammary tumors. M-Wnt, relative to E-Wnt, cells were tumor-initiating cell (TIC)-enriched (62% vs. 2.4% CD44high/CD24low) and displayed enhanced ALDEFLUOR positivity, epithelial-to-mesenchymal transition (EMT) marker expression, mammosphere-forming ability, migration, invasion, and tumorigenicity (P &lt; 0.001; each parameter). M-Wnt and E-Wnt cells clustered with claudin-low and basal-like breast tumors, respectively, in gene expression profiles and recapitulated these tumors when orthotopically transplanted into ovariectomized C57BL/6 mice. To assess the effects of energy balance interventions on tumor progression and EMT, mice were administered DIO, control, or CR diets for 8 weeks before orthotopic transplantation of M-Wnt or E-Wnt cells (for each cell line, n = 20 mice per diet) and continued on their diets for 6 weeks while tumor growth was monitored. Relative to control, DIO enhanced M-Wnt (P = 0.01), but not E-Wnt, tumor progression; upregulated EMT- and TIC-associated markers including N-cadherin,fibronectin, TGFβ, Snail, FOXC2, and Oct4 (P &lt; 0.05, each); and increased intratumoral adipocytes. Conversely, CR suppressed M-Wnt and E-Wnt tumor progression (P &lt; 0.02, each) and inhibited EMT and intratumoral adipocyte accumulation. Thus, dietary energy balance interventions differentially modulate EMT and progression of claudin-low and basal-like tumors. EMT pathway components may represent targets for breaking the obesity–breast cancer link, particularly for preventing and/or controlling TIC-enriched subtypes such as claudin-low breast cancer. Cancer Prev Res; 5(7); 930–42. ©2012 AACR.
Limitations of Ranking Lists Based on Cardiac Surgery Mortality Rates
Authors: Siregar Sabrina , Groenwold Rolf H.H. , Jansen Evert K. , Bots Michiel L. , van der Graaf Yolanda , van Herwerden Lex A. 
Published: May 2012

Background—
Ranking lists are a common way of reporting performance in cardiac surgery; however, rankings have shown to be imprecise, yet the extent of this imprecision is unknown. We aimed to determine the precision of, and fluctuations in, ranking lists in the comparison of cardiac surgery mortality rates.

Methods and Results—
Information on all adult cardiac surgery patients in all 16 cardiothoracic centers in The Netherlands from January 1, 2007, until December 31, 2009, was extracted from the database of the Netherlands Association for Cardio-Thoracic Surgery (n=46883). Ranks were assessed using crude and adjusted mortality rates, using a random effects logistic regression model. Risk adjustment was performed using the logistic EuroSCORE. Statistical precision of ranks was assessed with 95% confidence intervals. Additional analyses were performed for patients with isolated coronary artery bypass grafting. The ranking lists, based on mortality rates in 3 consecutive years, showed considerable reshuffling. When all data were pooled, the mean width of the 95% confidence intervals was 10 ranks using crude and 8 ranks using adjusted mortality rates. The large overlap of the confidence intervals across hospitals indicates that rank statistics were not materially different. Results were similar in the isolated coronary artery bypass grafting subgroup.

Conclusions—
Rankings are an imprecise statistical method to report cardiac surgery mortality rates and prone to (random) fluctuation. Hence, reshuffling of ranks can be expected solely due to chance. Therefore, we strongly discourage the use of ranking lists in the comparison of mortality rates.
Sensitivity of Cloud Liquid Water Content Estimates to the Temperature-Dependent Thermodynamic Phase: A Global Study Using CloudSat Data
Authors: Devasthale Abhay , Thomas Manu Anna 
Published: May 2012

Abstract
The main purpose of this study is to underline the sensitivity of cloud liquid water content (LWC) estimates purely to 1) the shape of computationally simplified temperature-dependent thermodynamic phase and 2) the range of subzero temperatures covered to partition total cloud condensate into liquid and ice fractions. Linear, quadratic, or sigmoid-shaped functions for subfreezing temperatures (down to −20° or −40°C) are often used in climate models and reanalysis datasets for partitioning total condensate. The global vertical profiles of clouds obtained from CloudSat for the 4-yr period June 2006–May 2010 are used for sensitivity analysis and the quantitative estimates of sensitivities based on these realistic cloud profiles are provided. It is found that three cloud regimes in particular—convective clouds in the tropics, low-level clouds in the northern high latitudes, and middle-level clouds over the midlatitudes and Southern Ocean—are most sensitive to assumptions on thermodynamic phase. In these clouds, the LWC estimates based purely on quadratic or sigmoid-shaped functions with a temperature range down to −20°C can differ by up to 20%–40% over the tropics (in seasonal means), 10%–30% over the midlatitudes, and up to 50% over high latitudes compared to a linear assumption. When the temperature range is extended down to −40°C, LWC estimates in the sigmoid case can be much higher than the above values over high-latitude regions compared to the commonly used case with quadratic dependency down to −20°C. This sensitivity study emphasizes the need to critically investigate radiative impacts of cloud thermodynamic phase assumptions in simplified climate models and reanalysis datasets.
Improving HF Radar Estimates of Surface Currents Using Signal Quality Metrics, with Application to the MVCO High-Resolution Radar System
Authors: Kirincich Anthony R. , de Paolo Tony , Terrill Eric 
Published: May 2012

Abstract
Estimates of surface currents over the continental shelf are now regularly made using high-frequency radar (HFR) systems along much of the U.S. coastline. The recently deployed HFR system at the Martha’s Vineyard Coastal Observatory (MVCO) is a unique addition to these systems, focusing on high spatial resolution over a relatively small coastal ocean domain with high accuracy. However, initial results from the system showed sizable errors and biased estimates of M2 tidal currents, prompting an examination of new methods to improve the quality of radar-based velocity data. The analysis described here utilizes the radial metric output of CODAR Ocean Systems’ version 7 release of the SeaSonde Radial Site Software Suite to examine both the characteristics of the received signal and the output of the direction-finding algorithm to provide data quality controls on the estimated radial currents that are independent of the estimated velocity. Additionally, the effect of weighting spatial averages of radials falling within the same range and azimuthal bin is examined to account for differences in signal quality. Applied to two month-long datasets from the MVCO high-resolution system, these new methods are found to improve the rms difference comparisons with in situ current measurements by up to 2 cm s−1, as well as reduce or eliminate observed biases of tidal ellipses estimated using standard methods.
Comparisons of Single- and Double-Moment Microphysics Schemes in the Simulation of a Synoptic-Scale Snowfall Event
Authors: Molthan Andrew L. , Colle Brian A. 
Published: May 2012

Abstract
The Canadian CloudSat/Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) Validation Project (C3VP) provided aircraft, surface, and remotely sensed observations of cloud and precipitation characteristics to support improved simulation of cold-season precipitation within weather forecast models and new developments in satellite and radar precipitation retrievals. On 22 January 2007, the C3VP campaign executed an intensive observation period to sample widespread snowfall that occurred as a midlatitude cyclone tracked along the U.S.–Canadian border. Surface air temperature and precipitation measurements, combined with aircraft measurement of hydrometeor content and size distribution, are used to examine various assumptions and parameterizations included within four bulk water microphysics schemes available within the Weather Research and Forecasting Model (WRF).
In a simulation of the 22 January 2007 event, WRF forecasts reproduced the overall precipitation pattern observed during aircraft sampling, allowing for a comparison between C3VP measurements and microphysics scheme assumptions. Single-moment schemes that provide flexibility in size distribution parameters as functions of temperature can represent much of the vertical variability observed in aircraft data, but variability is reduced in an environment where the simulated temperature profile is nearly isothermal. Double-moment prediction of total number concentration may improve the representation of ice crystal aggregation. Inclusion of both temperature dependence on distribution parameters and variability in mass–diameter or diameter–fall speed relationships suggest a means of improving upon single-moment predictions.
Two Overlooked Biases of the Advanced Research WRF (ARW) Model in Geopotential Height and Temperature
Authors: Wee Tae-Kwon , Kuo Ying-Hwa , Lee Dong-Kyou , Liu Zhiquan , Wang Wei , Chen Shu-Ya 
Published: May 2012

Abstract
The authors have discovered two sizeable biases in the Weather Research and Forecasting (WRF) model: a negative bias in geopotential and a warm bias in temperature, appearing both in the initial condition and the forecast. The biases increase with height and thus manifest themselves at the upper part of the model domain. Both biases stem from a common root, which is that vertical structures of specific volume and potential temperature are convex functions. The geopotential bias is caused by the particular discrete hydrostatic equation used in WRF and is proportional to the square of the thickness of model layers. For the vertical levels used in this study, the bias far exceeds the gross 1-day forecast bias combining all other sources. The bias is fixed by revising the discrete hydrostatic equation. WRF interpolates potential temperature from the grids of an external dataset to the WRF grids in generating the initial condition. Associated with the Exner function, this leads to the marked bias in temperature. By interpolating temperature to the WRF grids and then computing potential temperature, the bias is removed. The bias corrections developed in this study are expected to reduce the disparity between the forecast and observations, and eventually to improve the quality of analysis and forecast in the subsequent data assimilation. The bias corrections might be especially beneficial to assimilating height-based observations (e.g., radio occultation data).