bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roads, logging, and the large-mammal community of an eastern Canadian boreal forest
Authors: Bowman Jeff , Ray Justina C. , Magoun Audrey J. , Johnson Devin S. , Dawson F. Neil 
Published: May 2010

We evaluated hypotheses concerning the distributions of large mammals in a 60 000 km2study area that encompassed the contact zone between Ontario’s roadless north and the postlogging southern landscape. We estimated occurrence probability in 575 sample units for woodland caribou ( Rangifer tarandus caribou (Gmelin, 1788)), wolverine ( Gulo gulo (L., 1758)), gray wolf ( Canis lupus L., 1758), moose ( Alces alces (L., 1758)), and white-tailed deer ( Odocoileus virginianus (Zimmerman, 1780)). We used ordinations and spatial regressions to assess the contributions of parameters to species occurrence. Roads and cutovers were most abundant in the south, leading to an increased prevalence of deciduous forest. Mature coniferous forest, however, occurred most commonly in the north. Occurrence probabilities for moose and deer were greatest in the south, in close association with deciduous trees. Wolf occurrence was also greatest in the south, positively related to both deciduous forest and road density. Caribou occurrence, however, was positively related to mature coniferous forest and negatively related to both wolf occurrence and roads. Wolverine occurrence was negatively related to deciduous forest. Our surveys demonstrated distinct mammal communities in the northern and southern halves of our study area, a separation that appeared to be mediated by deciduous forest and roads.
Behavior and survival of white-tailed deer neonates in two suburban forest preserves
Authors: Piccolo B. P. , Van Deelen T. R. , Hollis-Etter K. , Etter D. R. , Warner R. E. , Anchor C. 
Published: May 2010

Neonatal survival influences growth of unhunted populations of suburban white-tailed deer ( Odocoileus virginianus (Zimmerman, 1780)). Understanding the interaction of habitat and survival may inform conservation efforts and studies of life history of cervids at high density. We chose two forest preserves representative of forests in suburban Chicago. We radio-marked 56 neonates (1999–2001) to investigate mortality and habitat use. Through 1 July, 21 of 29 (72%) neonates and 6 of 22 (27%) died mostly because of predation by coyotes ( Canis latrans Say, 1823). Akaike’s information criterion suggested that optimal mark–recapture models of survival contained covariates reflecting differences by preserve and timing chosen to coincide with behavioral change from hiding to accompanying the doe. Survival was lower during early parturition (0.26–0.78) relative to the latter part (0.90–0.96). Early fawns (hiders) at one site had lower survival (0.26–0.29) than fawns at the other (0.78). Lower survival associated with larger home ranges, greater movement, and reduced understory cover, suggesting that hiding cover may mediate fawn survival in the presence of predators. Our study demonstrates spatial heterogeneity in population biology of suburban deer and suggests that site-specific differences may influence neonate survival in the face of coyote predation.
Predictive Biomarkers of Sensitivity to the Phosphatidylinositol 3′ Kinase Inhibitor GDC-0941 in Breast Cancer Preclinical Models
Authors: O'Brien Carol , Wallin Jeffrey J. , Sampath Deepak , GuhaThakurta Debraj , Savage Heidi , Punnoose Elizabeth A. , Guan Jane , Berry Leanne , Prior Wei Wei , Amler Lukas C. , Belvin Marcia , Friedman Lori S. , Lackner Mark R. 
Published: May 2010

AbstractPurpose: The class I phosphatidylinositol 3′ kinase (PI3K) plays a major role in proliferation and survival in a wide variety of human cancers. A key factor in successful development of drugs targeting this pathway is likely to be the identification of responsive patient populations with predictive diagnostic biomarkers. This study sought to identify candidate biomarkers of response to the selective PI3K inhibitor GDC-0941.Experimental Design: We used a large panel of breast cancer cell lines and in vivo xenograft models to identify candidate predictive biomarkers for a selective inhibitor of class I PI3K that is currently in clinical development. The approach involved pharmacogenomic profiling as well as analysis of gene expression data sets from cells profiled at baseline or after GDC-0941 treatment.Results: We found that models harboring mutations in PIK3CA, amplification of human epidermal growth factor receptor 2, or dual alterations in two pathway components were exquisitely sensitive to the antitumor effects of GDC-0941. We found that several models that do not harbor these alterations also showed sensitivity, suggesting a need for additional diagnostic markers. Gene expression studies identified a collection of genes whose expression was associated with in vitro sensitivity to GDC-0941, and expression of a subset of these genes was found to be intimately linked to signaling through the pathway.Conclusion: Pathway focused biomarkers and the gene expression signature described in this study may have utility in the identification of patients likely to benefit from therapy with a selective PI3K inhibitor. Clin Cancer Res; 16(14); 3670–83. ©2010 AACR.
Nocturnal Cold-Air Intrusions into a Closed Basin: Observational Evidence and Conceptual Model
Authors: Whiteman C. David , Hoch Sebastian W. , Lehner Manuela , Haiden Thomas 
Published: May 2010

AbstractObservations are analyzed to explain an unusual feature of the nighttime atmospheric structure inside Arizona’s idealized, basin-shaped Meteor Crater. The upper 75%–80% of the crater’s atmosphere, which overlies an intense surface-based inversion on the crater’s floor, maintains a near-isothermal lapse rate during the entire night, even while continuing to cool. Evidence is presented to show that this near-isothermal layer is produced by cold-air intrusions that come over the crater’s rim. The intrusions are driven by a regional-scale drainage flow that develops over the surrounding inclined Colorado Plateau. Cold air from the drainage flow builds up on the upwind side of the crater and splits around the crater at low levels. A shallow layer of cold air, however, spills over the 30–60-m-high rim and descends partway down the crater’s upwind inner sidewall until reaching its buoyancy equilibrium level. Detrainment of cold air during its katabatic descent and compensatory rising motions in the crater atmosphere destabilize the basin atmosphere, producing the observed near-isothermal lapse rate. A conceptual model of this phenomenon is presented.
The Response of Simulated Nocturnal Convective Systems to a Developing Low-Level Jet
Authors: French Adam J. , Parker Matthew D. 
Published: May 2010

Abstract
Some recent numerical experiments have examined the dynamics of initially surface-based squall lines that encounter an increasingly stable boundary layer, akin to what occurs with the onset of nocturnal cooling. The present study builds on that work by investigating the added effect of a developing nocturnal low-level jet (LLJ) on the convective-scale dynamics of a simulated squall line. The characteristics of the simulated LLJ atop a simulated stable boundary layer are based on past climatological studies of the LLJ in the central United States. A variety of jet orientations are tested, and sensitivities to jet height and the presence of low-level cooling are explored.
The primary impacts of adding the LLJ are that it alters the wind shear in the layers just above and below the jet and that it alters the magnitude of the storm-relative inflow in the jet layer. The changes to wind shear have an attendant impact on low-level lifting, in keeping with current theories for gust front lifting in squall lines. The changes to the system-relative inflow, in turn, impact total upward mass flux and precipitation output. Both are sensitive to the squall line–relative orientation of the LLJ.
The variations in updraft intensity and system-relative inflow are modulated by the progression of the low-level cooling, which mimics the development of a nocturnal boundary layer. While the system remains surface-based, the below-jet shear has the largest impact on lifting, whereas the above-jet shear begins to play a larger role as the system becomes elevated. Similarly, as the system becomes elevated, larger changes to system-relative inflow are observed because of the layer of potentially buoyant inflowing parcels becoming confined to the layer of the LLJ.
Convectively Coupled Waves in a Sheared Environment
Authors: Han Ying , Khouider Boualem 
Published: May 2010

Abstract
A linear stability analysis, about a radiative–convective equilibrium in a sheared environment, on an equatorial beta plane, for a simple multicloud model for organized tropical convection is presented here. Both vertical/baroclinic and meridional/barotropic zonal wind shears are considered separately in a parameter regime for which the shear-free multicloud model exhibits synoptic-scale instability of Kelvin and n = 0 eastward inertio-gravity [eastward mixed Rossby–gravity (MRG)] waves only, with moderate growth rates. The maximum growth rates appear to increase significantly with the strength of the background wind shear, and new wave instabilities appear and/or disappear depending on the strength and type of the wind shear. It is found here that both high- and low-level vertical shears have a strong impact on the stability of convectively coupled waves (CCWs), consistent with the fact that the multicloud instability mechanism is controlled by both stratiform heating and low-level moisture and congestus heating. Typically, vertical shears with high-level easterly wind destabilize westward moving waves and stabilize eastward waves, whereas westerly winds aloft and on bottom tend to destabilize eastward moving and stabilize westward moving waves. In the mixed situation of high-level easterlies and low-level westerlies both eastward and westward waves are unstable, while in the case of high-level westerlies and low-level easterlies only eastward waves are unstable. In the presence of a barotropic/meridional shear, synoptic-scale convectively coupled westward MRG and Rossby waves emerge, when the shear strength is large enough, due essentially to pure shear instability of the dry dynamics. The meridional shear has also an important impact on the horizontal structure of the waves. Owing to the meridional shear, the Kelvin wave displays a nonzero meridional velocity that induces a significant contribution toward the horizontal convergence. The two-day waves adopt a crescentlike shape while the westward MRG, and somewhat the Rossby waves, become less trapped in the vicinity of the equator.
Contrails of Small and Very Large Optical Depth
Authors: Atlas David , Wang Zhien 
Published: May 2010

Abstract
This work deals with two kinds of contrails. The first comprises a large number of optically thin contrails near the tropopause. They are mapped geographically using a lidar to obtain their height and a camera to obtain azimuth and elevation. These high-resolution maps provide the local contrail geometry and the amount of optically clear atmosphere. The second kind is a single trail of unprecedentedly large optical thickness that occurs at a lower height. The latter was observed fortuitously when an aircraft moving along the wind direction passed over the lidar, thus providing measurements for more than 3 h and an equivalent distance of 620 km. It was also observed by Geostationary Operational Environmental Satellite (GOES) sensors. The lidar measured an optical depth of 2.3. The corresponding extinction coefficient of 0.023 km−1 and ice water content of 0.063 g m−3 are close to the maximum values found for midlatitude cirrus. The associated large radar reflectivity compares to that measured by ultrasensitive radar, thus providing support for the reality of the large optical depth.
Decadal Variations of North Atlantic Sea Surface Temperature in Observations and CMIP3 Simulations*
Authors: Jamison Nathan , Kravtsov Sergey 
Published: May 2010

Abstract
This study evaluates the ability of the global climate models that compose phase 3 of the Coupled Model Intercomparison Project (CMIP3) to simulate intrinsic decadal variations detected in the observed North Atlantic sea surface temperature (SST) record via multichannel singular spectrum analysis (M-SSA). M-SSA identifies statistically significant signals in the observed SSTs, with time scales of 5–10, 10–15, and 15–30 yr; all of these signals have distinctive spatiotemporal characteristics and are consistent with previous studies.
Many of the CMIP3 twentieth-century simulations are characterized by quasi-oscillatory behavior within one or more of the three observationally motivated frequency bands specified above; however, only a fraction of these models also capture the spatial patterns of the observed signals. The models best reproduce the observed quasi-regular SST variations in the high-frequency, 5–10-yr band, while the observed signals in the intermediate, 10–15-yr band have turned out to be most difficult to capture. A handful of models capture the patterns and, sometimes, the spectral character of the observed variability in the two or three bands simultaneously.
These results imply that the decadal prediction skill of the models considered—to be estimated within the CMIP5 framework—would be stratified according to the models’ performance in capturing the time scales and patterns of the observed decadal SST variations. They also warrant further research into the dynamical causes of the observed and simulated decadal variability, as well as into apparent differences in the representation of these variations by individual CMIP3 models.
The Influence of Assimilating Dropsonde Data on Typhoon Track and Midlatitude Forecasts
Authors: Weissmann Martin , Harnisch Florian , Wu Chun-Chieh , Lin Po-Hsiung , Ohta Yoichiro , Yamashita Koji , Kim Yeon-Hee , Jeon Eun-Hee , Nakazawa Tetsuo , Aberson Sim 
Published: May 2010

Abstract
A unique dataset of targeted dropsonde observations was collected during The Observing System Research and Predictability Experiment (THORPEX) Pacific Asian Regional Campaign (T-PARC) in the autumn of 2008. The campaign was supplemented by an enhancement of the operational Dropsonde Observations for Typhoon Surveillance near the Taiwan Region (DOTSTAR) program. For the first time, up to four different aircraft were available for typhoon observations and over 1500 additional soundings were collected.
This study investigates the influence of assimilating additional observations during the two major typhoon events of T-PARC on the typhoon track forecast by the global models of the European Centre for Medium-Range Weather Forecasts (ECMWF), the Japan Meteorological Agency (JMA), the National Centers for Environmental Prediction (NCEP), and the limited-area Weather Research and Forecasting (WRF) model. Additionally, the influence of T-PARC observations on ECMWF midlatitude forecasts is investigated.
All models show an improving tendency of typhoon track forecasts, but the degree of improvement varied from about 20% to 40% in NCEP and WRF to a comparably low influence in ECMWF and JMA. This is likely related to lower track forecast errors without dropsondes in the latter two models, presumably caused by a more extensive use of satellite data and four-dimensional variational data assimilation (4D-Var) of ECMWF and JMA compared to three-dimensional variational data assimilation (3D-Var) of NCEP and WRF. The different behavior of the models emphasizes that the benefit gained strongly depends on the quality of the first-guess field and the assimilation system.
Behind the Avatar: The Patterns, Practices, and Functions of Role Playing in MMOs
Authors: Williams Dmitri , Kennedy Tracy L. M. , Moore Robert J. 
Published: May 2010

A two-part quantitative and qualitative study of role players within a virtual game world examined their prevalence, practices, and identity formation. Drawing on unobtrusive behavioral data captured by the game, combined with a large survey and traditional ethnographic methods, the study found that role players both negotiate identity and use their time online as a moratorium for their offline lives. Descriptive results showed that role players are a relatively small, but psychologically burdened subgroup. When examined from the theoretical perspectives of Goffman’s Self-Presentation theory, Huizenga’s Magic Circle, and Turkle’s early work on online identity formation, these players were seen as largely using virtual spaces as creative outlets and for socialization. The worlds also functioned as coping mechanisms for players frequently unable to gain acceptance, social connectivity or social support offline due to their personal situation, psychological profile, or their minority status.
Extracellular protein disulfide isomerase regulates coagulation on endothelial cells through modulation of phosphatidylserine exposure
Authors: Popescu Narcis I. , Lupu Cristina , Lupu Florea 
Published: May 2010

AbstractTissue factor (TF) is the cellular receptor for plasma protease factor VIIa (FVIIa), and the TF-FVIIa complex initiates coagulation in both hemostasis and thrombosis. Cell surface-exposed TF is mainly cryptic and requires activation to fully exhibit the procoagulant potential. Recently, the protein disulfide isomerase (PDI) has been hypothesized to regulate TF decryption through the redox switch of an exposed disulfide in TF extracellular domain. In this study, we analyzed PDI contribution to coagulation using an in vitro endothelial cell model. In this model, extracellular PDI is detected by imaging and flow cytometry. Inhibition of cell surface PDI induces a marked increase in TF procoagulant function, whereas exogenous addition of PDI inhibits TF decryption. The coagulant effects of PDI inhibition were sensitive to annexin V treatment, suggesting exposure of phosphatidylserine (PS), which was confirmed by prothrombinase assays and direct labeling. In contrast, exogenous PDI addition enhanced PS internalization. Analysis of fluorescent PS revealed that PDI affects both the apparent flippase and floppase activities on endothelial cells. In conclusion, we identified a new mechanism for PDI contribution to coagulation on endothelial cells, namely, the regulation of PS exposure, where PDI acts as a negative regulator of coagulation.
Human T-cell leukemia virus type I (HTLV-1) proviral load and disease progression in asymptomatic HTLV-1 carriers: a nationwide prospective study in Japan
Authors: Iwanaga Masako , Watanabe Toshiki , Utsunomiya Atae , Okayama Akihiko , Uchimaru Kaoru , Koh Ki-Ryang , Ogata Masao , Kikuchi Hiroshi , Sagara Yasuko , Uozumi Kimiharu , Mochizuki Manabu , Tsukasaki Kunihiro , Saburi Yoshio , Yamamura Masaomi , Tanaka Junji , Moriuchi Yukiyoshi , Hino Shigeo , Kamihira Shimeru , Yamaguchi Kazunari ,   for the Joint Study on Predisposing Factors of ATL Development investigators
Published: May 2010

AbstractDefinitive risk factors for the development of adult T-cell leukemia (ATL) among asymptomatic human T-cell leukemia virus type I (HTLV-1) carriers remain unclear. Recently, HTLV-1 proviral loads have been evaluated as important predictors of ATL, but a few small prospective studies have been conducted. We prospectively evaluated 1218 asymptomatic HTLV-1 carriers (426 males and 792 females) who were enrolled during 2002 to 2008. The proviral load at enrollment was significantly higher in males than females (median, 2.10 vs 1.39 copies/100 peripheral blood mononuclear cells [PBMCs]; P < .001), in those 40 to 49 and 50 to 59 years of age than that of those 40 years of age and younger (P = .02 and .007, respectively), and in those with a family history of ATL than those without the history (median, 2.32 vs 1.33 copies/100 PBMCs; P = .005). During follow-up, 14 participants progressed to overt ATL. Their baseline proviral load was high (range, 4.17-28.58 copies/100 PBMCs). None developed ATL among those with a baseline proviral load lower than approximately 4 copies. Multivariate Cox analyses indicated that not only a higher proviral load, advanced age, family history of ATL, and first opportunity for HTLV-1 testing during treatment for other diseases were independent risk factors for progression of ATL.
Live imaging of Runx1 expression in the dorsal aorta tracks the emergence of blood progenitors from endothelial cells
Authors: Lam Enid Yi Ni , Hall Christopher J. , Crosier Philip S. , Crosier Kathryn E. , Flores Maria Vega 
Published: May 2010

AbstractBlood cells of an adult vertebrate are continuously generated by hematopoietic stem cells (HSCs) that originate during embryonic life within the aorta-gonad-mesonephros region. There is now compelling in vivo evidence that HSCs are generated from aortic endothelial cells and that this process is critically regulated by the transcription factor Runx1. By time-lapse microscopy of Runx1-enhanced green fluorescent protein transgenic zebrafish embryos, we were able to capture a subset of cells within the ventral endothelium of the dorsal aorta, as they acquire hemogenic properties and directly emerge as presumptive HSCs. These nascent hematopoietic cells assume a rounded morphology, transiently occupy the subaortic space, and eventually enter the circulation via the caudal vein. Cell tracing showed that these cells subsequently populated the sites of definitive hematopoiesis (thymus and kidney), consistent with an HSC identity. HSC numbers depended on activity of the transcription factor Runx1, on blood flow, and on proper development of the dorsal aorta (features in common with mammals). This study captures the earliest events of the transition of endothelial cells to a hemogenic endothelium and demonstrates that embryonic hematopoietic progenitors directly differentiate from endothelial cells within a living organism.
Bone marrow is a reservoir for proangiogenic myelomonocytic cells but not endothelial cells in spontaneous tumors
Authors: Dudley Andrew C. , Udagawa Taturo , Melero-Martin Juan M. , Shih Shou-Ching , Curatolo Adam , Moses Marsha A. , Klagsbrun Michael 
Published: May 2010

Abstract
The hypothesis that bone marrow–derived, circulating endothelial cells incorporate into tumor blood vessels is unresolved. We have measured the numbers of bone marrow–derived versus resident endothelial cells in spontaneous prostate cancers during different stages of tumor progression and in age-matched normal prostates. Bone marrow–derived endothelial cells were rare in dysplasia and in well differentiated cancers representing between 0 and 0.04% of the total tumor mass. Instead, approximately 99% of all tumor-associated bone marrow–derived cells were CD45+ hematopoietic cells, including GR-1+, F4-80+, and CD11b+ myeloid cells. Similar to peripheral blood mononuclear cells, these tumor-associated myeloid cells expressed matrix metalloproteinases (MMPs), consistent with their proposed catalytic role during tumor angiogenesis. Furthermore, freshly isolated CD11b+ cells stimulated tumor endothelial cell cord formation by 10-fold in an in vitro angiogenesis assay. The bone marrow is, therefore, a reservoir for cells that augment tumor angiogenesis, but the tumor endothelium is derived primarily from the local environment.