bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sediment supply versus storm winnowing in the development of muddy and shelly interbeds from the Upper Ordovician of the Cincinnati region, USAThis article is one of a series of papers published in this Special Issue on the themeThe dynamic reef and shelly communities of the Paleozoic. This Special is in honour of our colleague and friend Paul Copper.
Authors: Dattilo Benjamin F. , Brett Carlton E. , Tsujita Cameron J. , Fairhurst Robert 
Published: April 2008

Shell-bed development can be a product of complex sedimentological and biological factors. The Upper Ordovician sediments near Cincinnati, Ohio constitute a succession of thinly interbedded shelly carbonates and mudrocks. Despite years of study, the development of Cincinnatian shell beds and metre-scale cycles has, until recently, been attributed solely to storm reworking. This “storm-winnowing model” treats shells as passive sedimentary clasts, ignoring other factors of shell-bed development. A recently proposed alternative is Brett and Algeo’s idea that these shell beds grew during long periods of normally low sedimentation, while most mud accumulated during brief periods of high sedimentation. Under this “episodic starvation model,” any storms would winnow pre-existing muds and shell beds alike. We tested both models in the Edenian–Maysvillian (early to mid Katian) strata of the Cincinnati region by compiling observations on their petrologic, taphonomic, and paleoecologic characteristics. The storm-winnowing model does not explain several observed features that the episodic starvation model does, including (i) storm-related sedimentary structures in mudrocks and limestones; (ii) lack of a sufficiently fossiliferous precursor deposit to winnow; (iii) deep-water faunas in grainstones; (iv) mixed taphonomic conditions of shell-bed fossils; (v) ubiquitous discontinuity surfaces; (vi) carbonate concretion horizons; (vii) unwinnowed shell beds; and (viii) micrite in packstones. Episodic starvation is a superior explanation because it explains all of these features and allows for the complex interplay of other environmental and biological factors that contribute to shell-bed growth. It may also be applicable to other deposits, previously interpreted as tempestites.
Injury-induced expression of cytokeratins 8 and 18 by vascular smooth muscle cells requires concurrent activation of cytoskeletal and growth factor receptors
Authors: Moon Michael C. , Yau Lorraine , Wright Brenda , Zahradka Peter 
Published: April 2008

Cytokeratins are not present in the vascular smooth muscle cells (VSMCs) of normal arteries, but they are detectable in the VSMCs of atherosclerotic lesions. A correlation between cytokeratin expression and VSMC phenotype is proposed, but an examination of VSMCs after mechanical injury has yet to be performed. Immunohistochemistry was used to monitor proteins in arterial sections. Western blotting enabled quantification of protein levels. Angioplasty of porcine femoral artery in vivo and porcine coronary artery in vitro served as models of vascular injury. Cytokeratins 8 and 18 were expressed by VSMCs in porcine femoral artery lesions 14 days after balloon angioplasty. Cytokeratins were also present in the neointima of porcine coronary artery segments placed into organ culture for 4 days. Cytokeratin expression was decreased in the presence of inhibitors that affect MAP kinase, PI3 kinase, Src kinase, and G protein, but not in the presence of an AT1 receptor antagonist. Cytokeratin expression also occurred when VSMCs were plated onto collagen in the presence of serum. We conclude that mechanical injury induces expression of cytokeratin 8 and 18 both in vitro and in vivo by synthetic VSMCs that migrate into the neointima. Furthermore, cytokeratin expression requires cellular attachment to extracellular matrix proteins in conjunction with mitogenic stimulation.
Prolactin decreases expression of Runx2, osteoprotegerin, and RANKL in primary osteoblasts derived from tibiae of adult female rats
Authors: Charoenphandhu Narattaphol , Teerapornpuntakit Jarinthorn , Methawasin Methajit , Wongdee Kannikar , Thongchote Kanogwun , Krishnamra Nateetip 
Published: April 2008

Hyperprolactinemia caused by physiological or pathological conditions, such as those occurring during lactation and prolactinoma, respectively, results in progressive osteopenia. The underlying mechanisms, however, are controversial. Prolactin (PRL) may directly attenuate the functions of osteoblasts, since these bone cells express PRL receptors. The present study therefore aimed to investigate the effects of PRL on the expression of genes related to the osteoblast functions by using quantitative real-time PCR technique. Herein, we used primary osteoblasts that were derived from the tibiae of adult rats and displayed characteristics of differentiated osteoblasts, including in vitro mineralization. Osteoblasts exposed for 48 h to 1000 ng/mL PRL, but not to 10 or 100 ng/mL PRL, showed decreases in the mRNA expression of Runx2, osteoprotegerin (OPG), and receptor activator of nuclear factor κB ligand (RANKL) by 60.49%, 72.74%, and 87.51%, respectively. Nevertheless, PRL did not change the RANKL/OPG ratio, since expression of OPG and RANKL were proportionally decreased. These concentrations of PRL had no effect on the mRNA expression of osteocalcin and osteopontin, nor on mineralization. High pathologic concentrations of PRL (1000 ng/mL) may downregulate expression of genes that are essential for osteoblast differentiation and functions. The present results explained the clinical findings of hyperprolactinemia-induced bone loss.
Cloud Liquid Water Path from Satellite-Based Passive Microwave Observations: A New Climatology over the Global Oceans
Authors: O’Dell Christopher W. , Wentz Frank J. , Bennartz Ralf 
Published: April 2008

AbstractThis work describes a new climatology of cloud liquid water path (LWP), termed the University of Wisconsin (UWisc) climatology, derived from 18 yr of satellite-based passive microwave observations over the global oceans. The climatology is based on a modern retrieval methodology applied consistently to the Special Sensor Microwave Imager (SSM/I), the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI), and the Advanced Microwave Scanning Radiometer (AMSR) for Earth Observing System (EOS) (AMSR-E) microwave sensors on eight different satellite platforms, beginning in 1988 and continuing through 2005. It goes beyond previously published climatologies by explicitly solving for the diurnal cycle of cloud liquid water by providing statistical error estimates, and includes a detailed discussion of possible systematic errors.A novel methodology for constructing the climatology is used in which a mean monthly diurnal cycle as well as monthly means of the liquid water path are derived simultaneously from the data on a 1° grid; the methodology also produces statistical errors for these quantities, which decrease toward the end of the time record as the number of observations increases. The derived diurnal cycles are consistent with previous findings in the tropics, but are also derived for higher latitudes and contain more information than in previous studies. The new climatology exhibits differences with previous observationally based climatologies and is found to be more consistent with the 40-yr ECMWF Re-Analysis (ERA-40) than are the previous climatologies.Potential systematic errors of the order of 15%–30% or higher exist in the LWP climatology. A previously unexplored source of systematic error is caused by the assumption that all microwave-based retrievals of LWP must make regarding the partitioning of cloud water and rainwater, which cannot be determined using microwave observations alone. The potentially large systematic errors that result may hamper the usefulness of microwave-based climatologies of both cloud liquid water and especially rain rate, particularly in certain regions of the tropics and midlatitudes where the separation of rain from liquid cloud water is most critical.
Interdecadal Changes in the Major Modes of Asian–Australian Monsoon Variability: Strengthening Relationship with ENSO since the Late 1970s*
Authors: Wang Bin , Yang Jing , Zhou Tianjun , Wang Bin 
Published: April 2008

Abstract
The present paper develops an integral view of the year-to-year variability across the entire Asian–Australian monsoon (A–AM) system, which covers one-third of the global tropics between 40° and 160°E. Using season-reliant empirical orthogonal function (S-EOF) analysis, the authors identified two major modes of variability for the period 1956–2004. The first exhibits a prominent biennial tendency and concurs with the turnabout of El Niño–Southern Oscillation (ENSO), providing a new perspective of the seasonally evolving spatiotemporal structure for tropospheric biennial oscillation. The second mode leads ENSO by one year. The remote El Niño forcing, the monsoon–warm pool ocean interaction, and the influence of the annual cycle are three fundamental factors for understanding the behavior of the first mode. The monsoon–ocean interaction is characterized by a positive feedback between the off-equatorial convectively coupled Rossby waves and the underlying sea surface temperature (SST) “dipole” anomalies.
Since the late 1970s the overall coupling between the A–AM system and ENSO has become strengthened. The relationships between ENSO and the western North Pacific, East Asian, and Indonesian monsoons have all become enhanced during ENSO’s developing, mature, and decaying phases, overriding the weakening of the Indian monsoon–ENSO anticorrelation during the developing phase. Prior to the late 1970s (1956–79), the first mode shows a strong biennial tendency, and the second mode does not lead ENSO. After 1980, the first mode shows a weakening biennial tendency, and the second mode provides a strong precursory signal for ENSO. These interdecadal changes are attributed to increased magnitude and periodicity of ENSO and the strengthened monsoon–ocean interaction.
On the Use of Cool Materials as a Heat Island Mitigation Strategy
Authors: Synnefa A. , Dandou A. , Santamouris M. , Tombrou M. , Soulakellis N. 
Published: April 2008

Abstract
The mitigation of the heat island effect can be achieved by the use of cool materials that are characterized by high solar reflectance and infrared emittance values. Several types of cool materials have been tested and their optical and thermal properties reveal that these materials can be classified as “cool” with the ability to maintain lower surface temperatures. Cool materials can be used on buildings and other surfaces of the urban environment. Based on these results, a modeling study was undertaken to assess the urban heat island effect over Athens, Greece, a densely populated city, by trying to analyze the impacts of large-scale increases in surface albedo on ambient temperature. Numerical simulations were performed by the “urbanized” version of the nonhydrostatic fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5, version 3-6-1). Two scenarios of modified albedo were studied: a moderate and an extreme increase in albedo scenario. It was found that large-scale increases in albedo could lower ambient air temperatures by 2°C. Furthermore, the impact of high albedo measures on heat island magnitude was estimated by creating a spatial representation of the urban heat island effect over the modeled area. The results of this study can help to promote the adoption of high albedo measures in building energy codes and urban planning regulations.
Decadal Modulation of ENSO in a Hybrid Coupled Model
Authors: Burgman Robert J. , Schopf Paul S. , Kirtman Ben P. 
Published: April 2008

Abstract
Decadal variations in the amplitude of El Niño and the Southern Oscillation have been the subject of great interest in the literature for the past decade. One theory suggests that ENSO is best described as a stable system driven by linear dynamics and that stochastic atmospheric forcing is responsible for the development and modulation of ENSO on interannual as well as decadal time scales. Another theory suggests that ENSO is driven by strong nonlinear coupled feedbacks between the ocean and atmosphere and low frequency changes in ENSO amplitude are driven by decadal changes in the tropical Pacific mean state. Unfortunately, the observed record is too short to collect reliable statistics for such low frequency behavior. A hybrid coupled model composed of a simple statistical atmosphere coupled to the Poseidon isopycnal ocean model has been developed for the study of ENSO decadal variability. The model simulates realistic ENSO variability on interannual and decadal time scales with negligible climate drift over 1000 years. Through analysis and experimentation the authors show that low frequency changes in the atmospheric “weather noise” drive changes in the tropical Pacific mean state leading to changes in the amplitude of ENSO on decadal time scales. Additional model simulations suggest that, while predictability is limited by the presence of atmospheric noise, there are extended periods when the coupled instability, strengthened by changes in the mean state, is insensitive to noise on interannual time scales.
The relationship between decadal modulation of ENSO and mean state changes resides somewhere between the linear damped stochastically forced theory and the strongly unstable theory. Unlike the strongly unstable system, changes in ENSO amplitude on longer time scales are determined by the stochastic forcing. The stochastic forcing is not necessary in this model to sustain ENSO; however, its presence is crucial for low frequency changes in the mean state of the tropical Pacific. The strong relationship between the mean state and ENSO amplitude modulation in the model is in opposition to the linear damped stochastically forced theory. The fact that changes in the tropical Pacific mean state lead directly to changes in ENSO amplitude and predictability has positive implications for predictability.
On Multidecadal Variability of the Atlantic Meridional Overturning Circulation in the Community Climate System Model Version 3
Authors: Danabasoglu Gokhan 
Published: April 2008

Abstract
Multidecadal variability of the Atlantic meridional overturning circulation (MOC) is investigated diagnostically in the NCAR Community Climate System Model version 3 (CCSM3) present-day simulations, using the highest (T85 × 1) resolution version. This variability has a 21-yr period and is present in many other ocean fields in the North Atlantic. In MOC, the oscillation amplitude is about 4.5 Sv (1 Sv ≡ 106 m3 s−1), corresponding to 20% of the mean maximum MOC transport. The northward heat transport (NHT) variability has an amplitude of about 0.12 PW, representing 10% of the mean maximum NHT. In sea surface temperature (SST) and sea surface salinity (SSS), the peak-to-peak changes can be as large as 6°–7°C and 3 psu, respectively. The Labrador Sea region is identified as the deep-water formation (DWF) site associated with the MOC oscillations. In contrast with some previous studies, temperature and salinity contributions to the total density in this DWF region are almost equal and in phase. The heat and freshwater budget analyses performed for the DWF site indicate a complex relationship between the DWF, MOC, North Atlantic Oscillation (NAO), and subpolar gyre circulation anomalies. Their complicated interactions appear to be responsible for the maintenance of this multidecadal oscillation. In these interactions, the atmospheric variability associated with the model’s NAO plays a prominent role. In particular, the NAO modulates the subpolar gyre strength and contributes to the formation of the temperature and salinity anomalies that lead to positive/negative density anomalies at the DWF site. In addition, the wind stress curl anomalies occurring during the transition phase between the positive and negative NAO states produce fluctuations of the subtropical–subpolar gyre boundary, thus creating midlatitude SST and SSS anomalies. Comparisons with observations show that neither the pattern nor the magnitude of this dominant SST variability is realistic.
On the Steadiness of Separating Meandering Currents
Authors: van Leeuwen Peter Jan , de Ruijter Will P. M. 
Published: April 2008

Abstract
The existence of inertial steady currents that separate from a coast and meander afterward is investigated. By integrating the zonal momentum equation over a suitable area, it is shown that retroflecting currents cannot be steady in a reduced gravity or in a barotropic model of the ocean. Even friction cannot negate this conclusion. Previous literature on this subject, notably the discrepancy between several articles by Nof and Pichevin on the unsteadiness of retroflecting currents and steady solutions presented in other papers, is critically discussed. For more general separating current systems, a local analysis of the zonal momentum balance shows that given a coastal current with a specific zonal momentum structure, an inertial, steady, separating current is unlikely, and the only analytical solution provided in the literature is shown to be inconsistent. In a basin-wide view of these separating current systems, a scaling analysis reveals that steady separation is impossible when the interior flow is nondissipative (e.g., linear Sverdrup-like). These findings point to the possibility that a large part of the variability in the world’s oceans is due to the separation process rather than to instability of a free jet.
The Effects of Complex Terrain on Severe Landfalling Tropical Cyclone Larry (2006) over Northeast Australia
Authors: Ramsay Hamish A. , Leslie Lance M. 
Published: April 2008

Abstract
The interaction between complex terrain and a landfalling tropical cyclone (TC) over northeastern Australia is investigated using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5). Severe TC Larry (in March 2006) made landfall over an area of steep coastal orography and caused extensive damage. The damage pattern suggested that the mountainous terrain had a large influence on the TC wind field, with highly variable damage across relatively small distances. The major aims in this study were to reproduce the observed features of TC Larry, including track, intensity, speed of movement, size, decay rate, and the three-dimensional wind field using realistic high-resolution terrain data and a nested grid with a horizontal spacing of 1 km for the finest domain (referred to as CTRL), and to assess how the above parameters change when the terrain height is set to zero (NOTOPOG). The TC track for CTRL, including the timing and location of landfall, was in close agreement with observation, with the model eye overlapping the location of the observed eye at landfall. Setting the terrain height to zero resulted in a more southerly track and a more intense storm at landfall. The orography in CTRL had a large impact on the TC’s 3D wind field, particularly in the boundary layer where locally very high wind speeds, up to 68 m s−1, coincided with topographic slopes and ridges. The orography also affected precipitation, with localized maxima in elevated regions matching observed rainfall rates. In contrast, the precipitation pattern for the NOTOPOG TC was more symmetric and rainfall totals decreased rapidly with distance from the storm’s center. Parameterized maximum surface wind gusts were located beneath strong boundary layer jets. Finally, small-scale banding features were evident in the surface wind field over land for the NOTOPOG TC, owing to the interaction between the TC boundary layer flow and land surface characteristics.
Genome classification by gene distribution: An overlapping subspace clustering approach
Authors: Li Jason , Halgamuge Saman K , Tang Sen-Lin 
Published: April 2008

Abstract

Background
Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods.

Results
We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2, Clostridium phi3626, Geobacillus GBSV1, and Listeria monocytogenes PSA.

Conclusion
The method described in this paper can assist evolutionary study through objectively classifying genomes based on their resemblance in gene order, gene content and gene positions. The method is suitable for application to genomes with high genetic exchange and various conserved gene arrangement, as demonstrated through our application on phages.