bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Double-ITCZ Problem in IPCC AR4 Coupled GCMs: Ocean–Atmosphere Feedback Analysis
Authors: Lin Jia-Lin 
Published: October 2007

Abstract
This study examines the double–intertropical convergence zone (ITCZ) problem in the coupled general circulation models (CGCMs) participating in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4). The twentieth-century climate simulations of 22 IPCC AR4 CGCMs are analyzed, together with the available Atmospheric Model Intercomparison Project (AMIP) runs from 12 of them. To understand the physical mechanisms for the double-ITCZ problem, the main ocean–atmosphere feedbacks, including the zonal sea surface temperature (SST) gradient–trade wind feedback (or Bjerknes feedback), the SST–surface latent heat flux (LHF) feedback, and the SST–surface shortwave flux (SWF) feedback, are studied in detail.
The results show that most of the current state-of-the-art CGCMs have some degree of the double-ITCZ problem, which is characterized by excessive precipitation over much of the Tropics (e.g., Northern Hemisphere ITCZ, South Pacific convergence zone, Maritime Continent, and equatorial Indian Ocean), and are often associated with insufficient precipitation over the equatorial Pacific. The excessive precipitation over much of the Tropics usually causes overly strong trade winds, excessive LHF, and insufficient SWF, leading to significant cold SST bias in much of the tropical oceans. Most of the models also simulate insufficient latitudinal asymmetry in precipitation and SST over the eastern Pacific and Atlantic Oceans.
The AMIP runs also produce excessive precipitation over much of the Tropics, including the equatorial Pacific, which also leads to overly strong trade winds, excessive LHF, and insufficient SWF. This suggests that the excessive tropical precipitation is an intrinsic error of the atmospheric models, and that the insufficient equatorial Pacific precipitation in the coupled runs of many models comes from ocean–atmosphere feedback. Feedback analysis demonstrates that the insufficient equatorial Pacific precipitation in different models is associated with one or more of the following three biases in ocean–atmosphere feedback over the equatorial Pacific: 1) excessive Bjerknes feedback, which is caused by excessive sensitivity of precipitation to SST and overly strong time-mean surface wind speed; 2) overly positive SST–LHF feedback, which is caused by excessive sensitivity of surface air humidity to SST; and 3) insufficient SST–SWF feedback, which is caused by insufficient sensitivity of cloud amount to precipitation. Off the equator over the eastern Pacific stratus region, most of the models produce insufficient stratus–SST feedback associated with insufficient sensitivity of stratus cloud amount to SST, which may contribute to the insufficient latitudinal asymmetry of SST in their coupled runs. These results suggest that the double-ITCZ problem in CGCMs may be alleviated by reducing the excessive tropical precipitation and the above feedback-relevant errors in the atmospheric models.
Effects of Spatial and Temporal Variations in PBL Depth on a GCM
Authors: Shin Sun-Hee , Ha Kyung-Ja 
Published: October 2007

Abstract
The effect of variations in planetary boundary layer (PBL) height on a GCM was investigated using the Yonsei University (YONU) AGCM. This GCM assumes a convective boundary layer constrained to the two lowest model levels. As a consequence of this fixed PBL height, the model tends to produce excessive mixing. In this study the authors focuse on the impact of spatially and temporally varying PBL height. In addition to stability-dependent eddy diffusivity, the model adopts both bulk mixing due to the surface heat flux and z-less mixing under stable conditions. The variable-depth PBL strongly suppressed excessive mixing so that the model bias was reduced over stable regions such as the Antarctic continent. On the other hand, vertical mixing over continents in the summer hemisphere was stronger than for the fixed-PBL version, resulting in greater rising motion and warming effects in the lower atmosphere. The variable-PBL height reduces excess precipitation over the western Pacific and East Asian monsoon region. Based on the improved PBL parameterization, widespread decreases in surface sensible heat flux and rising motion in the lower troposphere occurred simultaneously over the East Asian continent. This implies that the precipitation simulation is very sensitive to PBL processes.
The Transient Atmospheric Circulation Response to North Atlantic SST and Sea Ice Anomalies
Authors: Deser Clara , Tomas Robert A. , Peng Shiling 
Published: October 2007

Abstract
The objective of this study is to investigate the transient evolution of the wintertime atmospheric circulation response to imposed patterns of SST and sea ice extent anomalies in the North Atlantic sector using a large ensemble of experiments with the NCAR Community Climate Model version 3 (CCM3). The initial adjustment of the atmospheric circulation is characterized by an out-of-phase relationship between geopotential height anomalies in the lower and upper troposphere localized to the vicinity of the forcing. This initial baroclinic response reaches a maximum amplitude in ∼5–10 days, and persists for 2–3 weeks. Diagnostic results with a linear primitive equation model indicate that this initial response is forced by diabatic heating anomalies in the lower troposphere associated with surface heat flux anomalies generated by the imposed thermal forcing. Following the initial baroclinic stage of adjustment, the response becomes progressively more barotropic and increases in both spatial extent and magnitude. The equilibrium stage of adjustment is reached in 2–2.5 months, and is characterized by an equivalent barotropic structure that resembles the hemispheric North Atlantic Oscillation–Northern Annular Mode (NAO–NAM) pattern, the model’s leading internal mode of circulation variability over the Northern Hemisphere. The maximum amplitude of the equilibrium response is approximately 2–3 times larger than that of the initial response. The equilibrium response is primarily maintained by nonlinear transient eddy fluxes of vorticity (and, to a lesser extent, heat), with diabatic heating making a limited contribution in the vicinity of the forcing.
Atlantic Subsurface Temperatures: Response to a Shutdown of the Overturning Circulation and Consequences for Its Recovery
Authors: Mignot J. , Ganopolski A. , Levermann A. 
Published: October 2007

Abstract
Using the coupled climate model of intermediate complexity, CLIMBER-3α, changes in the vertical thermal structure associated with a shutdown of the Atlantic meridional overturning circulation (AMOC) are investigated. When North Atlantic Deep Water formation is inhibited by anomalous freshwater forcing, intermediate depth ventilation can remain active and cool the subsurface water masses (i.e., the “cold case”). However, if intermediate ventilation is completely suppressed, relatively warm water coming from the south penetrates to a high northern latitude beneath the halocline and induces a strong vertical temperature inversion between the surface and intermediate depth (i.e., the “warm case”). Both types of temperature anomalies emerge within the first decade after the beginning of the freshwater perturbation. The sign of subsurface temperature anomaly has a strong implication for the recovery of the AMOC once the anomalous freshwater forcing is removed. While the AMOC recovers from the cold case on centennial time scales, the recovery is much more rapid (decadal time scales) when ventilation is completely suppressed and intermediate depths are anomalously warm. This is explained by a more rapid destabilization of the water column after cessation of the anomalous flux due to a strong vertical temperature inversion. A suite of sensitivity experiments with varying strength and duration of the freshwater perturbation and a larger value of background vertical diffusivity demonstrate robustness of the phenomenon. Implications of the simulated subsurface temperature response to the shutdown of the AMOC for future climate and abrupt climate changes of the past are discussed.
The Influence of a Weakening of the Atlantic Meridional Overturning Circulation on ENSO
Authors: Timmermann A. , Okumura Y. , An S.-I. , Clement A. , Dong B. , Guilyardi E. , Hu A. , Jungclaus J. H. , Renold M. , Stocker T. F. , Stouffer R. J. , Sutton R. , Xie S.-P. , Yin J. 
Published: October 2007

Abstract
The influences of a substantial weakening of the Atlantic meridional overturning circulation (AMOC) on the tropical Pacific climate mean state, the annual cycle, and ENSO variability are studied using five different coupled general circulation models (CGCMs). In the CGCMs, a substantial weakening of the AMOC is induced by adding freshwater flux forcing in the northern North Atlantic. In response, the well-known surface temperature dipole in the low-latitude Atlantic is established, which reorganizes the large-scale tropical atmospheric circulation by increasing the northeasterly trade winds. This leads to a southward shift of the intertropical convergence zone (ITCZ) in the tropical Atlantic and also the eastern tropical Pacific. Because of evaporative fluxes, mixing, and changes in Ekman divergence, a meridional temperature anomaly is generated in the northeastern tropical Pacific, which leads to the development of a meridionally symmetric thermal background state. In four out of five CGCMs this leads to a substantial weakening of the annual cycle in the eastern equatorial Pacific and a subsequent intensification of ENSO variability due to nonlinear interactions. In one of the CGCM simulations, an ENSO intensification occurs as a result of a zonal mean thermocline shoaling.
Analysis suggests that the atmospheric circulation changes forced by tropical Atlantic SSTs can easily influence the large-scale atmospheric circulation and hence tropical eastern Pacific climate. Furthermore, it is concluded that the existence of the present-day tropical Pacific cold tongue complex and the annual cycle in the eastern equatorial Pacific are partly controlled by the strength of the AMOC. The results may have important implications for the interpretation of global multidecadal variability and paleo-proxy data.
Dynamical Processes Related to the Appearance of the Okhotsk High during Early Midsummer
Authors: Sato Naoki , Takahashi Masaaki 
Published: October 2007

Abstract
The authors identified an upper-level pressure anomaly pattern corresponding to the interannual variability of the Okhotsk high in midsummer (late July and early August) as a predominant anomaly pattern in the Northern Hemisphere, by using objectively analyzed data. According to the results of empirical orthogonal function (EOF) analyses and composite analyses, a positive pressure anomaly appeared near the tropopause over eastern Siberia in years with strong Okhotsk highs. Examination of the heat budget in the lower troposphere revealed that a negative surface temperature anomaly observed in northern Japan was brought by the advection of the climatological temperature gradient from the anomalous wind associated with the upper-level anticyclonic anomaly. It was also demonstrated that the anomaly field over Siberia does not accompany predominant vorticity forcing or Rossby wave propagation from the west with a specific phase. However, positive kinetic energy conversion from the climatological basic field to the anomaly field is estimated. The energy conversion contributes to maintaining the anomaly pattern. By the numerical experiments using a linear barotropic model, it is suggested that the upper-level anomaly pattern related to the anomalous Okhotsk high appears through the interaction with the climatological basic field, even though the external forcings are homogeneously distributed.
Two-stage formation of kaolinite in shear-zone slates, southern Iberian Massif, SE Spain
Authors: Jiménez-Millán J. , Velilla N. , Vázquez M. 
Published: October 2007

AbstractKaolinite aggregates are the major alteration product in the strongly deformed areas of a shear zone developed in contact-metamorphosed slates from the Southern Iberian Massif near Jaén (SE Spain). Muscovite and Fe-rich chlorite in strain shadows of broken andalusite crystals were observed in slates from less deformed areas. The presence of phyllosilicate packets nearly perpendicular to each other and veinlets parallel to {110} of andalusite reveal the importance of cleavage-controlled fracturing of andalusite to the mineral reactions. The compositional similarity between kaolinite and andalusite suggests a direct transformation of andalusite to kaolinite in the strongly altered area. The absence of clear preferred orientation of phyllosilicates relative to andalusite, and the compositional differences of andalusite with muscovite and chlorite from the less altered samples, indicate andalusite dissolution and chlorite-muscovite precipitation during a first mineral-growth stage. Muscovite-kaolinite and chlorite-kaolinite intergrowths indicate a later retrograde replacement stage.
The effect of the octahedral cations on the dimensions of the palygorskite cell
Authors: Suárez M. , García-Romero E. , Sánchez Del Río M. , Martinetto P. , Dooryhée E. 
Published: October 2007

AbstractHigh-resolution synchrotron X-ray diffraction recorded on a collection of palygorskites with different chemical compositions (obtained by analytical electron microscopy) permits unambiguous correlation of the crystallographic parametersa(orasin β if a monoclinic phase is considered) with the nature of the octahedral sheet, i.e. with both the number of octahedral positions that are occupied and the type of octahedral cation. No significant changes in the lattice parametersbandcare observed. The unit cell modification consists essentially of an expansion inaas the number of cations with larger ionic radii (Mg2+and Fe3+) predominates over smaller cations (Al3+). A linear dependency ofa(orasin β) on the chemical composition of the octahedral sheet was obtained that can be used for classifying palygorskite into compositional groups, using only conventional diffraction data, without the need for chemical analyses.
Synthesis of linear alkylbenzene sulphonate intercalated iron(II) iron(III) hydroxide sulphate (green rust) and adsorption of carbon tetrachloride
Authors: Ayala-Luis K. B. , Kaldor D. K. , Bender Koch C. , Strobel B. W. , Hansen H. C. B. 
Published: October 2007

AbstractGreen rusts, GRs, can act as both sorbents and reductants towards selected pollutants. Organo-GRs are expected to combine these properties with a high affinity for hydrophobic substances. A novel organo-GR, GRLAS, was synthesized by incorporating a mixture of linear alkylbenzenesulphonates (LAS) into the interlayer space of synthetic sulphate green rust, GRSO4 . Mössbauer analysis of GRLAS indicates that the structure of the organo-GR is very similar to that of the initial GRSO4 with regard to the FeII/FeIII ratio and local coordination of Fe atoms. X-ray diffraction demonstrates that the GRLAS formed was well ordered, although a mixture of surfactant was used for intercalation. The basal spacings of the GRLAS and the kinetics of the ion-exchange process were dependent on the initial surfactant loading; basal spacings of ~2.85 nm were obtained at LAS solution concentrations >10 mM. The ratio LASadsorbed/SO42–desorbed significantly exceeded the stoichiometric ratio of 2 during the initial part of the ion-exchange process (t = 5 h). However, this ratio was reached progressively with time. GRSO4 preferentially sorbed LAS homologues with long alkyl chains over short ones. Carbon tetrachloride was successfully adsorbed into GRLAS. The adsorption isotherm was linear with a distribution coefficient, Kd, of 505±19 litre kg–1.
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
Authors: Horesh Yair , Doniger Tirza , Michaeli Shulamit , Unger Ron 
Published: October 2007

Abstract

Background
In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure.

Results
We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE) predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of vertices in a graph. The shortest path in this graph is the basis for structural predictions for the molecule. We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. We show that this approach allows us to more deeply explore the suboptimal structure space.

Conclusion
The algorithm was tested on three datasets which include several ncRNA families taken from the Rfam database. These datasets allowed for comparison of the algorithm with other methods. In these tests, RNAspa performed better than four other programs.
Forelimb-hindlimb developmental timing changes across tetrapod phylogeny
Authors: Bininda-Emonds Olaf RP , Jeffery Jonathan E , Sánchez-Villagra Marcelo R , Hanken James , Colbert Matthew , Pieau Claude , Selwood Lynne , ten Cate Carel , Raynaud Albert , Osabutey Casmile K , Richardson Michael K 
Published: October 2007

AbstractBackgroundTetrapods exhibit great diversity in limb structures among species and also between forelimbs and hindlimbs within species, diversity which frequently correlates with locomotor modes and life history. We aim to examine the potential relation of changes in developmental timing (heterochrony) to the origin of limb morphological diversity in an explicit comparative and quantitative framework. In particular, we studied the relative time sequence of development of the forelimbs versus the hindlimbs in 138 embryos of 14 tetrapod species spanning a diverse taxonomic, ecomorphological and life-history breadth. Whole-mounts and histological sections were used to code the appearance of 10 developmental events comprising landmarks of development from the early bud stage to late chondrogenesis in the forelimb and the corresponding serial homologues in the hindlimb.ResultsAn overall pattern of change across tetrapods can be discerned and appears to be relatively clade-specific. In the primitive condition, as seen in Chondrichthyes and Osteichthyes, the forelimb/pectoral fin develops earlier than the hindlimb/pelvic fin. This pattern is either retained or re-evolved in eulipotyphlan insectivores (= shrews, moles, hedgehogs, and solenodons) and taken to its extreme in marsupials. Although exceptions are known, the two anurans we examined reversed the pattern and displayed a significant advance in hindlimb development. All other species examined, including a bat with its greatly enlarged forelimbs modified as wings in the adult, showed near synchrony in the development of the fore and hindlimbs.ConclusionMajor heterochronic changes in early limb development and chondrogenesis were absent within major clades except Lissamphibia, and their presence across vertebrate phylogeny are not easily correlated with adaptive phenomena related to morphological differences in the adult fore- and hindlimbs. The apparently conservative nature of this trait means that changes in chondrogenetic patterns may serve as useful phylogenetic characters at higher taxonomic levels in tetrapods. Our results highlight the more important role generally played by allometric heterochrony in this instance to shape adult morphology.
Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection
Authors: Graham Neil S , Broadley Martin R , Hammond John P , White Philip J , May Sean T 
Published: October 2007

Abstract

Background
Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.

Results
Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.

Conclusion
This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays.
DNA copy number profiles of gastric cancer precursor lesions
Authors: Buffart Tineke E , Carvalho Beatriz , Mons Thomas , Reis Rui M , Moutinho Cátia , Silva Paula , van Grieken Nicole CT , Vieth Michael , Stolte Manfred , van de Velde Cornelis JH , Schrock Evelin , Matthaei Anja , Ylstra Bauke , Carneiro Fátima , Meijer Gerrit A 
Published: October 2007

Abstract

Background
Chromosomal instability (CIN) is the most prevalent type of genomic instability in gastric tumours, but its role in malignant transformation of the gastric mucosa is still obscure. In the present study, we set out to study whether two morphologically distinct categories of gastric cancer precursor lesions, i.e. intestinal-type and pyloric gland adenomas, would carry different patterns of DNA copy number changes, possibly reflecting distinct genetic pathways of gastric carcinogenesis in these two adenoma types.

Results
Using a 5K BAC array CGH platform, we showed that the most common aberrations shared by the 11 intestinal-type and 10 pyloric gland adenomas were gains of chromosomes 9 (29%), 11q (29%) and 20 (33%), and losses of chromosomes 13q (48%), 6(48%), 5(43%) and 10 (33%). The most frequent aberrations in intestinal-type gastric adenoma were gains on 11q, 9q and 8, and losses on chromosomes 5q, 6, 10 and 13, whereas in pyloric gland gastric adenomas these were gains on chromosome 20 and losses on 5q and 6. However, no significant differences were observed between the two adenoma types.

Conclusion
The results suggest that gains on chromosomes 8, 9q, 11q and 20, and losses on chromosomes 5q, 6, 10 and 13, likely represent early events in gastric carcinogenesis. The phenotypical entities, intestinal-type and pyloric gland adenomas, however, do not differ significantly (P = 0.8) at the level of DNA copy number changes.