bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indian Ocean Variability in the GFDL Coupled Climate Model
Authors: Song Qian , Vecchi Gabriel A. , Rosati Anthony J. 
Published: June 2007

Abstract
The interannual variability of the Indian Ocean, with particular focus on the Indian Ocean dipole/zonal mode (IODZM), is investigated in a 250-yr simulation of the GFDL coupled global general circulation model (CGCM). The CGCM successfully reproduces many fundamental characteristics of the climate system of the Indian Ocean. The character of the IODZM is explored, as are relationships between positive IODZM and El Niño events, through a composite analysis. The IODZM events in the CGCM grow through feedbacks between heat-content anomalies and SST-related atmospheric anomalies, particularly in the eastern tropical Indian Ocean. The composite IODZM events that co-occur with El Niño have stronger anomalies and a sharper east–west SSTA contrast than those that occur without El Niño. IODZM events, whether or not they occur with El Niño, are preceded by distinctive Indo-Pacific warm pool anomaly patterns in boreal spring: in the central Indian Ocean easterly surface winds, and in the western equatorial Pacific an eastward shift of deep convection, westerly surface winds, and warm sea surface temperature. However, delayed onsets of the anomaly patterns (e.g., boreal summer) are often not followed by IODZM events. The same anomaly patterns often precede El Niño, suggesting that the warm pool conditions favorable for both IODZM and El Niño are similar. Given that IODZM events can occur without El Niño, it is proposed that the observed IODZM–El Niño relation arises because the IODZM and El Niño are both large-scale phenomena in which variations of the Indo-Pacific warm pool deep convection plays a central role. Yet each phenomenon has its own dynamics and life cycle, allowing each to develop without the other.
The CGCM integration also shows substantial decadal modulation of the occurrence of IODZM events, which is found to be not in phase with that of El Niño events. There is a weak, though significant, negative correlation between the two. Moreover, the statistical relationship between the IODZM and El Niño displays strong decadal variability.
The Influence of Tropical Indian Ocean SST on the Indian Summer Monsoon
Authors: Cherchi Annalisa , Gualdi Silvio , Behera Swadhin , Luo Jing Jia , Masson Sebastien , Yamagata Toshio , Navarra Antonio 
Published: June 2007

AbstractThe Indian summer monsoon (ISM) is one of the main components of the Asian summer monsoon. It is well known that one of the starting mechanisms of a summer monsoon is the thermal contrast between land and ocean and that sea surface temperature (SST) and moisture are crucial factors for its evolution and intensity. The Indian Ocean, therefore, may play a very important role in the generation and evolution of the ISM itself. A coupled general circulation model, implemented with a high-resolution atmospheric component, appears to be able to simulate the Indian summer monsoon in a realistic way. In particular, the features of the simulated ISM variability are similar to the observations.In this study, the relationships between the ISM and tropical Indian Ocean (TIO) SST anomalies are investigated, as well as the ability of the coupled model to capture those connections. The recent discovery of the Indian Ocean dipole mode (IODM) may suggest new perspectives in the relationship between ISM and TIO SST. A new statistical technique, the coupled manifold, is used to investigate the TIO SST variability and its relation with the tropical Pacific Ocean (TPO). The analysis shows that the SST variability in the TIO contains a significant portion that is independent from the TPO variability. The same technique is used to estimate the amount of Indian rainfall variability that can be explained by the tropical Indian Ocean SST. Indian Ocean SST anomalies are separated in a part remotely forced from the tropical Pacific Ocean variability and a part independent from that. The relationships between the two SSTA components and the Indian monsoon variability are then investigated in detail.
Intraseasonal Variability of Equatorial Indian Ocean Zonal Currents
Authors: Sengupta Debasis , Senan Retish , Goswami B. N. , Vialard Jérôme 
Published: June 2007

Abstract
New satellite and in situ observations show large intraseasonal (10–60 day) variability of surface winds and upper-ocean current in the equatorial Indian Ocean, particularly in the east. An ocean model forced by the Quick Scatterometer (QuikSCAT) wind stress is used to study the dynamics of the intraseasonal zonal current. The model has realistic upper-ocean currents and thermocline depth variabilities on intraseasonal to interannual scales. The quality of the simulation is directly attributed to the accuracy of the wind forcing. At the equator, moderate westerly winds are punctuated by strong 10–40-day westerly wind bursts. The wind bursts force swift, intraseasonal (20–50 day) eastward equatorial jets in spring, summer, and fall. The zonal momentum balance is between local acceleration, stress, and pressure, while nonlinearity deepens and strengthens the eastward current. The westward pressure force associated with the thermocline deepening toward the east rapidly arrests eastward jets and, subsequently, generates (weak) westward flow. Thus, in accord with direct observations in the east, the spring jet is a single intraseasonal event, there are intraseasonal jets in summer, and the fall jet is long lived but strongly modulated on an intraseasonal scale. The zonal pressure force is almost always westward in the upper 120 m, and changes sign twice a year in the 120–200-m layer. Transient eastward equatorial undercurrents in early spring and late summer are associated with semiannual Rossby waves generated at the eastern boundary following thermocline deepening by the spring and fall jets. An easterly wind stress is not necessary to generate the undercurrents. Experiments with a single westerly wind burst forcing show that apart from the intraseasonal response, the zonal pressure force and current in the east have an intrinsic 90-day time scale that arises purely from equatorial adjustment.
Pathways and Effects of the Indonesian Throughflow Water in the Indian Ocean Using Particle Trajectory and Tracers in an OGCM
Authors: Valsala Vinu K. , Ikeda Motoyoshi 
Published: June 2007

Abstract
The 3D pathways of the Indonesian Throughflow (ITF) in the Indian Ocean are identified using an OGCM, with a combined set of tools: 1) Lagrangian particle trajectories, 2) passive tracers, and 3) active tracers (temperature and salinity). Each of these tools has its own advantages and limitations to represent the watermass pathways. The Lagrangian particles, without horizontal and vertical mixing, suggest that at the entrance region the surface ITF subducts along the northwestern coast of Australia and then travels across the Indian Ocean along the thermocline depths. The subsurface ITF more directly departs westward and crosses the Indian Ocean. Using the passive tracers, which are mixed vertically under convection as well as horizontally due to diffusion, the ITF is shown to undergo vigorous mixing as soon as it enters the Indian Ocean and modifies its upper temperature–salinity (T–S) characteristics. Thus, the surface and subsurface ITF watermasses lose their identities.
Upon reaching the western boundary, the ITF reroutes into three distinct depth ranges, owing to the seasonal reversal of the Somali region: route 1—across the Indian Ocean just to the south of the equator (200–300 m); route 2—across the Indian Ocean to the north of the equator (100–200 m); and route 3—upwells in the Somali region and spreads all over the surface of the northern Indian Ocean. The seasonality of the Somali Current is crucial to spread the ITF along route 3 during the summer monsoon (April–October) and route 2 during the winter monsoon (November–March). The basinwide spreading is responsible for a long residence time of the ITF in the Indian Ocean to be at least 20 yr.
The effects of the ITF on the temperature and salinity are mainly accompanied with the major pathways. However, indirect effects are visible in a few spots; that is, the warm and saline feature is produced in the subsurface off the southwestern coast of Australia around 30°S caused by the eastward surface current, which is under the thermal wind relationship owing to the warm and fresh ITF component. This component also enhances vertical convection and warms the surface around 40°S. The Arabian Sea high salinity water is produced extensively with the effects of the Somali upwelling, which is originally strengthened by the fresh and warm ITF.
Decadal Modulations of the Indian Ocean Dipole in the SINTEX-F1 Coupled GCM
Authors: Tozuka Tomoki , Luo Jing-Jia , Masson Sebastien , Yamagata Toshio 
Published: June 2007

Abstract
The decadal variation in the tropical Indian Ocean is investigated using outputs from a 200-yr integration of the Scale Interaction Experiment-Frontier Research Center for Global Change (SINTEX-F1) ocean–atmosphere coupled model. The first EOF mode of the decadal bandpass- (9–35 yr) filtered sea surface temperature anomaly (SSTA) represents a basinwide mode and is closely related with the Pacific ENSO-like decadal variability. The second EOF mode shows a clear east–west SSTA dipole pattern similar to that of the interannual Indian Ocean dipole (IOD) and may be termed the decadal IOD. However, it is demonstrated that the decadal air–sea interaction in the Tropics can be a statistical artifact; it should be interpreted more correctly as decadal modulation of interannual IOD events (i.e., asymmetric or skewed occurrence of positive and negative events). Heat budget analysis has revealed that the occurrence of IOD events is governed by variations in the southward Ekman heat transport across 15°S and variations in the Indonesian Throughflow associated with the ENSO. The variations in the southward Ekman heat transport are related to the Mascarene high activities.
Relationship between insertion/deletion (indel) frequency of proteins and essentiality
Authors: Chan Simon K , Hsing Michael , Hormozdiari Fereydoun , Cherkasov Artem 
Published: June 2007

Abstract

Background
In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient spatial differences between the pathogenic protein and human proteins to allow for selective targeting. In one example, an indel difference was targeted via large scale in-silico screening. This resulted in selective antibodies and small compounds which were capable of binding to the deletion-bearing essential pathogen protein without any cross-reactivity to the highly similar human protein. The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins.

Results
We have investigated three species, Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae, for which high-quality protein essentiality data is available. Using these data, we demonstrated with t-test calculations that the mean indel frequencies in essential proteins were greater than that of non-essential proteins in the three proteomes. The abundance of indels in both types of proteins was also shown to be accurately modeled by the Weibull distribution. However, Receiver Operator Characteristic (ROC) curves showed that indel frequencies alone could not be used as a marker to accurately discriminate between essential and non-essential proteins in the three proteomes. Finally, we analyzed the protein interaction data available for S. cerevisiae and observed that indel-bearing proteins were involved in more interactions and had greater betweenness values within Protein Interaction Networks (PINs).

Conclusion
Overall, our findings demonstrated that indels were not randomly distributed across the studied proteomes and were likely to occur more often in essential proteins and those that were highly connected, indicating a possible role of sequence insertions and deletions in the regulation and modification of protein-protein interactions. Such observations will provide new insights into indel-based drug design using bioinformatics and cheminformatics tools.
A curious coincidence: mosquito biodiversity and the limits of the Japanese encephalitis virus in Australasia
Authors: Hemmerter Stéphane , Šlapeta Jan , van den Hurk Andrew F , Cooper Robert D , Whelan Peter I , Russell Richard C , Johansen Cheryl A , Beebe Nigel W 
Published: June 2007

Abstract

Background
The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is the major vector of endemic arboviruses in Australia and is also responsible for the establishment of the Japanese encephalitis virus (JEV) in southern Papua New Guinea (PNG) as well as its incursions into northern Australia. Papua New Guinea and mainland Australia are separated by a small stretch of water, the Torres Strait, and its islands. While there has been regular JEV activity on these islands, JEV has not established on mainland Australia despite an abundance of Cx. annulirostris and porcine amplifying hosts. Despite the public health significance of this mosquito and the fact that its adults show overlapping morphology with close relative Cx. palpalis Taylor, its evolution and genetic structure remain undetermined. We address a hypothesis that there is significant genetic diversity in Cx. annulirostris and that the identification of this diversity will shed light on the paradox that JEV can cycle on an island 70 km from mainland Australia while not establishing in Australia itself.

Results
We sequenced 538 bp of the mitochondrial DNA cytochrome oxidase I gene from 273 individuals collected from 43 localities in Australia and the southwest Pacific region to describe the phylogeography of Cx. annulirostris and its sister species Cx. palpalis. Maximum Likelihood and Bayesian analyses reveal supporting evidence for multiple divergent lineages that display geographic restriction. Culex palpalis contained three divergent lineages geographically restricted to southern Australia, northern Australia and Papua New Guinea (PNG). Culex annulirostris contained five geographically restricted divergent lineages, with one lineage restricted to the Solomon Islands and two identified mainly within Australia while two other lineages showed distributions in PNG and the Torres Strait Islands with a southern limit at the top of Australia's Cape York Peninsula.

Conclusion
The existence of divergent mitochondrial lineages within Cx. annulirostris and Cx. palpalis helps explain the difficulty of using adult morphology to identify Cx. annulirostris and its ecological diversity. Notably, the southern limit of the PNG lineages of Cx. annulirostris coincides exactly with the current southern limit of JEV activity in Australasia suggesting that variation in these COI lineages may be the key to why JEV has not yet established yet on mainland Australia.
High-throughput genotyping of a common deletion polymorphism disrupting the TRY6 gene and its association with breast cancer risk
Authors: Wagner Kerstin , Grzybowska Ewa , Butkiewicz Dorota , Pamula-Pilat Jolanta , Pekala Wioletta , Tecza Karolina , Hemminki Kari , Försti Asta 
Published: June 2007

Abstract

Background
Copy number polymorphisms caused by genomic rearrangements like deletions, make a significant contribution to the genomic differences between two individuals and may add to disease predisposition. Therefore, genotyping of such deletion polymorphisms in case-control studies could give important insights into risk associations.

Results
We mapped the breakpoints and developed a fluorescent fragment analysis for a deletion disrupting the TRY6 gene to exemplify a quick and cheap genotyping approach for such structural variants. We showed that the deletion is larger than predicted and encompasses also the pseudogene TRY5. We performed a case-control study to test an association of the TRY6 deletion polymorphism with breast cancer using a single nucleotide polymorphism which is in 100% linkage disequilibrium with the deletion. We did not observe an effect of the deletion on breast cancer risk (OR 1.05, 95% CI 0.71–1.56).

Conclusion
Although we did not observe an association between the TRY6 deletion polymorphism and breast cancer risk, the identification and investigation of further deletions using the present approach may help to elucidate their effect on disease susceptibility.
Neurite outgrowth on a fibronectin isoform expressed during peripheral nerve regeneration is mediated by the interaction of paxillin with α4β1 integrins
Authors: Vogelezang Mariette , Forster Ulrike B , Han Jaewon , Ginsberg Mark H , ffrench-Constant Charles 
Published: June 2007

Abstract

Background
The regeneration of peripheral nerve is associated with a change in the alternative splicing of the fibronectin primary gene transcript to re-express embryonic isoforms containing a binding site for α4β1 integrins that promote neurite outgrowth. Here we use PC12 cells to examine the role of the interaction between paxillin and the α4 integrin cytoplasmic domain in neurite outgrowth.

Results
Expression of α4 with mutations in the paxillin-binding domain reduced neurite outgrowth on recombinant embryonic fibronectin fragments relative to wild type α4. Over-expression of paxillin promoted neurite outgrowth while a mutant isoform lacking the LD4 domain implicated in the regulation of ARF and Rac GTPases was less effective. Optimal α4-mediated migration in leucocytes requires spatial regulation of α4 phosphorylation at Ser988, a post-translational modification that blocks paxillin binding to the integrin cytoplasmic domain. In keeping with this α4(S988D), which mimics phosphorylated α4, did not promote neurite outgrowth. However, α4 was not phosphorylated in the PC12 cells, and a non-phosphorylatable α4(S988A) mutant promoted neurite outgrowth indistinguishably from the wild type integrin.

Conclusion
We establish the importance of the α4 integrin-paxillin interaction in a model of axonal regeneration and highlight differing dependence on phosphorylation of α4 for extension of neuronal growth cones and migration of non-neural cells.
Schizophrenia and psychotic symptoms in families of two American Indian tribes
Authors: Robin Robert W , Gottesman Irving I , Albaugh Bernard , Goldman David 
Published: June 2007

AbstractBackgroundThe risk of schizophrenia is thought to be higher in population isolates that have recently been exposed to major and accelerated cultural change, accompanied by ensuing socio-environmental stressors/triggers, than in dominant, mainstream societies. We investigated the prevalence and phenomenology of schizophrenia in 329 females and 253 males of a Southwestern American Indian tribe, and in 194 females and 137 males of a Plains American Indian tribe. These tribal groups were evaluated as part of a broader program of gene-environment investigations of alcoholism and other psychiatric disorders.MethodsSemi-structured psychiatric interviews were conducted to allow diagnoses utilizing standardized psychiatric diagnostic criteria, and to limit cultural biases. Study participants were recruited from the community on the basis of membership in pedigrees, and not by convenience. After independent raters evaluated the interviews blindly, DSM-III-R diagnoses were assigned by a consensus of experts well-versed in the local cultures.ResultsFive of the 582 Southwestern American Indian respondents (prevalence = 8.6 per 1000), and one of the 331 interviewed Plains American Indians (prevalence = 3.02 per 1000) had a lifetime diagnosis of schizophrenia. The lifetime prevalence rates of schizophrenia within these two distinct American Indian tribal groups is consistent with lifetime expectancy rates reported for the general United States population and most isolate and homogeneous populations for which prevalence rates of schizophrenia are available. While we were unable to factor in the potential modifying effect that mortality rates of schizophrenia-suffering tribal members may have had on the overall tribal rates, the incidence of schizophrenia among the living was well within the normative range.ConclusionThe occurrence of schizophrenia among members of these two tribal population groups is consistent with prevalence rates reported for population isolates and in the general population. Vulnerabilities to early onset alcohol and drug use disorders do not lend convincing support to a diathesis-stressor model with these stressors, commonly reported with these tribes. Nearly one-fifth of the respondents reported experiencing psychotic-like symptoms, reaffirming the need to examine sociocultural factors actively before making positive diagnoses of psychosis or schizophrenia.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
Authors: Kmiecik Sebastian , Gront Dominik , Kolinski Andrzej 
Published: June 2007

Abstract

Background
Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. For a considerable fraction of proteins whose structures will not be determined experimentally, computational methods can provide valuable information. The value of structural models in biological research depends critically on their quality. Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling.

Results
Large sets of structural decoys have been generated using reduced conformational space protein modeling tool CABS. Subsequently, the reduced models were subject to all-atom reconstruction. Then, the resulting detailed models were energy-minimized using state-of-the-art all-atom force field, assuming fixed positions of the alpha carbons. It has been shown that a very short minimization leads to the proper ranking of the quality of the models (distance from the native structure), when the all-atom energy is used as the ranking criterion. Additionally, we performed test on medium and low accuracy decoys built via classical methods of comparative modeling. The test placed our model evaluation procedure among the state-of-the-art protein model assessment methods.

Conclusion
These test computations show that a large scale high resolution protein structure prediction is possible, not only for small but also for large protein domains, and that it should be based on a hierarchical approach to the modeling protocol. We employed Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Our tests show that a physic-based approach, usually considered computationally too demanding for large-scale applications, can be effectively used in such studies.