bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms for the Advanced Asian Summer Monsoon Onset since the Mid-to-Late 1990s
Authors: Xiang Baoqiang , Wang Bin 
Published: October 2012

AbstractUnderstanding the variability and change of monsoon onset is of utmost importance for agriculture planning and water management. In the last three decades, the Asian summer monsoon onset (ASMO) has remarkably advanced, but the physical mechanisms underlying the change remain elusive. Since the overall ASMO occurs in May, this paper focuses on the change of mean fields in May and considers enhanced mean precipitation and monsoon westerly winds as signs of advanced ASMO. The results reveal that the advanced ASMO mainly represents a robust decadal shift in the mid-to-late 1990s, which is attributed to the mean state change in the Pacific basin characterized by a grand La Niña–like pattern. The La Niña–like mean state change controls the ASMO through the westward propagation of Rossby waves and its interaction with the asymmetric background mean states in the Indian Ocean and western Pacific, which intensifies the Northern Hemispheric perturbations and westerly winds. Intriguingly, the abrupt decadal shifts of monsoon onset in the Arabian Sea and Bay of Bengal occur in 1999, in contrast to the South China Sea with a decadal shift in 1994. Numerical experiments with a coupled climate model demonstrate that the advanced monsoon onset in the Arabian Sea and Bay of Bengal is governed by the enhanced zonal sea surface temperature (SST) gradients in the equatorial Pacific, while that in the South China Sea is primarily determined by the abrupt SST warming near the Philippine Sea.
Thermodynamic Bias in the Multimodel Mean Boreal Summer Monsoon
Authors: Boos William R. , Hurley John V. 
Published: October 2012

AbstractHere it is shown that almost all models participating in the Coupled Model Intercomparison Project (CMIP) exhibit a common bias in the thermodynamic structure of boreal summer monsoons. The strongest bias lies over South Asia, where the upper-tropospheric temperature maximum is too weak, is shifted southeast of its observed location, and does not extend as far west over Africa as it does in observations. Simulated Asian maxima of surface air moist static energy are also too weak and are located over coastal oceans rather than in their observed continental position. The spatial structure of this bias suggests that it is caused by an overly smoothed representation of topography west of the Tibetan Plateau, which allows dry air from the deserts of western Asia to penetrate the monsoon thermal maximum, suppressing moist convection and cooling the upper troposphere. In a climate model with a decent representation of the thermodynamic state of the Asian monsoon, the qualitative characteristics of this bias can be recreated by truncating topography just west of the Tibetan Plateau. This relatively minor topographic modification also produces a negative anomaly of Indian precipitation of similar sign and amplitude to the CMIP continental Indian monsoon precipitation bias. Furthermore, in simulations of next-century climate warming, this topographic modification reduces the amplitude of the increase in Indian monsoon precipitation. These results confirm the importance of topography west of the Tibetan Plateau for South Asian climate and illustrate the need for careful assessments of the thermodynamic state of model monsoons.
Range-Correcting Azimuthal Shear in Doppler Radar Data
Authors: Newman Jennifer F. , Lakshmanan Valliappa , Heinselman Pamela L. , Richman Michael B. , Smith Travis M. 
Published: October 2012

Abstract
The current tornado detection algorithm (TDA) used by the National Weather Service produces a large number of false detections, primarily because it calculates azimuthal shear in a manner that is adversely impacted by noisy velocity data and range-degraded velocity signatures. Coincident with the advent of new radar-derived products and ongoing research involving new weather radar systems, the National Severe Storms Laboratory is developing an improved TDA. A primary component of this algorithm is the local, linear least squares derivatives (LLSD) azimuthal shear field. The LLSD method incorporates rotational derivatives of the velocity field and is affected less strongly by noisy velocity data in comparison with traditional “peak to peak” azimuthal shear calculations. LLSD shear is generally less range dependent than peak-to-peak shear, although some range dependency is unavoidable. The relationship between range and the LLSD shear values of simulated circulations was examined to develop a range correction for LLSD shear. A linear regression and artificial neural networks (ANNs) were investigated as range-correction models. Both methods were used to produce fits for the simulated shear data, although the ANN excelled as it could capture the nonlinear nature of the data. The range-correction methods were applied to real radar data from tornadic and nontornadic events to measure the capacity of the corrected shear to discriminate between tornadic and nontornadic circulations. The findings presented herein suggest that both methods increased shear values during tornadic periods by nearly an order of magnitude, facilitating differentiation between tornadic and nontornadic scans in tornadic events.
Differential effects of γc cytokines on postselection differentiation of CD8 thymocytes
Authors: Rafei Moutih , Rouette Alexandre , Brochu Sylvie , Vanegas Juan Ruiz , Perreault Claude 
Published: October 2012

Abstract
The primary consequence of positive selection is to render thymocytes responsive to cytokines and chemokines expressed in the thymic medulla. In the present study, our main objective was to discover which cytokines could support the differentiation of positively selected thymocytes. To this end, we have developed an in vitro model suitable for high-throughput analyses of positive selection and CD8 T-cell differentiation. The model involves coculture of TCRhiCD5intCD69− double-positive (DP) thymocytes with peptide-pulsed OP9 cells and γc-cytokines. We report that IL-4, IL-7, and IL-21 have nonredundant effects on positively selected DP thymocytes. IL-7 signaling phosphorylates STAT5 and ERK; induces Foxo1, Klf2, and S1pr1; and supports the differentiation of classic CD8 T cells. IL-4 activates STAT6 and ERK and supports the differentiation of CD8intPD-L1hiCD44hiEOMES+ innate CD8 T cells. IL-21 is produced by thymic epithelial cells and the IL-21 receptor-α is strongly induced on DP thymocytes undergoing positive selection. IL-21 signaling phosphorylates STAT3 and STAT5, but not ERK, and does not support CD8 T-cell differentiation. However, IL-21 has a unique ability to up-regulate BCL-6, expand DP thymocytes undergoing positive selection, and increase the production of mature T cells. Our data suggest that injection of recombinant IL-21 might enhance thymic output in subjects with age- or disease-related thymic atrophy.
Evolutionary dynamics of rRNA gene clusters in cichlid fish
Authors: Nakajima Rafael T , Cabral-de-Mello Diogo C , Valente Guilherme T , Venere Paulo C , Martins Cesar 
Published: October 2012

AbstractBackgroundAmong multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity.ResultsThe present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching theOreochromis niloticusgenome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes.ConclusionsThe organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.
Molecular adaptation and resilience of the insect’s nuclear receptor USP
Authors: Chaumot Arnaud , Da Lage Jean-Luc , Maestro Oscar , Martin David , Iwema Thomas , Brunet Frederic , Belles Xavier , Laudet Vincent , Bonneton François 
Published: October 2012

Abstract

Background
The maintenance of biological systems requires plasticity and robustness. The function of the ecdysone receptor, a heterodimer composed of the nuclear receptors ECR (NR1H1) and USP (NR2B4), was maintained in insects despite a dramatic divergence that occurred during the emergence of Mecopterida. This receptor is therefore a good model to study the evolution of plasticity. We tested the hypothesis that selection has shaped the Ligand-Binding Domain (LBD) of USP during evolution of Mecopterida.

Results
We isolated usp and cox1 in several species of Drosophilidae, Tenebrionidae and Blattaria and estimated non-synonymous/synonymous rate ratios using maximum-likelihood methods and codon-based substitution models. Although the usp sequences were mainly under negative selection, we detected relaxation at residues located on the surface of the LBD within Mecopterida families. Using branch-site models, we also detected changes in selective constraints along three successive branches of the Mecopterida evolution. Residues located at the bottom of the ligand-binding pocket (LBP) underwent strong positive selection during the emergence of Mecopterida. This change is correlated with the acquisition of a large LBP filled by phospholipids that probably allowed the stabilisation of the new Mecopterida structure. Later, when the two subgroups of Mecopterida (Amphiesmenoptera: Lepidoptera, Trichoptera; Antliophora: Diptera, Mecoptera, Siphonaptera) diverged, the same positions became under purifying selection. Similarly, several positions of the heterodimerisation interface experienced positive selection during the emergence of Mecopterida, rapidly followed by a phase of constrained evolution. An enlargement of the heterodimerisation surface is specific for Mecopterida and was associated with a reinforcement of the obligatory partnership between ECR and USP, at the expense of homodimerisation.

Conclusions
In order to explain the episodic mode of evolution of USP, we propose a model in which the molecular adaptation of this protein is seen as a process of resilience for the maintenance of the ecdysone receptor functionality.
Drought yield index to select high yielding rice lines under different drought stress severities
Authors: Raman Anitha , Verulkar Satish , Mandal Nimai , Variar Mukund , Shukla V , Dwivedi J , Singh B , Singh O , Swain Padmini , Mall Ashutosh , Robin S , Chandrababu R , Jain Abhinav , Ram Tilatoo , Hittalmani Shailaja , Haefele Stephan , Piepho Hans-Peter , Kumar Arvind 
Published: October 2012

Abstract

Background
Drought is the most severe abiotic stress reducing rice yield in rainfed drought prone ecosystems. Variation in intensity and severity of drought from season to season and place to place requires cultivation of rice varieties with different level of drought tolerance in different areas. Multi environment evaluation of breeding lines helps breeder to identify appropriate genotypes for areas prone to similar level of drought stress. From a set of 129 advanced rice (Oryza sativa L.) breeding lines evaluated under rainfed drought-prone situations at three locations in eastern India from 2005 to 2007, a subset of 39 genotypes that were tested for two or more years was selected to develop a drought yield index (DYI) and mean yield index (MYI) based on yield under irrigated, moderate and severe reproductive-stage drought stress to help breeders select appropriate genotypes for different environments.

Results
ARB 8 and IR55419-04 recorded the highest drought yield index (DYI) and are identified as the best drought-tolerant lines. The proposed DYI provides a more effective assessment as it is calculated after accounting for a significant genotype x stress-level interaction across environments. For rainfed areas with variable frequency of drought occurrence, Mean yield index (MYI) along with deviation in performance of genotypes from currently cultivated popular varieties in all situations helps to select genotypes with a superior performance across irrigated, moderate and severe reproductive-stage drought situations. IR74371-70-1-1 and DGI 75 are the two genotypes identified to have shown a superior performance over IR64 and MTU1010 under all situations.

Conclusion
For highly drought-prone areas, a combination of DYI with deviation in performance of genotypes under irrigated situations can enable breeders to select genotypes with no reduction in yield under favorable environments compared with currently cultivated varieties. For rainfed areas with variable frequency of drought stress, use of MYI together with deviation in performance of genotypes under different situations as compared to presently cultivated varieties will help breeders to select genotypes with superior performance under all situations.
Biomechanical factors and physical examination findings in osteoarthritis of the knee: associations with tissue abnormalities assessed by conventional radiography and high-resolution 3.0 Tesla magnetic resonance imaging
Authors: Knoop Jesper , Dekker Joost , Klein Jan-Paul , van der Leeden Marike , van der Esch Martin , Reiding Dick , Voorneman Ramon E , Gerritsen Martijn , Roorda Leo D , Steultjens Martijn PM , Lems Willem F 
Published: October 2012

Abstract
Introduction
We aimed to explore the associations between knee osteoarthritis (OA)-related tissue abnormalities assessed by conventional radiography (CR) and by high-resolution 3.0 Tesla magnetic resonance imaging (MRI), as well as biomechanical factors and findings from physical examination in patients with knee OA.

Methods
This was an explorative cross-sectional study of 105 patients with knee OA. Index knees were imaged using CR and MRI. Multiple features from CR and MRI (cartilage, osteophytes, bone marrow lesions, effusion and synovitis) were related to biomechanical factors (quadriceps and hamstrings muscle strength, proprioceptive accuracy and varus-valgus laxity) and physical examination findings (bony tenderness, crepitus, bony enlargement and palpable warmth), using multivariable regression analyses.

Results
Quadriceps weakness was associated with cartilage integrity, effusion, synovitis (all detected by MRI) and CR-detected joint space narrowing. Knee joint laxity was associated with MRI-detected cartilage integrity, CR-detected joint space narrowing and osteophyte formation. Multiple tissue abnormalities including cartilage integrity, osteophytes and effusion, but only those detected by MRI, were found to be associated with physical examination findings such as crepitus.

Conclusion
We observed clinically relevant findings, including a significant association between quadriceps weakness and both effusion and synovitis, detected by MRI. Inflammation was detected in over one-third of the participants, emphasizing the inflammatory component of OA and a possible important role for anti-inflammatory therapies in knee OA. In general, OA-related tissue abnormalities of the knee, even those detected by MRI, were found to be discordant with biomechanical and physical examination features.
A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors
Authors: Li Zhen , Zheng Weiling , Wang Zhengyuan , Zeng Zhiqiang , Zhan Huiqing , Li Caixia , Zhou Li , Yan Cuan , Spitsbergen Jan M. , Gong Zhiyuan 
Published: October 2012

Summary
Myc is a pleiotropic transcription factor that is involved in many cellular activities relevant to carcinogenesis, including hepatocarcinogenesis. The zebrafish has been increasingly used to model human diseases and it is particularly valuable in helping to identify common and conserved molecular mechanisms in vertebrates. Here we generated a liver tumor model in transgenic zebrafish by liver-specific expression of mouse Myc using a Tet-On system. Dosage-dependent induction of Myc expression specifically in the liver was observed in our Myc transgenic zebrafish, TO(Myc), and the elevated Myc expression caused liver hyperplasia, which progressed to hepatocellular adenoma and carcinoma with prolonged induction. Next generation sequencing-based transcriptomic analyses indicated that ribosome proteins were overwhelmingly upregulated in the Myc-induced liver tumors. Cross-species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc-induced zebrafish liver tumors also possessed molecular signatures highly similar to human those of hepatocellular carcinoma. Finally, we found that a small Myc target gene set of 16 genes could be used to identify liver tumors due to Myc upregulation. Thus, our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species.
Regulation of synapse composition by protein acetylation: the role of acetylated cortactin
Authors: Catarino Tatiana , Ribeiro Luís , Santos Sandra D. , Carvalho Ana Luísa 
Published: October 2012

Summary
Protein acetylation affects synaptic plasticity and memory, but its effects on synapse composition have not been addressed. We found that protein acetylation promotes the dendritic clustering of the excitatory postsynaptic scaffold protein PSD95 in hippocampal neurons, without affecting the total levels of this protein. Cortactin, an F-actin-binding protein enriched in dendritic spines, is a substrate for acetylation and has a role in spine morphogenesis. Recent studies showed that cortactin acetylation changes its ability to bind F-actin and regulates cellular motility, but the function of cortactin acetylation in neuronal cells is so far unknown. We tested whether acetylation of cortactin influences its morphogenic function by overexpressing wild-type cortactin, or the mimetic mutants for acetylated or deacetylated cortactin, in hippocampal neurons, and found that cortactin acetylation has an impact on PSD95 clustering, independent from its function as actin dynamics regulator. Moreover, acetylated cortactin can rescue the reduction in PSD95 clustering mediated by knockdown of cortactin. We also found that acetylation of cortactin is correlated with decreased cortactin interaction with p140Cap and Shank1, and with lower cortactin phosphorylation at tyrosine 421. The neurotrophin BDNF promoted the acetylation of cortactin in hippocampal neurons, suggesting that BDNF may regulate excitatory synapses and PSD95 dendritic clustering at least in part by changing the acetylation level of cortactin. Our findings unravel an unsuspected role for cortactin acetylation in the regulation of PSD95 dendritic clustering, which may work in concert with cortactin's role in spine development.
MDC1 and RNF8 function in a pathway that directs BRCA1-dependent localization of PALB2 required for homologous recombination
Authors: Zhang Fan , Bick Gregory , Park Jung-Young , Andreassen Paul R. 
Published: October 2012

Summary
The PALB2 protein is associated with breast cancer susceptibility and Fanconi anemia. Notably, PALB2 is also required for DNA repair by homologous recombination (HR). However, the mechanisms that regulate PALB2, and the functional significance of its interaction with the BRCA1 breast cancer susceptibility protein, are poorly understood. Here, to better understand these processes, we fused PALB2, or the PALB2(L21P) mutant which cannot bind to BRCA1, with the BRCT repeats that are present in, and which localize, BRCA1. Our results yield important insights into the regulation of PALB2 function. Both fusion proteins can bypass BRCA1 to localize to sites of DNA damage. Further, the localized fusion proteins are functional, as determined by their ability to support the assembly of RAD51 foci, even in the absence of the capacity of PALB2 to bind BRCA1. Strikingly, the localized fusion proteins mediate DNA double-strand break (DSB)-initiated HR and resistance to mitomycin C in PALB2-deficient cells. Additionally, we show that the BRCA1–PALB2 heterodimer, rather than the PALB2–PALB2 homodimer, mediates these responses. Importantly, we offer the first insight into how BRCA1-dependent recruitment of PALB2 is integrated with other DNA damage signaling pathways. We find that PALB2 localization depends on the presence of MDC1, RNF8, RAP80 and Abraxas upstream of BRCA1. Thus, PALB2 may link HR to a key ubiquitin-related signaling pathway that responds to DSBs.
Involvement of the mRNA binding protein CRD-BP in the regulation of metastatic melanoma cell proliferation and invasion by hypoxia
Authors: Craig Evisabel A. , Weber Jonathan D. , Spiegelman Vladimir S. 
Published: October 2012

Summary
We have previously shown that the mRNA binding protein CRD-BP is overexpressed in human melanomas, where it promotes cell survival and resistance to chemotherapy. The present study investigates the role of hypoxia, a common characteristic of the tumor microenvironment, in the regulation of CRD-BP expression and melanoma cell responses. We found that hypoxia increases CRD-BP levels in metastatic melanoma cell lines but not in melanocytes or primary melanoma cells. Hypoxic stimulation transcriptionally regulates CRD-BP by facilitating the acetylation of histones within the CRD-BP gene and by modulating the extent of HIF1α binding to the CRD-BP promoter. Hypoxia significantly enhances the proliferative and invasive potential of metastatic melanoma cells but not that of normal or primary melanoma cells. Furthermore, inhibition of CRD-BP impairs the ability of metastatic cells to proliferate and invade in response to hypoxia. These findings identify CRD-BP as a novel effector of hypoxic responses that is relevant for the selection of metastatic cells. This work also describes a previously unknown role for CRD-BP in the regulation of melanoma cell invasion and highlights the importance of the hypoxic microenvironment in determining cell fate.