bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Abrupt Shift of Typhoon Activity in the Vicinity of Taiwan and Its Association with Western North Pacific–East Asian Climate Change
Authors: Tu Jien-Yi , Chou Chia , Chu Pao-Shin 
Published: March 2009

Abstract
Bayesian analysis is applied to detect changepoints in the time series of seasonal typhoon counts in the vicinity of Taiwan. An abrupt shift in the typhoon count series occurs in 2000. On average, 3.3 typhoons per year have been noted before 2000 (1970–99), with the rate increasing to 5.7 typhoons per year since 2000 (2000–06). This abrupt change is consistent with a northward shift of the typhoon track over the western North Pacific–East Asian region and an increase of typhoon frequency over the Taiwan–East China Sea region. The northward shift of the typhoon track tends to be associated with typhoon-enhancing environmental conditions over the western North Pacific, namely, the weakening of the western North Pacific subtropical high, the strengthening of the Asian summer monsoon trough, and the enhanced positive vorticity anomalies in the lower troposphere. Based on observational analysis and model simulations, warm sea surface temperature anomalies over the equatorial western and central Pacific appear to be a major factor contributing to a northward-shifted typhoon track.
Attribution of Projected Changes in Atmospheric Moisture Transport in the Arctic: A Self-Organizing Map Perspective
Authors: Skific Natasa , Francis Jennifer A. , Cassano John J. 
Published: March 2009

Abstract
Meridonal moisture transport into the Arctic derived from one simulation of the National Center for Atmospheric Research Community Climate System Model (CCSM3), spanning the periods of 1960–99, 2010–30, and 2070–89, is analyzed. The twenty-first-century simulation incorporates the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emission Scenarios (SRES) A2 scenario for CO2 and sulfate emissions. Modeled and observed [from the 40-yr ECMWF Re-Analysis (ERA-40)] sea level pressure (SLP) fields are classified using a neural network technique called self-organizing maps to distill a set of characteristic atmospheric circulation patterns over the region north of 60°N. Model performance is validated for the twentieth century by comparing the frequencies of occurrence of particular circulation regimes in the model to those from the ERA-40. The model successfully captures dominant SLP patterns, but differs from observations in the frequency with which certain patterns occur. The model’s twentieth-century vertical mean moisture transport profile across 70°N compares well in terms of structure but exceeds the observations by about 12% overall. By relating moisture transport to a particular circulation regime, future changes in moisture transport across 70°N are assessed and attributed to changes in frequency with which the atmosphere resides in particular SLP patterns and/or to other factors, such as changes in the meridional moisture gradient. By the late twenty-first century, the transport is projected to increase by about 21% in this model realization, with the largest contribution (32%) to the total change occurring in summer. Only about one-quarter of the annual increase is due to changes in pattern occupancy, suggesting that the majority is related to mainly thermodynamic factors. A larger poleward moisture transport likely constitutes a positive feedback on the system through related increases in latent heat release and the emission of longwave radiation to the surface.
Measurement of GCM Skill in Predicting Variables Relevant for Hydroclimatological Assessments
Authors: Johnson Fiona , Sharma Ashish 
Published: March 2009

Abstract
Simulations from general circulation models are now being used for a variety of studies and purposes. With up to 23 different GCMs now available, it is desirable to determine whether a specific variable from a particular model is representative of the ensemble mean, which is often assumed to indicate the likely state of that variable in the future. The answers are important for decision makers and researchers using selective model outputs for follow-on studies such as statistical downscaling, which currently assume all model outputs are simulated with equal reliability.
A skill score, termed the variable convergence score (VCS), has been derived that can be used to rank variables based on the coefficient of variation of the ensemble. The key benefit is the development of a simple methodology that allows for a quantitative assessment between different hydroclimatic variables.
The VCS methodology has been applied to the outputs of nine GCMs for eight different variables and two emission scenarios to provide a relative ranking of the variables averaged across Australia and over different climatic regions of the country. The methodology, however, would be applicable for any region or any variable of interest from GCMs.
It was found that the surface variables with the highest scores are pressure, temperature, and humidity. Regionally in Australia, models again show the best agreement in the surface pressure projections. The tropical and southwestern temperate zones show the overall highest variable convergence when all variables are considered. The desert zone shows relatively low model agreement, particularly in the projections of precipitation and specific humidity.
Do people with acquired brain impairment benefit from additional therapy specifically directed at the hand? A randomized controlled trial
Authors: Ross Leo F , Harvey Lisa A , Lannin Natasha A 
Published: March 2009

Objective: To determine the benefits of additional therapy specifically directed at the hand in people with acquired brain impairment. Design: An assessor-blinded randomized controlled trial. Setting: Rehabilitation hospital. Participants: A sample of 39 adults with hand impairment following stroke (90%) or traumatic brain injury (10%). The median (interquartile) time since injury was 1.6 months (0.5—3.5 months). Intervention: The experimental group (n = 20) received an additional one-hour session of task-specific motor training for the hand five times a week over a six-week period. The training was administered on a one-to-one basis. The control group (n = 19) received standard care which consisted of 10 minutes of hand therapy three times a week. Both groups continued to receive therapy directed at the shoulder and elbow. Outcome measures: Primary outcomes were the Action Research Arm and Summed Manual Muscle Tests measured at the beginning and end of the six-week period. Results: The mean (SD) Action Research Arm Test values for experimental participants improved from the beginning to the end of study from 10 points (15) to 21 points (23) and the equivalent values for the Summed Manual Muscle Test improved from 35% (33) to 49% (35). There were similar improvements in control participants. The mean between-group differences for the Action Research Arm and Summed Manual Muscle Tests were -6 points (95% confidence interval (CI), -20 to 8) and 3% (95% CI, -10 to 16), respectively. Conclusion: Hand and overall arm function of all participants improved over the six-week period, however there was not a clear benefit from providing additional hand therapy.
Plasma exchange in severe spinal attacks associated with neuromyelitis optica spectrum disorder
Authors: Bonnan M , Valentino R , Olindo S , Mehdaoui H , Smadja D , Cabre P 
Published: March 2009

Background Plasma exchange (PE) is increasingly undertaken in diseases involving humoral factors and is proven to be beneficial in acute demyelinating diseases. Spinal attacks in relapsing neuromyelitis optica (NMO) and in extensive transverse myelitis (ETM) – a truncated form of NMO with spinal involvement – are usually devastating. Objective We retrospectively studied the outcome of PE-treated versus steroid-only treated spinal attacks in relapsing NMO and ETM. Methods We included 96 severe spinal attacks in 43 Afro-Caribbean patients. PE was given as an add-on therapy in 29 attacks. Expanded disability status score (EDSS) was obtained before attack, during the acute and residual stage. We defined the ΔEDSS as the rise from basal to residual EDSS. Results The ΔEDSS was found to be lower in the PE-treated group (1.2 ± 1.6 vs 2.6 ± 2.3; P < 0.01). A low basal impairment is associated with a better outcome. Improvement was obtained in both NMO-IgG negative and positive NMO attacks. Minor adverse events manifested in seven PE sessions (24%). Conclusion PE appears to be a safe add-on therapy that may be employed early in severe spinal attacks in the NMO spectrum disorders in order to maximize improvement rate. PE efficiency is independent of NMO-IgG positivity.
Expression of Scl in mesoderm rescues hematopoiesis in the absence of Oct-4
Authors: Kong Kimi Y. , Williamson Elizabeth A. , Rogers Jason H. , Tran Tam , Hromas Robert , Dahl Richard 
Published: March 2009

AbstractIn embryonic stem cells, Oct-4 concentration is critical in determining the development of endoderm, mesoderm, and trophectoderm. Although Oct-4 expression is essential for mesoderm development, it is unclear whether it has a role in the development of specific mesodermal tissues. In this study, we have examined the importance of Oct-4 in the generation of hematopoietic cells using an inducible Oct-4 ESC line. We demonstrate that Oct-4 has a role in supporting hematopoiesis after specifying brachyury-positive mesoderm. When we suppressed Oct-4 expression before or after mesoderm specification, no hematopoietic cells are detected. However, hematopoiesis can be rescued in the absence of Oct-4 after mesoderm specification if the essential hematopoietic transcription factor stem cell leukemia is expressed. Our results suggest that, for hematopoiesis to occur, Oct-4 is required for the initial specification of mesoderm and subsequently is required for the development of hematopoietic cells from uncommitted mesoderm.
The roles of aldehyde dehydrogenases (ALDHs) in the PDH bypass of Arabidopsis
Authors: Wei Yanling , Lin Ming , Oliver David J , Schnable Patrick S 
Published: March 2009

Abstract

Background
Eukaryotic aldehyde dehydrogenases (ALDHs, EC 1.2.1), which oxidize aldehydes into carboxylic acids, have been classified into more than 20 families. In mammals, Family 2 ALDHs detoxify acetaldehyde. It has been hypothesized that plant Family 2 ALDHs oxidize acetaldehyde generated via ethanolic fermentation, producing acetate for acetyl-CoA biosynthesis via acetyl-CoA synthetase (ACS), similar to the yeast pathway termed the "pyruvate dehydrogenase (PDH) bypass". Evidence for this pathway in plants has been obtained from pollen.

Results
To test for the presence of the PDH bypass in the sporophytic tissue of plants, Arabidopsis plants homozygous for mutant alleles of all three Family 2 ALDH genes were fed with 14C-ethanol along with wild type controls. Comparisons of the incorporation rates of 14C-ethanol into fatty acids in mutants and wild type controls provided direct evidence for the presence of the PDH bypass in sporophytic tissue. Among the three Family 2 ALDHs, one of the two mitochondrial ALDHs (ALDH2B4) appears to be the primary contributor to this pathway. Surprisingly, single, double and triple ALDH mutants of Arabidopsis did not exhibit detectable phenotypes, even though a Family 2 ALDH gene is required for normal anther development in maize.

Conclusion
The PDH bypass is active in sporophytic tissue of plants. Blocking this pathway via triple ALDH mutants does not uncover obvious visible phenotypes.
Detection of genomic deletions in rice using oligonucleotide microarrays
Authors: Bruce Myron , Hess Ann , Bai Jianfa , Mauleon Ramil , Diaz M Genaleen , Sugiyama Nobuko , Bordeos Alicia , Wang Guo-Liang , Leung Hei , Leach Jan E 
Published: March 2009

Abstract

Background
The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.

Results
We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/.

Conclusion
We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.
Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae
Authors: Jo William J , Kim Jeung Hyoun , Oh Eric , Jaramillo Daniel , Holman Patricia , Loguinov Alex V , Arkin Adam P , Nislow Corey , Giaever Guri , Vulpe Chris D 
Published: March 2009

Abstract

Background
Iron-deficiency anemia is the most prevalent form of anemia world-wide. The yeast Saccharomyces cerevisiae has been used as a model of cellular iron deficiency, in part because many of its cellular pathways are conserved. To better understand how cells respond to changes in iron availability, we profiled the yeast genome with a parallel analysis of homozygous deletion mutants to identify essential components and cellular processes required for optimal growth under iron-limited conditions. To complement this analysis, we compared those genes identified as important for fitness to those that were differentially-expressed in the same conditions. The resulting analysis provides a global perspective on the cellular processes involved in iron metabolism.

Results
Using functional profiling, we identified several genes known to be involved in high affinity iron uptake, in addition to novel genes that may play a role in iron metabolism. Our results provide support for the primary involvement in iron homeostasis of vacuolar and endosomal compartments, as well as vesicular transport to and from these compartments. We also observed an unexpected importance of the peroxisome for growth in iron-limited media. Although these components were essential for growth in low-iron conditions, most of them were not differentially-expressed. Genes with altered expression in iron deficiency were mainly associated with iron uptake and transport mechanisms, with little overlap with those that were functionally required. To better understand this relationship, we used expression-profiling of selected mutants that exhibited slow growth in iron-deficient conditions, and as a result, obtained additional insight into the roles of CTI6, DAP1, MRS4 and YHR045W in iron metabolism.

Conclusion
Comparison between functional and gene expression data in iron deficiency highlighted the complementary utility of these two approaches to identify important functional components. This should be taken into consideration when designing and analyzing data from these type of studies. We used this and other published data to develop a molecular interaction network of iron metabolism in yeast.
Staged stromal extracellular 3D matrices differentially regulate breast cancer cell responses through PI3K and beta1-integrins
Authors: Castelló-Cros Remedios , Khan David R , Simons Jeffrey , Valianou Matthildi , Cukierman Edna 
Published: March 2009

Abstract

Background
Interactions between cancer cells and stroma are critical for growth and invasiveness of epithelial tumors. The biochemical mechanisms behind tumor-stromal interactions leading to increased invasiveness and metastasis are mostly unknown. The goal of this study was to analyze the direct effects of staged stroma-derived extracellular matrices on breast cancer cell behavior.

Methods
Early and late three-dimensional matrices were produced by NIH-3T3 and tumor-associated murine fibroblasts, respectively. After removing fibroblasts, extracted matrices were re-cultured with breast epithelial cells of assorted characteristics: MCF-10A (non-tumorigenic), MCF-7 (tumorigenic, non-invasive), and MDA-MB-231 (tumorigenic, invasive). Effects prompted by staged matrices on epithelial cell's growth, morphology and invasion were determined. Also, matrix-induced velocity, directionality and relative track orientation of invasive cells were assessed in the presence or absence of inhibitors of phosphoinositide-3 kinase (PI3K) and/or beta-1 integrin.

Results
We observed that assorted breast epithelial cells reacted differently to two-dimensional vs. staged, control (early) and tumor-associated (late), three-dimensional matrices. MCF-10A had a proliferative advantage on two-dimensional substrates while MCF-7 and MDA-MB-231 showed no difference. MCF-10A and MCF-7 formed morphologically distinguishable aggregates within three-dimensional matrices, while MDA-MB-231 exhibited increased spindle-shape morphologies and directional movements within three-dimensional matrices. Furthermore, MDA-MB-231 acquired a pattern of parallel oriented organization within tumor-associated, but not control matrices. Moreover, tumor-associated matrices induced PI3K and beta1-integrin dependent Akt/PKB activity in MDA-MB-231 cells. Interestingly, beta1-integrin (but not PI3K) regulated tumor-associated matrix-induced mesenchymal invasion which, when inhibited, resulted in a change of invasive strategy rather than impeding invasion altogether.

Conclusion
We propose that both cells and matrices are important to promote effective breast cancer cell invasion through three-dimensional matrices and that beta1-integrin inhibition is not necessarily sufficient to block tumor-matrix induced breast cancer cell invasion. Additionally, we believe that characterizing stroma staging (e.g., early vs. late or tumor-associated) might be beneficial for predicting matrix-induced cancer cell responses in order to facilitate the selection of therapies.
The incidence of co-morbidities related to obesity and overweight: A systematic review and meta-analysis
Authors: Guh Daphne P , Zhang Wei , Bansback Nick , Amarsi Zubin , Birmingham C Laird , Anis Aslam H 
Published: March 2009

AbstractBackgroundOverweight and obese persons are at risk of a number of medical conditions which can lead to further morbidity and mortality. The primary objective of this study is to provide an estimate of the incidence of each co-morbidity related to obesity and overweight using a meta-analysis.MethodsA literature search for the twenty co-morbidities identified in a preliminary search was conducted in Medline and Embase (Jan 2007). Studies meeting the inclusion criteria (prospective cohort studies of sufficient size reporting risk estimate based on the incidence of disease) were extracted. Study-specific unadjusted relative risks (RRs) on the log scale comparing overweight with normal and obese with normal were weighted by the inverse of their corresponding variances to obtain a pooled RR with 95% confidence intervals (CI).ResultsA total of 89 relevant studies were identified. The review found evidence for 18 co-morbidities which met the inclusion criteria. The meta-analysis determined statistically significant associations for overweight with the incidence of type II diabetes, all cancers except esophageal (female), pancreatic and prostate cancer, all cardiovascular diseases (except congestive heart failure), asthma, gallbladder disease, osteoarthritis and chronic back pain. We noted the strongest association between overweight defined by body mass index (BMI) and the incidence of type II diabetes in females (RR = 3.92 (95% CI: 3.10–4.97)). Statistically significant associations with obesity were found with the incidence of type II diabetes, all cancers except esophageal and prostate cancer, all cardiovascular diseases, asthma, gallbladder disease, osteoarthritis and chronic back pain. Obesity defined by BMI was also most strongly associated with the incidence of type II diabetes in females (12.41 (9.03–17.06)).ConclusionBoth overweight and obesity are associated with the incidence of multiple co-morbidities including type II diabetes, cancer and cardiovascular diseases. Maintenance of a healthy weight could be important in the prevention of the large disease burden in the future. Further studies are needed to explore the biological mechanisms that link overweight and obesity with these co-morbidities.