bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiscale Interactions in the Life Cycle of a Tropical Cyclone Simulated in a Global Cloud-System-Resolving Model. Part I: Large-Scale and Storm-Scale Evolutions*
Authors: Fudeyasu Hironori , Wang Yuqing , Satoh Masaki , Nasuno Tomoe , Miura Hiroaki , Yanase Wataru 
Published: August 2010

Abstract
The Nonhydrostatic Icosahedral Atmospheric Model (NICAM), a global cloud-system-resolving model, successfully simulated the life cycle of Tropical Storm Isobel that formed over the Timor Sea in the austral summer of 2006. The multiscale interactions in the life cycle of the simulated storm were analyzed in this study. The large-scale aspects that affected Isobel’s life cycle are documented in this paper and the corresponding mesoscale processes are documented in a companion paper.
The life cycle of Isobel was largely controlled by a Madden–Julian oscillation (MJO) event and the associated westerly wind burst (WWB). The MJO was found to have both positive and negative effects on the tropical cyclone intensity depending on the location of the storm relative to the WWB center associated with the MJO. The large-scale low-level convergence and high convective available potential energy (CAPE) downwind of the WWB center provided a favorable region to the cyclogenesis and intensification, whereas the strong large-scale stretching deformation field upwind of the WWB center may weaken the storm by exciting wavenumber-2 asymmetries in the eyewall and leading to the eyewall breakdown.
Five stages are identified for the life cycle of the simulated Isobel: the initial eddy, intensifying, temporary weakening, reintensifying, and decaying stages. The initial eddy stage was featured by small-scale/mesoscale convective cyclonic vortices developed in the zonally elongated rainband organized in the preconditioned environment characterized by the WWB over the Java Sea associated with the onset of an MJO event over the East Indian Ocean. As the MJO propagated eastward and the cyclonic eddies moved southward into an environment with weak vertical shear and strong low-level cyclonic vorticity, a typical tropical cyclone structure developed over the Java Sea, namely the genesis of Isobel. Isobel experienced an eyewall breakdown and a temporary weakening when it was located upwind of the WWB center as the MJO propagated southeastward and reintensified as its eyewall reformed as a result of the axisymmetrization of an inward spiraling outer rainband that originally formed downwind of the WWB center. Finally Isobel decayed as it approached the northwest coast of Australia.
Seasonal Prediction of Tropical Cyclone Activity Near Taiwan Using the Bayesian Multivariate Regression Method
Authors: Lu Mong-Ming , Chu Pao-Shin , Lin Yun-Ching 
Published: August 2010

AbstractA Poisson generalized linear regression model cast within a Bayesian framework is applied to forecast the seasonal tropical cyclone (TC) counts in the vicinity of Taiwan. The TC season considered is June–November and the data period used for model development is 1979–2007. A stepwise regression procedure is applied for predictor selection. Three large-scale climate variables, namely, relative vorticity at 850 hPa (Vor850), vertical wind shear, and sea level pressure over the western and central North Pacific from the antecedent May, are selected as predictors. Leave-one-out cross validation is performed and forecast skill is thoroughly evaluated. The skill level of the Bayesian regression model is better than what can be achieved by climatology and persistence methods. Most importantly, the Bayesian probabilistic inference can provide an uncertainty expression in the parameter estimation. Among the three predictors, Vor850 is found to be the most important because it reflects the variation of the ridge position of the westward extension of the western Pacific subtropical high. The model shows negative bias during the years with successive TCs, which are generated by easterly waves before approaching Taiwan. Recommendations for real-time operational forecast and future development are discussed.
Latin America: Underdevelopment and Surpluses of Population
Authors: Figueroa Sepúlveda Victor M. 
Published: August 2010

The present work discusses the origin and forms of manifestation of the surplus population in Latina America. It is argued that (a) the relations between developed and underdeveloped countries rest on an asymmetric production integration, which, in turn, results from the different production relations in both categories of countries; and (b) this integration determines a structurally unequal exchange as well as an unequal distribution of the energy to create a surplus population, concentrating it in underdeveloped countries, and (c) consequently, Latin America produces both a relative and an absolute surplus population. The surplus population’s meaning vis-a-vis the process of accumulation, of which it is a result, is spread heterogeneously throughout its ranks. In the discussion of this population’s position with respect to capital and its manifestation forms, special attention is paid to pirate capital and home-based domestic labor.
Th17 immune responses contribute to the pathophysiology of aplastic anemia
Authors: de Latour Regis Peffault , Visconte Valeria , Takaku Tomoiku , Wu Colin , Erie Andrew J. , Sarcon Annahita K. , Desierto Marie J. , Scheinberg Phillip , Keyvanfar Keyvan , Nunez Olga , Chen Jichun , Young Neal S. 
Published: August 2010

AbstractT helper type 17 (Th17) cells have been characterized based on production of interleukin-17 (IL-17) and association with autoimmune diseases. We studied the role of Th17 cells in aplastic anemia (AA) by isolating Th17 cells from patients blood (n = 41) and bone marrow (BM) mononuclear cells (n = 7). The frequency and total number of CD3+CD4+IL-17–producing T cells were increased in AA patients at presentation compared with healthy controls (P = .0007 and .02, respectively) and correlated with disease activity. There was an inverse relationship between the numbers of Th17 cells and CD4+CD25highFoxP3+ regulatory T cells (Tregs) in the blood of AA patients. Concomitant with the classical Th1 response, we detected the presence of CD4+ and CD8+ IL-17-producing T cells in a mouse model of lymph node infusion–induced BM failure. Although anti–IL-17 treatment did not abrogate BM failure, early treatment with the anti–IL-17 antibody reduced the severity of BM failure with significantly higher platelet (P < .01) and total BM cell (P < .05) counts at day 10. Recipients that received anti-IL-17 treatment had significantly fewer Th1 cells (P < .01) and more Treg cells (P < .05) at day 10 after lymph node infusion. Th17 immune responses contribute to AA pathophysiology, especially at the early stage during disease progression.
Persistent expression of the full genome of hepatitis C virus in B cells induces spontaneous development of B-cell lymphomas in vivo
Authors: Kasama Yuri , Sekiguchi Satoshi , Saito Makoto , Tanaka Kousuke , Satoh Masaaki , Kuwahara Kazuhiko , Sakaguchi Nobuo , Takeya Motohiro , Hiasa Yoichi , Kohara Michinori , Tsukiyama-Kohara Kyoko 
Published: August 2010

AbstractExtrahepatic manifestations of hepatitis C virus (HCV) infection occur in 40%-70% of HCV-infected patients. B-cell non-Hodgkin lymphoma is a typical extrahepatic manifestation frequently associated with HCV infection. The mechanism by which HCV infection of B cells leads to lymphoma remains unclear. Here we established HCV transgenic mice that express the full HCV genome in B cells (RzCD19Cre mice) and observed a 25.0% incidence of diffuse large B-cell non-Hodgkin lymphomas (22.2% in males and 29.6% in females) within 600 days after birth. Expression levels of aspartate aminotransferase and alanine aminotransferase, as well as 32 different cytokines, chemokines and growth factors, were examined. The incidence of B-cell lymphoma was significantly correlated with only the level of soluble interleukin-2 receptor α subunit (sIL-2Rα) in RzCD19Cre mouse serum. All RzCD19Cre mice with substantially elevated serum sIL-2Rα levels (> 1000 pg/mL) developed B-cell lymphomas. Moreover, compared with tissues from control animals, the B-cell lymphoma tissues of RzCD19Cre mice expressed significantly higher levels of IL-2Rα. We show that the expression of HCV in B cells promotes non-Hodgkin–type diffuse B-cell lymphoma, and therefore, the RzCD19Cre mouse is a powerful model to study the mechanisms related to the development of HCV-associated B-cell lymphoma.
A haplotype inference algorithm for trios based on deterministic sampling
Authors: Iliadis Alexandros , Watkinson John , Anastassiou Dimitris , Wang Xiaodong 
Published: August 2010

Abstract

Background
In genome-wide association studies, thousands of individuals are genotyped in hundreds of thousands of single nucleotide polymorphisms (SNPs). Statistical power can be increased when haplotypes, rather than three-valued genotypes, are used in analysis, so the problem of haplotype phase inference (phasing) is particularly relevant. Several phasing algorithms have been developed for data from unrelated individuals, based on different models, some of which have been extended to father-mother-child "trio" data.

Results
We introduce a technique for phasing trio datasets using a tree-based deterministic sampling scheme. We have compared our method with publicly available algorithms PHASE v2.1, BEAGLE v3.0.2 and 2SNP v1.7 on datasets of varying number of markers and trios. We have found that the computational complexity of PHASE makes it prohibitive for routine use; on the other hand 2SNP, though the fastest method for small datasets, was significantly inaccurate. We have shown that our method outperforms BEAGLE in terms of speed and accuracy for small to intermediate dataset sizes in terms of number of trios for all marker sizes examined. Our method is implemented in the "Tree-Based Deterministic Sampling" (TDS) package, available for download at http://www.ee.columbia.edu/~anastas/tds

Conclusions
Using a Tree-Based Deterministic sampling technique, we present an intuitive and conceptually simple phasing algorithm for trio data. The trade off between speed and accuracy achieved by our algorithm makes it a strong candidate for routine use on trio datasets.
Identification and characterization of potential NBS-encoding resistance genes and induction kinetics of a putative candidate gene associated with downy mildew resistance in Cucumis
Authors: Wan Hongjian , Zhao Zhenguo , Malik Ahmed Abbas , Qian Chuntao , Chen Jinfeng 
Published: August 2010

Abstract

Background
Due to the variation and mutation of the races of Pseudoperonospora cubensis, downy mildew has in recent years become the most devastating leaf disease of cucumber worldwide. Novel resistance to downy mildew has been identified in the wild Cucumis species, C. hystrix Chakr. After the successful hybridization between C. hystrix and cultivated cucumber (C. sativus L.), an introgression line (IL5211S) was identified as highly resistant to downy mildew. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes are the largest class of disease resistance genes cloned from plant with highly conserved domains, which can be used to facilitate the isolation of candidate genes associated with downy mildew resistance in IL5211S.

Results
Degenerate primers that were designed based on the conserved motifs in the NBS domain of resistance (R) proteins were used to isolate NBS-type sequences from IL5211S. A total of 28 sequences were identified and named as cucumber (C. sativus = CS) resistance gene analogs as CSRGAs. Polygenetic analyses separated these sequences into four different classes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that these CSRGAs expressed at different levels in leaves, roots, and stems. In addition, introgression from C. hystrix induced expression of the partial CSRGAs in cultivated cucumber, especially CSRGA23, increased four-fold when compared to the backcross parent CC3. Furthermore, the expression of CSRGA23 under P. cubensis infection and abiotic stresses was also analyzed at different time points. Results showed that the P. cubensis treatment and four tested abiotic stimuli, MeJA, SA, ABA, and H2O2, triggered a significant induction of CSRGA23 within 72 h of inoculation. The results indicate that CSRGA23 may play a critical role in protecting cucumber against P. cubensis through a signaling the pathway triggered by these molecules.

Conclusions
Four classes of NBS-type RGAs were successfully isolated from IL5211S, and the possible involvement of CSRGA23 in the active defense response to P. cubensis was demonstrated. These results will contribute to develop analog-based markers related to downy mildew resistance gene and elucidate the molecular mechanisms causing resistance in IL5211S in the future.
Modulation of flavonoid biosynthetic pathway genes and anthocyanins due to virus infection in grapevine (Vitis viniferaL.) leaves
Authors: Gutha Linga R , Casassa Luis F , Harbertson James F , Naidu Rayapati A 
Published: August 2010

AbstractBackgroundSymptoms of grapevine leafroll disease (GLRD) in red-fruited wine grape (Vitis viniferaL.) cultivars consist of green veins and red and reddish-purple discoloration of inter-veinal areas of leaves. The reddish-purple color of symptomatic leaves may be due to the accumulation of anthocyanins and could reflect an up-regulation of genes involved in their biosynthesis.ResultsWe examined six putative constitutively expressed genes,Ubiquitin, Actin,GAPDH,EF1-a, SANDandNAD5, for their potential as references for normalization of gene expression in reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). Using thegeNormprogram, a combination of two genes (ActinandNAD5) was identified as the stable set of reference genes for normalization of gene expression data obtained from grapevine leaves. By using gene-specific RT-qPCR in combination with a reliable normalization factor, we compared relative expression of the flavonoid biosynthetic pathway genes between leaves infected withGrapevine leafroll-associated virus 3(GLRaV-3) and exhibiting GLRD symptoms and virus-free green leaves obtained from a red-fruited wine grape cultivar (cv. Merlot). The expression levels of these different genes ranged from two- to fifty-fold increase in virus-infected leaves. Among them,CHS3,F3'5'H,F3H1,LDOX,LAR1andMybA1showed greater than 10-fold increase suggesting that they were expressed at significantly higher levels in virus-infected symptomatic leaves. HPLC profiling of anthocyanins extracted from leaves indicated the presence of cyanidin-3-glucoside and malvidin-3-glucoside only in virus-infected symptomatic leaves. The results also showed 24% higher levels of flavonols in virus-infected symptomatic leaves than in virus-free green leaves, with quercetin followed by myricetin being the predominant compounds. Proanthocyanidins, estimated as total tannins by protein precipitation method, were 36% higher in virus-infected symptomatic leaves when compared to virus-free green leaves.ConclusionsThe results, the first example to our knowledge, showed that modulation of the flavonoid biosynthetic pathway occurred in GLRaV-3-infected leaves of a red-fruited wine grape cultivar (cv. Merlot) leading tode novosynthesis of two classes of anthocyanins. These anthocyanins have contributed to the expression of reddish-purple color of virus-infected grapevine leaves exhibiting GLRD symptoms.
Acetic acid-indigo carmine chromoendoscopy for delineating early gastric cancers: its usefulness according to histological type
Authors: Lee Bong Eun , Kim Gwang Ha , Park Do Youn , Kim Dae Hwan , Jeon Tae Yong , Park Su Bum , You Hyun Seok , Ryu Dong Yup , Kim Dong Uk , Song Geun Am 
Published: August 2010

Abstract

Background
Endoscopic treatments, such as endoscopic submucosal dissection (ESD) and laparoscopic gastrectomy, are increasingly used to treat a subset of patients with early gastric cancer (EGC). To achieve successful outcomes, it is very important to accurately determine the lateral extent of the tumor. Therefore, we investigated the diagnostic performance of chromoendoscopy using indigo carmine dye added to acetic acid (AI chromoendoscopy) in delineating differentiated or undifferentiated adenocarcinomas in patients with EGC.

Methods
We prospectively included 151 lesions of 141 patients that had an endoscopic diagnosis of EGC. All the lesions were examined by conventional endoscopy and AI chromoendoscopy before ESD or laparoscopic gastrectomy. The border clarification between the lesion and the normal mucosa was classified as distinct or indistinct before and after AI chromoendoscopy.

Results
The borders of the lesions were distinct in 66.9% (101/151) with conventional endoscopy and in 84.1% (127/151) with AI chromoendoscopy (P < 0.001). Compared with conventional endoscopy, AI chromoendoscopy clarified the border in a significantly higher percentage of differentiated adenocarcinomas (74/108 [68.5%] vs 97/108 [89.8%], respectively, P < 0.001). However, the border clarification rate for undifferentiated adenocarcinomas did not differ between conventional endoscopy and AI chromoendoscopy (27/43 [62.8%] vs 30/43 [70.0%], respectively, P = 0.494).

Conclusions
AI chromoendoscopy is useful in determining the lateral extent of EGCs. However, its usefulness is reduced in undifferentiated adenocarcinomas.
Gender differences in age-related decline in glomerular filtration rates in healthy people and chronic kidney disease patients
Authors: Xu Rong , Zhang Lu-Xia , Zhang Pu-Hong , Wang Fang , Zuo Li , Wang Hai-Yan 
Published: August 2010

Abstract

Background
Since men with chronic kidney disease (CKD) progress faster than women, an accurate assessment of CKD progression rates should be based on gender differences in age-related decline of glomerular filtration rate (GFR) in healthy individuals.

Methods
A Chinese sample population from a stratified, multistage, and clustered CKD screening study was classified into healthy, at-risk, and CKD groups. The gender differences in estimated GFR (eGFR) and age-related eGFR decline were calculated for each group after controlling for blood pressure, fasting glucose levels, serum lipids levels, education level, and smoking status. After referencing to the healthy group, gender-specific multivariate-adjusted rates of decline in eGFR and differences in the rates of decline were calculated for both CKD and at-risk groups.

Results
The healthy, at-risk, and CKD groups consisted of 4569, 7434, and 1573 people, respectively. In all the 3 groups, the multivariate-adjusted eGFRs in men were lower than the corresponding eGFRs in women. In addition, in the healthy and at-risk groups, the rates of decline in eGFR in men were lower than the corresponding rates of decline in women (healthy group: 0.51 mL·min-1·1.73 m-2·yr-1
vs. 0.74 mL·min-1·1.73 m-2·yr-1 and at-risk group: 0.60 mL·min-1·1.73 m-2·yr-1
vs. 0.73 mL·min-1·1.73 m-2·yr-1). However, in the CKD group, the rates of decline in eGFR in men were similar to those in women (0.96 mL·min-1·1.73 m-2·yr-1
vs. 0.91 mL·min-1·1.73 m-2·yr-1). However, after referencing to the healthy group, the rates of decline in eGFR in men in the at-risk and CKD groups were greater faster than the corresponding rates in women (at-risk group: 0.10 mL·min-1·1.73 m-2·yr-1
vs. -0.03 mL·min-1·1.73 m-2·yr-1 and CKD group: 0.44 mL·min-1·1.73 m-2·yr-1
vs. 0.15 mL·min-1·1.73 m-2·yr-1).

Conclusion
To accurately assess gender differences in CKD progression rates, gender differences in age-related decline in GFR should be considered.
An investigation of breast cancer risk factors in Cyprus: a case control study
Authors: Hadjisavvas Andreas , Loizidou Maria A , Middleton Nicos , Michael Thalia , Papachristoforou Rena , Kakouri Eleni , Daniel Maria , Papadopoulos Panayiotis , Malas Simon , Marcou Yiola , Kyriacou Kyriacos 
Published: August 2010

Abstract

Background
Breast cancer is the most common form of malignancy affecting women worldwide. It is also the leading cancer in females in Cyprus, with approximately 400 new cases diagnosed annually. It is well recognized that genetic variation as well as environmental factors modulate breast cancer risk. The main aim of this study was to assess the strength of associations between recognized risk factors and breast cancer among Cypriot women. This is the first epidemiological investigation on risk factors of breast cancer among the Cypriot female population.

Methods
We carried out a case-control study, involving 1,109 breast cancer patients and a group of 1,177 controls who were recruited while participating in the National screening programme for breast cancer. Information on demographic characteristics and potential risk factors were collected from both groups during a standardized interview. Logistic regression analysis was used to assess the strength of the association between each risk factor and breast cancer risk, before and after adjusting for the possible confounding effect of other factors.

Results
In multivariable models, family history of breast cancer (OR 1.64, 95% CI 1.23, 2.19) was the strongest predictor of breast cancer risk in the Cypriot population. Late menarche (OR 0.64, 95% CI 0.45, 0.92 among women reaching menarche after the age of 15 vs. before the age of 12) and breastfeeding (OR 0.74, 95% CI 0.59, 0.92) exhibited a strong protective effect. In the case of breastfeeding, the observed effect appeared stronger than the effect of pregnancy alone. Surprisingly, we also observed an inverse association between hormone replacement therapy (HRT) although this may be a product of the retrospective nature of this study.

Conclusion
Overall the findings of our study corroborate with the results of previous investigations on descriptive epidemiology of risk factors for breast cancer. This investigation provides important background information for designing detailed studies that aim to improve our understanding of the epidemiology of breast cancer in the Cypriot population, including the study of gene-environment interactions. Furthermore, our study provides the first scientific evidence for formulating targeted campaigns for prevention and early diagnosis of breast cancer in Cyprus.
Phenotyping breast cancer cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis and affinity chromatography for glutathione-binding proteins
Authors: Mladkova Jana , Sanda Miloslav , Matouskova Eva , Selicharova Irena 
Published: August 2010

Abstract

Background
Transformed phenotypes are common to cell lines derived from various cancers. Proteome profiling is a valuable tool that may reveal uncharacteristic cell phenotypes in transformed cells. Changes in expression of glutathione S-transferases (GSTs) and other proteins interacting with glutathione (GSH) in model cell lines could be of particular interest.

Methods
We compared the phenotypes of breast cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis (2-DE). We further separated GSH-binding proteins from the cell lines using affinity chromatography with GSH-Sepharose 4B, performed 2-DE analysis and identified the main protein spots.

Results
Correlation coefficients among 2-DE gels from the cell lines were lower than 0.65, pointing to dissimilarity among the cell lines. Differences in primary constituents of the cytoskeleton were shown by the 2-D protein maps and western blots. The spot patterns in gels of GSH-binding fractions from primary carcinoma-derived cell lines HCC1937 and EM-G3 were similar to each other, and they differed from the spot patterns of cell lines MCF7 and MDA-MB-231 that were derived from pleural effusions of metastatic mammary carcinoma patients. Major differences in the expression of GST P1-1 and carbonyl reductase [NADPH] 1 were observed among the cell lines, indicating differential abilities of the cell lines to metabolize xenobiotics.

Conclusions
Our results confirmed the applicability of targeted affinity chromatography to proteome profiling and allowed us to characterize the phenotypes of four breast cancer cell lines.