bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Social Science of Democracy?
Authors: Welch Cheryl 
Published: June 2011

Alexis de Tocqueville, the First Social Scientist. By Jon Elster. New York: Cambridge University Press, 2009. 212p. $80.00 cloth, $22.99 paper.Alexis de Tocqueville is surely one of the most widely cited, discussed, and celebrated political theorists in the world. Jon Elster's book, Alexis de Tocqueville: the First Social Scientist proceeds from a provocative premise: that Tocqueville's major works were lacking in “system” and were “hugely incoherent,” and that Tocqeuville himself “was not a major political thinker” (xi). Elster argues that instead Tocqueville ought to be viewed as a penetrating historical sociologist and an exemplary social scientist who might well be considered the first true social scientist. Elster's argument is important for at least two reasons: first, because it offers a striking and challenging reading of Tocqueville; and second, because it expands on Elster's own contributions in the philosophy of social science, and develops interesting understandings of “causal mechanisms,” methodological individualism, and social explanation more generally. As Elster writes in his Introduction, “the main task of this book is to argue for the relevance of Tocqueville for social science in the twenty-first century (p. 5).” The purpose of this Perspectives symposium is to assess Elster's argument in broad terms. What are the strengths and limits of Elster's reading of Tocqueville? How ought we to assess Elster's understanding of Tocqueville's deficiencies as a “political theorist?” What is the relevance of Tocqueville for contemporary social science? And, most importantly, what are the challenges and possible trajectories facing social science in the twenty-first century, and to what extent does Elster's essay point us in the right direction?—Jeffrey C. Isaac, Editor
Comparative studies of de novo assembly tools for next-generation sequencing technologies
Authors: Lin Yong , Li Jian , Shen Hui , Zhang Lei , Papasian Christopher J. , Deng Hong−Wen 
Published: June 2011

Abstract
Motivation: Several new de novo assembly tools have been developed recently to assemble short sequencing reads generated by next-generation sequencing platforms. However, the performance of these tools under various conditions has not been fully investigated, and sufficient information is not currently available for informed decisions to be made regarding the tool that would be most likely to produce the best performance under a specific set of conditions.
Results: We studied and compared the performance of commonly used de novo assembly tools specifically designed for next-generation sequencing data, including SSAKE, VCAKE, Euler-sr, Edena, Velvet, ABySS and SOAPdenovo. Tools were compared using several performance criteria, including N50 length, sequence coverage and assembly accuracy. Various properties of read data, including single-end/paired-end, sequence GC content, depth of coverage and base calling error rates, were investigated for their effects on the performance of different assembly tools. We also compared the computation time and memory usage of these seven tools. Based on the results of our comparison, the relative performance of individual tools are summarized and tentative guidelines for optimal selection of different assembly tools, under different conditions, are provided.
Contact: hdeng2@tulane.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Robust biclustering by sparse singular value decomposition incorporating stability selection
Authors: Sill Martin , Kaiser Sebastian , Benner Axel , Kopp-Schneider Annette 
Published: June 2011

Abstract
Motivation: Over the past decade, several biclustering approaches have been published in the field of gene expression data analysis. Despite of huge diversity regarding the mathematical concepts of the different biclustering methods, many of them can be related to the singular value decomposition (SVD). Recently, a sparse SVD approach (SSVD) has been proposed to reveal biclusters in gene expression data. In this article, we propose to incorporate stability selection to improve this method. Stability selection is a subsampling-based variable selection that allows to control Type I error rates. The here proposed S4VD algorithm incorporates this subsampling approach to find stable biclusters, and to estimate the selection probabilities of genes and samples to belong to the biclusters.
Results: So far, the S4VD method is the first biclustering approach that takes the cluster stability regarding perturbations of the data into account. Application of the S4VD algorithm to a lung cancer microarray dataset revealed biclusters that correspond to coregulated genes associated with cancer subtypes. Marker genes for different lung cancer subtypes showed high selection probabilities to belong to the corresponding biclusters. Moreover, the genes associated with the biclusters belong to significantly enriched cancer-related Gene Ontology categories. In a simulation study, the S4VD algorithm outperformed the SSVD algorithm and two other SVD-related biclustering methods in recovering artificial biclusters and in being robust to noisy data.
Availability: R-Code of the S4VD algorithm as well as a documentation can be found at http://s4vd.r-forge.r-project.org/.
Contact: m.sill@dkfz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Chrysanthemum chlorotic mottle viroid in Chrysanthemum in China
Authors: Zhang Z. Z. , Pan S. , Li S. F. 
Published: June 2011

During the spring of 2008, a chrysanthemum plant showing mild mottle on young leaves was observed in a garden in Beijing, China. After the plant was moved into a greenhouse, symptoms became severe with obvious yellowing and complete chlorosis on new leaves. In addition, when a survey was conducted for chrysanthemum diseases in 2010, plants with mild chlorotic spots on leaves were also found occasionally in a commercial field in Hainan, China. These symptoms resembled symptoms induced by Chrysanthemum chlorotic mottle viroid (CChMVd). Therefore, total RNA of 13 samples collected from Beijing (cultivar unknown) and Hainan (cv. Golden) was extracted according to Li et al. (2) and tested for CChMVd by northern blot hybridization using DIG-labeled CChMVd cRNA probe (1). All samples were CChMVd positive, and the healthy control was negative. The viroid was further confirmed by reverse transcription (RT)-PCR using CChMVd specific primers (forward: 5′-AGGTCGTA(T)AAACTTCCCCTCTAAA(G)CG-3′, homologous to nucleotides 134 to 159; and reverse: 5′-TCCAGTCGAGACCTGAAGTGGGTTTC-3′, complementary to nucleotides 133 to 108) (1). Two amplified products of approximately 400 bp were cloned into the pGEM-T vector (Promega, Madison, WI) and transformed into E. coli DH5α competent cells. Two positive clones were obtained from each isolate and sequenced. Four sequences obtained have been submitted to GenBank (Accession Nos. HQ891014 to HQ891017). Sequence analysis revealed that the obtained sequences shared 96.49 to 96.99% similarity with the reference sequence CChMVd (GenBank Accession No. NC003540). All the clones are 399 nucleotides long and are thought to be the symptomatic type based on their UUUC sequence at positions 82 to 85 in the CChMVd tetraloop (1). In addition, both isolates were mechanically inoculated to three healthy chrysanthemum plants of the unknown cultivar from Beijing. All inoculated plants developed chlorosis after 5 weeks and CChMVd infections were confirmed by northern blot hybridization and RT-PCR. CChMVd is an important pathogen that may potentially cause losses to the chrysanthemum industry. It is necessary to survey for CChMVd infection in various chrysanthemums cultivated in China. To our knowledge, this is the first report of CChMVd in chrysanthemum in China. References: (1) P. M. De la Pena et al. Proc. Natl. Acad. Sci. USA. 96:9960, 1999. (2) S. F. Li et al. Ann. Phytopathol. Soc. Jpn. 61:381, 1995.
Susceptibility of Onion Relatives (Allium spp.) to Iris yellow spot virus
Authors: Cramer C. S. , Bag S. , Schwartz H. F. , Pappu H. R. 
Published: June 2011

Iris yellow spot virus (IYSV; family Bunyaviridae, genus Tospovirus) is becoming an increasingly important constraint to the production of bulb and seed onions (Allium cepa L.) in many onion-growing regions of the continental United States and the world (4). During an evaluation of onion germplasm for susceptibility to IYSV, six other Allium species (A. altaicum, A. galanthum, A. roylei, A. schoenoprasum, A. tuberosum, and A. vavilovii) were also evaluated under natural field conditions. In July 2010, symptoms suggestive of IYSV infection (straw-colored necrotic lesions) were observed on leaves of these Allium spp. in experimental plots in Las Cruces, NM. IYSV was detected in symptomatic leaves of A. altaicum, A. vavilovii, A. tuberosum, A. schoenoprasum and A. roylei with a commercially available ELISA kit (Agdia Inc., Elkhart, IN). IYSV infection was confirmed by reverse transcription (RT)-PCR with forward and complementary primers 5′-CTCTTAAACACATTTAACAAGCAC-3′ and 5′-TAAAACAAACATTCAAACAA-3′ flanking the nucleocapsid (N) gene encoded by the small RNA of IYSV as previously described (1,3). Amplicons, approximately 1.1 kb long, were obtained from all symptomatic Allium spp. samples but not from healthy samples or water controls. Sequencing of selected amplicons confirmed IYSV infection. The highest nucleotide identity of 98% was shared with IYSV isolates from Japan (GenBank Accession No. AB180921). A. altaicum, A. vavilovii, and A. pskemense were previously reported from Washington to be susceptible to IYSV (2). Current findings expand the list of Allium spp. that are susceptible to IYSV and underscores the need for continued screening of other members of the genus to find sources of resistance to IYSV. References: (1) H. R. Pappu et al. Arch. Virol. 151:1015, 2006. (2) H. R. Pappu et al. Plant Dis. 90:378, 2006. (3) H. R. Pappu et al. Plant Dis. 92:588, 2008. (4) H. R. Pappu et al. Virus Res. 141:219, 2009.
Efficacy of an MFGM‐enriched Complementary Food in Diarrhea, Anemia, and Micronutrient Status in Infants
Authors: Zavaleta Nelly , Kvistgaard Anne Staudt , Graverholt Gitte , Respicio Graciela , Guija Henry , Valencia Norma , Lönnerdal Bo 
Published: June 2011

ABSTRACTObjective:The aim of the present study was to evaluate the efficacy of a milkfat globule membrane (MFGM)–enriched protein fraction in a complementary food, on diarrhea, anemia, and micronutrient status.Subjects and Methods:A randomized, double‐blind controlled design to study 550 infants, 6 to 11 months old, who received daily for 6 months a complementary food (40 g/day) with the protein source being either the MFGM protein fraction or skim milk proteins (control). Health and nutritional status of infants were examined monthly in the outpatient clinic; product intake, food patterns, and diarrhea morbidity were assessed by home visits twice per week. Hemoglobin and micronutrient status were measured at 0 and 6 months of intervention. Results are presented as the entire group and as 6 to 8 and 9 to 11 months subgroups.Results:A total of 499 infants completed the study. Global prevalence of diarrhea was 3.84% and 4.37% in the MFGM group and control group, respectively (P < 0.05). Consumption of the MFGM protein fraction reduced episodes of bloody diarrhea (odds ratio 0.54; 95% confidence interval 0.31–0.93, P = 0.025) adjusting for anemia and potable water facilities as covariates. There were no differences between groups in anemia, serum ferritin, zinc, or folate.Conclusions:Addition of an MFGM‐enriched protein fraction to complementary food had beneficial effects on diarrhea in infants and may thus help to improve the health of vulnerable populations.
Tissue-Specific Differences in Cytosine Methylation and Their Association with Differential Gene Expression in Sorghum
Authors: Zhang Meishan , Xu Chunming , von Wettstein Diter , Liu Bao 
Published: June 2011

Abstract
It has been well established that DNA cytosine methylation plays essential regulatory roles in imprinting gene expression in endosperm, and hence normal embryonic development, in the model plant Arabidopsis (Arabidopsis thaliana). Nonetheless, the developmental role of this epigenetic marker in cereal crops remains largely unexplored. Here, we report for sorghum (Sorghum bicolor) differences in relative cytosine methylation levels and patterns at 5′-CCGG sites in seven tissues (endosperm, embryo, leaf, root, young inflorescence, anther, and ovary), and characterize a set of tissue-specific differentially methylated regions (TDMRs). We found that the most enriched TDMRs in sorghum are specific for the endosperm and are generated concomitantly but imbalanced by decrease versus increase in cytosine methylation at multiple 5′-CCGG sites across the genome. This leads to more extensive demethylation in the endosperm than in other tissues, where TDMRs are mainly tissue nonspecific rather than specific to a particular tissue. Accordingly, relative to endosperm, the other six tissues showed grossly similar levels though distinct patterns of cytosine methylation, presumably as a result of a similar extent of concomitant decrease versus increase in cytosine methylation that occurred at variable genomic loci. All four tested TDMRs were validated by bisulfite genomic sequencing. Diverse sequences were found to underlie the TDMRs, including those encoding various known-function or predicted proteins, transposable elements, and those bearing homology to putative imprinted genes in maize (Zea mays). We further found that the expression pattern of at least some genic TDMRs was correlated with its tissue-specific methylation state, implicating a developmental role of DNA methylation in regulating tissue-specific or -preferential gene expression in sorghum.
BBX32, an Arabidopsis B-Box Protein, Functions in Light Signaling by Suppressing HY5-Regulated Gene Expression and Interacting with STH2/BBX21
Authors: Holtan Hans E. , Bandong Simona , Marion Colleen M. , Adam Luc , Tiwari Shiv , Shen Yu , Maloof Julin N. , Maszle Don R. , Ohto Masa-aki , Preuss Sasha , Meister Rob , Petracek Marie , Repetti Peter P. , Reuber T. Lynne , Ratcliffe Oliver J. , Khanna Rajnish 
Published: June 2011

Abstract
A B-box zinc finger protein, B-BOX32 (BBX32), was identified as playing a role in determining hypocotyl length during a large-scale functional genomics study in Arabidopsis (Arabidopsis thaliana). Further analysis revealed that seedlings overexpressing BBX32 display elongated hypocotyls in red, far-red, and blue light, along with reduced cotyledon expansion in red light. Through comparative analysis of mutant and overexpression line phenotypes, including global expression profiling and growth curve studies, we demonstrate that BBX32 acts antagonistically to ELONGATED HYPOCOTYL5 (HY5). We further show that BBX32 interacts with SALT TOLERANCE HOMOLOG2/BBX21, another B-box protein previously shown to interact with HY5. Based on these data, we propose that BBX32 functions downstream of multiple photoreceptors as a modulator of light responses. As such, BBX32 potentially has a native role in mediating gene repression to maintain dark adaptation.
Dual cut‐off transient elastography to assess liver fibrosis in chronic hepatitis B: a cohort study with internal validation
Authors: Viganò M. , Paggi S. , Lampertico P. , Fraquelli M. , Massironi S. , Ronchi G. , Rigamonti C. , Conte D. , Colombo M. 
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 353–362SummaryBackground Transient elastography has gained popularity to stage liver fibrosis in chronic viral hepatitis, however, diagnostic cut‐offs for severe fibrosis in chronic hepatitis B are poorly defined.Aim To evaluate an algorithm with two distinct cut‐offs for positive and negative prediction of significant fibrosis and cirrhosis in chronic hepatitis B patients.Methods Two cohorts of treatment‐naïve patients with chronic hepatitis B (125 training and 92 validations) were consecutively and concurrently examined by percutaneous liver biopsy and transient elastography. Fibrosis was staged by Metavir (significant fibrosis = F ≥ 2; cirrhosis = F4) in ≥2 cm long liver tissue cores.Results A >13.1 kPa positive and a ≤9.4 kPa negative cut‐off for cirrhosis had a >90% sensitivity and specificity, with an accuracy of 94%. The corresponding cut‐offs for F ≥ 2 were >9.4 and ≤6.2 kPa, thus classifying 56% of patients with an overall accuracy of 90%. In the validation cohort, F4 and F ≥ 2 were predicted by the above transient elastography cut‐offs with an overall accuracy >90%. In 165 patients with higher than upper limit of normal transaminase activity the dual cut‐off algorithm of transient elastography was as accurate as in the 52 patients with normal alanine aminotransferase values in the prediction and exclusion of cirrhosis, only.Conclusions A dual cut‐off algorithm allowed for correctly classifying both significant fibrosis and cirrhosis in the majority of the patients with chronic hepatitis B, independent of alanine aminotransferase values, thus reducing the need for liver biopsy investigations.
Association between the presence of brown adipose tissue and non‐alcoholic fatty liver disease in adult humans
Authors: Yilmaz Y. , Ones T. , Purnak T. , Ozguven S. , Kurt R. , Atug O. , Turoglu H. T. , Imeryuz N. 
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 318–323SummaryBackground  The presence of active brown adipose tissue (BAT) has been associated with a reduced risk of obesity in adult humans.Aim  To examine whether the presence and activity of BAT in patients undergoing PET‐CT examinations is related to the presence of fatty liver.Method  We retrospectively analysed 3666 consecutive PET‐CT whole‐body scans performed on a total of 1832 patients who were referred for suspected malignancies. BAT‐positive subjects (BAT+) were defined as subjects who showed substantial amounts of brown adipose tissue on PET‐CT scans. In areas where uptake of [18F]FDG was identified by CT for BAT, the maximal standardised uptake values (SUVmax), defined as the maximum activity per millilitre within the region of interest divided by the injected dose in megabecquerels per gram of body weight, were determined. A ratio of mean liver attenuation to spleen attenuation <0.8 on CT scans was considered to indicate NAFLD.Results  Thirty patients of the 1832 screened individuals (2%) demonstrated brown fat uptake (BAT+ subjects). Ninety matched individuals without evidence of BAT on PET scans (BAT− subjects) were enrolled for comparison purposes. After adjustment for potential confounders, the odds ratio for having NAFLD was significantly higher for BAT− subjects (3.12, 95% confidence interval = 1.03–9.88, P < 0.05). The SUVmax for brown fat tissue was significantly correlated with the ratio of mean liver attenuation to spleen attenuation (P < 0.05).Conclusion  The presence of brown adipose tissue in adulthood is independently associated with a lower likelihood of NAFLD diagnosed by CT findings.
Very low birth weight survivors have reduced peak bone mass and reduced insulin sensitivity
Authors: Smith C. M. , Wright N. P. , Wales J. K. H. , Mackenzie C. , Primhak R. A. , Eastell R. , Walsh J. S. 
Published: June 2011

SummaryContext  Increasing numbers of very low birth weight (VLBW) infants are surviving into adulthood because of improvements in neonatal intensive care. Adverse events in early life can have long‐term effects through reprogramming of metabolic systems.Objective  To determine whether young adult VLBW survivors have abnormalities of skeletal development or endocrine function.Design  Cross‐sectional, observational, case‐control study.Participants  Thirty‐seven VLBW subjects and 27 healthy controls at peak bone mass (mean age 23).Measurements  Differences between cases and controls in body size, body composition, bone mass and bone geometry [assessed by dual‐energy X‐ray absorptiometry (DXA), hip structure analysis and peripheral quantitative computed tomography (pQCT)], bone turnover [urine N‐terminal telopeptide of type I collagen (NTX), serum C‐terminal telopeptide of type I collagen (CTX)], aminoterminal propeptide of type I procollagen (PINP) and bone alkaline phosphatase), hormones (sex steroids, IGF‐1, PTH and 25‐OH vitamin D) and insulin sensitivity (HOMA‐IR and oral glucose tolerance testing).Results  VLBW subjects had lower bone density at the lumbar spine (5.7%) and femoral neck (8.6%), which persisted after correction for bone size by the estimation of volumetric density (bone mineral apparent density). Urine NTX was higher in VLBW subjects than in controls, but there were no significant differences in other bone turnover markers. VLBW survivors had lower insulin sensitivity (mean INS‐30 controls = 57.0, VLBW subjects = 94.3, P < 0.01), but there were no differences in whole body fat mass or truncal fat mass between VLBW subjects and controls.Conclusions  Young adult VLBW survivors have reduced bone density for their bone size and reduced insulin sensitivity, which may have significant implications for their risk of fracture and diabetes in later life.
Inflamed gut mucosa: downstream of interleukin‐10
Authors: Paul Gregor , Khare Vineeta , Gasche Christoph 
Published: June 2011

Eur J Clin Invest 2012; 42 (1): 95–109AbstractBackground  Interleukin‐10 is a pleiotropic cytokine, whose main function is limitation and ultimately termination of immune responses. This is especially true for environmental interfaces such as the gastrointestinal tract. IL‐10 acts as a key mediator for maintaining gut homeostasis. IL‐10 knockout mice are well established as a genetic model for inflammatory bowel disease (IBD), and sequence variants in the IL‐10 locus contribute to ulcerative colitis (UC).Design  This review covers the significance of IL‐10 signalling in the intestinal immune response both in health and disease. It explains the biological role of IL‐10, its deregulation in IBD and its contribution to intestinal inflammation via endoplasmic reticulum stress response.Results  Many IBD susceptibility genes have been discovered in the past years, linking fundamental biological systems, like innate and adaptive immunity, stress responses, autophagy and mucosal barrier to the pathogenesis of Crohn’s disease (CD) and UC. IL‐10 has long been known for its substantial role in regulating gut immunity, but its contribution to IBD was somewhat elusive. A recent study identified mutations in either IL‐10 receptor subunits that are associated with early‐onset enterocolitis, a severe phenotype of IBD. Other than genetic variants of IL‐10 receptors, IL‐10 and STAT3 genes are also associated with IBD, emphasizing the involvement of the IL‐10 signalling cascade in the pathogenesis of CD and UC.Conclusions  The discovery of inherited deregulations in the IL‐10 signalling cascade is not only considered the missing link between IL‐10 and intestinal homeostasis, but also demonstrates how findings made in animal models help explaining human disease.