bluuebunny/crossref_metadata_2025_split huggingface dataset:
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
Authors: Delport Wayne , Poon Art F. Y. , Frost Simon D. W. , Kosakovsky Pond Sergei L. 
Published: July 2010

Abstract
Summary: Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. Since the original release in 2005, we have expanded the analysis options to include recently developed algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, which rapidly escape host-immune pressure and HIV-1 subtype assignment. The traditional selection tools have also been augmented to include recent developments in the field. Here, we summarize the analyses options currently available on Datamonkey, and provide guidelines for their use in evolutionary biology.
Availability and documentation: http://www.datamonkey.org
Contact: spond@ucsd.edu
Prediction of Specific Japanese Sponge Cake Volume Using Pasting Properties of Flour
Authors: Nakamura Kazuhiro , Taniguchi Yoshinori , Taira Masato , Ito Hiroyuki 
Published: July 2010

ABSTRACTIn Japanese soft wheat (Triticum aestivum L.) breeding programs, protein content (PC), and specific surface area (SSA) of flour have been used as important factors for the baking quality of Japanese sponge cake. We proposed batter pasting viscosity (BPV) as a parameter to predict the baking quality of Japanese sponge cake. BPV was measured using a Rapid Visco‐Analyser (RVA) with a modified heating profile. Twenty soft wheat samples from the 2006‐07 season and 22 from the 2007‐08 season, including Japanese soft wheat cultivars, advanced breeders' lines, and Western White (WW) imported from the United States, were milled and evaluated for solvent retention capacity (SRC) values of four solvents, batter pasting properties, flour pasting properties, PC, SSA, and specific cake volume (SCV) to investigate their relationships. BPV was the most strongly correlated of the parameters to SCV (r = –0.90, P < 0.001). Stepwise multiple regression analysis selected BPV and minimum viscosity (MV) of flour pasting as significant independent variables to predict SCV (corrected R2 = 0.848). The variability in BPV related to cake batter expansion was highly explained by PC and sucrose SRC (corrected R2 = 0.854, P < 0.001). MV was correlated to SSA (r = 0.56, P < 0.001) and might be related to the prevention of sponge cake shrinkage during baking.
Proper Levels of the Arabidopsis Cohesion Establishment Factor CTF7 Are Essential for Embryo and Megagametophyte, But Not Endosperm, Development
Authors: Jiang Ling , Yuan Li , Xia Ming , Makaroff Christopher A. 
Published: July 2010

Abstract
CTF7 is an essential gene in yeast that is required for the formation of sister chromatid cohesion. While recent studies have provided insights into how sister chromatid cohesion is established, less is known about how specifically CTF7 facilitates the formation of cohesion, and essentially nothing is known about how sister chromatid cohesion is established in plants. In this report, we describe the isolation and characterization of CTF7 from Arabidopsis (Arabidopsis thaliana). Arabidopsis CTF7 is similar to Saccharomyces cerevisiae CTF7 in that it lacks an amino-terminal extension, exhibits acetyltransferase activity, and can complement a yeast ctf7 temperature-sensitive mutation. CTF7 transcripts are found throughout the plant, with the highest levels present in buds. Seeds containing T-DNA insertions in CTF7 exhibit mitotic defects in the zygote. Interestingly, the endosperm developed normally in ctf7 seeds, suggesting that CTF7 is not essential for mitosis in endosperm nuclei. Minor defects were observed in female gametophytes of ctf7+/2 plants, and plants that overexpress CTF7 exhibited female gametophyte lethality. Pollen development appeared normal in both CTF7 knockout and overexpression plants. Therefore, proper levels of CTF7 are critical for female gametophyte and embryo development but not for the establishment of mitotic cohesion during microgametogenesis or during endosperm development.
Vernalization-Mediated VIN3 Induction Overcomes the LIKE-HETEROCHROMATIN PROTEIN1/POLYCOMB REPRESSION COMPLEX2-Mediated Epigenetic Repression
Authors: Kim Dong-Hwan , Zografos Brett R. , Sung Sibum 
Published: July 2010

Abstract
VERNALIZATION INSENSITIVE3 (VIN3) induction by vernalization is one of the earliest events in the vernalization response of Arabidopsis (Arabidopsis thaliana). However, the mechanism responsible for vernalization-mediated VIN3 induction is poorly understood. Here, we show that the constitutive repression of VIN3 in the absence of the cold is due to multiple repressive components, including a transposable element-derived sequence, LIKE-HETEROCHROMATIN PROTEIN1 and POLYCOMB REPRESSION COMPLEX2. Furthermore, the full extent of VIN3 induction by vernalization requires activating complex components, including EARLY FLOWERING7 and EARLY FLOWERING IN SHORT DAYS. In addition, we observed dynamic changes in the histone modifications present at VIN3 chromatin during the course of vernalization. Our results show that the induction of VIN3 includes dynamic changes at the level of chromatin triggered by long-term cold exposure.
Genome‐wide analysis of phenylpropanoid defence pathways
Authors: NAOUMKINA MARINA A. , ZHAO QIAO , GALLEGO‐GIRALDO LINA , DAI XINBIN , ZHAO PATRICK X. , DIXON RICHARD A. 
Published: July 2010

SUMMARYPhenylpropanoids can function as preformed and inducible antimicrobial compounds, as well as signal molecules, in plant–microbe interactions. Since we last reviewed the field 8 years ago, there has been a huge increase in our understanding of the genes of phenylpropanoid biosynthesis and their regulation, brought about largely by advances in genome technology, from whole‐genome sequencing to massively parallel gene expression profiling. Here, we present an overview of the biosynthesis and roles of phenylpropanoids in plant defence, together with an analysis of confirmed and predicted phenylpropanoid pathway genes in the sequenced genomes of 11 plant species. Examples are provided of phylogenetic and expression clustering analyses, and the large body of underlying genomic data is provided through a website accessible from the article.
Synergistic and persistent effect of T‐cell immunotherapy with anti‐CD19 or anti‐CD38 chimeric receptor in conjunction with rituximab on B‐cell non‐Hodgkin lymphoma
Authors: Mihara Keichiro , Yanagihara Kazuyoshi , Takigahira Misato , Kitanaka Akira , Imai Chihaya , Bhattacharyya Joyeeta , Kubo Takanori , Takei Yoshifumi , Yasunaga Shin’ichiro , Takihara Yoshihiro , Kimura Akiro 
Published: July 2010

SummaryUsing artificial receptors, it is possible to redirect the specificity of immune cells to tumour‐associated antigens, which is expected to provide a useful strategy for cancer immunotherapy. Given that B‐cell non‐Hodgkin lymphoma (B‐NHL) cells invariably express CD19 and CD38, these antigens may be suitable molecular candidates for such immunotherapy. We transduced human peripheral T cells or a T‐cell line with either anti‐CD19‐chimeric receptor (CAR) or anti‐CD38‐CAR, which contained an anti‐CD19 or anti‐CD38 antibody‐derived single‐chain variable domain respectively. Retroviral transduction led to anti‐CD19‐CAR or anti‐CD38‐CAR expression in T cells with high efficiency (>60%). The T cell line, Hut78, when transduced with anti‐CD19‐CAR or anti‐CD38‐CAR, exerted strong cytotoxicity against the B‐NHL cell lines, HT and RL, and lymphoma cells isolated from patients. Interestingly, use of both CARs had an additive cytotoxic effect on HT cells in vitro. In conjunction with rituximab, human peripheral T cells expressing either anti‐CD19‐CAR or anti‐CD38‐CAR enhanced cytotoxicity against HT‐luciferase cells in xenografted mice. Moreover, the synergistic tumour‐suppressing activity was persistent in vivo for over 2 months. These results provide a powerful rationale for clinical testing of the combination of rituximab with autologous T cells carrying either CAR on aggressive or relapsed B‐NHLs.
Application of genomics for risk stratification of childhood acute lymphoblastic leukaemia: from bench to bedside?
Authors: Izraeli Shai 
Published: July 2010

SummaryThe remarkable progress in the treatment of childhood acute lymphoblastic leukaemia (ALL) has been based on the adjustment of therapy to subgroups of leukaemia stratified by their prognostic implications. Here, the contribution of the last decade of advanced genomic research on the clinical management of childhood ALL is examined. The application of genomics for routine diagnosis of ALL is feasible but depends on commercial development of appropriate certified platforms. The discovery of several novel high‐risk markers, such as deletions in IKZF1 might be integrated into clinical protocols in the near future. Several novel targets for therapy have been identified and have led to phase I/II therapeutic trials. This and any future progress depends on the maintenance of high quality bio‐banks including biological material and clinical data of each patient enrolled on a prospective clinical protocol.
Plasma levels of advanced glycation end products are associated with haemolysis‐related organ complications in sickle cell patients
Authors: Nur Erfan , Brandjes Dees P. , Schnog John‐John B. , Otten Hans‐Martin , Fijnvandraat Karin , Schalkwijk Casper G. , Biemond Bart J. ,   the CURAMA Study Group
Published: July 2010

SummaryOxidative stress plays an important role in the pathophysiology of sickle cell disease (SCD). Plasma levels of advanced glycation end products (AGEs) are increased under oxidative conditions and are associated with disease severity in diabetes and inflammatory diseases. We investigated whether AGEs are increased in sickle cell patients and whether they are associated with SCD‐related complications. Plasma levels of the AGEs pentosidine, Nε‐(carboxymethyl)lysine (CML) and Nε‐(carboxyethyl)lysine (CEL) were measured using single‐column high performance liquid chromatography with fluorescence detection (pentosidine) and ultra performance liquid chromatography‐tandem mass spectrometry (CML and CEL). Plasma levels of pentosidine and CML were increased in HbSS/HbSβ0‐thalassaemia (n = 60) and HbSC/HbSβ+‐thalassaemia (n = 42) patients during steady state as compared to healthy HbAA controls (n = 30) without increments during painful crisis. CEL levels were comparable between all groups. Pentosidine and CML levels correlated significantly to haemolytic rate during the clinically asymptomatic state while pentosidine was significantly related to the number of haemolysis‐related organ complications. The increased plasma AGE levels in sickle cell patients and their association with haemolysis and haemolysis‐related complications suggest AGEs might be implicated in the pathophysiology of the haemolytic phenotype of SCD. Measurement of AGEs might be useful in predicting organ complications in SCD.
CD200R1 regulates the severity of arthritis but has minimal impact on the adaptive immune response
Authors: Šimelyte E , Alzabin S , Boudakov I , Williams R 
Published: July 2010

Summary
CD200R1 is a member of the immunoglobulin supergene family that is thought to play an inhibitory role in immunity. Previous studies have established the anti-arthritic effect of CD200Fc, an agonist of CD200R1. However, the physiological role played by CD200R1 in arthritis remains to be established. The aims of this study are to assess the contribution of endogenous CD200R1 in regulating the severity of arthritis and to determine its role in shaping the immune response to type II collagen within the context of collagen-induced arthritis, an animal model of rheumatoid arthritis. Arthritis was induced in DBA/1 mice by immunization with type II collagen and the kinetics of expression of CD200R1 and CD200 were monitored by quantitative reverse transcription–polymerase chain reaction. Next, a comparison was made between CD200R1−/− and wild-type mice in terms of the progression of collagen-induced arthritis, as well as the B and T cell responses to type II collagen. The expression of both CD200R1 and CD200 was increased after immunization and reached maximal levels at the height of the inflammatory response. In addition, the severity of arthritis was increased significantly in CD200R1−/− mice compared to wild-type mice. However, little or no differences were observed between CD200R1−/− and wild-type mice in terms of the T or B cell responses to type II collagen. It was concluded that the CD200R1/CD200 pathway is up-regulated in arthritis and plays a significant physiological role in regulating the severity of disease. In contrast, CD200R1 plays a minimal role in shaping the immune response to collagen in this model.
Non‐obese early onset diabetes mellitus in mutant cryptochrome1 transgenic mice
Authors: Okano Satoshi , Hayasaka Kiyoshi , Igarashi Masahiko , Iwai Harue , Togashi Yoshiyuki , Nakajima Osamu 
Published: July 2010

Eur J Clin Invest 2010; 40 (11): 1011–1017AbstractBackground  An earlier report described that transgenic mice ubiquitously expressing cryptochrome1 (CRY1) with a mutation in cystein414 (CRY1‐AP Tg mice) display diabetes mellitus in addition to anomalous circadian behaviours. This study examined characteristic aspects of symptoms to clarify the diabetes type and pathogenesis.Materials and methods  The body weights and blood glucose levels of CRY1‐AP Tg mice were measured for 7 weeks starting at 3 weeks after birth. Glucose tolerance test for the mice of various ages and insulin tolerance test at 6 weeks of age were conducted. Immunohistochemical analysis of islets was carried out for the mice of 19 and 40 weeks of age. Basal and glucose‐stimulated serum insulin levels of mice at 27 weeks were also measured.Results  Three‐week‐old CRY1‐AP Tg mice, which showed mild retardation in growth, already displayed glucose intolerance. Hyperglycaemia progressed with age, without accompanying insulin resistance. Insulin‐stained areas in islets in CRY1‐AP Tg mice were smaller than that in wild‐type controls. Both basal and glucose‐stimulated secretion of insulin decreased in CRY1‐AP Tg mice.Conclusion  The symptoms of diabetes in CRY1‐AP Tg mice turned out to be similar to those of maturity onset diabetes of the young (MODY) in humans in terms of early onset, non‐obesity and primary dysfunction of beta cells. The CRY1‐AP Tg mice might serve as an animal model of early onset insulin‐secretory defect of diabetes.
Item response modelling for clinical and laboratory testing
Authors: Cleophas Ton J. , Zwinderman Aeilko H. 
Published: July 2010

Eur J Clin Invest 2010; 40 (10): 911–917AbstractBackground  Item response models using exponential modelling are more sensitive than classical linear methods for making predictions from psychological questionnaires.Objective  To assess whether they can also be used for making predictions from quality of life questionnaires and clinical and laboratory diagnostic‐tests.Methods  Of 1000 anginal patients assessed for quality of life and 1350 patients assessed for peripheral vascular disease with diagnostic laboratory tests, items response modelling was applied using the Latent Trait Analysis program ‐2 of Uebersax.Results  The 32 different response patterns obtained from test batteries of five items produced 32 different quality of life scores ranging from 3·4% to 74·5% and 32 different levels of peripheral vascular disease ranging from 9·9% to 83·5% with overall mean scores, by definition, of 50%, whereas the classical method of analysis produced the discrete scores of only 0–5. The item response models produced an adequate fit for the data as demonstrated by chi‐square goodness of fit values/degrees of freedom of 0·86 and 0·64.Conclusions  1 Quality of life assessments and diagnostic tests can be analysed through item response modelling, and provide more sensitivity than do classical linear models.2 Item response modelling can change largely qualitative data into fairly accurate quantitative data, and can, even with limited sets of items, produce fairly accurate frequency distribution patterns of quality of life, severity of disease and other latent traits.
Source location using time‐reverse imaging
Authors: Artman Brad , Podladtchikov Igor , Witten Ben 
Published: July 2010

ABSTRACTWe present the chain of time‐reverse modeling, image space wavefield decomposition and several imaging conditions as a migration‐like algorithm called time‐reverse imaging. The algorithm locates subsurface sources in passive seismic data and diffractors in active data. We use elastic propagators to capitalize on the full waveforms available in multicomponent data, although an acoustic example is presented as well. For the elastic case, we perform wavefield decomposition in the image domain with spatial derivatives to calculate P and S potentials. To locate sources, the time axis is collapsed by extracting the zero‐lag of auto and cross‐correlations to return images in physical space. The impulse response of the algorithm is very dependent on acquisition geometry and needs to be evaluated with point sources before processing field data. Band‐limited data processed with these techniques image the radiation pattern of the source rather than just the location. We present several imaging conditions but we imagine others could be designed to investigate specific hypotheses concerning the nature of the source mechanism. We illustrate the flexible technique with synthetic 2D passive data examples and surface acquisition geometry specifically designed to investigate tremor type signals that are not easily identified or interpreted in the time domain.
Dental management of a child with EEC syndrome
Authors: TANBOǦA ILKNUR , PINÇE SEZER , DÜZDAR LALE 
Published: July 2010

Summary. The EEC syndrome is a condition characterized by ectrodactyly, ectodermal dysplasia and clefting of the lip and/or palate. Here we report a case of a boy with the EEC syndrome. The clinical and radiologic aspects of this condition, as well as the dental treatment, are reviewed.Résumé.La dysplasie ectodermique, l'ectrodactyle et la fente palatine et labiale sont caractéristiques d'un syndrôme. L'aspect clinique, radiologique et le traitement dentaire d'un patient atteint de ce syndrôme, sont étudiés dans cet article.Zusammenfassung.Das EEC Syndrom ist charakterisiert durch Ektrodaktylie, ektodermale Dysplasie und durch Lippenoder und Gaumenspalten. In diesem Bericht wird ein Fall mit EEC Syndrom beschrieben, die klinischen und röntgoloischen Aspekte dieses Syndromes, ebenso die zahnärztliche Behandlung dieses Falles.Resumen.El sindrome EEC (EDF) es una condición caracterizada por ectrodactilidad, displasia ectodérmica y fisura (hendidura) del labio y/o paladar. Se reporta un caso con el síndrome EEC y los aspectos clínicos y radiográficos de la condición así como el tratmiento odontológico realizado.
Classification and sequelae of arrested eruption of primary molars
Authors: KJÆR INGER , FINK‐JENSEN MERETE , ANDREASEN JENS OVE 
Published: July 2010

Aim.  The aim of this study was to classify early arrested eruption of primary molars and to analyse and explain the sequelae for the surrounding alveolar bone and the succeeding premolar.Design.  The position of the arrested primary molars in the mandible, the height of the local alveolar bone, and the morphology and location of the succeeding premolar were evaluated on radiographs from 29 children.Results.  Four groups of arrest from mild to severe with regards to infra‐position were categorized (Groups I–IV). Mean ages at the time of referral decreased from Groups I (8 years, 10 months) to Group IV (5 years, 9 months).Sequelae.  (i) Reduction of alveolar bone height (Groups I–III); (ii) delayed maturity of the succeeding premolar (two‐thirds of the cases); (iii) malformation of the succeeding premolar (mainly Groups III and IV); and (iv) ectopically located premolar occlusal to the retained molar (Group IV).Conclusions.  The deeper in the alveolar process a primary molar is retained, the earlier the disturbance in the eruption has occurred, and the greater is the risk of the permanent tooth germ being malformed and malpositioned. It is estimated that the earliest occurrences of arrested eruption of primary molars supposedly occur before the age of 3.
Restoring ecological balance to the British mammal fauna
Authors: GORMAN MARTYN L. 
Published: July 2010

ABSTRACT

The mammal fauna of the British Isles has seen major perturbations since the end of the last ice age, some natural and some anthropogenic. Today, 61 species of terrestrial mammals breed in the British Isles, but only 39 of them are native species, the rest have been introduced. Furthermore, 19 native species have disappeared from the fauna including all the large predators, lynx Lynx lynx, wolf Canis lupus and brown bear Ursus arctos.
Inevitably, these changes in species composition have been accompanied by major changes in community function including changes in patterns of energy flow through the mammalian community. For example, a high percentage of all the energy now flows through the introduced rabbit Oryctolagus cuniculus population and red deer Cervus elaphus, which, in the absence of natural predators, are living at extremely high densities.
Could the reintroduction of species help to reverse such changes in community structure and function? The successful return to the wild of species such as the Arabian oryx Oryx leucoryx and beaver Castor fiber has shown that reintroductions are certainly possible. However, the impact on community function of returned species is more difficult to evaluate.
This question is addressed in relation to the consequences for deer populations of any possible reintroduction of the wolf to Scotland. Based on what we know of wolves elsewhere, predictions are made about the likely demography and patterns of killing behaviour of introduced wolves. These values are then used to parameterize a Leslie matrix simulation of the impact of wolves on contemporary populations of red deer in Scotland. The simulations suggest very strongly that wolves are very unlikely to have any significant impact on the high‐density populations of deer now living in the Scottish landscape.