bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of the Barleyuroporphyrinogen III synthaseGene by aDsActivation Tagging Element Generates Developmental Photosensitivity
Authors: Ayliffe Michael A. , Agostino Anthony , Clarke Bryan C. , Furbank Robert , von Caemmerer Susanne , Pryor Anthony J. 
Published: April 2009

AbstractChlorophyll production involves the synthesis of photoreactive intermediates that, when in excess, are toxic due to the production of reactive oxygen species (ROS). A novel, activation-tagged barley (Hordeum vulgare) mutant is described that results from antisense suppression of a uroporphyrinogen III synthase (Uros) gene, the product of which catalyzes the sixth step in the synthesis of chlorophyll and heme. In homozygous mutant plants, uroporphyrin(ogen) I accumulates by spontaneous cyclization of hydroxyl methylbilane, the substrate of Uros. Accumulation of this tetrapyrrole intermediate results in photosensitive cell death due to the production of ROS. The efficiency of Uros gene suppression is developmentally regulated, being most effective in mature seedling leaves compared with newly emergent leaves. Reduced transcript accumulation of a number of nuclear-encoded photosynthesis genes occurs in the mutant, even under 3% light conditions, consistent with a retrograde plastid-nuclear signaling mechanism arising from Uros gene suppression. A similar set of nuclear genes was repressed in wild-type barley following treatment with a singlet oxygen-generating herbicide, but not by a superoxide generating herbicide, suggesting that the retrograde signaling apparent in the mutant is specific to singlet oxygen.
Tissue- and Expression Level–Specific Chromatin Looping at Maizeb1Epialleles
Authors: Louwers Marieke , Bader Rechien , Haring Max , van Driel Roel , de Laat Wouter , Stam Maike 
Published: April 2009

AbstractThis work examines the involvement of chromatin looping in the transcriptional regulation of two epialleles of the maize (Zea mays) b1 gene, B-I and B'. These two epialleles are tissue-specifically regulated and are involved in paramutation. B-I and B' are expressed at high and low levels, respectively. A hepta-repeat ∼100 kb upstream of the transcription start site (TSS) is required for both paramutation and high b1 expression. Using chromosome conformation capture, we show that the hepta-repeat physically interacts with the TSS region in a tissue- and expression level–specific manner. Multiple repeats are required to stabilize this interaction. High b1 expression is mediated by a multiloop structure; besides the hepta-repeat, other sequence regions physically interact with the TSS as well, and these interactions are epiallele- and expression level–specific. Formaldehyde-assisted isolation of regulatory elements uncovered multiple interacting regions as potentially regulatory.
Next‐generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology
Authors: ADAMS IAN P. , GLOVER RACHEL H. , MONGER WENDY A. , MUMFORD RICK , JACKEVICIENE ELENA , NAVALINSKIENE MELETELE , SAMUITIENE MARIJA , BOONHAM NEIL 
Published: April 2009

SUMMARYA novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next‐generation sequencing coupled with metagenomic analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata. This plant was found to contain a new cucumovirus, for which we suggest the name ‘Gayfeather mild mottle virus’. In both cases, the full viral genome was sequenced. This method expedites the entire process of novel virus discovery, identification, viral genome sequencing and, subsequently, the development of more routine assays for new viral pathogens.
Exploring outcomes in a therapeutic service response to the emotional and mental health needs of children who have experienced abuse and neglect in Victoria, Australia
Authors: Jackson Annette , Frederico Margarita , Tanti Chris , Black Carlina 
Published: April 2009

ABSTRACTChildren in the protection and care system are highly vulnerable and need more than protection and physical care. This paper outlines elements of an innovative therapeutic programme, Take Two, which combines trauma and attachment‐informed practice with a clinical outcomes focus. An important feature was the embedding of a research and evaluation partnership between the programme and a university. The paper discusses the challenges of implementing a research approach into a highly sensitive ‘messy’ or non‐routine environment. The paper portrays the value of a trauma and attachment perspective within a developmental and ecological framework to guide understanding and intervention with these children and their network. A description of the client group is followed by analysis of outcome measures: the Trauma Symptom Checklist for Children and the Social Network Map. Findings include the significant reduction of trauma‐related symptoms, an increase in the percentage of friends identified and an increase, albeit not significant, in the percentage of people described as very close. The results point to the importance of family in the lives of these children. This study explores this type of research in situ and its value in building knowledge and strengthening practice.
Intensive family preservation services in Flanders: an outcome study
Authors: Puyenbroeck Hubert Van , Loots Gerrit , Grietens Hans , Jacquet Wolfgang , Vanderfaeillie Johan , Escudero Valentin 
Published: April 2009

ABSTRACTSet up as a one‐group pre‐test–post‐test follow‐up design, this study examines the outcomes of intensive family preservation services (IFPS) in Flanders addressing the following research questions: Does IFPS make a significant difference concerning (1) the interaction between parent and child? (2) social support as experienced by the parent? (3) stress and empowerment of the parent? and (4) the strengths and difficulties of the minor? Families seem to indicate that their family situation is more manageable, although still, professional help is needed. Parents feel more resilient about the situation and indicate that they can get along with their child better than before the crisis intervention. Parents still feel uncertain about the future and about their role as a parent. There seems to be no indications that their level and quality of social contacts have changed. Further research is suggested to provide more in‐depth information about the conditions associated with processes of change during an IFPS intervention.
Velocity analysis using AB semblance
Authors: Fomel S. 
Published: April 2009

ABSTRACTI derive and analyse an explicit formula for a generalized semblance attribute, which is suitable for the velocity analysis of prestack seismic gathers with distinct amplitude trends. While the conventional semblance can be interpreted as a squared correlation with a constant, the AB semblance is defined as a correlation with a trend. This measure is particularly attractive for analysing class II AVO anomalies and converted waves. Analytical derivations and numerical experiments show that the resolution of the AB semblance is approximately twice as low as that of the conventional semblance. However, this does not prevent it from being an effective attribute. I use synthetic and field data examples to demonstrate the improvements in velocity analysis from AB semblance.
Scientific rationale for the Finnish Allergy Programme 2008–2018: emphasis on prevention and endorsing tolerance
Authors: Von Hertzen L. C. , Savolainen J. , Hannuksela M. , Klaukka T. , Lauerma A. , Mäkelä M. J. , Pekkanen J. , Pietinalho A. , Vaarala O. , Valovirta E. , Vartiainen E. , Haahtela T. 
Published: April 2009

In similarity to many other western countries, the burden of allergic diseases in Finland is high. Studies worldwide have shown that an environment rich in microbes in early life reduces the subsequent risk of developing allergic diseases. Along with urbanization, such exposure has dramatically reduced, both in terms of diversity and quantity. Continuous stimulation of the immune system by environmental saprophytes via the skin, respiratory tract and gut appears to be necessary for activation of the regulatory network including regulatory T‐cells and dendritic cells. Substantial evidence now shows that the balance between allergy and tolerance is dependent on regulatory T‐cells. Tolerance induced by allergen‐specific regulatory T‐cells appears to be the normal immunological response to allergens in non atopic healthy individuals. Healthy subjects have an intact functional allergen‐specific regulatory T‐cell response, which in allergic subjects is impaired. Evidence on this exists with respect to atopic dermatitis, contact dermatitis, allergic rhinitis and asthma. Restoration of impaired allergen‐specific regulatory T‐cell response and tolerance induction has furthermore been demonstrated during allergen‐specific subcutaneous and sublingual immunotherapy and is crucial for good therapeutic outcome. However, tolerance can also be strengthened unspecifically by simple means, e.g. by consuming farm milk and spending time in nature. Results so far obtained from animal models indicate that it is possible to restore tolerance by administering the allergen in certain circumstances both locally and systemically. It has become increasingly clear that continuous exposure to microbial antigens as well as allergens in foodstuffs and the environment is decisive, and excessive antigen avoidance can be harmful and weaken or even prevent the development of regulatory mechanisms. Success in the Finnish Asthma Programme was an encouraging example of how it is possible to reduce both the costs and morbidity of asthma. The time, in the wake of the Asthma Programme, is now opportune for a national allergy programme, particularly as in the past few years, fundamentally more essential data on tolerance and its mechanisms have been published. In this review, the scientific rationale for the Finnish Allergy Programme 2008–2018 is outlined. The focus is on tolerance and how to endorse tolerance at the population level.
Variation in properties of Phlebiopsis gigantea related to biocontrol against infection by Heterobasidion spp. in Norway spruce stumps
Authors: Sun H. , Korhonen K. , Hantula J. , Kasanen R. 
Published: April 2009

SummaryThe properties of 64 heterokaryotic strains of Phlebiopsis gigantea, isolated mostly from Norway spruce stumps, were tested for asexual spore production, growth rate and competitive ability against Heterobasidion spp. on agar medium, and for growth rate in spruce wood. Eighteen isolates were also tested for the efficacy of control against Heterobasidion spp. in stem pieces of spruce. The results revealed high variation in traits between different P. gigantea isolates. The efficacy of control against Heterobasidion spp. and the growth rate in spruce wood were closely related to each other (r = 0.727, p < 0.001). These preliminary tests indicate that the growth rate of a P. gigantea strain in spruce wood is the most important characteristic determining its efficiency in controlling the infection and spread of Heterobasidion spp. in spruce stumps.
EfCCNa survey: European intensive care nurses’ attitudes and beliefs towards end‐of‐life care
Authors: Latour Jos M , Fulbrook Paul , Albarran John W 
Published: April 2009

AbstractBackground:  Available literature suggests that critical care nurses have varied experiences in relation to end‐of‐life (EOL) care. Few studies have examined the involvement of European intensive care nurses’ involvement in EOL care decisions and the extent to which their nursing practice is based on shared beliefs, experiences and attitudes.Aim:  To investigate experiences and attitudes of European intensive care nurses regarding EOL care.Methods:  Using a survey method, delegates (n = 419) attending an international critical care nursing conference were invited to complete a self‐administered questionnaire about their involvement with EOL care practices. The questionnaire composed of 45 items and was available in three European languages.Results:  A total of 164 questionnaires were completed, yielding a response rate of 39%. The majority of respondents (91·8%) indicated direct involvement in EOL patient care, while 73·4% reported active involvement in decision‐making process. 78·6% of respondents expressed commitment to family involvement in EOL decisions, however only 59·3% of the participants said that this was routinely undertaken (p < 0·0005, Z = −4·778). In decisions to withdraw or withhold therapy, 65% would decrease the flow of inspired oxygen, 98·8% provide continuous pain relief and 91·3% endorse open visiting. The majority (78%) disagreed that dying patients should be transferred to a single room. A division of views was observed in relation to 44% agreeing that patients should be kept deeply sedated and equal numbers contesting the continuation of nutritional support (41·6% versus 42·3%).Conclusions:  The involvement of European intensive care nurses in EOL care discussions and decisions is reasonably consistent with many engaged in initiating dialogue with coworkers. In general, views and experiences of EOL care were similar, with the exception of the provision of nutrition and use of sedation.Relevance to practice:  Use of formal guidelines and education may increase nurses’ involvement and confidence with EOL decisions.
Characterization of ERG, AR and PTEN Gene Status in Circulating Tumor Cells from Patients with Castration-Resistant Prostate Cancer
Authors: Attard Gerhardt , Swennenhuis Joost F. , Olmos David , Reid Alison H.M. , Vickers Elaine , A'Hern Roger , Levink Rianne , Coumans Frank , Moreira Joana , Riisnaes Ruth , Oommen Nikhil Babu , Hawche George , Jameson Charles , Thompson Emilda , Sipkema Ronald , Carden Craig P. , Parker Christopher , Dearnaley David , Kaye Stan B. , Cooper Colin S. , Molina Arturo , Cox Michael E. , Terstappen Leon W.M.M. , de Bono Johann S. 
Published: April 2009

Abstract
Hormone-driven expression of the ERG oncogene after fusion with TMPRSS2 occurs in 30% to 70% of therapy-naive prostate cancers. Its relevance in castration-resistant prostate cancer (CRPC) remains controversial as ERG is not expressed in some TMPRSS2-ERG androgen-independent xenograft models. However, unlike these models, CRPC patients have an increasing prostate-specific antigen, indicating active androgen receptor signaling. Here, we collected blood every month from 89 patients (54 chemotherapy-naive patients and 35 docetaxel-treated patients) treated in phase I/phase II clinical trials of an orally available, highly specific CYP17 inhibitor, abiraterone acetate, that ablates the synthesis of androgens and estrogens that drive TMPRSS2-ERG fusions. We isolated circulating tumor cells (CTC) by anti–epithelial cell adhesion molecule immunomagnetic selection followed by cytokeratin and CD45 immunofluorescence and 4′,6-diamidino-2-phenylindole staining. We used multicolor fluorescence in situ hybridization to show that CRPC CTCs, metastases, and prostate tissue invariably had the same ERG gene status as therapy-naive tumors (n = 31). We then used quantitative reverse transcription–PCR to show that ERG expression was maintained in CRPC. We also observed homogeneity in ERG gene rearrangement status in CTCs (n = 48) in contrast to significant heterogeneity of AR copy number gain and PTEN loss, suggesting that rearrangement of ERG may be an earlier event in prostate carcinogenesis. We finally report a significant association between ERG rearrangements in therapy-naive tumors, CRPCs, and CTCs and magnitude of prostate-specific antigen decline (P = 0.007) in CRPC patients treated with abiraterone acetate. These data confirm that CTCs are malignant in origin and indicate that hormone-regulated expression of ERG persists in CRPC. [Cancer Res 2009;69(7):2912–8]
Phosphorylation of TRAF2 within Its RING Domain Inhibits Stress-Induced Cell Death by Promoting IKK and Suppressing JNK Activation
Authors: Thomas Gregory S. , Zhang Laiqun , Blackwell Ken , Habelhah Hasem 
Published: April 2009

Abstract
Tumor necrosis factor (TNF) receptor–associated factor 2 (TRAF2) is an adaptor protein that modulates the activation of the c-Jun NH2 terminal kinase (JNK)/c-Jun and IκB kinase (IKK)/nuclear factor-κB (NF-κB) signaling cascades in response to TNFα stimulation. Although many serine/threonine kinases have been implicated in TNFα-induced IKK activation and NF-κB–dependent gene expression, most of them do not directly activate IKK. Here, we report that protein kinase Cζ phosphorylates TRAF2 at Ser55, within the RING domain of the protein, after TNFα stimulation. Although this phosphorylation event has a minimal effect on induction of the immediate/transient phase of IKK and JNK activation by TNFα, it promotes the secondary/prolonged phase of IKK activation and inhibits that of JNK. Importantly, constitutive TRAF2 phosphorylation increased both basal and inducible NF-κB activation and rendered Ha-Ras-V12–transformed cells resistant to stress-induced apoptosis. Moreover, TRAF2 was found to be constitutively phosphorylated in some malignant cancer cell lines and Hodgkin's lymphoma. These results reveal a new level of complexity in TNFα-induced IKK activation modulated by TRAF2 phosphorylation and suggest that TRAF2 phosphorylation is one of the events that are responsible for elevated basal NF-κB activity in certain human cancers. [Cancer Res 2009;69(8):3665–72]
Prognostic Significance of p53 Codon 72 Polymorphism Differs with Race in Colorectal Adenocarcinoma
Authors: Katkoori Venkat R. , Jia Xu , Shanmugam Chandrakumar , Wan Wen , Meleth Sreelatha , Bumpers Harvey , Grizzle William E. , Manne Upender 
Published: April 2009

Abstract
Purpose: Several studies have examined the prognostic value of the codon 72 polymorphism of the p53 gene in colorectal adenocarcinoma, but none have addressed patient race/ethnicity. Therefore, this study assessed the prognostic value of this polymorphism in African American and Caucasian colorectal adenocarcinoma patients separately.
Experimental Design: Colorectal adenocarcinomas from 137 African Americans and 236 non-Hispanic Caucasians were assessed for p53 mutations and genotyped for the codon 72 polymorphism. The phenotypes were correlated with p53 mutational status, clinicopathologic features, and patient survival using the χ2 test and Kaplan-Meier and Cox regression models.
Results: The incidence of p53 mutations was similar in African American and Caucasian patients (50% versus 54%, respectively); however, the homozygous Pro72 allele frequency was higher in African Americans (17%) as compared with Caucasians (7%). In contrast, the homozygous Arg72 allele frequency was higher in Caucasians (36%) than in African Americans (19%). In African Americans but not Caucasians, the Pro/Pro phenotype significantly correlated with a higher incidence of missense p53 mutations and with nodal metastasis. African Americans, but not Caucasians, with the Pro/Pro phenotype had significantly higher mortality (log-rank P = 0.005 versus. P = 0.886) and risk of death due to colorectal adenocarcinoma (hazard ratio, 2.15; 95% confidence interval, 1.02-4.53 versus hazard ratio, 1.60; 95% confidence interval, 0.69-3.18) than those with the phenotype Arg/Arg or Arg/Pro.
Conclusions: The higher frequency of the Pro/Pro phenotype of p53 in African American patients with colorectal adenocarcinoma is associated with an increased incidence of p53 mutations, with advanced tumor stage, and with short survival.
Some like it cool? Intermorph comparison of preferred body temperature in a colour-dimorphic snake
Authors: Tanaka Koji 
Published: April 2009

AbstractOrganismal characteristics of ectotherms are profoundly affected by body temperature (Tb). Despite constraints imposed by environmental factors, they can adjust Tb by several means. However, if thermoregulatory ability is limited by their own property such as coloration and this constraint affects individual's fitness, selection may promote coevolution of coloration and thermal aspects. I investigated this topic using a colour-dimorphic (melanistic/striped) snake Elaphe quadrivirgata as a model species. Recent laboratory experiment revealed slower body warming in striped individuals than in melanistic individuals. Under this circumstance, one way that striped individuals can manage their slower body warming is to prefer low Tb. Contrary to this prediction, there was no intermorph difference in preferred Tb. Coupled with the results of field studies, I suggest that striped individuals manage their slower body warming by behavioural thermoregulation and that constraints (e.g., high predation risk due to conspicuousness under thermally superior habitats) imposed on melanistic individuals lessen their thermal advantages. The effect of melanism on thermal aspects may not be so advantageous for melanistic animals than generally thought.
Diagnosing declining grassland wader populations using simple matrix models
Authors: Klok Chris , Roodbergen Maja , Hemerik Lia 
Published: April 2009

Abstract
Many populations of wader species have shown a strong decline in number in Western-Europe in recent years. The use of simple population models such as matrix models can contribute to conserve these populations by identifying the most profitable management measures. Parameterization of such models is often hampered by the availability of demographic data (survival and reproduction). In particular, data on survival in the pre-adult (immature) stage of wader species that remain in wintering areas outside Europe are notoriously difficult to obtain, and are therefore virtually absent in the literature. To diagnose population decline in the wader species; Black-tailed Godwit, Curlew, Lapwing, Oystercatcher, and Redshank, we extended an existing modelling framework in which incomplete demographic data can be analysed, developed for species with a pre-adult stage of one year. The framework is based on a Leslie matrix model with three parameters: yearly reproduction (number of fledglings per pair), yearly pre-adult (immature) and yearly adult (mature) survival. The yearly population growth rate of these populations and the relative sensitivity of this rate to changes in survival and reproduction parameters (the elasticity) were calculated numerically and, if possible, analytically. The results showed a decrease in dependence on reproduction and an increase in pre-adult survival of the population growth rate with an increase in the duration of the pre-adult stage. In general, adult survival had the highest elasticity, but elasticity of pre-adult survival increased with time to first reproduction, a result not reported earlier. Model results showed that adult survival and reproduction estimates reported for populations of Redshank and Curlew were too low to maintain viable populations. Based on the elasticity patterns and the scope for increase in actual demographic parameters we inferred that conservation of the Redshank and both Curlew populations should focus on reproduction. For one Oystercatcher and the Black-tailed Godwit populations we suggested a focus on both reproduction and pre-adult survival. For the second Oystercatcher population pre-adult survival seemed the most promising target for conservation. And for the Lapwing populations all demographic parameters should be considered.