bluuebunny/crossref_metadata_2025 huggingface dataset:
Stem cell activation by light guides plant organogenesis
Authors: Yoshida Saiko , Mandel Therese , Kuhlemeier Cris
Published: July 2011

Leaves originate from stem cells located at the shoot apical meristem. The meristem is shielded from the environment by older leaves, and leaf initiation is considered to be an autonomous process that does not depend on environmental cues. Here we show that light acts as a morphogenic signal that controls leaf initiation and stabilizes leaf positioning. Leaf initiation in tomato shoot apices ceases in the dark but resumes in the light, an effect that is mediated through the plant hormone cytokinin. Dark treatment also affects the subcellular localization of the auxin transporter PIN1 and the concomitant formation of auxin maxima. We propose that cytokinin is required for meristem propagation, and that auxin redirects cytokinin-inducible meristem growth toward organ formation. In contrast to common wisdom over the last 150 years, the light environment controls the initiation of lateral organs by regulating two key hormones: auxin and cytokinin.
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Authors: Kim Jung H. , Dhanasekaran Saravana M. , Prensner John R. , Cao Xuhong , Robinson Daniel , Kalyana-Sundaram Shanker , Huang Christina , Shankar Sunita , Jing Xiaojun , Iyer Matthew , Hu Ming , Sam Lee , Grasso Catherine , Maher Christopher A. , Palanisamy Nallasivam , Mehra Rohit , Kominsky Hal D. , Siddiqui Javed , Yu Jindan , Qin Zhaohui S. , Chinnaiyan Arul M.
Published: July 2011

Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex–next-generation sequencing (M-NGS). Hidden Markov model–based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ∼12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10−16). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
Immersion Freezing of Cell Monolayers for Cryo-Electron Tomography
Authors: Resch Guenter P. , Brandstetter Marlene , Wonesch Veronika I. , Urban Edit
Published: July 2011

INTRODUCTION

Cryo-transmission electron microscopy (cryo-TEM) is not limited to the visualization of suspended macromolecules in their native hydrated state. It can also be used to elucidate the molecular architecture of peripheral parts of adherent cells: After cultivation of the cells directly on EM grids, they are physically fixed by immersion freezing to yield cells embedded in thin, crystal-free layers of frozen water. Subsequently, specimens can be visualized using cryo-electron tomography (cryo-ET). This protocol outlines the production of protein-coated gold particles as suitable fiducial markers for electron tomography, and how to cultivate cells on grids with a carbon support film. It also describes how to freeze cells to obtain optimal and reproducible results using the Leica EM GP immersion freezer, and how to assess the results.
Using Intravital Dyes to Ubiquitously Label Embryonic Zebrafish
Authors: Godinho Leanne
Published: July 2011

INTRODUCTION

In the last two decades, the small tropical freshwater-dwelling zebrafish has emerged as a popular model for developmental biologists. The exceptional optical accessibility of zebrafish embryos coupled with the ability to use genetic tools to indelibly tag cells have been exploited to watch developmental events as they unfold. Moreover, because zebrafish are vertebrates, the knowledge gained through such studies is broadly applicable. This protocol describes the use of intravital dyes to ubiquitously label embryonic zebrafish. Intravital dyes such as CellTrace BODIPY TR methyl ester can be used to counterstain embryos that express fluorescent proteins either through transient injections or by stable transgenics. BODIPY TR should only be used in combination with fluorescent proteins that can be spectrally separated from it. The BODIPY TR absorption spectrum peaks at 598 nm, and its emission spectrum peaks at 625 nm. Embryos should be stained just before imaging.
CCD Cameras for Fluorescence Imaging of Living Cells
Authors: Salmon Wendy C. , Waters Jennifer C.
Published: July 2011

INTRODUCTION

Charged-coupled device (CCD) cameras are commonly used to acquire wide-field, spinning-disk confocal, and total internal reflection fluorescence (TIRF) microscopy images. Collecting digital images for a live cell fluorescence microscopy experiment requires balancing the desire to acquire sufficiently high-quality images with the need to minimize exposure of the specimen to light to reduce phototoxicity and photobleaching. The choice of CCD camera and the camera acquisition settings are critical determinants in the quality of a digital image that one can acquire from a given fluorescent specimen. In this article, we discuss the characteristics of CCD cameras, how they affect digital-image quality, and how to properly use a CCD camera for fluorescence live cell imaging experiments.
Generating and Imaging Multicolor Brainbow Mice
Authors: Weissman Tamily A. , Sanes Joshua R. , Lichtman Jeff W. , Livet Jean
Published: July 2011

INTRODUCTION

Visualizing the precise morphology of closely juxtaposed cells and their interactions can be highly informative, particularly when studying the complex organization of neuronal and glial networks in the nervous system. To this end, one can use optical approaches to image-distinct markers that are differentially distributed among the cells of interest, such as fluorescent proteins of various colors (XFPs). The Brainbow strategies use Cre/lox recombination to stochastically express two to four XFPs in a cellular population from a single promoter. Integration of multiple Brainbow transgene copies results in combinatorial expression of these XFPs, creating a wide range of hues. In the nervous system, the multicolor labeling thus generated can be used to distinguish adjacent neuronal or glial cells and to verify the identity of neuronal processes while tracing circuitry. This article describes the generation of Brainbow transgenes and mice as well as their use to image and digitally reconstruct nerve cells and their interactions in fixed samples. This method also holds potential for studies in other tissues and model organisms as well as live imaging in vivo.
Imaging the Dynamics of Biological Processes via Fast Confocal Microscopy and Image Processing
Authors: Liebling Michael
Published: July 2011

INTRODUCTION

Confocal microscopy offers the ability to optically section biological samples and to build three-dimensional (3D) volumes that can be digitally rendered, viewed from arbitrary directions, and quantitatively analyzed. Capturing, in addition to their 3D structure, the dynamics of living cells and organisms, further requires that image acquisition be performed rapidly to avoid measurements that are corrupted by sample movement. Several variations of the confocal principle have been incorporated into microscopes that can achieve fine optical sectioning, high frame rate, and high signal-to-noise ratio (SNR), while minimally perturbing biological samples. In this article we present some of the challenges and the requirements that are tied to imaging live samples and discuss how these are addressed by three optical versions of fast confocal microscopes: single-beam point scanning, spinning-disk, and slit-scanning confocal microscopes. Finally, we show that, for samples undergoing periodic motions, dynamic 3D image representations with virtually identical frame rates as in the case of two-dimensional (2D) imaging can be achieved via postacquisition image synchronization. These tools and techniques open new avenues for imaging fast dynamic processes in biology.
Analysis of Cytokinin Mutants and Regulation of Cytokinin Metabolic Genes Reveals Important Regulatory Roles of Cytokinins in Drought, Salt and Abscisic Acid Responses, and Abscisic Acid Biosynthesis
Authors: Nishiyama Rie , Watanabe Yasuko , Fujita Yasunari , Le Dung Tien , Kojima Mikiko , Werner Tomás , Vankova Radomira , Yamaguchi-Shinozaki Kazuko , Shinozaki Kazuo , Kakimoto Tatsuo , Sakakibara Hitoshi , Schmülling Thomas , Tran Lam-Son Phan
Published: July 2011

Cytokinins (CKs) regulate plant growth and development via a complex network of CK signaling. Here, we perform functional analyses with CK-deficient plants to provide direct evidence that CKs negatively regulate salt and drought stress signaling. All CK-deficient plants with reduced levels of various CKs exhibited a strong stress-tolerant phenotype that was associated with increased cell membrane integrity and abscisic acid (ABA) hypersensitivity rather than stomatal density and ABA-mediated stomatal closure. Expression of the Arabidopsis thaliana ISOPENTENYL-TRANSFERASE genes involved in the biosynthesis of bioactive CKs and the majority of the Arabidopsis CYTOKININ OXIDASES/DEHYDROGENASES genes was repressed by stress and ABA treatments, leading to a decrease in biologically active CK contents. These results demonstrate a novel mechanism for survival under abiotic stress conditions via the homeostatic regulation of steady state CK levels. Additionally, under normal conditions, although CK deficiency increased the sensitivity of plants to exogenous ABA, it caused a downregulation of key ABA biosynthetic genes, leading to a significant reduction in endogenous ABA levels in CK-deficient plants relative to the wild type. Taken together, this study provides direct evidence that mutual regulation mechanisms exist between the CK and ABA metabolism and signals underlying different processes regulating plant adaptation to stressors as well as plant growth and development.
Interference of E2‐2‐mediated effect in endothelial cells by FAM96B through its limited expression of E2‐2
Authors: Yang Weiwen , Itoh Fumiko , Ohya Hirotoshi , Kishimoto Fukiko , Tanaka Aya , Nakano Naoko , Itoh Susumu , Kato Mitsuyasu
Published: July 2011

The basic helix–loop–helix protein E2‐2 is known to play a role in quiescence of endothelial cells (ECs). However, it is unclear how the activity of E2‐2 is controlled in the cells. In this study, we identified FAM96B as an interaction partner of E2‐2. FAM96B interfered with E2‐2‐mediated effects on luciferase reporter activities. Furthermore, the suppression of vascular endothelial growth factor receptor 2 promoter activity by E2‐2 was rescued by the expression of FAM96B in a dose‐dependent manner. Interestingly, FAM96B decreased the expression of ectopic and endogenous E2‐2 proteins. Mutational analysis revealed that the middle region of FAM96B is required for the limited expression of E2‐2 protein. When FAM96B was expressed in ECs, the EC migration, proliferation, and tube formation were potentiated. Taken together, these findings suggest that FAM96B acts as a regulator of E2‐2 through the control of its protein expression. (Cancer Sci 2011; 102: 1808–1814)
Cytoskeletal and membrane remodelling during malaria parasite invasion of the human erythrocyte
Authors: Zuccala Elizabeth S. , Baum Jake
Published: July 2011

Erythrocytes are remarkably dynamic structures, possessing multiple and complex pathways for regulating cell membrane properties to compensate for the absence of a nucleus and internal membranes. Unlike the invasion strategies of many viruses and bacteria into their eukaryotic hosts, however, the accepted model for malaria parasite entry into human erythrocytes casts the host cell in a largely passive role. This is in contrast to mounting evidence for a suite of dynamic alterations that the erythrocyte membrane undergoes during the rapid process of invasion by the blood stage malaria parasite – the merozoite. Here we review the cellular and molecular basis for merozoite invasion of the erythrocyte and explore the idea that radical changes in the erythrocyte membrane protein and lipid architecture probably accompany this key step in the establishment of human malaria disease.
Diagnosis of Burkitt lymphoma using an algorithmic approach – applicable in both resource‐poor and resource‐rich countries
Authors: Naresh Kikkeri N. , Ibrahim Hazem A. H. , Lazzi Stefano , Rince Patricia , Onorati Monica , Ambrosio Maria R. , Bilhou‐Nabera Chrystèle , Amen Furrat , Reid Alistair , Mawanda Michael , Calbi Valeria , Ogwang Martin , Rogena Emily , Byakika Bessie , Sayed Shahin , Moshi Emma , Mwakigonja Amos , Raphael Martine , Magrath Ian , Leoncini Lorenzo
Published: July 2011

Distinguishing Burkitt lymphoma (BL) from B cell lymphoma, unclassifiable with features intermediate between diffuse large B‐cell lymphoma (DLBCL) and BL (DLBCL/BL), and DLBCL is challenging. We propose an immunohistochemistry and fluorescent in situ hybridization (FISH) based scoring system that is employed in three phases – Phase 1 (morphology with CD10 and BCL2 immunostains), Phase 2 (CD38, CD44 and Ki‐67 immunostains) and Phase 3 (FISH on paraffin sections for MYC, BCL2, BCL6 and immunoglobulin family genes). The system was evaluated on 252 aggressive B‐cell lymphomas from Europe and from sub‐Saharan Africa. Using the algorithm, we determined a specific diagnosis of BL or not‐BL in 82%, 92% and 95% cases at Phases 1, 2 and 3, respectively. In 3·4% cases, the algorithm was not completely applicable due to technical reasons. Overall, this approach led to a specific diagnosis of BL in 122 cases and to a specific diagnosis of either DLBCL or DLBCL/BL in 94% of cases that were not diagnosed as BL. We also evaluated the scoring system on 27 cases of BL confirmed on gene expression/microRNA expression profiling. Phase 1 of our scoring system led to a diagnosis of BL in 100% of these cases.
Central cervical lymph node metastases in papillary thyroid cancer: a systematic review of imaging‐guided and prophylactic removal of the central compartment
Authors: Mulla Mubashir , Schulte Klaus‐Martin
Published: July 2011

Background  Papillary thyroid cancer (PTC) is a common endocrine cancer and commonly presents with lymph node (LN) metastases. The role of surgical removal of the central cervical LN compartment is poorly defined. There are no prospective randomized controlled trials addressing the relevance to the extent of the initial surgical approach.

Design and Methods  A systematic review of studies of patients with PTC undergoing either prophylactic or therapeutic lymphadenectomy of the central LNs was carried out. Studies involving imaging modalities in the detection of LNs in PTC were also analysed.

Results  Twenty‐one studies contained data on 4188 patients undergoing prophylactic or imaging‐guided removal of the central compartment. Imaging‐guided surgery retrieved cancerous central LNs in 346 or 30% of eligible patients, whilst prophylactic central neck dissection yielded histopathological proof of cancer in 898 or 26·2% of patients. Five imaging studies revealed data on the use of ultrasound (US) and/or computerized tomography (CT). The sensitivity of US and CT was poor, ranging from 50% to 70% when accurately calculated.

Conclusion  Metastatic central LNs are found in nearly half of all patients with PTC when prophylactic central lymph node dissection (CLND) is performed. With unreliable imaging modalities, prophylactic CLND should be performed on all patients with PTC.
Adenoma granulation pattern correlates with clinical variables and effect of somatostatin analogue treatment in a large series of patients with acromegaly
Authors: Fougner Stine Lyngvi , Casar‐Borota Olivera , Heck Ansgar , Berg Jens Petter , Bollerslev Jens
Published: July 2011

Context  Somatotroph adenomas have been classified into densely granulated (DG) and sparsely granulated (SG) tumours with a transitional, intermediate group. Gsp oncogenes are activating mutations in the Gsα subunit gene, found in approximately 40% of somatotroph adenomas.

Objectives  To explore granulation pattern and presence of gsp oncogene in acromegaly with correlations to clinical and biochemical variables and to the effect of treatment with somatostatin analogues (SA), as well as to describe granulation pattern in adenomas with and without SA pretreatment.

Design/settings/patients  Seventy‐eight patients with active acromegaly were included. Long‐term SA efficacy was evaluated in 29 patients treated preoperatively and in ten treated postoperatively. Granulation pattern was examined, as were immunohistochemical analyses for E‐cadherin and SSTR2a. Protein levels of E‐cadherin and SSTR2a were measured (Western blot). Gsp mutation analysis was available for 74 adenomas.

Results  DG adenomas and the transitional group had higher serum levels of IGF‐1 per tumour volume than SG (P = 0·009; P = 0·005). Acute and long‐term SA responses were lower in SG (P = 0·001; P = 0·043). No correlation between gsp mutation and granulation was found, and no difference in granulation pattern according to preoperative SA treatment was demonstrated. A significant correlation between granulation and E‐cadherin was found, where SG had lowest immunohistochemical expression, substantiated by protein levels, and a highly significant gradient was observed from DG, through the transitional group, to SG.

Conclusions  Densely granulated adenomas were highly responsive to somatostatin analogues in contrast to SG adenomas. The transitional group behaved clinically more like DG adenomas. However, based on E‐cadherin, a marker of dedifferentiation, the transitional group seemed to be a true intermediate.
The lack of reproducibility of different distillation techniques and its impact on pear spirit composition
Authors: García‐Llobodanin Laura , Roca Jordi , López José Ramón , Pérez‐Correa José Ricardo , López Francisco
Published: July 2011

We analysed the impact of operation variability on the composition of pear spirits obtained with a Charentais alembic and a packed distillation column. Lack of reproducibility significantly affected the spirits’ compositions, with batch distillation columns more difficult to operate reproducibly vs. traditional alembics. The composition of column distilled spirits differed more in esters, such as ethyl octanoate, ethyl decanoate and ethyl palmitate. In turn, alembic spirit compositions differed more in acetaldehyde and acetal. Moreover, column distilled spirits contained four times more esters, 20% more higher alcohols, 40% less acetaldehyde and 10% less methanol than alembic spirits. Spirits distilled with a rectification column were more concentrated in ethanol than alembic distilled spirits, although both distillation systems recovered the same amount of ethanol in the heart fraction.
The role of transient dynamics in biological pest control: insights from a host–parasitoid community
Authors: Kidd David , Amarasekare Priyanga
Published: July 2011

1.Identifying natural enemies that can maintain pests at low abundances is a priority in biological control. Here, we show that experiments combined with models generate new insights into identifying effective control agents prior to their release in the field. Using a host–parasitoid community (the harlequin bug and its egg parasitoids) as a model system, we report three key findings.

2.The interplay between the host's self‐limitation and the parasitoids’ saturating functional response causes the long‐term (steady‐state) outcomes for pest suppression to differ from those of short‐term (transient) dynamics. When the bug's self‐limitation is moderately strong, the parasitoid with the higher attack rate and conversion efficiency (Ooencyrtus) achieves greater host suppression in the long term, but its longer handling time causes long periods of transient dynamics during which the bug can reach high abundances; when the bug's self‐limitation is weak, host fluctuations amplify over time andOoencyrtusfails at host suppression altogether. In contrast, the parasitoid with the lower attack rate and conversion efficiency but the shorter handling time (Trissolcus) induces only weak transient fluctuations of short duration and can maintain the host at low abundances regardless of the strength of the bug's self‐limitation.

3.Release of multiple enemy species can compromise host suppression if an enemy that induces stronger transient fluctuations excludes one that induces weaker fluctuations. For instance,Ooencyrtusexcludes Trissolcus despite having a longer handling time because of its higher conversion efficiency. The model correctly predicts the time to exclusion observed in experiments, suggesting that it captures the key biological features of the host–parasitoid interaction.

4.Intraspecific interference reduces long‐term pest suppression but improves short‐term pest control by reducing the magnitude and duration of transient fluctuations.

5.These results highlight the importance of transient dynamics in pest suppression. Pests are unlikely to be strongly self‐limited because they attack crop monocultures. Hence, pest fluctuations are likely to dominate short‐term dynamics even when the long‐term outcome is a stable equilibrium. The tendency to induce strong transient fluctuations (e.g. through a long handling time) is therefore a crucial consideration when identifying effective pest control agents.
Predicting invasion success of forest pathogenic fungi from species traits
Authors: Philibert Aurore , Desprez‐Loustau Marie‐Laure , Fabre Bénédicte , Frey Pascal , Halkett Fabien , Husson Claude , Lung‐Escarmant Brigitte , Marçais Benoit , Robin Cécile , Vacher Corinne , Makowski David
Published: July 2011

1. Biological invasions are a major consequence of globalization and pose a significant threat to biodiversity. Because only a small fraction of introduced species become invasive, identification of those species most likely to become invasive after introduction is highly desirable to focus management efforts. The predictive potential of species‐specific traits has been much investigated in plants and animals. However, despite the importance of fungi as a biological group and the potentially severe effects of pathogenic fungi on agrosystems and natural ecosystems, the specific identification of traits correlated with the invasion success of fungi has not been attempted previously.

2. We addressed this question by constructing anad hocdata set including invasive and non‐invasive species of forest pathogenic fungi introduced into Europe. Data were analysed with a machine learning method based on classification trees (Random Forest). The performance of the classification rule based on species traits was compared with that of several random decision rules, and the principal trait predictors associated with invasive species were identified.

3. Invasion success was more accurately predicted by the classification rule including biological traits than by random decision rules. The effect of species traits was maintained when confounding variables linked to residence time and habitat availability were included. The selected traits were unlikely to be affected by a phylogenetic bias as invasive and non‐invasive species were evenly distributed in fungal clades.

4. The species‐level predictors identified as useful for distinguishing between invasive and non‐invasive species were traits related to long‐distance dispersal, sexual reproduction (in addition to asexual reproduction), spore shape and size, number of cells in spores, optimal temperature for growth and parasitic specialization (host range and infected organs).

5. Synthesis and applications. This study demonstrates that some species‐level traits are predictors of invasion success for forest pathogenic fungi in Europe. These traits could be used to refine current pest risk assessment (PRA) schemes. Our results suggest that current schemes, which are mostly based on sequential questionnaires, could be improved by taking into account trait interactions or combinations. More generally, our results confirm the interest of machine learning methods, such as Random Forest, for species classification in ecology.
Transient elastography for predicting clinical outcomes in patients with chronic liver disease
Authors: Klibansky D. A. , Mehta S. H. , Curry M. , Nasser I. , Challies T. , Afdhal N. H.
Published: July 2011

Summary.  There is increasing interest in developing noninvasive means to evaluate liver fibrosis in patients with chronic liver disease to determine disease severity, prognosis and optimal treatment. Transient elastography (TE) has previously been demonstrated to predict the presence or absence of advanced fibrosis. The current study was conducted to determine whether TE can identify patients with chronic liver disease at risk of clinical decompensation. A total of 667 patients underwent TE and were followed for a median of 861 days and 57 patients achieved the primary outcome, a composite of clinical endpoints including death, ascites, encephalopathy, increased Child Score ≥2, variceal bleed, hepatocellular carcinoma or listing for transplant. Overall, TE had an area under the receiver operating characteristic curve of 0.87 for predicting clinical outcome. Using a cut‐off of 10.5 kPa, TE has a sensitivity, specificity, positive predictive value and negative predictive value (NPV) of 94.7%, 63.0%, 19.3% and 99.2%, respectively. A predictive model for clinical events was developed using generalized cross‐validation for clinical endpoints considering TE, liver biopsy results and multiple other predictors. Individually, TE performed better than biopsy, or any other variable, for predicting clinical outcome [Harrell’s C Statistic 0.86 for TE, 0.78 for stage]. Patients with a TE score of >12.5 kPa were found to have a relative hazard for clinical event of 18.99 compared with patients with TE score <10.5. A combined variable model including TE, aspartate aminotransferase/alanine aminotransferase ratio and model for end‐stage liver disease (MELD) yielded the highest predictive accuracy with Harrell’s C value of 0.93. In the subset of patients with cirrhosis, TE was not found to be independently associated with clinical outcomes in univariate or multivariate analysis although it retained a high sensitivity and NPV of 97.5% and 92.3%, respectively, at a kPa cut‐off of 10.5. TE can successfully identify patients with chronic liver disease who are at low risk of clinical decompensation over a time period of 2 years.
Water stress, shoot growth and storage of non‐structural carbohydrates along a tree height gradient in a tall conifer
Authors: WOODRUFF DAVID R. , MEINZER FREDERICK C.
Published: July 2011

We analysed concentrations of starch, sucrose, glucose and fructose in upper branch wood, foliage and trunk sapwood of Douglas‐fir trees in height classes ranging from ∼2 to ∼57 m. Mean concentrations of non‐structural carbohydrates (NSC) for all tissues were highest in the tallest height class and lowest in the lowest height class, and height‐related trends in NSC were most pronounced in branches. Throughout a 17‐month sampling period, mean values of branch NSC from the 57 m trees ranged between 30 and 377% greater than the 2 m trees. Branch NSC was inversely correlated with midday shoot water potential (Ψl), shoot osmotic potential at full turgor (Ψ) and shoot extension. Temporal fluctuation in branch NSC was inversely correlated with height, and positively correlated with midday Ψl, Ψ and shoot extension. The positive correlation between height and storage of NSC, and the negative correlation between NSC storage and shoot extension provide evidence that size‐related growth decline in trees is not strongly associated with constraints on photosynthesis. The negative correlation between height and fluctuation in NSC suggests that mobilization of photosynthate in taller trees is constrained by some factor such as reductions in turgor‐driven cell expansion or constraints on phloem transport.
Regular provision of outreach increases acceptance of cataract surgery in South India
Authors: Finger Robert P. , Kupitz David G. , Holz Frank G. , Chandrasekhar Seetha , Balasubramaniam Bharath , Ramani Ramanathan V. , Gilbert Clare E.
Published: July 2011

Objectives  The prevalence of visual loss and blindness from cataract remains high in India. Marginalized communities are frequently reached through outreach clinics. The aim of this study was to explore the hypothesis that regular outreach, held in the same location by the same provider, leads to greater acceptance of cataract surgery than outreach clinics that are irregular in terms of timing and location.

Methods  The study was integrated into outreach clinics run in two districts by Sankara Eye Centre, Coimbatore, Southern India. A semi‐structured questionnaire was administered to patients who had attended outreach eye clinics and either accepted or not accepted the offer of cataract surgery.

Results  Overall acceptance of surgery was high (91.7%), being higher in the district with regular outreach (94.6%vs. 82.3%, P < 0.001). A total of 398 participants (240, 60% acceptors) were interviewed. Acceptors were more likely to live in smaller households and in supportive families than non‐acceptors who lived in larger families which could not provide support and where transport and distance were also barriers (P < 0.001). Attending regular outreach and having had first eye cataract surgery were independent predictors of acceptance in a logistic regression model.

Conclusion  The findings indicate the importance of providers building trust by organizing regular outreach in the same location. Previous eye surgery was also a strong predictor of accepting cataract surgery. To promote universal access to health care, marginalized rural communities will continue to need outreach for some time to come.
Comparable efficacy of a topical 0.0584% hydrocortisone aceponate spray and oral ciclosporin in treating canine atopic dermatitis
Authors: Nuttall Tim J. , McEwan Neil A. , Bensignor Emmanuel , Cornegliani Luisa , Löwenstein Christine , Rème Christophe A.
Published: July 2011

This study compared the efficacy of a 0.0584% hydrocortisone aceponate (HCA) spray (Cortavance®; Virbac SA) and ciclosporin (Atopica®; Novartis Animal Health) in canine atopic dermatitis in a single‐blind randomized controlled trial. Dogs received HCA (two sprays/100 cm2; n = 24) or ciclosporin (5 mg/kg; n = 21). Canine Atopic Dermatitis Extent and Severity Index (CADESI)‐03, pruritus (visual analog scale with grade descriptors) and owner scores (5‐point scales) were recorded every 28 days for 84 days. Intention‐to‐treat data were analysed. CADESI‐03 and pruritus significantly decreased over time (P < 0.0001), but there was no difference between the treatment groups (P = 0.91 and P = 0.52, respectively). Similar proportions of HCA‐ and ciclosporin‐treated dogs achieved ≥50% reductions in CADESI‐03 and pruritus scores at 28 days (CADESI‐03 58.3 and 57.1%, P = 0.76; pruritus 33.3 and 38.1%, P = 1.0), 56 days (CADESI‐03 70.8 and 81.0%, P = 1.0; pruritus 62.5 and 57.1%, P = 1.0) and 84 days (CADESI‐03 75 and 85.7%, P = 0.72; pruritus 65.2 and 57.1%, P = 0.76). The CADESI‐03 and pruritus scores were close to equivalence (0.47 and 0.51, respectively). By 84 days, every‐other‐day or twice‐weekly therapy was achieved in 13 of 24 HCA‐ and 12 of 21 ciclosporin‐treated dogs (P = 0.85). There were no significant differences in scores for efficacy (P = 0.82), tolerance (P = 0.62) and ease of administration (P = 0.25). Scores for tolerance (0.49) and administration (0.46) were close to equivalence. The score for efficacy favoured HCA (0.68). Mild adverse events were noted in six of 21 ciclosporin and none of 24 HCA dogs (P = 0.008). Five HCA‐treated dogs and three ciclosporin‐treated dogs were prematurely withdrawn (P = 0.7). In conclusion, HCA and ciclosporin proved equally effective in treating canine atopic dermatitis for up to 84 days.
Prediction of improved liver function after balloon‐occluded retrograde transvenous obliteration: Relation to hepatic vein pressure gradient
Authors: Uehara Hideo , Akahoshi Tomohiko , Tomikawa Morimasa , Kinjo Nao , Hashimoto Naotaka , Nagao Yoshihiro , Kamori Masahiro , Maehara Yoshihiko
Published: July 2011

Background and Aims:  Balloon‐occluded retrograde transvenous obliteration (B‐RTO) is an effective treatment for gastric varices (GVx), as well as hepatic encephalopathy. The aim of this study was to examine the changes of the hepatic vein pressure gradient (HVPG) after B‐RTO and determine the relation between the changes of HVPG and liver function.

Patients and Methods:  B‐RTO was performed in 30 patients with GVx and hepatic encephalopathy. HVPG was measured in 19 of 30 patients both before and after B‐RTO.

Results:  The B‐RTO was successful in all patients. The GVx and hepatic encephalopathy were improved, and no recurrence or bleeding was observed within the follow‐ up period. The serum albumin and prothrombin activity were significantly improved 6 months after B‐RTO in all patients. HVPG was elevated 44% above the baseline after B‐RTO. Liver function significantly improved 6 months after B‐RTO in patients whose HVPG increased ≥ 20% from baseline.

Conclusion:  An elevated HVPG after B‐RTO is one aspect of the effect of liver function, and an HVPG increase of ≥ 20% from baseline is a predictive factor for obtaining an improvement of liver function.
Is speech and language therapy effective for children with primary speech and language impairment? Report of a randomized control trial
Authors: Broomfield Jan , Dodd Barbara
Published: July 2011

Background:A randomized controlled trial was conducted of a whole‐service cohort of children referred to the Paediatric Speech and Language Therapy Service of Middlesbrough Primary Care Trust between January 1999 and April 2000. The 730 children involved, aged up to 16 years, were diagnosed with primary speech and/or language impairment in the absence of any learning, physical or sensory difficulty.

Aims:The study considered outcomes of treatment versus no treatment.

Methods & Procedures:Treatment involved clinic‐based interventions, provided according to local departmental criteria and care pathways, averaging 5.5 h (range 0–24 h) of contact during the 6‐month period immediately following initial assessment. Assessments occurred within 8 weeks of referral and intervention began immediately thereafter.

Outcomes & Results:Treatment was significantly more effective than no treatment, over 6 months, both overall (p< 0.001) and for each of the three diagnostic categories (comprehension, expression and speech, eachp< 0.001).

Conclusions:An average of 6 h of speech and language therapy in a 6‐month period can produce significant improvement in performance, and it has been shown to be more effective than no treatment over the same 6‐month period for children with primary speech and/or language impairment.
Primary full‐gland prostate cryoablation in older men (> age of 75 years): results from 860 patients tracked with the COLD Registry
Authors: Dhar Nivedita , Ward John F. , Cher Michael L. , Jones J. Stephen
Published: July 2011

Study Type – Therapy (outcomes research)

Level of Evidence 2c

What's known on the subject? and What does the study add?

Most elderly patient with prostate cancer undergo radiation therapy, but cryoablation has gained popularity. This study demonstrates the safety and efficiency of this new approach.

OBJECTIVE

To report on the largest data set regarding outcomes for whole gland prostate cryoablation as a primary treatment of prostate cancer in older men, which we empirically defined as age >75 years.

MATERIALS AND METHODS

The COLD (Cryo On‐Line Data) Registry consists of case report forms with pre‐ and post‐treatment information obtained from patients undergoing prostate cryoablation.

A total of 860 patients were stratified into low‐, intermediate‐ and high‐risk groups (D'Amico 2003 risk definitions).

Biochemical disease‐free survival (bDFS) was defined according to the traditional American Society for Therapeutic Radiology and Oncology definition (3 increases) and the newer (Phoenix) definition (nadir +2).

Biopsy was performed at physician discretion but most commonly for cause if a patient had an increasing or suspicious prostate‐specific antigen level (PSA).

RESULTS

The median age was 79 years (76–91) and the median follow‐up was 16 months (4–60).

The 5‐year [95% confidence interval (CI)] bDFS for the entire population using ASTRO and Phoenix definitions was 79% (4%) and 62.6% (8.3%), respectively.

Stratified by risk group, 5‐year bDFS (ASTRO) was 82.4% (7.9%), 78.3% (5.8%) and 77.6% (7.7%) for low, moderate and high risk, respectively.

Using the Phoenix definition, 5‐year bDFS was 74.9%± 15.3%, 61.4%± 13.2% and 58.0%± 11.9% for low‐, moderate‐ and high‐risk groups, respectively.

Incontinence was reported in eight patients (0.9%).

CONCLUSION

Whole gland cryoablation in older men maintains oncological efficacy similar to that of younger men without increased morbidity.
Multilocular cystic renal cell carcinoma: clinicopathological features and preoperative prediction using multiphase computed tomography
Authors: You Dalsan , Shim Myungsun , Jeong In Gab , Song Cheryn , Kim Jeong Kon , Ro Jae Y. , Hong Jun Hyuk , Ahn Hanjong , Kim Choung‐Soo
Published: July 2011

Study Type – Diagnostic (exploratory cohort)

Level of Evidence 2b

What’s known on the subject? and What does the study add?

Multilocular cystic renal cell carcinoma (MCRCC), defined according to the 2004 WHO classification, has good prognosis, which is not affected adversely by large tumour size or advanced stage. Thus nephron‐sparing surgery is proposed when MCRCC is suspected by preoperative radiologic criteria.

The present study confirms the low malignant potential of MCRCC. Additionally, the results of the present study provide a simple, useful criteria using a Bosniak classification and Hounsfield unit on multiphase computed tomography images to differentiate MCRCC from other cystic RCC.

OBJECTIVE

• To analyse the clinicopathological and radiological features of multilocular cystic renal cell carcinoma (MCRCC) and to determine the preoperative factors differentiating MCRCC from other cystic RCC (CRCC).

PATIENTS AND METHODS

• The medical records of 53 patients with complex cystic renal masses evaluated by multiphase computed tomography (CT), surgically removed and confirmed as sporadic RCC were reviewed.

• Of these 53 patients, 23 were classified as having MCRCC and 30 as other CRCCs, defined as RCCs with extensive cystic change or cystic necrosis.

• Another 22 patients were treated for complex cystic renal masses presumed to be RCC and diagnosed as having benign cyst.

RESULTS

• Benign cysts and MCRCCs were significantly more likely to be of Bosniak classification III than other CRCCs (77% vs 61% vs 27%, P= 0.001).

• The mean Hounsfield unit (HU) during the corticomedullary phase (CMP) was significantly higher in other CRCCs, with HU ≥38 having 83% sensitivity and 80% specificity for predicting other CRCCs.

• In a multiple regression model, Bosniak classification and mean HU during CMP were independent factors predictive of other CRCCs.

• In the 41 patients with masses >4 cm in diameter, the combination of Bosniak classification IV and HU ≥38 during CMP showed 63% sensitivity, 96% specificity, 91% positive predictive value and 80% negative predictive value, yielding 2% false‐positive and 15% false‐negative rates.

CONCLUSIONS

• The mean HU during CMP and Bosniak classification can differentiate MCRCC from other CRCCs.

• This could help in selecting an appropriate surgical method, such as nephron‐sparing surgery, for complex cystic renal masses >4 cm.
Evaluating the utility of a preoperative nomogram for predicting 90‐day mortality following radical cystectomy for bladder cancer
Authors: Taylor Jennifer M. , Feifer Andrew , Savage Caroline J. , Maschino Alexandra C. , Bernstein Melanie , Herr Harry W. , Donat S. Machele
Published: July 2011

Study Type – Prognosis (individual cohort)

Level of Evidence 2b

What's known on the subject? and What does the study add?

We know that patient fitness for surgery is a major predictor of morbidity and mortality after surgery.

We found the published nomogram did not incorporate several known clinical risk factors and its predictive value was only slightly better than using the patient's age and Charlson score to predict perioperative morality. This limitation may be related to the lack of availability of these factors in national databases for inclusion when creating a nomogram. In addition, there are elements that factor into postoperative patient care that are not easily measured, such as hospital‐stay pathways, ancillary staff expertise, supportive medical care, and surgeon ability.

OBJECTIVE

To evaluate the performance of the Isbarn nomogram for predicting 90‐day mortality following radical cystectomy in a contemporary series.

PATIENTS AND METHODS

We identified 1141 consecutive radical cystectomy patients treated at our institution between 1995 and 2005 with at least 90 days of follow‐up.

We applied the published nomogram to our cohort, determining its discrimination, with the area under the receiver operating characteristic curve (AUC), and calibration.

We further compared it with a simple model using age and the Charlson comorbidity score.

RESULTS

Our cohort was similar to that used to develop the Isbarn nomogram in terms of age, gender, grade and histology; however, we observed a higher organ‐confined (≤pT2, N0) rate (52% vs 24%) and a lower overall 90‐day mortality rate [2.8% (95% confidence interval 1.9%, 3.9%) vs 3.9%].

The Isbarn nomogram predicted individual 90‐day mortality in our cohort with moderate discrimination [AUC 73.8% (95% confidence interval 64.4%, 83.2%)].

In comparison, a model using age and Charlson score alone had a bootstrap‐corrected AUC of 70.2% (95% confidence interval 67.2%, 75.4%).

CONCLUSIONS

The Isbarn nomogram showed moderate discrimination in our cohort; however, the exclusion of important preoperative comorbidity variables and the use of postoperative pathological stage limit its utility in the preoperative setting.

The use of a simple model combining age and Charlson score yielded similar discriminatory ability and underscores the significance of individual patient variables in predicting outcomes.

An accurate tool for predicting postoperative morbidity/mortality following radical cystectomy would be valuable for treatment planning and counselling. Future nomogram design should be based on preoperative variables including individual risk factors, such as comorbidities.
Giving children a voice: children's positioning in family therapy
Authors: Moore Lynn , Seu Irene Bruna
Published: July 2011

Studies of users' views of family therapy have rarely explored the means by which children construct their experiences. Family interviews after a first session of therapy included thirteen children aged 8 to 15 years. An analysis of the transcripts demonstrated that, like adults, children draw on forms of explanation generated by acknowledged experts. They used discourses of counselling, therapy, consumerism and education to construct and assess their experiences. The ages of the children affected the construction and evaluation of therapy and the positions taken up in relation to adults. Older children demonstrated more independence from parents. Like adults, the children adopted a variety of stakes, their sophistication increasing with age, suggesting a developmental path towards full membership of adult discursive communities. Recognition that children are active in construing therapy should enhance therapists' insights and facilitate positive therapeutic relationships.
Political Culture, Flag Use and Freedom of Speech
Authors: Gelber Katharine
Published: July 2011

Flag use generates passionate debates that fundamentally turn on questions of the appropriate extent and limits of freedom of speech. The national flag is a natural and forceful medium with which to express one's views about a nation. Yet its use in this way also generates controversy and emotionally charged reactions. The purpose of this article is to assess attitudes in political culture towards flag use in the context of wider freedom of speech considerations. By analysing events in Australia, the United States and New Zealand, the article argues that public responses to flag use as a medium of political expression demonstrate a flawed understanding of the meaning, import and effect of freedom of speech and its limits. This has significant implications, exposing the extent of fragility of freedom of speech on controversial issues, and its persistence despite differences between jurisdictions in the manner and extent of free speech protection.
Estimation of a Conditional Copula and Association Measures
Authors: VERAVERBEKE NOËL , OMELKA MAREK , GIJBELS IRÈNE
Published: July 2011

Abstarct.  This paper is concerned with studying the dependence structure between two random variables Y1 and Y2 conditionally upon a covariate X. The dependence structure is modelled via a copula function, which depends on the given value of the covariate in a general way. Gijbels et al. (Comput. Statist. Data Anal., 55, 2011, 1919) suggested two non‐parametric estimators of the ‘conditional’ copula and investigated their numerical performances. In this paper we establish the asymptotic properties of the proposed estimators as well as conditional association measures derived from them. Practical recommendations for their use are then discussed.
Estimation of Stratified Mark‐Specific Proportional Hazards Models with Missing Marks
Authors: SUN YANQING , GILBERT PETER B.
Published: July 2011

Abstract.  An objective of randomized placebo‐controlled preventive HIV vaccine efficacy trials is to assess the relationship between the vaccine effect to prevent infection and the genetic distance of the exposing HIV to the HIV strain represented in the vaccine construct. Motivated by this objective, recently a mark‐specific proportional hazards (PH) model with a continuum of competing risks has been studied, where the genetic distance of the transmitting strain is the continuous ‘mark’ defined and observable only in failures. A high percentage of genetic marks of interest may be missing for a variety of reasons, predominantly because rapid evolution of HIV sequences after transmission before a blood sample is drawn from which HIV sequences are measured. This research investigates the stratified mark‐specific PH model with missing marks where the baseline functions may vary with strata. We develop two consistent estimation approaches, the first based on the inverse probability weighted complete‐case (IPW) technique, and the second based on augmenting the IPW estimator by incorporating auxiliary information predictive of the mark. We investigate the asymptotic properties and finite‐sample performance of the two estimators, and show that the augmented IPW estimator, which satisfies a double robustness property, is more efficient.