Methodological and reporting standards for quality-of-life data eligible for European Society for Medical Oncology-Magnitude of Clinical Benefit Scale (ESMO-MCBS) credit.

BACKGROUND: The European Society for Medical Oncology-Magnitude of Clinical Benefit Scale (ESMO-MCBS) has been developed to grade clinical benefit of cancer therapies. Improvement in quality of life (QoL) is considered relevant, especially in the non-curative setting. This is reflected by an upgrade of the preliminary ESMO-MCBS score if QoL is improved compared to the control arm or a downgrade if an improvement in progression-free survival is not paralleled by an improvement in QoL or overall survival. Given the importance of QoL for the final score, a need to ensure the robustness of QoL data was recognised. DESIGN: A checklist was created based on existing guidelines for QoL research. Field testing was carried out using clinical trials that either received an adjustment of the preliminary ESMO-MCBS score based on QoL or had QoL as the primary endpoint. Several rounds of revision and re-testing of the checklist were undertaken until a final consensus was reached. RESULTS: The final checklist consists of four items and can be applied if three prerequisites are met: (i) QoL is at least a secondary endpoint, (ii) evidence of reliability and validity of the instrument is provided, and (iii) a statistically and clinically significant improvement in QoL is observed. The four items on the checklist pertain to the (i) hypothesis, (ii) compliance and missing data, (iii) presentation of the results, and (iv) statistical and clinical relevance. Field testing revealed that a clear QoL hypothesis and correction for multiple testing were mostly lacking, while the main statistical method was always described. CONCLUSIONS: Implementation of the ESMO-MCBS QoL checklist will facilitate objective and transparent decision making on QoL data within the ESMO-MCBS scoring process. Trials published until 1 January 2025 will have to meet the prerequisites and at least two items for crediting QoL benefit in the final ESMO-MCBS score. Trials published thereafter will have to meet all four items.

Tuscany Sangiovese grape juice imparts cardioprotection by regulating gene expression of cardioprotective C-type natriuretic peptide.

PURPOSE: A regular intake of red grape juice has cardioprotective properties, but its role on the modulation of natriuretic peptides (NPs), in particular of C-type NP (CNP), has not yet been proven. The aims were to evaluate: (1) in vivo the effects of long-term intake of Tuscany Sangiovese grape juice (SGJ) on the NPs system in a mouse model of myocardial infarction (MI); (2) in vitro the response to SGJ small RNAs of murine MCEC-1 under physiological and ischemic condition; (3) the activation of CNP/NPR-B/NPR-C in healthy human subjects after 7 days' SGJ regular intake. METHODS: (1) C57BL/6J male and female mice (n = 33) were randomly subdivided into: SHAM (n = 7), MI (n = 15) and MI fed for 4 weeks with a normal chow supplemented with Tuscany SGJ (25% vol/vol, 200 µl/per day) (MI + SGJ, n = 11). Echocardiography and histological analyses were performed. Myocardial NPs transcriptional profile was investigated by Real-Time PCR. (2) MCEC-1 were treated for 24 h with a pool of SGJ small RNAs and cell viability under 24 h exposure to H2O2 was evaluated by MTT assay. (3) Human blood samples were collected from seven subjects before and after the 7 days' intake of Tuscany SGJ. NPs and miRNA transcriptional profile were investigated by Real-Time PCR in MCEC-1 and human blood. RESULTS: Our experimental data, obtained in a multimodal pipeline, suggest that the long-term intake of SGJ promotes an adaptive response of the myocardium to the ischemic microenvironment through the modulation of the cardiac CNP/NPR-B/NPR-C system. CONCLUSIONS: Our results open new avenue in the development of functional foods aimed at enhancing cardioprotection of infarcted hearts through action on the myocardial epigenome.

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks.

The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.

UNLABELLED: The version of this article published in BMC Genomics 2009, 10:558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper. BACKGROUND: MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. RESULTS: Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts. CONCLUSIONS: Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.

The role of barren stalk1 in the architecture of maize.

The architecture of higher plants is established through the activity of lateral meristems--small groups of stem cells formed during vegetative and reproductive development. Lateral meristems generate branches and inflorescence structures, which define the overall form of a plant, and are largely responsible for the evolution of different plant architectures. Here, we report the isolation of the barren stalk1 gene, which encodes a non-canonical basic helix-loop-helix protein required for the initiation of all aerial lateral meristems in maize. barren stalk1 represents one of the earliest genes involved in the patterning of maize inflorescences, and, together with the teosinte branched1 gene, it regulates vegetative lateral meristem development. The architecture of maize has been a major target of selection for early agriculturalists and modern farmers, because it influences harvesting, breeding strategies and mechanization. By sampling nucleotide diversity in the barren stalk1 region, we show that two haplotypes entered the maize gene pool from its wild progenitor, teosinte, and that only one was incorporated throughout modern inbreds, suggesting that barren stalk1 was selected for agronomic purposes.

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.

BACKGROUND: MicroRNAs are short (approximately 21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. RESULTS: Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts. CONCLUSION: Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.

Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in two maize recombinant inbred line populations.

The genetic architecture underlying resistance in maize to southern leaf blight (SLB) caused by Cochliobolus heterostrophus race O is not well understood. The objective of this study was to identify loci contributing to SLB resistance in two recombinant inbred line populations and to compare these to SLB resistance loci in other populations. The two populations used were derived from crosses between maize inbred lines H99 and B73 (HB population-142 lines) and between B73 and B52 (BB population-186 lines). They were evaluated for SLB resistance and for days from planting to anthesis (DTA) in 2005 and 2006. Two replications arranged as randomized complete blocks were assessed in each year for each population. Entry mean heritabilities for disease resistance were high for both populations (0.876 and 0.761, respectively). Quantitative trait loci (QTL) for SLB resistance were identified in bins 3.04 (two QTL), 6.01, and 8.05 in the HB population and in bin 2.07 in the BB population. No overlap of DTA and SLB resistance QTL was observed, nor was there any phenotypic correlation between the traits. A comparison of the results of all published SLB resistance QTL studies suggested that bins 3.04 and 6.01 are 'hotspots' for SLB resistance QTL.

Characterization of transformation related genes in oral cancer cells.

A cDNA representational difference analysis (cDNA-RDA) and an arrayed filter technique were used to characterize transformation-related genes in oral cancer. From an initial comparison of normal oral epithelial cells and a human papilloma virus (HPV)-immortalized oral epithelial cell line, we obtained 384 differentially expressed gene fragments and arrayed them on a filter. Two hundred and twelve redundant clones were identified by three rounds of back hybridization. Sequence analysis of the remaining clones revealed 99 unique clones corresponding to 69 genes. The expression of these transformation related gene fragments in three nontumorigenic HPV-immortalized oral epithelial cell lines and three oral cancer cell lines were simultaneously monitored using a cDNA array hybridization. Although there was a considerable cell line-to-cell line variability in the expression of these clones, a reliable prediction of their expression could be made from the cDNA array hybridization. Our study demonstrates the utility of combining cDNA-RDA and arrayed filters in high-throughput gene expression difference analysis. The differentially expressed genes identified in this study should be informative in studying oral epithelial cell carcinogenesis.

Ritleng intubation system for treatment of congenital nasolacrimal duct obstruction.

Twenty-eight patients (34 eyes) with congenital nasolacrimal duct obstruction underwent silicone intubation with the Ritleng lacrimal intubation system. The technique involves introduction of a Prolene (Ethicon Inc, Somerville, NJ) monofilament guide thread, securely fastened to the silicone tubing, into a tubular metal probe that opens into the inferior meatus. The outcome was evaluated in terms of ease of intubation and objective success rate. Thirty-two (94%) of the 34 lacrimal systems were successfully intubated with the Ritleng system. Difficulty passing the Prolene thread through the probe and out the tip, necessitating conversion to a Crawford intubation system, was encountered in only 2 eyes (6%). The Prolene spontaneously emerged from the nose in 24 (75%) of 32 eyes, making retrieval simple and uncomplicated. The success rate for relieving signs and symptoms of obstruction was 97% (31/32) for the eyes with the Ritleng system and 100% (2/2) for the eyes with the Crawford system. Bicanalicular silicone intubation with the Ritleng intubation system is an easy and effective technique for treatment of congenital nasolacrimal duct obstruction.

Application of magnetic resonance imaging and ultrasonography to preoperative evaluation of masseteric hypertrophy.

A case of unilateral masseteric hypertrophy in a 30-year-old man is described. Preoperative evaluation was performed by magnetic resonance imaging (MRI), computed tomography (CT) and ultrasonography (USG). MRI could delineate not only the border between medial and lateral layers of the masseter but also delineate the hypertrophic portion. MRI also provided more information in respect of the masseter muscle as well as the other masticatory muscles and the surrounding tissues than CT. USG was useful because of its real-time processing, especially in this case where facial asymmetry was emphasized during mastication. We resected the medial lower-half of the masseter intraorally based on these imagings and obtained a successful result.

The anti-tumor effect of photodynamic therapy evaluated by bromodeoxyuridine immunohistochemistry.

The anti-tumor effect of photodynamic therapy (PDT) on mouse tumors was evaluated with bromodeoxyuridine (BrdU) immunohistochemistry. BrdU was injected into the mice intraperitoneally (40 mg/kg body weight). Immediately after injection of BrdU, PDT using a photosensitizing drug (hematoporphyrin oligomers: 20 mg/kg body weight) was carried out on the experimental group but not on the control group. BrdU labeling indices (LIs) of the tumor cells close to blood vessels and adjacent to the surrounding normal tissue were investigated. In the tumor cells close to blood vessels, the LIs of the experimental group were significantly lower than those of the control group. As for the tumor cells adjacent to the surrounding normal tissue, the LIs of the experimental group were similar to those of the control group. Thus, the effect of PDT was significant in the tumor cells close to the blood vessels, while the tumor cells adjacent to the surrounding normal tissue resisted PDT.

Bromodeoxyuridine immunohistochemistry for evaluating age-related changes in the rat mandibular condyle decalcified by intravenous infusion.

Age-related changes in cell proliferation kinetics of the mandibular condyle were studied in Sprague-Dawley rats using bromodeoxyuridine (BrdUrd) immunohistochemistry in decalcified, paraffin-embedded tissues. Intraperitoneal injection of 40 mg/kg BrdUrd was given 1 hr before animal sacrifice. Continuous perfusion of EDTA solution via the left ventricle shortened the decalcification time. Immunohistochemical staining was performed with monoclonal anti-BrdUrd antibody. BrdUrd labeled cells, i.e., the S-phase cells, were clearly visible with well-preserved cytological detail. Their nuclei exhibited homogeneously stained granules. The labeling index in the intermediate zone of the condyle decreased with increasing age of the animals. This method is useful for evaluating physiological and pathological changes of the rat mandibular condyle as well as other bones and joints.

Enhanced polymer one-step staining for proliferating cell nuclear antigen in squamous cell carcinoma of the tongue.

A rapid enhanced polymer one-step staining for proliferating cell nuclear antigen (EPOS-PCNA) in formalin fixed, paraffin embedded sections of tongue squamous cell carcinoma is described. EPOS-PCNA was compared with PCNA immunohistochemistry using the avidin-biotin complex (ABC) method, with or without autoclave pretreatment. Significant correlation of PCNA labeling index (percentage of labeled cells/total cells counted) was observed between EPOS-PCNA and the immunohistochemical protocol using autoclave pretreatment. We consider this method a reliable, timesaving technique that would be useful in quantitative histopathology and in performing double immunostaining.

[Sarmiento's method of conservative treatment of leg fractures]. / Fractures de jambe traitement conservateur selon Sarmiento.

The authors present a prospective series of 32 fractures of the tibia, treated by Sarmiento's technique. Consolidation of the fracture has been obtained in 3 to 4 months. Five open tibia fractures healed in 4 months. Functional recovery is complete in 90% of the cases. Two failures needed late surgical treatment (one centro-medullary nailing and one plate-fixation). These fractures are studied in detail.

Exploring the genetic diversity of Ethiopian grass pea (Lathyrus sativus L.) using EST-SSR markers.

Expressed sequence tags (ESTs) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers for less-studied species. In this study, EST-simple sequence repeat (SSR) markers developed from Lathyrus sativus L. EST sequences and cross-transferable EST-SSRs derived from Medicago truncatula L. were utilized to investigate the genetic diversity among grass pea populations from Ethiopia. A total of 45 alleles were detected using eleven EST-SSRs with an average of four alleles per locus. The average polymorphism information content for all primers was 0.416. The average gene diversity was 0.477, ranging from 0.205 for marker Ls942 to 0.804 for MtBA32F05. F(ST) values estimated by analysis of molecular variance were 0.01, 0.15, and 0.84 for among regions, among accessions and within accessions respectively, indicating that most of the variation (84%) resides within accessions. Model-based cluster analysis grouped the accessions into three clusters, grouping accessions irrespective of their collection regions. Among the regions, high levels of diversity were observed in Gojam, Gonder, Shewa and Welo regions, with Gonder region showing a higher number of different alleles. From breeding and conservation aspects, conducting a close study on a specific population would be advisable for genetic improvement in the crop, and it would be appropriate if future collection and conservation plans give due attention to under-represented regions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9662-y) contains supplementary material, which is available to authorized users.

Addressing drought tolerance in maize by transcriptional profiling and mapping.

In order to unravel the genetic architecture underlying plant response to drought, we adopted an integrated approach, combining transcript profiling and quantitative trait loci (QTL) mapping. In fact, improving plant tolerance to water stress is an important, but, at the same time, a difficult task, since plant tolerance is the result of many complex mechanisms acting at different levels of plant organization, and its genetic basis is largely unknown. The phenotypic data, concerning yield components and flowering time, of a population of 142 maize Recombinant Inbred Lines (RILs), grown under well watered conditions or under water stress, were submitted to linkage analysis to detect drought-tolerance QTLs. Thirty genomic regions containing 50 significant QTLs distributed on nine chromosomes were identified. At the same time, a customized targeted oligoarray was used to monitor the expression levels of 1,000 genes, representative of the immature maize kernel transcriptome. Using this DNA array we compared transcripts from 10 days after pollination kernels of two susceptible and two drought tolerant genotypes (extracted from our RILs) grown under control and water stress field conditions. Two hundred and fifty-two genes were significantly affected by stress in at least one genotype. From a set of these, 49 new molecular markers were developed. By mapping most of them and by in silico mapping other regulated sequences, 88 differentially expressed genes were localized onto our linkage map, which, added to the existing 186 markers, brought their total number on the map to 274. Twenty-two of the 88 differentially expressed genes mapped in the same chromosomal segments harbouring QTLs for tolerance, thus representing candidate genes for further functional studies.

Effects of photodynamic therapy in the normal mouse tongue.

The effects of photodynamic therapy (PDT) on the normal mouse tongue were investigated. After using various doses (2.5, 10, and 20 mg/kg body wt) of the photosensitizing drug hematoporphyrin oligomers and 90 or 180 J/cm2 red light (630-nm) emitted from a pulsed neodymium:yttrium-aluminum-garnet dye laser was used to activate it 3 or 24 hours later. It was found that the 20-mg/kg dose elicited a severe response that included extensive vesicular and edema formation. A less severe response was observed with 10 mg/kg of the drug and low-power light (5 mJ/cm2/pulse) periodically delivered (1 hour interval between two 30-minute photoradiations). Such a regimen, however, produced more damage when compared with the higher power (15 mJ/cm2), continuous light delivery counterpart. Healing, except for the protocol with only a 3-hour drug-light interval, was attained by 5 days post-PDT as indicated by regeneration with histologically normal tissues and quantitatively a return to untreated, control values for cross-sectional areas and number of blood vessels. Bromodeoxyuridine immunohistochemistry disclosed an immediate increase in the labeling indices, ie, the percentage of S phase cycling cells, indicating stimulated cell proliferation secondary to repair and fast repopulation of the epithelium. Under the commonly used protocols, PDT was provided safely to the mouse tongue. The regimen of low drug dose and low power of light periodically delivered appears to be the most acceptable method. These parameter-dependent results may partly form the basis for the judicious application of PDT to the oral cavity.