bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of Multiple Virus Infections in the Conifer Pathogenic Fungi, Diplodia pinea and Diplodia scrobiculata
Authors: De Wet Juanita , Preisig Oliver , Wingfield Brenda D. , Wingfield Michael J. 
Published: July 2008

Abstract Diplodia pinea and Diplodia scrobiculata are opportunistic pathogens associated with various disease symptoms on conifers that most importantly include die‐back and stem cankers. Two viruses with dsRNA genomes, Sphaeropsis sapinea RNA virus 1 and 2 (SsRV1 and SsRV2) are found in D. pinea and an undescribed dsRNA element is known to occur in D. scrobiculata. We have partially characterized the putative RNA‐dependent RNA polymerase (RdRp) of the undescribed dsRNA element and designed virus‐specific primers from the RdRp regions of all three virus genomes. This made it possible to screen for the presence of the three viruses in a collection of D. pinea and D. scrobiculata isolates using real‐time PCR. Triple infections with all three viruses occurred in D. pinea and D. scrobiculata. Co‐infections with SsRV1 and SsRV2 were common but found only in D. pinea. Co‐infection with SsRV1 and the undescribed dsRNA element was rare and observed only in D. pinea. Single infections with either SsRV1 or SsRV2 were equally common, while the undescribed dsRNA element never occurred alone. SsRV1 occurred alone in both D. pinea and D. scrobiculata while SsRV2 occurred alone only in D. pinea. There were only two instances where the undescribed dsRNA element was observed in D. pinea and it was otherwise found only in D. scrobiculata. This study highlights the complex interactions between the viruses found in the closely related plant pathogenic fungi, D. pinea and D. scrobiculata. It illustrates the importance of not only characterizing viruses infecting fungi but also of determining the interactions between mycoviruses and their fungal hosts.
Occurrence and Partial Characterization of a Phytoplasma Associated with Phyllody Disease of Fennel (Foeniculum vulgare Mill.) in India
Authors: Bhat Alangar I. , Jiby Mary V. , Anandaraj Muthuswamy , Bhadramurthy Vemulapati , Patel Kirtikumar D. , Patel Nareshkumar R. , Jaiman Rakeshkumar K. , Agalodia Abbasbhai V. 
Published: July 2008

AbstractIn India, fennel showing symptoms of phyllody disease were noticed since 2003. As symptoms were suggestive of a phytoplasma infection, tissues were assayed by nested PCR using universal primers that amplify a 1.2‐kb phytoplasma 16S rDNA fragment. The phytoplasma specific fragment was amplified from diseased plants, but not from healthy plants, indicating that a phytoplasma was associated with fennel phyllody (FP) disease. On the basis of 16S rDNA sequence identity and phylogenetic relationship, it is concluded that FP belongs to peanut witches’ broom group and may be considered as a strain of the ‘Candidatus Phytoplasma aurantifolia’. This is the first report of occurrence and association of phytoplasma in fennel.
Granule‐bound starch synthase (GBSS) diversity of ancient wheat and related species
Authors: Caballero L. , Bancel E. , Debiton C. , Branlard G. 
Published: July 2008

AbstractGranule‐bound starch synthase of ancient wheat and related species was examined by sodium dodecyl sulphate polyacrylamide gel. A total of 13 different alleles were revealed in a collection of three accessions of diploid wheat, six accessions of tetraploid wheat, 49 accessions of spelt wheat, nine accessions of Sitopsis and two accessions of Aegilops tauschii. A new allele named Wx‐A1a′ appeared in four spelt wheat accessions. The tetraploid wheat accessions evaluated did not show any polymorphism; nevertheless the tetraploid accessions of Sitopsis section revealed three novel alleles. The novel allele Wx‐Ddn1g was found in two accessions of A. ventricosa and the Wx‐Ddcm1h and Wx‐Ddcm1i in two accessions of A. crassa. A novel allele named Wx‐Au1g was found in Triticum urartu, which is different from the also new Wx‐Am1h allele of T. monococcum. The diploid‐related species accessions revealed two novel alleles named Wx‐Bsl1h and Wx‐Bs1g found, respectively, in A. longissima and A. speltoides. The amylose content was measured for the different alleles found in all evaluated species and no significant effects of the allele composition on the amylose content were detected.
Barley adaptation and improvement in the Mediterranean basin
Authors: Pswarayi A. , Van Eeuwijk F. A. , Ceccarelli S. , Grando S. , Comadran J. , Russell J. R. , Francia E. , Pecchioni N. , Li Destri O. , Akar T. , Al‐Yassin A. , Benbelkacem A. , Choumane W. , Karrou M. , Ouabbou H. , Bort J. , Araus J. L. , Molina‐Cano J. L. , Thomas W. T. B. , Romagosa I. 
Published: July 2008

AbstractTo study barley adaptation and improvement in the Mediterranean basin, a collection of 188 entries comprising landraces and old genotypes and current modern varieties from the Mediterranean basin and elsewhere was tested on moisture‐contrasted environments in seven Mediterranean countries, during 2004 and 2005 harvest seasons. The experimental design consisted of an unreplicated trial for all entries, augmented by four repeated checks to which a partial replicate containing a quarter of the entries was added. Best Linear Unbiased Predictions (BLUPs) representing adjusted genotypic means were generated for individual trials using a mixed model. BLUPs were used for genotype by environment interaction analysis using main effect plus genotype by environment interaction (GGE) biplots of yield ranked data and for comparisons of landraces, old and modern genotypes using analysis of variance. Mean yields ranged from near crop failure to 6 t/ha. Local landraces were better adapted to environments yielding below 2 t/ha, thus breeding has mostly benefited environments yielding above 2 t/ha where modern genotypes out yielded landraces and old cultivars by 15%. Current barley selection is leading to specifically adapted genotypes.
The use of ISSR markers to identify Texas bluegrass interspecific hybrids
Authors: Goldman J. J. 
Published: July 2008

AbstractSeventeen ISSR primers were screened on Texas bluegrass (Poa arachnifera), Kentucky bluegrass (P. pratensis), Canadian bluegrass (P. compressa), Argentine bluegrass (P. ligularis), cv. ‘Sherman’ (P. secunda), putative Texas × Kentucky (TK) (P. arachnifera ×P. pratensis) hybrids and hybrids involving Texas, Canadian, and Sherman bluegrass [(P. arachnifera × P. compressa) × (P. arachnifera ×P. secunda)], to determine whether they could be used to produce robust and reproducible DNA fingerprints and identify interspecific hybrids. Nine of the 17 primers consistently produced robust fingerprints and nine 2‐way primer combinations were also selected. DNA fingerprints were highly reproducible and the majority of the selected primers (16/18) amplified hybrid profiles using two putative TK full‐sib hybrids. Combined with a rapid DNA extraction protocol, the ISSR technique enabled a fast and practical way to detect F1 interspecific hybrids early in the breeding programme and could also be useful for other applications that require DNA‐based markers.
Clinical Effect of alpha 1D/A adrenoceptor inhibitor naftopidil on Benign Prostatic Hyperplasia: An International Prostate Symptom Score and King's Health Questionnaire assessment
Authors: Awa Yusuke , Suzuki Hiroyoshi , Hamano Satoshi , Okano Tatsuya , Sakurayama Yuri , Ohki Takemasa , Egoshi Ken‐ichi , Ota Sho , Mori Ikuo , Ichikawa Tomohiko 
Published: July 2008

Objectives:  To examine the effect of alpha 1D/A adrenoceptor inhibitor naftopidil on health‐related quality of life (QOL) in men with benign prostatic hyperplasia (BPH).Methods:  A total of 56 newly diagnosed patients with symptomatic BPH were prospectively enrolled and treated with 50 mg naftopidil daily for more than 12 weeks. All underwent pre‐treatment documentation of lower urinary tract symptoms, QOL assessment using the international prostate symptom score (IPSS) and King's Health Questionnaire (KHQ), and uroflowmetry. A post‐treatment assessment was performed at 12 weeks.Results:  IPSS scores as well as QOL index showed a significant improvement after naftopidil administration. Similarly, all seven domains except general health perceptions and social limitations in the KHQ questionnaire were significantly improved. When dividing the patients into overactive bladder (OAB) and non‐OAB groups, only the OAB group showed significant improvement in almost all the domains of KHQ. Change ratios of the IPSS were not associated with those of KHQ domain scores in the OAB group. On the other hand, in the non‐OAB group more domains presented improvements, which were associated with those of IPSS scores.Conclusions:  Twelve‐week treatment with naftopidil for symptomatic BPH patients is associated with significant improvement in the IPSS, QOL index, maximum urinary flow rate, post‐void residual urine volume (PVR) and almost all domains in KHQ. KHQ is useful for the evaluation of clinical response in BPH patients, particularly in those with associated OAB.
A nomogram predicting metastatic progression after radical prostatectomy
Authors: Porter Christopher R , Suardi Nazareno , Kodama Koichi , Capitanio Umberto , Gibbons Robert P , Correa Roy , Jeldres Claudio , Perrotte Paul , Montorsi Francesco , Karakiewicz Pierre I 
Published: July 2008

Objectives:  To develop and internally validate a nomogram predicting the individual probability of metastatic progression after radical prostatectomy according to the length of disease‐free interval.Methods:  Cox regression modeled the probability of metastatic progression of prostate cancer in 752 patients treated with radical prostatectomy with a mean follow up of 11.6 years (median 11.4; range 0.1–40.5). The significance of the predictors was confirmed in competing risks analysis, which accounts for other causes of mortality. The Cox regression model‐based nomogram was internally validated with 200 bootstrap resamples.Results:  Eighty‐five of 752 patients (11.3%) developed metastatic progression. The 5, 10, 15 and 20‐year actuarial rates of metastatic progression‐free survival were, respectively, 95.9, 90.5, 84.8 and 80.5%. Pathological stage T3, elevated radical prostatectomy Gleason sum and delivery of adjuvant radiotherapy represented independent predictors of metastatic progression in both Cox and competing risks regression models, and constituted the nomogram predictors along with a fourth variable describing the presence of co‐morbidities. After 200 bootstrap resamples the nomogram achieved 80.2, 77.7, 77.6 and 76.0% accuracy in predicting metastatic progression at 5, 10, 15 and 20 years after radical prostatectomy.Conclusions:  Metastatic progression is a sign of poor prognosis in men with prostate cancer. Our nomogram is able to accurately predict the conditional probability of metastatic progression up to 20 years after radical prostatectomy.
Nine cases of nonpalpable testicular mass: an incidental finding in a large scale ultrasonography survey
Authors: Avci Ali , Erol Bulent , Eken Cenker , Ozgok Yasar 
Published: July 2008

Objectives:  Nonpalpable testicular masses are usually diagnosed during routine ultrasonography (US) examinations for other conditions. There are conflicting results on the final diagnosis and management of these lesions. In the present study we report the results of a large US series of 5104 patients on nonpalpable testicular masses and discuss the management of these patients.Methods:  This retrospective observational study was performed in a secondary care military hospital. A total of 5104 patients underwent a US and 11 of them were diagnosed as having a nonpalpable testicular mass. These 11 patients also underwent magnetic resonance imaging (MRI). Two of them refused surgery and were excluded from the study. The remaining nine patients underwent intraoperative US‐guided localization and excisional biopsy of the non‐palpable testicular parenchymal mass. A radical orchiectomy was required in all of them. US and MRI findings, frozen and final pathology results were recorded.Results:  The median age of study subjects was 24 years. The final pathology revealed a malign tumor in eight patients and an inflammatory mass in one patient. There were inconsistent results in four patients between frozen section analysis and final pathology. MRI improved the definition of the solid masses in all patients.Conclusions:  MRI enhances the certainty of the diagnosis of malignity in nonpalpable testicular masses, particularly in conditions that generally can not be diagnosed with ultrasonography alone. Frozen section analysis is not an accredited method in diagnosing malign lesions in non‐palpable testicular masses.
The identification of response regulator‐specific binding sites reveals new roles of two‐component systems in Bacillus cereus and closely related low‐GC Gram‐positives
Authors: de Been Mark , Bart Marieke J. , Abee Tjakko , Siezen Roland J. , Francke Christof 
Published: July 2008

SummaryIn bacteria, environmental challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two‐component systems (TCSs). A phylogenetic footprinting/shadowing approach was designed and used to identify many novel RR‐specific operators for species of the Bacillus cereus group and related Gram‐positives. Analysis of the operator sequences revealed characteristic traits for each RR subfamily. For instance, operators related to the largest subfamily (OmpR) typically consisted of direct repeats (e.g. TTAAGA‐N5‐TTAAGA), whereas operators related to the second largest family (NarL) consisted of inverted repeats (e.g. ATGACA‐N2‐TGTCAT). This difference indicates a fundamentally different organization of the bound RR dimers between the two subfamilies. Moreover, the identification of the specific operator motifs allowed relating several RRs to a minimal regulon and thereby to a characteristic transcriptional response. Mostly, these regulons comprised genes encoding transport systems, suggesting a direct coupling of stimulus perception to the transport of target compounds. New biological roles could be attributed to various TCSs, including roles in cytochrome c biogenesis (HssRS), transport of carbohydrates, peptides and/or amino acids (YkoGH, LytSR), and resistance to toxic ions (LiaSR), antimicrobial peptides (BceRS) and beta‐lactam antibiotics (BacRS, YcbLM). As more and more bacterial genome sequences are becoming available, the use of comparative analyses such as the approach applied in this study will further increase our knowledge of bacterial signal transduction mechanisms and provide directions for the assessment of their role in bacterial performance and survival strategies.
The microbial community of Vetiver root and its involvement into essential oil biogenesis
Authors: Del Giudice Luigi , Massardo Domenica Rita , Pontieri Paola , Bertea Cinzia M. , Mombello Domenico , Carata Elisabetta , Tredici Salvatore Maurizio , Talà Adelfia , Mucciarelli Marco , Groudeva Veneta Ivanova , De Stefano Mario , Vigliotta Giovanni , Maffei Massimo E. , Alifano Pietro 
Published: July 2008

SummaryVetiver is the only grass cultivated worldwide for the root essential oil, which is a mixture of sesquiterpene alcohols and hydrocarbons, used extensively in perfumery and cosmetics. Light and transmission electron microscopy demonstrated the presence of bacteria in the cortical parenchymatous essential oil‐producing cells and in the lysigen lacunae in close association with the essential oil. This finding and the evidence that axenic Vetiver produces in vitro only trace amounts of oil with a strikingly different composition compared with the oils from in vivo Vetiver plants stimulated the hypothesis of an involvement of these bacteria in the oil metabolism. We used culture‐based and culture‐independent approaches to analyse the microbial community of the Vetiver root. Results demonstrate a broad phylogenetic spectrum of bacteria, including α‐, β‐ and γ‐Proteobacteria, high‐G+C‐content Gram‐positive bacteria, and microbes belonging to the Fibrobacteres/Acidobacteria group. We isolated root‐associated bacteria and showed that most of them are able to grow by using oil sesquiterpenes as a carbon source and to metabolize them releasing into the medium a large number of compounds typically found in commercial Vetiver oils. Several bacteria were also able to induce gene expression of a Vetiver sesquiterpene synthase. These results support the intriguing hypothesis that bacteria may have a role in essential oil biosynthesis opening the possibility to use them to manoeuvre the Vetiver oil molecular structure.
Diversity of ring‐hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels
Authors: Bordenave Sylvain , Goñi‐urriza Marisol , Vilette Cécile , Blanchard Sophie , Caumette Pierre , Duran Robert 
Published: July 2008

SummaryThe aim of this work was to characterize bacterial ring‐hydroxylating dioxygenase (RHD) diversity in a pristine microbial mat and follow their diversity changes in response to heavy fuel oil contamination. In order to describe the RHDs diversity, new degenerate primers were designed and a nested‐PCR approach was developed to gain sensitivity and wider diversity. RHD diversity in artificially contaminated mats maintained in microcosms and in chronically contaminated mats was analysed by clone libraries and terminal restriction fragment length polymorphism (T‐RFLP) at genomic and transcriptomic levels. The RHD diversity in the pristine microbial mat was represented by Pseudomonas putida nahAc‐like genes and no increase of diversity was detected after 1 year of oil contamination. The diversity observed in a 30 year chronically polluted microbial mat was represented by four main RHD clusters and two new genes revealing higher polyaromatic hydrocarbon (PAH) degradation capacity. This study illustrates that a single petroleum contamination (such as oil spill) is not enough to involve a detectable modification of RHD diversity. The new degenerate primers described here allowed RHD gene amplification from pristine and contaminated samples thereby showing their diversity. The proposed approach solves one of the main problems of functional gene analysis providing effective amplification of the environmental diversity of the targeted genes.
Hand‐assisted laparoscopic colectomy versus standard laparoscopic colectomy: a cost analysis
Authors: Roslani A. C. , Koh D. C. , Tsang C. B. , Wong K. S. , Cheong W. K. , Wong H. B. 
Published: July 2008

AbstractObjective There is a relative dearth of literature comparing hand‐assisted (HALC) to standard (SLC) laparoscopic colectomies. HALC seems beneficial in terms of shorter operative times and lower conversion rates, but this is counterbalanced by a greater inflammatory response, larger incisions and higher direct costs. Nevertheless, these results are not consistent throughout existing studies and there are to date no detailed cost comparisons. Our hypothesis was that HALC would not incur significantly higher institutional costs compared with standard laparoscopic techniques.Method Patients undergoing either SLC or HALC between August 2004 and September 2006 were retrospectively reviewed. All patients were managed using a standard protocol. Outcomes assessed included operative times, conversion rates, pain scores, time to resolution of ileus, length of stay and complications. Total costs were calculated from the day of surgery. Statistical analyses included χ2, Fisher’s exact test, the Mann–WhitneyU‐test or nonparametric bootstrapping method.Results Seventy‐three patients underwent SLC while 101 had HALC. Demographics and indications for surgery in both groups were similar; the majority were performed for colorectal cancers. Operative times were shorter (147.5vs172.5 min,P < 0.05) and complication rates lower (28.7%vs45.2%,P < 0.025) for HALC. There was no significant difference in the other clinical outcomes. Operative costs and cost of consumables were higher for HALC (US$4024.2vsUS$3568.1,P = 0.01 and US$1724.7vsUS$1302.7,P < 0.001, respectively). However, total costs were not significantly different (HALC US$8999.8, SLC US$7910.7,P = 0.11).Conclusion Institutional costs are not significantly higher for HALC compared with SLC.
Extended total mesorectal excision in locally advanced rectal cancer (T4a) and the clinical role of MRI‐evaluated neo‐adjuvant downstaging
Authors: Larsen S. G. , Wiig J. N. , Emblemsvaag H. L. , Grøholt K. K. , Hole K. H. , Bentsen A. , Dueland S. , Vetrhus T. , Giercksky K.‐E. 
Published: July 2008

AbstractObjective  To compare the clinical ability of MRl taken before and after neo‐adjuvant treatment in locally advanced rectal cancer (LARC) to predict the necessary extension of TME (ETME) and the possibility to achieve a R0 resection.Method  Prospective registration of 92 MRI evaluated T4a cancers undergoing elective surgery between 2002 and 2007 in a tertiary referral centre for multimodal treatment of rectal cancer.Results  MRI identified patients in need of neo‐adjuvant treatment and predicted T‐downstaging in 10% and N‐downstaging in 59%. Seventy‐nine percent R0 resections, 18% R1 and 3% R2 were obtained after ETME in 95% of the patients and TME in the rest. Higher tumour regression grade (TRG) was achieved in higher ypT‐stage (P < 0.01). Preoperative chemo radiotherapy resulted in that more patients obtained TRG1‐3 compared to those receiving radiotherapy (79% vs. 57%, P = 0.02). The pelvic wall was the area of failure in 70% of the R1 resections. Tumour cells outside the mesorectal fascia scattered within fibrosis was found in 18 TRG2‐3 among 33 ypT4 tumours (55%).Conclusion  MRl cannot discriminate tumour within fibrosis. Therefore, if a R0 resection is the goal, we advocate optimal surgery in accordance with the pre‐treatment MRI. Post treatment MRI is a poor predictor of final histology and should not be relied upon to guide the extent of surgical resection. The study has initiated a new approach to histopathological classification of the removed specimen where we introduce a MRI assisted technique for investigating the areas at risk outside the mesorectal fascia in the specimen.
The use of a wound protector to prevent port site recurrence may not be totally logical
Authors: Seow‐Choen F. , Wan W.‐H. , Tan K.‐Y. 
Published: July 2008

AbstractThe wound protector has been used widely to prevent port site metastases (PSM). Although port site metastases ties in with poor survival, it is not because of PSM itself, but rather because PSM is a sign of more widespread metastatic disease. Whilst being touted as a method of preventing PSM, it fails to address the bigger issue of preventing intra‐abdominal recurrence. Proper surgical technique in tumour handling following rigorous oncological principles, and not just putting in a wound protector is the key to good surgery with low recurrences and excellent survival rates.