bluuebunny/crossref_metadata_2025_split huggingface dataset:
A strategy for developing scientific sampling tools for fishery-independent surveys of estuarine fish in New South Wales, Australia
Authors: Rotherham D. , Underwood A. J. , Chapman M. G. , Gray C. A. 
Published: July 2007

Abstract
Rotherham, D., Underwood, A. J., Chapman, M. G., and Gray, C. A. 2007. A strategy for developing scientific sampling tools for fishery-independent surveys of estuarine fish in New South Wales, Australia. – ICES Journal of Marine Science, 64: 1512–1516. The limitations of using fishery-dependent data, i.e. from commercial and recreational fisheries to assess harvested stocks of fish and invertebrates, are well known. Increasingly, fishery-independent surveys are used to validate data from fishery-dependent sources and to provide indices of recruitment and broader ecological information about species not normally retained in fishing operations. Any large-scale, long-term, fishery-independent study must develop sampling gear and designs that are standardized, representative, optimal with respect to the quantity and structure of catch, and replicated over relevant spatial and temporal scales. We present a strategy for achieving appropriate sampling designs. This involves: (i) identifying suitable sampling gears for target species; (ii) testing different configurations of gear and sampling practices to ensure that samples are optimal, representative, and cost efficient; (iii) understanding scales of spatial and temporal variability; and (iv) cost–benefit analyses to optimize replication. Examples of this strategy are illustrated, with brief considerations of the values of pilot research in developing fishery-independent sampling.
First Report of Potato spindle tuber viroid in Tomato in Belgium
Authors: Verhoeven J. Th. J. , Jansen C. C. C. , Roenhorst J. W. , Steyer S. , Michelante D. 
Published: July 2007

During August of 2006, a sample of a tomato plant (Solanum lycopersicum, formerly Lycopersicum esculentum) from a greenhouse in Belgium was received for diagnosis. The plant showed severe growth reduction and the young leaves were chlorotic and distorted. In the greenhouse, the disease had been spreading slowly along the row. These observations suggested the presence of a viroid infection, and reverse transcriptase (RT)-PCR with two sets of universal pospiviroid primers (Pospi1-RE/FW and Vid-FW/RE; 3) yielded amplicons of the expected size (approximately 196 and 360 bp). Sequence analysis of the larger PCR product revealed that the genome was 358 nt and 100% identical to two isolates of Potato spindle tuber viroid (PSTVd) previously submitted to the NCBI GenBank (Accession Nos. AJ583449 from the United Kingdom and AY962324 from Australia). A pathogen associated with the symptomatic tomato plants was therefore identified as PSTVd. Tracing the origin of the infection revealed the following information: during November of 2005, 8-day-old tomato seedlings raised from seed by a Dutch nursery were transferred to a small part of the greenhouse of the Belgian grower; 7 to 8 weeks later, the plants were transplanted to their final destination; during May of 2006, the grower first observed growth reduction in a single plant; several weeks later, similar symptoms were observed in two more plants in the same row close to the first symptomatic plant; and by September, there were approximately 20 symptomatic tomato plants, all located in two adjacent rows. The viroid outbreak was fully eradicated by destroying all tomato plants in the affected rows as well as in two adjacent rows at both sides. The absence of further infections was confirmed by testing approximately 1,200 tomato plants in pooled samples for PSTVd by RT-PCR (2) and real-time RT-PCR (1). The origin and the method of introduction and spread of the viroid remain unclear. References: (1) N. Boonham et al. J. Virol. Methods 116:139, 2004. (2) R. A. Mumford et al. Plant Pathol. 53:242, 2004. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004.
First Report of Phytophthora ramorum and P. inflata in Ornamental Rhododendrons in Finland
Authors: Lilja A. , Rytkönen A. , Kokkola M. , Parikka P. , Hantula J. 
Published: July 2007

Phytophthora ramorum was found for the first time in Finland during the spring of 2004 on marketed plants of Rhododendron spp. originating in other EU member states. During August of 2004, the pathogen was also found in one Finnish nursery on German Rhododendron catawbiense plants and several Finnish Rhododendron spp. cultivars. P. ramorum was detected by species-specific PCR and isolated (1). It was first characterized by an abundant production of chlamydospores on PARP and V8 agar, absence of oogonia and antheridia, and elongate, ellipsoid, deciduous, semipapillate sporangia produced in soil extract water (3). A partial sequence of the β-tubulin gene was identical to that of P. ramorum deposited in GenBank. Despite strict regulations governing the movement of plants, the pathogen has been found every year since 2004 on materials transported to Finland from other EU countries. A total of 586 samples were taken from symptomatic plants of several susceptible species from 2004 to 2006. P. ramorum was detected in 51 rhododendron samples and the number of the outbreak sites was 28. In domestic plant production, P. ramorum was found in only one nursery. The infected plants in this nursery were destroyed in 2005 according to the EU regulation 2004/426/EG. During the 2006 growing season, 84 samples from trace-forward inspections and reinspections of the nursery were tested and P. ramorum was not detected in any of the samples. In 2005, surveys for P. ramorum on Finnish Rhododendron spp. cultivars with necrotic lesions on leaves and blackened tips yielded, in addition to P. ramorum, another Phytophthora sp. On V8 agar, this homothallic species showed a stellate growth pattern with sparse aerial mycelium. Oogonia had both paragynous and amphigynous antheridia, and sporangia produced in soil extract water were ellipsoid in shape and semipapillate. A 763-bp segment of the β-tubulin gene was sequenced and was identical to the β-tubulin sequence of P. inflata strain IMI342898 (GenBank), which was isolated in 1990 from Syringa sp. in the UK. It is likely that this P. inflata strain has been spreading in Europe with the ornamental plant trade. To fulfill Koch's postulates, rhododenrdon plants were inoculated (2) with P. inflata or P. ramorum, typical symptoms observed, and the pathogens were reisolated from inoculated plants. Both Phytophthora species also caused necrotic lesions on Alnus glutinosa, A. incana, and Betula pendula. Pinus sylvestris was resistant to both Phytophthora spp., whereas Picea abies was susceptible to P. inflata but not P. ramorum. References: (1) EPPO Bull. 36:145, 2006. (2) E. Hansen et al. Plant Dis. 89:63, 2005. (3) S. Werres et al. Mycol. Res. 105:1155, 2001.
Occurrence of Tomato yellow leaf curl virus in Tomato in Martinique, Lesser Antilles
Authors: Urbino C. , Dalmon A. 
Published: July 2007

During April of 2002, symptoms of stunting and chlorotic curled leaves of reduced size, similar to those caused by Tomato yellow leaf curl virus (TYLCV), were observed for the first time in commercial tomato (Solanum lycopersicum) in the northwest region of Martinique. Six months later, many tomato fields had more than 80% of plants expressing these symptoms and yield was drastically reduced. Samples from two symptomatic plants were collected and analyzed by PCR. Primers PC1 (5′-TGACTATGTCGAAGCGACCAGG-3′) and PC2 (5′-CGACATTACAGCCTCAGACTGG-3′) were used to amplify a 950-bp fragment within the coat protein gene (CP) of TYLCV species (1). Primer pair MP16-MP82 (2) amplified a 550-bp fragment from the conserved nonanucleotide sequence (TAATATTAC) to the 5′ end of the CP gene. Products of expected sizes were obtained with both pairs of primers from symptomatic samples but not from uninfected ones. The two overlapping PCR products were cloned into a pGEM-T Easy Vector (Promega, Madison, WI) and sequenced. A BLAST analysis was conducted with begomovirus sequences available in the GenBank database at the NCBI, and DNAMAN software (Lynnon Corporation, Quebec, Canada) was used for further comparisons. The 1275-bp sequence (GenBank Accession No. EF490995) shared 99% nucleotide identity with the partial sequences of TYLCV from Antigua and Barbuda (GenBank Accession No. EF028240), Saint Kitts and Nevis (GenBank Accession No. EF028239), and the two overlapping sequences from Guadeloupe (GenBank Accessions No. AY319645 and AY319646). It was at least 98% identical to TYLCV isolates from Florida (GenBank Accession No AY530931), Dominican Republic (GenBank Accession No. AF024715), and Cuba (GenBank Accession No. AJ223505). These results confirm the introduction of TYLCV into Martinique, possibly from a nearby Caribbean country, and reveal its southward spread in the Lesser Antilles. The nearness of the islands in the Lesser Antilles (20 to 100 km distant) probably permitted the rapid spread of TYLCV through the movement of plant material or wind transport of viruliferous whiteflies from one island to the next. Monitoring the spread of TYLCV in this Caribbean archipelago is important for regional virus management and in forecasting the spread of TYLCV to nearby countries in South America. References: (1) Y. Martinez et al. Rev. Prot. Veg. 18:168, 2003. (2) P. Umaharan et al. Phytopathology 88:1262, 1998.
First Report of Cylindrocarpon liriodendri Causing Black Foot Disease of Grapevine in California
Authors: Petit E. , Gubler W. D. 
Published: July 2007

Black foot disease is a recently identified but worsening problem in vineyards worldwide (2). Roots of symptomatic grapevines show black, sunken, necrotic lesions (2). In cross section, the base of the trunk appears necrotic and xylem vessels are plugged with black inclusions and tyloses (2). Aboveground, leaves of infected vines appear to be scorched, and the entire vine becomes stunted and frequently dies (2). In California, we previously identified two Cylindrocarpon species as causal agents of this disease: C. macrodidymum and C. destructans (2). In earlier molecular phylogenetic studies, tremendous variation in C. destructans from diverse hosts was found, indicating that this species might encompass more than one species (2). On the basis of analysis of sequences of three independent DNA regions, we concluded that the group of C. destructans isolated from grapevines in France, South Africa, and California have nearly identical sequences and form a well-supported sister clade divergent from the clade containing C. destructans found in numerous hosts (2). Further studies compared DNA sequences of C. destructans causing black foot in France, Portugal, and South Africa with an ex-type strain of C. liriodendri isolated from tulip poplar (Liriodendron tulipifera) (1). Because these species had identical sequences, C. destructans causing black foot in France, Portugal, and South Africa was renamed C. liriodendri (1). The objective of the current study was to clarify the taxonomy of C. destructans causing black foot in California. We compared C. liriodendri isolate CBS112602 from South Africa (1) with three C. destructans isolates (USME116, USST148, and USSO150) from California (2). We analyzed four sequences on three genomic regions: the internal transcribed spacer of ribosomal DNA, partial sequences of the beta tubulin gene, and the mitochondrial small subunit ribosomal DNA. We used sequences from the South African C. liriodendri isolate CBS112602 (AY997566, AY997586, AY997581, and AY997532) and sequences from Californian isolates of C. destructans (AY997568, AY997588, AY997534, AY997583, AY997569, AY997601, AY997547, AY997584, AY997570, AY997598, AY997544, and AY997585) previously deposited in GenBank (2). Sequences were aligned using Clustal X 1.8 (3). On the basis of visual inspection of each DNA region alignment, the South African C. liriodendri isolate was identical to Californian isolates of C. destructans. Thus, Californian isolates of C. destructans causing black foot (2) are renamed C. liriodendri. To our knowledge, this is the first report of C. liriodendri causing black foot disease of grapevine in California. References: (1) F. Halleen et al. Stud. Mycol. 55:227, 2006. (2) E. Petit and W. D. Gubler. Plant Dis. 89:1051, 2005. (3) J. D. Thompson et al. Nucleic Acids Res. 25:4876, 1997.
Discarding practices in a Mediterranean small‐scale fishing fleet (Patraikos Gulf, Greece)
Authors: Tzanatos E. , Somarakis S. , Tserpes G. , Koutsikopoulos C. 
Published: July 2007

Abstract  Discarding practices from 110 fishing operations in a Mediterranean small‐scale fishing fleet (Patraikos Gulf, western Greece) from August 2004 to July 2005 were analysed. On average, 1 kg of fish was discarded per fishing operation (10% of the catch). The reasons for discarding were: low commercial value (78% of discards), damage at sea before retrieval of the gear (5%), and bad handling on‐board (17%). More than half of discards belonged to Spicara flexuosa (L.), Lepidopus caudatus (Euphrasen), Sardinella aurita Valenciennes and Merluccius merluccius (L.). The bulk of discards of each species were associated with a single fishing method (metier). A Generalized Linear Model (Delta‐X – error‐model) indicated that, when discards were present, significant differences existed in the discard ratio among different métier groups (groups comprising métiers with similar characteristics). Longlines and trammel nets with small mesh‐sizes had the highest discard ratios. Discarding practices for the species Diplodus annularis (L.), S. aurita, Squilla mantis (L.), S. flexuosa and Scorpaena scrofa (L.) did not follow a consistent pattern (these species were either fully discarded or fully retained during a fishing operation). The decision seemed to be dependent on market demands rather than fish size. Significant correlation was found between discarded and catch weight, but the presence of many outliers indicated deviance from a case where discards are high when there is an abundant catch. The findings of the study imply that monitoring and management should be carried out preferably on the métier level. Discards could be reduced by technical measures, controlling effort regulations and by improving working conditions on‐board fishing vessels.
Concordance between ecotypes and macroinvertebrate assemblages in Mediterranean streams
Authors: SÁNCHEZ‐MONTOYA MARIA DEL MAR , PUNTÍ TURA , SUÁREZ MARIA LUISA , VIDAL‐ABARCA MARIA DEL ROSARIO , RIERADEVALL MARIA , POQUET JOSÉ MANUEL , ZAMORA‐MUÑOZ CARMEN , ROBLES SANTIAGO , ÁLVAREZ MARUXA , ALBA‐TERCEDOR JAVIER , TORO MANUEL , PUJANTE ANA MARIA , MUNNÉ ANTONI , PRAT NARCÍS 
Published: July 2007

Summary1. According to the guidelines of the European Water Framework Directive, assessment of the ecological quality of streams and rivers should be based on ecotype‐specific reference conditions. Here, we assess two approaches for establishing a typology for Mediterranean streams: a top‐down approach using environmental variables and bottom‐up approach using macroinvertebrate assemblages.2. Classification of 162 sites using environmental variables resulted in five ecotypes: (i) temporary streams; (ii) evaporite calcareous streams at medium altitude; (iii) siliceous headwater streams at high altitude; (iv) calcareous headwater streams at medium to high altitude and (v) large watercourses.3. Macroinvertebrate communities of minimally disturbed sites (n = 105), grouped using UPGMA (unweighted pair‐group method using arithmetic averages) on Bray–Curtis similarities, were used to validate four of the five ecotypes obtained using environmental variables; ecotype 5, large watercourses, was not included as this group had no reference sites.4. Analysis of similarities (anosim) showed that macroinvertebrate assemblage composition differed among three of the four ecotypes, resulting in differences between the bottom‐up and top‐down classification approaches. Siliceous streams were clearly different from the other three ecotypes, evaporite and calcareous ecotypes did not show large differences in macroinvertebrate assemblages and temporary streams formed a very heterogeneous group because of large variability in salinity and hydrology.5. This study showed that stream classification schemes based on environmental variables need to be validated using biological variables. Furthermore, our findings indicate that special attention should be given to the classification of temporary streams.
Utilization of recombinant activated factor VII in southern Ontario in 85 patients with and without haemophilia
Authors: WEBERT K. E. , ARNOLD D. M. , CARRUTHERS J. , MOLNAR L. , ALMONTE T. , DECKER K. , SEROSKI W. , REED J. , CHAN A. K. , PAI M. , WALKER I. R. 
Published: July 2007

Summary.  Recombinant activated factor VII (rFVIIa) is licensed for the treatment of bleeding in individuals with haemophilia and inhibitors. The use of rFVIIa appears to be increasing, and an increase in unlicensed use is suspected. There are currently few data about the specific indications for its use.The aim of this study was to describe the patterns of utilization of rFVIIa.We performed a retrospective cohort study using rFVIIa infusion data collected prospectively and clinical data collected retrospectively. Patients were identified using a tracking system designed to account for use of all coagulation factor concentrates issued in southern Ontario.Between 1 January 2001 and 31 December 2005, 85 patients received rFVIIa. 1164 infusions were given (8246.4 mg). Haemophilia patients with inhibitors accounted for 82.9% of rFVIIa infused and represented 8.2% of patients. The total amount of rFVIIa used increased each year from 2001 to 2004 and then decreased in 2005. The total number of infusions of rFVIIa administered annually increased. Both on‐label and off‐label use of rFVIIa increased. The number of patients with haemophilia receiving rFVIIa remained small and constant. The number of patients receiving rFVIIa for off‐label indications increased markedly.Most rFVIIa infusions were given for licensed indications; however, these infusions represented <10% of patients treated. Overall, the utilization of rFVIIa is increasing, mostly for approved indications; however, the number of patients being prescribed rFVIIa for off‐label indications has increased. The tracking system used in this study is a valuable tool to describe ongoing utilization patterns of rFVIIa.
Intramural duodenal haematoma presenting as a complication after endoscopic biopsy
Authors: Borsaru AD , Nandurkar D 
Published: July 2007

SummaryIntramural duodenal haematoma is an uncommon lesion, usually a complication of blunt abdominal trauma in children and young adults. We present a case of intramural duodenal haematoma following endoscopic biopsy, which caused partial duodenal obstruction and pancreatitis and resolved with conservative management.
Management options for echogenic intracardiac focus and choroid plexus cysts: A review including Australian Association of Obstetrical and Gynaecological Ultrasonologists consensus statement
Authors: Bethune M 
Published: July 2007

SummaryEchogenic intracardiac focus and choroid plexus cysts are common findings at the midtrimester ultrasound. These findings have been linked with an increased risk of Down syndrome and trisomy 18. Most fetuses with these findings will, however, not have chromosomal abnormalities, especially when these findings are isolated. Patients experience considerable anxiety when informed of these findings and require extensive counselling in order to minimize anxiety not only about aneuploidy but also about the structure and development of the heart and brain. Although early studies showed an association with aneuploidies, several recent studies have cast doubt on this association. Many of the early studies were carried out in high‐risk populations or in populations that had not had the benefit of other screening tests. Many Australian and New Zealand patients will access screening tests designed to detect these aneuploidies before presenting for a midtrimester ultrasound. Patients who have been screened by nuchal translucency, maternal serum screening or some combination of the two will already have had most cases of Down syndrome and trisomy 18 detected, and any soft marker found will almost certainly be a false positive. It is time to rethink the management of these markers. Recent evidence indicates that if these markers are found in isolation in an otherwise low‐risk pregnancy, then there is minimal or no increase in the risk of Down syndrome or trisomy 18: these markers should be considered normal variants.The Australian Association of Obstetrical and Gynaecological Ultrasonologists consensus statement on these markers is included.
Capillary haemangioma involving the middle and external ear: Radiotherapy as a treatment method
Authors: Pavamani SP , Surendrababu NRS , Ram TS , Thomas M , Viswanathan PN , Viswanathan FR 
Published: July 2007

SummaryCapillary haemangiomas rarely occur in the auditory canal and have mainly been managed with surgical excision or kept on close follow up for development of symptoms. Radiotherapy, as a treatment method, has not been reported previously in the published work. We describe a study of a capillary haemangioma in the auditory canal of a 26‐year‐old woman who presented with bleeding. She was treated with radiotherapy, after the lesion was found to be unsuitable for surgery and embolization. The patient remains well 5 years after completion of treatment.
Lactate quantification by proton magnetic resonance spectroscopy using a clinical MRI machine: A basic study
Authors: Isobe T , Matsumura A , Anno I , Kawamura H , Shibata Y , Muraishi H , Minami M 
Published: July 2007

SummaryThe purpose of this study was to establish quantification method of lactate concentration by proton magnetic resonance spectroscopy (MRS) carried out using a conventional 1.5‐T MRI machine. We used a lactate phantom with known concentrations (1, 1.5, 3, 6, 12 and 14 mmol/L). As a clinical example, a patient with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke‐like episodes (MELAS) was evaluated. Proton MRS was carried out using a clinical 1.5‐T super‐conducting magnetic resonance whole‐body system. Data were acquired by point resolved spectroscopy. A coupling constant of J = 7.35 Hz (2/J = 272 ms) and two long in‐phase echo time of 272 ms and 544 ms were used to calculate the T2 relaxation time. The tissue water signal was used as an internal standard to quantify lactate. The correlation coefficient R between the calculated lactate concentrations and the known concentration of lactate was 0.99 with a constant factor of 0.32 (1/3.14). In patients with MELAS, the lactate concentration measured by MRS was 6.2 mmol/kg wet weight, which is similar to the value obtained in previous studies. In the present study, we have established a reliable method for lactate quantification in a phantom study and have shown a sample of clinical case of MELAS.
Infusion of 50% glucose solution before injection of ethanolamine oleate during balloon‐occluded retrograde transvenous obliteration
Authors: Yamagami T , Kato T , Hirota T , Yoshimatsu R , Matsumoto T , Nishimura T 
Published: July 2007

SummaryThe feasibility of infusion of 50% glucose solution before balloon‐occluded retrograde transvenous obliteration (BRTO) to occlude collateral vessels draining gastric varices other than gastrorenal shunt was evaluated. In five patients with such collateral vessels, 50% glucose solution was infused from the balloon catheter inflated within the gastrorenal shunt. The degree of collateral vessels had decreased when BRTO was carried out so that sclerotic agents sufficiently occupied the gastric varices in all patients. In three patients, embolization of collateral vessels with coils was unnecessary. There were no complications. In conclusion, retrograde infusion of 50% glucose solution assists in effectively carrying out BRTO.