bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rectal cancer staging post neoadjuvant therapy – how should the changes be assessed?
Authors: Bateman Adrian C , Jaynes Eleanor , Bateman Andrew R 
Published: April 2009

Aims:  To compare the utility and reproducibility of tumour regression grade scoring systems during histopathological assessment of rectal cancers resected after neoadjuvant (i.e. pre‐operative) chemoradiotherapy.Methods and results:  The histopathological features of tumour regression were assessed independently in 54 rectal cancer resection specimens using three scoring systems: the Tumour Regression Grade (TRG), modified Rectal Cancer Regression Grade (m‐RCRG) and RCPath Cancer Dataset (RCPath) methods. Good interobserver agreement was achieved for all three systems (κ scores: TRG system 0.719, m‐RCRG system 0.734, RCPath system 0.742). Both observers diagnosed complete tumour regression and little/no regression in 11 cases (20% of all cases) and four cases (11% of all cases), respectively. A mean of 5.6 tumour blocks/case were taken and the mean lymph node yield was 8.4/case.Conclusions:  All three scoring systems were usable in a diagnostic setting. The clinical significance of differing degrees of tumour regression is not yet universally agreed and, with this in mind, the m‐RCRG system provided the optimum balance between applicability and the accurate recording of low, moderate and high degrees of tumour regression, thus facilitating future clinicopathological studies of moderate and high degrees of tumour regression and clinical outcome.
Value of immunohistochemistry in the differential diagnosis of pleural sarcomatoid mesothelioma from lung sarcomatoid carcinoma
Authors: Takeshima Yukio , Amatya Vishwa J , Kushitani Kei , Kaneko Mayumi , Inai Kouki 
Published: April 2009

Aims:  The differential diagnosis of pleural sarcomatoid mesothelioma (SM) from lung sarcomatoid carcinoma (LSC) invading parietal pleura and chest wall is a challenging issue. The aim of this study was to identify useful antibodies that can be used for the differential diagnosis of pleural SM from LSC.Methods and results:  Forty‐five cases of pleural SM and 27 cases of LSC were immunohistochemically analysed by using 15 commercially available antibodies, including D2‐40 and antibodies to calretinin, thrombomodulin, Wilms’ Tumour 1, carcinoembryonic antigen (CEA), Napsin A, thyroid transcription factor (TTF)‐1, pan‐cytokeratin, CAM5.2, epithelial membrane antigen, Ber‐EP4, MOC‐31, α‐smooth muscle actin, h‐caldesmon and desmin. The results revealed that D2‐40 positivity was significantly higher in pleural SM (86.7%) than in LSC (25.9%). The positivity of the adenocarcinoma markers, including CEA, Napsin A, and TTF‐1, was low even in LSC.Conclusions:  Evaluating the positivity and degree of staining of the well‐known mesothelial marker D2‐40 could be applied to differentiate pleural SM from the sarcomatoid component of LSC, in addition to assessing clinical and radiological information.
An initial linkage map of the West Nile Virus vector Culex tarsalis
Authors: Venkatesan M. , Broman K. W. , Sellers M. , Rasgon J. L. 
Published: April 2009

AbstractWe have constructed the first genetic linkage map for the North American arboviral vector Culex tarsalis. 120 F2 offspring from a cross between two colonies were genotyped using 25 microsatellites and six inter‐simple sequence repeat (ISSR) markers. We resolved four linkage groups which likely correspond to two full‐length chromosomes and two arms of the final chromosome. The longest linkage group contains the sex locus and corresponds to chromosome 3. Recombination rates around the sex locus were dramatically higher in females compared to males. The majority of microsatellite loci share sequence identity with regions of the Culex quinquefasciatus genome, whose assembly should aid in anchoring linkage groups to physical chromosomes. This map will aid in identification of loci involved with variable phenotypes in C. tarsalis including WNV susceptibility.
Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites
Authors: NAGAI S. , NISHITANI G. , SAKAMOTO S. , SUGAYA T. , LEE C. K. , KIM C. H. , ITAKURA S. , YAMAGUCHI M. 
Published: April 2009

AbstractTo determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides, 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise FST, global amova, and genetic admixture analysis identified three clusters — the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations — indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals (PSAxy) analyses between the Sea of Japan and the other samples, PSAxy was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation‐by‐distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, PSAxy data among the samples were extremely high compared with those among other samples, clearly showing that a large‐scale transfer from west to east has occurred via the Tushima Warm Current. In the PSAxy data of the Seto Inland Sea and Pacific samples, individuals showing relatively high PSAxy were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human‐assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.
Interpopulation variation in mating system and late‐stage inbreeding depression in Magnolia stellata
Authors: TAMAKI ICHIRO , ISHIDA KIYOSHI , SETSUKO SUZUKI , TOMARU NOBUHIRO 
Published: April 2009

AbstractInbreeding has the potential to cause evolutionary changes in populations, although these changes are likely to drive populations to extinction through inbreeding depression and reductions in genetic diversity. We investigated the mating system and late‐stage inbreeding depression (δ) in 10 populations of Magnolia stellata using nine microsatellite markers and evaluated the effects of population size and the degree of population isolation through inbreeding and inbreeding depression on the persistence of populations. The outcrossing rates were very similar (~0.7) among populations, but the correlations of paternity, fractions of biparental inbreeding and inbreeding coefficients at the seed stage (FS) varied among populations, suggesting that the level of outcrossing was similar among populations, while the quality of it was not. A significant negative correlation was detected between FS and population size. The average value of δ was 0.709, and the values in six of the 10 populations were significant. The values of δ differed among populations, although clear relationships with population size and the degree of population isolation were not detected. However, in one population, which was very small and located in the edge of the species’ range, we obtained a very low value of δ (–0.096), which may be indicative of purging or the fixation of deleterious alleles. Existing M. stellata populations that are small (and thus might be expected to have higher frequencies of inbreeding) and have large values of δ may be in danger of declining, even if the populations are located within the central region of the species’ range.
Tales from scales: old DNA yields insights into contemporary evolutionary processes affecting fishes
Authors: QUINN THOMAS P. , SEAMONS TODD R. 
Published: April 2009

Salmon and trout populations are suffering declines in abundance and diversity over much of their range around the Atlantic and Pacific rims as a consequence of many factors. One method of dealing with the decline has been to produce them in hatcheries but the wisdom of this approach has been hotly debated (e.g. Hilborn & Winton 1993; Waples 1999; Brannon et al. 2004). One concern is that domesticated hatchery strains will interbreed with locally adapted wild fish; but how do we study the genetic effects if the introgression might have occurred in the past? Hansen (2002) used DNA isolated from archived scales from brown trout, Salmo trutta (Fig. 1), to show that domesticated trout had, to varying degrees, genetically introgressed with wild, native trout in two Danish rivers. Extending that study, Hansen et al. (2009) have examined DNA from brown trout scales in six Danish rivers collected during historical (1927–1956) and contemporary (2000–2006) periods and from two hatchery source populations, to assess the effects of stocking nonlocal strains of hatchery trout and declining abundance on genetic diversity. Using 21 microsatellite loci, they revealed that genetic change occurred between the historic and contemporary time periods. Many populations appeared to have some low level of introgression from hatchery stocks and two populations apparently experienced high levels of introgression. Hansen et al. (2009) also showed that population structure persists in contemporary populations despite apparent admixture and migration among populations, providing evidence that the locally adapted populations have struggled against and, to some extent, resisted being overwhelmed by repeated introductions of and interbreeding with non‐native, hatchery‐produced conspecifics.Photograph of a brown trout, Salmo trutta, one of many species of salmon and trout (Family Salmonidae) that are widely produced in hatcheries to enhance recreational and commercial fisheries. Photo by Peter Westley, Memorial University of Newfoundland, St John's NFLD, Canada.image
Patchy population structure in a short‐distance migrant: evidence from genetic and demographic data
Authors: MAYER C. , SCHIEGG K. , PASINELLI G. 
Published: April 2009

AbstractSpecies often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland‐restricted reed bunting (Emberiza schoeniclus) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour‐banded individuals among subpopulations, immigration rates and extinction‐/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.
Plant genomes do a balancing act
Authors: HUDSON MATTHEW E. , KANE NOLAN C. 
Published: April 2009

Balancing selection is one mechanism that may explain why diversity is maintained in wild populations. However, relatively few examples of genes showing evidence of balancing selection have been identified, particularly in plants. In this issue, Reininga et al. (2009) present three Arabidopsis loci that show strong evidence of balancing selection. The loci, discovered using a genome‐scanning approach, encode proteins with diverse predicted functions: starch synthesis and control of gene expression. These three genes were identified by scanning only a small fraction of the Arabidopsis genome, suggesting that balancing selection may be more prevalent than previously known.
Normal values for the satiety drinking test in healthy children between 5 and 15 years
Authors: Hoffman I. , Vos R. , Tack J. 
Published: April 2009

Abstract In adults, a slow caloric drinking test has been proposed as a non‐invasive tool to estimate gastric accommodation and to quantify meal‐induced symptoms in functional dyspepsia (FD). The same test has been proposed for paediatric FD, but normal values are only available for adolescents and adults. The aim of the study was (i) to establish normal values for the satiety drinking test in young children and (ii) to study the influence of demographic factors. In all, 59 healthy children [27 girls; age range 5–16 years, body mass index (BMI) 17.4 ± 2.5 kg m−2] were studied in the morning after an overnight fast. They drank a liquid nutrient meal (1.5 kcal mL−1) from beakers that were filled by a peristaltic pump filled at a rate of 15 mL min−1 with. For every 5 min, satiety was scored on a graphic rating scale grade 0–5 (1 = threshold, 5 = maximum), until a score of 5 was reached. Values are given as mean ± SEM and compared by t‐test; correlation analysis was performed using Spearman rank test. All children performed the test as indicated except for one 5 years old who stopped prematurely for dislike of the taste. The endpoint was reached at 360 ± 23 mL (540 ± 34 kcal), and was age‐dependent (Spearman r = 0.28, P = 0.03). No correlation was found between the maximum volume ingested and gender, weight, height or BMI. Age‐dependent normal ranges were determined for ages 5–16 at 3‐year intervals, and were found to increase with age. We established feasibility of and normal values for a non‐invasive satiety drinking test in children with an age range of 5–15 years. This tool can now be used in the assessment of paediatric FD and eating disorders.
Diagnostic performance and costs of Capilia TB for Mycobacterium tuberculosis complex identification from broth‐based culture in Bangkok, Thailand
Authors: Ngamlert Keerataya , Sinthuwattanawibool Chalinthorn , McCarthy Kimberly D. , Sohn Hojoon , Starks Angela , Kanjanamongkolsiri Photjanart , Anek‐vorapong Rapeepan , Tasaneeyapan Theerawit , Monkongdee Patama , Diem Lois , Varma Jay K. 
Published: April 2009

SummaryObjectives  Broth‐based culture (BBC) systems are increasingly being used to detect Mycobacterium tuberculosis complex (MTBC) in resource‐limited. We evaluated the performance, time to detection and cost of the Capilia TB identification test from broth cultures positive for acid‐fast bacilli (AFB) in Thailand.Methods  From October–December 2007, broth cultures that grew AFB from specimens submitted by district TB clinics to the Bangkok city laboratory were tested for MTBC using Capilia TB and standard biochemical tests. Isolates that were identified as MTBC by biochemical tests but not by Capilia TB underwent repeat testing using Capilia TB, Accuprobe (Gen‐Probe, San Diego, CA, USA) and sequencing. Costs of time, labour, infrastructure and consumables for all procedures were measured.Results  Of 247 isolates evaluated, the sensitivity of Capilia TB was 97% and its true specificity 100% compared with biochemical testing. The median time from specimen receipt to confirmed MTBC identification was 20 days (range 7–53 days) for Capilia TB and 45 days (range 35–79 days) for biochemical testing (P < 0.01). Six isolates that were Capilia TB negative but positive by biochemical testing were confirmed as MTBC and mutations in the mpb64 gene were detected in all. The unit cost of using Capilia TB was 2.67 USD that of biochemical testing was 8.78 USD.Conclusions  In Thailand, Capilia TB had acceptable sensitivity and specificity, was lower in cost and had shorter turn‐around times. Laboratories investing in BBC should consider Capilia TB for identification of MTBC, after validation of performance in their setting.
Sensitivity and specificity of Chagas Stat‐Pak® test in Bolivia
Authors: Chippaux Jean‐Philippe , Santalla Jose A. , Postigo Jorge R. , Romero Mario , Salas Clavijo Nadin A. , Schneider Dominique , Brutus Laurent 
Published: April 2009

SummaryObjective  To compare the results of an immunochromatographic test performed on whole blood, Chagas Stat‐Pak®, with those of an ELISA test using recombinant antigens.Method  We tested 995 subjects of a rural population of all ages in the south of Bolivia, 459 pregnant women of the same population and 1030 urban women giving birth from the east of Bolivia.Results  The sensitivity of the CSP test for the entire studied population (n = 2484) was 94.73% [93.35–96.10]; the specificity was 97.33% [96.50–98.15]. However, the specificity differed significantly between rural pregnant and urban birthing women, which could be attributed either to differences of parasite strain or Chagas prevalence.Conclusion  The test is simple of use, reliable, relatively inexpensive (<2 US$ each test) and its performances are compatible with a field use for large‐scale screenings.
Potentilla reptans is an Alternative Host for Two Strawberry Viruses
Authors: Yohalem David , Lower Karen , Harvey Nick , Passey Tom 
Published: April 2009

AbstractStrawberry [Fragaria x ananassa Duchesne = Potentilla x ananassa (Rozier) Mabb] has accumulated a variety of viruses in its relatively short history. Strawberry crinkle virus and Strawberry mild yellow edge virus are transmitted obligately by the aphid Chaetosiphon fragaefolii (Cockerell), which also occasionally infests other species of Potentilla. Several wild strawberry species have been shown previously to be hosts of the viruses. Leaves infected with these strawberry viruses were grafted into plants of UC‐5, an indicator strawberry cultivar, and then UC‐5 leaves were grafted into Potentilla reptans. Leaves from P. reptans were subsequently grafted back to uninfected UC‐5 plants to demonstrate their potential as reservoirs for the virus. UC‐5, Fragaria vesca and P. reptans plants were indexed for strawberry viruses by end‐point reverse transcriptase PCR subsequent to back grafting.
Trichosporon on humans: a practical account
Authors: Guého Eveline , Improvisi Luce , de Hoog G. S. , Dupont B. 
Published: April 2009

Summary. Six human pathogenic Trichosporon species are described with respect to criteria for routine identification, epidemiology and clinical origin: T. ovoides, T. inkin, T. asahii, T. asteroides (Fissuricella filamenta), T. cutaneum, and T. mucoides. These species are causative agents of white piedra and cutaneous infections and are involved in systemic, localized or disseminated mycoses, particularly in patients with underlying haematological malignancy. Data on in vitro sensitivity to antifungal drugs are provided.Zusammenfassung. Sechs humanpathogene Trichosporon‐Arten werden anhand von routinediagnostischen Merkmalen, der Epidemiologic sowie ihrer klinischen Herkunft beschrieben: T. ovoides, T. inkin, T. asahii, T. asteroides (Fissuricella filamenta), T. cutaneum und T. mucoides. Es handelt sich um Erreger der weißen Piedra und von Hautinfektionen sowie lokalisierter oder disseminierter tiefer Mykosen, insbesondere bei Patienten mit malignen hämatologischen Erkrankungen. Ferner werden Ergebnisse über in votro‐Empfindlichkeiten gegenüber Antimykotika mitgeteilt.
Mycoflora inhabiting water closet environments
Authors: Ismail M. A. , Abdel‐Sater M. A. 
Published: April 2009

Summary.Sixty‐six fungal species in addition to two species varieties belonging to 31 genera were isolated during the current study from water closet (WC) sewage samples (39 species and two varieties in 20 genera) and WC air (53 species and two varieties in 25 genera). There were more fungi in the WC air than in sewage. The most prevalent fungi in WC sewage and air were members of the generaAspergillus, CladosporiumandPenicillium. Acremonium, Alternaria, Emericella, MycosphaerellaandPleosporawere dominant only in WC air. Some species of these genera are considered to be true or opportunistic pathogens. The pollution level due to the bacterial flora either in the air or in the sewage of WCs was relatively higher than that of the fungal flora. Testing the capability to produce urease, nearly all fungal isolates (65 out of 67) and bacteria tested (35 out of 36) proved to be good urease producers.Zusammenfassung.Sechsundsechzig Pilzarten und zwei Varietäten aus 31 Genera konnten in der vorgelegten Untersuchung im WC‐Abwasser (39 Arten und 2 Varietäten in 20 Genera) und in WC‐Luft (53 Arten und 2 Varietäten in 25 Genera) nachgewiesen werden. Die Pilzflora in der WC‐Luft war reichhaltiger als die des WC‐Abwassers. In beiden Habitats herrschten Arten der GattungenAspergillus, CladosporiumundPenicilliumvor. Dagegen warenAcremonium, Alternaria, Emericella, MycosphaerellaundPleosporanur in der WC‐Luft bedeutsam. Einige Arten dieser Gattungen werden als primäre oder opportunistische Erreger angesehen. Die Keimbelastung sowohl der Luft als auch des Abwassers durch Bakterien war relativ höher als durch Pilze. Im Urease‐Nachweis erwiesen sich fast alle geprüften Pilze (65 von 67) und Bakterien (35 von 36) als gute Urease‐Bildner.
Comparative studies on the detection of delayed dermal hypersensitivity in experimental animals with lysate and filtrate antigens of Blastomyces dermatitidis
Authors: Abuodeh R. O. , Scalarone G. M. 
Published: April 2009

Summary.Yeast cell and mycelial lysate and filtrate antigens prepared in our laboratory from two strains of Blastomyces dermatitidis (canine isolate T‐58 and human isolate Le) were evaluated with respect to the detection of delayed dermal hypersensitivity in hairless guinea pigs previously immunized with killed whole yeast cells from two strains of Blastomyces dermatitidis (T‐58 and Le) and Histoplesma capsulattum (strain G‐217A). The optimal potential reactivity (reactivity minus cross‐reactivity) with regard to eliciting a dermal response in animals sensitized with B. dermatitidis was achieved with the yeast phase lysate and filtrate antigens prepared from both T‐58 and Le isolates (mean axes of induration values ranging from 14.0 to 15.9mm). In contrast, the mycelial phase reagents exhibited lower potential reactivity (mean axes of induration values ranging from 5.3 to 10.5 mm).Zusammenfassung. Lysat‐ und Filtratantigene wurden von der Hefe‐ und der Myzelphase zweier Blastomyces dermatitidis‐Stämme (Isolat T‐58 vom Hund und Isolat Le vom Menschen) hergestellt und in ihrer Reaktionsstärke im Nachweis der Überempfindlichkeit vom verzögerten Typ an unbehaarten Meerschweinchen validiert, die sowohl mit abgetöteten Ganzzellen der beiden B. dermatitidis‐Stämme als auch eines Histoplasma capsulatum‐Stammes (G‐217A) vorimmunisiert worden waren. Optimale Reaktivität (Reaktivität abzüglich Kreuzreaktionen) wurde im Hauttest an B. dematitidis‐sensibilisierten Tieren mit Lysav‐ und Filtratantigenen der Hefephase beider Stämme erreicht (mittlerer Duchmesser der Indurationen 14.0–15.9 mm). Dagegen zeigten die aus der Myzelphase präparierten Antigene ein geringeres Reaktionspotential (mittlerer Durchmesser der Indurationen 5.3–10.5 mm).