bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular identification of species comprising an unusual biofilm from a groundwater treatment plant
Authors: Gillings M. R. , Holley M. P. , Selleck M. 
Published: May 2007

ABSTRACTOrica's groundwater treatment plant in Botany, NSW, Australia, was designed to remove and destroy volatile organic compounds from polluted groundwater and to treat the water for reuse on the Botany Industrial Park. The initial steps in this process involved acidification of the groundwater and air stripping. During this operation, very large quantities of a biofilm formed within the air stripper, necessitating weekly clean-outs. We investigated the composition of this biofilm using molecular methods. Total DNA extracted from biofilm material was used as a template for amplification of both bacterial 16 S ribosomal DNA (rDNA) and the eukaryotic rDNA internal transcribed spacer region. Cloning and sequencing of these products showed that the biofilm was composed primarily of a bacterium belonging to the genusAcidocella, a filamentous fungus (Trichoderma asperellum), and the ascomycetous yeastsPichia,CandidaandGeotrichum. This unusual biofilm was composed of acidophiles that were capable of rapidly generating large amounts of biomass under these conditions. When acidification of the groundwater ceased, the biofilm no longer formed.
Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts
Authors: van Elsas Jan Dirk , Hill Patrick , Chroňáková Alica , Grekova Martyna , Topalova Yana , Elhottová Dana , Krištůfek Václav 
Published: May 2007

Abstract
A loamy sand soil sampled from a species-rich permanent grassland at a long-term experimental site (Wildekamp, Bennekom, The Netherlands) was used to construct soil microcosms in which the microbial community compositions had been modified by fumigation at different intensities (depths). As expected, increasing depth of fumigation was shown to result in progressively increasing effects on the microbiological soil parameters, as determined by cultivation-based as well as cultivation-independent (PCR-DGGE, PLFA) methods. Both at 7 and at 60 days after fumigation, shifts in the bacterial, fungal and protozoan communities were noted, indicating that altered community compositions had emerged following a transition phase. At the level of bacteria culturable on plates, an increase of the prevalence of bacterial r-strategists was noted at 7 days followed by a decline at 60 days, which also hinted at the effectiveness of the fumigation treatments. The survival of a non-toxigenic Escherichia coli O157:H7 derivative, strain T, was then assessed over 60 days in these microcosms, using detection via colony forming units counts as well as via PCR-DGGE. Both data sets were consistent with each other. Thus, a clear effect of fumigation depth on the survival of the invading strain T was noted, as a progressive increase of depth coincided with a progressively enhanced inoculant survival rate. As fumigation depth was presumably inversely related to community complexity, this was consistent with the hypothesis that soil systems with reduced biological complexity offer enhanced opportunities for invading microbial species to establish and persist. The significance of this finding is discussed in the light of the ongoing discussion about the complexity–invasiveness relationship within microbial communities, in particular regarding the opportunities of pathogens to persist.
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Authors: Xu Xing , Ji Yongmei , Stormo Gary D. 
Published: May 2007

AbstractMotivation: Non-coding RNA genes and RNA structural regulatory motifs play important roles in gene regulation and other cellular functions. They are often characterized by specific secondary structures that are critical to their functions and are often conserved in phylogenetically or functionally related sequences. Predicting common RNA secondary structures in multiple unaligned sequences remains a challenge in bioinformatics research.Methods and Results: We present a new sampling based algorithm to predict common RNA secondary structures in multiple unaligned sequences. Our algorithm finds the common structure between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures and subsequently recalculates stem conservation using the updated probabilities. The iterative process terminates upon convergence of the sampled structures. We extend the algorithm to multiple sequences by a consistency-based method, which iteratively incorporates and reinforces consistent structure information from pairwise comparisons into consensus structures. The algorithm has no limitation on predicting pseudoknots. In extensive testing on real sequence data, our algorithm outperformed other leading RNA structure prediction methods in both sensitivity and specificity with a reasonably fast speed. It also generated better structural alignments than other programs in sequences of a wide range of identities, which more accurately represent the RNA secondary structure conservations.Availability: The algorithm is implemented in a C program, RNA Sampler, which is available at http://ural.wustl.edu/software.htmlContact: xingxu@ural.wustl.edu and stormo@genetics.wustl.edu.Supplementary information: Supplementary data are available at Bioinformatics online.
Fruit Rot Caused by Penicillium italicum on Lemon (Citrus aurantifolia) in Colima, Mexico
Authors: Hernández-Montiel L. G. , Ochoa J. L. 
Published: May 2007

Postharvest rotting caused by Penicillium italicum Wermer is responsible for significant economic losses of orange (Citrus sinensis (L.) Osbeck) and lemon (C. limon Burm. f.) worldwide, but until now was not described on lemons (C. aurantifolia (Chistm.) Swingle) in Mexico. During May 2002, we analyzed 400 fruits of lemon collected in the state of Colima, which is the most important lemon producer in Mexico. Rotting and softened areas covered with a white mycelium and blue conidia were observed on approximately 30% of the fruits. Affected tissue was plated onto potato dextrose agar (PDA) for fungal isolation and identification. Following the morphological criteria (1) and the internal transcribed spacer 1 (ITS1), 5.8S, and ITS2 region of the ribosomal DNA (2) (GenBank Accession No. DQ991463), the fungus was identified as P. italicum and deposited in the Colección Microbiana y de Cultivos Celulares CINVESTAV-IPN, México. For the pathogenicity test, the fungus was grown on PDA for 1 week. Four drops (15 μl each) of a sterile water suspension of 106 conidia per ml were placed in four wounds of 3 × 3 × 3 mm produced with a scalpel on the fruit surface. Five plastic boxes with six fruits each were placed in an environmental chamber at 12°C and 90% relative humidity. After 10 days, all fruit rotted in a similar way as naturally infected fruit on trees. Control fruits inoculated with sterile distilled water were symptomless. The test was repeated and the results were similar, confirming Koch's postulates. To our knowledge, this is the first report describing the isolation and pathogenicity of P. italicum on lemon (C. aurantifolia) in Colima, Mexico, which may have important implications in fruit quality and storage. References: (1) Z. Kozakieweicz. IMI Descriptions of Fungi and Bacteria. 155, Sheet 1548, 2002. (2) M. J. Pianzzola et al. Plant. Dis. 88:23, 2004.
First Report of Tomato yellow leaf curl virus in Venezuela
Authors: Zambrano K. , Carballo O. , Geraud F. , Chirinos D. , Fernández C. , Marys E. 
Published: May 2007

Tomato yellow leaf curl virus (TYLCV), a member of the family Geminiviridae, is a serious production constraint to tomato worldwide. In the new world, the virus had been identified as the causal agent of tomato yellow leaf curl disease in the Caribbean countries of the Dominican Republic, Cuba, and Guadeloupe and also in Florida and the Yucatan Peninsula (1). Molecular data from these TYLCV isolates identified the virus as the TYLCV prototype from Israel. During April 2004, tomato plants showing symptoms such as chlorotic leaf edges, upward leaf cupping, leaf mottling, and reduced leaf size indicative of TYLCV were observed in commercial fields in Zulia state, Venezuela. Whiteflies (Bemisia tabaci Gennadius) were present in the field and appeared to be associated with the disease. Leaf samples from nine symptomatic plants were collected and brought to the lab at Instituto Venezolano de Investigaciones Científicas (IVIC) for further analyses. Geminivirus infection of samples was confirmed by PCR amplification with the degenerate primer pair PAL1v1978 and PAR1c494 (2). TYLCV coat protein gene-specific primers KL04-06_TYLCV CP F and KL04-07_TYLCV CP R (3) were used to confirm the diagnosis. These primers amplified the expected 842-bp PCR product from the nine symptomatic samples. One of the resulting amplicons was cloned into the pCR-TOPO vector (Invitrogen, Carlsbad, CA) and sequenced (GenBank Accession No. DQ302033). Sequence comparison with those available in the NCBI database indicated that the sequenced portion of the genome shared 99% nucleotide identity with the TYLCV mild strain from Portugal (GenBank Accession No. AF105975) and 98% nucleotide identity with the TYLCV mild strain from Spain (GenBank Accession No. AF071228), TYLCV Israel isolate (GenBank Accession No. AM234066), and TYLCV Mexico isolate (GenBank Accession No. DQ631892). To our knowledge, this is the first report of TYLCV infecting tomato crops in South America. Further studies are needed to clarify how TYLCV has been introduced into Venezuela. References: (1) J. E. Polston and P. K. Anderson. Plant Dis. 81:1358, 1997. (2) M. R. Rojas et al. Plant Dis. 77:340, 1993. (3) K. S. Ling et al. Plant Dis. 90:379, 2006.
First Report of Aloe Root and Stem Rot in China Caused by Fusarium solani
Authors: Ji G. , Wei L. , He Y. , Wu Y. 
Published: May 2007

During the springs of 2003 and 2004, a serious outbreak of root and stem disease occurred on Aloe barbadensis L. grown in commercial fields in Yuanjiang, Yunnan Province, Southwest China. The disease began with brown root rots that advanced to collars and stems, followed by internal decay of the lower stem. Diseased tissue samples collected from plants in different fields were surface disinfested and plated on potato dextrose agar (PDA). A Fusarium species was consistently isolated, and pure cultures were established by initiating new cultures with single spores. Grayish white and fluffy mycelium with a deep violet-blue pigment developed on PDA agar, with a growth rate of 3.4 cm in 3 days, and a dark, blue-green mass of confluent sporodochia or pionnotes covering the central part of the culture. Microconidia in false heads on long phialides were abundant when initially isolated but were infrequent in later cultures. Microconidia were generally single celled, oval to kidney shaped, and 8 to 16 × 2.5 to 4 μm. Macroconidia were abundant, cylindrical, slightly curved with blunt and rounded apical cells, and foot-shaped or notched basal cells, and mostly three to four septate, 27 to 50 × 3.6 to 5.7 μm. Chlamydospores were sparse, single or in short chains, thick walled, and 7 to 10 μm in diameter. This description corresponds to Fusarium solani (Mart.) Appel & Wollenw. emend. Snyd. & Hans as described by Nelson et al. (1). Inoculations with F. solani were made by dipping healthy aloe roots into a 300-ml suspension of 3 × 105 conidia/ml. Control plants were dipped in sterile water. All plants were potted in soil and kept in a greenhouse (2). After 30 days, all inoculated plants developed root rots followed by collar and stem rots that were similar to those observed in the field. Cultures of F. solani were reisolated from the diseased plants and identification was confirmed by conidial characteristics. No symptoms were observed on the control plants. Tests were repeated with similar results. In China, the Yunnan Province produces one-third of all aloe grown and this disease has a major impact on production. Aloe is grown in certified organic fields and chemical pesticides are not used. To our knowledge, this is the first report of F. solani causing root and stem rot of A. barbadensis. References: (1) P. E. Nelson et al. Fusarium Species: An Illustrated Manual for Identification. Pennsylvania State University Press, University Park, PA, 1983. (2) X. Ruan et al. Pages 211–215 in: Phytopathology Laboratory of Yunnan Province. Vol. 2. Y. Y. Shengfu, ed. Yunnan Science and Technology Press, Kunming, Yunnan, China, 1998.
Awareness of and adherence to cancer screening guidelines among health professionals in Japan
Authors: Hamashima Chisato , Saito Hiroshi , Sobue Tomotaka 
Published: May 2007

Since 1998 in Japan, guidelines for cancer screening programs have been developed and revised by a research group funded by the Ministry of Health, Labour and Welfare. However, little is known about health professionals’ awareness of and adherence to the cancer screening guidelines. Surveys were conducted by mailing questionnaires to two target groups of health professionals: local government officers of municipal cancer screening programs of 3327 municipalities in 47 prefectures (local government officers group; n = 3327) and councilors of an academic society dealing with a mass survey of gastroenterological cancer (expert group; n = 195). The questionnaire contained questions dealing with: (1) awareness of and adherence to the cancer screening guidelines published in 2001, and (2) basic knowledge of and attitude towards cancer screening. We compared the responses of the two groups. The response rate in both groups was approximately 65%. Over 70% of the respondents were aware of the cancer screening guidelines. However, 20% of the local government officers and 35% of the experts thought that non‐recommended methods could be used for population‐based screening. Fifty‐six percent of the local government officers and 76% of the experts responded that there was no problem with using non‐recommended methods for opportunistic screening. Almost all health professionals believed that screening was ‘almost always a good idea’. Although the two groups’ backgrounds differed, both did not sufficiently understand the evidence‐based approach for cancer screening. To properly conduct evidence‐based cancer screening, it is necessary that health professionals have an appropriate understanding of the guidelines. (Cancer Sci 2007; 98: 1241–1247)
C‐Myc Expression In Exfoliated Cells In Serous Effusions
Authors: TAWFIK M. S. , COLEMAN D. V. 
Published: May 2007

In an attempt to improve the discrimination between benign and malignant cells in pleural and peritoneal fluids, 32 effusions were investigated for c‐myc expression. Smears were prepared from cells harvested from the fluids for immunocytochemical staining to identify the presence of c‐myc protein. Recombinant DNA technology (Northern blotting, slot blotting and in situ hybridization) was used to detect c‐myc mRNA. No significant difference in expression of c‐myc was noted in benign or malignant effusions.Although the results are inconclusive, the recombinant DNA technology developed for this research could be used to investigate the expression of other oncogenes in cytological material.
The Cytological Prediction of Cervical Intraepithelial Neoplasia In Colposcopically Directed Biopsies
Authors: PARHAM D. M. , WIREDU E. K. , HUSSEIN K. A. 
Published: May 2007

The tissue sections and preceding cervical smears of 1262 women who had colposcopic cervical biopsies were reviewed and the reports correlated. Close correlation between the cytological and histological findings, to within one histological grade of cervical intraepithelial neoplasia (CIN), was noted in 86% of cases. However, the biopsy was negative, or contained evidence of wart virus infection only, in 24% of cases where dyskaryotic cells had been observed in the cervical smear. of particular concern was the fact that negative histological findings were recorded in 13% of cases where the smear contained cells showing a moderate dyskaryosis and in 1.26% of cases where the smear showed severe dyskaryosis. This suggests that colposcopically directed biopsies do not always reflect the underlying pathological changes in the cervix. Management of these cases is discussed.In 45 women with a normal cervical smear prior to biopsy, histology revealed seven cases of CIN 3 and one case of invasive squamous carcinoma. This indicates that referral for colposcopy is advisable whenever there is clinical suspicion of cancer, even if the cervical smear report is normal.
Comparison of Planimetry and Image Analysis For the Discrimination Between Normal and Abnormal Cells In Cytological Smears of Suspicious Lesions of the Oral Cavity
Authors: COWPE J. G. , OGDEN G. R. , GREEN M. W. 
Published: May 2007

Light microscope analysis of cytological smears of suspicious lesions of the oral cavity is used as a method for detecting early cancer in the oral cavity. the sensitivity of this approach can be improved by quantitative analysis of the cells in the cytological smears.We have compared the efficiency of planimetry and the Vids V system of image analysis, as quantitative methods for discriminating between normal and abnormal cells in cytological smears of suspicious lesions in the oral cavity. Both methods detected an increase in nuclear area and a decrease in cytoplasmic area in abnormal epithelial cells from dysplastic lesions of increasing severity. However, image analysis was better able to discriminate between benign and malignant cells on the basis of nuclear size. Thus the Vids V system of image analysis is more appropriate than planimetry for quantitative analysis of cytological smears from the oral cavity.
Quality assurance in cervical cancer screening
Authors: GIFFORD C. , COLEMAN D. V. 
Published: May 2007

Objectives. to examine the effectiveness of introducing External Quality Assessment (EQA) into all laboratories which undertake gynaecological cytopathology. to assess pathologists and cytotechnologists regularly for their competence to screen cervical smears, regardless of their standing in the laboratory hierarchy or their experience of gynaecological cytopathology. Methods. Each participant was asked to screen and report on 10 slides during a 2 h period. the assessment was carried out by a facilitator under the direction of a specially appointed EQA Committee. A maximum score of 20 points was awarded for a completely correct set of answers. A minus score was awarded for a missed abnormal smear. Seventeen pathology laboratories in North West Thames Regional Health Authority participated; 146 cytologists were assessed. Results. A pilot and four rounds of EQA have been completed and a total 5350 smears examined. Out of 2568 dyskaryotic (abnormal) smears screened, 0.7% were not identified correctly. of the 146 cytologists taking part in the assessment, 95% achieved a score of 17 or more. Three participants were identified who did not reach an acceptable level of competence and appropriate remedial action was taken. Conclusion. the EQA scheme detected unacceptable levels of performance which can be quickly rectified. Participation of 100% has been maintained on a voluntary basis, and 4 years experience of the scheme confirms that a very high standard of screening prevails in the Region. the study illustrates that voluntary self‐regulation is acceptable in the NHS, and the introduction of similar EQA schemes on a national scale will go a long way to establishing confidence in the cervical cancer screening programme.
Involving the General Practitioner In Screening For Cervical Cancer
Authors: BOON M. E. , BECK S. , WIJSMAN‐GROOTENDORST A. 
Published: May 2007

In the Leiden region, the cervical cancer screening programme for the age group 35–54 years shifted in 1989 from one in which the smears were taken by specially trained paramedical personnel in health centres to a programme where the general practitioner is the smear taker. Hence, it is possible to compare the results of the two types of screening to evaluate whether involvement of general practitioners leads to better uptake of screening. In the 6 year period evaluated in this paper, the 3‐yearly cytological rate per thousand for severe dysplasia or worse increased from 1.00 to 3.40; when stratified by age the positive rates were significantly higher. the histological rate per thousand for severe dysplasia increased from 0.60 to 2.09, and for carcinoma in situ from 0.35 to 1.36. All six invasive carcinomata were detected in the GP programme (0.31%). the general practitioner is clearly more able to attract the ‘high‐risk’groups.Dans la reéion de Leiden, le programme de dépistage du cancer du col pour les tranches d'âge de 35–54 ans a été modifié en 1989. Le programme était initialement basé sur des frottis faits dans des centres de santé, par un personnel paramédical ayant suivi une formation particulière. Après 1989, le médecin généraliste est devenu le préleveur. II est done possible de comparer les résultats de ces 2 types de dépistage et d'apprécier si la participation des médecins généralistes a pour conséquence un meilleur dépistage. Au cours de la période d'étude, les taux pour 1000 de positivité cytologique pour les lésions graves (de type dysplasie sévère et plus) et par période de 3 ans ont augmenté de 1,00 à 3,40. Lorsque l'on stratifie sur l'âge, les taux de cas positifs sont significativement supérieurs. Le taux histologique des dysplasies sévères pour 1000 passe de 0,60 à 2,09 et celui du carcinome in situ de 0,35 à 1,36. Les 6 cas de carcinome invasif ont été détectés par le programme impliquant les médecins généralistes (0,31%). II est clair que le médecin généraliste est mieux placé pour dépister les patientes à“haut risque”.Im Bezirk von Leiden wurden die Abstriche der 35‐ bis 54 jährigen vor 1989 von speziell ausgebildeten Hilfskräften in Gesundheitszentren hergestellt, während diese Aufgabe dann von den Allgemeinmedizinern übernommen wurde. Dies erlaubt einen Vergleich zwische den Präparaten von zwei jeweils 3 Jahre umfassenden Perioden. Der Anteil schwerer Dysplasien und stärkerer Veränderungen nahm von 1.00 auf 3.40 pro Tausend zu. Der histologische Anteil der schweren Dysplasien erhöhte sich von 0.60 auf 2.09 und der der Carcinomata in situ von 0.35 auf 1.36. Alle 6 nachgewiesenen invasiven Carcinome wurden in den Abstrichen der Allgemeinmediziner entdeckt (0.31%o). Damit ist klar, daß die Allgemeinmediziner die Risikogruppen besser zu erfassen vermögen.