bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of PI and NNRTI HAART‐based therapy on oral lesions of Brazilian HIV‐infected patients
Authors: Ortega Karem L. , Vale Daniela A. , Magalhães Marina H. C. G. 
Published: July 2009

Background:  The incidence of oral lesions related to human immunodeficiency virus (HIV) infection have been investigated after treatment with highly active antiretroviral therapy (HAART) including protease inhibitors (PI) but no data are available on the effect of non‐nucleoside reverse transcriptase inhibitor (NNRTI)‐based therapy on incidence of acquired immunodeficiency syndrome (AIDS) oral manifestations or impact of HAART on oral manifestations of HIV infection in Brazil. The aim of this study was to describe the effects of anti‐HIV therapy on the incidence of oral lesions during 17 years of AIDS epidemics in a Brazilian population.Methods:  From 1989 to 2006, we collected data from 1595 consecutive HIV patients at the Special Care Dentistry Center, São Paulo, Brazil. We compared the effect of PI‐ and NNRTI‐based antiretroviral therapy (ARVT) on the annual incidence of Kaposi sarcoma (KS), oral candidiasis (OC) and hairy leukoplakia (HL). The chi‐squared test was used to test the association between oral lesions and therapeutic regimen (P < 0.05).Results:  None of patients on ARVT presented with KS. Patients who used (nucleoside reverse transcriptase inhibitors) NRTI + PI were 0.9 times as likely to present with HL as those who used NRTI + NNRTI. This finding, however, was not statistically significant (P = 0.5). The relative risk for OC was 0.8 in patients with PI‐based HAART. The increased risk among those on PIs was statistically significant (P = 0.004).Conclusions:  The superiority of NNRTI regimens in decreasing OC incidence is consistent with current therapeutic guidelines which recommend NNRTI‐based therapy as the treatment of choice for initial ARVT.
A clinico‐pathologic study of 311 intra‐oral salivary gland tumors in Thais
Authors: Dhanuthai Kittipong , Boonadulyarat Mingkwun , Jaengjongdee Thitipa , Jiruedee Kanyarat 
Published: July 2009

Background:  There have been several epidemiologic studies on intra‐oral salivary gland tumors in several countries, but little is known of these tumors in Thailand.Objectives:  To determine the relative frequency and distribution of various types of intra‐oral salivary gland tumors in the Thai population.Methods:  The files of the Department of Oral Pathology, Faculty of Dentistry, Chulalongkorn University, from 1969 to 2007 were searched for intra‐oral salivary gland tumors. Histopathologic slides were reviewed and reclassified according to the 2005 WHO Classification of Head and Neck Tumors. The age, gender, race, and anatomical distribution of the tumors were collected from the patients’ records.Results:  Of the 16,358 accessioned cases, 311 cases (1.90%) were diagnosed as intra‐oral salivary gland tumors. One hundred and forty‐seven cases (47.27%) were benign tumors, while 164 cases (52.73%) were malignant tumors. The mean age of the patient ± SD = 41.57 ± 16.65 years. Females outnumbered male patients by a ratio of M:F = 1:1.38. Almost all except one patient were Thais. Pleomorphic adenoma was the most common intra‐oral salivary gland tumor. The majority of cases occurred at the palate.Conclusions:  Pleomorphic adenoma is the most common intra‐oral salivary gland tumor and the most common benign intra‐oral salivary gland tumor, while mucoepidermoid carcinoma is the most common malignant intra‐oral salivary gland tumor. Intra‐oral salivary gland tumors in Thailand elicit similar trend as in previous studies, with only minor differences such as the ranking of some tumors, the higher incidence of intra‐bony location, and the lower incidence of polymorphous low‐grade adenocarcinoma.
A PSYCHOSIS MORE ORDINARY: A LACANIAN TREATMENT OF PARANOIA
Authors: Schwartz Susan 
Published: July 2009

abstractMany patients who are diagnosed as borderline within psychiatric discourse are, within the Lacanian orientation, more likely to be considered to have a psychotic structure even though there has been no psychotic break. The concept of ‘ordinary psychosis’ was developed by Jacques‐Alain Miller to describe a psychosis that has not been triggered, or has been triggered and has since stabilized. This is not a diagnostic category but rather an epistemic one; it provides a way of thinking about and treating patients who are not clearly neurotic but do not present with any obvious psychotic phenomena.
LE DÉSIR DE VIVRE: AN INTRODUCTION TO THE LIFE AND WORK OF FRANÇOISE DOLTO
Authors: Hall Guy 
Published: July 2009

abstractThis paper serves as a brief introduction into the life and works of the French psychoanalyst, Françoise Dolto. Although acclaimed around the world, she is almost unknown in the United Kingdom as most of her books are not available in translation. It is suggested that this omission is largely due to the complicated post‐war politics amongst Parisian psychoanalytic organizations and with the IPA. With reference to four questions, it is hoped that this paper will stimulate a greater interest into her life, her theoretical ideas and her clinical work, so that they become better known and her contribution to psychoanalysis can receive the recognition it deserves.
THE FUTURE OF THE TRANSFERENCE‐BASED THERAPIES
Authors: Murdin Lesley 
Published: July 2009

abstractMuch demonology has grown up round the acronym IAPT. This paper considers the current state of its effect on the discipline in which we practise. The paper sets out the current landscape and begins to address the implications for those who are practising models of psychotherapy other than the cognitive–behavioural model. The outlook may not be a disaster but we need to heed the warnings and gather our thoughts so that we can ensure not only the continued existence of our model but its continued availability for those who need us.
TEACHING AND TRANSFORMATION: A PSYCHOANALYTIC PERSPECTIVE ON PSYCHOTHERAPEUTIC TRAINING
Authors: Rizq Rosemary 
Published: July 2009

abstractWhile there has been much recent interest in the impact of organizational structures underpinning psychotherapeutic training (e.g. Davies 2008; Kernberg 2006), there has been curiously little interest in the impact of interpersonal dynamics on the process of teaching psychotherapy. In this paper, I draw on my experience as a university lecturer and tutor on a postgraduate counselling and psychotherapy training programme to explore some of the unconscious dynamics underpinning the psychotherapy trainee's development towards a mature professional identity. The implicit expectations that trainee psychotherapists hold at the start of their training are initially discussed; I then turn to psychoanalytic writers such as Bollas, Winnicott and Jessica Benjamin in an attempt to articulate and explore how trainees may progress from relating, to constructive use of their tutors in their quest for personal transformation and professional recognition.
PSYCHOANALYSIS AS AN ART FORM
Authors: Williams Meg Harris 
Published: July 2009

abstractThis paper takes Bion's question ‘What sort of artists can we be?’ and begins the quest for an answer. In the light of the later aesthetic model posited by Bion and Meltzer, I consider first the nature and properties of symbols as containers for meaning, then the problem of how symbols are formed and metabolized by means of the transference–countertransference. Finally attention is drawn to the musical resonances of the ‘countertransference dream’ which have traditionally been overshadowed by verbal and visual considerations.
Role of Flagella in Virulence of the Coral Pathogen
Vibrio coralliilyticus
Authors: Meron Dalit , Efrony Rotem , Johnson Wesley R. , Schaefer Amy L. , Morris Pamela J. , Rosenberg Eugene , Greenberg E. Peter , Banin Ehud 
Published: July 2009

ABSTRACT

A recently available transposition system was utilized to isolate a nonmotile mutant of the coral-bleaching pathogen
Vibrio coralliilyticus
. The mutation was localized to the
fhlA
gene, and the mutant lacked flagella. The
flhA
mutant was unable to exhibit chemotaxis toward coral mucus or to adhere to corals and subsequently cause infection.
Overproduction of Geranylgeraniol by Metabolically Engineered
Saccharomyces cerevisiae
Authors: Tokuhiro Kenro , Muramatsu Masayoshi , Ohto Chikara , Kawaguchi Toshiya , Obata Shusei , Muramoto Nobuhiko , Hirai Masana , Takahashi Haruo , Kondo Akihiko , Sakuradani Eiji , Shimizu Sakayu 
Published: July 2009

ABSTRACT

(
E
,
E
,
E
)-Geranylgeraniol (GGOH) is a valuable starting material for perfumes and pharmaceutical products. In the yeast
Saccharomyces cerevisiae
, GGOH is synthesized from the end products of the mevalonate pathway through the sequential reactions of farnesyl diphosphate synthetase (encoded by the
ERG20
gene), geranylgeranyl diphosphate synthase (the
BTS1
gene), and some endogenous phosphatases. We demonstrated that overexpression of the diacylglycerol diphosphate phosphatase (
DPP1
) gene could promote GGOH production. We also found that overexpression of a
BTS1
-
DPP1
fusion gene was more efficient for producing GGOH than coexpression of these genes separately. Overexpression of the hydroxymethylglutaryl-coenzyme A reductase (
HMG1
) gene, which encodes the major rate-limiting enzyme of the mevalonate pathway, resulted in overproduction of squalene (191.9 mg liter
−1
) rather than GGOH (0.2 mg liter
−1
) in test tube cultures. Coexpression of the
BTS1
-
DPP1
fusion gene along with the
HMG1
gene partially redirected the metabolic flux from squalene to GGOH. Additional expression of a
BTS1
-
ERG20
fusion gene resulted in an almost complete shift of the flux to GGOH production (228.8 mg liter
−1
GGOH and 6.5 mg liter
−1
squalene). Finally, we constructed a diploid prototrophic strain coexpressing the
HMG1
,
BTS1
-
DPP1
, and
BTS1
-
ERG20
genes from multicopy integration vectors. This strain attained 3.31 g liter
−1
GGOH production in a 10-liter jar fermentor with gradual feeding of a mixed glucose and ethanol solution. The use of bifunctional fusion genes such as the
BTS1
-
DPP1
and
ERG20
-
BTS1
genes that code sequential enzymes in the metabolic pathway was an effective method for metabolic engineering.
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology
Authors: Caron David A. , Countway Peter D. , Savai Pratik , Gast Rebecca J. , Schnetzer Astrid , Moorthi Stefanie D. , Dennett Mark R. , Moran Dawn M. , Jones Adriane C. 
Published: July 2009

ABSTRACT
DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.
Quantitative PCR for Genetic Markers of Human Fecal Pollution
Authors: Shanks Orin C. , Kelty Catherine A. , Sivaganesan Mano , Varma Manju , Haugland Richard A. 
Published: July 2009

ABSTRACT

Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting
Bacteroidales
-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 × 10
6
copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total
Bacteroidales
and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.
Quantitative PCR for Determining the Infectivity of Bacteriophage MS2 upon Inactivation by Heat, UV-B Radiation, and Singlet Oxygen: Advantages and Limitations of an Enzymatic Treatment To Reduce False-Positive Results
Authors: Pecson Brian M. , Martin Luisa Valério , Kohn Tamar 
Published: July 2009

ABSTRACT
Health risks posed by waterborne viruses are difficult to assess because it is tedious or impossible to determine the infectivity of many viruses. Recent studies hypothesized that quantitative PCR (qPCR) could selectively quantify infective viruses if preceded by an enzymatic treatment (ET) to reduce confounding false-positive signals. The goal of this study was to determine if ET with qPCR (ET-qPCR) can be used to accurately quantify the infectivity of the human viral surrogate bacteriophage MS2 upon partial inactivation by three treatments (heating at 72°C, singlet oxygen, and UV radiation). Viruses were inactivated in buffered solutions and a lake water sample and assayed with culturing, qPCR, and ET-qPCR. To ensure that inactivating genome damage was fully captured, primer sets that covered the entire coding region were used. The susceptibility of different genome regions and the maximum genomic damage after each inactivating treatment were compared. We found that (i) qPCR alone caused false-positive results for all treatments, (ii) ET-qPCR significantly reduced (up to >5.2 log units) but did not eliminate the false-positive signals, and (iii) the elimination of false-positive signals differed between inactivating treatments. By assaying the whole coding region, we demonstrated that genome damage only partially accounts for virus inactivation. The possibility of achieving complete accordance between culture- and PCR-based assays is therefore called into doubt. Despite these differences, we postulate that ET-qPCR can track infectivity, given that decreases in infectivity were always accompanied by dose-dependent decreases in ET-qPCR signal. By decreasing false-positive signals, ET-qPCR improved the detection of infectivity loss relative to qPCR.
Quantitative Physiology of
Saccharomyces cerevisiae
at Near-Zero Specific Growth Rates
Authors: Boender Léonie G. M. , de Hulster Erik A. F. , van Maris Antonius J. A. , Daran-Lapujade Pascale A. S. , Pronk Jack T. 
Published: July 2009

ABSTRACT

Growth at near-zero specific growth rates is a largely unexplored area of yeast physiology. To investigate the physiology of
Saccharomyces cerevisiae
under these conditions, the effluent removal pipe of anaerobic, glucose-limited chemostat culture (dilution rate, 0.025 h
−1
) was fitted with a 0.22-μm-pore-size polypropylene filter unit. This setup enabled prolonged cultivation with complete cell retention. After 22 days of cultivation, specific growth rates had decreased below 0.001 h
−1
(doubling time of >700 h). Over this period, viability of the retentostat cultures decreased to ca. 80%. The viable biomass concentration in the retentostats could be accurately predicted by a maintenance coefficient of 0.50 mmol of glucose g
−1
of biomass h
−1
calculated from anaerobic, glucose-limited chemostat cultures grown at dilution rates of 0.025 to 0.20 h
−1
. This indicated that, in contrast to the situation in several prokaryotes, maintenance energy requirements in
S. cerevisiae
do not substantially change at near-zero specific growth rates. After 22 days of retentostat cultivation, glucose metabolism was predominantly geared toward alcoholic fermentation to meet maintenance energy requirements. The strict correlation between glycerol production and biomass formation observed at higher specific growth rates was not maintained at the near-zero growth rates reached in the retentostat cultures. In addition to glycerol, the organic acids acetate,
d
-lactate, and succinate were produced at low rates during prolonged retentostat cultivation. This study identifies robustness and by-product formation as key issues in attempts to uncouple growth and product formation in
S. cerevisiae
.
Absence of
Escherichia coli
Phylogenetic Group B2 Strains in Humans and Domesticated Animals from Jeonnam Province, Republic of Korea
Authors: Unno Tatsuya , Han Dukki , Jang Jeonghwan , Lee Sun-Nim , Ko GwangPyo , Choi Ha Young , Kim Joon Ha , Sadowsky Michael J. , Hur Hor-Gil 
Published: July 2009

ABSTRACT

Multiplex PCR analyses of DNAs from genotypically unique
Escherichia coli
strains isolated from the feces of 138 humans and 376 domesticated animals from Jeonnam Province, South Korea, performed using primers specific for the
chuA
and
yjaA
genes and an unknown DNA fragment, TSPE4.C2, indicated that none of the strains belonged to
E. coli
phylogenetic group B2. In contrast, phylogenetic group B2 strains were detected in about 17% (8 of 48) of isolates from feces of 24 wild geese and in 3% (3 of 96) of isolates obtained from the Yeongsan River in Jeonnam Province, South Korea. The distribution of
E. coli
strains in phylogenetic groups A, B1, and D varied depending on the host examined, and there was no apparent seasonal variation in the distribution of strains in phylogenetic groups among the Yeongsan River isolates. The distribution of four virulence genes (
eaeA
,
hlyA
,
stx
1
, and
stx
2
) in isolates was also examined by using multiplex PCR. Virulence genes were detected in about 5% (38 of 707) of the total group of unique strains examined, with 24, 13, 13, and 9 strains containing
hlyA
,
eaeA
,
stx
2
, and
stx
1
, respectively. The virulence genes were most frequently present in phylogenetic group B1 strains isolated from beef cattle. Taken together, results of these studies indicate that
E. coli
strains in phylogenetic group B2 were rarely found in humans and domesticated animals in Jeonnam Province, South Korea, and that the majority of strains containing virulence genes belonged to phylogenetic group B1 and were isolated from beef cattle. Results of this study also suggest that the relationship between the presence and types of virulence genes and phylogenetic groupings may differ among geographically distinct
E. coli
populations.
Large Sequence Polymorphisms Unveil the Phylogenetic Relationship of Environmental and Pathogenic Mycobacteria Related to
Mycobacterium ulcerans
Authors: Käser Michael , Hauser Julia , Small Pamela , Pluschke Gerd 
Published: July 2009

ABSTRACT

Mycolactone is an immunosuppressive cytotoxin responsible for the clinical manifestation of Buruli ulcer in humans. It was believed to be confined to its etiologic agent,
Mycobacterium ulcerans
. However, the identification of other mycolactone-producing mycobacteria (MPMs) in other species, including
Mycobacterium marinum
, indicated a more complex taxonomic relationship. This highlighted the need for research on the biology, evolution, and distribution of such emerging and potentially infectious strains. The reliable genetic fingerprinting analyses presented here aim at both the unraveling of phylogenetic relatedness and of dispersal between environmental and pathogenic mycolactone producers and the identification of genetic prerequisites that enable lateral gene transfer of such plasmids. This will allow for the identification of environmental reservoirs of virulence plasmids that encode enzymes required for the synthesis of mycolactone. Based on dynamic chromosomal loci identified earlier in
M. ulcerans
, we characterized large sequence polymorphisms for the phylogenetic analysis of MPMs. Here, we identify new insertional-deletional events and single-nucleotide polymorphisms that confirm and redefine earlier strain differentiation markers. These results support other data showing that all MPMs share a common ancestry. In addition, we found unique genetic features specific for
M. marinum
strain M, the genome sequence strain which is used widely in research.
Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria
Authors: Miot Jennyfer , Benzerara Karim , Obst Martin , Kappler Andreas , Hegler Florian , Schädler Sebastian , Bouchez Camille , Guyot François , Morin Guillaume 
Published: July 2009

ABSTRACT

Iron oxidation at neutral pH by the phototrophic anaerobic iron-oxidizing bacterium
Rhodobacter
sp. strain SW2 leads to the formation of iron-rich minerals. These minerals consist mainly of nano-goethite (α-FeOOH), which precipitates exclusively outside cells, mostly on polymer fibers emerging from the cells. Scanning transmission X-ray microscopy analyses performed at the C K-edge suggest that these fibers are composed of a mixture of lipids and polysaccharides or of lipopolysaccharides. The iron and the organic carbon contents of these fibers are linearly correlated at the 25-nm scale, which in addition to their texture suggests that these fibers act as a template for mineral precipitation, followed by limited crystal growth. Moreover, we evidence a gradient of the iron oxidation state along the mineralized fibers at the submicrometer scale. Fe minerals on these fibers contain a higher proportion of Fe(III) at cell contact, and the proportion of Fe(II) increases at a distance from the cells. All together, these results demonstrate the primordial role of organic polymers in iron biomineralization and provide first evidence for the existence of a redox gradient around these nonencrusting, Fe-oxidizing bacteria.
New Design Strategy for Development of Specific Primer Sets for PCR-Based Detection ofChlorophyceaeandBacillariophyceaein Environmental Samples
Authors: Valiente Moro Claire , Crouzet Olivier , Rasconi Séréna , Thouvenot Antoine , Coffe Gérard , Batisson Isabelle , Bohatier Jacques 
Published: July 2009

ABSTRACTStudying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers forChlorophyceaeandBacillariophyceaeby using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were excluded. These newly developed PCR primer sets were also able to amplify microalgal rRNA genes from environmental samples with accurate specificity. These tools could be of great interest for studying freshwater microalgal ecology and for developing bioindicators of the health status of aquatic environments.