bluuebunny/crossref_metadata_2025 huggingface dataset:
The yeast kinase Yck2 has a tripartite palmitoylation signal
Authors: Roth Amy F. , Papanayotou Irene , Davis Nicholas G.
Published: June 2011

The yeast kinase Yck2 tethers to the cytoplasmic surface of the plasma membrane through dual palmitoylation of its C-terminal Cys-Cys dipeptide, mediated by the Golgi-localized palmitoyl-transferase Akr1. Here, the Yck2 palmitoylation signal is found to consist of three parts: 1) a 10-residue-long, conserved C-terminal peptide (CCTP) that includes the C-terminal Cys-Cys dipeptide; 2) the kinase catalytic domain (KD); and mapping between these two elements; and 3) a 176-residue-long, poorly conserved, glutamine-rich sequence. The CCTP, which contains the C-terminal cysteines as well as an important Phe-Phe dipeptide, likely serves as an Akr1 recognition element, because CCTP mutations disrupt palmitoylation within a purified in vitro palmitoylation system. The KD contribution appears to be complex with roles for both KD activity (e.g., Yck2-mediated phosphorylation) and structure (e.g., Akr1 recognition elements). KD and CCTP mutations are strongly synergistic, suggesting that, like the CCTP, the KD may also participate at the Yck2-Akr1 recognition step. The long, glutamine-rich domain, which is located between the KD and CCTP, is predicted to be intrinsically disordered and may function as a flexible, interdomain linker, allowing a coupled interaction of the KD and CCTP with Akr1. Multipart palmitoylation signals may prove to be a general feature of this large class of palmitoylation substrates. These soluble proteins have no clear means of accessing membranes and thus may require active capture out of the cytoplasm for palmitoylation by their membrane-localized transferases.
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Authors: Westra Harm-Jan , Jansen Ritsert C. , Fehrmann Rudolf S. N. , te Meerman Gerard J. , van Heel David , Wijmenga Cisca , Franke Lude
Published: June 2011

Motivation: Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels.

Results: We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets.

Availability and implementation:  MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/

Contact:  lude@ludesign.nl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays
Authors: Paliy Oleg , Foy Brent D.
Published: June 2011

Motivation: Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR.

Results: Here we describe the development of a mathematical model aimed to simulate multitemplate amplification of 16S ribosomal DNA sample and subsequent detection of these amplified 16S rDNA species by phylogenetic microarray. Using parameters estimated from the experimental results obtained in the analysis of intestinal microbial communities with Microbiota Array, we show that both species detection and the accuracy of species abundance estimates depended heavily on the number of PCR cycles used to amplify 16S rDNA. Both parameters initially improved with each additional PCR cycle and reached optimum between 15 and 20 cycles of amplification. The use of more than 20 cycles of PCR amplification and/or more than 50 ng of starting genomic DNA template was, however, detrimental to both the fraction of detected community members and the accuracy of abundance estimates. Overall, the outcomes of the model simulations matched well available experimental data. Our simulations also showed that species detection and the accuracy of abundance measurements correlated positively with the higher sample-wide PCR amplification rate, lower template-to-template PCR bias and lower number of species in the interrogated community. The developed model can be easily modified to simulate other multitemplate DNA mixtures as well as other microarray designs and PCR amplification protocols.

Contact:  oleg.paliy@wright.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
nucleR: a package for non-parametric nucleosome positioning
Authors: Flores Oscar , Orozco Modesto
Published: June 2011

Summary: nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

Availability: Additional information and methodological details can be found at http://mmb.pcb.ub.es/nucleR

Contact:  modesto.orozco@irbbarcelona.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A method of detecting patterns in mean lengths of samples of discarded fish, applied to the self-sampling programme of the Dutch bottom-trawl fishery
Authors: Uhlmann Sebastian S. , Bierman Stijn M. , van Helmond Aloysius T. M.
Published: June 2011

Uhlmann, S. S., Bierman, S. M., and van Helmond, A. T. M. 2011. A method of detecting patterns in mean lengths of samples of discarded fish, applied to the self-sampling programme of the Dutch bottom-trawl fishery. – ICES Journal of Marine Science, 68: 1712–1718. In 2009, a self-sampling programme was organized in the Netherlands, fishers sampling ca. 80 kg of discards from randomly selected bottom trawls in the North Sea. A statistical procedure is proposed to highlight samples, trips (with multiple samples), or vessels (which may have multiple trips within a year) where extreme mean lengths of discarded fish were observed. Randomization methods were used to test for evidence of non-randomness in patterns of highlighted discard samples, e.g. repeated observations of extreme mean lengths for consecutive discard samples across trips from the same vessel. European plaice (Pleuronectes platessa), common dab (Limanda limanda), grey gurnard (Eutrigla gurnardus), and whiting (Merlangius merlangus) were considered because these were the most abundant species in most of the discard samples. A linear mixed model was used to estimate random-sample effects on the estimated mean lengths by species. These random effects were incorporated into uni- and bivariate procedures to identify extreme samples that were summed for each vessel, and the probability of observing such numbers was estimated. Excluding these samples from the dataset had marginal effects on estimated size distributions of fish.
Sporisorium reilianumInfection Changes Inflorescence and Branching Architectures of Maize
Authors: Ghareeb Hassan , Becker Annette , Iven Tim , Feussner Ivo , Schirawski Jan
Published: June 2011

Sporisorium reilianum is a biotrophic maize (Zea mays) pathogen of increasing economic importance. Symptoms become obvious at flowering time, when the fungus causes spore formation and phyllody in the inflorescences. To understand how S. reilianum changes the inflorescence and floral developmental program of its host plant, we investigated the induced morphological and transcriptional alterations. S. reilianum infection promoted the outgrowth of subapical ears, suggesting that fungal presence suppressed apical dominance. Female inflorescences showed two distinct morphologies, here termed “leafy ear” and “eary ear.” In leafy ears, all floral organs were replaced by vegetative organs. In eary ears, modified carpels enclosed a new female inflorescence harboring additional female inflorescences at every spikelet position. Similar changes in meristem fate and organ identity were observed in the tassel of infected plants, which formed male inflorescences at spikelet positions. Thus, S. reilianum triggered a loss of organ and meristem identity and a loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied by transcriptional regulation of genes proposed to regulate floral organ and meristem identity as well as meristem determinacy in maize. S. reilianum colonization also led to a 30% increase in the total auxin content of the inflorescence as well as a dramatic accumulation of reactive oxygen species. We propose a model describing the architectural changes of infected inflorescence as a consequence of transcriptional, hormonal, and redox modulation, which will be the basis for further molecular investigation of the underlying mechanism of S. reilianum-induced alteration of floral development.
AUXIN UP-REGULATED F-BOX PROTEIN1 Regulates the Cross Talk between Auxin Transport and Cytokinin Signaling during Plant Root Growth
Authors: Zheng Xiaohua , Miller Nathan D. , Lewis Daniel R. , Christians Matthew J. , Lee Kwang-Hee , Muday Gloria K. , Spalding Edgar P. , Vierstra Richard D.
Published: June 2011

Plant root development is mediated by the concerted action of the auxin and cytokinin phytohormones, with cytokinin serving as an antagonist of auxin transport. Here, we identify the AUXIN UP-REGULATED F-BOX PROTEIN1 (AUF1) and its potential paralog AUF2 as important positive modifiers of root elongation that tether auxin movements to cytokinin signaling in Arabidopsis (Arabidopsis thaliana). The AUF1 mRNA level in roots is strongly up-regulated by auxin but not by other phytohormones. Whereas the auf1 single and auf1 auf2 double mutant roots grow normally without exogenous auxin and respond similarly to the wild type upon auxin application, their growth is hypersensitive to auxin transport inhibitors, with the mutant roots also having reduced basipetal and acropetal auxin transport. The effects of auf1 on auxin movements may be mediated in part by the misexpression of several PIN-FORMED (PIN) auxin efflux proteins, which for PIN2 reduces its abundance on the plasma membrane of root cells. auf1 roots are also hypersensitive to cytokinin and have increased expression of several components of cytokinin signaling. Kinematic analyses of root growth and localization of the cyclin B mitotic marker showed that AUF1 does not affect root cell division but promotes cytokinin-mediated cell expansion in the elongation/differentiation zone. Epistasis analyses implicate the cytokinin regulator ARR1 or its effector(s) as the target of the SKP1-Cullin1-F Box (SCF) ubiquitin ligases assembled with AUF1/2. Given the wide distribution of AUF1/2-type proteins among land plants, we propose that SCFAUF1/2 provides additional cross talk between auxin and cytokinin, which modifies auxin distribution and ultimately root elongation.
Total intravenous anaesthesia
Authors: MORGAN M.
Published: June 2011

Total intravenous anaesthesia is a feasible alternative to the use of inhalational agents and the rationale behind such a technique is presented. The various intravenous agents are discussed, particularly with regard to their suitability for this form of anaesthesia, and their physiological effects compared with those of the inhalational anaesthetics. Some of the problems associated with the use of total intravenous anaesthesia are mentioned.
Profile of etomidate
Authors: WAUQUIER A.
Published: June 2011

A review of the hypnotic, anticonvulsant and brain protective action of etomidate in animals shows that when given as a single injection in different animal species recovery from hypnosis is quick and that the safety margin is large. In dogs a bolus or infusion produces high amplitude theta activity on the electroencephalogram (EEC). During infusion burst suppression is seen. After high doses, behaviour and EEG changes returned to normal within 3 hours. The wide spectrum of anticonvulsant activity suggests that etomidate may be useful in the treatment of status epilepticus. Studies in various animal models show that etomidate might have brain resuscitative properties. In hypoxic‐ischaemic conditions etomidate has some protective effects, where its anticonvulsant action is probably important. Lowering of the cerebral metabolic rate of oxygen consumption, and reducing the rise of intracranial pressure, coupled with immobilisation and prevention of hyperactivity enables animals to resist a hypoxic insult.
Pharmacokinetics as applied to total intravenous anaesthesia
Authors: SCHWILDEN H. , SCHÜTTLER J. , STOEKEL H.
Published: June 2011

Some theoretical considerations of pharmacokinetics as applied to total intravenous anaesthesia are discussed. The problem is the need to achieve a concentration within the therapeutic range at the receptor site. The use of linear compartment models, and of the superposition principle within these models, is discussed.
Etomidate anaesthesia in patients with cirrhosis of the liver: pharmacokinetic data
Authors: VAN BEEM H. , MANGER F. W. , VAN BOXTEL C. , VAN BENTEM N.
Published: June 2011

Five patients undergoing endoscopic injection of oesphageal varices were anaesthetised with etomidate 0.2 mg/kg followed by an infusion at a rate of 20 μg/kg/minute. Fentanyl 100–200 μg was also given intravenously and the patients' lungs were ventilated with oxygen in air. The postinfusion plasma etomidate concentration was described by a three compartment model with a mean half‐life of 540 minutes (SEM 66.9) and volume of distribution of 8.9 litres/kg (SEM 0.6). Clearance was 12.7 ml/kg/minute (SEM 2.3). Compared to results in the literature obtained from normal patients, these cirrhotic patients had normal clearance rates, but the distribution volume and elimination half‐life were twice as great. This suggests that cirrhotic patients metabolise etomidate normally, but the volume of distribution is doubled, thus resulting in prolonged elimination half‐lives.
Expression of the CD117 antigen (C‐Kit) on normal and myelomatous plasma cells
Authors: Ocqueteau M. , Orfao A. , García‐Sanz R. , Almeida J. , Gonzalez M. , San Miguel J. F.
Published: June 2011

Summary. The surface expression of CD117 on plasma cells (PCs) from normal individuals and patients with multiple myeloma (MM) has been analysed using triple‐stained cells for flow cytometry. In addition, the clinical significance of CD117 expression in MM patients and its possible value for the evaluation of minimal residual disease was explored. A total of 11 healthy volunteers and 56 untreated MM patients were included in the study. The expression of CD117 was analysed by flow cytometry, using simultaneous staining with the MAbs BB4, CD117 and CD38. Cell acquisition was performed in two consecutive steps using a live gate drawn on SSC/CD38+++ cells and a total of 300000 events were acquired. For data analysis, the Paint‐a‐Gate Plus software (Becton Dickinson) was used. PCs were identified according to their strong reactivity for CD38 and their positivity for BB4, as well as by their light scatter distribution. Dilution experiments of CD117+ myelomatous PCs with normal bone marrow (BM) cells were performed in order to assess the sensitivity level of the technique for detection of CD117+ residual PCs. None of the PCs from normal BM samples showed reactivity for the CD117 antigen. In contrast, CD117 antigen was present in 18/56 MM patients (32%), the proportion of positive cells in these cases being as high as 92·1 ± 9%. Therefore, within PC lineage the c‐Kit antigen would be restricted to the myelomatous population and thus could be considered as a “tumour‐associated marker” for monitoring minimal residual disease in about one third of MM patients. Dilution experiments indicate that the detection limit with this marker would be 10−4 (one myelomatous PC/104 normal BM cells). Upon comparing the clinical and haematological disease characteristics of CD117‐positive and CD117‐negative cases, no significant differences were found.
Maternal depression and perceived social support as predictors of cognitive function trajectories during the first 3 years of life for preterm infants in Wisconsin
Authors: McManus B. M. , Poehlmann J.
Published: June 2011

Background  Among families of infants born preterm, the association between post‐natal depression and children's cognitive function is not well understood, but thought to be compromised. The purpose of this study is to investigate maternal depressive symptoms and perceived social support as predictors of children's cognitive function trajectories.

Methods  This is a longitudinal study of a sample of infants born preterm (less than 37 weeks) in Wisconsin. This study includes 130 infants who were hospitalized in one of three Wisconsin neonatal intensive care units in 2002–2005 and followed until 36 months of age. Maternal depressive symptoms were measured using the Center for Epidemiologic Studies Depression Scale. Social support was measured using the Maternal Support Scale. Children's cognitive function was measured using the Bayley Scales of Infant Development, 2nd Edition, and the Stanford–Binet Intelligence Scale, 5th Edition.

Results  Children's cognitive function trajectories declined initially and then increased. Being female (coefficient = 5.14, SE = 1.89) and non‐poor (coefficient = 11.26, SE = 5.78), and having a mother who has a graduate degree (coefficient = 7.67, SE = 3.37) was associated with higher levels of cognition initially. Being white was associated with a more optimal cognitive trajectory. Although depression did not predict children's cognitive trajectories, the presence of clinically elevated depressive symptoms at 9 months post term was associated with lower cognitive functioning at 16 months when mothers reported low social support.

Conclusion  Post‐natal depressive symptoms appear to have a meaningful, dynamic influence on the cognitive outcomes of children born preterm, above and beyond family socio‐demographic risk when the presence and timing of perceived social support are considered. Interventions to ameliorate developmental risk associated with preterm birth should include repeated assessments of maternal social support and post‐natal depression and be targeted towards socially disadvantaged families.
The ability to mentally represent action is associated with low motor ability in children: a preliminary investigation
Authors: Gabbard Carl , Caçola Priscila , Bobbio Tatiana
Published: June 2011

Background  Theory and anatomical research suggest that the ability to mentally represent intended actions affect level of execution. This study presents preliminary data examining the association between children's ability to mentally represent action and general motor ability.

Methods  Children aged 7‐ to 10 years were assessed for motor imagery ability using a simulation of reach task and motor ability via the Movement ABC‐2. Motor ability values, based on percentile rank, ranged from 2 to 91, with a mean of 36.

Results  The overall correlation between mental representation and motor ability yielded a moderately positive relationship (r = .39). Interestingly, when looking at motor ability subcategories, only Balance was significant in the model, explaining 20% of the variance.

Conclusions  These results provide preliminary evidence that children's motor ability and the ability to mentally represent action are associated in a positive direction. Furthermore, given the results for Balance, we speculate that there are clinical implications regarding work with potentially at‐risk children.
Clinical accuracy of a non‐contact infrared skin thermometer in paediatric practice
Authors: Teran C. G. , Torrez‐Llanos J. , Teran‐Miranda T. E. , Balderrama C. , Shah N. S. , Villarroel P.
Published: June 2011

Background  Rectal thermometry is considered the most reliable method for measuring the temperature in the paediatric population. Recently, a new non‐contact skin infrared thermometer for children was introduced in the market with excellent acceptance by parents.

Methods  A prospective, analytical, cross‐sectional study was designed in order to assess the effectiveness of the infrared non‐contact thermometer (Thermofocus) in comparison with two other known methods used to measure body temperature. Children aged 1 to 48 months were included from the emergency room and inpatient unit. All patients selected were assessed with three different thermometers: (1) non‐contact infrared thermometer (Thermofocus); (2) temporal artery thermometer (Exergen); and (3) rectal glass mercury thermometer.

Results  Four hundred and thirty‐four patients were eligible to complete the study. One hundred and sixty‐seven were identified with fever. The mean age of the patients studied was 14.6 ± 10.7 months. Both devices were strongly correlated with the rectal temperature: r= 0.950 for Exergen and r= 0.952 for Thermofocus. The mean difference in temperature between the rectal temperature and the non‐contact thermometer was 0.029 ± 0.01°C (P < 0.001), while the mean difference between the temporal artery thermometer and the rectal temperature was −0.20 ± 0.27°C (P < 0.001). The sensitivity and specificity for the non‐contact thermometer is 97%. The negative predictive value is 99%, which is especially important to rule out fever and avoid unnecessary laboratory work‐up.

Conclusions  The non‐contact infrared thermometer is a reliable, comfortable and accurate option for measurement of temperature and is very useful for the screening of fever in the paediatric population. More studies are recommended to support the evidence found in this study and compare its accuracy with more complex devices.
Evaluation of bone mineral density in Turkish children with severe haemophilia A: Ankara hospital experience
Authors: ALIOGLU B. , SELVER B. , OZSOY H. , KOCA G. , OZDEMIR M. , DALLAR Y.
Published: June 2011

Summary.  This study was conducted to understand the pathogenetic mechanisms that are involved in the development of bone loss in children with severe haemophilia A (HA). Fourty‐four children with severe HA and 40 age‐ and gender‐matched healthy control subjects were enrolled in this study. Markers of bone remodelling and osteoclast regulation including serum bone specific alkaline phosphatase, parathormone, 25‐hydroxy‐vitamin D3 (25HOvitD3), osteocalcin and calcitonin levels were studied. Bone mineral density (BMD) was also studied in all children. The measurement of markers of bone remodelling and osteoclast regulation suggested increased osteoclast‐mediated resorption activity in children with severe HA. Although serum parathormone levels were significantly increased, serum 25HOvitD3 and osteocalcin levels were significantly reduced. BMD was significantly reduced in severe haemophilics compared with healthy controls. There was also significant inverse correlation between BMD z‐score and total joint scores, and insignificant inverse correlation between BMD z‐score and single joint scores. There were also significant inverse correlation between 25HOvitD3 and osteocalcin levels and total joint scores. Children with severe HA could have significantly reduced BMD, compared with gender‐ and age‐matched healthy control subjects. Our results of the markers of bone remodelling and osteoclast regulation suggested that increased osteoclast‐mediated resorption and decreased osteoblastic activity in children with severe HA. All children with severe HA should be routinely screened in terms of BMD.
Investigating the impact of psychosocial risks and occupational stress on psychiatric hospital nurses' mental well‐being in Japan
Authors: LEKA S. , HASSARD J. , YANAGIDA A.
Published: June 2011

Accessible summary

A high level of work‐related stress was reported by psychiatric nurses (20.8%).

Several work‐related stressors were found to predict poor well‐being among psychiatric nurses (feeling uptight and emotional exhaustion), including high psychological job demands, low level of social support in the workplace, occupational stress and occupational stress paired with low social support.

The current study highlights the importance of examining and addressing work‐related stressors associated with the organization and management of nurses' work in order to promote and protect their health and performance.

In order to protect the mental health of nurses, it is important to implement workplace strategies and policies to prevent occupational stress and high levels of job demands, while promoting a socially supportive environment that will be conducive to nurses' well‐being.

A cross‐sectional survey was conducted, with the aim to examine what stressors in the workplace and demographic factors were associated with signs and symptoms of poor well‐being among psychiatric nurses. A structured questionnaire was distributed to nurses within six psychiatric hospitals in Japan. Information was collected on demographic information, work characteristics and two dimensions of well‐being: feeling uptight and emotional exhaustion. Three hundred and sixty‐one questionnaires were completed by participants. High rates of emotional exhaustion in psychiatric nurses were found to be predicted by young age, high psychological demands paired with low social support in the workplace, job strain (a proxy to occupational stress) and job strain paired with low social support. In addition, high rates of being tense/uptight were associated with high psychological job demand, low psychological job control, low social support in the workplace, high job strain and high job strain paired with low social support. The current study has found evidence of significant relationships between demographic factors and several work and organizational stressors and poor mental health among Japanese psychiatric nurses.
Concurrence of alopecia areata and vitiligo at the same anatomical site
Authors: Özcan Deren , Çevlik Aydoğan Filiz
Published: June 2011

Both alopecia areata and vitiligo are common skin disorders that are considered to be caused by an autoimmune response targeted to hair follicle and melanocyte antigens, respectively. The association of these two diseases in the same patient is well known, however, coexistence of alopecia areata and vitiligo within the same lesion is very rare. Herein, we report an 8‐year‐old boy who had colocalization of alopecia areata and vitiligo on the frontal portion of his scalp.
Methotrexate toxicity presenting as ulcerated psoriatic plaques
Authors: Wong Su‐ming , Chong Yew Thong , Thevarajah Suganthi , Baba Roshidah
Published: June 2011

Methotrexate toxicity is known to cause erosions of existing psoriatic plaques, although rare. We describe two patients who developed painful ulcerated psoriatic plaques as an early presenting sign of methotrexate toxicity and review the risk factors associated with this manifestation.
Primary adenoid cystic carcinoma of sweat glands in vulva: Report of an unusual case and review of the literature
Authors: Tang Qiong‐Lan , Jiang Xue‐Feng , Lin Zhong‐Qiu , Li Hai‐gang , Wang Yong‐an , Luo Xin
Published: June 2011

Adenoid cystic carcinoma arising from the vulvar sweat glands is a rare malignancy of the female genital tract. We report a case of adenoid cystic carcinoma of sweat glands occurring in the left labia majora of a 52‐year‐old female patient. The patient underwent radical hemivulvectomy and left inguinal lymph node dissection with negative surgical margins and negative inguinal lymph node metastasis. Then, four episodes of combined chemotherapy without further radiotherapy were given. However, the tumor recurred after 3 months. Currently, the patient has been followed up for 2 years with no distant metastasis. According to our experience, although the tumor has a high tendency of local recurrence after resection, an acceptable survival time of the patient can be achieved with primary surgery.
Velamentous cord insertion caused by oblique implantation after in vitro fertilization and embryo transfer
Authors: Hasegawa Junichi , Iwasaki Shinji , Matsuoka Ryu , Ichizuka Kiyotake , Sekizawa Akihiko , Okai Takashi
Published: June 2011

We present a case of a 36‐year‐old pregnant female after intracytoplasmic sperm injection. Ultrasonographic examination at 8 weeks' gestation revealed umbilical cord insertion with a viable fetus located on the septum membrane of dichorionic twin pregnancy near the anterior wall, while the other fetus was observed to have vanished. Next, this umbilical cord was seen to connect to the anterior wall and the placenta developed on the posterior wall later in the pregnancy. As a result, velamentous cord insertion with long membranous umbilical vessels developed at the time of delivery. The present case indicates that the assessment of the cord insertion site during the early gestation period is very important to predict any abnormality of the cord insertion site at the time of delivery. Furthermore, this case is valuable to understand the pathophysiological development of the placenta and velamentous cord insertion.
Prospective comparison of biopsy results from curettage and hysteroscopy in postmenopausal uterine bleeding
Authors: Lee Dong Ock , Jung Min Hyung , Kim Heung Yeol
Published: June 2011

Aim:  To evaluate the diagnostic accuracy of biopsy by dilatation and curettage in postmenopausal women with abnormal uterine bleeding.

Material and Methods:  A prospective observational study conducted with 112 consecutive postmenopausal women. Biopsy by dilatation and curettage was immediately followed by hysteroscopic biopsy and the histologic results were compared.

Results:  By curettage, although performed under anesthesia, 3/3 (100%) cases of endometrial hyperplasia were reported as normal proliferative endometrium. There were two endometrial cancers (1.8%) and one case was missed as normal endometrium by curettage. Among endometrial polyps, only 3/39 (7.7%) cases were diagnosed by curettage.

Conclusions:  In postmenopausal women with abnormal uterine bleeding, biopsy by curettage may be not reliable for evaluation of endometrial pathology.
Multi‐locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus
Authors: Mazard Sophie , Ostrowski Martin , Partensky Frédéric , Scanlan David J.
Published: June 2011

Conserved markers such as the 16S rRNA gene do not provide sufficient molecular resolution to identify spatially structured populations of marine Synechococcus, or ‘ecotypes’ adapted to distinct ecological niches. Multi‐locus sequence analysis targeting seven ‘core’ genes was employed to taxonomically resolve Synechococcus isolates and correlate previous phylogenetic analyses encompassing a range of markers. Despite the recognized importance of lateral gene transfer in shaping the genomes of marine cyanobacteria, multi‐locus sequence analysis of more than 120 isolates reflects a clonal population structure of major lineages and subgroups. A single core genome locus, petB, encoding the cytochrome b6 subunit of the cytochrome b6f complex, was selected to expand our understanding of the diversity and ecology of marine Synechococcus populations. Environmental petB sequences cloned from contrasting sites highlight numerous genetically and ecologically distinct clusters, some of which represent novel, environmentally abundant clades without cultured representatives. With a view to scaling ecological analyses, the short sequence, taxonomic resolution and accurate automated alignment of petB is ideally suited to high‐throughput and high‐resolution sequencing projects to explore links between the ecology, evolution and biology of marine Synechococcus.
Characterization of the cryptic Escherichia lineages: rapid identification and prevalence
Authors: Clermont Olivier , Gordon David M. , Brisse Sylvain , Walk Seth T. , Denamur Erick
Published: June 2011

Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi‐locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large‐scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele‐specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2–3% frequency) and even less likely to be isolated from extra‐intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3–8% in non‐human mammals to 8–28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of ‘E. coli’ as an indicator of water quality.
Mentalization‐based Therapeutic Interventions for Families
Authors: Asen Eia , Fonagy Peter
Published: June 2011

This article attempts to bridge two seemingly different and yet related worlds, the intra‐psychic and the interpersonal, by viewing systemic practice(s) through a mentalization‐based lens. It is argued that in therapy there needs to be a deliberate, conscious and consistent focus on mentalizing. The emerging mentalization‐based therapy for families is an innovative approach and a distinctive model which is systemic in essence, deriving its ideas and practices from a variety of diverse systemic approaches, yet enriching family work by adding mentalizing ingredients.
When Media and Politics Overlap: Inferences from the Italian Case
Authors: Fabbrini Sergio
Published: June 2011

There is broad agreement that the most important transformation undergone by democratic politics since the second half of the twentieth century has been the diffusion of the means of mass-communication (television in particular). Teledemocracy especially has changed democratic politics in a specific way: the leaders rather than the parties now stand at the centre of the electoral and political process. This article does not aim to go over the relationship between media and politics; that has already been done. Instead, it focuses on how to deal with a situation in which media and politics overlap.
Efficacy and cost‐benefit analysis of risk‐adaptive use of plerixafor for autologous hematopoietic progenitor cell mobilization
Authors: Vishnu Prakash , Roy Vivek , Paulsen Athena , Zubair Abba C.
Published: June 2011

BACKGROUND: Plerixafor (P) reduces mobilization failure rates but it is very expensive. For better utilization of P, we employed a risk‐adaptive strategy of using it only in patients who are at high risk of mobilization failure, defined by peripheral blood (PB) CD34+ cell count of fewer than 10 × 106/L after 4 days of filgrastim (F) alone.

STUDY DESIGN AND METHODS: Herein, we present the results of efficacy and cost‐benefit analysis of this risk‐adaptive approach for hematopoietic progenitor cell (HPC) collection. All patients received daily F for 4 days, and P was added for those “at‐risk” patients from Day 4 with apheresis commencing the following morning. F and P were continued daily for up to a maximum of 4 days or until more than 5 × 106 CD34+ cells/kg were collected. Forty‐two transplant‐eligible patients underwent HPC mobilization.

RESULTS: Eighteen patients mobilized with F alone and 24 patients required P with F. Two patients failed adequate HPC mobilization after F+P. Addition of P increased the PB CD34+ count by 6.8‐fold with a mean yield of 4.9 × 106 CD34+ cells/kg. Decision‐analysis model estimated cost‐effectiveness for this risk‐adaptive approach of using P with savings of $19,300/patient. Engraftment after HPC infusion was similar among the patients regardless of mobilization regimens.

CONCLUSION: These results suggest that addition of P to F based on a risk‐adaptive strategy significantly reduces the frequency of mobilization failures and is also cost‐effective.
Philodendron bernardopazii and P. ricardoi spp. nov. (Araceae) from Espírito Santo State, Brazil
Authors: Gonçalves Eduardo G.
Published: June 2011

Two new species of Philodendron– Araceae (Philodendron bernardopazii E. G. Gonç. and Philodendron ricardoi E. G. Gonç.), so far known to be endemic to the Espirito Santo State, Brazil, are here described and illustrated for the first time. Philodendron bernardopazii has been traded as an ornamental plant for more than 30 years, as one of several species popularly called Philodendron“Santa Leopoldina”, because of the Brazilian county where it has been collected. This new species is so far known from two cultivated stocks, both supposedly collected at the same location (around the village of Santa Leopoldina) and if it still exists in nature, it is probably threatened. Philodendron ricardoi has only been observed on rocks around the village of Estrela do Norte where huge populations can be seen growing in rocky outcrops in open areas.
Quorum sensing regulation of virulence gene expression in Vibrio harveyi in vitro and in vivo during infection of gnotobiotic brine shrimp larvae
Authors: Ruwandeepika H. A. Darshanee , Bhowmick Patit Paban , Karunasagar Indrani , Bossier Peter , Defoirdt Tom
Published: June 2011

In this study, we investigated quorum sensing regulation of virulence genes in Vibrio harveyi by determining their expression levels, both in vitro and in vivo during infection of gnotobiotic brine shrimp. The quorum sensing master regulator luxR and the vhp metalloprotease showed around threefold and fivefold higher expression levels in a luxO mutant with maximum quorum sensing activity than in a luxO mutant with minimum quorum sensing activity. There was no difference in expression of the vhh haemolysin gene between the two mutants. There was however more than 2.5‐fold lower expression in an AI‐2‐negative mutant, suggesting that this gene is specifically regulated by AI‐2 quorum sensing through a yet unknown signal transduction cascade. The in vivo expression data showed a peak in expression of the quorum sensing master regulator luxR and the vhp metalloprotease after 24 h of incubation in wild‐type V. harveyi and the luxO mutant mimicking a maximally activated quorum sensing system, whereas the expression remained low in the luxO mutant mimicking a completely inactivated quorum sensing system. The vhh haemolysin gene showed a peak in expression after 24 h in the wild type and a constantly low expression in an AI‐2‐negative mutant.
Community pharmacy in the United Arab Emirates: characteristics and workforce issues
Authors: Hasan Sanah , Sulieman Hana , Chapman Colin , Stewart Kay , Kong David C M
Published: June 2011

Objectives

To determine the characteristics and workforce issues of community pharmacy practice in the United Arab Emirates (UAE).

Methods

Data collection was by anonymous cross-sectional survey. Questionnaires were distributed by hand to 700 community pharmacies to collect information about the participating pharmacists, pharmacy characteristics, the types of products and professional pharmacy services available to patients, and the barriers to offering professional services.

Key findings

A total of 344 pharmacists (49%) responded. Most were male (64%), had been in practice for less than 10 years (mean = 9.3, 95% confidence interval (CI) = 8.4–10.0) and were trained in India (35%) or Egypt (15%). The pharmacies were open for business 7 days/week (mean = 6.8, 95% CI = 6.7–8.8) with an average working day of 13 h (mean = 12.9, 95% CI = 12.7–13.2) and were mostly owned by independent non-pharmacists (70%). The pharmacies employed on average 2.6 full-time-equivalent (FTE) pharmacists (95% CI = 2.3–2.8) with 74% employing 1.8 FTE pharmacy assistants (95% CI = 1.7–2.0) and 47% employing trainee pharmacists (mean = 1.8 FTE, 95% CI = 1.6–2.0). Around three-quarters of the pharmacies dispensed fewer than 100 prescriptions (75%) and responded to fewer than 100 requests for over-the-counter medicines (69%) per day. Most pharmacists encountered limited immediate access to up-to-date resources.

Conclusions

This is the first study to explore the characteristics of community pharmacy practice in the UAE. The study provides baseline data which are critical to inform the development of strategies to improve the quality of community pharmacy services in the UAE.
Crystallinity-retaining removal of germanium by direct-write focused electron beam induced etching
Authors: Roediger Peter , Wanzenboeck Heinz D. , Hochleitner Gottfried , Bertagnolli Emmerich
Published: June 2011

In this work, a well-controllable, direct-write, resistless, and crystallinity-retaining etching process for germanium using a focused electron beam with nanometer resolution has been developed. This process allows for precise, local, and efficient removal of germanium from a surface without showing any spontaneous etching effects. This focused electron beam induced etching process of germanium substrates employs pure chlorine gas as etchant. The presented process was carried out in a conventional scanning electron microscope equipped with a custom-tailored gas injection system. The etch rate of this etching process was observed to be up to 0.32 μm3 min−1 or 12 nm min−1 for an area of 1.5×1.5 μm2. The influence of various etching parameters such as electron beam current, acceleration voltage and chlorine gas flow on the etch rate as well as the shape of the etch pits have been studied systematically by atomic force microscopy analysis. It is demonstrated that etching of amorphous germanium films can be performed significantly faster (∼8 times) than etching of crystalline germanium. Finally, a comparison between silicon etching and germanium etching by chlorine is presented.
Identification, Bioinformatics Analyses, and Expression of Immunoreactive Antigens of Mycoplasma haemofelis
Authors: Messick Joanne B. , Santos Andrea P.
Published: June 2011

Mycoplasma haemofelisinfection frequently causes anemia in cats. Despite an intense immune response and/or antibiotic treatment, cats often remain asymptomatic carriers following infection. Our hypothesis is that detection of antibodies toM. haemofelisis a sensitive approach for identifying infected cats, particularly carriers. To date, no immunoassay has been developed. This is due largely to the inability to cultureM. haemofelis in vitro; hence, a source of antigen is not readily available. The objective of this study was to identify, express, and purify immunogenic proteins ofM. haemofelis. To accomplish this, two whole-genomic expression libraries were created in the Lambda ZapII vector and immunoscreened with preimmune plasma, plasma from specific-pathogen-free cats, and pooled acute- and convalescent-phase plasma from experimentally infected cats. The inserts from 21 immunoreactive clones were sequenced, resulting in the identification of 60 genes coding for putative proteins necessary for diverse cellular functions, along with several novel genes ofM. haemofelis. Fragments of selected genes based on bioinformatic analyses were PCR amplified, cloned into a high-level protein expression system, and subsequently expressed inEscherichia colias a His6-fusion protein. The recombinant fusion proteins ofM. haemofeliswere purified and evaluated as an antigen in a Western blot to verify the findings of previous immunoscreening. Together with bioinformatics analyses of individual genes, this approach provided several putative candidate antigens. Five antigens ofM. haemofeliswere reactive by Western blotting against the immune plasma and negative against nonimmune plasma; these antigens might be useful serologic or even vaccine targets.
Statistical modelling of falls count data with excess zeros
Authors: Khan Asaduzzaman , Ullah Shahid , Nitz Jenny
Published: June 2011

Objective

To examine the appropriateness of different statistical models in analysing falls count data.

Methods

Six count models (Poisson, negative binomial (NB), zero-inflated Poisson (ZIP), zero-inflated NB (ZINB), hurdle Poisson (HP) and hurdle NB (HNB)) were used to analyse falls count data. Empirical evaluation of the competing models was performed using model selection criteria and goodness-of-fit through simulation. Data used were from a prospective cohort study of women aged 40–80 years.

Results

Of the 465 women analysed, 330 (71%) did not fall at all. The analyses identified strong evidence of overdispersion in the falls data. The NB-based regression models (HNB, ZINB, NB) were better performed than the Poisson-based regression models (Poisson, ZIP, HP). Vuong tests favoured the HNB model over the NB and ZINB models and the NB model over the ZINB model. Model accuracy measures and Monte Carlo simulation of goodness-of-fit confirmed the lack of fit of the Poisson-based regression models and demonstrated the best fit for the HNB model with comparable good fit for the ZINB and NB models.

Conclusions

Falls count data consisting of a considerable number of zeros can be appropriately modelled by the NB-based regression models, with the HNB model offering the best fit. The evaluation procedure presented in this paper provides a defensible guideline to appropriately model falls or similar count data with excess zeros.
Ezrin expression predicts local recurrence and development of metastases in soft tissue sarcomas
Authors: Carneiro Ana , Bendahl Pär-Ola , Åkerman Måns , Domanski Henryk A , Rydholm Anders , Engellau Jacob , Nilbert Mef
Published: June 2011

Background

Ezrin is a cytoskeletal protein involved in tumour growth and invasion. Ezrin expression has been suggested to play a role in metastasis in paediatricosteosarcoma and rhabdomyosarcoma.

Aim

To evaluate the prognostic role of ezrin in a large series of soft tissue sarcoma of the extremities and trunk wall.

Methods

Ezrin expression was evaluated by immunohistochemistry on tissue microarrays from a mixed series of 256 soft tissue sarcomas. The expression patterns were correlated to local recurrence and metastasis as well as to established prognostic factors in soft tissue sarcoma.

Results

Increased ezrin expression predicted development of metastasis (HR=1.8, 95% CI 1.1 to 2.8; p=0.007) and local recurrence, also after adjustment for surgical margin (HR=2.4, 95% CI 1.4 to 4.3; p=0.02). Correlations to established prognostic factors showed strong associations between ezrin and necrosis (OR=3.9, p<0.0001) and ezrin and growth pattern (OR=3.1, p=0.03).

Conclusions

Ezrin independently predicts development of local recurrences and metastases in soft tissue sarcomas. The possibility of preoperative evaluation makes ezrin a potential marker for identification of high-risk sarcoma patients who would benefit from neoadjuvant therapy.