bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABACAS: algorithm-based automatic contiguation of assembled sequences
Authors: Assefa Samuel , Keane Thomas M. , Otto Thomas D. , Newbold Chris , Berriman Matthew 
Published: June 2009

Abstract
Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated.
Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net
Contact: sa4@sanger.ac.uk
Division-inhibition capacity of penicillin in Escherichia coli is growth-rate dependent
Authors: Hadas Hilla , Einav Monica , Fishov Itzhak , Zaritsky Arieh 
Published: June 2009

SUMMARY
Growing bacteria are sensitive to various
-lactam derivatives due to their interference with peptidogly can biosynthesis. At low concentrations, penicillin G (benzylpenicillin) blocks cell division without affecting mass growth rate. The MIC for division of Escherichia coli B/r (H266) was found to depend on the growth rate, which was modified by the nutritional conditions. Our hypothesis, that division sensitivity is proportional to the rate of peptidoglycan synthesis for septum formation, as well as to cell circumference, was thus confirmed.
An operon encoding aspartokinase and purine phosphoribosyltransferase in Thermus flavus
Authors: Nishiyama Makoto , Kukimoto Mutsuko , Beppu Teruhiko , Horinouchi Sueharu 
Published: June 2009

SUMMARY
The nucleotide sequence of a 1:1 kb Xhol-HindIII fragment downstream of the malate dehydrogenase (mdh) gene of Thermus flavus revealed the presence of an ORF and an incomplete ORF lacking its NH2-terminal portion, in the opposite orientation to that of the mdh gene. These two genes overlapped with each other, sharing two base pairs, suggesting that these genes are co-transcribed in a single mRNA. One ORF (termed gpt) encoded a protein of 154 amino acids showing significant amino acid sequence similarity to purine phosphoribosyltransferases, such as xanthine-guanine phosphoribosyltransferase of Escherichia coli and human hypoxanthine phosphoribosyltransferase. Cloning and sequencing of the upstream region of the gpt gene, together with sequence comparison of the gene product encoded by the region upstream of gpt, suggested that the upstream ORF encoded two in-frame overlapping aspartokinase genes, askA, encoding the β-subunit of 405 amino acids, and askB, encoding the β-subunit of 161 amino acids, which was part of the 3′ portion of askA. Consistent with the sequence data, the askAB and the gpt genes conferred the heat-stable enzyme activities of aspartokinase and phosphoribosyltransferase, respectively, on E. coli. Preliminary characterization of these enzymes produced in E. coli is described.
Bacterial contamination of PCA and epidural infusion devices
Authors: Rothwell M. , Pearson D. , Wright K. , Barlow D. 
Published: June 2009

SummaryWe prospectively audited the bacterial contamination of re‐useable analgesia infusion pumps. In a one‐month period, 112 samples from the handset and keypads of our analgesia infusion pumps were cultured for bacterial contamination. Forty‐five percent of handset swabs and 46% of keypad swabs grew bacteria; the commonest organism being coagulase‐negative staphylococcus. An additional cleaning step using 70% isopropyl alcohol wipes was introduced and the contamination rate was re‐audited in 100 samples. The contamination rate was reduced to 6% of handset swabs and 4% of keypad swabs. A high initial rate of bacterial contamination of re‐useable analgesia infusion pumps was significantly reduced by the implementation of a simple, additional cleaning procedure.
Optimal remifentanil dosage for providing excellent intubating conditions when co‐administered with a single standard dose of propofol
Authors: Bouvet L. , Stoian A. , Rimmelé T. , Allaouchiche B. , Chassard D. , Boselli E. 
Published: June 2009

SummaryThis dose–response study aimed to determine the dose of remifentanil combined with propofol 2.5 mg.kg−1 which provided excellent intubation conditions in 95% of patients. Ninety premedicated female ASA 1 and 2 patients were randomly allocated to five remifentanil dose groups (1, 2, 3, 4 or 5 μg.kg−1). Induction of anaesthesia was performed with a blinded dose of remifentanil infused over 60 s simultaneously co‐administered with propofol 2.5 mg.kg−1 infused over 45 s. Tracheal intubation was attempted 150 s after the beginning of induction. Intubating conditions were assessed with the Copenhagen score. A probit analysis was performed to calculate the intubating efficient doses (IED) of remifentanil in 95% of patients (IED95). Our data revealed that the IED95 of remifentanil was 4.0 (95% CI: 3.4–5.6) μg.kg−1, which was associated with a maximum decrease in heart rate and mean arterial pressure of < 30%, a finding which also applied to the other groups.
Agreement between children with cancer and their parents in reporting the child's health‐related quality of life during a stay at the hospital and at home
Authors: Speyer E. , Herbinet A. , Vuillemin A. , Chastagner P. , Briançon S. 
Published: June 2009

AbstractBackground  Although parent–child agreement is widely studied in the paediatric clinical sample, no study has compared parent–child agreement during home and hospital stays. We aimed to determine the level of agreement in reports of health‐related quality of life (HRQoL) between parents of children with cancer and the children themselves during a stay in the hospital and a stay at home.Methods  The sample consisted of 28 children, aged 9–18 years old, hospitalized and treated for cancer in a Children's University Hospital in France. The child's HRQoL was assessed by the parent and child versions of the Child Health Questionnaire. Parent–child agreement was estimated by the intraclass correlation coefficient. Potential predictors influencing the parent–child agreement were investigated.Results  For both locations of stay, parent scores from the HRQoL survey were lower than those for their children for all domains, except for the general behaviour during the home stay. Scores for both parents and children, for all domains, were lower during the hospital than the home stay. The parent–child agreement was better for mental health, self‐esteem, general health and family activities during the hospital stay (range 0.32–0.66), but was better for physical function, role/physical and general behaviour during the home stay (range 0.45–0.71). Few predictors of parent–child agreement were found.Conclusions  Agreement between parents and their children who have cancer in reporting the child's HRQoL differed by location of stay. For the home stay, the agreement was better for domains related to the child's physical life, but for the hospital stay, it was better for domains related to the child's behaviour/psychological life.
A psychometric evaluation of the Chinese version of the Hospital Anxiety and Depression Scale in patients with coronary heart disease
Authors: Wang Wenru , Chair Sek Ying , Thompson David R , Twinn Sheila F 
Published: June 2009

Aim.  To evaluate further the psychometric properties of the Chinese version of the Hospital Anxiety and Depression Scale (HADS) as a screening instrument for anxiety and depression in Chinese patients with coronary heart disease (CHD) in Xian, China.Background.  There is considerable evidence that anxiety and depression are common in patients with CHD and are associated with increased morbidity and mortality. A valid, reliable and sensitive screening tool that can be used readily on this group of patients would be useful for assessment, intervention and outcome evaluation.Design.  A single group, cross‐sectional study.Method.  Measurement performance was tested on 314 Chinese patients with CHD and repeated on 173 of them two weeks later.Results.  The Chinese version of HADS (C‐HADS) had acceptable internal consistency and test‐retest reliability, with a Cronbach's alpha of 0·85 and intraclass correlation coefficient of 0·90, respectively. There was acceptable concurrent validity with significant (p < 0·05) correlations between the anxiety and depression subscales of the C‐HADS and CHD patients’ perceived health status as measured by the Chinese‐Mandarin version of the Short Form‐36 health survey (CM:SF‐36). Principal components analysis revealed a three‐factor solution accounting for 53% of the total variance. The three underlying sub‐scale dimensions are depression, psychic anxiety and psychomotor anxiety. The responsiveness of the C‐HADS was also satisfactory with significant correlation between the changes in the C‐HADS score and the changes in the mental health domain of the CM:SF‐36 (p < 0·01). Finally, over one‐third of the patients demonstrated psychological distress.Conclusion.  Empirical data support the C‐HADS as a reliable and valid screening instrument for the assessment of anxiety and depression in Chinese‐speaking patients with CHD. A tri‐dimensional scoring approach should be considered as potentially clinically useful for this group of patients.Relevance to clinical practice.  The C‐HADS can guide and evaluate the delivery of psychological care for Chinese patients with CHD.
An evaluation of strategies to improve the quality and content of hospital‐based postnatal care in a metropolitan Australian hospital
Authors: Schmied Virginia , Cooke Margaret , Gutwein Rosalind , Steinlein Elizabeth , Homer Caroline 
Published: June 2009

Aim and objective.  This study aimed to design, implement and evaluate strategies to improve the quality and content of hospital‐based postnatal care.Background.  Following birth, women report physical health problems, difficulties with breastfeeding, a lack of parenting self‐efficacy and there is high occurrence of postnatal distress and depression. Despite these significant needs, women are frequently dissatisfied with the advice and support they receive from hospital‐based postnatal care.Design.  A pre/post test design compared the effect of multifaceted strategies on perceptions of quality and content of postnatal care, knowledge and experience of postnatal problems, parenting self‐efficacy and breastfeeding outcomes. The key strategy, ‘one‐to‐one time’, focused on providing women an uninterrupted period of time each day when a midwife would be available to discuss women’s concerns about their health and that of their baby.Method.  A convenience sample of 146 women at baseline and 148 women postintervention completed a postal self‐report questionnaire between 2–4 weeks postpartum.Results.  There were no significant differences between baseline and postintervention groups in perceived quality of care, breastfeeding outcomes and maternal self‐efficacy. Women experiencing health issues, including insufficient milk supply, backache, abnormal bleeding and urinary incontinence, were more likely to report that they received good or excellent care and advice in the postintervention group. Strategies to increase rest appeared effective with women less likely to report excessive tiredness postintervention. The key strategy, ‘one‐to‐one time’ was not consistently implemented, 57% of women reported they received 10 minutes or less of uninterrupted time with a midwife and only 11% reported that they were provided with 20 minutes or more.Conclusion.  There is the potential for individualised care to impact on outcomes for women but established routines and institutional priorities are difficult to change.Relevance to clinical practice.  Midwives require both skill development and time to be able to sensitively listen to women’s needs in the hospital postnatal setting.
Are older patients’ cardiac rehabilitation needs being met?
Authors: Tolmie Elizabeth P , Lindsay Grace M , Kelly Tim , Tolson Debbie , Baxter Susan , Belcher Philip R 
Published: June 2009

Aims.  The primary aim of this study was to examine the needs of older people in relation to cardiac rehabilitation and to determine if these were currently being met. A secondary aim was to compare illness representations, quality of life and anxiety and depression in groups with different levels of attendance at a cardiac rehabilitation programme.Background.  Coronary heart disease accounted for over seven million cardiovascular deaths globally in 2001. Associated deaths increase with age and are highest in those older than 65. Effective cardiac rehabilitation can assist independent function and maintain health but programme uptake rates are low. We have, therefore, focussed specifically on the older patient to determine reasons for the low uptake.Design.  Mixed methods.Methods.  A purposive sample of 31 older men and women (≥65 years) completed three questionnaires to determine illness representations, quality of life and anxiety and depression. They then underwent a brief clinical assessment and participated in a face‐to‐face audio‐taped interview.Results.  Quantitative: Older adults, who did not attend a cardiac rehabilitation programme, had significantly poorer personal control and depression scores (p < 0·01) and lower quality of life scores than those who had attended. Few achieved recommended risk factor reduction targets. Qualitative: The three main themes identified as reflecting the views and experiences of and attendance at the cardiac rehabilitation programme were: ‘The sensible thing to do’, ‘Assessing the impact’ and ‘Nothing to gain’.Conclusions.  Irrespective of level of attendance, cardiac rehabilitation programmes are not meeting the needs of many older people either in terms of risk factor reduction or programme uptake. More appropriate programmes are needed.Relevance to clinical practice.  Cardiac rehabilitation nurses are ideally placed to identify the rehabilitation needs of older people. Identifying these from the older person’s perspective could help guide more appropriate intervention strategies.
Susceptibility of selected freshwater fish species to a UK Lactococcus garvieae isolate
Authors: Algöet M , Bayley A E , Roberts E G , Feist S W , Wheeler R W , Verner‐Jeffreys D W 
Published: June 2009

AbstractGram‐positive cocci recovered from diseased rainbow trout from a farm in England were characterized by different methods, including pulsed field gel electrophoresis, as virulent Lactococcus garvieae serogroup 2 (pulsotype A1). Groups of rainbow trout were kept at a range of temperatures and injected intraperitoneally (i.p.) with one of the UK isolates, L. garvieae 00021. The 18 °C and 16 °C groups showed 67% and 28% mortality, respectively, by day 27 post‐injection. Fish kept at 14 °C or lower were less susceptible (≤3% mortality). Raising the temperature of all groups to 18 °C at day 27 post‐injection did not result in recurrence of the disease, even though viable bacteria were recovered from all groups 42 days later. Grayling were highly susceptible, with 65% mortalities when challenged with 200 colony forming unit fish−1 by i.p. injection and 37% mortalities when exposed to effluent water from tanks containing affected rainbow trout. Other fish species tested, Atlantic salmon, brown trout and seven cyprinid species, were less susceptible. Viable L. garvieae was isolated from the internal organs of all species tested at the end of the trials, suggesting that they may pose a threat as possible carriers to susceptible farmed and wild fish.
Tetrahymena sp. infection in guppies, Poecilia reticulata Peters: parasite characterization and pathology of infected fish
Authors: Leibowitz M P , Zilberg D 
Published: June 2009

Abstract Tetrahymena sp. infection was diagnosed in guppies imported from Singapore. The parasite was isolated (Tet‐NI) and optimally cultured in vitro in RM‐9 medium. Cytological analyses [silver‐staining and scanning electron microscopy (SEM)] revealed a pyriform‐shaped, 64 × 41‐μm holotrich ciliate without caudal cilium, containing a macro‐nucleus (18.25 × 16.83 μm) and micro‐nucleus (5.73 × 5.40 μm). Wet‐mount examination and histological analyses of fish exposed to the parasite by co‐habitation, immersion and infection by i.p. (intra‐peritoneal) and i.m. (intra‐muscular) injection revealed numerous ciliates on the skin, and in the gill and caudal fin blood vessels. Ciliates surrounded internal organs, the peri‐orbital region of the eye, and were observed inside developing guppy embryos. Some muscle necrosis was associated with infection, but little or no inflammatory response. Immersion, co‐habitation and i.m. injection caused relatively high infection rates and levels in the skin and tail, and lower infection in the gill blood vessels and internal organs; i.p. injection caused higher infection in the gill blood vessels and internal organs. Co‐habited fish had relatively high infection levels in the hind‐gut sub‐mucosa. This is the first report of controlled systemic infection by Tetrahymena sp.
Foliar and tuber late blight resistance in a Solanum tuberosum breeding population
Authors: Mayton H. , Griffiths H. , Simko I. , Cheng S. , Lorenzen J. , De Jong W. , Fry W. E. 
Published: June 2009

With 2 figures and 2 tables AbstractThe purpose of this research was to identify the genetic basis of foliar and tuber resistance to Phytophthora infestans in a potato breeding population developed from a cross between two tetraploid Solanum tuberosum lines, NY121 and NY115. The parent with high foliar resistance, NY121, was highly susceptible to tuber blight. Foliar resistance was assessed in field trials, while tuber blight was assessed both in the field and in the laboratory. A quantitative trait locus (QTL) explaining ca. 50% of the phenotypic variance for foliar resistance was located on the lower arm of linkage group V, and was loosely associated with tuber blight resistance (significantly in one of two trials). This QTL was confirmed in a separate sample from the same population. Tuber blight detected via laboratory assays was not correlated with tuber blight incidence in the field. Most markers associated with tuber blight resistance were not associated with foliar resistance and most markers associated with foliar resistance were not associated with tuber blight resistance.
No evidence for compensatory thermal adaptation of soil microbial respiration in the study of Bradford et al. (2008)
Authors: Hartley Iain P. , Hopkins David W. , Garnett Mark H. , Sommerkorn Martin , Wookey Philip A. 
Published: June 2009

Abstract Bradford et al. (2008) conclude that thermal adaptation will reduce the response of soil microbial respiration to rising global temperatures. However, we question both the methods used to calculate mass‐specific respiration rates and the interpretation of the results. No clear evidence of thermal adaptation reducing soil microbial activity was produced.
New nitrogen uptake strategy: specialized snow roots
Authors: Onipchenko Vladimir G. , Makarov Mikhail I. , Van Logtestijn Richard S. P. , Ivanov Viktor B. , Akhmetzhanova Assem A. , Tekeev Dzhamal K. , Ermak Anton A. , Salpagarova Fatima S. , Kozhevnikova Anna D. , Cornelissen Johannes H. C. 
Published: June 2009

AbstractThe evolution of plants has yielded a wealth of adaptations for the acquisition of key mineral nutrients. These include the structure, physiology and positioning of root systems. We report the discovery of specialized snow roots as a plant strategy to cope with the very short season for nutrient uptake and growth in alpine snow‐beds, i.e. patches in the landscape that remain snow‐covered well into the summer. We provide anatomical, chemical and experimental 15N isotope tracking evidence that the Caucasian snow‐bed plant Corydalis conorhiza forms extensive networks of specialized above‐ground roots, which grow against gravity to acquire nitrogen directly from within snow packs. Snow roots capture nitrogen that would otherwise partly run off down‐slope over a frozen surface, thereby helping to nourish these alpine ecosystems. Climate warming is changing and will change mountain snow regimes, while large‐scale anthropogenic N deposition has increased snow N contents. These global changes are likely to impact on the distribution, abundance and functional significance of snow roots.
Palmitoylation of the synaptic vesicle fusion machinery
Authors: Prescott Gerald R. , Gorleku Oforiwa A. , Greaves Jennifer , Chamberlain Luke H. 
Published: June 2009

AbstractThe fusion of synaptic vesicles with the pre‐synaptic plasma membrane mediates the secretion of neurotransmitters at nerve terminals. This pathway is regulated by an array of protein–protein interactions. Of central importance are the soluble NSF (N‐ethylmaleimide‐sensitive factor) attachment protein receptor (SNARE) proteins syntaxin 1 and SNAP25, which are associated with the pre‐synaptic plasma membrane and vesicle‐associated membrane protein (VAMP2), a synaptic vesicle SNARE. Syntaxin 1, SNAP25 and VAMP2 interact to form a tight complex bridging the vesicle and plasma membranes, which has been suggested to represent the minimal membrane fusion machinery. Synaptic vesicle fusion is stimulated by a rise in intraterminal Ca2+ levels, and a major Ca2+ sensor for vesicle fusion is synaptotagmin I. Synaptotagmin is likely to couple Ca2+ entry to vesicle fusion via Ca2+‐dependent and independent interactions with membrane phospholipids and the SNARE proteins. Intriguingly, syntaxin 1, SNAP25, VAMP2 and synaptotagmin I have all been reported to be modified by palmitoylation in neurons. In this review, we discuss the mechanisms and dynamics of palmitoylation of these proteins and speculate on how palmitoylation might contribute to the regulation of synaptic vesicle fusion.
Perceptions by and of lonely people in social networks
Authors: TSAI FEN‐FANG , REIS HARRY T. 
Published: June 2009

AbstractAlthough past research has associated loneliness with negative perceptions of others, P. Christensen and D. A. Kashy (1998), using the social relations model (SRM), found that among new acquaintances, loneliness was associated with more positive other‐perceptions. SRM was used to examine loneliness and interpersonal perception within existing social networks. Seventy‐three university students in the United States rated themselves and others on 19 attributes and also judged how they thought others saw them (meta‐perceptions). Results indicated that lonely people tended to be more negative toward closer targets and somewhat positive toward less close acquaintances. Lonely people had lower self‐regard and perceived self‐regard, invariant across acquaintanceship, and were rated more negatively by others. Relationship contexts thus moderate effects of loneliness on other‐perceptions.