bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-Throughput Fatty Acid Profiling Screen Reveals Novel Variations in Fatty Acid Biosynthesis in Chlamydomonas reinhardtii and Related Algae
Authors: Pflaster Erin L. , Schwabe Michael J. , Becker Joyanne , Wilkinson Melissa S. , Parmer Ashley , Clemente Thomas E. , Cahoon Edgar B. , Riekhof Wayne R. 
Published: September 2014

ABSTRACT

Analysis of fatty acid methyl esters (FAMEs) by gas chromatography (GC) is a common technique for the quantitative and qualitative analysis of acyl lipids. Methods for FAME preparation are typically time-consuming and labor-intensive and require multiple transfers of reagents and products between reaction tubes and autosampler vials. In order to increase throughput and lower the time and materials costs required for FAME preparation prior to GC analysis, we have developed a method in which 10-to-20-mg samples of microbial biomass are transferred to standard GC autosampler vials, transesterified using an emulsion of methanolic trimethylsulfonium hydroxide and hexane, and analyzed directly by GC without further sample handling. This method gives results that are essentially identical to those obtained by the more labor- and material-intensive FAME preparation methods, such as transmethylation with methanolic HCl. We applied this method to the screening of laboratory and environmental isolates of the green alga
Chlamydomonas
for variations in fatty acid composition. This screening method facilitated two novel discoveries. First, we identified a common laboratory strain of
C. reinhardtii
, CC-620, completely lacking all ω-3 fatty acids normally found in this organism and showed that this strain contains an inactivating mutation in the CrFAD7 gene, encoding the sole ω-3 desaturase activity in this organism. Second, we showed that some species of
Chlamydomonas
make Δ6-unsaturated polyunsaturated fatty acids (PUFA) rather than the Δ5 species normally made by the previously characterized laboratory strains of
Chlamydomonas
, suggesting that there is species-specific variation in the regiospecificity and substrate selectivity of front-end desaturases in this algal genus.
Genomic Insights into Processes Driving the Infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp
Authors: Lu Yameng , Wohlrab Sylke , Glöckner Gernot , Guillou Laure , John Uwe 
Published: September 2014

ABSTRACTThe regulatory circuits during infection of dinoflagellates by their parasites are largely unknown on the molecular level. Here we provide molecular insights into these infection dynamics.Alexandrium tamarenseis one of the most prominent harmful algal bloom dinoflagellates. Its pathogen, the dinoflagellate parasitoidAmoebophryasp., has been observed to infect and control the blooms of this species. We generated a data set of transcripts from three time points (0, 6, and 96 h) during the infection of this parasite-host system. Assembly of all transcript data from the parasitoid (>900,000 reads/313 Mbp with 454/Roche next-generation sequencing [NGS]) yielded 14,455 contigs, to which we mapped the raw transcript reads of each time point of the infection cycle. We show that particular surface lectins are expressed at the beginning of the infection cycle which likely mediate the attachment to the host cell. In a later phase, signal transduction-related genes together with transmembrane transport and cytoskeleton proteins point to a high integration of processes involved in host recognition, adhesion, and invasion. At the final maturation stage, cell division- and proliferation-related genes were highly expressed, reflecting the fast cell growth and nuclear division of the parasitoid. Our molecular insights into dinoflagellate parasitoid interactions point to general mechanisms also known from other eukaryotic parasites, especially from the Alveolata. These similarities indicate the presence of fundamental processes of parasitoid infection that have remained stable throughout evolution within different phyla.
Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii
Authors: Jiang Wenzhi , Brueggeman Andrew J. , Horken Kempton M. , Plucinak Thomas M. , Weeks Donald P. 
Published: September 2014

ABSTRACT

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a powerful and precise tool for targeted gene modification (e.g., gene knockout and gene replacement) in numerous eukaryotic organisms. Initial attempts to apply this technology to a model, the single-cell alga,
Chlamydomonas reinhardtii
, failed to yield cells containing edited genes. To determine if the Cas9 and single guide RNA (sgRNA) genes were functional in
C. reinhardtii
, we tested the ability of a codon-optimized Cas9 gene along with one of four different sgRNAs to cause targeted gene disruption during a 24-h period immediately following transformation. All three exogenously supplied gene targets as well as the endogenous
FKB12
(rapamycin sensitivity) gene of
C. reinhardtii
displayed distinct Cas9/sgRNA-mediated target site modifications as determined by DNA sequencing of cloned PCR amplicons of the target site region. Success in transient expression of Cas9 and sgRNA genes contrasted with the recovery of only a single rapamycin-resistant colony bearing an appropriately modified
FKB12
target site in 16 independent transformation experiments involving >10
9
cells. Failure to recover transformants with intact or expressed Cas9 genes following transformation with the Cas9 gene alone (or even with a gene encoding a Cas9 lacking nuclease activity) provided strong suggestive evidence for Cas9 toxicity when Cas9 is produced constitutively in
C. reinhardtii
. The present results provide compelling evidence that Cas9 and sgRNA genes function properly in
C. reinhardtii
to cause targeted gene modifications and point to the need for a focus on development of methods to properly stem Cas9 production and/or activity following gene editing.
Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology Studies
Authors: Broberg Christopher A. , Wu Weisheng , Cavalcoli James D. , Miller Virginia L. , Bachman Michael A. 
Published: September 2014

ABSTRACT

Klebsiella pneumoniae
is an urgent public health threat due to the spread of carbapenem-resistant strains causing serious, and frequently fatal, infections. To facilitate genetic, molecular, and immunological studies of this pathogen, we report the complete chromosomal sequence of a genetically tractable, prototypical strain used in animal models.
Complete Genome Sequence of
Chryseobacterium
sp. Strain StRB126, an
N
-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Root
Authors: Morohoshi Tomohiro , Wang Wen-Zhao , Someya Nobutaka , Ikeda Tsukasa 
Published: September 2014

ABSTRACT

Chryseobacterium
sp. strain StRB126 was isolated from a potato root and showed
N
-acylhomoserine lactone-degrading activity. Here, we present the complete 5,503,743-bp genome sequence of StRB126, which has a G+C content of 35.6% and carries 4,828 protein-coding genes, six rRNA operons, and 80 tRNA genes.
Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853)
Authors: Daligault H. E. , Davenport K. W. , Minogue T. D. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Gibbons H. S. , Jaissle J. , Lo C.-C. , Meincke L. , Munk A. C. , Rosenzweig C. N. , Johnson S. L. 
Published: September 2014

ABSTRACT

We present the genome assembly of
Ralstonia pickettii
K-288 (ATCC 27511), consisting of 27 contigs placed into a single scaffold. This 4.76-Mbp genome has 64.0% G+C content and 4,425 coding sequences. Because this is the type strain, inclusion of its data set among other
Ralstonia
genomes should provide a historical genomic perspective.
Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC 13637)
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Gibbons H. S. , Jaissle J. , Li P.-E. , Rosenzweig C. N. , Scholz M. B. , Johnson S. L. 
Published: September 2014

ABSTRACT

An emerging nosocomial pathogen,
Stenotrophomonas maltophila
has a high mortality rate in those it infects. Here, we present the complete genome sequence of
Stenotrophomonas maltophilia
810-2 (ATCC 13637), the type strain of the species. The 5-Mb (66.1% G+C content) genome has been deposited in NCBI under accession number CP008838.
HIV status and sexual behaviour among gay men in Ottawa: considerations for public health
Authors: O'Byrne Patrick , Phillips J Craig , Kitson Cynthia , Bryan Alyssa 
Published: September 2014

ObjectivesHIV prevention efforts, particularly among men who have sex with men (MSM), have not achieved maximum effectiveness. A survey of MSM in Ottawa, Canada was completed to ascertain whether there were differences in how the perceived HIV status of participants and their partners influenced sexual practices.MethodsSelf-directed surveys were administered to a convenience sample of 721 MSM in Ottawa, Canada from November 2011 through May 2012. Data collection occurred at 14 sites. The survey identified whether participants identified as HIV positive, negative or unsure of their HIV status.ResultsThe findings indicated variation between HIV-negative MSM and those who are unsure of their HIV status. Men who were unsure of their HIV status were less likely to report that they asked sexual partners or have had their partners ask about HIV status.ConclusionsThe results of this study indicate that some MSM may base decisions about HIV prevention on discussion about HIV status with their partners, rather than condom use. These practices may increase, rather than decrease, HIV transmission. Survey findings and extant literature demonstrate a need to inform MSM about the limitations of serosorting as a prevention strategy, and to provide facilitated access to sexually transmitted infection testing and treatment to further reduce onward HIV transmission.
State-specific, racial and ethnic heterogeneity in trends of firearm-related fatality rates in the USA from 2000 to 2010
Authors: Kalesan Bindu , Vasan Sowmya , Mobily Matthew E , Villarreal Marcos D , Hlavacek Patrick , Teperman Sheldon , Fagan Jeffrey A , Galea Sandro 
Published: September 2014

ObjectivesTo document overall, racial, ethnic and intent-specific spatiotemporal trends of firearm-related fatality rates (FRF rates) in the USA.DesignCross-sectional study per year from 2000 to 2010.SettingUSA.ParticipantsAggregate count of all people in the USA from 2000 to 2010.Outcome measuresData from the Web-based Injury Statistics Query and Reporting System from 2000 to 2010 was used to determine annual FRF rates per 100 000 and by states, race, ethnicity and intent.ResultsThe average national 11-year FRF rate was 10.21/100 000, from 3.02 in Hawaii to 18.62 in Louisiana: 60% of states had higher than national rates and 41 states showed no temporal change. The average national FRF rates among African-Americans and Caucasians were 18.51 and 9.05/100 000 and among Hispanics and non-Hispanics were 7.13 and 10.13/100 000; Hispanics had a decreasing change of −0.18, p trend<0.0001. In states with increasing trends (Florida and Massachusetts), Caucasians and non-Hispanics drove the rise; while in states with decreasing trends (California, North Carolina, Arizona, Nevada, New York, Illinois, Maryland), Hispanics and African-Americans drove the fall. The average national FRF rates due to homicides (4.1/100 000) and suicides (5.8/100 000) remained constant, but varied between states.ConclusionsEndemic national FRF rates mask a wide variation in time trends between states. FRF rates were twice as high in African-Americans than Caucasians but decreased among Hispanics. Efforts to identify state-specific best practices can contribute to changes in national FRF rates that remain high.
Are schoolteachers able to teach first aid to children younger than 6 years? A comparative study
Authors: Ammirati Christine , Gagnayre Rémi , Amsallem Carole , Némitz Bernard , Gignon Maxime 
Published: September 2014

ObjectivesThis study was designed to assess the knowledge acquired by very young children (<6 years) trained by their own teachers at nursery school. This comparative study assessed the effect of training before the age of 6 years compared with a group of age-matched untrained children.SettingSome schoolteachers were trained by emergency medical teams to perform basic first aid.ParticipantsEighteen classes comprising 315 pupils were randomly selected: nine classes of trained pupils (cohort C1) and nine classes of untrained pupils (cohort C2).Primary and secondary outcome measuresThe test involved observing and describing three pictures and using the phone to call the medical emergency centre. Assessment of each child was based on nine criteria, and was performed by the teacher 2 months after completion of first aid training.ResultsThis study concerned 285 pupils: 140 trained and 145 untrained. The majority of trained pupils gave the expected answers for all criteria and reacted appropriately by assessing the situation and alerting emergency services (55.7−89.3% according to the questions). Comparison of the two groups revealed a significantly greater ability of trained pupils to describe an emergency situation (p<0.005) and raise the alert (p<0.0001).ConclusionsThis study shows the ability of very young children to assimilate basic skills as taught by their own schoolteachers.
A longitudinal study to identify the influence of quality of chronic care delivery on productive interactions between patients and (teams of) healthcare professionals within disease management programmes
Authors: Cramm Jane Murray , Nieboer Anna Petra 
Published: September 2014

ObjectiveThe chronic care model is an increasingly used approach to improve the quality of care through system changes in care delivery. While theoretically these system changes are expected to increase productive patient–professional interaction empirical evidence is lacking. This study aims to identify the influence of quality of care on productive patient–professional interaction.SettingLongitudinal study in 18 Dutch regions.ParticipantsQuestionnaires were sent to all 5076 patients participating in 18 Disease Management Programmes (DMPs) in 2010 (2676 (53%) respondents). One year later (T1), 4693 patients still participating in the DMPs received a questionnaire (2191 (47%) respondents) and 2 years later (in 2012; T2) 1722 patients responded (out of 4350; 40% response).InterventionsDMPsPrimary outcome measurePatients’ perceptions of the productivity of interactions (measured as relational coordination/coproduction of care) with professionals. Patients were asked about communication dimensions (frequent, accurate, and problem-solving communication) and relationship dimensions (shared goals and mutual respect).FindingsAfter controlling for background characteristics these results clearly show that quality of chronic care (T0), first-year changes in quality of chronic care (T1—T0) and second-year changes in quality of chronic care (T2—T1) predicted productive interactions between patients and professionals at T2 (all at p≤0.001). Furthermore, we found a negative relationship between lower educational level and productive interactions between patients and professionals 2 years later.ConclusionsWe can conclude that successfully dealing with the consequences of chronic illnesses requires proactive patients who are able to make productive decisions together with their healthcare providers. Since patients and professionals share responsibility for management of the chronic illness, they must also share control of interactions and decisions. The importance of patient-centeredness is growing and this study reports a first example of how quality of chronic care stimulates productive interactions between patients and professionals.
A systematic review of qualitative research on the contributory factors leading to medicine-related problems from the perspectives of adult patients with cardiovascular diseases and diabetes mellitus
Authors: Al Hamid A , Ghaleb M , Aljadhey H , Aslanpour Z 
Published: September 2014

ObjectivesTo synthesise contributing factors leading to medicine-related problems (MRPs) in adult patients with cardiovascular diseases and/or diabetes mellitus from their perspectives.DesignA systematic literature review of qualitative studies regarding the contributory factors leading to MRPs, medication errors and non-adherence, followed by a thematic synthesis of the studies.Data sourcesWe screened Pubmed, EMBASE, ISI Web of Knowledge, PsycInfo, International Pharmaceutical Abstract and PsycExtra for qualitative studies (interviews, focus groups and questionnaires of a qualitative nature).Review methodsThematic synthesis was achieved by coding and developing themes from the findings of qualitative studies.ResultsThe synthesis yielded 21 studies that satisfied the inclusion and exclusion criteria. Three themes emerged that involved contributing factors to MRPs: patient-related factors including socioeconomic factors (beliefs, feeling victimised, history of the condition, lack of finance, lack of motivation and low self-esteem) and lifestyle factors (diet, lack of exercise/time to see the doctor, obesity, smoking and stress), medicine-related factors (belief in natural remedies, fear of medicine, lack of belief in medicines, lack of knowledge, non-adherence and polypharmacy) and condition-related factors (lack of knowledge/understanding, fear of condition and its complications, and lack of control).ConclusionsMRPs represent a major health threat, especially among adult patients with cardiovascular diseases and/or diabetes mellitus. The patients’ perspectives uncovered hidden factors that could cause and/or contribute to MRPs in these groups of patients.
Management of behavioural change in patients presenting with a diagnosis of dementia: a video vignette study with Australian general practitioners
Authors: Jiwa Moyez , Nichols Pam , Magin Parker , Pagey Georgina , Meng Xingqiong , Parsons Richard , Pillai Vinita 
Published: September 2014

ObjectiveTo test the impact of feedback on the proposed management of standardised patients presenting with behavioural change with a diagnosis of dementia in Australian primary care.Materials and methodsA video vignette study was performed with Australian general practitioners (GPs) in 2013. Participants viewed six pairs of matched videos depicting people presenting changed behaviour in the context of a dementia diagnosis in two phases. In both phases GPs indicated their diagnosis and management. After phase 1, GPs were offered feedback on management strategies for the patients depicted. Analyses focused on identification of change in management between the two phases of the study. Factors impacting on the intention to coordinate care for such patients were tested in a questionnaire based on the Theory of Planned Behaviour.ResultsForty-five GPs completed the study. There was significant improvement in the proposed management of three of the six scenarios after the intervention. Older GPs were more likely to refer appropriately (OR=1.11 (1.01 to 1.23), p=0.04.). Overall referral to support agencies was more likely after the intervention (OR=2.52 (1.53 to 4.14), p<0.001). Older GPs were less likely to intend to coordinate care for such patients (OR=0.89 (0.81 to 0.98) p=0.02). Participants who felt confident about their ability to coordinate care were more likely to do so (OR=3.79 (1.08 to 13.32) p=0.04).ConclusionsThe intervention described in this study promoted multidisciplinary management of patients with behavioural problems with a diagnosis of dementia. Increasing practitioner confidence in their ability to coordinate care may increase the proportion of GPs who will respond to patients and carers in this context. Older GPs may benefit in particular.
Improving cardiac assessment and monitoring in methadone prescribing at an addiction service
Authors: Ramage Mark , Fadaka Kate 
Published: September 2014

AbstractThe assessment and monitoring of cardiac risk in patients prescribed methadone is important for patient safety. Although uncommon, QTc interval prolongation is potentially life-threatening. Known risk factors for QTc prolongation include methadone, particularly at doses above 100 milligrams daily. This project aimed to improve the cardiac assessment and monitoring at Barnet Drug and Alcohol Service through raising the awareness of this clinically importance issue as well as through amending the medical assessment guidance to promote the comprehensive assessment of QTc prolongation risk factors and ensure the identification of cardiac risk in patients prescribed methadone.The project also provided guidance on QTc prolongation management and monitoring (including performance of an electrocardiogram) at the service to provide a baseline measurement and arrangement of annual monitoring. Prior to the intervention, a randomised sample of 26 patients that had been prescribed methadone revealed no comprehensive cardiac risk assessments. Analysing 52 medical assessments in the month following the intervention suggested an improvement in assessment and management of QTc interval prolongation risk, with seven comprehensive cardiac risks assessments performed and one patient having QTc interval prolongation identified following an electrocardiogram and appropriately managed. This project was limited by small sample sizes and the relatively low incidence of QTc prolongation. The poor rate of attendance for requested electrocardiograms in this population was noted as a challenge that needed further consideration.
Transport cyclists and road rules: what influences the decisions they make?
Authors: Shaw Louise , Poulos Roslyn G , Hatfield Julie , Rissel Chris 
Published: September 2014

ObjectiveTo determine the level of adherence by transport cyclists to road rules in traffic situations and their reasons for non-adherence.DesignThe Safer Cycling Study was a prospective cohort study of transport and recreational cyclists. Over 2000 cyclists were recruited between March and November 2011.Subjects and Setting770 Transport cyclists aged 18 years and older, who lived in New South Wales, Australia. Participants completed a baseline questionnaire plus provided data during a further six survey weeks over 12 months. In one of their survey weeks, cyclists were asked how often they infringed road rules and what contributory factors led to their road rule infringement. Data were collected via web-based online questionnaires.MethodsQuantitative data were analysed descriptively. Qualitative data were analysed to identify themes derived from the text.ResultsRiding on the footpath and red light infringement were the most commonly reported road rule breaches. Poor infrastructure design was the most frequently identified contributing factor to road rule breaches, followed by the speed of motorised traffic and the behaviour of other road users.ConclusionsA transport network needs to facilitate cyclists of all capabilities to reach their required destination in a safe and timely manner, and encourage compliance with the road rules.