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1.  Physiotherapy practice in the private sector: organizational characteristics and models 
Background
Even if a large proportion of physiotherapists work in the private sector worldwide, very little is known of the organizations within which they practice. Such knowledge is important to help understand contexts of practice and how they influence the quality of services and patient outcomes. The purpose of this study was to: 1) describe characteristics of organizations where physiotherapists practice in the private sector, and 2) explore the existence of a taxonomy of organizational models.
Methods
This was a cross-sectional quantitative survey of 236 randomly-selected physiotherapists. Participants completed a purpose-designed questionnaire online or by telephone, covering organizational vision, resources, structures and practices. Organizational characteristics were analyzed descriptively, while organizational models were identified by multiple correspondence analyses.
Results
Most organizations were for-profit (93.2%), located in urban areas (91.5%), and within buildings containing multiple businesses/organizations (76.7%). The majority included multiple providers (89.8%) from diverse professions, mainly physiotherapy assistants (68.7%), massage therapists (67.3%) and osteopaths (50.2%). Four organizational models were identified: 1) solo practice, 2) middle-scale multiprovider, 3) large-scale multiprovider and 4) mixed.
Conclusions
The results of this study provide a detailed description of the organizations where physiotherapists practice, and highlight the importance of human resources in differentiating organizational models. Further research examining the influences of these organizational characteristics and models on outcomes such as physiotherapists’ professional practices and patient outcomes are needed.
doi:10.1186/1472-6963-14-362
PMCID: PMC4161767  PMID: 25168160
Organizational characteristics; Organizational models; Physiotherapy; Private sector; Survey
2.  Interprofessional practices of physiotherapists working with adults with low back pain in Québec’s private sector: results of a qualitative study 
Background
Collaboration and interprofessional practices are highly valued in health systems, because they are thought to improve outcomes of care for persons with complex health problems, such as low back pain. Physiotherapists, like all health providers, are encouraged to take part in interprofessional practices. However, little is known about these practices, especially for private sector physiotherapists. This study aimed to: 1) explore how physiotherapists working in the private sector with adults with low back pain describe their interprofessional practices, 2) identify factors that influence their interprofessional practices, and 3) identify their perceived effects.
Methods
Participants were 13 physiotherapists, 10 women/3 men, having between 3 and 21 years of professional experience. For this descriptive qualitative study, we used face-to-face semi-structured interviews and conducted content analysis encompassing data coding and thematic regrouping.
Results
Physiotherapists described interprofessional practices heterogeneously, including numerous processes such as sharing information and referring. Factors that influenced physiotherapists’ interprofessional practices were related to patients, providers, organizations, and wider systems (e.g. professional system). Physiotherapists mostly viewed positive effects of interprofessional practices, including elements such as gaining new knowledge as a provider and being valued in one’s own role, as well as improvements in overall treatment and outcome.
Conclusions
This qualitative study offers new insights into the interprofessional practices of physiotherapists working with adults with low back pain, as perceived by the physiotherapists’ themselves. Based on the results, the development of strategies aiming to increase interprofessionalism in the management of low back pain would most likely require taking into consideration factors associated with patients, providers, the organizations within which they work, and the wider systems.
doi:10.1186/1471-2474-15-160
PMCID: PMC4032868  PMID: 24884757
Interprofessional collaboration; Physiotherapy; Physical therapy; Low back pain; Private sector; Qualitative research
3.  Production of cecropin A antimicrobial peptide in rice seed endosperm 
BMC Plant Biology  2014;14:102.
Background
Cecropin A is a natural antimicrobial peptide that exhibits rapid, potent and long-lasting lytic activity against a broad spectrum of pathogens, thus having great biotechnological potential. Here, we report a system for producing bioactive cecropin A in rice seeds.
Results
Transgenic rice plants expressing a codon-optimized synthetic cecropin A gene drived by an endosperm-specific promoter, either the glutelin B1 or glutelin B4 promoter, were generated. The signal peptide sequence from either the glutelin B1 or the glutelin B4 were N-terminally fused to the coding sequence of the cecropin A. We also studied whether the presence of the KDEL endoplasmic reticulum retention signal at the C-terminal has an effect on cecropin A subcellular localization and accumulation. The transgenic rice plants showed stable transgene integration and inheritance. We show that cecropin A accumulates in protein storage bodies in the rice endosperm, particularly in type II protein bodies, supporting that the glutelin N-terminal signal peptides play a crucial role in directing the cecropin A to this organelle, independently of being tagged with the KDEL endoplasmic reticulum retention signal. The production of cecropin A in transgenic rice seeds did not affect seed viability or seedling growth. Furthermore, transgenic cecropin A seeds exhibited resistance to infection by fungal and bacterial pathogens (Fusarium verticillioides and Dickeya dadantii, respectively) indicating that the in planta-produced cecropin A is biologically active.
Conclusions
Rice seeds can sustain bioactive cecropin A production and accumulation in protein bodies. The system might benefit the production of this antimicrobial agent for subsequent applications in crop protection and food preservation.
doi:10.1186/1471-2229-14-102
PMCID: PMC4032361  PMID: 24755305
Rice; Antimicrobial peptides; Cecropin A; Endosperm; Protein bodies; Pathogen resistance; Fusarium verticillioides; Dickeya dadantii; Oryza sativa
4.  Management of Upper Respiratory Tract Infections by Different Medical Practices, Including Homeopathy, and Consumption of Antibiotics in Primary Care: The EPI3 Cohort Study in France 2007–2008 
PLoS ONE  2014;9(3):e89990.
Background
Prescribing of antibiotics for upper respiratory tract infections (URTI) varies substantially in primary care.
Objectives
To describe and compare antibiotic and antipyretic/anti-inflammatory drugs use, URTI symptoms' resolution and occurrence of potentially-associated infections in patients seeking care from general practitioners (GPs) who exclusively prescribe conventional medications (GP-CM), regularly prescribe homeopathy within a mixed practice (GP-Mx), or are certified homeopathic GPs (GP-Ho).
Method
The EPI3 survey was a nationwide population-based study of a representative sample of 825 GPs and their patients in France (2007–2008). GP recruitment was stratified by self-declared homeopathic prescribing preferences. Adults and children with confirmed URTI were asked to participate in a standardized telephone interview at inclusion, one-, three- and twelve-month follow up. Study outcomes included medication consumption, URTI symptoms' resolution and potentially-associated infections (sinusitis or otitis media/externa) as reported by patients. Analyses included calibration to account for non-respondents and groups were compared using multivate analyses adjusting for baseline differences with a propensity score.
Results
518 adults and children with URTI (79.3% rhinopharyngitis) were included (36.9% response rate comparable between groups). As opposed to GP-CM patients, patients in the GP-Ho group showed significantly lower consumption of antibiotics (Odds ratio (OR) = 0.43, 95% confidence interval (CI): 0.27–0.68) and antipyretic/anti-inflammatory drugs (OR = 0.54, 95% CI: 0.38–0.76) with similar evolution in related symptoms (OR = 1.16, 95% CI: 0.64–2.10). An excess of potentially-associated infections (OR = 1.70, 95% CI: 0.90–3.20) was observed in the GP-Ho group (not statistically significant). No difference was found between GP-CM and GP-Mx patients.
Conclusion
Patients who chose to consult GPs certified in homeopathy used less antibiotics and antipyretic/anti-inflammatory drugs for URTI than those seen by GPs prescribing conventional medications. No difference was observed in patients consulting GPs within mixed-practice. A non-statistically significant excess was estimated through modelling for associated infections in the GP-Ho group and needs to be further studied.
doi:10.1371/journal.pone.0089990
PMCID: PMC3960096  PMID: 24646513
5.  Microgravity Induces Changes in Microsome-Associated Proteins of Arabidopsis Seedlings Grown on Board the International Space Station 
PLoS ONE  2014;9(3):e91814.
The “GENARA A” experiment was designed to monitor global changes in the proteome of membranes of Arabidopsis thaliana seedlings subjected to microgravity on board the International Space Station (ISS). For this purpose, 12-day-old seedlings were grown either in space, in the European Modular Cultivation System (EMCS) under microgravity or on a 1 g centrifuge, or on the ground. Proteins associated to membranes were selectively extracted from microsomes and identified and quantified through LC-MS-MS using a label-free method. Among the 1484 proteins identified and quantified in the 3 conditions mentioned above, 80 membrane-associated proteins were significantly more abundant in seedlings grown under microgravity in space than under 1 g (space and ground) and 69 were less abundant. Clustering of these proteins according to their predicted function indicates that proteins associated to auxin metabolism and trafficking were depleted in the microsomal fraction in µg space conditions, whereas proteins associated to stress responses, defence and metabolism were more abundant in µg than in 1 g indicating that microgravity is perceived by plants as a stressful environment. These results clearly indicate that a global membrane proteomics approach gives a snapshot of the cell status and its signaling activity in response to microgravity and highlight the major processes affected.
doi:10.1371/journal.pone.0091814
PMCID: PMC3950288  PMID: 24618597
6.  Sinorhizobium meliloti Sigma Factors RpoE1 and RpoE4 Are Activated in Stationary Phase in Response to Sulfite 
PLoS ONE  2012;7(11):e50768.
Rhizobia are soil bacteria able to establish a nitrogen-fixing symbiosis with legume plants. Both in soil and in planta, rhizobia spend non-growing periods resembling the stationary phase of in vitro-cultured bacteria. The primary objective of this work was to better characterize gene regulation in this biologically relevant growth stage in Sinorhizobium meliloti. By a tap-tag/mass spectrometry approach, we identified five sigma factors co-purifying with the RNA polymerase in stationary phase: the general stress response regulator RpoE2, the heat shock sigma factor RpoH2, and three extra-cytoplasmic function sigma factors (RpoE1, RpoE3 and RpoE4) belonging to the poorly characterized ECF26 subgroup. We then showed that RpoE1 and RpoE4 i) are activated upon metabolism of sulfite-generating compounds (thiosulfate and taurine), ii) display overlapping regulatory activities, iii) govern a dedicated sulfite response by controlling expression of the sulfite dehydrogenase SorT, iv) are activated in stationary phase, likely as a result of endogenous sulfite generation during bacterial growth. We showed that SorT is required for optimal growth of S. meliloti in the presence of sulfite, suggesting that the response governed by RpoE1 and RpoE4 may be advantageous for bacteria in stationary phase either by providing a sulfite detoxification function or by contributing to energy production through sulfite respiration. This paper therefore reports the first characterization of ECF26 sigma factors, the first description of sigma factors involved in control of sulphur metabolism, and the first indication that endogenous sulfite may act as a signal for regulation of gene expression upon entry of bacteria in stationary phase.
doi:10.1371/journal.pone.0050768
PMCID: PMC3511301  PMID: 23226379
7.  Who seeks primary care for sleep, anxiety and depressive disorders from physicians prescribing homeopathic and other complementary medicine? Results from the EPI3 population survey 
BMJ Open  2012;2(6):e001498.
Objectives
To describe and compare patients seeking treatment for sleep, anxiety and depressive disorders (SADD) from physicians in general practice (GPs) with three different practice preferences: strictly conventional medicine (GP-CM), mixed complementary and conventional medicine (GP-Mx) and certified homeopathic physicians (GP-Ho).
Design and setting
The EPI3 survey was a nationwide, observational study of a representative sample of GPs and their patients, conducted in France between March 2007 and July 2008.
Participants
1572 patients diagnosed with SADD.
Primary and secondary outcomes
The patients’ attitude towards complementary and alternative medicine; psychotropic drug utilisation.
Results
Compared to patients attending GP-CM, GP-Ho patients had healthier lifestyles while GP-Mx patients showed similar profiles. Psychotropic drugs were more likely to be prescribed by GP-CM (64%) than GP-Mx (55.4%) and GP-Ho (31.2%). The three groups of patients shared similar SADD severity.
Conclusion
Our results showed that patients with SADD, while differing principally in their sociodemographic profiles and conventional psychotropic prescriptions, were actually rather similar regarding the severity of SADD in terms of comorbidities and quality of life. This information may help to better plan resource allocation and management of these common health problems in primary care.
doi:10.1136/bmjopen-2012-001498
PMCID: PMC3532988  PMID: 23180389
Epidemiology
8.  Phosphoproteomic analysis reveals major default phosphorylation sites outside long intrinsically disordered regions of Arabidopsis plasma membrane proteins 
Proteome Science  2012;10:62.
Background
Genome-wide statistics established that long intrinsically disordered regions (over 30 residues) are predicted in a large part of proteins in all eukaryotes, with a higher ratio in trans-membrane proteins. At functional level, such unstructured and flexible regions were suggested for years to favour phosphorylation events. In plants, despite increasing evidence of the regulation of transport and signalling processes by phosphorylation events, only few data are available without specific information regarding plasma membrane proteins, especially at proteome scale.
Results
Using a dedicated phosphoproteomic workflow, 75 novel and unambiguous phosphorylation sites were identified in Arabidopsis plasma membrane. Bioinformatics analysis showed that this new dataset concerned mostly integral proteins involved in key functions of the plasma membrane (such as transport and signal transduction, including protein phosphorylation). It thus expanded by 15% the directory of phosphosites previously characterized in signalling and transport proteins. Unexpectedly, 66% of phosphorylation sites were predicted to be located outside long intrinsically disordered regions. This result was further corroborated by analysis of publicly available data for the plasma membrane.
Conclusions
The new phosphoproteomics data presented here, with published datasets and functional annotation, suggest a previously unexpected topology of phosphorylation in the plant plasma membrane proteins. The significance of these new insights into the so far overlooked properties of the plant plasma membrane phosphoproteome and the long disordered regions is discussed.
doi:10.1186/1477-5956-10-62
PMCID: PMC3537754  PMID: 23110452
Arabidopsis; Plasma membrane; Phosphoproteome; Intrinsically disordered regions
9.  Identification of the protein sequence of the type III effector XopD from the B100 strain of Xanthomonas campestris pv campestris 
Plant Signaling & Behavior  2012;7(2):184-187.
During evolution, pathogens have developed sophisticated strategies to suppress plant defense responses and promote successful colonization of their hosts. In their attempt to quell host resistance, Gram-negative phytopathogenic bacteria inject type III effectors (T3Es) into plant cells, where they typically target plant components essential for the establishment of defense responses. We have recently shown that the XopD T3E from the strain B100 of Xanthomonas campestris pathovar campestris (XopDXccB100) is able to target AtMYB30, a positive regulator of Arabidopsis defense responses. This protein interaction leads to inhibition of AtMYB30 transcriptional activity and promotion of bacterial virulence. Here, we describe the identification of the complete protein sequence of XopDXccB100, which presents an N-terminal extension of 40 amino acids with respect to the protein annotated in public databases. The implications of this finding are discussed.
doi:10.4161/psb.18828
PMCID: PMC3405711  PMID: 22353870
mass spectrometry; type III effector; Xanthomonas; XopD
10.  Proteomic characterisation of endoplasmic reticulum-derived protein bodies in tobacco leaves 
BMC Plant Biology  2012;12:36.
Background
The N-terminal proline-rich domain (Zera) of the maize storage protein γ-zein, is able to induce the formation of endoplasmic reticulum (ER)-derived protein bodies (PBs) when fused to proteins of interest. This encapsulation enables a recombinant fused protein to escape from degradation and facilitates its recovery from plant biomass by gradient purification. The aim of the present work was to evaluate if induced PBs encapsulate additional proteins jointly with the recombinant protein. The exhaustive analysis of protein composition of PBs is expected to facilitate a better understanding of PB formation and the optimization of recombinant protein purification approaches from these organelles.
Results
We analysed the proteome of PBs induced in Nicotiana benthamiana leaves by transient transformation with Zera fused to a fluorescent marker protein (DsRed). Intact PBs with their surrounding ER-membrane were isolated on iodixanol based density gradients and their integrity verified by confocal and electron microscopy. SDS-PAGE analysis of isolated PBs showed that Zera-DsRed accounted for around 85% of PB proteins in term of abundance. Differential extraction of PBs was performed for in-depth analysis of their proteome and structure. Besides Zera-DsRed, 195 additional proteins were identified including a broad range of proteins resident or trafficking through the ER and recruited within the Zera-DsRed polymer.
Conclusions
This study indicates that Zera-protein fusion is still the major protein component of the new formed organelle in tobacco leaves. The analysis also reveals the presence of an unexpected diversity of proteins in PBs derived from both the insoluble Zera-DsRed polymer formation, including ER-resident and secretory proteins, and a secretory stress response induced most likely by the recombinant protein overloading. Knowledge of PBs protein composition is likely to be useful to optimize downstream purification of recombinant proteins in molecular farming applications.
doi:10.1186/1471-2229-12-36
PMCID: PMC3342223  PMID: 22424442
11.  Benchmarking the burden of 100 diseases: results of a nationwide representative survey within general practices 
BMJ Open  2011;1(2):e000215.
Objective
To assess the burden of diseases and quality of life (QOL) of patients for a large variety of diseases within general practice.
Design
In a representative nationwide cross-sectional study, a total of 825 general practitioners (GPs) were randomly selected from across France. Independent investigators recruited 8559 patients attending the GPs' practices. Data on QOL (12-Item Short Form questionnaire) and other individual characteristics were documented by the independent investigators for all participants in the waiting room. Medical information was recorded by GPs. Sampling was calibrated to national standards using the CALMAR (CALage sur MARges) weighting procedure. Associations of lower scores (ie, below vs above the first quartile) of physical and mental component scores (physical component summary score (PCS) and mental component summary score (MCS), respectively) with main diseases and patients characteristics were estimated using multivariate logistic regression. Weighted morbidity rates, PCS and MCS were computed for 100 diagnoses using the International Classification of Diseases (9th version).
Results
Overall mental impairment was observed among patients in primary care with an average MCS of 41.5 (SD 8.6), ranging from 33.0 for depressive disorders to 45.3 for patients exhibiting fractures or sprains. Musculoskeletal diseases were found to have the most pronounced effect on impaired physical health (OR=2.31; 95% CI 2.08 to 2.57) with the lowest PCS (45.6 (SD 8.8)) and ranked first (29.0%) among main diagnoses experienced by patients followed by cardiovascular diseases (26.7%) and psychological disorders (22.0%). When combining both prevalence and QOL, musculoskeletal diseases represented the heaviest burden in general practice.
Conclusions
Etude épidémiologique de l'Impact de santé public sur 3 groupes de pathologies (EPI3) is the first study to provide reference figures for burden of disease in general practice across a wide range of morbidities, particularly valuable for health-economics and healthcare-system evaluation.
Article summary
Article focus
The impact of diseases on quality of life (QOL) in general practice has been assessed among selected samples of patients, usually from studies including a limited number of medical practices and/or focusing mainly on chronic conditions.
There is a clear need for more data on QOL of patients in primary care; the aim of the Etude épidémiologique de l'Impact de santé public sur 3 groupes de pathologies (EPI3) survey was to provide reference figures for disease burden in this setting.
Key messages
The EPI3 study was a cross-sectional survey combining unique data from patients and general practitioners (GPs), and allowed provision of reference figures for the vast majority of diseases encountered in primary care for a large number of patients.
The study highlighted the burden of musculoskeletal and psychological disorders, experienced by more than half the patients.
Although social and medical determinants of patients' QOL were somewhat similar than those found in previous studies in primary care, the EPI3 survey showed more pronounced mental impairment in French patients.
Strengths and limitations of this study
No nationwide study on burden of disease combining both prevalence measures and QOL assessment has been conducted to date, addressing such a large variety of diseases in general practice.
On-site selection and recruitment by an independent investigator limited the possibility of selection bias among patients, and the participation of physicians added high specificity to medical data collection.
A study design providing a high specificity in data collection led to a relatively low response rate from GPs. However, stratified recruitment phases and sample sizes from both GPs and patients highly representative of national standards ensured the strong external validity of the results.
Home consultations, which are common among GPs in France, were not surveyed which could have led to an underestimation of the burden of disease.
doi:10.1136/bmjopen-2011-000215
PMCID: PMC3221295  PMID: 22102638
12.  Benchmarking clinical management of spinal and non-spinal disorders using quality of life: results from the EPI3-LASER survey in primary care 
European Spine Journal  2011;20(12):2210-2216.
Concerns have been raised regarding sub-optimal utilization of analgesics and psychotropic drugs in the treatment of patients with chronic musculoskeletal disorders (MSDs) and their associated co-morbidities. The objective of this study was to describe drug prescriptions for the management of spinal and non-spinal MSDs contrasted against a standardized measure of quality of life. A representative population sample of 1,756 MSDs patients [38.5% with spinal disorder (SD) and 61.5% with non-spinal MSDs (NS-MSD)] was drawn from the EPI3-LASER survey of 825 general practitioners (GPs) in France. Physicians recorded their diagnoses and prescriptions on that day. Patients provided information on socio-demographics, lifestyle and quality of life using the Short Form 12 (SF-12) questionnaire. Chronicity of MSDs was defined as more than 12 weeks duration of the current episode. Chronic SD and NS-MSD patients were prescribed less analgesics and non-steroidal anti-inflammatory drugs than their non-chronic counterpart [odds ratios (OR) and 95% confidence intervals (CI), respectively: 0.4, 0.2–0.7 and 0.5, 0.3–0.6]. They also had more anxio-depressive co-morbidities reported by their physicians (SD: 16.1 vs.7.4%; NS-MSD: 21.6 vs. 9.5%) who prescribed more antidepressants and anxiolytics with a difference that was statistically significant only for spinal disorder patients (OR, 95% CI: 2.0, 1.1–3.6). Psychotropic drugs were more often prescribed in patients in the lower quartile of SF-12 mental score and prescriptions of analgesics in the lower quartile of SF-12 physical score (P < 0.001). In conclusion, anxiety and depressive disorders were commonly reported by GPs among chronic MSD patients. Their prescriptions of psychotropic and analgesic drugs were consistent with patients’ self-rated mental and physical health.
doi:10.1007/s00586-011-1780-z
PMCID: PMC3229736  PMID: 21487774
Spinal disorders; Musculoskeletal disorders; Epidemiology; Population health
13.  Who seeks primary care for musculoskeletal disorders (MSDs) with physicians prescribing homeopathic and other complementary medicine? Results from the EPI3-LASER survey in France 
Background
There is a paucity of information describing patients with musculoskeletal disorders (MSDs) using complementary and alternative medicines (CAMs) and almost none distinguishing homeopathy from other CAMs. The objective of this study was to describe and compare patients with MSDs who consulted primary care physicians, either certified homeopaths (Ho) or regular prescribers of CAMs in a mixed practice (Mx), to those consulting physicians who strictly practice conventional medicine (CM), with regard to the severity of their MSD expressed as chronicity, co-morbidity and quality of life (QOL).
Methods
The EPI3-LASER study was a nationwide observational survey of a representative sample of general practitioners and their patients in France. The sampling strategy ensured a sufficient number of GPs in each of the three groups to allow comparison of their patients. Patients completed a questionnaire on socio-demographics, lifestyle and QOL using the Short Form 12 (SF-12) questionnaire. Chronicity of MSDs was defined as more than twelve weeks duration of the current episode. Diagnoses and co-morbidities were recorded by the physician.
Results
A total of 825 GPs included 1,692 MSD patients (predominantly back pain and osteoarthritis) were included, 21.6% in the CM group, 32.4% Ho and 45.9% Mx. Patients in the Ho group had more often a chronic MSD (62.1%) than the CM (48.6%) or Mx (50.3%) groups, a result that was statistically significant after controlling for patients' characteristics (Odds ratio = 1.43; 95% confidence interval (CI): 1.07 - 1.89). Patients seen by homeopaths or mixed practice physicians who were not the regular treating physician, had more often a chronic MSD than those seen in conventional medicine (Odds ratios were1.75; 95% CI: 1.22 - 2.50 and 1.48; 95% CI: 1.06 - 2.12, respectively). Otherwise patients in the three groups did not differ for co-morbidities and QOL.
Conclusion
MSD patients consulting primary care physicians who prescribed homeopathy and CAMs differed from those seen in conventional medicine. Chronic MSD patients represented a greater proportion of the clientele in physicians offering alternatives to conventional medicine. In addition, these physicians treated chronic patients as consulting rather than regular treating physicians, with potentially important impacts upon professional health care practices and organisation.
doi:10.1186/1471-2474-12-21
PMCID: PMC3034723  PMID: 21247493
14.  Detection and Functional Characterization of a 215 Amino Acid N-Terminal Extension in the Xanthomonas Type III Effector XopD 
PLoS ONE  2010;5(12):e15773.
During evolution, pathogens have developed a variety of strategies to suppress plant-triggered immunity and promote successful infection. In Gram-negative phytopathogenic bacteria, the so-called type III protein secretion system works as a molecular syringe to inject type III effectors (T3Es) into plant cells. The XopD T3E from the strain 85-10 of Xanthomonas campestris pathovar vesicatoria (Xcv) delays the onset of symptom development and alters basal defence responses to promote pathogen growth in infected tomato leaves. XopD was previously described as a modular protein that contains (i) an N-terminal DNA-binding domain (DBD), (ii) two tandemly repeated EAR (ERF-associated amphiphillic repression) motifs involved in transcriptional repression, and (iii) a C-terminal cysteine protease domain, involved in release of SUMO (small ubiquitin-like modifier) from SUMO-modified proteins. Here, we show that the XopD protein that is produced and secreted by Xcv presents an additional N-terminal extension of 215 amino acids. Closer analysis of this newly identified N-terminal domain shows a low complexity region rich in lysine, alanine and glutamic acid residues (KAE-rich) with high propensity to form coiled-coil structures that confers to XopD the ability to form dimers when expressed in E. coli. The full length XopD protein identified in this study (XopD1-760) displays stronger repression of the XopD plant target promoter PR1, as compared to the XopD version annotated in the public databases (XopD216-760). Furthermore, the N-terminal extension of XopD, which is absent in XopD216-760, is essential for XopD type III-dependent secretion and, therefore, for complementation of an Xcv mutant strain deleted from XopD in its ability to delay symptom development in tomato susceptible cultivars. The identification of the complete sequence of XopD opens new perspectives for future studies on the XopD protein and its virulence-associated functions in planta.
doi:10.1371/journal.pone.0015773
PMCID: PMC3008746  PMID: 21203472
15.  Exocytosis and protein secretion in Trypanosoma 
BMC Microbiology  2010;10:20.
Background
Human African trypanosomiasis is a lethal disease caused by the extracellular parasite Trypanosoma brucei. The proteins secreted by T. brucei inhibit the maturation of dendritic cells and their ability to induce lymphocytic allogenic responses. To better understand the pathogenic process, we combined different approaches to characterize these secreted proteins.
Results
Overall, 444 proteins were identified using mass spectrometry, the largest parasite secretome described to date. Functional analysis of these proteins revealed a strong bias toward folding and degradation processes and to a lesser extent toward nucleotide metabolism. These features were shared by different strains of T. brucei, but distinguished the secretome from published T. brucei whole proteome or glycosome. In addition, several proteins had not been previously described in Trypanosoma and some constitute novel potential therapeutic targets or diagnostic markers. Interestingly, a high proportion of these secreted proteins are known to have alternative roles once secreted. Furthermore, bioinformatic analysis showed that a significant proportion of proteins in the secretome lack transit peptide and are probably not secreted through the classical sorting pathway. Membrane vesicles from secretion buffer and infested rat serum were purified on sucrose gradient and electron microscopy pictures have shown 50- to 100-nm vesicles budding from the coated plasma membrane. Mass spectrometry confirmed the presence of Trypanosoma proteins in these microvesicles, showing that an active exocytosis might occur beyond the flagellar pocket.
Conclusions
This study brings out several unexpected features of the secreted proteins and opens novel perspectives concerning the survival strategy of Trypanosoma as well as possible ways to control the disease. In addition, concordant lines of evidence support the original hypothesis of the involvement of microvesicle-like bodies in the survival strategy allowing Trypanosoma to exchange proteins at least between parasites and/or to manipulate the host immune system.
doi:10.1186/1471-2180-10-20
PMCID: PMC3224696  PMID: 20102621
16.  Excreted/Secreted Proteins from Trypanosome Procyclic Strains 
Trypanosoma secretome was shown to be involved in parasite virulence and is suspected of interfering in parasite life-cycle steps such as establishment in the Glossina midgut, metacyclogenesis. Therefore, we attempted to identify the proteins secreted by procyclic strains of T. brucei gambiense and T. brucei brucei, responsible for human and animal trypanosomiasis, respectively. Using mass spectrometry, 427 and 483 nonredundant proteins were characterized in T. brucei brucei and T. brucei gambiense secretomes, respectively; 35% and 42% of the corresponding secretome proteins were specifically secreted by T. brucei brucei and T. brucei gambiense, respectively, while 279 proteins were common to both subspecies. The proteins were assigned to 12 functional classes. Special attention was paid to the most abundant proteases (14 families) because of their potential implication in the infection process and nutrient supply. The presence of proteins usually secreted via an exosome pathway suggests that this type of process is involved in trypanosome ESP secretion. The overall results provide leads for further research to develop novel tools for blocking trypanosome transmission.
doi:10.1155/2010/212817
PMCID: PMC2789517  PMID: 20011064
17.  The interpretation of systematic reviews with meta-analyses: an objective or subjective process? 
Background
Discrepancies between the conclusions of different meta-analyses (quantitative syntheses of systematic reviews) are often ascribed to methodological differences. The objective of this study was to determine the discordance in interpretations when meta-analysts are presented with identical data.
Methods
We searched the literature for all randomized clinical trials (RCT) and review articles on the efficacy of intravenous magnesium in the early post-myocardial infarction period. We organized the articles chronologically and grouped them in packages. The first package included the first RCT, and a summary of the review articles published prior to first RCT. The second package contained the second and third RCT, a meta-analysis based on the data, and a summary of all review articles published prior to the third RCT. Similar packages were created for the 5th RCT, 10th RCT, 20th RCT and 23rd RCT (all articles). We presented the packages one at a time to eight different reviewers and asked them to answer three clinical questions after each package based solely on the information provided. The clinical questions included whether 1) they believed magnesium is now proven beneficial, 2) they believed magnesium will eventually be proven to be beneficial, and 3) they would recommend its use at this time.
Results
There was considerable disagreement among the reviewers for each package, and for each question. The discrepancies increased when the heterogeneity of the data increased. In addition, some reviewers became more sceptical of the effectiveness of magnesium over time, and some reviewers became less sceptical.
Conclusion
The interpretation of the results of systematic reviews with meta-analyses includes a subjective component that can lead to discordant conclusions that are independent of the methodology used to obtain or analyse the data.
doi:10.1186/1472-6947-8-19
PMCID: PMC2408567  PMID: 18495019
18.  Determinants of “return to work in good health” among workers with back pain who consult in primary care settings: a 2-year prospective study 
European Spine Journal  2006;16(5):641-655.
Many factors have been linked to return to work after a back pain episode, but our understanding of this phenomenon is limited and cross-sectional dichotomous indices of return to work are not valid measures of this construct. To describe the course of “return to work in good health” (RWGH—a composite index of back pain outcome) among workers who consulted in primary care settings for back pain and identify its determinants, a 2-year prospective study was conducted. Subjects (n = 1,007, 68.4%) were workers who consulted in primary care settings of the Quebec City area for a nonspecific back pain. They completed five telephone interviews over 2 years (follow-up = 86%). Analyses linking baseline variables with 2-year outcome were conducted with polytomous logistic regression. The proportion of “success” in RWGH increased from 18% at 6 weeks to 57% at 2 years. In women, persistent pain, pain radiating to extremities, increasing job seniority, not having a unionized job, feeling that the physician did listen carefully and increasing fear-avoidance beliefs towards work and activity were determinants of “failure” in RWGH. In men, decreasing age, cigarette smoking, poor self-reported health status, pain in the thoracic area, previous back surgeries, a non-compensated injury, high pain levels, belief that job is below qualifications, likelihood of losing job, job status, satisfaction with health services and fear-avoidance beliefs towards work were all significant. RWGH among workers with back pain receives multiple influences, especially among men. In both genders, however, fear-avoidance beliefs about work are associated with failure and high self-efficacy is associated with success.
doi:10.1007/s00586-006-0180-2
PMCID: PMC2213556  PMID: 16868783
Back pain; Cohort studies; Return to work; Risk factors
19.  An interdisciplinary clinical practice model for the management of low-back pain in primary care: the CLIP project 
Background
Low-back pain is responsible for significant disability and costs in industrialized countries. Only a minority of subjects suffering from low-back pain will develop persistent disability. However, this minority is responsible for the majority of costs and has the poorest health outcomes. The objective of the Clinic on Low-back pain in Interdisciplinary Practice (CLIP) project was to develop a primary care interdisciplinary practice model for the clinical management of low-back pain and the prevention of persistent disability.
Methods
Using previously published guidelines, systematic reviews and meta-analyses, a clinical management model for low-back pain was developed by the project team. A structured process facilitating discussions on this model among researchers, stakeholders and clinicians was created. The model was revised following these exchanges, without deviating from the evidence.
Results
A model consisting of nine elements on clinical management of low-back pain and prevention of persistent disability was developed. The model's two core elements for the prevention of persistent disability are the following: 1) the evaluation of the prognosis at the fourth week of disability, and of key modifiable barriers to return to usual activities if the prognosis is unfavourable; 2) the evaluation of the patient's perceived disability every four weeks, with the evaluation and management of barriers to return to usual activities if perceived disability has not sufficiently improved.
Conclusion
A primary care interdisciplinary model aimed at improving quality and continuity of care for patients with low-back pain was developed. The effectiveness, efficiency and applicability of the CLIP model in preventing persistent disability in patients suffering from low-back pain should be assessed.
doi:10.1186/1471-2474-9-54
PMCID: PMC2390556  PMID: 18426590
20.  A critical appraisal of guidelines for the management of knee osteoarthritis using Appraisal of Guidelines Research and Evaluation criteria 
Clinical practice guidelines have been elaborated to summarize evidence related to the management of knee osteoarthritis and to facilitate uptake of evidence-based knowledge by clinicians. The objectives of the present review were summarizing the recommendations of existing guidelines on knee osteoarthritis, and assessing the quality of the guidelines using a standardized and validated instrument – the Appraisal of Guidelines Research and Evaluation (AGREE) tool. Internet medical literature databases from 2001 to 2006 were searched for guidelines, with six guidelines being identified. Thirteen clinician researchers participated in the review. Each reviewer was trained in the AGREE instrument. The guidelines were distributed to four groups of three or four reviewers, each group reviewing one guideline with the exception of one group that reviewed two guidelines. One independent evaluator reviewed all guidelines. All guidelines effectively addressed only a minority of AGREE domains. Clarity/presentation was effectively addressed in three out of six guidelines, scope/purpose and rigour of development in two guidelines, editorial independence in one guideline, and stakeholder involvement and applicability in none. The clinical management recommendation tended to be similar among guidelines, although interventions addressed varied. Acetaminophen was recommended for initial pain treatment, combined with exercise and education. Nonsteroidal anti-inflammatory drugs were recommended if acetaminophen failed to control pain, but cautiously because of gastrointestinal risks. Surgery was recommended in the presence of persistent pain and disability. Education and activity management interventions were superficially addressed in most guidelines. Guideline creators should use the AGREE criteria when developing guidelines. Innovative and effective methods of knowledge translation to health professionals are needed.
doi:10.1186/ar2339
PMCID: PMC2246248  PMID: 18062805
21.  An interdisciplinary guideline development process: the Clinic on Low-back pain in Interdisciplinary Practice (CLIP) low-back pain guidelines 
Background
Evaluation of low-back pain guidelines using Appraisal of Guidelines Research and Evaluation (AGREE) criteria has shown weaknesses, particularly in stakeholder involvement and applicability of recommendations. The objectives of this project were to: 1) develop a primary care interdisciplinary clinical practice guideline aimed at preventing prolonged disability from low-back pain, using a community of practice approach, and 2) assess the participants' impressions with the process, and evaluate the relationship between participant characteristics and their participation.
Methods
Ten stakeholder representatives recruited 136 clinicians to participate in this community of practice. Clinicians were drawn from the following professions: physiotherapists (46%), occupational therapists (37%), and family physicians (17%). Using previously published guidelines, systematic reviews, and meta-analyses, a first draft of the guidelines was presented to the community of practice. Four communication tools were provided for discussion and exchanges with experts: a web-based discussion forum, an anonymous comment form, meetings, and a symposium. Participants were prompted for comments on interpretation, clarity, and applicability of the recommendations. Clinical management recommendations were revised following these exchanges. At the end of the project, a questionnaire was sent to the participants to assess satisfaction towards the guidelines and the development process.
Results
Twelve clinical management recommendations on management of low-back pain and persistent disability were initially developed. These were discussed through 188 comments posted on the discussion forum and 103 commentary forms submitted. All recommendations were modified following input of the participants. A clinical algorithm summarizing the guidelines was also developed. A response rate of 75% was obtained for the satisfaction questionnaire. The majority of respondents appreciated the development process and agreed with the guideline content. Most participants thought recommendations improved between versions, and that participant comments contributed to this improvement. All stakeholders officially endorsed the guidelines.
Conclusion
The community of practice approach was a successful method to develop guidelines on low-back pain, with participants providing information to improve guideline recommendations. The information technology infrastructure that was developed remains for continuous interdisciplinary exchanges and updating of the guidelines.
doi:10.1186/1748-5908-2-36
PMCID: PMC2206051  PMID: 18036241
22.  Comorbidity and age are both independent predictors of length of hospitalization in trauma patients 
Canadian Journal of Surgery  2005;48(5):361-366.
Background
Length of hospitalization is a good indicator of resource utilization. Older patients are increasingly suffering trauma, and comorbid medical conditions are also increasing. Our objective was to determine the separate and combined effect of these 2 factors on length of hospital stay for trauma patients in a tertiary trauma centre.
Methods
All 994 consecutive trauma patients surviving to hospital discharge between Apr. 1, 2000, and Mar. 31, 2001, were identified. Patient characteristics, injury severity and length of hospitalization were obtained from the hospital trauma registry. Each medical record was then reviewed for completeness of information and assessment of comorbid conditions. A multivariate linear regression model was developed to predict logarithmic length of stay from age and presence of a cormorbid condition while adjusting for the Injury Severity Score (ISS).
Results
The mean age of the patients was 49.7 (range from 14–100) years and median ISS was 9 (range from 1–50). At least 1 comorbid condition was present in 321 (32%) patients. Mean length of hospital stay was 15.3 days. The proportion of patients with a comorbid condition increased steadily with age, from 8.7% before the age of 55 years to 92% at 85 or more years of age (p < 0.001). According to the multivariate model, the presence of comorbidity, age and ISS were all independent predictors of hospital stay (p < 0.001). When applied to patients with the mean ISS value of 9, the model showed an increase in length of hospitalization for patients with a comorbid condition over those without; (3.6 v. 13.1 d for patients <55 and ≥85 yr respectively). Length of hospital stay increased particularly with neurologic and pulmonary problems.
Conclusions
Comorbidity and age were both independently significant predictors of length of hospitalization over and beyond that which is expected based on the severity of the injuries. With an aging population, this phenomenon should severely affect resource utilization in trauma centres in the near future. Researchers should take account of both age and comorbidity in order to compare trauma populations.
PMCID: PMC3211888  PMID: 16248133
23.  A clinical return-to-work rule for patients with back pain 
Background
Tools for early identification of workers with back pain who are at high risk of adverse occupational outcome would help concentrate clinical attention on the patients who need it most, while helping reduce unnecessary interventions (and costs) among the others. This study was conducted to develop and validate clinical rules to predict the 2-year work disability status of people consulting for nonspecific back pain in primary care settings.
Methods
This was a 2-year prospective cohort study conducted in 7 primary care settings in the Quebec City area. The study enrolled 1007 workers (participation, 68.4% of potential participants expected to be eligible) aged 18–64 years who consulted for nonspecific back pain associated with at least 1 day's absence from work. The majority (86%) completed 5 telephone interviews documenting a large array of variables. Clinical information was abstracted from the medical files. The outcome measure was “return to work in good health” at 2 years, a variable that combined patients' occupational status, functional limitations and recurrences of work absence. Predictive models of 2-year outcome were developed with a recursive partitioning approach on a 40% random sample of our study subjects, then validated on the rest.
Results
The best predictive model included 7 baseline variables (patient's recovery expectations, radiating pain, previous back surgery, pain intensity, frequent change of position because of back pain, irritability and bad temper, and difficulty sleeping) and was particularly efficient at identifying patients with no adverse occupational outcome (negative predictive value 78%– 94%).
Interpretation
A clinical prediction rule accurately identified a large proportion of workers with back pain consulting in a primary care setting who were at a low risk of an adverse occupational outcome.
doi:10.1503/cmaj.1041159
PMCID: PMC558170  PMID: 15939915

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