The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked

Minimum detectable and minimal clinically important changes for pain in patients with nonspecific neck pain

<p>Abstract</p> <p>Background</p> <p>The minimal detectable change (MDC) and the minimal clinically important changes (MCIC) have been explored for nonspecific low back pain patients and are similar across different cultural settings. No data on MDC and MCIC for pain severity are available for neck pain patients. The objectives of this study were to estimate MDC and MCIC for pain severity in subacute and chronic neck pain (NP) patients, to assess if MDC and MCIC values are influenced by baseline values and to explore if they are different in the subset of patients reporting referred pain, and in subacute versus chronic patients.</p> <p>Methods</p> <p>Subacute and chronic patients treated in routine clinical practice of the Spanish National Health Service for neck pain, with or without pain referred to the arm, and a pain severity ≥ 3 points on a pain intensity number rating scale (PI-NRS), were included in this study. Patients' own "global perceived effect" over a 3 month period was used as the external criterion. The minimal detectable change (MDC) was estimated by means of the standard error of measurement in patients who self-assess as unchanged. MCIC were estimated by the mean value of change score in patients who self-assess as improved (mean change score, MCS), and by the optimal cutoff point in receiver operating characteristics curves (ROC). The effect on MDC and MCIC of initial scores, duration of pain, and existence of referred pain were assessed.</p> <p>Results</p> <p>658 patients were included, 487 of them with referred pain. MDC was 4.0 PI-NRS points for neck pain in the entire sample, 4.2 for neck pain in patients who also had referred pain, and 6.2 for referred pain. MCS was 4.1 and ROC was 1.5 for referred and for neck pain, both in the entire sample and in patients who also complained of referred pain. ROC was lower (0.5 PI-NRS points) for subacute than for chronic patients (1.5 points). MCS was higher for patients with more intense baseline pain, ranging from 2.4 to 4.9 PI-NRS for neck pain and from 2.4 to 5.3 for referred pain.</p> <p>Conclusion</p> <p>In general, improvements ≤ 1.5 PI-NRS points could be seen as irrelevant. Above that value, the cutoff point for clinical relevance depends on the methods used to estimate MCIC and on the patient's baseline severity of pain. MDC and MCIC values in neck pain patients are similar to those for low back pain and other painful conditions.</p

Avoidable costs of physical treatments for chronic back, neck and shoulder pain within the Spanish National Health Service: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Back, neck and shoulder pain are the most common causes of occupational disability. They reduce health-related quality of life and have a significant economic impact. Many different forms of physical treatment are routinely used. The objective of this study was to estimate the cost of physical treatments which, despite the absence of evidence supporting their effectiveness, were used between 2004 and 2007 for chronic and non-specific neck pain (NP), back pain (BP) and shoulder pain (SP), within the Spanish National Health Service in the Canary Islands (SNHSCI).</p> <p>Methods</p> <p>Chronic patients referred from the SNHSCI to private physical therapy centres for NP, BP or SP, between 2004 and 2007, were identified. The cost of providing physical therapies to these patients was estimated. Systematic reviews (SRs) and clinical practice guidelines (CPGs) for NP, BP and SP available in the same period were searched for and rated according to the Oxman and AGREE criteria, respectively. Those rated positively for ≥70% of the criteria, were used to categorise physical therapies as Effective; Ineffective; Inconclusive; and Insufficiently Assessed. The main outcome was the cost of physical therapies included in each of these categories.</p> <p>Results</p> <p>8,308 chronic cases of NP, 4,693 of BP and 5,035 of SP, were included in this study. Among prescribed treatments, 39.88% were considered Effective (physical exercise and manual therapy with mobilization); 23.06% Ineffective; 13.38% Inconclusive, and 23.66% Insufficiently Assessed. The total cost of treatments was € 5,107,720. Effective therapies accounted for € 2,069,932.</p> <p>Conclusions</p> <p>Sixty percent of the resources allocated by the SNHSCI to fund physical treatment for NP, BP and SP in private practices are spent on forms of treatment proven to be ineffective, or for which there is no evidence of effectiveness.</p

Psychometric characteristics of the Spanish version of instruments to measure neck pain disability

Background: The NDI, COM and NPQ are evaluation instruments for disability due to NP. There was no Spanish version of NDI or COM for which psychometric characteristics were known. The objectives of this study were to translate and culturally adapt the Spanish version of the Neck Disability Index Questionnaire (NDI), and the Core Outcome Measure (COM), to validate its use in Spanish speaking patients with non-specific neck pain (NP), and to compare their psychometric characteristics with those of the Spanish version of the Northwick Pain Questionnaire (NPQ). Methods: Translation/re-translation of the English versions of the NDI and the COM was done blindly and independently by a multidisciplinary team. The study was done in 9 primary care Centers and 12 specialty services from 9 regions in Spain, with 221 acute, subacute and chronic patients who visited their physician for NP: 54 in the pilot phase and 167 in the validation phase. Neck pain (VAS), referred pain (VAS), disability (NDI, COM and NPQ), catastrophizing (CSQ) and quality of life (SF-12) were measured on their first visit and 14 days later. Patients' self-assessment was used as the external criterion for pain and disability. In the pilot phase, patients' understanding of each item in the NDI and COM was assessed, and on day 1 test-retest reliability was estimated by giving a second NDI and COM in which the name of the questionnaires and the order of the items had been changed. Results: Comprehensibility of NDI and COM were good. Minutes needed to fill out the questionnaires [median, (P25, P75)]: NDI. 4 (2.2, 10.0), COM: 2.1 (1.0, 4.9). Reliability: [ICC, (95%CI)]: NDI: 0.88 (0.80, 0.93). COM: 0.85 (0.75,0.91). Sensitivity to change: Effect size for patients having worsened, not changed and improved between days 1 and 15, according to the external criterion for disability: NDI: -0.24, 0.15, 0.66; NPQ: -0.14, 0.06, 0.67; COM: 0.05, 0.19, 0.92. Validity: Results of NDI, NPQ and COM were consistent with the external criterion for disability, whereas only those from NDI were consistent with the one for pain. Correlations with VAS, CSQ and SF-12 were similar for NDI and NPQ (absolute values between 0.36 and 0.50 on day 1, between 0.38 and 0.70 on day 15), and slightly lower for COM (between 0.36 and 0.48 on day 1, and between 0.33 and 0.61 on day 15). Correlation between NDI and NPQ: r = 0.84 on day 1, r = 0.91 on day 15. Correlation between COM and NPQ: r = 0.63 on day 1, r = 0.71 on day 15. Conclusion: Although most psychometric characteristics of NDI, NPQ and COM are similar, those from the latter one are worse and its use may lead to patients' evolution seeming more positive than it actually is. NDI seems to be the best instrument for measuring NP-related disability, since its results are the most consistent with patient's assessment of their own clinical status and evolution. It takes two more minutes to answer the NDI than to answer the COM, but it can be reliably filled out by the patient without assistance

Utilisation des activitées enzymatiques anti-oxydantes comme biomarqueurs de contaminations métalliques faibles en cours d'eau

International audienceThe goal of this study was to assess the use of antioxidant enzyme activities (AEA) in periphyton communities as biomarkers of low metal pollution under multiple stress field conditions. With this purpose, the effects of metal exposure were investigated in situ in a low order stream, located in a former mining area. Translocation experiments were performed along a gradient of metal pollution including a control and five polluted sites. Physical and chemical parameters, metal bioaccumulation, AEA and diatom species composition in periphyton were followed over the five weeks of translocation. Dissolved Zn concentration wa

Une approche multi-biomarqueurs pour évaluer les effets des toxiques sur les écosystèmes fluviaux

International audienceHuman activity is responsible for the entrance of toxic substances to aquatic ecosystems. These substances entail a risk for the components of the ecosystem (toxicological stress). Now, in addition, as a result of the global change, aquatic ecosystems are under strong environmental stress due to changes in water flow, light regime, temperature or nutrient concentration. Fluvial biofilms are attached communities consisting of bacteria, algae and fungi embedded within a polysaccharide matrix. In rivers, these communities are the first to interact with dissolved substances such as nutrients, organic matter, and toxicants. Fluvial biofilms, provide a community ecotoxicology perspective suitable for the assessment of acute and chronic effects of ecosystems' perturbations. Since species in a community differ in their range of tolerance to environmental and chemical stressors, it is expected that multi-stress situations of different magnitude and duration will cause structural and functional changes detectable at the community level. In this presentation, the assessment of ecosystem damage is addressed from a multi-biomarker perspective including functional and structural biomarkers measured in the fluvial biofilm. The main objective of this presentation is to update and illustrate the pros and contras of this multi-biomarker approach. Structural changes and functional responses of biofilm communities exposed to different organic (diuron, triclosan and b-bockers) and inorganic (Cu, Zn and Cd) toxic substances in experimental studies will be summarized and contrasted with the effects recorded in the field, under fairly uncontrolled multi-stress conditions. The advantages and limitations in the use of fluvial biofilms as multi-biomarkers of stress will be discussed

Discharge and the response of biofilms to metal exposure in Mediterranean rivers

The expected response of fluvial biofilms to the environment and metal pollution prevailing under different discharge conditions was investigated. The relationship between inter-annual hydrological variability and metal concentration in water and sediments was explored in Mediterranean rivers (Catalonia, NE Spain) affected by low but chronic metal pollution, using monitoring data provided by the Catalan Water Agency (ACA). During the period investigated (2000-2006), metal pollution was characterized by low water concentrations and high concentrations in sediments. The most consistent pattern was observed for sediment cadmium (Cd) concentrations, showing a positive relationship with annual discharge, reaching values of environmental concern (above ecotoxicological benchmarks). A different pattern was observed for Cu, Zn, and As increasing with flow in some sites and decreasing in others. While Cd seems to proceed from diffuse sources being washed by surface runoff, Zn, Pb, and As may proceed from either diffuse or point-sources in the different river sites investigated. The relevance of diffuse metal pollution in the area of study indicates that polluted landfills runoff might be an important source of metals causing repetitive pulses of high metal concentration in the receiving water courses. The experimental results presented demonstrate that metal effects in fluvial biofilms may be accumulative, increasing the toxicity after repetitive pulse exposures. Since draughts and extreme rain events are expected to increase at higher latitudes due to global change, the sources of metal pollution, its final concentration and potential effects on the fluvial ecosystem may also change following the patterns expected for human-impacted Mediterranean rivers. © 2010 Springer Science+Business Media B.V.Family Process Institute Sixth Framework Programme: MODELKEY 511237-2 GOCE, KEYBIOEFFECTS MRTN-CT-2006-035695 Ministry of Education and Science: FLUVIALFITOMARC CGL2006-12785, FLUVIALMULTISTRESS CTM2009-14111-CO2-01-745Acknowledgments The ‘‘Serveis Científics i Tècnics’’ at the University of Girona provided its facilities and technical help for ICP-MS metal analysis. The research was funded by the Spanish Ministry Science and Education (FLUVIALFITOMARC CGL2006-12785 and FLUVIALMULTISTRESS CTM2009-14111-CO2-01-745), and the EC Sixth Framework Program (MODELKEY 511237-2 GOCE and KEYBIOEFFECTS MRTN-CT-2006-035695). Alexandra Serra and Berta Bonet benefit from a FPI grant of the Spanish Ministry Science and Education. Güluzar Atli benefit from an Erasmus grant between the University of C¸ ukurova (Turkey) and the University of Girona (Spain)

Impact de stress multiples sur les communautés de diatomées : le cumul de stress de différentes natures augmente la vulnérabilité des communautés

International audienceChronic, non-lethal stressors occurring gradually (in space or time) can result in cumulative impacts that are more dramatic than higher intensities or occasional critical levels of any single one of these stressors. The negative effects of the chronic stressors trigger lasting impacts that may grow in intensity and become problematic over time and/or to higher trophic levels. In rivers, aquatic organisms experience this type of cumulative stress along the up- to downstream gradient in natural and anthropogenic contaminants generally observed in inhabited watersheds. Diatoms are a major component of the periphyton in rivers; their richness and diversity in natural communities are directly related to their varied ecological preferences and sensitivity to disturbance. In this study, we monitored from 2003 to 2008 the changes in the diversity of taxonomic and non-taxonomic features along a small river (Riou-Mort, South West France), at three sites: one site upstream considered as a reference for this watershed, one intermediate site with high nutrient load, and one downstream site exposed to both nutrient and metal pollution. The cumulative impacts of nutrients plus metals led to a gradual decrease in species richness and diversity, and in a potential capacity to cope with additional stresses, e.g. climate change-related ones. This is reflected by a decrease in species richness downstream, more dramatic in the hot summer of 2003 than in cooler summers. With the increasingly protective environmental regulations (e.g. Water Framework Directive in Europe), accumulation of stresses on aquatic resources are recommended to receive increasing attention, in particular considering the expected changes in climate

Impact de stress multiples sur les communautés de diatomées : Cumul de stress de différentes natures et évolution de la vulnérabilité des communautés

International audienceChronic, non-lethal stressors occurring gradually (in space or time) can result in cumulative impacts, more dramatic than higher intensity or occasional critical level of one of these contaminants singly. The negative effects of these stressors trigger enduring impacts that may grow in intensity and become problematic over time and/or to higher trophic levels. In a river, for instance, aquatic organisms experience this type of cumulative stress along the up- to downstream gradient in natural and anthropogenic contaminants generally observed in inhabited watersheds. Diatoms are a major component of the periphyton in rivers; their richness and diversity in natural communities are directly related to their varied ecological preferences. In this study, we monitored from 2003 to 2008 the changes in structural features and traits along a small river (Riou-Mort, South West France), at three sites: one site upstream considered as a reference, one intermediate site with high nutrient load, and one downstream site exposed to both nutrient and metal pollution. The cumulative impacts of nutrients plus metals led to a gradual decrease in species richness and diversity, and potential capacity to cope with additional stresses, e.g. climate change-related ones. This is reflected by, for example, the decrease in species richness downstream, more dramatic in Summer 2003 (heat wave) than in cooler summers. With the increasingly protective environmental regulations (e.g. Water Framework Directive in Europe), cumulated stresses on aquatic resources are recommended to receive increasing attention, in particular considering the expected changes in global climate