A multidisciplinary cognitive behavioural programme for coping with chronic neuropathic pain following spinal cord injury: the protocol of the CONECSI trial

<p>Abstract</p> <p>Background</p> <p>Most people with a spinal cord injury rate neuropathic pain as one of the most difficult problems to manage and there are no medical treatments that provide satisfactory pain relief in most people. Furthermore, psychosocial factors have been considered in the maintenance and aggravation of neuropathic spinal cord injury pain. Psychological interventions to support people with spinal cord injury to deal with neuropathic pain, however, are sparse. The primary aim of the CONECSI (COping with NEuropathiC Spinal cord Injury pain) trial is to evaluate the effects of a multidisciplinary cognitive behavioural treatment programme on pain intensity and pain-related disability, and secondary on mood, participation in activities, and life satisfaction.</p> <p>Methods/Design</p> <p>CONECSI is a multicentre randomised controlled trial. A sample of 60 persons with chronic neuropathic spinal cord injury pain will be recruited from four rehabilitation centres and randomised to an intervention group or a waiting list control group. The control group will be invited for the programme six months after the intervention group. Main inclusion criteria are: having chronic (> 6 months) neuropathic spinal cord injury pain as the worst pain complaint and rating the pain intensity in the last week as 40 or more on a 0-100 scale. The intervention consists of educational, cognitive, and behavioural elements and encompasses 11 sessions over a 3-month period. Each meeting will be supervised by a local psychologist and physical therapist. Measurements will be perfomed before starting the programme/entering the control group, and at 3, 6, 9, and 12 months. Primary outcomes are pain intensity and pain-related disability (Chronic Pain Grade questionnaire). Secondary outcomes are mood (Hospital Anxiety and Depression Scale), participation in activities (Utrecht Activities List), and life satisfaction (Life Satisfaction Questionnaire). Pain coping and pain cognitions will be assessed with three questionnaires (Coping Strategy Questionnaire, Pain Coping Inventory, and Pain Cognition List).</p> <p>Discussion</p> <p>The CONECSI trial will reveal the effects of a multidisciplinary cognitive behavioural programme for people with chronic neuropathic spinal cord injury pain. This intervention is expected to contribute to the rehabilitation treatment possibilities for this population.</p> <p>Trial Registration</p> <p>Dutch Trial Register NTR1580.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Regime shift in sandy beach microbial communities following Deepwater Horizon oil spill remediation efforts.

Sandy beaches support a wide variety of underappreciated biodiversity that is critical to coastal ecosystems. Prior to the 2010 Deepwater Horizon oil spill, the diversity and function of supratidal beach sediment microbial communities along Gulf of Mexico coastlines were not well understood. As such, it was unclear if microbial community compositional changes would occur following exposure to beached oil, if indigenous communities could biodegrade oil, or how cleanup efforts, such as sand washing and sediment redistribution, would impact microbial ecosystem resiliency. Transects perpendicular to the shoreline were sampled from public beaches on Grand Isle, Louisiana, and Dauphin Island, Alabama, over one year. Prior to oil coming onshore, elevated levels of bacteria associated with fecal contamination were detected (e.g., Enterobacteriales and Campylobacterales). Over time, significant shifts within major phyla were identified (e.g., Proteobacteria, Firmicutes, Actinobacteria) and fecal indicator groups were replaced by taxa affiliated with open-ocean and marine systems (e.g., Oceanospirillales, Rhodospirillales, and Rhodobacterales). These new bacterial groups included putative hydrocarbon degraders, similar to those identified near the oil plume offshore. Shifts in the microbial community composition strongly correlated to more poorly sorted sediment and grain size distributional changes. Natural oceanographic processes could not account for the disrupted sediment, especially from the backshore well above the maximum high-tide levels recorded at these sites. Sand washing and tilling occurred on both open beaches from August through at least December 2010, which were mechanisms that could replace fecal indicator groups with open-ocean groups. Consequently, remediation efforts meant to return beaches to pre-spill compositions caused a regime shift that may have added potential ecosystem function, like hydrocarbon degradation, to the sediment. Future research will need to assess the persistence and impact of the newly formed microbial communities to the overall sandy beach ecosystems

Microbial contributions to cave formation: New insights into sulfuric acid speleogenesis

The sulfuric acid speleogenesis (SAS) model was introduced in the early 1970s from observations of Lower Kane Cave, Wyoming, and was proposed as a cave-enlargement process due to primarily H2S autoxidation to sulfuric acid and subaerial replacement of carbonate by gypsum. Here we present a reexamination of the SAS type locality in which we make use of uniquely applied geochemical and microbiological methods. Little H2S escapes to the cave atmosphere, or is lost by abiotic autoxidation, and instead the primary H2S loss mechanism is by subaqueous sulfur-oxidizing bacterial communities that consume H2S. Filamentous “Epsilonproteobacteria” and Gammaproteobacteria, characterized by fluorescence in situ hybridization, colonize carbonate surfaces and generate sulfuric acid as a metabolic byproduct. The bacteria focus carbonate dissolution by locally depressing pH, compared to bulk cave waters near equilibrium or slightly supersaturated with calcite. These findings show that SAS occurs in subaqueous environments and potentially at much greater phreatic depths in carbonate aquifers, thereby offering new insights into the microbial roles in subsurface karstification

Bray-Curtis similarity distances among groups of samples for sampling times and beach locations.

<p>For Grand Isle, comparisons are (A) between different sampling times and (B) between different locations along the beach profile, and for Dauphin Island comparisons are (C) between different sampling times and (D) between different locations along the beach profile. N.S. = comparisons were not significant. *weakly significant, between <i>p</i>-values 0.051 to 0.1; **significant, between 0.0001 to 0.05; ***highly significant, <0.0001.</p

Order-level taxonomic results for Grand Isle and Dauphin Island.

<p>Summaries are organized as (A) Gammaproteobacteria, (B) Alphaproteobacteria, and (C) Firmicutes<b>,</b> by beach, sample location, and sampling time. Numbers included to right of each bar represent the percentages that the class or phylum represented in the complete dataset for that sample, at that specific sampling time and location.</p

Non-metric multidimensional scaling (NMDS) plots based on microbial community compositions for all beach sand.

<p>(A) Grand Isle and (B) Dauphin Island community compositions from 16S rRNA gene pyrosequences that correspond to environmental variables and the extent of physical remediation at the beaches, shown as vectors. For (A), stress = 0.11, axis 1 R² = 0.61 and axis 2 = 0.35. For (B), stress = 0.16, axis 1 R² = 064 and axis 2 = 0.23. Colored arrows indicate the temporal shifts in community ordination for the dune, open beach areas, and swash zone.</p