A realistic assessment of methods for extracting gene/protein interactions from free text

Background: The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger. Results: Our results show: that performance across different evaluation corpora is extremely variable; that the use of tagged (as opposed to gold standard) gene and protein names has a significant impact on performance, with a drop in F-score of over 20 percentage points being commonplace; and that a simple keyword-based benchmark algorithm when coupled with a named entity tagger outperforms two of the tools most widely used to extract gene/protein interactions. Conclusion: In terms of availability, ease of use and performance, the potential non-specialist user community interested in automatically extracting gene and/or protein interactions from free text is poorly served by current tools and systems. The public release of extraction tools that are easy to install and use, and that achieve state-of-art levels of performance should be treated as a high priority by the biomedical text mining community

The value and effectiveness of geriatric assessments for older adults with cancer: an umbrella review.

PURPOSE: This umbrella review aimed to summarise and synthesize the evidence on the outcomes reported and used to assess the value and or efficacy of geriatric assessments (GAs) for older adults with cancer. METHODS: Six electronic databases, PsycINFO, MEDLINE, Embase, CINAHL, Cochrane Library and Web of Science databases, were searched to identify systematic reviews with or without meta-analyses that described the value or outcomes of GAs for older adults with cancer. RESULTS: Twenty-six systematic reviews were included, of which six included a meta-analysis of the data. Thirteen associations and or outcomes were identified. Overall geriatric impairments predicted or were associated with majority of identified outcomes. However, the type of domains associated with outcomes differed within and across reviews. Only treatment toxicity was statistically significantly lower for patients allocated to the GA intervention group compared to standard care. Systematic reviews without meta-analyses demonstrated a positive impact of GA with management on treatment completion, communication and care planning and patient satisfaction with care. CONCLUSION: There is evidence demonstrating the predictive value of GAs for older adults with cancer. GAs seems to be beneficial for older adults with cancer across some outcomes, with strong evidence demonstrating the impact of GA with management for treatment toxicity. However, there is mixed or limited evidence demonstrating the effect of GA in other treatment modalities, and on quality of life and economic outcomes

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

Circumstellar disks and planets. Science cases for next-generation optical/infrared long-baseline interferometers

We present a review of the interplay between the evolution of circumstellar disks and the formation of planets, both from the perspective of theoretical models and dedicated observations. Based on this, we identify and discuss fundamental questions concerning the formation and evolution of circumstellar disks and planets which can be addressed in the near future with optical and infrared long-baseline interferometers. Furthermore, the importance of complementary observations with long-baseline (sub)millimeter interferometers and high-sensitivity infrared observatories is outlined.Comment: 83 pages; Accepted for publication in "Astronomy and Astrophysics Review"; The final publication is available at http://www.springerlink.co

The importance of baseline viral load when assessing relative efficacy in treatment-naïve HBeAg-positive chronic hepatitis B: a systematic review and network meta-analysis.

BACKGROUND: To date no network meta-analysis (NMA) has accounted for baseline variations in viral load when assessing the relative efficacy of interventions for chronic hepatitis B (CHB). We undertook baseline-adjusted and unadjusted analyses using the same data to explore the impact of baseline viral load (BVL) on CHB treatment response. METHODS: We searched Embase, Medline, Medline in Process and the Cochrane CENTRAL databases for randomised clinical trials (RCTs) of monotherapy interventions at licensed doses for use in CHB. Search strategies comprised CHB disease and drug terms (a combination of controlled vocabulary and free text terms) and also a bespoke RCT filter.The NMA was undertaken in WinBUGs using fixed and random effects methods, using data obtained from a systematic review. Individual patient data (IPD) from an entecavir clinical trial were used to quantify the impact of different baseline characteristics (in particular undetectable viral load (UVL) at 1 year) on relative treatment effect. Study level mean baseline values from all identified studies were used. Results were generated for UVL and presented as relative risks (RRs) and 95% credible intervals (CrIs) using entecavir as reference treatment. RESULTS: Overall, for all eight relevant interventions we identified 3,000 abstracts. Following full text review a total of 35 (including the contents of six clinical study reports) met the inclusion critera; 19 were in hepatitis B e antigen (HBeAg)-positive patients and 14 of the 19 contained outcome information of relevance to the NMA.Entecavir and tenofovir studies had heterogeneous patient populations in terms of BVL (mean values 9.29 and 8.65 log10 copies/ml respectively). After adjusting UVL for BVL using an informative prior based on the IPD analysis, the difference between entecavir and tenofovir was not statistically significant (RR 1.27, 95% CrI 0.96 to 1.47-fixed effects). A similar conclusion was found in all sensitivity analyses. Adjusted tenofovir results were more consistent with observed clinical trial response rates. CONCLUSIONS: This study demonstrates the importance of adjusting for BVL when assessing the relative efficacy of CHB interventions in achieving UVL. This has implications for both clinical and economic decision making

Monoclonal antibodies directed to fucoidan preparations from brown algae

Cell walls of the brown algae contain a diverse range of polysaccharides with useful bioactivities. The precise structures of the sulfated fucan/fucoidan group of polysaccharides and their roles in generating cell wall architectures and cell properties are not known in detail. Four rat monoclonal antibodies, BAM1 to BAM4, directed to sulfated fucan preparations, have been generated and used to dissect the heterogeneity of brown algal cell wall polysaccharides. BAM1 and BAM4, respectively, bind to a non-sulfated epitope and a sulfated epitope present in the sulfated fucan preparations. BAM2 and BAM3 identified additional distinct epitopes present in the fucoidan preparations. All four epitopes, not yet fully characterised, occur widely within the major brown algal taxonomic groups and show divergent distribution patterns in tissues. The analysis of cell wall extractions and fluorescence imaging reveal differences in the occurrence of the BAM1 to BAM4 epitopes in various tissues of Fucus vesiculosus. In Ectocarpus subulatus, a species closely related to the brown algal model Ectocarpus siliculosus, the BAM4 sulfated epitope was modulated in relation to salinity levels. This new set of monoclonal antibodies will be useful for the dissection of the highly complex and yet poorly resolved sulfated polysaccharides in the brown algae in relation to their ecological and economic significance

Decision making in early-stage colorectal cancer treatments:a literature review

Background:The introduction of the National Bowel Cancer Screening Programme has led to an increase in colorectal cancer diagnosed at an early stage. Advances in the options for treatmentof early-stage disease may have similar survival benefits but different risks and side effects. The decision on treatment for early stage bowel cancers can therefore be described as preference sensitive.Method:A literature review was conducted of 12 studies and reviews published 2007–2017, focusing on patient involvement in decisions on treatment following a diagnosis of colorectal cancer. The review covered both patient and clinician perspectives.Results:The review highlighted key themes that influence how far patients are involved in decisions regarding treatment. These themes include: patient understanding of the preference-sensitive nature of the decision, time pressures and perceived inapplicability of involving patients.Conclusion:Further studies are necessary to understand the experiences of patients and clinicians making treatment decisions in the context of early colorectal cancer, including polyp cancers. There is a lack of studies specifically addressing clinician experiences in this area.<br/

A mixed methods pilot and feasibility open trial of internet-delivered cognitive behaviour therapy (iCanADAPT Advanced) for people with advanced cancer with depression and/or anxiety

Purpose: Evaluate the feasibility, acceptability and potential efficacy of a form of online therapy for clinical depression and/or anxiety in people living with advanced cancer. Methods: A single-arm open trial of a six-lesson clinician-supervised, internet-delivered cognitive behavioural therapy (iCBT) transdiagnostic intervention (iCanADAPT Advanced) was undertaken. Qualitative (semi-structured telephone interview conducted at 3-months) and quantitative data (questionnaires collected at pre-, post-, and 3-month follow-up) were analysed. Results: 27 participants partook (26 women, 56% breast cancer, mean age 56yo; average number of mental health diagnoses 1.8, with majority (81%) meeting criteria for generalised anxiety disorder). Feasibility - Unanticipated numbers (48%) of participants had physical health deterioration (cancer progression or death). iCBT had high adherence overall (completion rates: 37% did 6 lessons; 70% did 4 lessons) but adherence was higher for those whose cancer remained stable (completion rates: 43% did 6 lessons; 85% did 4 lessons). Acceptability - the intervention was acceptable to the majority of participants, with high treatment satisfaction. Advisory data was achieved regarding future versions. Potential efficacy - regardless of physical health status, participants who completed the iCBT showed a significant decrease over time in anxiety and depression symptoms. Conclusions: Online therapies may be useful in assisting those living with advanced cancer dealing with clinical depression and anxiety disorders. The specific modality of clinician supervised iCBT has significant potential to be a suitable modality of online therapy

Piloting a shared decision-making clinician training intervention in maternity care in Australia: A mixed methods study

Problem: Implementation of woman-centred care in evidence-based maternity practice requires clinicians to be skilled in shared decision-making, yet there is limited training or research into such interventions. Background: Shared decision-making enables women to make informed decisions in partnership with clinicians where there are varied clinical options in relation to indications for and timing of planned birth. Aim: We aimed to develop a shared decision-making training intervention and evaluate its feasibility and acceptability to midwives and obstetricians. Methods: The intervention was co-designed by midwifery and medical clinician-researchers, and a consumer representative. Online training and demonstration videos were distributed to midwives and obstetricians in three Sydney hospitals, followed by two online workshops in 2021 and 2022 where participants practised shared decision-making in roleplaying scenarios tailored to timing of birth. Training was evaluated using post-workshop and post-training surveys and semi-structured qualitative interviews. Findings: The training workshop format, duration and content were well received. Barriers to the uptake of shared decision-making were time, paternalistic practices and fear of repercussions of centring women in the decision-making process. Discussion: The intervention enabled midwifery and medical colleagues to learn communication repertoires from each other in woman-centred discussions around timing of birth. Roleplay scenarios enabled participants to observe and provide feedback on their colleagues’ shared decision-making practices, while providing a space for collective reflection on ways to promote, and mitigate barriers to, its implementation in practice. Conclusion: Shared decision-making training supports maternity clinicians in developing skills that implement woman-centred care in the timing of planned birth