Epidemiology of depression and factors associated with depression in cancer patients’ in Ethiopia: protocol for systematic review and meta-analysis

BackgroundThere is no pooled evidence regarding the prevalence and potential associated factors of depression among cancer patients in East Africa community. Hence, the current review aimed to examine the prevalence and associated factors of depression among cancer patients in East Africa.Method: A computerized systematic literature search was made in MEDLINE, Scopus, PubMed, Science Direct, and Google Scholar. Each database was searched from its start date to June 2020. All included articles were published in English, which evaluated prevalence and associated factors of depression among cancer patients in East Saharan Africa. Pooled estimations with 95% confidence interval (CI) were calculated with DerSimonian-Laird random-effects model. Publication bias was evaluated by using inspection of funnel plots and statistical tests.DiscussionSince we are using existing anonymized data, ethical approval is not required for this study. Our results can be used to guide clinical decisions about the most efficient way to prevent and treat depression among cancer patients.Systematic review registrationsubmitted to Prospero

Association of the rs17250932, rs4794067 and rs2240017 polymorphism in the TBX21 gene with autoimmune diseases

Objective: To evaluate systematically the association between TBX21 gene polymorphisms (rs17250932, rs2240017, and rs4794067) and the risk of autoimmune diseases in Asian populations. Methods: The Medline, Web of Science, and Chinese Biomedical Literature Database were used to retrieve eligible studies that were published before July 2020. Pooled odds ratios (OR) and 95% confidence intervals (95% CI) were calculated by using the dominant model, heterozygote contrast model, and allelic contrast model. Publication bias was evaluated using contour-enhanced funnel plots and Egger’s regression test. Sensitivity analysis was conducted to assess the robustness of this meta-analysis.Results: A total of 12 eligible studies, including 3834 patients and 4824 healthy controls, were recruited in this meta-analysis. The pooled data demonstrated that TBX21 rs2240017 and rs4794067 polymorphisms were significantly associated with the risk of autoimmune diseases in Asian populations in allelic contrast model (OR: 1.456, 95% CI: 1.131–1.875, P = 0.004; OR: 0.766, 95% CI: 0.615–0.954, P = 0.017), heterozygote comparison model (OR: 1.647, 95% CI: 1.239–2.189, P = 0.001; OR: 0.796, 95% CI: 0.634–0.999, P = 0.049), and dominant model (OR: 1.572, 95% CI: 1.194–2.071, P = 0.004; OR: 0.767, 95% CI: 0.607–0.970, P = 0.027). The G allele of rs2240017 may be a risk factor for autoimmune diseases, and the T allele of rs4794067 may increase the risk of autoimmune diseases. However, we failed to find evidence of the association between TBX21 rs17250932 polymorphism and susceptibility to autoimmune diseases. No publication bias was established in this meta-analysis.Conclusion: This meta-analysis indicated that TBX21 rs2240017 and rs4794067 polymorphism confer susceptibility to autoimmune diseases, but not rs17250932.

Clinicians’ Publication Output: Self-Report Survey and Bibliometric Analysis

The uncertainties around disease management and control measures have not only motivated clinicians to keep abreast of new evidence available in the scholarly literature, but also to be rigorously engaged in medical research, dissemination and knowledge transfer. We aimed to explore clinicians’ publication output from the Malaysian perspective. A self-report survey and bibliometric analysis was conducted. A total of 201/234 clinicians participated in the survey. Items consisted of demographics, researching habits, publication output and level of importance of journal selection metrics. Descriptive, bivariate and multivariate analyses were conducted. Bibliometric analysis using retrieved records from PubMed between 2009 and October 2019 was conducted and co-occurrence and co-authorship analyses were executed. Self-reported publication output was 16.9%. In the logistic regression model, publication output was significantly higher amongst consultants or clinical specialists (aOR = 2.5, 95% CI 1.1–10.0, p = 0.023); clinicians previously involved in research (aOR = 4.2, 95% CI 1.5–11.4, p = 0.004); clinicians who ever used reference citation managers (aOR = 3.2, 95% CI 1.3–7.7, p = 0.010); and journal publication speed (aOR = 2.9, 95% CI 1.2–7.1, p = 0.019). Most clinicians published original research papers (76.4%) in international journals (78.2%). Published papers were mostly observational studies, genetic, stroke and health services or systems research. In conclusion, socio-demographics, researching habits and journal selection metrics were significantly associated with self-reported publication output. Real outputs from bibliometrics were predominantly focused across five clusters.

ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models

Motivation The number and complexity of genome-scale metabolic models is steadily increasing, empowered by automated model-generation algorithms. The quality control of the models, however, has always remained a significant challenge, the most fundamental being reactions incapable of carrying flux. Numerous automated gap-filling algorithms try to address this problem, but can rarely resolve all of a model’s inconsistencies. The need for fast inconsistency checking algorithms has also been emphasized with the recent community push for automated model-validation before model publication. Previously, we wrote a graphical software to allow the modeller to solve the remaining errors manually. Nevertheless, model size and complexity remained a hindrance to efficiently tracking origins of inconsistency. Results We developed the ErrorTracer algorithm in order to address the shortcomings of existing approaches: ErrorTracer searches for inconsistencies, classifies them and identifies their origins. The algorithm is ∼2 orders of magnitude faster than current community standard methods, using only seconds even for large-scale models. This allows for interactive exploration in direct combination with model visualization, markedly simplifying the whole error-identification and correction work flow. Availability and implementation Windows and Linux executables and source code are available under the EPL 2.0 Licence at https://github.com/TheAngryFox/ModelExplorer and https://www.ntnu.edu/almaaslab/downloads. Supplementary information Supplementary data are available at Bioinformatics online.

Conference presentation in palliative medicine: predictors of subsequent publication

ObjectivesConcerns have been raised about poor-quality palliative care research and low publication rate from conference abstracts. The study objectives: to estimate the publication rate for European Association for Palliative Care research conference abstracts (2008) and explore associated characteristics and to understand reasons for non-publication.MethodsFull published papers were searched to March 2015 (Medline; Pubmed; Google Scholar) and data extracted: country of origin, study design/population/topic. Multivariate logistic regression was used to identify predictors of publication.Members of two different palliative care associations were surveyed to understand reasons for non-publication. χ2 statistic was used to explore associations with publication.ResultsOverall publication rate of the 445 proffered abstracts was 57%. In the final model, publication was more likely for oral presentations (OR 2.13; 95% CI 1.28 to 3.55; P=0.003), those from Europe (3.24; 1.09 to 9.56; P=0.033) and much less likely for non-cancer topics (0.21; 0.07 to 0.64; P=0.006). Funding status, academic unit or study design were not associated with publication.Survey407/1546 (26.3%) physicians responded of whom 254 (62%) had submitted a conference abstract. Full publication was associated with: oral presentation (P<0.001), international conference abstracts (P=0.01) and academic clinicians versus clinicians (P<0.001). Reasons for non-publication included: low priority for workload (53%) and time constraints (43%).ConclusionsThe publication rate was similar to 2005 clinical conference. Probable quality markers were associated with publication: oral presentations selected by conference committee, international conference abstracts and abstracts from those with an academic appointment. Publication was given a low priority among clinical time pressures.

The Open Science Framework: Improving Science by Making It Open and Accessible

There currently exists a gap between scientific values and scientific practices. This gap is strongly tied to the current incentive structure that rewards publication over accurate science. Other problems associated with this gap include reconstructing exploratory narratives as confirmatory, the file drawer effect, an overall lack of archiving and sharing, and a singular contribution model - publication - through which credit is obtained. A solution to these problems is increased disclosure, transparency, and openness. The Open Science Framework (http://openscienceframework.org) is an infrastructure for managing the scientific workflow across the entirety of the scientific process, thus allowing the facilitation and incentivization of openness in a comprehensive manner. The current version of the OSF includes tools for documentation, collaboration, sharing, archiving, registration, and exploration.

Using argument notation to engineer biological simulations with increased confidence

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using A rtoo ( www.york.ac.uk/ycil/software/artoo ), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions.

Editorial: The publication of geoscientific model developments v1.0

In 2008, the first volume of the European Geosciences Union (EGU) journal Geoscientific Model Development (GMD) was published. GMD was founded because we perceived there to be a need for a space to publish comprehensive descriptions of numerical models in the geosciences. The journal is now well established, with the submission rate increasing over time. However, there are several aspects of model publication that we believe could be further improved. In this editorial we assess the lessons learned over the first few years of the journal's life, and describe some changes to GMD's editorial policy, which will ensure that the models and model developments are published in such a way that they are of maximum value to the community. These changes to editorial policy mostly focus on improving the rigour of the review process through a stricter requirement for access to the materials necessary to test the behaviour of the models. Throughout this editorial, "must" means that the stated actions are required, and the paper cannot be published without them; "strongly encouraged" means that we encourage the action, but papers can still be published if the criteria are not met; "may" means that the action may be carried out by the authors or referees, if they so wish. We have reviewed and rationalised the manuscript types into five new categories. For all papers which are primarily based on a specific numerical model, the changes are as follows: – The paper must be accompanied by the code, or means of accessing the code, for the purpose of peer-review. If the code is normally distributed in a way which could compromise the anonymity of the referees, then the code must be made available to the editor. The referee/editor is not required to review the code in any way, but they may do so if they so wish. – All papers must include a section at the end of the paper entitled "Code availability". In this section, instructions for obtaining the code (e.g. from a supplement, or from a website) should be included; alternatively, contact information should be given where the code can be obtained on request, or the reasons why the code is not available should be clearly stated. – We strongly encourage authors to upload any user manuals associated with the code. – For models where this is practicable, we strongly encourage referees to compile the code, and run test cases supplied by the authors where appropriate. – For models which have been previously described in the "grey" literature (e.g. as internal institutional documents), we strongly encourage authors to include this grey literature as a supplement, when this is allowed by the original authors. – All papers must include a model name and version number (or other unique identifier) in the title. It is our perception that, since Geoscientific Model Development (GMD) was founded, it has become increasingly common to see model descriptions published in other more traditional journals, so we hope that our insights may be of general value to the wider geoscientific community.

A physiome standards-based model publication paradigm

In this era of widespread broadband Internet penetration and powerful Web browsers on most desktops, a shift in the publication paradigm for physiome-style models is envisaged. No longer will model authors simply submit an essentially textural description of the development and behaviour of their model. Rather, they will submit a complete working implementation of the model encoded and annotated according to the various standards adopted by the physiome project, accompanied by a traditional human-readable summary of the key scientific goals and outcomes of the work. While the final published, peer-reviewed article will look little different to the reader, in this new paradigm, both reviewers and readers will be able to interact with, use and extend the models in ways that are not currently possible. Here, we review recent developments that are laying the foundations for this new model publication paradigm. Initial developments have focused on the publication of mathematical models of cellular electrophysiology, using technology based on a CellML- or Systems Biology Markup Language (SBML)-encoded implementation of the mathematical models. Here, we review the current state of the art and what needs to be done before such a model publication becomes commonplace.

Mefenamate, an Agent that Fails to Attenuate Experimental Cerebral Infarction

Background:Blockade of nonselective cation channels is a potential therapeutic approach that has not been attempted in cerebral ischemia, in spite of the ability of these channels to allow cellular calcium influx into neurons. Fenamates are a class of molecules that block these channels, and many congeners are also anti-inflammatory and free radical scavenging. These three mechanisms may contribute to brain damage in ischemia.Methods:Pretreatment or posttreatment with mefenamate (30 mg/kg) was evaluated in a temperature-controlled rat transient focal ischemia model. Quantitative histopathology on 26 coronal sections allowed determination of tissue necrosis and tissue atrophy at one week survival.Results:Neither pre- nor postischemic administration of a dose previously shown effective in preventing epileptic neuronal necrosis was found to reduce necrosis in cortex, nor in any subcortical structures.Conclusions:We conclude that nonselective cation channel blockade with mefenamate affords no neuroprotection in this model. Publication bias against negative studies exists in the literature, but we here report negative findings due to the multiple potentially positive actions of the drug. Closer examination of the effects of the molecule, however, reveals several potentially negative effects as well. We conclude there may be inherent weakness in pharmacologic monotherapy, even with molecules having protean potentially beneficial effects. This conclusion seems to have been borne out by the results of recent clinical trials.