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Background: Some sputum smear microscopy protocols recommend placing filter paper over sputum smears during staining for Mycobacterium tuberculosis (TB). We found no published evidence assessing whether this is beneficial. We aimed to evaluate the effect of filter paper on sputum smear microscopy results. Methods: Sputum samples were collected from 30 patients with confirmed pulmonary TB and 4 healthy control participants. From each sputum sample, six smears (204 smears in total) were prepared for staining with Ziehl-Neelsen (ZN), auramine or viability staining with fluorescein diacetate (FDA). Half of the slides subjected to each staining protocol were randomly selected to have Whatman grade 3 filter paper placed over the dried smears prior to stain application and removed prior to stain washing. The counts of acid-fast bacilli (AFB) and precipitates per 100 high-power microscopy fields of view, and the proportion of smear that appeared to have been washed away were recorded. Statistical analysis used a linear regression model adjusted by staining technique with a random effects term to correct for between-sample variability. Results: The inclusion of filter paper in the staining protocol significantly decreased microscopy positivity independent of staining with ZN, auramine or FDA (p=0.01). Consistent with this finding, there were lower smear grades in slides stained using filter paper versus without (p=0.04), and filter paper use reduced AFB counts by 0.28 logarithms (95% confidence intervals, CI=0.018, 0.54, p=0.04) independent of staining technique. In all analyses, auramine was consistently more sensitive with higher AFB counts versus ZN (p=0.001), whereas FDA had lower sensitivity and lower AFB counts (p Conclusions: Filter paper reduced the sensitivity of AFB microscopy and had no detectable beneficial effects so is not recommended.

Background: Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. In Ireland, a dearth of research means that we neither know the number of people affected by TBI, nor have the required data to improve neuro-rehabilitation services. This is a study protocol to examine the epidemiology and pathways through rehabilitation for a cohort of TBI survivors in the Republic of Ireland. Aims: To document the epidemiological data of TBIs in Ireland.To explore the pathway of TBI survivors through rehabilitation/health services.To document the experiences of those providing care for TBI survivors in Ireland Methods: This is a quantitative cohort study. Existing routine datasets will be used to report epidemiological data. Participants with moderate or severe TBI will be recruited through two brain injury service providers, two acute hospitals that provide neurosurgical services, and the National Rehabilitation Hospital. Participants with TBI will be surveyed on two separate occasions, to explore their use of health and rehabilitation services. Those providing care or support to TBI survivors will be surveyed, on one occasion. Additionally, data from the medical records of TBI survivors will be extracted to capture key information about their TBI, such as mechanism of injury, severity, hospitalisation and follow-up. TBI survivors’ use of health care will be followed prospectively for six months. Expected outcomes: The epidemiological data of TBI in Ireland will be documented. Data on survivors’ experiences of how rehabilitation services are accessed, and any barriers encountered with rehabilitation/health services will be reported. The experiences of those providing care or support for TBI survivors will be captured. It is expected that the outcomes of the study will support advocacy efforts toward the redevelopment of neuro-rehabilitation services in the Republic of Ireland.

Background: Publication and co-authorship rates have been increasing over decades. In response, calls are being made to restrict the number of publications included in research evaluations. Yet there is little evidence to guide publication expectations and inform research evaluation for early career researchers (ECRs). Methods: Here we examine the early career publication and co-authorship records between 1970 and 2019 of >140,000 authors of 2.8 million publications, to identify how publication and co-authorship rates have changed over the last 50 years. This examination is conducted in order to develop benchmarks of median publication rates for sensibly evaluating ECR research productivity, and to explore success in meeting these benchmarks with different co-authorship strategies using regression models. Results: Publication rates of multidisciplinary ECRs publishing in Nature, Science and PNAS have increased by 46% over the last 50 years and that publications rates in a set of disciplinary journals have increased by 105%. Co-authorship rates have increased even more, particularly for the multidisciplinary sample which now has 572% more co-authors per publication. Benchmarks based on median publication rates for all authors increased from one publication per year at the start of a career, to four publications per year after 10 years of publishing, and one first-author publication across all years. The probability of meeting these benchmarks increases when authors publish with different co-authors, and first authorship rates decrease for ECRs with many co-authors per publication. Conclusion: This evidence could be used to inform sensible publishing expectations for ECRs and the institutions they work for, and to inform calls to limit the number of publications produced by researchers and those used in research evaluations.

Background: The ‘impact’ of a scientific paper is a measure of influence in its field. In recent years, traditional, citation-based measures of impact have been complemented by Altmetrics, which quantify outputs including social media footprint. As authors and research institutions seek to increase their visibility both within and beyond the academic community, it is important to identify and compare the determinants of traditional and alternative metrics. We explored this using Stroke – a leading journal in its field. Methods: We described the impact of original research papers published in Stroke (2015-2016) using citation count and Altmetric Attention Score (Altmetrics). Using these two metrics as our outcomes, we assessed univariable and multivariable associations with 21 plausibly relevant publication features. We set the significance threshold at p Results: Across 911 papers published in Stroke, there was an average citation count of 21.60 (±17.40) and Altmetric score of 17.99 (±47.37). The two impact measures were weakly correlated (r=0.15, p Conclusion: Papers published in Stroke have impact. Certain aspects of content and format may contribute to impact, but these differ for traditional measures and Altmetrics, and explain only a very modest proportion of variance in the latter. Citation counts and Altmetrics seem to represent different constructs and, therefore, should be used in conjunction to allow a more comprehensive assessment of publication impact.

Background: Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. In Ireland, a dearth of research on TBI means that we neither know the number of people affected by this injury, nor have the information required to improve neuro-rehabilitation services. Aims: This is the protocol for a study that will examine pathways through rehabilitation for survivors of TBI in the Republic of Ireland. The experiences of family members providing care or support to a person with TBI will also be explored. Additionally, the study will estimate the incidence and prevalence of TBI in Ireland. Epidemiological data and information on how people with TBI access rehabilitation and health services will support advocacy efforts towards the redevelopment of neuro-rehabilitation services. Methods: The research is a mixed method, observational cohort study design. Participants with moderate to severe TBI will be recruited through two brain injury service providers, two acute hospitals that provide neurosurgical services, and the National Rehabilitation Hospital. Questionnaires will be administered to participants with TBI on two separate occasions, six months apart, and to family members providing care or support to an individual with TBI, on one occasion. Data from the medical records of participants will be abstracted to capture key information about their brain injury. TBI survivor participants’ use of health care will be followed prospectively for six months. Expected outcomes: The study will outline participants’ pathways through rehabilitation in Ireland, to understand how rehabilitation services are accessed, and the barriers to accessing these services. The incidence and prevalence of TBI in Ireland will be estimated. Experiences of family members providing care or support to an individual with TBI will be detailed. The outcomes of the study will support ongoing efforts to improve care for TBI survivors in Ireland and to redevelop neuro-rehabilitation services.

Background: Pertussis is a highly infectious respiratory illness caused by the bacteria Bordetella pertussis. A resurgence of pertussis, even in countries with good vaccine coverage, has led to an increase in infant deaths. In response to this, many countries have introduced pertussis vaccination in pregnancy. This strategy is effective at preventing infant disease, but there remains uncertainty about what gestational timing is best to ensure maximal protection of the infant. These uncertainties are the rationale for this randomised controlled trial and a sub-study investigating pertussis-specific antibody in breastmilk. Protocol: We will recruit 354 pregnant women and will randomise them to receive their pertussis vaccination in one of three gestational age windows: ≤23+6, 24-27+6 and 28-31+6 weeks of gestation. Vaccination will be with Boostrix-IPV® and participants will be asked to complete a symptom diary for seven days following vaccination. Blood sampling will be performed prior to vaccination, two weeks following vaccination and at the time of delivery. A cord blood sample will be collected at delivery and a blood sample collected from the infant 4-10 weeks after completion of the primary immunisations. Individuals participating in the breastmilk sub-study will provide a sample of colostrum within 48 hours of delivery and samples of breastmilk at two weeks and around five-six months. Blood samples will be analysed using enzyme linked immunosorbent assay (ELISA) techniques for pertussis toxin, filamentous haemagglutinin and pertactin. A subset of serum samples will also be analysed using a functional assay. Colostrum and breastmilk samples will be analysed using functional assays. Discussion: Although pertussis vaccination has been shown to be safe and effective in pregnancy there remains debate about the optimal timing for the administration during pregnancy. This study will investigate antibody responses in serum and breastmilk when vaccination is performed in three different time periods. Clinicaltrials.gov registration: NCT03908164 (09/04/2019)

Background: The moment of hospital discharge is a time for vulnerability for many patients and might jeopardize their safety. We found that the current structure of the discharge card at Soba University Hospital (SUH) does not improve the quality of the discharge summary. This hinders the delivery of valid, relevant and adequate health information and can negatively affect outpatient care. Methods: We implemented a new discharge card design with structured headings at the Department of Medicine at Soba University Hospital from the beginning of March to April 15th, 2017. This was coupled with educational sessions highlighting the problems that might occur if there were gaps in patient transition from inpatient to outpatient. Results: There was a significant improvement in documentation of the majority (>90%) of the items, including name, age, source of admission treating doctor, diagnosis and medication, but there was a drop in documentation of comorbidities. We also noticed that the new discharge summary format significantly improved the documentation of the majority of the headings (all P values were Conclusions: Recording of paper-based health records like discharge summaries could be substantially improved by use of well-structured formats and practical training sessions. Improvement is a dynamic process. Some gaps might appear during execution, these need monitoring and continuous improvement to establish sustainability.

Scientific evidence has established several links between metabolic and neurocognitive dysfunction, and epidemiologic evidence has revealed an increased risk of Alzheimer’s disease and vascular dementia in patients with diabetes. In July 2015, the National Institute of Diabetes, Digestive, and Kidney Diseases gathered experts from multiple clinical and scientific disciplines, in a workshop entitled “The Intersection of Metabolic and Neurocognitive Dysfunction”, to clarify the state-of-the-science on the mechanisms linking metabolic dysfunction, and insulin resistance and diabetes in particular, to neurocognitive impairment and dementia. This perspective is intended to serve as a summary of the opinions expressed at this meeting, which focused on identifying gaps and opportunities to advance research in this emerging area with important public health relevance.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders. BW was funded by a grant from the BBSRC [BB/P024092/1]. AB, SO and PLM were supported by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIGMS), and National Institute of Mental Health (NIMH) of the National Institutes of Health under Award Number [U24HG007822] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health), by European Molecular Biology Laboratory (EMBL) and by the Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI. AG was supported by the European Molecular Biology Laboratory (EMBL) and the Wellcome Trust [104948]. AE was supported by a Vetenskapsrådet grant [2016-03798]. EP was supported by Danmarks Grundforskningsfond [DNRF125] and a Carlsberg Foundation Distinguished Fellowship [CF18-0314]. JLS was supported by the Israel I-CORE Project: Integrated Structural Cell Biology and by Instruct-ERIC. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement [778247] and COST Action BM1405 NGP-net.

Background: Latest advances in information and health technologies enabled dentistry to follow the paradigm shift occurring in medicine – the transition to so called smart medicine. Consequently, the aim of this paper is to assess how ‘smart’ is smart dentistry as of the end of 2018. Methods: We analysed the state of the art in smart dentistry, performing bibliometric mapping on a corpus of smart dentistry papers found in the Scopus bibliographical database. Results: The search resulted in a corpus of 3451 papers, revealing that smart dentistry research is following the progress in smart medicine; however, there are some gaps in some specific areas like gamification and use of holistic smart dentistry systems. Conclusions: Smart dentistry is smart; however, it must become smarter.

Background: Decentralized drinking water treatment methods generally apply membrane-based treatment approaches. Ozonation of drinking water, which previously has only been possible at large centralized facilities, can now be accomplished on a small-scale using microplasma technology. The efficacy of decentralized solar-powered drinking water treatment systems has not previously been described. Methods: We established a 1,000L decentralized solar-powered water treatment system located in Kisumu County, Kenya. Highly contaminated surface water is pumped to the treatment system, which includes flocculation and filtration steps prior to ozonation. Turbidity, total coliform bacteria, and E. coli were measured at various stages of water treatment, and bacterial log reduction values (LRVs) were calculated. Results: Forty-seven trials were conducted in which1000L of water were flocculated, filtered, and ozonated for 180 minutes. Baseline turbidity and E. coli concentrations were reduced from a median of 238 nephelometric turbidity units (NTU) and 2,419.7 most probable number/100mL, respectively, in surface water to 1.0 NTU and undetectable E. coli after ozonation for 180 minutes. The median E. coli LRV was 3.99. Conclusions: The solar-powered, decentralized water treatment system that utilizes ozonation for disinfection was founded to reduce E. coli by more than 3 log-orders of magnitude despite the high turbidity of the raw water. Further research is needed to characterize limitations, scalability, economic viability, and community perspectives that could help determine the role for similar systems in other settings.

Background: Environmental sustainability is the driver for finding the optimal bioremediation cocktail with the combination of highly potent hydrocarbonoclastic strains and the nutrient additives that significantly enhance mineralization of crude oil in polluted soil in order to mitigate its deleterious effects on the environment. In this study, four hydrocarbon-degrading bacterial strains were pre-selected from mined rhizobacterial isolates in aged crude oil-contaminated soil. Method: Agrowaste residues of poultry-droppings, corn chaff, and plantain peel were selected among others for their ability to support high biomass of selected bacterial strains. Baseline proximate analysis was performed on the agrowaste residues. Simplified, one variable at a time (OVAT) was employed in the validation of the variables for optimization using the Multivariate analysis tool of Response Surface Methodology (RSM). To test the significant formulation variables, the Box-Behnken approach using 15 runs design was adopted. Results: The rate of contaminant removal was observed to fit into a quadratic function. For optimal rate or contaminant removal, the fitted model predicted the optimal formulation cocktail condition to be within 0.54 mg/kg (Corn steep liquor), phosphate 137.49 mg/kg (poultry droppings) and 6.4% inocula for initial TPH of 9744 mg kg-1 and THC of 9641 mg kg-1 contaminant level. The model for the application of the bioremediation product and the variables evaluated had a significant p-value < 0.005 for the attainment of 85 to 96 % of TPH and THC removal after 56 days of treatment. Conclusions: This study has shown the need to harness the abundant agrowaste nutrients in supporting high throughput rhizobacteria in the formulation of a bioremediation agent suitable for use in the reclamation of oil spill sites in the Niger Delta oil-producing region.

The tanning industry generates effluents with a high contaminant load represented in a considerable amount of liquid, solid, and gaseous waste. Solid waste, such as residual hair, fat, and meat, are dumped directly in landfills, triggering serious environmental problems. The objective of this research was to compost this waste, previously desulfurized, in a mixture with remnants from pruning as a bulking agent. This low-cost strategy may reduce the total amount of waste. A composting pile was created using residual hair and pruning remnants in a proportion of 3:1 (w/w) and then an inoculum was added. The waste degrading process ran for 141 days, followed by a maturation period of 64 days. Throughout the process, the temperature, moisture, pH, and electrical conductivity (EC) were monitored. The highest temperature reached was 69.7°C, which secured good disinfection. The EC was 0.27 dS/cm, having lower values than Spanish regulations, possibly due to the salt removal over the irrigation periods. The organic matter content decreased continuously, to reach an endpoint of 42%; this result agrees with the high organic matter content of the tannery waste and the pruning remnants. Germination index was 43.55%, which indicates the presence of phytotoxic substances. As compared to the initial value (10.73%) there was partial degrading of these substances. The challenge is to improve this parameter by identifying new mixtures and adding efficient microorganisms that help to degrade phytotoxic substances.

Background: This short-term study was carried out in 2013 at the Pollution Research Group at the University of KwaZulu-Natal (Durban, South Africa) as an asisgnemnt of a final year Chemical engineering student project. It focussed on the effect of storage time on the properties of fresh human faeces, more particularly moisture content, thermal conductivity, volatile solids and chemical oxygen demand (COD). These properties are important as they are often used in the design of drying or thermal treatment technologies for faeces. A storage period of one week was hypothesised at room ambient temperature. Methods: The samples were tested for chemical properties using standard operational procedures developed at the Pollution Research Group with parameters such as totals solids, moisture content, suspended solids, volatile solids, COD and thermal conductivity. Results: The thermal conductivity on average was 0.44 W/m.K. The moisture content was observed to decrease by 16%, from 77% to 61%. Thermal conductivity was plotted over the range of moisture contents to observe any trends, varying from 0.074 W/m.K to 0.61 W/m.K for dry faeces and water respectively. The use of a composition weighted average model fitted the data well and was found to be within 95% of the confidence interval of the best fit line. Conclusions: The effect of storage time was found to be negligible on COD and thermal conductivity however moisture content decreased as days progressed and the volatile solids increased with an increase in storage time. Examining the relationship between thermal conductivity and moisture content, it was found that thermal conductivity increase with an increase in moisture content.

This study aimed to utilize food industry waste (i.e. banana (Musa paradisiaca L.) peel), as a raw material for making banana peel activated carbon (BPAC). The activated carbon-making process was conducted at varying temperatures (200, 400 and 600°C) and furnacing times (1, 2 and 3 hours). The purification function of the BPAC obtained from the optimization process was assessed with used cooking oil (UCO) from the food industry. The purified oil was tested for three quality parameters, the peroxide value, free fatty acid value and iodine value. The results of this testing showed that BPAC could slightly improve the quality of used cooking oil.

Onsite reuse of blackwater requires removal of considerable amounts of suspended solids and organic material in addition to inactivation of pathogens. Previously, we showed that electrochemical treatment could be used for effective pathogen inactivation in blackwater, but was inadequate to remove solids and organics to emerging industry standards. Further, we found that as solids and organics accumulate with repeated recycling, electrochemical treatment becomes less energetically sustainable. Here, we describe a pilot study in which concentrated blackwater is pretreated with ultrafiltration and granular activated carbon prior to electrochemical disinfection, and show that this combination of treatments removes 75-99% of chemical oxygen demand, 92-100% of total suspended solids, and improves the energy efficiency of electrochemical blackwater treatment by an order of magnitude.