Spike sorting for large, dense electrode arrays

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%

Unsupervised home use of an overnight closed-loop system over 3-4 weeks: a pooled analysis of randomized controlled studies in adults and adolescents with type 1 diabetes.

AIMS: To compare overnight closed-loop and sensor-augmented pump therapy in patients with type 1 diabetes by combining data collected during free-living unsupervised randomized crossover home studies. METHODS: A total of 40 participants with type 1 diabetes, of whom 24 were adults [mean ± standard deviation (s.d.) age 43 ± 12 years and glycated haemoglobin (HbA1c) 8.0 ± 0.9%] and 16 were adolescents (mean ± s.d. age 15.6 ± 3.6 years and HbA1c 8.1 ± 0.8%), underwent two periods of sensor-augmented pump therapy in the home setting, in combination with or without an overnight closed-loop insulin delivery system that uses a model predictive control algorithm to direct insulin delivery. The order of the two interventions was random; each period lasted 4 weeks in adults and 3 weeks in adolescents. The primary outcome was time during which sensor glucose readings were in the target range of 3.9-8.0 mmol/l. RESULTS: The proportion of time when sensor glucose was in the target range (3.9-8.0 mmol/l) overnight (between 24:00 and 08:00 hours) was 18.5% greater during closed-loop insulin delivery than during sensor-augmented therapy (p < 0.001). Closed-loop therapy significantly reduced mean overnight glucose levels by 0.9 mmol/l (p < 0.001), with no difference in glycaemic variability, as measured by the standard deviation of sensor glucose. Time spent above the target range was reduced (p = 0.001), as was time spent in hypoglycaemia (<3.9 mmol/l; p = 0.014) during closed-loop therapy. Lower mean overnight glucose levels during closed-loop therapy were brought about by increased overnight insulin delivery (p < 0.001) without changes to the total daily delivery (p = 0.84). CONCLUSION: Overnight closed-loop insulin therapy at home in adults and adolescents with type 1 diabetes is feasible, showing improvements in glucose control and reducing the risk of nocturnal hypoglycaemia.Juvenile Diabetes Research Foundation (#22-2009-802) and Diabetes UK (BDA07/0003549) with additional support for the Artificial Pancreas work by National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK085621), and National Institute for Health Research Cambridge Biomedical Research Centre. Abbott Diabetes Care supplied continuous glucose delivery devices and sensors and modified devices to facilitate real-time connectivity.This if the final version of the article. It was originally published by Wiley in Diabetes, Obesity and Metabolism at http://onlinelibrary.wiley.com/doi/10.1111/dom.12427/abstrac

recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio

Costs of Testing for Ocular Chlamydia trachomatis Infection Compared to Mass Drug Administration for Trachoma in The Gambia: Application of Results from the PRET Study

Background Mass drug administration (MDA) treatment of active trachoma with antibiotic is recommended to be initiated in any district where the prevalence of trachoma inflammation, follicular (TF) is ≥10% in children aged 1–9 years, and then to continue for at least three annual rounds before resurvey. In The Gambia the PRET study found that discontinuing MDA based on testing a sample of children for ocular Chlamydia trachomatis(Ct) infection after one MDA round had similar effects to continuing MDA for three rounds. Moreover, one round of MDA reduced disease below the 5% TF threshold. We compared the costs of examining a sample of children for TF, and of testing them for Ct, with those of MDA rounds. Methods The implementation unit in PRET The Gambia was a census enumeration area (EA) of 600–800 people. Personnel, fuel, equipment, consumables, data entry and supervision costs were collected for census and treatment of a sample of EAs and for the examination, sampling and testing for Ct infection of 100 individuals within them. Programme costs and resource savings from testing and treatment strategies were inferred for the 102 EAs in the study area, and compared. Results Census costs were $103.24 per EA plus initial costs of$108.79. MDA with donated azithromycin cost $227.23 per EA. The mean cost of examining and testing 100 children was$796.90 per EA, with Ct testing kits costing $4.80 per result. A strategy of testing each EA for infection is more expensive than two annual rounds of MDA unless the kit cost is less than$1.38 per result. However stopping or deciding not to initiate treatment in the study area based on testing a sample of EAs for Ct infection (or examining children in a sample of EAs) creates savings relative to further unnecessary treatments. Conclusion Resources may be saved by using tests for chlamydial infection or clinical examination to determine that initial or subsequent rounds of MDA for trachoma are unnecessary

Targeting Antibiotics to Households for Trachoma Control

Repeated ocular infection with the bacterium Chlamydia trachomatis leads to the development of trachoma, a major cause of infectious blindness worldwide. Mass distribution of antibiotics, a component of the current trachoma control strategy, has had success in reducing infection in some areas, but results in a large number of uninfected people receiving antibiotics. We have previously shown that transmission of the bacteria between people in the same household is very efficient. Here, we investigated the effectiveness and cost-effectiveness of targeting antibiotics to households with active trachoma (inflammatory disease) compared to mass distribution, using data from four trachoma-endemic populations and a mathematical model of transmission. We found a high correspondence between households with active trachoma and infected households. In all populations the household targeted approach was predicted to be as effective as mass distribution, but it reduced the number of uninfected individuals receiving antibiotics, making the targeted strategy more cost-effective when antibiotics are not donated. Assuming antibiotics are donated, we predicted the targeted strategy to be more cost effective if it increases the proportion of infected individuals receiving treatment. Further work to address the feasibility and the cost variability in implementing the targeted approach in different settings is now required

Where form and substance meet: using the narrative approach of re-storying to generate research findings and community rapprochement in (university) mathematics education

Storytelling is an engaging way through which lived experience can be shared and reflected upon, and a tool through which difference, diversity—and even conflict—can be acknowledged and elaborated upon. Narrative approaches to research bring the richness and vibrancy of storytelling into how data is collected and interpretations of it shared. In this paper, I demonstrate the potency of the narrative approach of re-storying for a certain type of university mathematics education research (non-deficit, non-prescriptive, context-specific, example-centred and mathematically focused) conducted at the interface of two communities: mathematics education and mathematics. I do so through reference to Amongst Mathematicians (Nardi, 2008), a study carried out in collaboration with 20 university mathematicians from six UK mathematics departments. The study deployed re-storying to present data and analyses in the form of a dialogue between two fictional, yet entirely data-grounded, characters—M, mathematician, and RME, researcher in mathematics education. In the dialogues, the typically conflicting epistemologies—and mutual perceptions of such epistemologies—of the two communities come to the fore as do the feasibility-of, benefits-from, obstacles-in and conditions-for collaboration between these communities. First, I outline the use of narrative approaches in mathematics education research. Then, I introduce the study and its use of re-storying, illustrating this with an example: the construction of a dialogue from interview data in which the participating mathematicians discuss the potentialities and pitfalls of visualisation in university mathematics teaching. I conclude by outlining re-storying as a vehicle for community rapprochement achieved through generating and sharing research findings—the substance of research—in forms that reflect the fundamental principles and aims that underpin this research. My conclusions resonate with sociocultural constructs that view mathematics teacher education as contemporary praxis and the aforementioned inter-community discussion as taking place within a third space

The Global Burden of Trachoma: A Review

Trachoma is the commonest infectious cause of blindness worldwide. Recurrent infection of the ocular surface by Chlamydia trachomatis, the causative agent, leads to inturning of the eyelashes (trichiasis) and blinding corneal opacification. Trachoma is endemic in more than 50 countries. It is currently estimated that there are about 1.3 million people blind from the disease and a further 8.2 million have trichiasis. Several estimates for the burden of disease from trachoma have been made, giving quite variable results. The variation is partly because different prevalence data have been used and partly because different sequelae have been included. The most recent estimate from the WHO placed it at around 1.3 million Disability-Adjusted Life Years (DALYs). A key issue in producing a reliable estimate of the global burden of trachoma is the limited amount of reliable survey data from endemic regions

The prevalence and functional impact of musculoskeletal conditions amongst clients of a primary health care facility in an under-resourced area of Cape Town

BACKGROUND:The extent of disease burden of musculoskeletal conditions (MSC) not due to injury has not been well determined in sub-Saharan Africa. The 1999 Global Burden of Disease study estimated the prevalence of osteoarthritis and rheumatoid arthritis to be 150/100,000 compared to 1,500/100,000 in Europe. The objective of the study was to determine the prevalence of MSC and the functional implications in a sample of people attending community health centres in Cape Town, South Africa. METHODS: A cross-sectional, descriptive study was conducted in clinics in two resource poor communities. Phase I consisted of screening and those who screened positive for peripheral or spinal joint pain went on to complete Phase II, which included the Stanford Health Assessment Questionnaire. RESULTS: 1005 people were screened in Phase I. Of these, 362 (36%) reported MSC not due to injury in the past three months. Those with MSC had higher rates of co-morbidities in every category than those without. The mean Disability Index for those with MSC was mild to moderate and moderate to severe in those over 55 years. CONCLUSIONS: Although the sample may not be representative of the general community, the prevalence is considerably greater than those reported elsewhere even when the population of the catchment area is used as a denominator, (367/100 000). The common presentation of MSC with co-morbid diabetes and hypertension requires holistic management by appropriately trained health care practitioners. Any new determination of burden of disease due to MSC should recognise that these disorders may be more prevalent in developing countries than previously estimated

Theory in and for mathematics education: in pursuit of a critical agenda

© 2016 The Author(s)This special issue of Educational Studies in Mathematics, developed from the Mathematics Education and Contemporary Theory (MECT) conferences in Manchester, U.K., follows up an earlier double special issue in Volume 80 (2012) of this journal, which comprised 18 papers authored from a dozen countries. These efforts—both in conference and in print—to develop theory in and for mathematics education should be seen as part of our community’s collective effort to offer mathematics education broader yet more rigorous “thinking tools”. We argue in this introduction that in these times where ideology so often defines “improvement” in preference to rigorous analysis, this effort is more important than ever before. The selected papers span two broad areas: theory is used to develop critical conceptual frameworks for studies in mathematics education by Llewellyn, Nolan, Barwell, Nardi, Pais; and philosophical dimensions of mathematical learning are discussed by Ernest, Skovsmose, and Boylan