Burrows–Wheeler compression: Principles and reflections

AbstractAfter a general description of the Burrows–Wheeler transform and a brief survey of recent work on processing its output, the paper examines the coding of the zero-runs from the MTF recoding stage, an aspect with little prior treatment. It is concluded that the original scheme proposed by Wheeler is extremely efficient and unlikely to be much improved.The paper then proposes some new interpretations and uses of the Burrows–Wheeler transform, with new insights and approaches to lossless compression, perhaps including techniques from error correction

Using quicksand to improve debugging practice in post-novice level students

The ability to debug existing code is an important skill to develop in student programmers. However, debugging may not receive the same amount of explicit teaching attention as other material and the main expression of debugging competence is students' ability to undo problems which they themselves have injected into their assignments. Further, as the literature points out, debugging skills do not necessarily develop at the same rate as code writing skills. This paper discusses an intervention in a second year course designed to improve students' application of simple debugging techniques. We use a puzzle based approach where students are graded based on the number of attempts they take to locate misbehaving code in a program which they did not write but whose function they understand. An existing assignment component addresses another aspect of debugging practice

Soil-transmitted helminth infections

More than a quarter of the world's population is at risk of infection with the soil-transmitted helminths Ascaris lumbricoides, hookworm (Ancylostoma duodenale and Necator americanus), Trichuris trichiura, and Strongyloides stercoralis. Infected children and adults present with a range of medical and surgical conditions, and clinicians should consider the possibility of infection in individuals living in, or returning from, endemic regions. Although safe and effective drugs are donated free to endemic countries, only half of at-risk children received treatment in 2016. This Seminar describes the epidemiology, lifecycles, pathophysiology, clinical diagnosis, management, and public health control of soil-transmitted helminths. Previous work has questioned the effect of population-level deworming; however, it remains beyond doubt that treatment reduces the severe consequences of soil-transmitted helminthiasis. We highlight the need for refined diagnostic tools and effective control options to scale up public health interventions and improve clinical detection and management of these infections

As experiências de quase morte (EQM) podem contribuir para o debate sobre a consciência?

A EQM é um estado alterado de consciência que no ocidente inclui uma experiência emocional e de conteúdo estereotipado. Algumas características da experiência são transculturais e sugerem ou um mecanismo cerebral similar ou acesso a uma realidade transcendente. Características individuais da experiência indicam mais persuasivamente para transcendência que para um simples mecanismo cerebral limitado. Além disso, não há, até agora, nenhuma explicação reducionista que possa dar conta satisfatoriamente de algumas dessas características: o encontro com parentes falecidos, a aparente capacidade visual em cegos durante a EQM, a aparente aquisição de dons psíquicos e espirituais após a EQM, relato de cura ocorrida durante uma EQM e experiências verídicas durante a ressuscitação pós-parada cardíaca. Embora uma mente não local pudesse explicar muita das características das EQM, a não localidade ainda não é aceita pela corrente predominante da neurociência. Somente aquelas teorias baseadas num entendimento mais amplo da mente poderiam explicar totalmente a experiência subjetiva dos que vivenciaram uma EQM.The NDE is an altered state of consciousness which in the West has stereotyped content and emotional experience. Some features of the experience are trans-cultural and suggest either a similar brain mechanism or access to a transcendent reality. Individual features of the experience point more persuasively to transcendence than to simple limited brain mechanisms. Moreover there are, so far, no reductionist explanations which can account satisfactorily for some of its features; the meeting of dead relatives, the apparent "sightedness" in the blind during an NDE, the apparent acquisition after an NDE of psychic and spiritual gifts, accounts of healing occurring during an NDE, and of veridical experience during the resuscitation after a cardiac arrest. Although non-local mind would explain many of the NDE features, non locality is not yet accepted by mainstream neuroscience. Only those theories based on a wider understanding of mind could fully explain the subjective experience of the NDEr

The new COVID-19 poor and the neglected tropical diseases resurgence

More than 100 million people are facing a return to extreme poverty because of coronavirus disease 2019 (COVID-19), while new estimates suggest that threenations—India, Nigeria, and the Democratic Republic of the Congo—may suffer the greatest economic contractions. Such findings will have profound consequences in terms of our ability to control or eliminate the most widely prevalent neglected tropical diseases

Is the near-death experience only N-methyl-D-aspartate blocking?

ABSTRACT: Karl Jansen's interesting hypothesis that near-death experi ences (NDEs) result from blockade of the N-methyl-D-aspartate receptor has several weaknesses. Some NDEs occur to individuals who are neither near death nor experiencing any event likely to upset cerebral physiology as Jan sen proposed; thus his hypothesis applies only to a subset of NDEs that occur in catastrophic circumstances. For that subset, the clarity of NDEs and the clear memory for the experience afterward are inconsistent with compromised cerebral function. Jansen's analogy between NDEs and ketamine-induced hallucinations is weakened by the fact that most ketamine users do not believe the events they perceived really happened. 'Iemporal lobe seizures do not resemble NDEs as Jansen postulated; they are confu sional, rarely ecstatic, and never clear, as are NDEs, nor are they remem bered afterward. Jansen's hypothesis assumes the standard scientific view that brain processes are entirely responsible for subjective experience; how ever, NDEs suggest that that concept of the mind may be too limited, and that in fact personal experience may continue beyond death of the brain. Karl L. R. Jansen has proposed a hypothesis describing a mecha nism that makes a major contribution to the understanding of the near-death experience (NDE). He suggested that the NDE is the re sult of the blocking of the phencyclidine (PCP) site on the N-methyl D-aspartate (NMDA) receptor

The impact of diabetes-related complications on preference-based measures of health-related quality of life in adults with Type I diabetes

Introduction: This study estimates health-related quality of life (HRQoL) or utility decrements associated with type 1 diabetes mellitus (T1DM) using data from a UK research programme on the Dose Adjustment For Normal Eating (DAFNE) education programme. Methods: A wide range of data was collected from 2,341 individuals who undertook a DAFNE course in 2009-12, at baseline and for two subsequent years. We use fixed and random effects linear models to generate utility estimates for T1DM using different instruments: EQ-5D, SF-6D and EQ-VAS. We show models with and without controls for HbA1c and depression, which may be endogenous (if, for example, there is reverse causality in operation). Results: We find strong evidence of an unobserved individual effect, suggesting the superiority of the fixed effects model. Depression shows the greatest decrement across all the models in the preferred fixed effects model. The fixed effects EQ-5D model also finds a significant decrement from retinopathy, BMI and HbA1c(%). Estimating a decrement using the fixed effects model is not possible for some conditions where there are few new cases. In the random effects model diabetic foot disease shows substantial utility decrements, yet these are not significant in the fixed effects models. Conclusion: Utility decrements have been calculated for a wide variety of health states in T1DM which can be used in economic analyses. However, despite the large dataset, the low incidence of several complications leads to uncertainty in calculating the utility weights. Depression and diabetic foot disease result in a substantial loss in HRQoL for patients with T1DM. HbA1c(%) appears to have an independent negative impact upon HRQoL, although concerns remain regarding the potential endogeneity of this variable