Algorithmic statistics revisited

The mission of statistics is to provide adequate statistical hypotheses (models) for observed data. But what is an "adequate" model? To answer this question, one needs to use the notions of algorithmic information theory. It turns out that for every data string $x$ one can naturally define "stochasticity profile", a curve that represents a trade-off between complexity of a model and its adequacy. This curve has four different equivalent definitions in terms of (1)~randomness deficiency, (2)~minimal description length, (3)~position in the lists of simple strings and (4)~Kolmogorov complexity with decompression time bounded by busy beaver function. We present a survey of the corresponding definitions and results relating them to each other

Trends in quality of care and dying perceived by family caregivers of nursing home residents with dementia 2005-2019

BACKGROUND: Dementia palliative care is increasingly subject of research and practice improvement initiatives. AIM: To assess any changes over time in the evaluation of quality of care and quality of dying with dementia by family caregivers. DESIGN: Combined analysis of eight studies with bereaved family caregivers’ evaluations 2005–2019. SETTING/PARTICIPANTS: Family caregivers of nursing home residents with dementia in the Netherlands (n = 1189) completed the End-of-Life in Dementia Satisfaction With Care (EOLD-SWC; quality of care) and Comfort Assessment in Dying (EOLD-CAD, four subscales; quality of dying) instruments. Changes in scores over time were analysed using mixed models with random effects for season and facility and adjustment for demographics, prospective design and urbanised region. RESULTS: The mean total EOLD-SWC score was 33.40 (SD 5.08) and increased by 0.148 points per year (95% CI, 0.052–0.244; adjusted 0.170 points 95% CI, 0.055–0.258). The mean total EOLD-CAD score was 30.80 (SD 5.76) and, unadjusted, there was a trend of decreasing quality of dying over time of −0.175 points (95% CI, −0.291 to −0.058) per year increment. With adjustment, the trend was not significant (−0.070 EOLD-CAD total score points, 95% CI, −0.205 to 0.065) and only the EOLD-CAD subscale ‘Well being’ decreased. CONCLUSION: We identified divergent trends over 14 years of increased quality of care, while quality of dying did not increase and well-being in dying decreased. Further research is needed on what well-being in dying means to family. Quality improvement requires continued efforts to treat symptoms in dying with dementia

A Simple Stochastic Model with Environmental Transmission Explains Multi-Year Periodicity in Outbreaks of Avian Flu

Avian influenza virus reveals persistent and recurrent outbreaks in North American wild waterfowl, and exhibits major outbreaks at 2–8 years intervals in duck populations. The standard susceptible-infected- recovered (SIR) framework, which includes seasonal migration and reproduction, but lacks environmental transmission, is unable to reproduce the multi-periodic patterns of avian influenza epidemics. In this paper, we argue that a fully stochastic theory based on environmental transmission provides a simple, plausible explanation for the phenomenon of multi-year periodic outbreaks of avian flu. Our theory predicts complex fluctuations with a dominant period of 2 to 8 years which essentially depends on the intensity of environmental transmission. A wavelet analysis of the observed data supports this prediction. Furthermore, using master equations and van Kampen system-size expansion techniques, we provide an analytical expression for the spectrum of stochastic fluctuations, revealing how the outbreak period varies with the environmental transmission

Making sense of health information technology implementation: A qualitative study protocol

BACKGROUND: Implementing new practices, such as health information technology (HIT), is often difficult due to the disruption of the highly coordinated, interdependent processes (e.g., information exchange, communication, relationships) of providing care in hospitals. Thus, HIT implementation may occur slowly as staff members observe and make sense of unexpected disruptions in care. As a critical organizational function, sensemaking, defined as the social process of searching for answers and meaning which drive action, leads to unified understanding, learning, and effective problem solving -- strategies that studies have linked to successful change. Project teamwork is a change strategy increasingly used by hospitals that facilitates sensemaking by providing a formal mechanism for team members to share ideas, construct the meaning of events, and take next actions. METHODS: In this longitudinal case study, we aim to examine project teams' sensemaking and action as the team prepares to implement new information technology in a tiertiary care hospital. Based on management and healthcare literature on HIT implementation and project teamwork, we chose sensemaking as an alternative to traditional models for understanding organizational change and teamwork. Our methods choices are derived from this conceptual framework. Data on project team interactions will be prospectively collected through direct observation and organizational document review. Through qualitative methods, we will identify sensemaking patterns and explore variation in sensemaking across teams. Participant demographics will be used to explore variation in sensemaking patterns. DISCUSSION: Outcomes of this research will be new knowledge about sensemaking patterns of project teams, such as: the antecedents and consequences of the ongoing, evolutionary, social process of implementing HIT; the internal and external factors that influence the project team, including team composition, team member interaction, and interaction between the project team and the larger organization; the ways in which internal and external factors influence project team processes; and the ways in which project team processes facilitate team task accomplishment. These findings will lead to new methods of implementing HIT in hospitals

Brain energy rescue:an emerging therapeutic concept for neurodegenerative disorders of ageing

The brain requires a continuous supply of energy in the form of ATP, most of which is produced from glucose by oxidative phosphorylation in mitochondria, complemented by aerobic glycolysis in the cytoplasm. When glucose levels are limited, ketone bodies generated in the liver and lactate derived from exercising skeletal muscle can also become important energy substrates for the brain. In neurodegenerative disorders of ageing, brain glucose metabolism deteriorates in a progressive, region-specific and disease-specific manner — a problem that is best characterized in Alzheimer disease, where it begins presymptomatically. This Review discusses the status and prospects of therapeutic strategies for countering neurodegenerative disorders of ageing by improving, preserving or rescuing brain energetics. The approaches described include restoring oxidative phosphorylation and glycolysis, increasing insulin sensitivity, correcting mitochondrial dysfunction, ketone-based interventions, acting via hormones that modulate cerebral energetics, RNA therapeutics and complementary multimodal lifestyle changes

The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates

The CD209 gene family that encodes C-type lectins in primates includes CD209 (DC-SIGN), CD209L (L-SIGN) and CD209L2. Understanding the evolution of these genes can help understand the duplication events generating this family, the process leading to the repeated neck region and identify protein domains under selective pressure. We compiled sequences from 14 primates representing 40 million years of evolution and from three non-primate mammal species. Phylogenetic analyses used Bayesian inference, and nucleotide substitutional patterns were assessed by codon-based maximum likelihood. Analyses suggest that CD209 genes emerged from a first duplication event in the common ancestor of anthropoids, yielding CD209L2 and an ancestral CD209 gene, which, in turn, duplicated in the common Old World primate ancestor, giving rise to CD209L and CD209. K(A)/K(S) values averaged over the entire tree were 0.43 (CD209), 0.52 (CD209L) and 0.35 (CD209L2), consistent with overall signatures of purifying selection. We also assessed the Toll-like receptor (TLR) gene family, which shares with CD209 genes a common profile of evolutionary constraint. The general feature of purifying selection of CD209 genes, despite an apparent redundancy (gene absence and gene loss), may reflect the need to faithfully recognize a multiplicity of pathogen motifs, commensals and a number of self-antigen

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.

Plant-derived lignans, consumed daily by most individuals, are thought to protect against cancer and other diseases1; however, their bioactivity requires gut bacterial conversion to enterolignans2. Here, we dissect a four-species bacterial consortium sufficient for all five reactions in this pathway. A single enzyme (benzyl ether reductase, encoded by the gene ber) was sufficient for the first two biotransformations, variable between strains of Eggerthella lenta, critical for enterolignan production in gnotobiotic mice and unique to Coriobacteriia. Transcriptional profiling (RNA sequencing) independently identified ber and genomic loci upregulated by each of the remaining substrates. Despite their low abundance in gut microbiomes and restricted phylogenetic range, all of the identified genes were detectable in the distal gut microbiomes of most individuals living in northern California. Together, these results emphasize the importance of considering strain-level variations and bacterial co-occurrence to gain a mechanistic understanding of the bioactivation of plant secondary metabolites by the human gut microbiome