Medical SANSformers: Training self-supervised transformers without attention for Electronic Medical Records

We leverage deep sequential models to tackle the problem of predicting healthcare utilization for patients, which could help governments to better allocate resources for future healthcare use. Specifically, we study the problem of \textit{divergent subgroups}, wherein the outcome distribution in a smaller subset of the population considerably deviates from that of the general population. The traditional approach for building specialized models for divergent subgroups could be problematic if the size of the subgroup is very small (for example, rare diseases). To address this challenge, we first develop a novel attention-free sequential model, SANSformers, instilled with inductive biases suited for modeling clinical codes in electronic medical records. We then design a task-specific self-supervision objective and demonstrate its effectiveness, particularly in scarce data settings, by pre-training each model on the entire health registry (with close to one million patients) before fine-tuning for downstream tasks on the divergent subgroups. We compare the novel SANSformer architecture with the LSTM and Transformer models using two data sources and a multi-task learning objective that aids healthcare utilization prediction. Empirically, the attention-free SANSformer models perform consistently well across experiments, outperforming the baselines in most cases by at least $\sim 10$\%. Furthermore, the self-supervised pre-training boosts performance significantly throughout, for example by over $\sim 50$\% (and as high as $800$\%) on $R^2$ score when predicting the number of hospital visits.Comment: 25 pages, 8 figures, 5 tables, Submitted to a journa

Analgesic purchases among older adults - a population-based study

Background: Pain is a frequent and inevitable factor affecting the quality of life among older people. Several studies have highlighted the ineffectiveness of treating chronic pain among the aged population, and little is known about the prevalence of analgesics administration among community-dwelling older adults. The objective was to examine older adults' prescription analgesic purchases in relation to SF-36 pain in a population-based setting. Methods: One thousand four hundred twenty community-dwelling citizens aged 62-86 years self-reported SF-36 bodily pain (pain intensity and pain-related interference) scores for the previous 4 weeks. The Social Insurance Institution of Finland register data on analgesic purchases for 6 months prior to and 6 months after the questionnaire data collection were considered. Special interest was focused on factors related to opioid purchases. Results: Of all participants, 84% had purchased prescription analgesics during 1 year. NSAIDs were most frequently purchased (77%), while 41% had purchased paracetamol, 32% opioids, 17% gabapentinoids, and 7% tricyclic antidepressants. Age made no marked difference in purchasing prevalence. The number of morbidities was independently associated with analgesic purchases in all subjects and metabolic syndrome also with opioid purchases in subjects who had not reported any pain. Discussion: Substantial NSAID and opioid purchases emerged. The importance of proper pain assessment and individual deliberation in terms of analgesic contraindications and pain quality, as well as non-pharmacological pain management, need to be highlighted in order to optimize older adults' pain management.Peer reviewe

A test of the effort equalization hypothesis in children with cerebral palsy who have an asymmetric gait

Healthy people can walk nearly effortlessly thanks to their instinctively adaptive gait patterns that tend to minimize metabolic energy consumption. However, the economy of gait is severely impaired in many neurological disorders such as stroke or cerebral palsy (CP). Moreover, self-selected asymmetry of impaired gait does not seem to unequivocally coincide with the minimal energy cost, suggesting the presence of other adaptive origins. Here, we used hemiparetic CP gait as a model to test the hypothesis that pathological asymmetric gait patterns are chosen to equalize the relative muscle efforts between the affected and unaffected limbs. We determined the relative muscle efforts for the ankle and knee extensors by relating extensor joint moments during gait to maximum moments obtained from all-out hopping reference test. During asymmetric CP gait, the unaffected limb generated greater ankle (1.36 +/- 0.15 vs 1.17 +/- 0.16 Nm/kg, p = 0.002) and knee (0.74 +/- 0.33 vs 0.44 +/- 0.19 Nm/kg, p = 0.007) extensor moments compared with the affected limb. Similarly, the maximum moment generation capacity was greater in the unaffected limb versus the affected limb (ankle extensors: 1.81 +/- 0.39 Nm/kg vs 1.51 +/- 0.34 Nm/kg, p = 0.033; knee extensors: 1.83 +/- 0.37 Nm/kg vs 1.34 +/- 0.38 Nm/kg, p = 0.021) in our force reference test. As a consequence, no differences were found in the relative efforts between unaffected and affected limb ankle extensors (77 +/- 12% vs 80 +/- 16%, p = 0.69) and knee extensors (41 +/- 17% vs 38 +/- 23%, p = 0.54). In conclusion, asymmetric CP gait resulted in similar relative muscle efforts between affected and unaffected limbs. The tendency for effort equalization may thus be an important driver of self-selected gait asymmetry patterns, and consequently advantageous for preventing fatigue of the weaker affected side musculature.Peer reviewe

The impact of host metapopulation structure on the population genetics of colonizing bacteria

Many key bacterial pathogens are frequently carried asymptomatically, and the emergence and spread of these opportunistic pathogens can be driven, or mitigated, via demographic changes within the host population. These inter-host transmission dynamics combine with basic evolutionary parameters such as rates of mutation and recombination, population size and selection, to shape the genetic diversity within bacterial populations. Whilst many studies have focused on how molecular processes underpin bacterial population structure, the impact of host migration and the connectivity of the local populations has received far less attention. A stochastic neutral model incorporating heightened local transmission has been previously shown to fit closely with genetic data for several bacterial species. However, this model did not incorporate transmission limiting population stratification, nor the possibility of migration of strains between subpopulations, which we address here by presenting an extended model. We study the consequences of migration in terms of shared genetic variation and show by simulation that the previously used summary statistic, the allelic mismatch distribution, can be insensitive to even large changes in microepidemic and migration rates. Using likelihood-free inference with genotype network topological summaries we fit a simpler model to commensal and hospital samples from the common nosocomial pathogens Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Enterococcus faecium. Only the hospital data for E. faecium display clearly marked deviations from the model predictions which may be attributable to its adaptation to the hospital environment

Ensemble approach to predict specificity determinants: benchmarking and validation

<p>Abstract</p> <p>Background</p> <p>It is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking protocol was employed to provide a reliable evaluation of methods which predict the specificity determining sites. Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results.</p> <p>Results</p> <p>It was shown that the analysis of structural characteristics of predicted specificity determining sites might provide the means to validate their prediction accuracy. For example, we found that for smaller distances it holds true that the more reliable the prediction method is, the closer predicted specificity determining sites are to each other and to the ligand.</p> <p>Conclusion</p> <p>We observed certain similarities of structural features between predicted and actual subsites which might point to their functional relevance. We speculate that majority of the identified potential specificity determining sites might be indirectly involved in specific interactions and could be ideal target for mutagenesis experiments.</p

OXA1L mutations cause mitochondrial encephalopathy and a combined oxidative phosphorylation defect

OXA1, the mitochondrial member of the YidC/Alb3/Oxa1 membrane protein insertase family, is required for the assembly of oxidative phosphorylation complexes IV and V in yeast. However, depletion of human OXA1 (OXA1L) was previously reported to impair assembly of complexes I and V only. We report a patient presenting with severe encephalopathy, hypotonia and developmental delay who died at 5 years showing complex IV deficiency in skeletal muscle. Whole exome sequencing identified biallelic OXA1L variants (c.500507dup, p.(Ser170Glnfs*18) and c.620G>T, p.(Cys207Phe)) that segregated with disease. Patient muscle and fibroblasts showed decreased OXA1L and subunits of complexes IV and V. Crucially, expression of wild-type human OXA1L in patient fibroblasts rescued the complex IV and V defects. Targeted depletion of OXA1L in human cells or Drosophila melanogaster caused defects in the assembly of complexes I, IV and V, consistent with patient data. Immunoprecipitation of OXA1L revealed the enrichment of mtDNA-encoded subunits of complexes I, IV and V. Our data verify the pathogenicity of these OXA1L variants and demonstrate that OXA1L is required for the assembly of multiple respiratory chain complexes.Peer reviewe

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages

Objectives ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. Methods We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. Results Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. Conclusions There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html

Normal growth and intravascular volume status with good metabolic control during peritoneal dialysis in infancy

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