Pangenome graph construction from genome alignments with Minigraph-Cactus

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Towards Fast Plume Source Estimation with a Mobile Robot

The estimation of the parameters of an odour source is of high relevance for multiple applications, but it can be a slow and error prone process. This work proposes a fast particle filter-based method for source term estimation with a mobile robot. Two strategies are implemented in order to reduce the computational cost of the filter and increase its accuracy: firstly, the sampling process is adapted by the mobile robot in order to optimise the quality of the data provided to the estimation process; secondly, the filter is initialised only after collecting preliminary data that allow limiting the solution space and use a shorter number of particles than it would be normally necessary. The method assumes a Gaussian plume model for odour dispersion. This models average odour concentrations, but the particle filter was proved adequate to fit instantaneous concentration measurements to that model, while the environment was being sampled. The method was validated in an obstacle free controlled wind tunnel and the validation results show its ability to quickly converge to accurate estimates of the plume’s parameters after a reduced number of plume crossings.

Long term prognosis of acute pulmonary embolism

BACKGROUND

Acute pulmonary embolism (PE) can be fatal if left untreated. Long-term prognosis of acute PE in the 21st century has not been fully reported. We aimed to determine the long-term prognosis of patients hospitalized with acute PE and compare survivalof patients with idiopathic and secondary PE.

MATERIALS AND METHODS

We retrospectively analysed a cohort of hospitalized patients with acute PE between 2006 and 2013.

EXCLUSION CRITERIA

<18 years, venous embolism of non-pulmonary veins, chronic thromboembolic pulmonary hypertension, and presumptive diagnosis without image confirmation. Only patients with a first PE episode were included. End-point: all-cause mortality. Patients were compared according to PE aetiology: idiopathic, secondary to neoplastic conditions and secondary to non-neoplastic conditions. A Cox-regression analysis was used to study the prognostic impact of PE aetiology.

RESULTS

We studied 872 hospitalized acute PE patients. Median age 70 years, 56.9% were women. PE was idiopathic in 376 (43.1%), secondary to a neoplastic condition in 284 (32.6%) and secondary to a condition other than neoplasia in 212 (24.3%). Patients were followed for a median 25 months period and 508 (58.3%) died. Patients with PE attributed to a neoplastic condition had the worst survival. Patients with idiopathic PE had a multivariate-adjusted HR of mortality of 1.46 (1.08-1.99) during the over 2-year follow-up period when compared to those with acute PE attributed to a non-neoplastic condition.

CONCLUSIONS

Patients with idiopathic acute PE have an almost 50% higher death risk in a median 2-year follow-up period than those with acute PE secondary to a condition other than neoplasia.

Influence of HOTAIR rs920778 and rs12826786 genetic variants on prostate cancer risk and progression-free survival

Aim: Evaluate the impact of the single nucleotide polymorphisms rs920778 and rs12826786 in the long noncoding RNA HOTAIR in the susceptibility and prognosis of prostate cancer (PCa) patients. Patients & methods: HOTAIR single nucleotide polymorphisms were genotyped by restriction fragment length polymorphism in 151 PCa cases and 180 cancer-free controls. Odds ratio, 95% CIs and prognostic significance were calculated. Results: Our data showed no statistically significant associations between HOTAIR polymorphic variants in rs920778 and rs12826786 and PCa susceptibility. However, the CC genotype in rs12826786 was significantly associated with shorter biochemical recurrence-free survival in pT3-stage PCa patients. Conclusion: Our results indicate that HOTAIR rs12826786 CC genotype may be an independent prognostic biomarker in a particular subset of PCa tumors.

Principais alterações no leite por agentes causadores de mastite no rebanho caprino dos estados de Minas Gerais e Rio de Janeiro

A mastite subclínica caprina ocasiona prejuízos econômicos em decorrência do descarte, dos gastos com medidas terapêuticas e da redução da quantidade e qualidade do leite e seus derivados. Nesse estudo, 129 amostras de leite de cabra in natura, provenientes de 11 propriedades foram avaliadas pelo teste da caneca telada, California Mastitis Test (CMT), exame bacteriológico, pesquisa de Mycoplasma spp. e pela determinação dos parâmetros físico-químicos. No teste da caneca telada e no CMT, 3,1% e 4,6% das amostras foram positivas, respectivamente. No exame bacteriológico, 57,4% das amostras foram positivas e o patógeno mais frequente foi Staphylococcus coagulase negativa com 56% das cepas resistentes à penicilina e 100% de sensíveis à gentamicina. Mycoplasma spp. não foi identificado nas amostras. O diagnóstico da mastite subclínica pelo CMT e pelo exame bacteriológico diferiu de forma significativa e não houve associação entre o número de UFC/mL obtidas no exame microbiológico e o resultado do CMT (Qui-quadrado p < 0,05). Os parâmetros físico-químicos diferiram significativamente entre os rebanhos (ANOVA, Tukey-Kramer, p < 0,05) e a gordura foi o constituinte que demonstrou maior amplitude, sendo que 63,4% dos rebanhos apresentaram os valores abaixo do exigido pela legislação brasileira. Não houve associação significativa entre a presença de mastite diagnosticada pelo exame bacteriológico e os valores obtidos para os parâmetros físico-químicos (t-Student p > 0,05). Com base nos resultados obtidos, recomenda-se a associação do exame bacteriológico quando na utilização do CMT para diagnóstico da mastite subclínica caprina.

Observer design in switching control of neuromuscular blockade: clinical cases

This paper concerns the application of multiple model switched methods to the control of neuromuscular blockade of patients undergoing anaesthesia. Since the model representing the neuromuscular blockade process is subject to a high level of uncertainty due both to inter-patient variability and time variations, switched methods provide the adaptation capability needed to achieve the desired performance. The paper contributions are twofold: first, it is shown that, for the type of process control problem considered, the design of the associated observer must be carefully performed. Guidelines are provided for adequate selection of the characteristic polynomial defining the observer error dynamics. Second, clinical results using atracurium as blocking agent are reported in order to illustrate the use of the proposed control structure in actual clinical practice.

Control of Neuromuscular Blockade in the Presence of Sensor Faults

The problem of embedding sensor fault tolerance in feedback control of neuromuscular blockade is considered. For tackling interruptions of feedback measurements, a structure based upon Bayesian inference as well as a predictive filter is proposed. This algorithm is general and can be applied to different situations. Here, it is incorporated in an adaptive automatic system for feedback control of neuromuscular blockade using continuous infusion of muscle relaxants. A significant contribution consists in the experimental clinical testing of the algorithm in patients undergoing surgery.

Hipocrates: a robust system for the control of neuromuscular blockade

OBJECTIVE

Development of an automatic system (software package Hipocrates) for the control of neuromuscular blockade by continuous infusion of the non-depolarising types of muscle relaxant drugs presently used in anaesthesia, namely atracurium, cisatracurium, vecuronium and rocuronium.

METHODS

Hipocrates incorporates control strategies based upon classical, adaptive and robust control, as well as a wide range of noise reduction techniques and on-line adaptation to patient-specific characteristics. Therefore, the system provides strong robustness to inter- and intra-individual variability of the patients responses or unexpected circumstances and adaptation to the individual requirements.

RESULTS

The control system is easy to set up and to use in a clinical environment. It consists of a portable PC computer, a Datex AS/3 NMT sensor and a B/Braun compact perfusion pump. In the simulation mode the software package incorporates sophisticated generation of pharmacokinetic/pharmacodynamic models driven by simulated drug administration regimes (bolus, continuous infusion and a combination of both).

CONCLUSIONS

Hipocrates is an advanced standalone application for the control of neuromuscular blockade with a friendly graphic interface. It has been extensively validated, and it can be used on patients undergoing surgery as well as for simulation studies. Therefore Hipocrates also provides an excellent environment for education and training purposes.