polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

Subjective sleep quality and fatigue assessment in Polish adult patients with primary immunodeficiencies: A pilot study

Introduction

Primary immunodeficiencies (PIDs) are clinically heterogeneous disorders caused by abnormalities in the immune system. However, PIDs are genetically determined and may occur at any age from early childhood to elderly age. Due to chronic patterns, the risk of malignancy and organ damage in patients with PIDs may affect any aspect of life, including sleep patterns. To our knowledge, the prevalence of insomnia and subjective sleep quality have not been investigated in patients with PIDs. Therefore, this pilot study was conducted to investigate sleep quality, the prevalence of sleep disturbances, and fatigue in adult patients with PIDs in Poland.

Methods

All participants were surveyed using the Athens Insomnia Scale, Pittsburgh Sleep Quality Index, Fatigue Severity Scale, and a questionnaire concerning general health and demographic data. We included 92 participants: 48 women (52.2%) and 44 men (47.8%).

Results

Participants' mean age was 41.9 ± 13.9 years. The mean sleep duration was 7.0 ± 1.5 hours, and the mean sleep latency was 41.2 ± 53.1 minutes. Additionally, 44.6% of patients (n=41) had symptoms of insomnia and 44.6% (n=42) had poor sleep quality. Less than one-fourth (n=22; 23.9%) of the patients reported the use of sleeping pills; moreover, clinically significant fatigue was reported in 52.2% (n=48).

Discussion

Our investigation provides insight into the problem of sleep disturbances in patients with PIDs. Data have demonstrated that sleeping disorders with concomitant fatigue are common in patients with PID. Further studies are needed to determine the determinants of poor sleep quality in this specific group of patients.

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American Fundulus killifish

BACKGROUND

Whole-genome sequencing data from wild-caught individuals of closely related North American killifish species (Fundulus xenicus, Fundulus catenatus, Fundulus nottii, and Fundulus olivaceus) were obtained using long-read Oxford Nanopore Technology (ONT) PromethION and short-read Illumina platforms.

FINDINGS

Draft de novo reference genome assemblies were generated using a combination of long and short sequencing reads. For each species, the PromethION platform was used to generate 30-45× sequence coverage, and the Illumina platform was used to generate 50-160× sequence coverage. Illumina-only assemblies were fragmented with high numbers of contigs, while ONT-only assemblies were error prone with low BUSCO scores. The highest N50 values, ranging from 0.4 to 2.7 Mb, were from assemblies generated using a combination of short- and long-read data. BUSCO scores were consistently >90% complete using the Eukaryota database.

CONCLUSIONS

High-quality genomes can be obtained from a combination of using short-read Illumina data to polish assemblies generated with long-read ONT data. Draft assemblies and raw sequencing data are available for public use. We encourage use and reuse of these data for assembly benchmarking and other analyses.

Polishing mechanism of light-initiated dental composite: Geometric optics approach

BACKGROUND/PURPOSE

For light-initiated dental hybrid composites, reinforcing particles are much stiffer than the matrix, which makes the surface rugged after inadequate polish and favors bacterial adhesion and biofilm redevelopment. The aim of the study was to investigate the polishing mechanism via the geometric optics approach.

METHODS

We defined the polishing abilities of six instruments using the obtained gloss values through the geometric optics approach (micro-Tri-gloss with 20°, 60°, and 85° measurement angles). The surface texture was validated using a field emission scanning electron microscope (FE-SEM). Based on the gloss values, we sorted polishing tools into three abrasive levels, and proposed polishing sequences to test the hypothesis that similar abrasive levels would leave equivalent gloss levels on dental composites.

RESULTS

The three proposed, tested polishing sequences included: S1, Sof-Lex XT coarse disc, Sof-Lex XT fine disc, and OccluBrush; S2, Sof-Lex XT coarse disc, Prisma Gloss polishing paste, and OccluBrush; and S3, Sof-Lex XT coarse disc, Enhance finishing cups, and OccluBrush. S1 demonstrated significantly higher surface gloss than the other procedures (p < 0.05). The surface textures (FE-SEM micrographs) correlated well with the obtained gloss values.

CONCLUSION

Nominally similar abrasive abilities did not result in equivalent polish levels, indicating that the polishing tools must be evaluated and cannot be judged based on their compositions or abrasive sizes. The geometric optic approach is an efficient and nondestructive method to characterize the polished surface of dental composites.

Motivation towards medical career choice and future career plans of Polish medical students

This longitudinal study aimed at investigating Polish medical students' career choice motivation, factors influencing specialty choices, professional plans and expectations. The same cohort of students responded to the same questionnaire, at the end of Year 1 and Year 6. The Chi-square, Mann-Whitney U tests and logistic regression were used in analyses. The results showed that altruistic and scientific reasons were the main motives for choosing a medical career. The motives remained stable over time. The effect of gender on altruistic motivation was stronger at the end of the study, with females' rating higher. The most favored career paths were associated with non-primary care specializations and work in a hospital. Results of the multivariate logistic regression showed that primary care specializations were more attractive to females, final year students, those from small agglomerations, and those less concerned about high earnings. Preferences regarding sector of work were formed at later stages of training. A preference shift was observed, between Year 1 and Year 6, towards favoring work in the public sector. Predictors of the desire to work in the public sector were: being a male and the final year student, paying less attention to high earnings, wanting certainty of finding work, having a stronger need for interesting and socially important work. A significant decline in the level of interest in seeking employment abroad was observed with the progress of studies. Our findings are likely to provide useful information for educators, policy planners and policy makers.

Population-based centile curves for triceps, subscapular, and abdominal skinfold thicknesses in Polish children and adolescents--the OLAF study

Skinfold thicknesses are used as valid anthropometric indicators of regional body fatness. Actual population-based values for skinfold thicknesses for Polish children are not available. The purpose of this study was to provide population-based values for triceps, subscapular, and abdominal skinfold thicknesses in healthy children and adolescents. A total number of 17,416 boys and girls aged 6.5-18.5 years, randomly selected from whole Polish population of children and adolescents, were enrolled in the study. Skinfold thicknesses (triceps, subscapular, and abdominal) were measured using Harpenden skinfold caliper. All measurements were taken after the training of participating investigators. The LMS method was used to fit percentile curves across age for each skinfold. Q tests for fit were used to assess the global goodness of fit of our final models. The study shows for the first time smoothed population-based values of body fat distribution indices for Polish children and adolescents 7-18 years of age. Reported skinfold centiles are higher compared to previously established for Warsaw children and very close to the actual US data.

CONCLUSION

Our study provided for the first time population-based values for skinfold thicknesses evaluation in a way allowing to calculate reliable Z scores. The early detection of abnormal fat stores, using our population-based values and respective Z scores, may be now implemented for practice.