A reference-free algorithm discovers regulation in the plant transcriptome.

Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered differential homolog expression during maize pollen development, and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from hybrid parental haplotypes, without the use of alignment to a reference genome.

SPLASH2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads.

SPLASH is an unsupervised, reference-free, and unifying algorithm that discovers regulated sequence variation through statistical analysis of k-mer composition, subsuming many application-specific methods. Here, we introduce SPLASH2, a fast, scalable implementation of SPLASH based on an efficient k-mer counting approach. SPLASH2 enables rapid analysis of massive datasets from a wide range of sequencing technologies and biological contexts, delivering unparalleled scale and speed. The SPLASH2 algorithm unveils new biology (without tuning) in single-cell RNA-sequencing data from human muscle cells, as well as bulk RNA-seq from the entire Cancer Cell Line Encyclopedia (CCLE), including substantial unannotated alternative splicing in cancer transcriptome. The same untuned SPLASH2 algorithm recovers the BCR-ABL gene fusion, and detects circRNA sensitively and specifically, underscoring SPLASH2's unmatched precision and scalability across diverse RNA-seq detection tasks.

Relative bioavailability of budesonide/glycopyrrolate/formoterol fumarate triple therapy delivered using next generation propellants with low global warming potential.

INTRODUCTION: The climate crisis poses an immediate threat to human health and well-being, demanding urgent adaptions across sectors, including healthcare. The development of pressurized metered dose inhalers (MDIs) with greater sensitivity to the climate emergency using novel propellants with lower global warming potentials (GWPs), but comparable pharmacokinetic (PK) parameters to currently marketed MDIs, is a vital step toward reducing the impact of healthcare for respiratory disorders on climate change. This study evaluated the relative bioavailabilities of the individual components of a fixed-dose combination of budesonide/glycopyrrolate/formoterol fumarate (BGF) 160/9/4.8 µg per actuation between three different propellant formulations. METHODS: Healthy male participants (aged 18-60 years) were randomized into a single-blind, three-period, single-dose, single-center, crossover study (NCT04600505). The PK and safety and tolerability profiles of BGF MDI formulated with two novel propellants with low GWP (hydrofluoroolefin-1234ze [HFO]; hydrofluorocarbon-152a [HFC]) were compared with BGF MDI formulated with the propellant used in the currently marketed reference product (hydrofluoroalkane-134a [HFA]). The study included a screening period, three treatment periods (with 3- to 7-day washout periods between each dose), and a follow-up. The primary PK parameters assessed were maximum observed plasma concentration (Cmax), area under the plasma concentration curve (AUC) from time zero extrapolated to infinity (AUCinf), and AUC from time zero to the time of the last quantifiable analyte concentration (AUClast). The study was not powered to statistically demonstrate bioequivalence. RESULTS: Forty-seven participants completed the study, and 24 participants were evaluable for PK assessments. Systemic exposure, based on geometric mean ratios (90% confidence interval), to each BGF component from the test propellants delivered in a standard MDI was comparable with the reference propellant for AUClast (HFO vs. HFA: budesonide, 107.30 [94.53, 121.90]; glycopyrrolate, 106.10 [86.18, 130.60]; formoterol, 98.13 [86.44, 111.40]; HFC vs. HFA: budesonide, 98.80 [84.59, 115.40]; glycopyrrolate, 99.71 [80.84, 123.00]; formoterol, 107.00 [88.82, 128.90]); AUCinf (where evaluable) and Cmax followed the same trend. There were no serious adverse events or adverse events leading to treatment discontinuation. No new safety signals were observed. CONCLUSIONS: Systemic BGF component exposure was similar for both test propellants (HFO and HFC) compared with the HFA reference propellant, with an acceptable safety profile in the studied population. Therefore, both novel low GWP propellants show strong potential as candidates for development of MDIs with greater sensitivity to the climate crisis, a vital step toward ameliorating the detrimental impact of healthcare on the environment. Further investigation in larger studies is warranted.

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.

The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54-58 h, using considerably more memory.

The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

SUMMARY: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools. AVAILABILITY AND IMPLEMENTATION: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CoLoRd: compressing long reads.

The cost of maintaining exabytes of data produced by sequencing experiments every year has become a major issue in today's genomic research. In spite of the increasing popularity of third-generation sequencing, the existing algorithms for compressing long reads exhibit a minor advantage over the general-purpose gzip. We present CoLoRd, an algorithm able to reduce the size of third-generation sequencing data by an order of magnitude without affecting the accuracy of downstream analyses.

VCFShark: how to squeeze a VCF file.

SUMMARY: Variant Call Format (VCF) files with results of sequencing projects take a lot of space. We propose the VCFShark, which is able to compress VCF files up to an order of magnitude better than the de facto standards (gzipped VCF and BCF). The advantage over competitors is the greatest when compressing VCF files containing large amounts of genotype data. The processing speeds up to 100 MB/s and main memory requirements lower than 30 GB allow to use our tool at typical workstations even for large datasets. AVAILABILITY AND IMPLEMENTATION: https://github.com/refresh-bio/vcfshark. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Monitoring of the Static and Dynamic Displacements of Railway Bridges with the Use of Inertial Sensors.

In the case of the monitoring of bridges, the determination of vertical displacements is one of the most important issues. A new measuring system has been developed and implemented for assessment of railway bridges based on measurements of the structural response to passing trains. The system uses inertial sensors: Inclinometers and accelerometers that do not need any referential points. The system records signals related to the passage of a train over a monitored bridge. The signals from inclinometers before the train's entry are used to determine the static movement. Integrated signals from inclinometers and accelerometers are used to determine dynamic displacements when the train goes through the bridge. Signals from inclinometers are used to determine the so-called "quasi-static" component of the displacement and signal from the accelerometer to determine the dynamic component. Field tests have been carried out on a viaduct along a high-speed railway line. Periodic comparative measurements are carried out using a Total Station to verify static measurements and using inductive sensors to verify dynamic measurements. Tests of the system carried out so far have proven its usefulness for monitoring bridges in a high-speed railway (up to 200 km/h) with high accuracy while determining dynamic displacements.

Kmer-db: instant evolutionary distance estimation.

Summary: Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor. Availability and implementation: https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db. Supplementary information: Supplementary data are available at Bioinformatics online.

KMC 3: counting and manipulating k-mer statistics.

SUMMARY: Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems. AVAILABILITY AND IMPLEMENTATION: Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc . CONTACT: sebastian.deorowicz@polsl.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KMC 2: fast and resource-frugal k-mer counting.

MOTIVATION: Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory. RESULTS: We present a novel method for k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM. Our disk-based method bears some resemblance to MSPKmerCounter, yet replacing the original minimizers with signatures (a carefully selected subset of all minimizers) and using (k, x)-mers allows to significantly reduce the I/O and a highly parallel overall architecture allows to achieve unprecedented processing speeds. For example, KMC 2 counts the 28-mers of a human reads collection with 44-fold coverage (106 GB of compressed size) in about 20 min, on a 6-core Intel i7 PC with an solid-state disk.

Pharmacological consequences of inhaled drug delivery to small airways in the treatment of asthma.

Small peripheral airways are an important target for the anti-inflammatory treatment of asthma. To make anti-inflammatory drugs (inhaled corticosteroids [ICS]) effectively reach small airways, they should be delivered using inhalation techniques containing high proportions of fine or super-fine particles. Higher proportions of fine particles are associated with higher systemic absorption of ICS leading to an increased risk of endogenous cortisol suppression. Ciclesonide, despite the highest proportion of fine and super-fine particle fractions, is the only ICS not associated with an increased risk of systemic adverse effects, including cortisol suppression. In contrary to ICS, bronchodilators should not be administered to peripheral airways. This does not improve their efficacy and may increase their risk of cardiotoxicity. Thus, from a pharmacological point of view and the theory of aerosols' deposition, fixed combinations of ICS and long-acting beta agonists are always suboptimal. In many cases, the best solution may be to use fine-particle ciclesonide and a non-fine particle beta agonist administered from separate inhalers.

Asthma-chronic obstructive pulmonary disease overlap syndrome in Poland. Findings of an epidemiological study.

INTRODUCTION: Recent years have seen an increased interest in asthma-chronic obstructive pulmonary disease (COPD) overlap syndrome (ACOS). AIM: In 2012, Takeda Polska conducted a non-interventional epidemiological study aimed at identifying the typical phenotype of ACOS patients receiving pulmonary care. MATERIAL AND METHODS: The study enrolled a total of 12,103 of smoking patients above 45 years of age (mean age: 61.5 years; mean duration of smoking: 28.4 pack-years). A total of 68.6% of patients represented the frequent-exacerbation phenotype (mean number of exacerbations during 12 months: 2.11), and 56.4% of patients from the group comprising 12,103 participants were hospitalized at least once during their lifetime due to a respiratory system disease (mean number: 3.82 ±3.76). RESULTS: The most commonly found asthma symptoms included paroxysmal dyspnoea with wheezing, and good response to inhaled steroids. The most frequently identified COPD-associated symptoms were: long-lasting reduction in forced expiratory volume in 1 s (FEV1) (< 80% after administering a bronchodilator) and chronic productive cough. Eighty-five percent of patients were diagnosed with concomitant diseases, predominantly arterial hypertension (62.9%) and metabolic diseases (metabolic syndrome, obesity, type 2 diabetes - 46.4% in total). CONCLUSIONS: A clinically severe course of ACOS and the presence of concomitant diseases should be regarded as factors justifying an individual selection of inhalation therapy which specifically takes into account anti-inflammatory treatment and patient safety.