WFA-GPU: gap-affine pairwise read-alignment using GPUs.

MOTIVATION: Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like those produced by PacBio and Nanopore technologies. The recently proposed wavefront alignment (WFA) algorithm paves the way for more efficient alignment tools, improving time and memory complexity over previous methods. However, high-performance computing (HPC) platforms require efficient parallel algorithms and tools to exploit the computing resources available on modern accelerator-based architectures. RESULTS: This paper presents WFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute exact gap-affine alignments based on the WFA algorithm. We present the algorithmic adaptations and performance optimizations that allow exploiting the massively parallel capabilities of modern GPU devices to accelerate the alignment computations. In particular, we propose a CPU-GPU co-design capable of performing inter-sequence and intra-sequence parallel sequence alignment, combining a succinct WFA-data representation with an efficient GPU implementation. As a result, we demonstrate that our implementation outperforms the original multi-threaded WFA implementation by up to 4.3× and up to 18.2× when using heuristic methods on long and noisy sequences. Compared to other state-of-the-art tools and libraries, the WFA-GPU is up to 29× faster than other GPU implementations and up to four orders of magnitude faster than other CPU implementations. Furthermore, WFA-GPU is the only GPU solution capable of correctly aligning long reads using a commodity GPU. AVAILABILITY AND IMPLEMENTATION: WFA-GPU code and documentation are publicly available at https://github.com/quim0/WFA-GPU.

Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples.

BACKGROUND: Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. METHODS AND RESULTS: The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. CONCLUSIONS: We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.

Fast gap-affine pairwise alignment using the wavefront algorithm.

MOTIVATION: Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields. RESULTS: In this article, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory. Furthermore, our algorithm exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code. We evaluate the performance of our algorithm, together with other state-of-the-art implementations. As a result, we demonstrate that the WFA runs 20-300× faster than other methods aligning short Illumina-like sequences, and 10-100× faster using long noisy reads like those produced by Oxford Nanopore Technologies. AVAILABILITY AND IMPLEMENTATION: The WFA algorithm is implemented within the wavefront-aligner library, and it is publicly available at https://github.com/smarco/WFA.

A rapid Soxhlet and mini-SPE method for analysis of polycyclic aromatic hydrocarbons in atmospheric particles.

An analytical method was validated with two reference materials of polycyclic aromatic hydrocarbons in atmospheric particles. Standard reference materials (SRMs) were incorporated into the matrix of unexposed cut quartz filters. The methodology was previously designed and extraction of polycyclic aromatic hydrocarbons (PAHs) from fortified filters was based on a rapid low-cost method, for a low consumption of volume and time. The optimisation combined a low-volume Soxhlet apparatus used in hot Soxhlet mode with a quick clean-up by solid-phase extraction with special cartridges. The quantification of target compounds was performed by gas chromatography/mass spectroscopy in SIM mode. Temperatures of injector and oven program of the GC-MS were also optimised. Experimental variables of both systems were successfully optimised and validated, achieving a robust analytical methodology.

Land use and land cover mapping in wetlands one step closer to the ground: Sentinel-2 versus landsat 8.

Environmental studies with Landsat images have revealed many of the problems faced by wetland ecosystem, which are crucial for the conservation of biodiversity and the natural values of our planet. The study of LULC changes in wetlands through remote sensing constantly helps to identify and combat their main environmental threats improving the conservation of these natural habitats. Starting in mid-2015, the Sentinel-2 satellite opens new possibilities in the field of earth observation thanks to its higher spatial, spectral and temporal resolution becoming a powerful source of information for LULC monitoring in wetland areas. However, researchers may ask them selves to what extent Sentinel-2 is an improvement over Landsat 8 for general purposes. This research test if there is a real difference in the quality of the results delivered by both Sentinel-2 and Landsat 8 imagery when basic classification methods are applied. The study uses Sentinel-2 and Landsat 8 imagery to produce LULC maps in a Mediterranean wetland area applying an object based classification method in order to compare the accuracy and reliability in the surface detected by both satellites. The results show that an object based classification using only the Sentinel-2 and Landsat 8 image information, without band indexes or ancillary data, offers very similar results for most LULC classes, being the overall accuracy around 87-88% with slightly better results when using Sentinel-2. Although using Sentinel-2 leads to an increase in file size and processing times, the analysis of certain LULC classes presents an improvement compared to Landsat 8, detecting more linear and small size elements with a better delineation of image features in the classified map. However, these improvements should not underestimate the value of Landsat imagery in the future since both satellites provide high precision information, so they can and should coexist and be used together to increase data availability in order to have the best possible results in remote sensing research.

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.

As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample. Results have been compared between them and against the NIST Genome in a Bottle (GIAB) variants reference dataset. We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome. SNV, and especially InDel, detection is less reliable in 20% of the genome, and almost unfeasible in the remaining 10%. These findings will aid in choosing the appropriate tools bearing in mind objectives, workload, and computing infrastructure available.

Improving the mining soil quality for a vegetation cover after addition of sewage sludges: inorganic ions and low-molecular-weight organic acids in the soil solution.

We assessed the effects of applying stabilized sewage sludge (SSL) and composted sewage sludge (CLV), at 5 and 10% to an acid mining soil. Limed soil (NCL) amended or not with SSL and CLV was incubated for 47 days. We studied the cations and organic and inorganic anions in the soil solution by means of ion chromatography. Liming led to big increases in Ca(2+) and SO4(2-) and to significant decreases in K(+), Mg(2+), NH4(+) and NO3(-). Addition of both organic amendments increased some cations (NH4(+), K(+), Mg(2+), Na(+)) and anions (Cl(-), NO3(-) only with CLV and PO4(3-) only with SSL) and provided a greater amount of low-molecular-weight organic acids (LMWOAs) (SSL more than CLV). Incubation led to decreases in all cations, particularly remarkable for Ca(2+) and Mg(2+) in SSL-10. A decrease in NH4(+) was associated with variations in NO2(-) and NO3(-) resulting from nitrification reactions. During incubation the LMWOAs content tended to decrease similarly to the cations, especially in SSL-10. Chemometric tools revealed a clear discrimination between SSL, CLV and NCL. Furthermore, treatment effects depended upon dose, mainly in SSL. Amendment nature and dose affect the quality of a mining soil and improve conditions for plant establishment.

1H, 13C NMR studies of new 3-aminophenol isomers linked to pyridinium salts.

(1)H and (13)C NMR spectroscopic data of 20 new non-symmetrical compounds were assigned by a combination of 1D and 2D NMR experiments (DEPT, HSQC, and HMBC). These compounds contain a 4-(N,N-dimethylamino)- or 4-(pyrrolidin-1-yl)pyridinium moiety and a 3-nitro-, 3-amino-, or 3-hydroxyphenyl ring, linked by p-xylene, 4,4'-dimethylbiphenyl, 1,2-bis(p-tolyl)ethane, or 1,4-bis(p-tolyl)butane.

Protecting effect of recycled urban wastes (sewage sludge and wastewater) on ryegrass against the toxicity of pesticides at high concentrations.

Degraded landscapes, like those from abandoned mine areas, could be restored by revegetating them with appropriate plant species, after correction for acidity and improvement by adding exogenous organic material. Application of urban wastes to large areas of derelict land helps in the sustainable development of this landscape. However, the development of plant species in these soils could require in the future the management of possible pests or diseases by pesticide applications which could also affect plant yield. Therefore, ryegrass (Lolium perenne L.) was planted in a limed soil from the mining area of Riotinto (SW Spain), using an indoor pot experiment and the effects of amendment with sewage sludge, as well as irrigation with urban wastewater on plant uptake of the insecticide thiacloprid and the fungicide fenarimol were examined. Ryegrass biomass was reduced up to 3-fold by pesticide application. Fenarimol residues were the highest in soil, while those of thiacloprid were lower in soil and higher in ryegrass. Addition of sewage sludge and irrigation with wastewater led to a reduction of pesticide translocation to the aerial plant parts, representing a lower hazard to ryegrass quality grown in this mine soil.

New non-symmetrical choline kinase inhibitors.

Identification of novel and selective anticancer agents remains an important and challenging goal in pharmacological research. Choline kinase (ChoK) is the first enzyme in the CDP-choline pathway that synthesizes phosphatidylcholine (PC), the major phospholipid in eukaryotic cell membranes. In the present paper, a new family of non-symmetrical monocationic compounds is developed including a 3-aminophenol moiety, bound to 4-(dimethylamino)- or 4-(pyrrolidin-1-yl)pyridinium cationic heads through several linkers. The most promising compounds in these series as ChoK inhibitors are 3f and 4f, while compounds 3c, 3d and 4c are the better antiproliferative agents. The analysis of the biological data observed in the described series of compounds mays represents a platform for the design of more active molecules.

The mechanism of allosteric coupling in choline kinase†α1 revealed by the action of a rationally designed inhibitor.

Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.

Toxic metals from atmospheric particulate matter in food species of tomato (Solanum lycopersicum) and strawberry (Fragaria x ananassa) used in urban gardening. A closed chamber study.

In this work, two plant foods, strawberry and tomato, were subjected to exposure to metals from synthetic airborne particles in a closed chamber experiment. The synthetic particles were obtained in the laboratory. Within the closed chamber, particles were added and recirculated for 4 days in a turbulent air stream, causing deposition on the different parts of the plants. They were evaluated because of their increasingly frequent cultivation in urban gardens of cities. The main objectives were to determine whether the species accumulate metals significantly, which species accumulate the most, and in which parts of the plant. Finally, an attempt was made to differentiate the accumulation of pollutants by surface deposition on leaves and fruits from the adsorbed metals into the leaf or the fruit by their stomata or cuticles. The concentration of heavy metals was quantified in fruits, leaves and the soil after exposure. Metals were evaluated as a whole and individually, both in dry and fresh weight basis. The decrease of particulate matter and metals in the air inside the chamber was also studied in order to evaluate the use of both food species as air purifier by vertical gardens. The concentration of metals in plants (mg kg-1) and airborne particles (mg m-3) was measured by microwave plasma optical emission spectroscopy (MP-AES). For the sake comparison of total amount of metals in the samples concentrations were normalized. Strawberries was the food species that accumulated the largest amount of metals. In a dry weight basis, tomato leaves and strawberry fruits were the parts of the plants with higher accumulation capacity of particles and metals. The potential toxic elements Cd, Ni and Cr in tomato leaves and in strawberry fruits had a higher presence in the interior of the plant system. In a fresh weight basis, the strawberry fruit had the most accumulation capacity for metals.

Non-Invasive Wildlife Disease Surveillance Using Real Time PCR Assays: The Case of the Endangered Galemys pyrenaicus Populations from the Central System Mountains (Extremadura, Spain).

The Iberian desman (Galemys pyrenaicus) is a small semi-aquatic mammal that inhabits mountainous areas from the centre to the north of the Iberian Peninsula and the Pyrenees and is listed as endangered because it has suffered a serious decline. Since 1960, only three species of digeneans (Omphalometra flexuosa, Maritrema pyrenaica and Mathovius galemydis) and two nematodes (Aonchotheca galemydis and Paracuaria hispanica) have been reported from the desman, but no further information on health status and no data from Extremadura has been available. The aim of our study was to characterise the diversity and distribution of parasites and microbiomes of desmans in different areas of the Central System of Extremadura. Between 2019 and 2021 we collected 238 fecal samples and one tissue (intestine) sample that was obtained from a dead desman. DNA templates were processed by commercial or customised real-time PCR using TaqMan probes. Representative data were obtained for Cryptosporidium spp., Omphalometra spp., Eimeria spp., Salmonella spp., Staphylococcus spp. and Leptospira spp. Omphalometra spp. was studied using a newly developed PCR test. The screening of the dead desman allowed us to obtain, for the first time, a partial sequence of the 18SrDNA. This study is the most complete study of the desman, allowing us to identify parasites and the microbiome in populations of G. pyrenaicus using non-invasive sampling.

1H and 13C NMR spectral assignments of pyridinium salts linked to a N-9 or N-3 adenine moiety.

(1)H and (13)C NMR spectral data of 13 new compounds containing a 4-(dimethylamino)- or 4-(pyrrolidin-1-yl)pyridinium moiety linked to the N-9 or N-3 nitrogen atom of an adenine moiety were assigned. 1D and 2D NMR experiments (DEPT, HSQC and HMBC) allowed the unequivocal identification of N-9 and N-3 isomers.

Characterization of 4,5-dihydro-1H-pyrazole derivatives by (13) C NMR spectroscopy.

The (13) C NMR resonances of 19 1-acyl-3-(2-nitro-5-substitutedphenyl)-4,5-dihydro-1H-pyrazoles, and 19 1-acyl-3-(2-amino-5-substituted)-4,5-dihydro-1H-pyrazoles, were completely assigned using the concerted application of one- and two-dimensional NMR experiments (DEPT, gs-HSQC and gs-HMBC).

NMR spectroscopic characterization of new 2,3-dihydro-1,3,4-thiadiazole derivatives.

The (1) H and (13) C NMR resonances of twenty-seven 2,2-dimethyl-5-(2-nitrophenyl-5-substituted)-2,3-dihydro-1,3,4-thiadiazoles, and twenty-seven 3-acyl-5-(2-amino-5-substituted)-2,2-dimethyl-2,3-dihydro-1,3,4-thiadiazoles were assigned completely using the concerted application of one-dimensional and two-dimensional experiments (DEPT, HMQC and HMBC). NOESY experiments, X-ray crystallography and conformational analysis confirm the preferred conformation of these compounds.

Fabrication of paper-based microfluidic devices using a 3D printer and a commercially-available wax filament.

In this work, we developed an alternative manufacturing paper-based microfluidics method through 3D printing and wax filament. Microfluidic paper-based analytical devices (µPADs) are low-cost and easy-to-manufacture tools used for various chemical and biological analyses and studies. Paper-based microfluidics with wax has been limited as the manufacturers have discontinued most wax printing equipment. We aim to develop a low-cost and accessible manufacturing method that can replace conventional wax-on paper-based microfluidic manufacturing methods. Using highly available commercial 3D printing technology and wax filament, we could create hydrophobic wax barriers on the surface of different paper types. The properties and limits of this manufacturing method were characterized. Moreover, using this paper-based microfluidic manufacturing method, we were able to measure dopamine electrochemically using µPAD as a passive flow-based method in concentrations as low as 1 nM using injections as small as 15 µL.

Assessment of the sequential principal component analysis chemometric tool to identify the soluble atmospheric pollutants in rainwater.

In this study a new method of principal component (PC) analysis, sequential PC analysis (SPCA), is proposed and assessed on real samples. The aim was to identify the atmospheric emission sources of soluble compounds in rainwater samples, and the sample collection was performed with an automatic sampler. Anions and cations were separated and quantified by ion chromatography, whereas trace metals and metalloids were determined by inductively coupled plasma mass spectrometry. SPCA results showed eight interfering PCs and ten significant PCs. The interfering cases originated from different atmospheric sources, such as resuspended crustal particles, marine aerosols, urban traffic and a fertilizer factory. The significant PCs explained 84.6% of the total variance; 28.1% accounted for the main contribution, which was resuspended industrial soil from a fertilizer factory containing NO(2)(-), NH(4)(+), NO(3)(-), SO(4)(2-), F(-), Al, K(+), Mn, Sb and Ca(2+) as indicators of the fertilizer factory. Another important source (15.0%) was found for Na(+), Mg(2+), K(+), Cl(-) and SO(4)(2-) , which represents the marine influence from south and southwest directions. Emissions of Ba(2+), Pb, Sr(2+), Sb and Mo, which represent a traffic source deposited in soils, were identified as another abundant contribution (12.1%) to the rainwater composition. Other important contributions to the rainwater samples that were identified through SPCA included the following: different urban emissions (Cu, As, Cd, Zn, Mo and Co, 18.1%), emissions from vegetation (HCOO(-), 7.7%) and emissions from industrial combustion processes (Ni, V 15.6%). The application of SPCA proved to be a useful tool to identify the complete information on rainwater samples as indicators of urban air pollution in a city influenced mainly by vehicle traffic emissions and resuspended polluted soils.

Gait kinematic analysis in patients with a mild form of central cord syndrome.

BACKGROUND: Central cord syndrome (CCS) is considered the most common incomplete spinal cord injury (SCI). Independent ambulation was achieved in 87-97% in young patients with CCS but no gait analysis studies have been reported before in such pathology. The aim of this study was to analyze the gait characteristics of subjects with CCS and to compare the findings with a healthy age, sex and anthropomorphically matched control group (CG), walking both at a self-selected speed and at the same speed. METHODS: Twelve CCS patients and a CG of twenty subjects were analyzed. Kinematic data were obtained using a three-dimensional motion analysis system with two scanner units. The CG were asked to walk at two different speeds, at a self-selected speed and at a slower one, similar to the mean gait speed previously registered in the CCS patient group. Temporal, spatial variables and kinematic variables (maximum and minimum lower limb joint angles throughout the gait cycle in each plane, along with the gait cycle instants of occurrence and the joint range of motion - ROM) were compared between the two groups walking at similar speeds. RESULTS: The kinematic parameters were compared when both groups walked at a similar speed, given that there was a significant difference in the self-selected speeds (p < 0.05). Hip abduction and knee flexion at initial contact, as well as minimal knee flexion at stance, were larger in the CCS group (p < 0.05). However, the range of knee and ankle motion in the sagittal plane was greater in the CG group (p < 0.05). The maximal ankle plantar-flexion values in stance phase and at toe off were larger in the CG (p < 0.05). CONCLUSIONS: The gait pattern of CCS patients showed a decrease of knee and ankle sagittal ROM during level walking and an increase in hip abduction to increase base of support. The findings of this study help to improve the understanding how CCS affects gait changes in the lower limbs.

Relation between kinematic analysis of wheelchair propulsion and wheelchair functional basketball classification.

The objective was to conduct a methodological pilot study to analyze wheelchair propulsion upper limb kinematics in standard competitive play considering the functional classification of each athlete. Ten basketball players with a functional classification ranging from 1 to 4 were included in the study. Four camcorders (Kinescan-IBV) and a treadmill for wheelchairs were used. Temporal parameters were analyzed and the upper limb kinematics was obtained using ISB recommendations. The value of the temporal parameters such as push phase duration, the ratio of push phase/recovery phase, contact, and propulsion angle seems to reduce as the functional classification increases. A methodological protocol has been developed that allows the analysis of kinematic characteristics of wheelchair propulsion in basketball players taking into account their functional classification.