Towards pocket-sized genomic analyses: cross-platform benchmark of multi-organism genomic data indexing and alignment

The current socio-economic situation as well as international objectives set by the United Nation (2030 Sustainable Agenda) underline the urgency of low-cost and environmental-friendly computational alternatives. Moreover, in recent years the bioinformatic community has shown renewed interest for Raspberry Pi (RPi) application in teaching and research projects. In the context of the BioVRPi project - which aims to develop and offer a low-cost, stable and tested bioinformatic environment - we propose an exploratory cross-platform benchmarking of multi-organism genomic analyses. The benchmark of indexing and alignment processes was carried out on the following devices: RPi 4 (Raspberry Pi OS 04-04-2022) RAM 8GB HDD storage, laptop (MacOS Big Sur v11.2.3) Intel Core i5 2GHz quad-core processor RAM 16GB SSD, and desktop (Ubuntu 20.04.4 LTS) Intel Core i7 3GHz octa-core processor RAM 32GB HDD storage. Performance assessment was evaluated on SARS-CoV-2 virus, Escherichia coli and Caenorhabditis elegans genome sequences (respective RefSeq accessions: GCF_009858895.2, GCF_000005845.2, GCF_000002985.6) since they present different degrees of genomic complexity: virus, bacterium, and nematode. To minimize variability and possible biases due to sequencing technologies used, sample reads were generated in silico from their respective reference genomes using ART Illumina v2.5.8 with the following parameters: read length 150, paired end, coverage 30X, mean fragment length 200, standard deviation 10, HiSeqX v2.5 TruSeq built-in profile. Indexing and alignment were performed with 3 alignment tools: BWA v0.7.17-r1188, Bowtie2 v2.4.5, and Minimap2 v2.17, using default parameters and scaling from 1 up to 4 threads. Benchmarking was evaluated using Hyperfine v1.13.0 with a warmup step of 3 simulations and 10 runs for each process. We performed a cross-platform benchmark of multi-organism genomic indexing and short reads alignment to evaluate RPi as a viable alternative to common bioinformatic devices. To assess its performance, we tested some of the most widely used alignment tools on SARS-CoV-2, E. coli and C. elegans genomic data (respective genome sizes: 29.9Kbp, 4.6Mbp, 100.3Mbp). The computational times for indexing and alignment are reported in Table 1. As regards indexing, we observed comparable runtimes among RPi and other platforms using BWA and Bowtie2 for SARS-CoV-2 and E. coli, whereas Minimap2 indexing showed an increase of one order of magnitude in runtimes for RPi. Nonetheless, Minimap2 showed the fastest runtimes for indexing overall. In addition, we found an increase of one order of magnitude in RPi runtimes for C. elegans for all considered tools, even though differences in runtimes across platforms showed to be stable across organisms. As regards the alignment process, we observed consistency in runtimes differences across all organisms and tools. Overall, Minimap2 performances proved to be the fastest whereas Bowtie2 displayed poor performances across all platforms, exacerbating its inefficiency on RPi. Even though BWA seems to work more efficiently on RPi than on desktop for SARS-COV-2 data, desktop and laptop showed better performances on more complex organisms as expected. Benchmarking analyses considered multi-threading up to 4 threads, the maximum available on RPi. As regards indexing on Bowtie2, multi-threading proved to be effective for C. elegans data, showing no improvement in runtimes for SARS-CoV-2 and E. coli. Conversely, alignment showed the best performances using multi-threading as expected. In conclusion, RPi showed promising results, proved to be a viable low-cost and environmental-friendly alternative to perform genomic data analysis on different organisms and turned out to be particularly efficient for microorganisms. Further advances and tools optimization for RPi ARM architecture will lead to a greater scalability for complex organisms and will be carried out by the BioVRPi project in future exploratory analyses

Leveraging multi-view deep learning for next activity prediction

Predicting the next activity in a running trace is a fundamental problem in business process monitoring since such predictive information may allow analysts to intervene proactively and prevent undesired behaviors. This paper describes a predictive process approach that couples multi-view learning and deep learning, in order to gain accuracy by accounting for the variety of information possibly recorded in event logs. Experiments with benchmark event logs show the accuracy of the proposed approach compared to several recent state-of-the-art methods

Generalized aggressive periodontitis in prepubertal age: description and comparison of two cases.

Aggressive periodontitis is a rare form of periodontal disease and it can involve both the deciduous dentition and the permanent one. It causes a rapid loss of periodontal attachment. The paper aims to describe two cases of severe generalized prepubertal periodontitis: the first child doesn't suffer from neither systemic diseases nor alteration of functionality of polymorphonuclear and periodontal disease involved both his deciduous dentition and the first permanent molars. The second child had a deficiency of functionality of polymorphonuclear but periodontal disease involved only primary dentition thanks to his immediate improvement of home dental hygiene. This comparison shows the importance of early diagnosis and especially of optimal dental oral hygiene. Infant healthcare professionals, as pediatric dentists and pediatricians, should have the necessary knowledge for early and correct diagnosis and clinical management of disease

Frontal brain asymmetries as effective parameters to assess the quality of audiovisual stimuli perception in adult and young cochlear implant users

How is music perceived by cochlear implant (CI) users? This question arises as "the next step" given the impressive performance obtained by these patients in language perception. Furthermore, how can music perception be evaluated beyond self-report rating, in order to obtain measurable data? To address this question, estimation of the frontal electroencephalographic (EEG) alpha activity imbalance, acquired through a 19-channel EEG cap, appears to be a suitable instrument to measure the approach/withdrawal (AW index) reaction to external stimuli. Specifically, a greater value of AW indicates an increased propensity to stimulus approach, and vice versa a lower one a tendency to withdraw from the stimulus. Additionally, due to prelingually and postlingually deafened pathology acquisition, children and adults, respectively, would probably differ in music perception. The aim of the present study was to investigate children and adult CI users, in unilateral (UCI) and bilateral (BCI) implantation conditions, during three experimental situations of music exposure (normal, distorted and mute). Additionally, a study of functional connectivity patterns within cerebral networks was performed to investigate functioning patterns in different experimental populations. As a general result, congruency among patterns between BCI patients and control (CTRL) subjects was seen, characterised by lowest values for the distorted condition (vs. normal and mute conditions) in the AW index and in the connectivity analysis. Additionally, the normal and distorted conditions were significantly different in CI and CTRL adults, and in CTRL children, but not in CI children. These results suggest a higher capacity of discrimination and approach motivation towards normal music in CTRL and BCI subjects, but not for UCI patients. Therefore, for perception of music CTRL and BCI participants appear more similar than UCI subjects, as estimated by measurable and not self-reported parameters

Iron chromium potential to model high-chromium ferritic alloys

We present an Fe­Cr interatomic potential to model high-Cr ferritic alloys.The potential is fitted to thermodynamic and point-defect propertiesobtained from density functional theory (DFT) calculations and experi-ments. The developed potential is also benchmarked against otherpotentials available in literature. It shows particularly good agreementwith the DFT obtained mixing enthalpy of the random alloy, the formationenergy of intermetallics and experimental excess vibrational entropy andphase diagram. In addition, DFT calculated point-defect properties,both interstitial and substitutional, are well reproduced, as is the screwdislocation core structure. As a first validation of the potential, we studythe precipitation hardening of Fe­Cr alloys via static simulations of theinteraction between Cr precipitates and screw dislocations. It is concludedthat the description of the dislocation core modification near a precipitatemight have a significant influence on the interaction mechanisms observedin dynamic simulations.Fil: Bonny, G.. No especifíca;Fil: Pasianot, Roberto Cesar. Universidad Nacional de San Martín. Instituto Sabato; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica; ArgentinaFil: Terentyev, D.. No especifíca;Fil: Malerba, L.. No especifíca

State of art in intra-articular hip injections of different medications for osteoarthritis: a systematic review

Background: Intra-articular hip injections for osteoarthritis represent a useful instrument to reduce pain and disability in the common clinical practice. Several medications can be injected locally with different level of evidence-based efficacy. Objective: The objective of this systematic review is to investigate the effectiveness of intra-articular injections of different medications or substances for the pain treatment and the management of disability in subjects affected by hip osteoarthritis. Methods: Two reviewers selected independently randomised controlled trials published in the last 10 years, using PubMed and Scopus databases. The risk of bias was evaluated with Cochrane library assessment tool. Results: 12 randomised controlled trials have been selected. We found 8 papers comparing hyaluronic acid with platelet rich plasma, with corticosteroids and with saline solution; 1 paper compares two types of hyaluronic acid with different molecular weights; 3 papers study the effects of corticosteroids alone or compared to ketorolac or saline solution. Conclusions: The studies reviewed were heterogeneous regarding sample size, level of osteoarthritis, evaluated with Kellegren-Lawrence score, medications used and follow up timings. However, we have observed that intra-articular injections of platelet-rich plasma seem to decrease pain at short term and disability at long term, in patients affected by hip osteoarthritis better than hyaluronic acid. The association of hyaluronic acid and corticosteroids could give better results compared to hyaluronic acid alone, while the use of intra-articular ketorolac and saline solution requires more studies

Relation Between EEG Measures and Upper Limb Motor Recovery in Stroke Patients: A Scoping Review

Current clinical practice does not leverage electroencephalography (EEG) measurements in stroke patients, despite its potential to contribute to post-stroke recovery predictions. We review the literature on the effectiveness of various quantitative and qualitative EEG-based measures after stroke as a tool to predict upper limb motor outcome, in relation to stroke timeframe and applied experimental tasks. Moreover, we aim to provide guidance on the use of EEG in the assessment of upper limb motor recovery after stroke, suggesting a high potential for some metrics in the appropriate context. We identified relevant papers (N = 16) from databases ScienceDirect, Web of Science and MEDLINE, and assessed their methodological quality with the Joanna Briggs Institute (JBI) Critical Appraisal. We applied the Preferred Reporting Systems for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) Framework. Identified works used EEG to identify properties including event-related activation, spectral power in physiologically relevant bands, symmetry in brain dynamics, functional connectivity, cortico-muscular coherence and rhythmic coordination. EEG was acquired in resting state or in relation to behavioural conditions. Motor outcome was mainly evaluated with the Upper Limb Fugl-Meyer Assessment. Despite great variability in the literature, data suggests that the most promising EEG quantifiers for predicting post-stroke motor outcome are event-related measures. Measures of spectral power in physiologically relevant bands and measures of brain symmetry also show promise. We suggest that EEG measures may improve our understanding of stroke brain dynamics during recovery, and contribute to establishing a functional prognosis and choosing the rehabilitation approach

Functional rescue of dystrophin deficiency in mice caused by frameshift mutations using Campylobacter jejuni Cas9

Duchenne muscular dystrophy (DMD) is a fatal, X-linked muscle wasting disease caused by mutations in the DMD gene. In 51% of DMD cases, a reading frame is disrupted because of deletion of several exons. Here, we show that CjCas9 derived from Campylobacter jejuni can be used as a gene editing tool to correct an out-of-frame Dmd exon in Dmd knockout mice. Herein, we used Cas9 derived from S. pyogenes to generate Dmd knockout (KO) mice with a frameshift mutation in Dmd gene. Then, we expressed CjCas9, its single-guide RNA, and the eGFP gene in the tibialis anterior muscle of the Dmd KO mice using an all-in-one adeno-associated virus (AAV) vector. CjCas9 cleaved the target site in the Dmd gene efficiently in vivo and induced small insertions or deletions at the target site. This treatment resulted in conversion of the disrupted Dmd reading frame from out-of-frame to in-frame, leading to the expression of dystrophin in the sarcolemma. Importantly, muscle strength was enhanced in the CjCas9-treated muscles, without off-target mutations, indicating high efficiency and specificity of CjCas9. This work suggests that in vivo DMD frame correction, mediated by CjCas9 has great potential for the treatment of DMD and other neuromuscular diseases

Early cardiovascular involvement in Chronic Obstructive Pulmonary Disease

Cardiovascular (CV) disease represents a considerable risk factor in terms of both morbidity and mortality in elderly patients with chronic obstructive pulmonary disease (COPD). In fact, there is a considerable evidence of this association: for only 20 years forced expiratory volume in 1 second (FEV1) has been considered as predictive of cardiovascular mortality especially in elderly patients. At present, the emerging evidence suggests that hypoxia, systemic inflammation, oxidative stress may cause an early sub-clinical cardiovascular involvement in patients with COPD. Aging is a selective process dramatically affecting certain portions of the cardiovascular system for example: diminished beta-adrenergic responsiveness, increased myocardial and vascular stiffness, decreased arterial baroreflex, vagal outflow and compromission of diastolic function. The nature of these interactions is complex and involves not only mechanisms of aging but also multiple defined and undefined (e.g., genetic) risk factors. Cardiovascular diseases are the main causes of mortality among the subjects with impaired lung function. Even mild reductions in expiratory flow volumes amplify the risk of ischemic heart diseases, strokes, and sudden cardiac deaths 2-to 3-fold, independent of other risk factors. The mechanism or mechanisms responsible for this association, however, remain largely unknown