Additional File Research Articles

A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora

BackgroundPlants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora.ResultsWe began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k–900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao’s defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp.ConclusionsOur results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.

ShetlandsUAVmetry: unmanned aerial vehicle-based photogrammetric dataset for Antarctic environmental research

The study of the functioning and responses of Antarctica to the current climate change scenario is a priority and a challenge for the scientific community aiming to predict and mitigate impacts at a regional and global scale. Due to the difficulty of obtaining aerial data in such extreme, remote, and difficult-to-reach region of the planet, the development of remote sensing techniques with Unmanned Aerial Vehicles (UAVs) has revolutionized polar research. ShetlandsUAVmetry comprises original datasets collected by UAVs during the Spanish Antarctic Campaign 2021–2022 (January to March 2022), along with the photogrammetric products resulting from their processing. It includes data recorded during twenty-eight distinct UAV flights at various study sites on Deception and Livingston islands (South Shetland Islands, Antarctica) and consists of a total of 15,691 high-resolution optical RGB captures. In addition, this dataset is accompanied by additional associated files that facilitate its use and accessibility. It is publicly accessible and can be downloaded from the figshare data repository.

Long-term safety of Ixekizumab in adults with psoriasis, psoriatic arthritis, or axial spondyloarthritis: a post-hoc analysis of final safety data from 25 randomized clinical trials

BackgroundWe report long-term, end-of-study program safety outcomes from 25 randomized clinical trials (RCTs) in adult patients with psoriasis (PsO), psoriatic arthritis (PsA), or axial spondyloarthritis (axSpA) [including ankylosing spondylitis (AS) and non-radiographic axial spondyloarthritis (nr-axSpA)] who received ≥ 1 dose of Ixekizumab (IXE) over 5 years (PsO) or up to 3 years (PsA, axSpA).MethodsThis integrated safety analysis consists of data from patients who received any dose of IXE, across 25 RCTs (17 PsO, 4 PsA, 4 axSpA). Rates of treatment-emergent adverse events (TEAEs), serious adverse events (SAEs) and selected adverse events (AEs) of interest were analyzed for all pooled studies by years of therapy and overall, through March 2022. Results were reported as exposure-adjusted incidence rates (IRs) per 100 patient-years (PY) overall and at successive year intervals.ResultsSix thousand eight hundred ninety two adult patients with PsO, 1401 with PsA, and 932 with axSpA (including AS and nr-axSpA), with a cumulative IXE exposure of 22,371.1 PY were included. The most commonly reported TEAE across indications was nasopharyngitis (IRs per 100 PY: 8.8 (PsO), 9.0 (PsA), 8.4 (axSpA)). SAEs were reported by 969 patients with PsO (IR 5.4), 134 patients with PsA (IR 6.0), and 101 patients with axSpA (IR 4.8). Forty-five deaths were reported (PsO, n = 36, IR 0.2; PsA, n = 6, IR 0.3; axSpA, n = 3, IR 0.1). TEAEs did not increase during IXE exposure: IRs per 100 PY, PsO: 88.9 to 63.2 (year 0–1 to 4–5), PsA: 87 to 67.3 (year 0–1 to 2–3), axSpA: 82.1 to 55.4 (year 0–1 to > = 2). IRs per 100 PY of discontinuation from IXE due to AE were 2.9 (PsO), 5.1 (PsA), and 3.1 (axSpA). IRs per 100 PY of injection site reactions were 5.9 (PsO), 11.6 (PsA) and 7.4 (axSpA); Candida: 1.9 (PsO), 2.0 (PsA), and 1.2 (axSpA); depression, major adverse cerebro-cardiovascular events and malignancies: ≤ 1.6 across all indications. Adjudicated IRs per 100 PY of inflammatory bowel disease were ≤ 0.8 across indications (0.1 [PsO]; 0.1 [PsA]; 0.8 [axSpA]).ConclusionsIn this integrated safety analysis, consisting of over 22,000 PY of exposure, the long-term safety profile of IXE was found to be consistent with previous, earlier reports, with no new safety signals identified.Trial registrationNCT registration numbers for RCTs included in this integrated analysis can be found in Additional File 1.

Vitamin E-enriched medium cross-linked polyethylene in total knee arthroplasty (VIKEP): clinical outcome, oxidation profile, and wear analysis in comparison to standard polyethylene—study protocol for a randomized controlled trial

BackgroundThe gliding surface of total knee endoprostheses is exposed to high loads due to patient weight and activity. These implant components are typically manufactured from ultra-high molecular weight polyethylene (UHMWPE). Crosslinking of UHMWPE by ionizing radiation results in higher wear resistance but induces the formation of free radicals which impair mechanical properties after contact with oxygen. Medium-crosslinked UHMWPE enriched with vitamin E (MXE) provides a balance between the parameters for a sustainable gliding surface, i.e., mechanical strength, wear resistance, particle size, and oxidation stability. Therefore, a gliding surface for knee endoprostheses made up from this material was developed, certified, and launched. The aim of this study is to compare this new gliding surface to the established predecessor in a non-inferiority design.MethodsThis multicenter, binational randomized controlled trial will enroll patients with knee osteoarthritis eligible for knee arthroplasty with the index device. Patients will be treated with a knee endoprosthesis with either MXE or a standard gliding surface. Patients will be blinded regarding their treatment. After implantation of the devices, patients will be followed up for 10 years. Besides clinical and patient-related outcomes, radiological data will be collected. In case of revision, the gliding surface will be analyzed biomechanically and regarding the oxidative profile.DiscussionThe comparison between MXE and the standard gliding surface in this study will provide clinical data to confirm preceding biomechanical results in vivo. It is assumed that material-related differences will be identified, i.e., that the new material will be less sensitive to wear and creep. This may become obvious in biomechanical analyses of retrieved implants from revised patients and in radiologic analyses.Trial registrationClinicalTrials.gov, NCT04618016. Registered 27 October 2020, https://clinicaltrials.gov/study/NCT04618016?term=vikep&checkSpell=false&rank=1.All items from the World Health Organization Trial Registration Data Set can be found in Additional file 1.

Application of culturomics in fungal isolation from mangrove sediments

BackgroundFungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties.ResultsThis study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1).ConclusionsOur study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments.Dds2rK-5aaMj4bHfhLGEseVideo

Study protocol of a randomized controlled trial to assess safety of teleconsultation compared with face-to-face consultation: the ECASeT study

BackgroundThe use of remote consultation modalities has exponentially grown in the past few years, particularly since the onset of the COVID-19 pandemic. Although a huge body of the literature has described the use of phone (tele) and video consultations, very few of the studies correspond to randomized controlled trials, and none of them has assessed the safety of these consultation modalities as the primary objective. The primary objective of this trial was to assess the safety of remote consultations (both video and teleconsultation) in the follow-up of patients in the hospital setting.MethodsMulticenter, randomized controlled trial being conducted in four centers of an administrative healthcare area in Catalonia (North-East Spain). Participants will be screened from all individuals, irrespective of age and sex, who require follow-up in outpatient consultations of any of the departments involved in the study. Eligibility criteria have been established based on the local guidelines for screening patients for remote consultation. Participants will be randomly allocated into one of the two study arms: conventional face-to-face consultation (control) and remote consultation, either teleconsultation or video consultation (intervention). Routine follow-up visits will be scheduled at a frequency determined by the physician based on the diagnostic and therapy of the baseline disease (the one triggering enrollment). The primary outcome will be the number of adverse reactions and complications related to the baseline disease. Secondary outcomes will include non-scheduled visits and hospitalizations, as well as usability features of remote consultations. All data will either be recorded in an electronic clinical report form or retrieved from local electronic health records. Based on the complications and adverse reaction rates reported in the literature, we established a target sample size of 1068 participants per arm. Recruitment started in May 2022 and is expected to end in May 2024.DiscussionThe scarcity of precedents on the assessment of remote consultation modalities using randomized controlled designs challenges making design decisions, including recruitment, selection criteria, and outcome definition, which are discussed in the manuscript.Trial registrationNCT05094180. The items of the WHO checklist for trial registration are available in Additional file 1. Registered on 24 November 2021.

Validation of a German-language modified Rankin Scale structured telephone interview at 3 months in a real-life stroke cohort

BackgroundThe modified Rankin scale (mRS) at 3 months is established as the primary outcome measure in clinical stroke trials. Traditionally, the mRS is assessed through an unstructured face-to-face interview. This approach can be labor-intensive and lead to suboptimal inter-rater reliability. Recently, the Covid-19 pandemic made face-to-face contact even more challenging. To address these issues, we developed and validated a structured German-language questionnaire for mRS testing by telephone.MethodsIn this prospective cohort study, we compared the mRS testing results of the standard face-to-face interview with those obtained in a structured interview by telephone using Cohen’s Kappa.ResultsAt our tertiary care stroke center, we included 108 patients who underwent both assessments. In 80.6% of cases (87/108) face-to-face and telephone interview reached identical scores. Linear weighted Kappa was 0.82 (p < 0.001). Unweighted Kappa for dichotomized mRS between fair (0–2) and poor (3–6) functional outcome was κ = 0.97 (p < 0.001).ConclusionsOur study validates the use of the German-language structured telephone interview as a reliable instrument for the use in clinical trials. We encourage others to utilize the questionnaire. It is available as an Appendix (Additional file 1) to this publication.

PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches

BackgroundTechnical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candidate positions within a reference sequence. We may create pairs (“position”, “subsequence”) for the reference sequence and keep all such records without compression, even on a budget computer. As sequences for new and reference genomes differ, the goal is to find anchors, so we tolerate differences and keep the number of candidate positions with the same anchors to a minimum. Spaced seeds (masks ignoring symbols at specific locations) are a way to approach the task. An ideal (full sensitivity) spaced seed should enable us to find all such positions subject to a given maximum number of mismatches permitted.ResultsSeveral algorithms to assist seed generation are presented. The first one finds all permitted spaced seeds iteratively. We observe specific patterns for the seeds of the highest weight. There are often periodic seeds with a simple relation between block size, length of the seed and read. The second algorithm produces blocks for periodic seeds for blocks of up to 50 symbols and up to nine mismatches. The third algorithm uses those lists to find spaced seeds for reads of an arbitrary length. Finally, we apply seeds to a real dataset and compare results for other popular seeds.ConclusionsPerFSeeB approach helps to significantly reduce the number of reads’ possible alignment positions for a known number of mismatches. Lists of long, high-weight spaced seeds are available in Additional file 1. The seeds are best in weight compared to seeds from other papers and can usually be applied to shorter reads. Codes for all algorithms and periodic blocks can be found at https://github.com/vtman/PerFSeeB.

A pilot randomised controlled parallel arm trial evaluating treatment satisfaction with the Omnipod DASH® Insulin Management System compared with usual care in adults with type 1 diabetes in Australia: rationale, study design and methodologies

BackgroundInsulin pump therapy (IPT) improves glucose control in people with type 1 diabetes (T1D) compared with multiple daily injections (MDI). However, their size, the tethered insulin infusion set, intrusiveness when operating the device and the need to disconnect during showering limit their acceptance to many who may benefit. The Omnipod DASH® Insulin Management System is a small waterproof tubeless device which is wirelessly controlled by a handheld device which may be an acceptable alternative. However, there are no randomised controlled trials focusing on the impact on user perceptions of tubeless insulin pump therapy. This pilot study aims to assess study feasibility and acceptability of patch pump therapy compared with usual care in adults with T1D in Australia to inform power calculations and progression to a large-scale multi-site randomised controlled study.MethodsA pilot multi-site parallel randomised controlled study will be conducted in sixty-four adults with T1D who are managed on MDI or IPT and self-monitoring with finger-stick blood glucose from four specialist diabetes centres in Victoria, Australia. Following carbohydrate counting education, participants will be randomised to use Omnipod DASH® System (Omnipod group) or continue usual care (usual care group) for 12 weeks, followed by a 12-week extension phase where all participants will use Omnipod DASH® System. The primary outcome measure is feasibility determined by study completion rates with a threshold of 0.80. Acceptability of the intervention (Omnipod DASH® System) will be assessed by the difference in Diabetes Technology Questionnaire ‘current’ (DTQ-current) score at 12 weeks post-randomisation compared to baseline. Secondary outcomes will include other measures of user acceptance, process outcomes, resource outcomes, participant-centred outcomes, healthcare professional perceptions and glycaemic outcomes.DiscussionThis pilot study will provide insights regarding the feasibility of the study design and the first data regarding user acceptance of insulin patch pump technology in Australian T1D adults. We anticipate that this study will provide information informing the design of a larger study evaluating the impact of patch pumps on subjective outcomes that are of significance to the person living with T1D.Trial registrationAustralian New Zealand Clinical Trials Registry (https://anzctr.org.au/) ACTRN12621001195842 (8th September 2021). Please refer to Additional file 1: Appendix 1 for full details.

Young adults’ sought gratifications from, and perceptions of food advertising by, social media influencers: a qualitative approach

BackgroundThis study aims to explore young adults’ sought gratifications from social media influencers and whether they are exposed to food advertising by influencers. Further, it aims to understand how young individuals perceive food advertisements by social media influencers.MethodsThis qualitative study was conducted on 17 students from two public universities—King Abdul Aziz and Jeddah universities—located in the City of Jeddah, Saudi Arabia, using in-depth, face-to-face, and semi-structured interviews. The participants were active users of social media platforms who followed at least one influencer. Thematic analysis was used to analyse the data. The COREQ guidelines for reporting qualitative research (see Additional file 2) were followed when stating the findings.ResultsThe findings reveal ten themes, that is, seven gratifications sought by young adults—broadening knowledge, perceived usefulness, self-improvement, boosting positivity, fostering morale, reinforcing inspiration, and passing time/enjoyment—and three themes (i.e. repeated, authentic, and unhealthy) that describe how Saudi young adults perceive food advertising.ConclusionThis study contributes to social media influencer marketing by identifying the factors that motivate young consumers to follow influencers, and it elucidates the extent to which young adults are exposed to food marketing, adding to the body of literature on food advertising.

Structural ultrasound of joints and tendons in healthy children: development of normative data

BackgroundMusculoskeletal ultrasound is a well accessible technique to assess disease activity in children with juvenile idiopathic arthritis. Knowledge of reference values of joint structures is indispensable to differentiate between physiological and pathological finding. The aim of this study was to assess the structural sonographic features of joints and tendons in healthy children from several age groups (0.2–18 year), and develop a set of normative data.MethodsGreyscale ultrasound was performed in 500 healthy children (age 0.2–18 years) according to a predefined scanning protocol (Additional file 1) including the shoulder, elbow, wrist, second metacarpophalangeal joint, hip, knee, ankle, and first metatarsophalangeal joint). Demographic data and values of cartilage thickness, tendon diameters, and the degree of capsular distention measured by bone-capsular distance (BCD) were collected. Differences according to the sex were assessed by unpaired t-test. Single and multiple regression analyses were performed between the ultrasound outcomes and covariates such as age, height, weight and body mass index. Growth charts and tables were developed with respect to age. Nonparametric quantile regression was applied using the R-packages quantreg and quantregGrowth.ResultsA total of 195 male and 305 female volunteers were included between the age of 0 and 18 years (mean age 8.9; range: 0.2–17.9 years). Cartilage diminished markedly as children aged, and cartilage of the boys was significantly thicker compared to the girls in all joints (p < 0.001). In addition, cartilage became thinner as children’s height and weight increased (beta regression coefficients between − 0.27 and − 0.01, p < 0.0001). Capsular distention (i.e., BCD > 0 mm) was uncommon in the ankle, wrist and MCP2 (resp. in 3, 6, and 3% of cases). It was more common in the suprapatellar and parapatellar knee, MTP1 and posterior recess of the elbow (resp. in 34, 32, 46, and 39% of cases). In the hip, some capsular distention was always present. Age was found to be the best predictor for BCD (beta regression coefficients between 0.05 and 0.13, p < 0.0001). Height was, in addition to age, a good predictor of tendon diameter (beta regression coefficients between 0.03 and 0.14, p < 0.0001). Growth curves and tables for each variable were developed.ConclusionsReference values of sonographic cartilage thickness, BCD and diameters of tendons at several joints were established from 500 healthy children, aged between 0.2 and 18 years. Growth charts and tables were developed to distinguish normal findings from pathology in children with complaints suspicious of arthritis.

On Image Quality Metadata, FAIR in ML, AI-Readiness and Reproducibility: Fish-AIR example

A new science discipline has emerged within the last decade at the intersection of informatics, computer science and biology: Imageomics. Like most other -omics fields, Imageomics also uses emerging technologies to analyze biological data but from the images. One of the most applied data analysis methods for image datasets is Machine Learning (ML). In 2019, we started working on a United States National Science Foundation (NSF) funded project, known as Biology Guided Neural Networks (BGNN) with the purpose of extracting information about biology by using neural networks and biological guidance such as species descriptions, identifications, phylogenetic trees and morphological annotations (Bart et al. 2021). Even though the variety and abundance of biological data is satisfactory for some ML analysis and the data are openly accessible, researchers still spend up to 80% of their time preparing data into a usable, AI-ready format, leaving only 20% for exploration and modeling (Long and Romanoff 2023). For this reason, we have built a dataset composed of digitized fish specimens, taken either directly from collections or from specialized repositories. The range of digital representations we cover is broad and growing, from photographs and radiographs, to CT scans, and even illustrations. We have added new groups of vocabularies to the dataset management system including image quality metadata, extended image metadata and batch metadata. With the image quality metadata and extended image metadata, we aimed to extract information from the digital objects that can possibly help ML scientists in their research with filtering, image processing and object recognition routines. Image quality metadata provides information about objects contained in the image, features and condition of the specimen, and some basic visual properties of the image, while extended image metadata provides information about technical properties of the digital file and the digital multimedia object (Bakış et al. 2021, Karnani et al. 2022, Leipzig et al. 2021, Pepper et al. 2021, Wang et al. 2021) (see details on Fish-AIR vocabulary web page). Batch metadata is used for separating different datasets and facilitates downloading and uploading data in batches with additional batch information and supplementary files. Additional flexibility, built into the database infrastructure using an RDF framework, will enable the system to host different taxonomic groups, which might require new metadata features (Jebbia et al. 2023). By the combination of these features, along with FAIR (Findable, Accessable, Interoperable, Reusable) principles, and reproducibility, we provide Artificial Intelligence Readiness (AIR; Long and Romanoff 2023) to the dataset. Fish-AIR provides an easy-to-access, filtered, annotated and cleaned biological dataset for researchers from different backgrounds and facilitates the integration of biological knowledge based on digitized preserved specimens into ML pipelines. Because of the flexible database infrastructure and addition of new datasets, researchers will also be able to access additional types of data—such as landmarks, specimen outlines, annotated parts, and quality scores—in the near future. Already, the dataset is the largest and most detailed AI-ready fish image dataset with integrated Image Quality Management System (Jebbia et al. 2023, Wang et al. 2021).

Serum and 24-hour urinary tests cost-effectiveness in stone formers

ObjectiveTo assess the routine serum and 24-hour urine tests proficiency in diagnosing the baseline metabolic abnormality of kidney stone formers.MethodsThis study analyzes the routine serum and 24-hour urine tests proficiency in diagnosing the baseline metabolic abnormality of kidney stone formers. The sensitivity and specificity, false positive, and negative results of the tests are extracted from diagnostic kits used in the laboratories of the target community. To accurately infer the results, a simulation based on 1000 people was used through 22 standard laboratory tests (Additional File 2), including calcium, oxalate, phosphate, uric acid, sulfate, potassium, sodium, citrate, and magnesium in 24-hour urine; and calcium, creatinine, Vit D, uric acid, and intact parathyroid hormone (PTH) in serum. The incremental cost-effectiveness ratio (ICER) was calculated and compared for each diagnostic test versus other diagnostic tests according to the incremental cost required for correct diagnoses of stone causes.ResultsUrinary uric acid, citrate, and serum potassium constitute the cost-effectiveness boundary curve in this study. This means that other diagnostic tests are not cost-effective compared to these three tests in terms of indexing at least one item of cost and effectiveness. The ICER index for each correct diagnosis with the urinary uric acid test was $ 1.25 per diagnosis, the most cost-effective test compared to serum potassium and urinary citrate.ConclusionThe simplified blood and 24-hour urine metabolic evaluation, including urinary uric acid, citrate, and serum potassium, constitute the cost-effectiveness boundary curve. The most cost-effective test was urinary uric acid measurement.

FastqToGenCounts: Converting Fastq Files to Gene Counts Matrices

Abstract FastqToGeneCounts is a computational pipeline built on Snakemake to process and analyze bulk RNA sequencing data to determine gene expression. It can handle raw data from the Gene Expression Omnibus or local FastQ files and runs on a supercomputing cluster. The primary function of FastqToGeneCounts is to align FastQ files to a reference genome. To ensure accurate outputs, it also offers trimming, quality control, and contaminant screening options. One of the benefits of using FastqToGeneCounts is that it addresses the issues commonly encountered with traditional alignment workflows. These include the need for manual file naming and directory setup, which can lead to errors and problems resuming failed workflows. Additionally, these workflows often require many resources requested at once, leading to long “wait times” for cluster access. Modifying parameters can also be challenging, as most settings are not localized to a single file. In contrast, FastqToGeneCounts integrates with Snakemake to improve resume-ability, minimize resource usage, and provide easy parameter modification. Jobs can be resumed from a failed state, only the minimum required resources are requested to reduce waiting time, and a single YAML file can be used to configure parameters within the pipeline. FastqToGeneCounts has been used to analyze four immature natural killer datasets and has successfully determined gene expression in these samples. It is capable of analyzing a single raw RNA-seq input file in approximately 15 compute minutes, and additional files do not increase runtime due to Snakemake’s high interoperability with SLURM. FastqToGeneCounts removes poor-quality reads from downstream analysis and presents results in an easy-to-read report.

Video File Allocation for Wear-Leveling in Distributed Storage Systems With Heterogeneous Solid-State-Disks (SSDs)

With the advent of new large-capacity solid-state disks (SSDs) such as quad-level-cells (QLC), SSD arrays can be effectively used in video storage systems that require large-capacity storage space. Typically, SSD manufacturers specify a drive-writes-per-day (DWPD) metric, which is the ratio of bytes written per day to the total capacity in bytes, to ensure an SSD’s specified lifetime; it is important to limit the number of write operations by considering the DWPD for each SSD. We propose a new video file allocation technique to effectively manage the heterogeneous DWPD characteristics of SSDs in distributed storage systems. To express the degree of wear-leveling for heterogeneous SSDs, we first introduce the concept of ADWD, which is the actual number of bytes written per day compared to DWPD. We then propose two algorithms for file placement and migration. The file placement algorithm places files greedily based on the bandwidth-to-space ratio (BSR) of each file and SSD to balance the bandwidth usage and storage of the SSD. The file migration algorithm moves files from overloaded to underloaded SSDs to meet bandwidth limit requirements while minimizing the overall ADWD as a result of migration, and then migrates additional popular files to improve SSD bandwidth utilization. To use these algorithms in actual distributed file systems, we implemented a suite of tools for file placement and migration in the Hadoop distributed file system (HDFS). Experimental results show that the proposed algorithm reduces the mean of ADWD by 35.44% and its standard deviation by 69.78% compared to the benchmark methods on average.

An Examination of the Impact of Blue Heat Treatment on the Forced Caused by the Vertical Motion of Endodontic Files

Objective: To assess the vertical forces produced during canal shaping by the Reciproc Blue (RB) and Reciproc (R) systems. Place and Duration: In the Operative Dentistry Department, Altamash Institute of Dental Medicine Karachi for one-year duration from January 2022 to December 2022. Methods: A total of 32 maxillary premolar teeth were selected, each with two distinct constricted and straight canals. Every tooth was positioned in a standing position on a platform attached to a force analysing device after access cavity preparation (M5-20 Advanced Digital Force Gauge; Mark-10 Corporation, NY, USA). Until the K file size was up to 15, the glide route was prepared manually. Then, using an R25/RB25 file, all of the groups' canals were completely shaped (0.08 taper, size 25). The canal was shaped with a mild and steady pressure on the file that produced a gradual, 2 mm amplitude "in-and-out" movement. It took three attempts for the file to successfully reach the WL. The canal was irrigated and recapitulated with sodium hypochlorite (1%) solution following each insertion. The Student's t-test was used to analyze the shaping time. The Mann Whitney test was applied to analyse the upward and inward peak forces. With a 95% level of confidence, SPSS software was used for all statistical analyses. Results: A single file was inserted into each root canal successfully three times for shaping till the WL achieved. With each additional file insertion, the overall real-time force increased in each group grew. The R group displayed lower peak forces in comparison to the RB group in the 3 insertions, and both groups inward peak forces varied from 1.76 to 8.64 N. (P&lt;0.05). Complete canal shaping of the RB and R systems took an average of 24.30±3.98 s and 21.91±3.56s, respectively (P&gt;0.05). During canal shaping in this experiment, no file fracture occurred. Conclusion: The forces generated during canal shaping were influenced by the blue heat treatment. Higher inward peak forces were higher in the RB file than the R file. Keywords: Root canal preparation, Endodontics, vertical force and shaping time.

Corticosterone mediates FKBP51 signaling and inflammation response in the trigeminal ganglion in chronic stress-induced corneal hyperalgesia mice

Stress-induced hyperalgesia is a health-threatening condition that lacks effective therapeutic intervention, impairing the quality of life. Interestingly, a high prevalence of corneal pain symptoms was also found in patients experienced severe stressors. Excessive secretion corticosterone in rodents has been shown to contribute to the development of visceral and mechanical hyperalgesia under stressful conditions. The co-chaperone protein FK506-binding protein 5 (FKBP5) was reported to modulate steroid sensitivity and inhibition of FKBP51 possessed anxiolytic and anti-hyperalgesic in the stressed-mice model. However, whether corticosterone and FKBP5 play a role in chronic stress-induced corneal hyperalgesia remains unknown. The aim of this study was to evaluate the corneal sensitivity after exposure to chronic restraint stress (CRS) and investigate the potential role of corticosterone and FKBP5 mediated proinflammatory cytokines release in trigeminal ganglion (TG) in corneal hyperalgesia under chronic stressful situations. Firstly, mice displayed increased corneal sensitivity without changes in tear production and corneal injury after CRS for 4 hours/day for 14 days. Meanwhile, corticosterone deficiency via adrenalectomy could prevent CRS-induced corneal hyperalgesia, whereas chronic corticosterone feeding increased the corneal sensitivity accompanied by increasing proinflammatory cytokines levels of phospho-NF-κB (p-NF-κB), tumor necrosis factor (TNF)-α and interleukin (IL)-1β in the TG on d14. Notably, we found that FKBP51 was significantly upregulated in the TG in the stressed-mice. Intraperitoneal injection of FKBP51 inhibitor significantly alleviated CRS-induced corneal hyperalgesia, and reversed calcitonin gene related peptide (CGRP) increase and proinflammatory cytokines production in the TG. Moreover, FKBP51 inhibitor could also exert its anti-hyperalgesic effect on corneal pain through intra-TG injection. Our study proves that CRS can induce corneal hyperalgesia in mice and uncovers the role of corticosterone and FKBP51 in modulating corneal sensitivity, providing a novel treatment strategy for stress-induced corneal hyperalgesia. Availability of data and materialsAll data and additional file are available upon request from the corresponding author.

CD74: a prospective marker for reactive microglia?

CD74: a prospective marker for reactive microglia?

Simulation device for shoulder reductions: overview of prototyping, testing, and design instructions

BackgroundShoulder dislocations are common occurrences, yet there are few simulation devices to train medical personnel on how to reduce these dislocations. Reductions require a familiarity with the shoulder and a nuanced motion against strong muscle tension. The goal of this work is to describe the design of an easily replicated, low-cost simulator for training shoulder reductions.Materials and methodsAn iterative, stepwise engineering design process was used to design and implement ReducTrain. A needs analysis with clinical experts led to the selection of the traction-countertraction and external rotation methods as educationally relevant techniques to include. A set of design requirements and acceptance criteria was established that considered durability, assembly time, and cost. An iterative prototyping development process was used to meet the acceptance criteria. Testing protocols for each design requirement are also presented. Step-by-step instructions are provided to allow the replication of ReducTrain from easily sourced materials, including plywood, resistance bands, dowels, and various fasteners, as well as a 3D-printed shoulder model, whose printable file is included at a link in the Additional file 1: Appendix.ResultsA description of the final model is given. The total cost for all materials for one ReducTrain model is under US $200, and it takes about 3 h and 20 min to assemble. Based on repetitive testing, the device should not see any noticeable changes in durability after 1000 uses but may exhibit some changes in resistance band strength after 2000 uses.DiscussionThe ReducTrain device fills a gap in emergency medicine and orthopedic simulation. Its wide variety of uses points to its utility in several instructional formats. With the rise of makerspaces and public workshops, the construction of the device can be easily completed. While the device has some limitations, its robust design allows for simple upkeep and a customizable training experience.ConclusionA simplified anatomical design allows for the ReducTrain model to serve as a viable training device for shoulder reductions.

The effect of vitamin D and magnesium supplementation on clinical symptoms and serum inflammatory and oxidative stress markers in patients with COVID-19: a structured summary of a study protocol for a randomized controlled trial

ObjectivesThis study aims to evaluate the effect of vitamin D and magnesium supplementation on clinical symptoms and serum inflammatory and oxidative stress markers in patients with COVID-19.Trial designThis study is a 4-arm randomized, double-blind, placebo-controlled clinical trial with a factorial design and the intervention period is 3 weeks.ParticipantsThis study is conducted on COVID-19 patients admitted to the Shahid Mohammadi hospital in Bandar Abbas, Iran, who are eligible for inclusion in the study. Patients are included only if they meet all of the following criteria: (1) aged from 18 to 65 years old; (2) confirmation of COVID-19 by RT-PCR test; (3) completing informed consent; (4) passing less than 48 h since the patient's hospitalization; (5) no skin or gastrointestinal allergies due to taking multivitamin supplements, vitamin D, and magnesium; and (6) having more than 30 breaths per minute and less than 93% oxygen saturation in room air and sea level. Patients are excluded if they have any of the following conditions: (1) pregnancy or lactation; (2) taking a daily multivitamin or take a vitamin D or magnesium supplement in the last month; (3) participating in other clinical trials; (4) renal failure or dialysis, severe liver disease or cirrhosis; (5) known diagnosis of hypercalcemia; (6) discharging from the hospital less than 24 h after the start of the intervention; (7) history of kidney stones in the last year; (8) transfer the patient to the ICU; (9) baseline vitamin D levels above 80 ng/ml; (10) baseline magnesium levels above 2.6 mg/dl; and (11) unwillingness of the patient to continue the study.Intervention and comparatorParticipants will be randomly allocated to one of the four following groups: (A) vitamin D (two 50,000 IU capsules at the beginning of the study, two 50,000 IU capsules on the 4th day, one 50,000 IU capsule on the 11th day, and one 50,000 IU capsule on the 17th day) and magnesium supplement (300 mg/day); (B) vitamin D capsule and magnesium placebo; (C) magnesium supplement and vitamin D placebo; and (D) vitamin D placebo and magnesium placebo.Main outcomesThe resolution of clinical symptoms (fever, dry cough, shortness of breath, headache, myalgia, oxygen saturation, and mortality rate) and interpretation of laboratory assays (CRP, MDA, TAC, WBC, neutrophils count, lymphocytes count, ratio of neutrophils to lymphocytes, levels of 25 hydroxyvitamin D and magnesium) will be assessed in the study groups.RandomizationA computer-generated block randomization list is used for randomization.Blinding (masking)Investigators and patients are blinded to group allocation and treatment. A double-blind design is achieved using matched placebos.Numbers to be randomized (sample size)A total of 104 eligible patients are randomized into four groups of 26 subjects (1:1:1:1 allocation ratio).DiscussionWith the rapid prevalence of COVID-19 in recent years, more attention has been paid to effective dietary supplementation to improve clinical symptoms and biochemical parameters in these patients. To our knowledge, this is the first study to evaluate the effects of vitamin D supplementation in combination with magnesium or alone with respect to this infectious disease. The findings of the current RCT will provide evidence regarding the effectiveness of dietary supplementation strategies to improve COVID-19 outcomes.Trial statusEthical approval of the first version of the study protocol was obtained from the medical ethics committee of Hormozgan University of Medical Sciences, Bandar Abbas, Iran on May 30, 2021 (IR.HUMS.REC.1400.085). Currently, the recruitment phase is ongoing since August 23, 2021, and is anticipated to be complete by the end of August 2022.Trial registrationThe study protocol was registered in the Iranian Registry of Clinical Trials (https://www.irct.ir; IRCT20210702051763N1) on August 14, 2021. https://www.irct.ir/trial/57413Full protocolThe full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this letter serves as a summary of the key elements of the full protocol.