F1000Research

Aims: Our primary aim was to determine the immediate effects of using a supported stepping device on the real-time locomotor behavior of pre-walking infants with Down syndrome (DS). Our secondary aim was to characterize the role of the caregiver in facilitating infant locomotor behavior by quantifying infant-initiated and caregiver-initiated walker movement, and to test whether walker movement encourages stepping behavior. Methods: Pre-walking infants with DS played with their caregiver in two conditions--with and without assistance from a wheeled suspension walker. To examine changes across development, we recorded infants across one to four sessions from 10 to 19 months of age. Results: Across developmental stages, we found that suspension walkers robustly increased infants' locomotor behavior: The walker increased upright time, percent time stepping, stepping rate, upright bout rate, percent time locomoting, and total bout rate. Most walker movement was initiated by caregivers, and infants stepped more while the walker was moving compared to stationary. Conclusions: Even without practice, pre-walking infants with DS were able to take advantage of the suspension walker to increase their locomotor behavior. Caregivers facilitated infants' activity by moving the walker. Future work will examine the potential of overground suspension walkers for home-based intervention.

Sepsis is a global health problem. Patients in the Intensive Care Unit (ICU) are at risk of having sepsis because of their vulnerability and use of invasive medical devices. Emerging antimicrobial-resistance complicates treatment. Understanding bacterial profiles and antibiotic sensitivity patterns in the ICU plays an important role in managing sepsis, optimizing antimicrobial use, and improving patient outcomes. The aim of this study was to show bacterial profiles and antibiotic sensitivity patterns among patients who were admitted to the ICU at Mbeya Zonal Referral Hospital for 12 months. This was a prospective cross-sectional study among 187 sepsis-suspected patients. Data analysis was performed using SPSS Version 27. Categorical data were summarized by frequency and percentage. Fishers exact test, chi-square test, and modified Poisson regression were used to show the association between patients clinical variables and culture positivity at a 95% CI. Statistical significance was set at a p-value < 0.05. Out of 187 samples, 41.7% were culture positive. Gram-negative bacteria were commonly isolated (65.4%, with Klebsiella pneumoniae and Escherichia coli being commonly isolated. Commonly isolated Gram-positive bacteria were Coagulase-negative Staphylococcus species (19%). 100% of gram-positive bacteria and 96% of gram-negative bacteria were Multi-Drug Resistant (MDR), respectively. In multivariable analysis, patients who were intubated and mechanically ventilated (aPR = 2.208, 95% CI: 1.133-4.305, p = 0.020) and post-laparotomy patients (aPR = 3.241,95% CI: 1.320-7.958, p = 0.010) independently had a higher proportion of Gram-negative bacteria. The study reveals a high level of resistance to commonly used antimicrobials in our setting, necessitating strengthening of the antimicrobial stewardship program and routine surveillance of antimicrobial resistance patterns.

We used Scopus data on 243949 top-cited scientists to map scientific cosmopolitanism defined as having at least two different countries that contribute alone at least 10 percent of an author published record as indexed in Scopus. 20.4 percent of the top-cited authors were cosmopolitan based on this definition. Based on current author affiliation, rates varied widely from 9% to 76% across countries with at least 250 top-cited authors. Countries with few top-cited authors had almost always high rates of cosmopolitanism. The proportion of top-cited authors who are cosmopolitan has steadily increased over time in younger generations among those who started publishing after 1965 reaching 43% recently. Large differences were also seen across scientific subfields from 1% in General Psychology and Cognitive Sciences to 46% in Econometrics. Across the 30 country pairs that were most over-represented, countries shared borders, languages, most common religion pairs, or any of these features in 15, 19, 26, and 29 cases, respectively. The map of cosmopolitan authors reveals a large and increasing proportion of the most influential scientists who share two or more scientific homes that each has made a substantial contribution to their career. Cosmopolitanism among scientists requires better study to help facilitate its potential positive contributions not only to individual scientists but to science and society more broadly.

At-home sampling can address obstacles to participation in transcriptomics research. We previously developed the homeRNA and homeRNAmax platforms; these custom-designed tubes containing RNA stabilizer interface with a blood tube compatible with upper-arm blood collection devices, allowing for blood collection and RNA stabilization to occur from a participant's home. In this work we introduce homeRNAdrop, an insert for a commercially available blood tube (BD Microtainer) that divides the tube into two compartments: the top compartment holds 200 L blood and the bottom compartment holds ~590 L liquid stabilizer (RNAlater). By combining blood collection and RNA stabilization into the same tube, homeRNAdrop streamlines sample preparation for participants and allows for more compact sample storage for the lab. In a remote pilot study, n=25 participants from across the United States tested the homeRNAdrop kit. The n=23 samples successfully received by the lab show that samples collected using homeRNAdrop are of sufficient RNA quality (all RINs > 6, a common cutoff for analysis) and yield (mean yield=1.44 g) for downstream gene expression analysis. Almost all participants who successfully collected blood using the Tasso Mini device found the homeRNAdrop device easy to use (n=23/24). Overall, this work adds a simplified, user-friendly platform to the growing suite of tools for remote blood RNA stabilization.

Frailty assessment is important while awaiting lung transplantation (LTx), as frailty is associated with disability and death before and after LTx. We assessed known risk factors and/or frailty indicators in frail, pre-frail, and non-frail patients according to the Short Physical Performance Battery (SPPB) and the Frailty Instrument for primary care of the Survey of Health, Ageing and Retirement in Europe (SHARE-FI), and evaluated the value of SHARE-FI as a proxy to detect frail patients. Frailty was assessed using SPPB and SHARE-FI in 82 patients on a waiting list for LTx. Demographic, anthropomorphic, and clinical variables were collected, and patients underwent respiratory/cardiorespiratory, biochemical, and quadriceps muscle performance assessments. The mean age was 57.3 {+/-} 9.4 years. Chronic obstructive pulmonary disease (COPD) (41.5%) and interstitial lung disease (ILD) (30.6%) were the most common indications for LTx. Four (4.9%), 13 (15.9%), and 65 (79.3%) patients were classified as frail, pre-frail, and non-frail by SPPB, respectively. These figures were 26 (31.7%), 41 (50%), and 15 (18.3%) with SHARE-FI. SPPB found differences between frail/pre-frail and non-frail patients in physical performance (6-minute walking distance) and muscular assessment, while SHARE-FI found differences in age, 6-minute walking distance, and oxygen saturation, and a trend in muscular strength. For COPD and ILD, frailty discrimination was better with SPPB. Concordance between the two measurements was weak, although all SPPB-frail ILD patients were detected by SHARE-FI. In patients awaiting LTx, SPPB showed better discrimination than SHARE-FI for COPD and ILD. SHARE-FI seems appropriate as a preliminary screening instrument for patients with ILD.

Sepsis is a substantial contributor to neonatal mortality in Africa, with Klebsiella pneumoniae as the leading causative pathogen. Incorporating molecular tools such as whole genome sequencing (WGS) into routine surveillance of important bacterial pathogens, including those causing neonatal sepsis, can support targeted deployment of infection prevention and control measures and treatment interventions. This study aimed to understand the current practices and capacity for culture, identification and genomic analysis of bacterial pathogens in Africa, with a particular focus on K. pneumoniae, to support standardised genomic surveillance. A cross-sectional online survey was distributed to various clinician and scientist networks across Africa. All respondents completed a demographics section, while sections on laboratory test capacity, blood culture practices, WGS, and bioinformatics analysis were completed based on experience in these aspects. Responses were received from 52 institutions in 25 African countries. Among 51 institutions completing the laboratory test capacity section, 61% reported performing blood cultures, with the majority using manual commercial biochemical systems for species identification (71%) and manual disk diffusion for antibiotic susceptibility testing (82%). Participating institutions reported near-universal access to a -80{degrees}C freezer, centrifuge and thermocycler, but shaking incubators were less commonly available (67%). More than half of respondents (54%) indicated that they perform the entire WGS workflow (including DNA extraction, library preparation and WGS) internally, with most performing DNA extraction internally (88%) using column-based kits (70%). Outsourcing was progressively more common at later workflow stages. Infrastructure challenges that limit bioinformatics analysis capabilities were reported by all 23 respondents who completed this question, including limited access to high-performance computing and data storage space. This survey found sufficient capacity to support genomic surveillance of neonatal sepsis pathogens across participating African institutions. However, investments in blood culture, supply chains, sequencing, bioinformatics, and data dissemination capacity are needed to realise its full potential. These findings will support the development of standardised genomic surveillance protocols tailored to the diverse capacities of African laboratories.

Introduction and objectives Hydrocephalus is a common complication of aneurysmal subarachnoid haemorrhage. This is one of several standard indications for the insertion of an external ventricular drain, but there are no standard guidelines for timing of extraventricular drain discontinuation in this population. Therefore, the study aims were to examine the 1) factors associated with extraventricular drain duration in aneurysmal subarachnoid haemorrhage and 2) association between extraventricular drain duration and clinical and resource-based outcomes. Methods In this single centre retrospective cohort study, data for adult patients treated in the ICU between 2015-2023 with aneurysmal subarachnoid haemorrhage and requiring an extraventricular drain were analysed. Data were extracted from both a prospective patient registry and the electronic medical record. Linear regression modelling was used to identify the factors associated with extraventricular drain duration. Measures used to examine the association between extraventricular drain duration, and the outcomes of interest included hazard ratio, relative risk, and mean differences as appropriate for a specific outcome. Results Of the participants (n=205), 68% (n = 140) were female, mean age was 60.7 (SD 13.3) years and 71% (n = 145) had a modified Fisher score of 4. Mean extraventricular drain duration was 15.3 (SD 8.6) days. The number of days mechanically ventilated and extraventricular drain challenge by clamp trial were associated with an increased duration of extraventricular drain treatment. Increased extraventricular drain duration was associated with an increased incidence of ventriculoperitoneal shunt insertion, and an increase in ICU and hospital length of stay when extraventricular drain duration exceeded 20 days. Conclusion The factors associated with an increased duration of extraventricular drain treatment were a longer duration of mechanical ventilation. The outcomes associated with an increased duration of extraventricular drain treatment were an increased incidence of ventriculoperitoneal shunt insertion, an increased incidence of ventriculitis when extraventricular drain duration exceeded 20 days, and an increase in ICU length of stay. These study findings may inform the conduct of a larger multi-centre study to examine the factors associated with duration of treatment with extraventricular drain, and outcomes associated with extraventricular drain duration.

Background Training in grant proposal writing is an essential component of professional development for academic scientists in the biomedical and behavioral sciences. Despite the expansion of inter- and intra-institutional grant writing coaching groups as an approach to honing these skills, specific features that enhance or limit coaching group effectiveness have not been rigorously studied. Methods Qualitative inerviews were conducted with a subset of early-career investigators (n=204 and coaches (n=36) engaged in a national, U.S. based, group-randomized trial of grant writing coaching groups to test the effects of two variables on submission and funding of national-level proposals: (1) coaching duration (regular/extended dose) and (2) mode of engaging a scientific advisor (someone with content-aligned expertise) in the coaching process. This report focuses on interviews conducted upon completion of the regular coaching dose - 5 months of biweekly, group-based coaching sessions to support active proposal writing. Interviews were designed to identify which coaching group elements were perceived to be the most critical. Transcribed interviews were analyzed using deductive (participants) or open (coaches) coding to identify themes. Results Triangulation of results from participant and coach interviews showed strong concordance that coaches, peers, and scientific advisors all played key roles in supporting intervention efficacy. Sufficient alignment of scientific fields and/or methodologies among group members was important, although breadth of perspectives was also valued. Other critical group features were skilled and well-organized coaches, detailed feedback, peer-to-peer support (technical and psychosocial), and clear expectations for group functioning. Factors attenuating impact included variation in participants' engagement and "readiness to write," within-group mismatches of expertise or grant mechanisms, and limited research support at some participants' home institutions. Conclusion This study identified key elements of successful grant writing coaching groups and potential barriers to their effectiveness, while yielding insights about tailoring this approach for individuals at different stages of proposal development.

Funding and publishing scientific research has become increasingly competitive, highlighting a growing need for clear and accurate scientific communication. Scientific editors are professionals who help ensure that grant proposals and research manuscripts meet the standards of funding agencies and peer-reviewed journals while effectively communicating research significance to diverse audiences. However, detailed information characterizing the scientific editing profession is scarce. While some organizations have conducted salary surveys, to our knowledge, no comprehensive survey of the scientific editing field has been conducted. Here, we report findings from a 2024 comprehensive survey of 132 scientific editors. We collected data on demographics and education, career experience and current employment, skills and types of editing, and outcomes and satisfaction. Our data reveal that scientific editors have homogenous demographic characteristics but considerable variability in job titles, employment mechanisms, and career pathways. As the responsibilities of many scientific editors, including supporting proposal development, applying best practices in grantsmanship, and identifying strategies to enhance competitiveness for research funding, overlap with those of research development professionals, our findings provide considerations for further incorporating or defining the role of scientific editors within research development offices. Our results also suggest avenues for scientific editors to start or advance their careers. We anticipate that our results will serve as a foundation for discussions on the future directions of the scientific editing profession as well as areas for future research and professional development.

Motivation: High-throughput sequencing technologies have driven rapid growth of biological sequence databases. Public repositories must therefore rely on automated computational heuristics to screen submitted sequences for errors and low quality. For example, SILVA SSU Ref, which exploits the conserved nature of 16S and 18S rRNA sequences, applies strict algorithmic quality controls yet still accepts sequences with up to 30% of their nucleotides deviating from any previously accepted sequence. This permissiveness creates opportunities for the admission of modified sequences, such as biologically plausible sequences generated by DNA foundation models. The vulnerability of public sequence databases to becoming polluted or poisoned with modified sequences necessitates the development of methods to detect such sequences. Results: We present the first investigation, to our knowledge, of the detectability of modified sequences. We consider simple computationally-modified 16S rRNA sequences that pass the quality control inclusion criteria of the SILVA database, which we generate via random substitutions. We present classifiers that can distinguish such modified sequences from natural 16S rRNA using conserved motifs. Our best classifier achieves over 90% sensitivity and specificity on our testing set when using a 5% artificial mutation rate. One feature used in our classifiers, gapped k-mers constructed from universally conserved nucleotides, was conserved across all three domains of life despite relying on exact matches to patterns found in E. coli, advancing our understanding of conserved grammatical structure in small subunit rRNA sequences. Availability and Implementation: Our source code is available at https://github.com/rainhaworth/16S-Mutation-Classifiers.

Background: Emergency conversion from labor epidural analgesia to Category I cesarean section leaves little time for epidural top-up to produce a surgical block. We examined whether low-dose intravenous esketamine could provide short-term bridging analgesia and sedation while maintaining maternal hemodynamics, oxygenation, and early neonatal safety. Methods: In this randomized study, parturients requiring Category I cesarean section after labor epidural analgesia received either esketamine 0.15 mg/kg or normal saline 1 min before skin incision, together with epidural alkalinized lidocaine. The primary outcome was the longitudinal change in maternal systolic blood pressure during the 20-min observation window. Secondary outcomes included heart rate, SpO2, intraoperative pain, surgeon satisfaction with muscle relaxation, Ramsay sedation score, and neonatal Apgar scores. We analyzed repeated continuous outcomes with linear mixed-effects models and repeated binary outcomes with generalized estimating equations. The single post-administration Ramsay outcome was analyzed using logistic regression. Apgar scores were summarized descriptively using medians, interquartile ranges, and counts.Results: We analyzed 55 parturients, 31 in the esketamine group and 24 in the normal saline group. Esketamine did not meaningfully alter the systolic blood pressure trajectory. Heart rate and SpO2 showed broadly similar patterns between groups, with no signal of esketamine-related respiratory deterioration. The esketamine group had lower odds of intraoperative pain at 5, 15, and 20 min and a higher probability of target Ramsay sedation. Surgeon satisfaction with muscle relaxation showed no clear between-group difference. Apgar scores remained high in both groups. Conclusion: Low-dose intravenous esketamine 0.15 mg/kg may be a practical bridging adjunct during emergency conversion from labor epidural analgesia to Category I cesarean section. It improved early pain control and target sedation without a clear adverse signal in systolic blood pressure, heart rate, oxygenation, or early Apgar scores. Trial Registration: Chinese Clinical Trial Registry, ChiCTR2600121948; retrospectively registered.

Background: School-based implementation of robot-assisted walking may support increased physical and social participation for children with physical disabilities, but evidence from an adequately powered trial is needed. This pilot study evaluated implementation strategies and study procedures to inform a future definitive trial. Methods: Participants were randomized to 12-weeks of robot-assisted walking or control, with subsequent crossover to the other condition. In the intervention arm, targeted dose was 75 minutes of robot-assisted walking, spread across three days/week. Implementation strategies for the child's classroom team included educational materials, centralized technical assistance, school champions, and on-going training. Implementation strategy evaluation focused on intervention protocol feasibility (i.e., weekly device use, troubleshooting) and fidelity (documentation of implementation strategy modifications). Preliminary estimates participation goal changes were obtained using the Canadian Occupational Performance Measure (COPM) 'Performance' scale (/10). Results: Eight children with neurodevelopmental physical disabilities participated (mean age 3.5, SD 0.5 years). Device use varied from 2.1 to 4.3 days/week (median 3.3) with a range of 48 to 96 minutes/week (median 80). Target use of >= 3 days/week was achieved for 66% of weeks and met the >=75-minute target for 33% of weeks. Troubleshooting occurred in 18.5% of sessions. Two implementation strategies were modified to improve feasibility. COPM mean change was 3.56 (SD 1.07) for robot-assisted walking and 2.11 (SD 2.41) for control (dz=0.74). Conclusions: This pilot study provided preliminary evidence regarding both the feasibility of robot-assisted walking implementation in schools and its potential effectiveness for children with physical disabilities. Findings support progression to a definitive trial.

Incidence of ventilator-associated pneumonia (VAP) is increased in patients admitted for brain injury. Staphylococcus aureus appears to be a particularly common pathogen in these respiratory infections. Our aim was to confirm the extent of S. aureus involvement in VAP among patients with neurological injuries. We conducted a retrospective, multicenter study including patients with and without neurological injuries who developed VAP during their ICU stay. Among 15 702 patients admitted in the participant centers during the study period. 407 were finally included in the study. S. aureus was involved in 122 (61.6%) VAP in brain-injured patients and 63 (30.1%) of non-brain-injured patients. In brain-injured patients, multivariate analysis identified age (0.97 [0.95; 0.98]), antibioprophylaxis (0.31 [0.18; 0.53]; p < 0.0001), subarachnoid hemorrhage (2.18 [1.01; 4.68]; p=0.0461), lower Glasgow coma score (0.92 [0.87; 0.97]; p= 0.004) and SAPS II (0.98 [0.97; 1]; p=0.0174) as critical factors associated with the risk of S. aureus in VAP. In the non-brain-injured population, multivariate analysis identified antibioprophylaxis (0.38 [0.22; 0.65]; p=0.0006), age (0.96 [0.95; 0.98]; p<0.0001), SAPS II (0.98 [0.97; 1]; p=0.0265), thoracic surgery (0.21 [0.09; 0.48]; p=0.0002) and peripheral neurosurgery (1.95 [1.2; 3.19]; p=0.0076) as critical factors. A total of 172 patients (42.3%) died during their ICU stay and 90-days mortality was 194 (47.7%). No difference of mortality was noticed function of VAP-associated pathogen.

PURPOSEPancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy with poor prognosis. A transcriptomic-based algorithm called Purity Independent Subtyping of Tumors (PurIST) relies on expression profiling of a defined set of genes to stratify PDAC into classical and basal-like molecular subtypes and assigns a confidence level to the subtypes as either "strong," "likely," or "lean." In this study, we apply PurIST to Appalachian and non-Appalachian patient cohorts and assess demographic variables between groups that may influence treatment outcomes. PATIENTS AND METHODSThis 13-site study includes 780 PDAC patients. Patients were divided into Appalachian and non-Appalachian cohorts according to Appalachian Regional Commission guidelines, and differences in PurIST classification, tobacco use, and alcohol use were analyzed. RESULTSIndividuals from Appalachian regions were more likely to receive a subtype classification from PurIST with "strong" confidence as opposed to "likely" or "lean" (P=0.0175; odds ratio=1.66). We did not observe any significant difference between basal and classical subtype classification in Appalachia (P=0.1457), yet an exploratory analysis showed that individuals aged [&ge;]85 were significantly more likely to have basal-like tumor classifications (P=0.005817; odds ratio=3.79). Appalachian patients were more likely to have a history of smoking (59.6% vs 49.9%; P=0.01756) and less likely to report alcohol consumption (50.5% vs 65.6%; P=0.000229). CONCLUSIONWe conducted the largest comparison of the PurIST algorithm in Appalachia to date and found PurIST is more likely to have higher confidence in molecular subtype classifications for Appalachian PDAC tumors compared to non-Appalachian tumors. If PurIST is to be considered as a prognostic or decision-making tool for PDAC patients, we must account for variability in different populations and model the likelihood that tumors will have a strong molecular signature.

Background: Qualitative research provides insights into human behavior, perspectives, and lived experience. While existing standards like the Consolidated Criteria for Reporting Qualitative Research (COREQ) have improved transparency and rigor, the integration of large language models (LLMs) into qualitative research introduces new challenges for not covered by current guidelines. LLMs transform analytic processes and blur the line between human interpretation and algorithmic text generation, raising concerns about transparency, authorship, and epistemic trust. The here presented COREQ+LLM guideline extends COREQ to establish comprehensive reporting standards for LLM use in qualitative research. Methods: The study followed the EQUATOR Network's guideline development framework in two phases: (1) a systematic scoping review to identify best practices for reporting LLM use in qualitative research, and (2) a Delphi consensus process with international experts in qualitative research, AI, medicine, ethics, and journal editing to develop a comprehensive reporting checklist. Findings: The scoping review identified 149 studies relevant for full-text review. From this literature, 29 preliminary reporting items were extracted. In the first Delphi round, international experts (N=141) assessed the items' relevance. 20 items were accepted for inclusion in the guideline (>75% agreement); however, four required reevaluation in the second round, five underwent wording revisions, and six new items were proposed. In the second Delphi round (N=115; retention rate 82%), one was excluded, while four items still lacked consensus. Remaining items were discussed in a virtual consensus conference with nine representatives of the expert panel, resulting in the inclusion of two and the exclusion of two others. The final checklist comprises 31 items grouped into seven categories, serving as an extension of the original COREQ checklist. Interpretation: COREQ+LLM offers structured, consensus-based guidance to enhance transparency, reproducibility, and methodological rigor in qualitative research using LLMs. Its adoption will support researchers, reviewers, and editors in maintaining trust and scientific integrity.

Purpose Delirium affects around 40% of intensive care unit (ICU) patients and adversely affects survival, length of stay, and cognitive recovery. Despite this, implementation of systematic clinical delirium assessments is variable. We sought to validate a point-of-care electroencephalography (EEG)-based system (Ceribell, Inc.) for the detection of delirium in the ICU. Methods In this multicenter, prospective cohort study, we monitored adult ICU patients with the Ceribell EEG system for 6-8 hours for a minimum of three days. Up to three times per day, expert clinicians assessed participants for delirium and research coordinators completed Confusion Assessment Method for the ICU (CAM-ICU) assessments, which we used to calculate CAM-ICU-7 severity scores. We compared expert clinician diagnoses with Ceribell EEG algorithm output using data from 30-minute periods surrounding each clinician assessment. Results Among 225 participants analyzed (median age: 64 years, 60% male, 21% mechanically ventilated), expert clinicians performed 857 assessments and found 24% of participants were delirious during at least one assessment. The Ceribell EEG system detected delirium with a sensitivity of 81% (95% CI: 76% to 87%) and specificity of 81% (95% CI: 78% to 84%). The continuous Ceribell EEG system score correlated with CAM-ICU-7 delirium severity scores (bootstrapped median rho 0.58, IQR: 0.54-0.62, p <0.001). Conclusion In a mixed adult ICU population, the Ceribell EEG system identified delirium with good sensitivity and specificity. Its continuous output was associated with delirium severity, highlighting its potential ability to characterize underlying physiological patterns across the clinical delirium spectrum.

Small RNA (sRNA) sequencing is widely used to study siRNA, miRNA and piRNA pathways and to profile sRNAs derived from viruses, transposons and host transcripts. However, many sRNA workflows rely on command-line mapping and separate software for downstream analysis and visualisation. We present sRNAMap, an HTML5/JavaScript application for mapping and analysing sRNA sequencing data. sRNAMap accepts either raw FASTA/FASTQ reads or pre-aligned BAM files. For raw reads, sRNAMap uses a k-mer-seeded alignment algorithm that runs directly in the browser using parallel Web Workers where supported. It generates strand-specific per-base coverage, 5'- and 3';-end profiles, read-length distributions and nucleotide-bias summaries, with optional library-size normalisation. It also quantifies characteristic read-overlap signatures, including 5';-to-5'; overlaps associated with ping-pong-like processing. Additional modules quantify phased sRNA production, non-templated 3'- and 5'-additions, and sequence diversity. Analyses can be saved and restored as JSON or exported as self-contained HTML reports containing figures and analysis metadata. Benchmarking against Bowtie 2 under approximately matched alignment settings using a representative virus-infected arthropod small-RNA dataset showed highly concordant mapping profiles. Per-position depth showed an R^2 of approximately 0.998, while 5';- and 3';-end counts showed R^2 values of approximately 0.97. sRNAMap is available at https://github.com/rhparry/sRNAMap under the MIT licence.

Purpose Autistic adults have diverse communication characteristics that are not well captured by standard demographic measures. Communication affects self-determination, relationships, access to healthcare, and services. Characterizing communication differences may improve research and intervention targeting for meaningful subgroups of autistic adults. Methods The Academic Autism Spectrum Partnership in Research and Education (AASPIRE) Outcomes Project team used a community based participatory research (CBPR) approach to develop a self- or caregiver-report module to characterize communication among autistic adults. The 10-item module asks about receptive and expressive communication, literacy, speech reliability, usage of digital communication, use of alternatives to speech, and communication fluency. It can be completed directly, with or without support, or via a caregiver. We used baseline survey data from 844 autistic adults to evaluate the module and derived a five-level variable, Communication Profile, from selected module items to stratify participants. We examined completion feasibility, response consistency, and construct validity. We also assessed test-retest reliability in a 15% random subsample who completed a 2-week retest following the 6-month survey, with oversampling of caregiver-report respondents. Results The Communication Characteristics module demonstrated high completion feasibility, minimal systematic error, and strong construct validity. The Communication Profile variable stratified participants into five meaningful communication profiles and demonstrated strong construct validity and substantial test-retest reliability ({kappa} = .69). Conclusion The Communication Characteristics module and Communication Profile variable provide a valid approach for characterizing communication diversity among autistic adults for research, clinical, and service settings. The full AASPIRE Measurement Toolkit is available at https://aaspire.org/measurement. Lay Summary Autistic people communicate in many different ways, and their communication may change in different situations. We developed and tested a set of survey questions to describe an individuals communication. We also used the results to describe 5 groups of autistic people based on how they communicate, without treating these groups as different types of autism.

Motivation: Tree sets appear naturally when performing model based phylogenetic analyses. When tracking host-parasite co-evolution, testing sensitivity of different model assumptions, or even just checking convergence of individual runs of the same analysis, the question arises: are a given pair of tree sets the same? And if they are not the same, how do they differ? Results: We provide DensiTree 3, an interactive tool for inspecting pairs of sets of trees that allow visualising both tree sets using a single panel. Incorporation of CCDs provide better summary trees, taxon orderings and extra functionality like rogue detection, making it easier to interpret tree samples. Furthermore, a clade comparison graph allows inspection of differences in clade support and clade heights linked to the double-DensiTree panel. Together, these visualisations of tree sets make it easy to identify potential differences in the tree sets and interactively inspect these differences. Furthermore, recent advances in conditional clade distributions (CCDs) to represent tree distributions have been incorporated in DensiTree 3, and the most visible part of the user interface has been updated for a more modern look. Availability: DensiTree 3 is freely available from https://cs.auckland.ac.nz/~remco/DensiTree/. The program is licensed under GPL and source code is available via the link above.

Bioinformatics software plays a central role in biological research, yet many academic projects lack robust testing and continuous integration (CI) practices. This absence can compromise reproducibility, accessibility, and long-term maintainability. In this study, we conduct an empirical analysis of GitHub repositories spanning bioinformatics and other scientific software domains to examine the relationship between CI, software testing, and software quality. Repository discovery was performed using domain-specific search terms via GitHub's Application Programming Interface (API). This was followed by a layered data extraction pipeline, which included a Large Language Model (LLM) validation step, that connected repositories to published works, institutions, authors, funding, and citation counts. By integrating repository activity, community engagement, and backlog health into a composite Repository Quality Index (RQI), we find that the presence of CI and software tests is significantly associated with higher repository quality. Additionally, repositories with higher academic citation counts tend to cluster in higher RQI tiers, suggesting that software quality, which is driven by proper testing and integration, is associated with academic impact and funding status. These results demonstrate that adopting industry-standard development practices, such as CI and software testing, is a tractable path toward more sustainable and impactful academic software and funding opportunities.