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Processing of 10X 500 PBMC single cell ATAC-seq data with SnapATAC2

Input files for SnapATAC2 tutorial on Galaxy

Processed scRNA and scATAC data in DRCTdb

Understanding the molecular mechanisms underlying genetic diseases is challenging due to the involvement of both environmental and genetic factors. Genome-wide association studies (GWAS) have identified numerous genetic loci, but their functional implications remain largely unknown. Single-cell multiomics sequencing has emerged as a powerful tool to study disease-specific cell types and their relationship with genetic variants. However, there is a lack of comprehensive databases for exploring genetic disease-related cell types and their mechanisms across different human tissues. In this study, we present the disease-related cell type database (DRCTdb), a database that integrates GWAS data and single-cell multiomics data to identify disease-related cell types and elucidate their regulatory mechanisms. DRCTdb contains well-processed single-cell multiomics data in 16 studies, encompassing transcriptome and epigenetic information overall 4 million cells within 28 tissues. Through DRCTdb, user can easily browse relationships and regulatory mechanisms between SNPs of 42 genetic disease and cell type in different human tissue based on GWAS and single cell multiomics data. Moreover, DRCTdb also provides data download, which allowing users to download well-processed <a name="_Int_HEP27DcN"></a>single-cell multiomics data and analysis result from DRCTdb

Process-based Modeling of Ecosystem-Level Monoterpene from a Japanese Larch (Larix Kaempferi) Forest

Title ''Process-based Modeling of Ecosystem-Level Monoterpene from a Japanese Larch (Larix Kaempferi) Forest'' Zhanzhuo Chen 1,2, Tomomichi Kato 3, Akihiko Ito 4,5, Tatsuya Miyauchi 3, Yoshiyuki Takahashi 4, and Jing Tang 2 1 Graduate School of Global Food Resources, Hokkaido University, Sapporo, Hokkaido, 060-0809, Japan 2 Center for Volatile Interactions (VOLT), Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark 3 Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan 4 Earth System Division, National Institute for Environmental Studies (NIES), Onogawa, Tsukuba, Ibaraki, 305-8506, Japan 5 Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan Correspondence to: Tomomichi Kato (tkato@agr.hokudai.ac.jp)

Prismatic Wave Imaging Reveals Details of Highly Steep Structures: Processed 1994 BP benchmark model

This zip file contains our processed 1994 BP model, some of the synthetic seismic data, and the Matlab drawing code. Each part has its own folder and README file, check these files for more information

WarpTools and MCore processing of a 5 tilt series subset of EMPIAR-10491

This dataset contains an example of cryo-electron tomography (cryo-ET) data processed using command line tools available in <a href="https://anaconda.org/warpem/warp">Warp v2.0.0dev9.</a> Processing a 5 tilt series subset led to a 2.92 Å reconstruction of apoferritin. The subset processed includes <ul> <li>TS_1</li> <li>TS_11</li> <li>TS_17</li> <li>TS_23</li> <li>TS_32</li> </ul> External packages used for processing include <a href="https://github.com/czimaginginstitute/AreTomo2">AreTomo2</a> for tilt series alignment and <a href="https://github.com/3dem/relion/tree/ver5.0">RELION 5</a> for initial 3D refinement. The raw data is not included but can be downloaded from <a href="https://www.ebi.ac.uk/empiar/">EMPIAR</a> using the following code snippet on UNIX systems <pre><code>wget --show-progress -N -q -nd -P ./ ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/gain_ref.mrc; for i in 1 11 17 23 32; do echo "======================================================" echo "================= Downloading TS_${i} ================" wget --show-progress ---timestamping --quiet --no-directories --directory-prefix ./mdoc ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/mdoc/TS_${i}.mrc.mdoc; wget --show-progress ---timestamping --quiet --no-directories --directory-prefix ./frames ftp://ftp.ebi.ac.uk/empiar/world_availability/10491/data/tiltseries/data/*-${i}_*.tif; done </code></pre> Processing is detailed in the `processing.sh` shell script. This script is not designed to be run end to end and instead should be run one command at a time.

Data from: CoZr nanocomposites in a ceramic-metal AlOx(OH)y/Al matrix with different Co/Zr ratio and its potential for syngas processing

Data from article in Dalton Transaction

Towards Immersive Process Simulation for Declarative Models - Accompanying Material

<div>This dataset contains the research protocol, transcripts and codings for the paper “Towards Immersive Process Simulation for Declarative Models.” Accepted for publication at the International Conference on Business Process Management - Forum. 2024.</div> <div> </div> <div>The documents are ordered by number. We describe their contents below:</div> <div> </div> <div>1. Appendix A - Consent Form used in research and validation interviews in section 4 and section 6</div> <div>2. Appendix B - DCR Training Material used to familiarize the research participants with DCR in section 4</div> <div>3. Appendix C - Elicitation Interview Script & Validation Session Interview Protocol used in sections 4 and 6</div> <div>4. Appendix D - First round of coding of Elicitation interviews</div> <div>5. Appendix E - Second round of coding of Elicitation interviews</div> <div>6. Appendix F - Third round of coding of Elicitation interviews</div> <div>7. Appendix G - First round of coding of Validation interviews</div> <div>8. Appendix H - Second round of coding of Validation interviews</div> <div>9. Appendix I1 - Third round of coding of Validation interviews, part 1</div> <div>10. Appendix I2 - Third round of coding of Validation interviews, part 2</div> <div>11. Appendix J - Validation participant DCR graph representation preferences: questionnaire and answers</div> Moreover, we included all the transcripts of the interviews in raw form.  <div>The file transcript_ideation.pdf contains the transcripts of the requirement elicitation interviews conducted during the research phase.</div> <div>The file transcript_validation.pdf contains the the transcripts of the validation interviews.</div>   The github repository https://github.com/GloriousHypnotoad/DCR-Graph-artifact contains the source code of the software artifact used in the paper.

Experimental datasets on "Real-time Observation of sub-100-fs Charge and Energy Transfer Processes in DNA Dinucleotides"

Experimental datasets referring to the manuscript entitled "Real-time Observation of sub-100-fs Charge and Energy Transfer Processes in DNA Dinucleotides"

Data from: Invertebrate diversity in groundwater filled lava caves is influenced by both neutral and niche-based processes

Aim: Understanding which factors shape and maintain biodiversity is essential to understand how ecosystems respond to crises. Biodiversity in ecological communities is a result of the interaction of various factors which can be classified as neutral or niche-based. The importance of these processes has been debated, but many scientists believe that both processes are important. Here we examined the importance of neutral vs. niche-based factors for shaping invertebrate communities. We hypothesized that if neutral processes are the main drivers of community structure we would not see any clear relationship between the structure of community and ecological factors. If niche-based processes are important we should see clear relationships between community structure and variation in ecological variables. Location: Groundwater-filled lava caves near Lake Mývatn, Iceland. Methods: We collected various ecological variables from these caves. Invertebrate communities were collected on the hard bottom using stone scrubbing and from epibenthic traps. Results: Both communities were species-poor, with low densities of invertebrates, showing the resource-limited and oligotrophic nature of these systems. Unusually for Icelandic freshwater ecosystems, the benthic communities were not dominated by Chironomidae (Diptera) larvae, but rather by crustaceans, mainly Cladocera. The epibenthic communities were not shaped by environmental variables, suggesting that they may be structured primarily by neutral processes. The benthic communities were shaped by the availability of energy, and to some extent pH, suggesting that niche-based processes were important drivers of community structure, although neutral processes may still be relevant. Main conclusions: The results suggest that both processes are important for invertebrate communities in freshwater, and research should focus on understanding both of these processes. The ponds we studied are representative of a number of freshwater ecosystems that are extremely vulnerable to human disturbance, making it even more important to understand how their biodiversity is shaped and maintained.

Supporting Information for the submitted manuscript by Rajič et al. The origin of tectonic mélanges and implication for the subduction interface processes

Files shared here contain supporting information for the submitted manuscript by Rajič et al. Appendix 1 file contains Text A.1, Tables A.1-2 and Figures A.1-8. Appendix 2 file contains all raw Raman spectra acquired in this study, along with READ ME text file.

opencc-by-nc-nd-1.0Jun 2024View details →

DNS dataset for modelling homogeneous ignition processes of clustering solid particle clouds in isotropic turbulence

<h2>Abstract</h2> This dataset is being published to enable the development of models for igniting and combusting solid particles in isotropic turbulence using flamelet tabulated chemistry. This dataset is generated using the forced homogeneous isotropic turbulence in order to investigate the effect of active turbulent forces on the ignition of particles, and it is used as the supplementary material for the manuscript "Modeling homogeneous ignition processes of clustering solid particle clouds in isotropic turbulence", which was accepted for publication in the special issue of Fuel Journal for the proceeding of the 4th international Oxyflame workshop. The particles are chosen to have near unity Stokes numbers, which promote particle clustering to study the ignition phenomenon for particle clusters, which is common during ignition and combustion of particle clouds in large industrial solid fuel-powered burners. Since the ignition process of clustering solid particle clouds is transient, different time instances during the ignition process are presented to facilitate the modelling effort for the transient ignition behaviour of the particles. The dataset consists of gas-phase data, particle data and the most important routines required to process the dataset.    This database is a valuable resource for users developing solid fuel ignition and combustion in turbulent conditions.  It should be noted that this dataset is a reduced version of the full dataset in order to size limitations in the sharing platforms. More information and full dataset can be provided upon request. For more information, contact: p.farmand@itv.rwth-aachen.de <h2>Technical details</h2> The data provided in this dataset contains gas phase data, particle data, and some post-processing scripts for visualization of the data. The data is generated in forced homogeneous isotropic turbulence (HIT) with an initial preferential concentration of the particles in a hot atmosphere to study the impact of particle clustering on ignition. Simulations were performed within a region with the physical size of 12.8mm * 12.8mm * 12.8mm with periodic boundary conditions in all directions. The domain size is discretized with a three-dimensional cartesian mesh with a resolution of Δx = 50 μm. A forced isotropic turbulent field with Re_λ=30 and the Kolmogorov length scale η =100 microns has been chosen. The dispersed phase consists of 10,000 particles of Colombian coal with D_p= 20 microns and T0=300K and with an apparent density of 700kg/m3. Non-reactive particles are first randomly distributed in the box filled with air with 20% oxygen and an initial gas temperature of T = 1500K, which is relevant to practical PCC applications. These conditions lead to an initial Stokes number of around 5, for which a clustering behaviour in particle cloud motion is expected. The employed forced isotropic turbulence ensures maintaining the same turbulence statistics during non-reactive and reactive simulations, as summarised in the following table: <table> <tbody> <tr> <td> time [ms] </td> <td> Re_λ </td> <td> Re_Turb </td> <td> η[m] </td> <td> l_t[m] </td> <td> t_η[ms] </td> <td> t_l[ms] </td> <td> St </td> </tr> <tr> <td>0</td> <td>30.7</td> <td>141.8</td> <td>1.04e-4</td> <td>4.27e-3</td> <td>4.47e-2</td> <td>5.33e-1</td> <td>6.199</td> </tr> <tr> <td>0.46</td> <td>30.9</td> <td>143.9</td> <td>9.94e-5</td> <td>4.13e-3</td> <td>4.16e-2</td> <td>4.99e-1</td> <td>6.207</td> </tr> <tr> <td>0.5</td> <td>30.5</td> <td>140.1</td> <td>9.96e-5</td> <td>4.06e-3</td> <td>4.27e-2</td> <td>5.05e-1</td> <td>6.333</td> </tr> <tr> <td>0.55</td> <td>29.4</td> <td>129.8</td> <td>1.01e-4</td> <td>3.88e-3</td> <td>4.34e-2</td> <td>4.94e-1</td> <td>6.032</td> </tr> <tr> <td>0.6</td> <td>28.5</td> <td>122.1</td> <td>1.02e-4</td> <td>3.76e-3</td> <td>4.46e-2</td> <td>4.92e-1</td> <td>5.775</td> </tr> <tr> <td>0.65</td> <td>27.7</td> <td>115.2</td> <td>1.04e-4</td> <td>3.66e-3</td> <td>4.48e-2</td> <td>4.81e-1</td> <td>5.365</td> </tr> </tbody> </table> η and t_η are the respective Kolmogorov length and time scales, and l_t and t_l correspond to the integral length and time scales.   <h3>Gas phase and particle data:</h3> The gas phase data has HDF5 formation, which contains selected scalars relevant to model developments. Since the ignition process is a transient process, two different time instances, t=0.5ms with the maximum number of ignited regions during the ignition process and t=0.65ms at the end of the ignition process, are chosen. Before starting the reactive simulations, a non-reactive simulation for 20.5ms was performed to form the particle clusters, and then the reactive simulation was started. Therefore, the data.out_2.100E-02.h5 corresponds to t = 0.5ms and data.out_2.115E-02.h5 corresponds to t = 0.65ms. Each HDF5 dataset has the following structure: Group Flow: <ul> <li>U, V, W</li> </ul> Group scalar:  <ul> <li>CO, CO2, H2O, C2H2, O2, N2, OH, progress variable (PV), temperature(T), enthalpy(h), heat capacity (Cp), density(RHO), pressure(P), mixture fraction(Z), dissipation rate, heat conductivity</li> </ul> Group C_dot: <ul> <li>Molar production rate of CO, CO2, O2, OH</li> </ul> Group ST: <ul> <li>Mass fraction rate of OH</li> </ul> Group var (data required for subfilter analysis and PDF modelling): <ul> <li>RHO * h</li> <li>RHO * h * h</li> <li>RHO * PV</li> <li>RHO * PV * PV</li> <li>RHO * RHO</li> <li>RHO * RHO * RHO</li> <li>RHO * T</li> <li>RHO * T * T</li> <li>RHO * Z</li> <li>RHO * Z * Z</li> </ul> These gas phase data can be used to study the Eulerian field, which is impacted by the particles through the source terms, which are obtained from the Lagrangian framework. For the particle data, two CSV files containing information about each particle's position and temperature are provided.  In each CSV file, which corresponds to the same time instance as the gas phase data, this structure can be found: <ul> <li>Points_0, Points_1, Points_2: particle position x,y,z</li> <li>coal_defaultT: particle temperature</li> </ul> <h3>Scripts:</h3> Different scripts are provided for a reader to enable the first-time use of the data, such as visualising the gas phase quantities, calculating the conditional mean and statistical analysis, and clustering analysis for the particles. Here is a brief information regarding the scripts: <ul> <li>hdf5_2D_Con_Mean_Plots.m: This script can be used for loading the HDF5 file and visualising the field, joint PDF, and joint correlation of different quantities with respect to different parameters. This script requires another module to calculate the conditional mean of the data.</li> <li>Compute_ConditionalMean_histograms_2D.m: This module calculates the conditional average of a 2D array.</li> <li>clustering_voronoi_3D.m: This script can analyse the particle data and calculate the clustering limit based on the Voronoi algorithm. It can also filter the clustered particles and separate different clusters using the nearest neighbour and DB-SCAN methods.</li> </ul>

Affordances of Scan Processing Methods

An INTRODUCTION to SCAN PROCESSING    This survey inquires about the affordances of historic and contemporary implementations of scan processing technology. Scan processing, also known as raster manipulation, refers to the separation and independent manipulation of the horizontal, vertical, and brightness components of a video image. It is often associated with the Rutt/Etra Video Synthesizer, which was designed in the early 1970s and used extensively by Steina and Woody Vasulka, Gary Hill, and other pioneering video artists.    Scan processing differs from other methods of video synthesis or processing in that it does not generate a normal video signal which can be displayed on a standard analog or digital video monitor. Rather, it outputs three independent signals (horizontal sweep, vertical sweep, and brightness) which must be rendered on an XY display of some kind (oscilloscope, vector monitor, ILDA laser, etc). The look of the scan processing effect can also be emulated by digital video software. Scan processing relies on an input image or video, and thus does not include other XY image techniques, such as Lissajous figures or vector line art and animations.     THREE METHODS of SCAN PROCESSING    The three methods of scan processing covered in this survey utilize the following technologies:    1) Analog scan processing hardware such as the Rutt/Etra Video Synthesizer, the Dave Jones Raster Manipulator, or the LZX Cadet series modules with output displayed on an analog Cathode Ray Tube monitor    2) Digital software designed to produce a set of analog horizontal, vertical, and brightness signals to be displayed on an analog Cathode Ray Tube monitor, such as the REWereHere or Vector Synthesis scan processing patches for Max and Pure Data.    3) Software which emulates the Rutt/Etra, scan processing, or Z-displacement effect entirely in the digital video domain, such as the v002 Rutt/Etra Quartz Composer plugin, the Rutt/Etra-Izer, or a number of filters and plugins for other softwares. ABOUT AFFORDANCES    "Affordances" is a term from interface design which describes the various possibilities an object suggests or offers to its users. These possibilities may or may not be part of the object's intended design, and may also be specific to certain users. For example, a coffee mug is designed for drinking a hot beverage, but just as easily I can scoop dry rice out of a bag, hold a dozen pens ready for writing, or elevate another object such as my laptop off the table by using it.    See: <a href="https://en.wikipedia.org/wiki/Affordance">https://en.wikipedia.org/wiki/Affordance</a>

Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf

This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section. This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>. To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.

Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication

Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication.

Data from: Severity of topsoil compaction controls the impact of skid trails on soil ecological processes

Skid trails are a major management-induced disturbance in temperate forest ecosystems with considerable impact on soil ecological processes that are so far poorly understood. In German forests, skid trails comprise 10 – 20 % of the forest area that is potentially affected by soil compaction through heavy machinery. We systematically investigated the influence of skid trails on physical, chemical, and microbiological soil parameters at 84 paired plots across four Central European forest types. In low mountain forests with steeper topography, skid trails had more drastic effects than in lowland forests. Skid trails in low mountain areas showed a decrease in the C to N ratio of microbial biomass (MBC/MBN), as well as increased microbial (MBC/SOC) and enzyme activities leading to faster carbon turnover (lower C/N, EOC/EN) and increased CO2 losses (CO2/SOC) from the soil. The overall effects of the skid trails in lowland forests were small. On base-poor soils, we found an increase in the MBC/MBN ratio, while skid trails in base-rich lowland soils showed a reduction in CO2/SOC, suggesting a proportional increase in soil carbon storage. Regardless of region-specific effects, the relative increase in the bulk density of the fine soil was identified as a 'golden trait' that determined the effects of skid trails on many soil parameters, as shown by negative correlations with SOC, N, MBC, MBN, MBP, MBC/SOC and CO2/SOC and positive ones with the activities of certain hydrolytic enzymes. Synthesis and Applications: Our data clearly showed that carbon conversion processes and soil respiration leading to significant carbon and nutrient losses increased significantly on skid trails in low mountain regions with relatively steep slopes, which was in sharp contrast to lowland sites. The strong context dependence of our findings suggests that the mapping of soil conditions in terms of slope, substrate and moisture with high spatial resolution is mandatory to assess the vulnerability of sites to soil compaction by heavy machinery. Based on such vulnerability analysis, negative impacts can be minimized through the designation of permanently fixed skid trails, the technical adaptation of vehicles (e.g., wide base tyres) as well as careful planning and timing of management operations that should be restricted to dry weather and soil moisture conditions or periods of frost.

Isogeochemical characterization of mountain system recharge processes in the Sierra Nevada, California

Mountain System Recharge processes are significant natural recharge pathways in many arid and semi-arid mountainous regions. However, Mountain System Recharge processes are often poorly understood and characterized in hydrologic models. Mountains are the primary water supply source to valley aquifers via lateral groundwater flow from the mountain block (Mountain Block Recharge) and focused recharge from mountain streams contributing to focused Mountain Front Recharge at the piedmont zone. Here, we present a multi-tool isogeochemical approach to characterize mountain flow paths and Mountain System Recharge in the northern Tulare Basin, California. We used groundwater chemistry data to delineate hydrochemical facies and explain the chemical evolution of groundwater from the Sierra Nevada to the Central Valley aquifer. Stable isotopes and radiogenic groundwater tracers validated Mountain System Recharge processes by differentiating focused from diffuse recharge, and estimating apparent groundwater age, respectively. Novel application of End-Member Mixing Analysis (EMMA) using conservative chemical components revealed three Mountain System Recharge end-members: (1) evaporated Ca-HCO3 water type associated with focused Mountain Front Recharge, (2) non-evaporated Ca-HCO3 and Na-HCO3 water types with short residence times associated with shallow Mountain Block Recharge, and (3) Na-HCO3 groundwater type with long residence time associated with deep Mountain Block Recharge. We quantified the contribution of each Mountain System Recharge process to the valley aquifer by calculating mixing ratios. Our results show that deep Mountain Block Recharge is a significant recharge component, representing 31 to 53 % of the valley groundwater. Greater hydraulic connectivity between the Sierra Nevada and Central Valley has significant implications for parameterizing groundwater flow models. Our framework is useful for understanding Mountain System Recharge processes in other snow-dominated mountain watersheds.

Evolutionary and ecological processes determining properties of the $\bm G$-matrix

The $\bm G$-matrix is the matrix of additive genetic variances and covariances for a vector of phenotypes. Here we apply the classical theory for the balance between selection drift and mutations to find the contributions to $\bm G$ from each locus. The fitness is approximated by a linear function of phenotypes. Fluctuations in the environment generate variation in the coefficients of the fitness function. We show that the $\bm G$-matrix can be decomposed into 4 additive components generated by selection, drift, mutations and environmental fluctuations. Selection is on average counteracted by the other three processes included in Fisher's concept of the deterioration of the environment, in accordance with Frank's approximate conservation law proposing that the response to selection at stasis on average is canceled by effects of drift and mutations. The theory illustrates that Fisher's fundamental theorem cannot be used to accumulate selection through time to describe adaption unless the other effects are corrected for. Another implication of the analyses is that the factor loadings to the eigenvector of the $\bm G$-matrix with the least eigenvalue are likely to indicate which characters contributing the most to the fitness function. This is information notoriously difficult to obtain in natural populations.

The extended 'common cause': causal links between punctuated evolution and sedimentary processes

The common-cause hypothesis suggests that the factors that control the availability of the Earth's sedimentary record may also affect probabilities of speciation and extinction and thus exert macroevolutionary controls on standing biodiversity. Here I show through computational modeling that common causes may also link sedimentary biases and microevolutionary processes of trait evolution. Using Gould's classic "evolutionary microcosm" of Bermuda and its diverse endemic clade of land snails, Poecilozonites, I show that the glacial-interglacial sea level cycles that toggle local sedimentation between rapid eolian accumulation and slow pedogenesis could easily toggle trait evolution between rapid bursts of morphological change driven small effective population size, disruptions in gene flow, and "genetic surfing" expansion events punctuated with long periods of slow morphological evolution associated with geographic range coalescence, large effective population size, and panmixia. The pattern produced by this interaction is expected to be similar to that produced by punctuated equilibria, even without accompanying speciation events. The spatial dynamics of this system are expected to produce patterns of random trait evolution that are more likely multi-rate evolutionary models than like the standard single-rate Brownian motion models that are currently used as the null model in many phylogenetic comparative methods. The Bermudian example of links between sedimentation and evolution is arguably extreme, but the principles of the extended common cause are likely to extend to many other paleontological systems.

Intervention fidelity and factors affecting the process of a mobile phone text messaging intervention among adolescents living with HIV: A convergent mixed methods study in southern Ethiopia

Objective: To assess the intervention fidelity and explore contextual factors affecting the process of a mobile phone text messaging intervention in improving adherence to and retention in care among adolescents living with HIV, their families, and their healthcare providers in southern Ethiopia. Design: A convergent mixed-methods design guided by the process evaluation theoretical framework and the RE-AIM framework was used alongside a randomised controlled trial to examine the fidelity and explore the experiences of participants in the intervention. Setting: Six hospitals and five health centres providing HIV treatment and care to adolescents in five zones in southern Ethiopia. Participants: adolescents (aged 10–19), their families and their healthcare providers. Intervention: Mobile phone text messages daily for 6 months or standard care (control). Results: 306 participants were enrolled in the process evaluation. Among the intervention participants (N =153), 171 (55.9%) of whom were men, most resided in an urban area 225 (73.5%), and participants had a mean age of 15 (2.62). The overall experiences of implementing the text messages reminder intervention were described as helpful in terms of treatment support for adherence but had room for improvement. During the study, 30,700 text messages were sent, and fidelity was high, with 99.4% successfully receiving text messages during the intervention. Barriers such as failed text messages delivery, limitations in phone ownership, and technical limitations affected fidelity. Technical challenges can hinder maintenance, but a belief in the future of digital communication permeates the experiences of the text messages reminders. Conclusions: Overall fidelity was high, and participants' overall experiences of mobile phone text messages were expressed as helpful. Contextual factors, such as local telecommunications networks and local electric power, as well as technical and individual factors must be considered when planning future interventions.

Compilation of existing underwater PAM repositories, libraries, and applications for sound processing

Resources for passive acoustic monitoring (PAM) are continuously expanding and being developed, yet a major challenge for users is staying up-to-date and finding the best software or application for their acoustics investigation. We expand on previous efforts (Rhinehart & Nicholson, 2022; Felgate, 2023) with the aim of providing a current, comprehensive list of 1) underwater sound repositories of raw sound data without significant processing, 2) biological sound reference libraries, with species or taxa identification, and 3) sound processing tools for visualization, annotation, or analysis. This spreadsheet contains three pages, one dedicated to each of the aforementioned items, along with some descriptive information to help users identify the best resources for their needs. This work was done to support the Global Library of Underwater Biological Sounds (GLUBS) project and funded in part by the Richard Lounsbery Foundation and from funding to SCOR WG #169 (GLUBS) provided by national committees of the Scientific Committee on Oceanic Research (SCOR) and from a grant to SCOR from the US National Science Foundation (OCE--2140395), with support from the International Quiet Ocean Experiment.