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544 results for “integrated models”
Data from: Prospective comparison of two models of integrating early infant male circumcision with maternal child health services in Kenya: the Mtoto Msafi Mbili Study
As countries scale up adult voluntary medical male circumcision (VMMC) for HIV prevention, they are looking ahead to long term sustainable strategies, including introduction of early infant male circumcision (EIMC). To address the lack of evidence regarding introduction of EIMC services in sub-Saharan African settings, we conducted a simultaneous, prospective comparison of two models of EIMC service delivery in Homa Bay County, Kenya. In one division a standard delivery package (SDP) was introduced and included health facility-based provision of EIMC services with community engagement for client referral versus in a different division a standard package plus (SDPplus) that included community-delivered EIMC services. Babies 1–60 days old were eligible for EIMC. A representative sample of mothers and fathers of baby boys at 16 health facilities was surveyed. We examined differences between mothers and fathers in the SDP and SDPplus divisions and identified factors associated with EIMC uptake. We report adjusted prevalence ratios (aPR). Of 1660 mothers interviewed, 1501 (89%) gave approval to contact the father, and 1259 fathers (84%) were interviewed. The proportion of babies circumcised was slightly greater in the SDPplus division than the SDP division (27.3% vs 23.7%), but the difference was not significant (p = 0.08). In adjusted analyses, however, the prevalence of babies being circumcised was greater in the SDPplus division (aPR = 1.23, 95% CI:1.04–1.45) and the factors associated with a baby being circumcised were the mother having received information about EIMC (during pregnancy, aPR = 4.81, 95% CI: 2.21–3.42), having discussed circumcision with the father if married or cohabiting (aPR = 5.39, 95% CI: 3.31–8.80) or being single (aPR = 5.67, 95% CI: 3.31–9.69), perceiving herself to be living with HIV (aPR = 1.39, 95% CI: 1.15–1.67), or having a post-secondary education (aPR = 1.33, 95% CI: 1.04–1.69), and the father being Muslim (aPR = 1.85, 95% CI: 1.29–2.65) or circumcised (aPR = 1.34, 95% CI: 1.13–1.59). The median age of 2117 babies circumcised was 8 days (IQR: 1–36), and the median weight was 3.6 kg (IQR: 3.2–4.4). There were 6 moderate adverse events (AEs) (0.28%); 5 severe AEs (0.24%), all involving an injury to the glans penis, requiring hospitalization and corrective surgery; and one death probably related to the procedure. There were no AEs among the 365 procedures performed outside health facilities. Information and education campaigns must reach members of the general population, especially men and fathers, who are influential to the EIMC decision. Serious AEs using the Mogen clamp are rare, but do occur and require efficient, reliable emergency back-up. Our results can assist countries considering scale-up of EIMC services for HIV prevention as their adult VMMC programs mature.
Data from: Quantifying demographic uncertainty: Bayesian methods for integral projection models (IPMs)
Integral projection models (IPMs) are a powerful and popular approach to modeling population dynamics. Generalized linear models form the statistical backbone of an IPM. These models are typically fit using a frequentist approach. We suggest that hierarchical Bayesian statistical approaches offer important advantages over frequentist methods for building and interpreting IPMs, especially given the hierarchical nature of most demographic studies. Using a stochastic IPM for a desert cactus based on a 10-year study as a worked example, we highlight the application of a Bayesian approach for translating uncertainty in the vital rates (e.g., growth, survival, fertility) to uncertainty in population-level quantities derived from them (e.g., population growth rate). The best-fit demographic model, which would have been difficult to fit under a frequentist framework, allowed for spatial and temporal variation in vital rates and correlated responses to temporal variation across vital rates. The corresponding posterior probability distribution for the stochastic population growth rate (λS) indicated that, if current vital rates continue, the study population will decline with nearly 100% probability. Interestingly, less-supported candidate models that did not include spatial variance and vital rate correlations gave similar estimates of λS. This occurred because the best-fitting model did a much better job of fitting vital rates to which the population growth rate was weakly sensitive. The cactus case study highlights several advantages of Bayesian approaches to IPM modeling, including that they: (1) provide a natural fit to demographic data, which are often collected in a hierarchical fashion (e.g., with random variance corresponding to temporal and spatial heterogeneity); (2) seamlessly combine multiple data sets or experiments; (3) readily incorporate covariance between vital rates; and, (4) easily integrate prior information, which may be particularly important for species of conservation concern where data availability may be limited. However, constructing a Bayesian IPM will often require the custom development of a statistical model tailored to the peculiarities of the sampling design and species considered; there may be circumstances under which simpler methods are adequate. Overall, Bayesian approaches provide a statistically sound way to get more information out of hard-won data, the goal of most demographic research endeavors.
Data from: Demography of Euterpe precatoria and Mauritia flexuosa in the Amazon: application of integral projection models for their harvest
Non-Timber Forest Products like palm fruits are fundamental in the livelihood of Amerindian groups. For the last 10 years the fruits of wild palm species, like Euterpe precatoria and Mauritia flexuosa, have been entering into global markets. These species are mostly harvested felling the adults, a practice that may have a disproportionate impact in the conservation of the populations. We studied the demography of E. precatoria and M. flexuosa, two important palms of the Amazon, using integral projection models, to characterize the population dynamics and project impact of different fruit harvest methods: adult felling and direct fruit harvest. We followed over 1400 individuals from populations with low harvest intensities in the Tikuna community of Amacayacu, Amazonas, Colombia from 2011 to 2013, establishing four plots for E. precatoria in seasonally inundated forests and two for M. flexuosa in swamps. The population growth in E. precatoria was slightly declining, whereas M. flexuosa was stable. As expected, the simulations of adult felling diminished λ and the number of available adults under any scenario for either species. On the contrary, the simulations support existing information that climbing and other non-destructive harvest methods would probably allow a sustainable management, satisfying the demand and preserving wild populations.
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.
Integration of protein and coding sequences enables mutual augmentation of the language model
<p><strong>The file structure is as follows:</strong></p> <p>Project Root<br>├── TE_MRL<br>│ ├── MRL_dataset.zip<br>│ └── TE_dataset.zip<br>│<br>├── finetuned_model<br>│ ├── FoldP<br>│ ├── LocP<br>│ ├── SSP<br>│ └── SolP<br>│<br>├── tax_tsne<br>│ └── emb_3models.zip<br>│<br>└── training_data<br> ├── FoldP.csv<br> ├── LocP.csv<br> ├── SolP.csv<br> ├── SSP.pkl<br> └── pretrain_source_GCF.txt</p>
Supplementary Data for "Exploring the Integration of Large Language Models in Industrial Test Maintenance Processes"
<p>This package contains supplementary data not directly included in the paper, including per-commit results for each prototype and the prompts used in the proof-of-concept implementations.</p>
Figure 2 in Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Figure 2. Map of Storeria ranges and sampling locations, showing geographical extent of populations, and range of former species with respect to re-delimited taxa. A, previous geographical extent of Storeria occipitomaculata is shown in red; circles indicate sampling localities. The asterisk indicates the sample of Storeria 'hidalgoensis' examined for morphology, with the range of this subpopulation, now considered part of S. occipitomaculata, indicated in pink. The range of Storeria storerioides is indicated in blue, with the sampling locality indicated by a square. B, previous geographical extent of Storeria dekayi is shown in yellow, with pentagons indicating sampling localities of S. dekayi, triangles indicating Storeria victa, and a line drawn to approximate the range boundary. The asterisk in the Central American population indicates the collection location of the specimen of Storeria 'tropica' examined for morphology, which is now considered part of S. dekayi.
Integration of 3D-printed middle ear models and middle ear prostheses in otosurgical training
<p>Additional files for article: Integration of 3D-printed middle ear models and middle ear prostheses in otosurgical training</p><p>Additional file 1: Simulation Video of drilling, scooping and placing a 3D-printed prosthesis (PORP) in the 3D-printed middle ear</p><p>Additional file 2: Responses of otosurgeons and ORL-HNS residents to the simulation questionnaire</p>
spatiAlign: An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics
<p>Integrative analysis of spatially resolved transcriptomics datasets empowers a deeper understanding of complex biological systems. However, integrating multiple tissue sections presents challenges for batch effect removal, particularly when the sections are measured by various technologies or collected at different times. Here, we propose spatiAlign, an unsupervised contrastive learning model that employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections. It enables the joint downstream analysis of multiple datasets not only in low-dimensional embeddings but also in the reconstructed full expression space. In benchmarking analysis, spatiAlign outperforms state-of-the-art methods in learning joint and discriminative representations for tissue sections, each potentially characterized by complex batch effects or distinct biological characteristics. Furthermore, we demonstrate the benefits of spatiAlign for the integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires a corrected gene expression matrix.</p>
Data from: Future projections of biodiversity and ecosystem services in Europe with two integrated assessment models
<p>Projections of future changes in biodiversity and ecosystem services (BES) are of increasing importance to inform policy and decision-making on options for conservation and sustainable use of BES. Scenario-based modelling is a powerful tool to assess these future changes. This study assesses the consequences for BES in Europe under four socio-environmental scenarios designed from a BES perspective. We evaluated these scenarios using two integrated assessment models (IMAGE-GLOBIO and CLIMSAVE IAP, respectively). </p> <p><strong>Veerkamp, C. J</strong>., Dunford. R. W., Harrison, P. A., Mandryk, M., Priess, J. A., Schipper, A. M., Stehfest, E., & Alkemade, R. (2020). Future projections of biodiversity and ecosystem services in Europe with two integrated assessment models. <em>Regional Environmental Change,</em> 20, 103. <a href="https://doi.org/10.1007/s10113-020-01685-8">https://doi.org/10.1007/s10113-020-01685-8</a> </p>
The dataset for Evaluation of plume-induced continental crust growth rate in early Earth: Insight from integrated petrological-thermo-mechanical modeling
<p>All data of model results for the paper <em>Evaluation of plume-induced continental crust growth rate in early Earth: Insight from integrated petrological-thermo-mechanical modeling</em>.</p> <p>Contents of this dataset includes:</p> <p>A list for models and data of model results are provided in the zip file. </p> <p>The files suffixed *.grd are grid datas that can be draw by GMT.</p> <p>The files suffixed *.info are datas of the evolution of volume of the continental crust and TTGs in the model.</p> <p>The files suffixed *.prn are datas of P-T condtions of continental crust generation by partial melting.</p> <p>The files suffixed *.py are python codes for visualization of the volume of continental crust and P-T datas.</p>
Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts
<p>Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .</p>
Enhancing Credit Risk Assessment in Digital Finance through a Hybrid Deep Learning Model Integrated with Blockchain on the Edge of Things F
<p><span>This work proposes a credit risk assessment model using deep learning models such as self-attention generative adversarial networks (SA-GAN) and deep multi-layer perceptron (DMLP). Blockchain is used to improve the security aspects of the model by employing Brakerski-Gentry-Vaikuntanathan (BKV) encryption technique. Further, the proposed system is implemented in Edge-of-things network and communications are enabled via LoRaWAN server.</span></p>
Field and Lab_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Field and Lab observations_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
Meteorological data_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Meteorological data_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
Depressions and Boundary_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Depressions and Boundary_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
Aerial Images_Part 3_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Aerial Images_Part 3_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
Orthomosaic_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>Orthomosaic of the aerial images_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
DSM_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria
<p>DSM_Integrating Remote Sensing and Machine Learning for Developing Spatio-Temporal Model to Predict Aquatic Larval Habitats of Malaria</p>
Raw IMC files for Spatial subsetting enables integrative modeling of oral squamous cell carcinoma multiplex imaging data.
<p>Raw MCD files for the Stanford cohort of oral squamous cell carcinoma patients in this publication:</p> <p>Spatial subsetting enables integrative modeling of oral squamous cell carcinoma multiplex imaging data (DOI:<span> <a href="https://doi.org/10.1016/j.isci.2023.108486" target="_blank" rel="noopener">10.1016/j.isci.2023.108486</a>).</span></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.