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Measurement of the B-band Galaxy Luminosity Function with Approximate Bayesian Computation
<p>In our recent paper Tortorelli et al. 2020 (arXiv: 2001.07727), we presented the first measurement in literature of galaxy population properties using the Approximate Bayesian Computation (ABC), specifically the B-band Galaxy Luminosity function. The novel methodology we developed that combines forward-modeling and ABC offers excellent prospects to robustly measure galaxy population properties as a function of redshift in large wide-field galaxy surveys, such as LSST and NGRST. The methodology has the advantage of overcoming part of the limitations that arise in wide-field galaxy studies, such as incorrect redshift estimation or separation of galaxies into red and blue. We forward model wide-field broad-band galaxy surveys using the fast image simulator UFig. We use ABC to constrain the galaxy population model parameters of the simulations and match data from the CFHTLS. We define a number of distance metrics between the simulated and the survey data. By exploring the parameter space of the galaxy population model through ABC to find the set of parameters that minimize these distance metrics, we obtain constraints on the LFs of blue and red galaxies as a function of redshift. We compare our results to other measurements, finding good agreement at all redshifts, for both blue and red galaxies. We also compare the redshift distribution we obtain applying the same cuts as the VIPERS survey on our image simulations, finding good agreement with survey data.</p>
Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada
The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is probably the best understood of all fossil fishes. In contrast, the anatomy of the lower jaw – crucial for both phylogenetics and biomechanical analyses – has been only superficially described. Computed tomography data of three Eusthenopteron skulls were segmented using visualization software to digitally separate bone from matrix and individual bones from each other. Here, we present a new description of the lower jaw of Eusthenopteron based on microcomputed tomography data, including the following: detailed description of sutural morphology and the mandibular symphysis; confirmed occurrence of pre- and intercoronoid fossae on the dorsal aspect of the lower jaw; and the arrangement of the submandibular bones. Furthermore, we identify a novel dermal ossification, the postsymphysial, present on the anteromedial aspect of the lower jaw in Eusthenopteron and describe its distribution in other stem tetrapod taxa. Sutural morphology is used to infer load regimes and, along with overall skull and lower jaw morphology, suggests that Eusthenopteron may have used biting along with suction feeding to capture and consume large prey. Finally, visualization software was used to repair and reconstruct the lower jaw, resulting in a three-dimensional digital reconstruction.
Data from: Oscillatory signatures underlie growth regimes in Arabidopsis pollen tubes: computational methods to estimate tip location, periodicity and synchronization in growing cells
Oscillations in pollen tubes have been reported for many cellular processes, including growth, extracellular ion fluxes, and cytosolic ion concentrations. However, there is a shortage of quantitative methods to measure and characterize the different dynamic regimes observed. Herein, a suite of open-source computational methods and original algorithms were integrated into an automated analysis pipeline that we employed to characterize specific oscillatory signatures in pollen tubes of Arabidopsis thaliana (Col-0). Importantly, it enabled us to detect and quantify a Ca2+ spiking behaviour upon growth arrest and synchronized oscillations involving growth, extracellular H+ fluxes, and cytosolic Ca2+, providing the basis for novel hypotheses. Our computational approach includes a new tip detection method with subpixel resolution using linear regression, showing improved ability to detect oscillations when compared to currently available methods. We named this data analysis pipeline 'Computational Heuristics for Understanding Kymographs and aNalysis of Oscillations Relying on Regression and Improved Statistics', or CHUKNORRIS. It can integrate diverse data types (imaging, electrophysiology), extract quantitative and time-explicit estimates of oscillatory characteristics from isolated time series (period and amplitude) or pairs (phase relationships and delays), and evaluate their synchronization state. Here, its performance is tested with ratiometric and single channel kymographs, ion flux data, and growth rate analysis.
Data from: The appropriateness of language found in research consent form templates: a computational linguistic analysis
Background: To facilitate informed consent, consent forms should use language below the grade eight level. Research Ethics Boards (REBs) provide consent form templates to facilitate this goal. Templates with inappropriate language could promote consent forms that participants find difficult to understand. However, a linguistic analysis of templates is lacking. Methods: We reviewed the websites of 124 REBs for their templates. These included English language medical school REBs in Australia/New Zealand (n=23), Canada (n=14), South Africa (n=8), the United Kingdom (n=34), and a geographically-stratified sample from the United States (n=45). Template language was analyzed using Coh-Metrix linguistic software (v.3.0, Memphis, USA). We evaluated the proportion of REBs with five key linguistic outcomes at or below grade eight. Additionally, we compared quantitative readability to the REBs' own readability standards. To determine if the template's country of origin or the presence of a local REB readability standard influenced the linguistic variables, we used a MANOVA model. Results: Of the REBs who provided templates, 0/94 (0%, 95% CI=0-3.9%) provided templates with all linguistic variables at or below the grade eight level. Relaxing the standard to a grade 12 level did not increase this proportion. Further, only 2/22 (9.1%, 95% CI= 2.5-27.8) REBs met their own readability standard. The country of origin (DF= 20, 177.5, F=1.97, p=0.01), but not the presence of an REB-specific standard (DF=5, 84, F=0.73, p=0.60), influenced the linguistic variables. Conclusions: Inappropriate language in templates is an international problem. Templates use words that are long, abstract, and unfamiliar. This could undermine the validity of participant informed consent. REBs should set a policy of screening templates with linguistic software.
Data from: Reconstructing the demographic history of orang-utans using approximate Bayesian computation
Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the Southeast Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an approximate Bayesian computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. Therefore, we showed that orang-utans went through drastic changes in population size and connectedness, caused by the recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations, and probably also by the impact of hunting by early humans. Our findings also emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.
Data from: X-Ray computed tomography of two mammoth calf mummies
Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.
Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates
We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.
Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modelling using 27 EST associated microsatellites. We also performed the species distribution modelling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
Data from: Is computer-assisted instruction more effective than other educational methods in achieving ECG competence amongst medical students and residents? A systematic review and meta-analysis.
Objectives It remains unclear whether computer-assisted instruction (CAI) is more effective than other teaching methods in acquiring and retaining ECG competence amongst medical students and residents. Design This systematic review and meta-analysis followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Data sources Electronic literature searches of PubMed, databases via EBSCOhost, Scopus, Web of Science, Google Scholar and grey literature were conducted on 28 November 2017. We subsequently reviewed the citation indexes of articles identified by the search. Eligibility criteria Studies were included if a comparative research design was used to evaluate the efficacy of CAI versus other methods of ECG instruction, as determined by the acquisition and/or retention of ECG competence of medical students and/or residents. Data extraction and synthesis Two reviewers independently extracted data from all eligible studies and assessed the risk of bias. After duplicates were removed, 559 papers were screened. Thirteen studies met the eligibility criteria. Eight studies reported sufficient data to be included in the meta-analysis. Results In all studies, CAI was compared to face-to-face ECG instruction. There was a wide range of computer-assisted and face-to-face teaching methods. Overall, the meta-analysis found no significant difference in acquired ECG competence between those who received computer-assisted or face-to-face instruction. However, sub-analyses showed that CAI in a blended learning context was better than face-to-face teaching alone, especially if trainees had unlimited access to teaching materials and/or deliberate practice with feedback. There was no conclusive evidence that CAI was better than face-to-face teaching for longer-term retention of ECG competence. Conclusion CAI was not better than face-to-face ECG teaching. However, this meta-analysis was constrained by significant heterogeneity amongst studies. Nevertheless, the finding that blended learning is more effective than face-to-face ECG teaching is important in the era of increased implementation of e-learning. PROSPERO registration number CRD42017067054
Commodore SX-64 computer
The Commodore SX-64 is a portable ("suitcase") version of one of the most popular computers of the 1980s, i.e., the Commodore C64. It is also the first portable computer equipped with a colour screen (a 5-inch CRT monitor). It has 64 kB of built-in operating memory. As it was to serve people who travelled frequently, it was advertised in the US with the slogan "designed for the movers of this word". Suitcase resembling, weighting ca 10 kg was lighter and smaller than the computers produced at the time. The model, however, does not have a built-in battery, which in fact prevents the device from being used while travelling. In contrast to the Commodore 64, it has only one built-in 5.25-inch floppy disk drive, yet its ports allow connection of peripherals such as a tape recorder, audio-video devices, or an external monitor. Commodore Intl., USA/Japan, 1984-86 Inv. No. MIM1749/VII-145 License: CC BY-NC-SA Source: Objaverse 1.0 / Sketchfab
A genetic and computational approach to structurally classify neuronal types
<p>This a missing piece of supplemental information that should accompany the article</p> <p>A genetic and computational approach to structurally classify neuronal types</p> <ul> <li>Uygar Sümbül,</li> <li>Sen Song,</li> <li>Kyle McCulloch,</li> <li>Michael Becker,</li> <li>Bin Lin,</li> <li>Joshua R. Sanes,</li> <li>Richard H. Masland</li> <li>& H. Sebastian Seung</li> </ul> <p>The file was kindly supplied by Uygar Sumbul, but has not yet appeared on the nature communications website.</p> <p> </p>
Programs for chemoinformatics and computational medicinal chemistry
<p>Programs provided herein are a part of a freely available database of annotated compound data sets and software tools developed in our laboratory for chemoinformatics and computational medicinal chemistry. The original release is described in the following article:<br /> <br /> Hu Y, Bajorath J: Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications [v1; ref status: indexed, http://f1000r.es/Mu9krs] <em>F1000Research</em> 2012; 1:11 (doi: 10.12688/f1000research.1-11.v1).<br /> <br /> The updated version containing the data provided herein will be described in a forthcoming data note in <em>F1000Research</em>.</p>
Huntingtin linker sequence determination by computational methods - correspondence with Alex Holehouse
<p>Huntingtin open lab notebook project</p>
Data sets for chemoinformatics and computational medicinal chemistry
<p>Data sets provided herein are a part of a freely available database of annotated compound data sets and software tools developed in our laboratory for chemoinformatics and computational medicinal chemistry. The original release is described in the following article:<br /> <br /> Hu Y, Bajorath J: Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications [v1; ref status: indexed, http://f1000r.es/Mu9krs] <em>F1000Research </em>2012; 1:11 (doi: 10.12688/f1000research.1-11.v1).<br /> <br /> The updated version containing the data provided herein will be described in a forthcoming data note in <em>F1000Research</em>.</p>
Computing Safe Contention Bounds for Multicore Resources with Round-Robin and FIFO Arbitration
<p>This dataset contains processed data in format of an microsoft excel spreadsheet referring to simulations and measurements of multicore contention described in the publication "Computing Safe Contention Bounds for Multicore Resources with Round-Robin and FIFO Arbitration" published in IEEETC.</p>
FIGURES 11–12 in First fossil Micropholcommatidae (Araneae), imaged in Eocene Paris amber using X-Ray Computed Tomography
FIGURES 11–12. Photographs of Cenotextricella simoni sp. nov. (male holotype, MNHN PA 327) using traditional light microscopy. (1) dorsal view; (2) ventral view. See Fig. 5 for scale.
FIGURES 1–10 in First fossil Micropholcommatidae (Araneae), imaged in Eocene Paris amber using X-Ray Computed Tomography
FIGURES 1–10. VHR-CT scans of Cenotextricella simoni sp. nov. (male holotype, MNHN PA 327). (1) dorsal view; (2) ventral view; (3) anterior view; (4) posterior view; (5) lateral view; (6) lateral sectioned view; (7) right pedipalp dorsal view; (8) right pedipalp posterior view; (9) left pedipalp retrolateral view; (10) right pedipalp prolateral view. Abbreviations: ALE, anterior lateral eye; AME, anterior median eye; c, conductor; cy, cymbium; ds, dorsal abdominal scutum; e, embolus; fe, femur; mt/t, metatarsus/tarsus joint; pa, patella; PLE, posterior lateral eye; PME, posterior median eye; st, sternum; th, tibial hook; ti, tibia; vs, ventral abdominal scutum.
FIGURE 2 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography
FIGURE 2. Comparative osteology of Rhombophryne vaventy sp. nov. (ZSM 357/2005, left in all pairs), and Rhombophryne serratopalpebrosa (MNHN 1975.24, right in all pairs), scaled to be equal in size; see Supplementary Figure S1 for manipulable model and scale. a: spinal columns in dorsal view (A = Atlas, T = Thoracic Vertebra, L = Lumbar Vertebra, S = Sacrum, U = Urostyle); b: ilia in dorsal view, with arrows indicating the third lumbar vertebrae and anterior-most end of the ilia; c: hands in ventral view, with arrows indicating the prepollex; d: head in ventral view, with arrows indicating the postchoanal prevomerine palate; e: columellae in dorsal view.
FIGURE 1. Holotype ZSM 357 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography
FIGURE 1. Holotype ZSM 357/2005 (FGZC 2876) (a–b) and paratype UADBA uncatalogued (FGZC 2842) (c–d) of Rhombophryne vaventy sp. nov. in dorsolateral and ventral views. Inset in c depicts the superciliary spines of the paratype. Note the variance in length of these spines.
FIGURE 3 in A new microhylid frog, genus Rhombophryne, from northeastern Madagascar, and a re-description of R. serratopalpebrosa using micro-computed tomography
FIGURE 3. Comparative skull osteology of Rhombophryne serratopalpebrosa (MNHN 1975.24, right in all pairs) and Rhombophryne vaventy sp. nov. (ZSM 357/2005, left in all pairs), scaled to be equal in size. a: lateral view; b: ventral view; c: dorsal view. Abbreviations: angspl = angulosplenial, col = columella, fpar = frontoparietal, max = maxillary, mmk = mentomeckelian bone, pmax = premaxilla, pro = prootic, prsph = parasphenoid, pter = pterygoid, pvom = prevomer, pvom/ neopl = prevomer/neopalatine (either fused or replaced), qj = quadratojugal, spheth = sphenethmoid, spmax = septomaxilla, sq = squamosal.
ScienceDex guides
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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.