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18,621 results for “development;”
Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma
<p>Lack of accurate methods for early lymphoma detection limits the ability to cure patients. Patients with Non-Hodgkin lymphomas (NHL) who present with advanced disease have worse outcomes.</p> <p>We developed a DNA methylation-based prediction tool for NHL, based on blood samples collected prospectively from 278 apparently healthy patients who were followed for up to 16 years to monitor for NHL development. A predictive score was developed using machine learning methods in a robust training/validation framework.</p> <p>Our predictive score incorporates CpG DNA methylation at 135 genomic positions, with higher scores predicting higher risk. It was 85% and 78% accurate for identifying patients at risk of developing future NHL, in patients with high or low epigenetic mitotic clock respectively, in a validation cohort. It was also sensitive at detecting active NHL (96.3% accuracy) and healthy status (95.6% accuracy) in additional independent cohorts. Scores optimized for specific NHL subtypes showed significant but lower accuracy for predicting other subtypes. Our score incorporates hyper-methylation of Polycomb and <em>HOX</em> genes, which have roles in NHL development, as well as <em>PAX5</em> - a master transcriptional regulator of B-cell fate. Subjects with higher risk scores showed higher regulatory T-cells, memory B-cells, but lower naïve T helper lymphocytes fractions in the blood.</p> <p>A score based on DNA methylation in blood is accurate at predicting NHL development with lead time of up to 16 years. Future prospective studies will be required to confirm the utility of our signature for managing patients who are at high risk for developing future NHL.</p>
Data from: Detecting seminal research contributions to the development of ethnobotany by reference publication year spectroscopy (RPYS)
<p>This study aims to assess the growth in overall publication output in ethnobotany as well as provide a systematic examination of the history of ethnobotanical publications using reference publication year spectroscopy (RPYS). The study is based on 5201 papers published between 1974 and 2019 covering 290006 non-distinct cited references (CRs), indexed in Science Citation Index-Expanded (SCI-Expanded) of Web of Science (WoS). The regression analysis indicated a compound annual growth rate of approximately 11% globally in ethnobotanical publications and the volume of publications doubles every approximately 6 years. The reference publication period was divided into four sub-periods in which a total of 31 peaks are clearly identifiable, including five peaks from the first period (earliest to 1800), ten from the second (1801–1900), nine from the third (1901–1950) and seven from the last period (1951–2000). A total of 44 publications were found to have been especially influential and landmark. Out of them, 31 (70%) were books and 11 (25%) were articles. Out of the 11 articles, 5 (45%) were published in the same journal (Economic Botany). The first period had the lowest number of publications (5), including classic books like the Spanish translation of Dioscorides' <em>Materia Medica </em>and Carolus Linnaeus' <em>Systema naturæ.</em> Interestingly, about 30% of the studies that laid the foundation of ethnobotany and are discussed in this paper come from South Africa, pointing to the contribution of the African Continent to the foundation of the field of ethnobotany.</p>
A mechanism for punctuating equilibria during mammalian vocal development
<p>Evolution and development are typically characterized as the outcomes of gradual changes, but sometimes such changes are abrupt: States of equilibrium can be punctuated by sudden change. Here, we studied the early vocal development of three different mammals: common marmoset monkeys, Egyptian fruit bats, and humans. Consistent with the notion of punctuated equilibria, we found that all three species undergo at least one sudden transition in the acoustics of their developing vocalizations. This was expected. To understand the mechanism, we modeled different developmental landscapes. We found that the transition was best described as a shift in the balance of two vocalization landscapes. We show that the natural dynamics of these two landscapes are consistent with the dynamics of energy expenditure and information transmission. By using them as constraints for each species, we predicted the differences in transition timing from immature to mature vocalizations. Using marmoset monkeys, we were able to manipulate both infant energy expenditure (vocalizing in a heliox environment) and information transmission (closed-loop contingent parental vocal playback). These experiments supported our predictions regarding the role of energy and information in leading to punctuating equilibrium states of vocal development.</p>
Data for the journal article: 'Ecology of testate amoebae along an environmental gradient from bogs to calcareous fens in East-Central Europe: development of transfer functions for palaeoenvironmental reconstructions'
<p><strong>DATA DESCRIPTION</strong>: This repository provides training sets and R scripts for the development of three transfer function models that allow reconstructions of Holocene hydrochemical or hydrological (hydroclimatic) conditions from testate amoeba assemblages preserved in mires of East-Central Europe. Specifically, the repository contains (<em>i</em>) <strong>the full dataset and an R script for the development of the final MLRC model</strong> for inferring past water-mineral richness (expressed as pH) in various types of mires; (<em>ii</em>) <strong>the minerotrophic subset and an R script for the development of the final WAPLS com1 model</strong> for the reconstructions of past water-mineral richness (expressed as pH) in calcareous and rich fens; and (<em>iii</em>) <strong>the ombrotrophic subset and an R script for the development of the final PLS com2 model</strong> for inferring past depth to water table (DWT) in bogs and poor fens. Additionally, the repository includes <strong>the original versions of the full, minerotrophic and ombrotrophic training sets</strong> (i.e., the versions before removing outlier samples and rare taxa due to transfer function optimisation), and <strong>the compiled dataset</strong>, from which the three above-mentioned training sets were generated. For details, see <a href="https://doi.org/10.1016/j.palaeo.2022.111145">Šímová et al. (2022)</a>.</p> <p><strong>ARTICLE ABSTRACT</strong>: Testate amoebae play an important role in biomonitoring and the understanding of peatland (palaeo)ecology. However, their application has been mainly limited to <em>Sphagnum</em>-dominated peatlands, especially ombrotrophic bogs. To facilitate wider use of these microorganisms, we explored their ecology along a gradient from mineral-poor acidic bogs to mineral-rich calcareous fens with tufa formation using a new calibration dataset of over 250 samples from East-Central Europe. Specifically, we examined environmental controls on testate amoebae along the complete gradient and separately in the minerotrophic (pH >5.5) and ombrotrophic (pH <5) parts. Based on these findings, we developed and statistically evaluated transfer function models for the dominant factors controlling the community composition of these protists. Multivariate statistical analysis showed that groundwater pH was the main driver of species composition in the full and minerotrophic datasets. In contrast, testate amoeba communities in the ombrotrophic dataset were primarily structured by depth to water table (DWT). Under leave-one-out cross-validation (LOO), the best-performing model for DWT gave a prediction error (RMSEP) of 5.43 cm. The most robust models for groundwater mineral richness yielded RMSEP<sub>LOO</sub> of 0.45 and 0.27 pH units, for the full and the minerotrophic dataset respectively. This is the first study to present a complete set of testate amoeba-based transfer functions that allow reconstructions of Holocene hydrochemical and hydrological (hydroclimatic) variability in different mire types within one region. The new models open up the possibility for testate amoebae to become a valuable tool in palaeoecological research, although further work is needed to fully assess their performance and usefulness in practice.</p>
LPCAT1 promotes cSCC development via EGFR
<p>Cutaneous squamous cell carcinoma (cSCC) is the second most common form of skin cancer. LPCAT1, a lysophosphatidylcholine acyltransferase, takes a center stage in membrane lipid remodeling. LPCAT1 is elevated in several cancers and contributes to cancer development. However, its role and molecular mechanisms in cSCC remain to be elucidated. In this study, we found that LPCAT1 was upregulated in cSCC tissues and in cell lines. In vitro, loss-of-function and gain-of-function experiments demonstrated that LPCAT1 facilitated cSCC cell proliferation, protected cells against apoptosis, accelerated epithelial‒mesenchymal transition, and enhanced cell metastasis. Mechanistically, LPCAT1 regulated EGFR signaling. The oncogenic effect of LPCAT1 was mediated by EGFR/protein kinase B and EGFR/p38MAPK pathways in cSCC. Using the xenograft mouse model, we consolidated the results mentioned earlier. In conclusion, LPCAT1 contributed to cSCC progression through EGFR-mediated protein kinase B and p38MAPK signaling pathways. LPCAT1 may serve as a target for therapeutic intervention in cSCC. And the datasets related to this study are available in this repository.</p>
Raw Data Survival, Development and Reproduction of Gonipterus platensis on Eucalyptus genotypes
<p>Data used in the paper "The survival, development, and reproduction of <em>Gonipterus platensis </em>(Coleoptera: Curculionidae) on the main <em>Eucalyptus </em>(Myrtaceae) genotypes planted in Brazil"</p>
Figure 3 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)
Figure 3. Ventral view of hands showing the comparative size of discs on fingers I and II in frogs of genus Pristimantis. A, Pristimantis appendiculatus (Werner, 1894) (KU 165140). B, Pristimantis penelopus (Lynch & Rueda-Almonacid, 1999) (ICN
Figure 1 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)
Figure 1. Lateral view of pelvic and thigh musculature showing origins of the m. iliacus externus (ile) and m. tensor fasciae latae (tfl) from the iliac shaft (ish) in frogs of the superfamily Brachycephaloidea. A, Pristimantis kelephus (Lynch, 1998) (ICN 39671). B, Pristimantis cristinae (Lynch & Ruiz-Carranza, 1985) (ICN 3950). C, Craugastor longirostris (Boulenger, 1898) (ICN 42787). D, Ceuthomantis sp1 Colombia (JDL 32489). The red and green colours denote the portion anterior of the iliac shaft free of muscle fibres and the tensor fasciae latae (tfl), respectively. Scale bars = 2 mm.
Figure 4 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)
Figure 4. Distribution of unambiguously optimized phenotypic synapomorphies recovered in the current character analysis. The phylogenetic hypothesis for Brachycephaloidea is that of Padial et al. (2014) and relationships outside Brachycephaloidea follow Jetz & Pyron (2018). Genera and subgenera were collapsed, but the complete distribution of character states is shown in Table 1. Character numbers are given beneath each square, with primitive-derived character states inside each square (see text and Table 1 for character definitions). Colour coding: red = untransformed, homoplastic; blue = transformed, homoplastic.
Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development
MicroRNAs (miRNAs) have been shown to be key modulators of post-transcriptional gene silencing in many cellular processes. In previous studies designed to understand the role of miRNAs in thymic development, we globally deleted miRNA exclusively in thymic epithelial cells (TECs), which are critical in thymic selection. This resulted in the loss of stromal cells that instruct T cell lineage commitment and affect thymocyte positive selection, required for mature T cell development. Since murine miR-181 is expressed in the thymus and miR-181 deficiency disrupts thymocyte development, we first quantified and thereby demonstrated that miR181a1 and miR181b1 are expressed in purified TECs. By generating mice with TEC targeted loss of miR-181a1 and miR-181b1 expression, we observed that neither TEC cellularity nor thymocyte number nor differentiation was adversely affected. Thus, disrupted thymopoiesis in miR-181 deficient mice was not due to miR-181 loss of expression in TECs. Importantly, in mice with restricted TEC deficiency of miR-181a1 and miR-181b1, there were similar numbers of mature T cells in the periphery in regards to frequencies, differentiation, and function as compared to controls. Moreover miR-181a1 and miR-181b1 were not required for maintenance of thymus integrity over time, as thymic involution was not accelerated in gene-targeted mice. Taken together our data indicate that miR-181a1 and miR-181b1 are dispensable for TEC differentiation, their control of thymocyte development and mature T cell export to and homeostasis within the periphery.
Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome
<p>Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (~2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image intact cerebral organoids generated from Rett Syndrome patients, we show defects in the ventricular zone volumetric structure of mutant organoids compared to isogenic control organoids. Long-term imaging of live organoids reveals that shorter migration distances and slower migration speeds of mutant radially migrating neurons are associated with more tortuous trajectories. Our label-free imaging system constitutes a particularly useful platform for tracking normal and abnormal development in individual organoids, as well as for screening therapeutic molecules via intact organoid imaging.</p>
Data for Chromatin compaction precedes apoptosis in developing neurons by Rose et al.
<p>Data for Chromatin compaction precedes apoptosis in developing neurons by Rose et al.</p>
Supporting Information: Assessing the Social Dimension in Strategic Network Design for a Sustainable Development: The Case of Bioethanol Production in the EU
<p>Supporting Information S2 provides all parameters of the optimization model, both those associated with the social objective and hotspot functions of the study at hand, and those from the underlying model by Wietschel et al. (2021). To put the method of the study into perspective, it also gives an overview of referenced frameworks (GSLCAPO, SHDB, SDGs) and their categories, subcategories, and indicators. Furthermore, it includes detailed results for all social, environmental, and economic objective functions in all scenarios, and of the Pareto optimization. Lastly, the underlying data for all figures of the manuscript and Supporting Information S1 is provided.</p>
FIGURE. Seedlings, seeds, embryos, anthers, and pollen in Dicorynia. A–D. Different stages of development in seedlings of D. paraensis, First eophiles unifoliolate and opposite; E–G. Seed of D. guianensis: E. External surface; F. Endosperm of the longitudinally sectioned seed, note the slightly gelatinous upper region; G. Cotyledon and embryo of longitudinally sectioned seed; H. SEM of seed's testa in D. paraensis; I. SEM of endosperm's surface in D. guianensis (notice the presence of circular perforations); J–K. SEM of the hypocotyl-radicular axis of the seed in D. guianensis and D. paraensis; L. SEM of seed's testa in D. guianensis; M–N. SEM of plumule region in embryo of D. guianensis and D. paraensis (note the developed leaf primordia); O. Apex of anther in longer stamen of D. paraensis, showing 4 sporangia and two pores covered by an apicle; P. Apex of anther in shorter stamen of D. guianensis, at least 9 sporangia; Q. Apex of anther in longer stamen of D. guianensis, 8 sporangia; R. Pollen grains in D. paraensis. A–D: Falcão, M.J. 91; E–G, I–J, L–M: Gentry 63030; H, K, N: Berry, P.E. 7460; O: Amaral, E. 618; P, Q: Unknown collector MO1576407; Scale bar. A–D: 2cm; E–G: 3mm; H–L: 1mm; M–N: 100 μm; O-Q: 200μm; R: 5 μm. in A Taxonomic Revision of the Amazonian Genus Dicorynia (Fabaceae: Dialioideae)
FIGURE. Seedlings, seeds, embryos, anthers, and pollen in Dicorynia. A–D. Different stages of development in seedlings of D. paraensis, First eophiles unifoliolate and opposite; E–G. Seed of D. guianensis: E. External surface; F. Endosperm of the longitudinally sectioned seed, note the slightly gelatinous upper region; G. Cotyledon and embryo of longitudinally sectioned seed; H. SEM of seed's testa in D. paraensis; I. SEM of endosperm's surface in D. guianensis (notice the presence of circular perforations); J–K. SEM of the hypocotyl-radicular axis of the seed in D. guianensis and D. paraensis; L. SEM of seed's testa in D. guianensis; M–N. SEM of plumule region in embryo of D. guianensis and D. paraensis (note the developed leaf primordia); O. Apex of anther in longer stamen of D. paraensis, showing 4 sporangia and two pores covered by an apicle; P. Apex of anther in shorter stamen of D. guianensis, at least 9 sporangia; Q. Apex of anther in longer stamen of D. guianensis, 8 sporangia; R. Pollen grains in D. paraensis. A–D: Falcão, M.J. 91; E–G, I–J, L–M: Gentry 63030; H, K, N: Berry, P.E. 7460; O: Amaral, E. 618; P, Q: Unknown collector MO1576407; Scale bar. A–D: 2cm; E–G: 3mm; H–L: 1mm; M–N: 100 μm; O-Q: 200μm; R: 5 μm.
Eight archetypes of Sustainable Development Goal (SDG) synergies and trade-offs
<p>Data S1 - Details of system archetype application articles reviewed systematically.</p>
Less-well-developed crustal flow in the central Tibetan Plateau revealed by receiver function and surface wave joint inversion
<p>A crustal flow model has been previously used to explain the crustal extension of the Tibetan Plateau. However, the existence of massive crustal flow in the central plateau is still controversial. We conducted a joint inversion of receiver functions and surface wave dispersions from the 2-D broadband seismic array SANDWICH deployed in the central plateau. The crustal S-wave velocity structure with high vertical resolution shows a low-velocity layer (LVL) in the middle-lower crust beneath most stations. The S-wave velocity of this LVL is mostly within 3.0-3.4 km/s, reflecting a melt volume percentage (MVP) ≤ 7%, except at two stations. Our study suggests that there is not a high enough melt volume in central Tibet to develop crustal flow, which requires an MVP ≥ 7% to decrease rock strength. The formation of extensional structures in the central plateau may contribute to ductile deformation in the middle-lower crust but not crustal flow.</p>
Raw data used in the paper User involvement before the development of an indoor RPAS for the creative industries
<p>This file includes the data used in the paper: de-Miguel-Molina, B., de-Miguel-Molina, M., Santamarina-Campos, V., & Segarra-Oña, M. (2021). User involvement before the development of an indoor RPAS for the creative industries. <em>International Journal of Micro Air Vehicles</em>, <em>13</em>, 1756829321992140.</p> <p>Please, cite the paper if you use the data.</p> <p> </p>
Distribution. SE Iran (Kerman Province), Pakistan, India, S Nepal, and Sri Lanka; range may have expanded with development of agricultural landscapes. in Muridae
Distribution. SE Iran (Kerman Province), Pakistan, India, S Nepal, and Sri Lanka; range may have expanded with development of agricultural landscapes.
Distribution. NE Egypt (coastal region of Sinai), S Israel (Negev Desert), and Palestine. Descriptive notes. Head-body 130-170 mm, tail 120-180 mm, ear 17-22 mm, hindfoot 30-41 mm; weight 125-275 g. A medium-sized jird, Buxton's Jird has tail of about same length as head-body length and partially hairy soles of hindfeet. Bicolored tail ends with well-developed pencil of black hairs. Dorsal pelage is reddish sandy, diffusely speckled with black hairs, and ventral is white. Enlarged tympanic bullae project over back of skull and represent c.35-37% ofskull length. Karyotype 2n = 46. in Muridae
Distribution. NE Egypt (coastal region of Sinai), S Israel (Negev Desert), and Palestine. Descriptive notes. Head-body 130-170 mm, tail 120-180 mm, ear 17-22 mm, hindfoot 30-41 mm; weight 125-275 g. A medium-sized jird, Buxton's Jird has tail of about same length as head-body length and partially hairy soles of hindfeet. Bicolored tail ends with well-developed pencil of black hairs. Dorsal pelage is reddish sandy, diffusely speckled with black hairs, and ventral is white. Enlarged tympanic bullae project over back of skull and represent c.35-37% ofskull length. Karyotype 2n = 46.
Human and Organizational Factors and their Influence on Turnover in Global Software Development Projects
<p><strong>LIST OF PAPERS - Human and Organizational Factors and their Influence on Turnover in Global Software Development Projects</strong></p> <p> </p>
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.