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Challenges and directions for open ecosystems biodiversity restoration: An overview of the techniques applied for Cerrado
<p>1. Ecological restoration of tropical open ecosystems remains challenging for both science and practice. Over the last decade, innovative techniques have been developed, but whether they have been successful or not remains to be demonstrated. Assessing the outcomes of these initiatives is crucial to drive the following steps to improve tropical grasslands and savanna restoration.</p> <p>2. Analyzing 82 data sets from the literature and primary data collection, we assessed the effectiveness of passive and active restoration techniques applied in Cerrado open ecosystems. We used plant diversity variables (species and growth forms) as indicators, considering ruderals and exotics as non-target species. Specifically, we aimed to answer: (i) How does the diversity of target species change through time in areas subject to passive restoration? (ii) Are active and passive restoration techniques effective in restoring the proportion of target species found in old-growth reference ecosystems? (iii) Have the current techniques been successful in recovering the proportions of growth forms of reference ecosystems?</p> <p>3. We found that target species proportions do not increase with time, suggesting limitations of typical species to colonize degraded sites. Hence, passive restoration will promote the conservation of a limited and constant number of target species. This number will depend on the magnitude of degradation and previous land use.</p> <p>4. The restoration techniques currently applied to restore the biodiversity of Cerrado open ecosystems are not reaching the reference standards, with distinct techniques driving plant communities to different sets of growth forms. Active restoration based on propagules obtained from pristine donor sites (topsoil translocation, plant material transplant, and seeding) performed better than passive restoration for most of the growth forms analyzed.</p> <p>5. Synthesis and Applications: Different growth forms have different roles in determining the structure and functioning of Cerrado vegetation. A mix of techniques can better approximate plant diversity and the proportionality of target species of pristine ecosystems. Singular restoration approaches are insufficient for restoring Cerrado open ecosystem biodiversity. Mixed efforts encompassing various techniques are required instead. Furthermore, it is likely restoration success can be improved with greater investment in improving our understanding of and developing existing restoration techniques.</p>
Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)
<p>To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.</p>
Transgenerational coexistence history attenuates negative direct interactions and strengthens facilitation
<p>Data set for the study <strong>Transgenerational coexistence history attenuates negative direct interactions and strengthens facilitation</strong></p>
Data for "Convective Organization and Dry Tropical Cyclones in Direct Numerical Simulations of Idealized Fluid Setups"
<p>Supporting data and analysis scripts for work contained in the manuscript Velez-Pardo, Martin & Cronin, Timothy W. (2023) Convective Organization and Dry Tropical Cyclones in Direct Numerical Simulations of Idealized Fluid Setups. README and scripts for running simulations and for data post-processing are found in README_and_scripts.zip. Data obtained using supercomputer Cheyenne (doi:10.5065/D6RX99HX) provided by NCAR's Computational and Information Systems Laboratory (CISL), sponsored by the National Science Foundation.</p>
Raw Data for the article: How important is the role of iterative liver direct surgery in patients with hepatocellular carcinoma for a transplant center located in an area with a low rate of deceased donation?
<p><strong>Introduction: </strong>Hepatocellular carcinoma (HCC) accounts for nearly 90% of primary liver cancers, with estimates of over 1 million people affected by 2025. We aimed to explore the impacting role of an iterative surgical treatment approach in a cohort of HCC patients within the Milan criteria, associated with clinical risk factors for tumor recurrence (RHCC) after liver transplant (LT) and loco-regional therapies (LRT), as well as liver resection (LR) and/or microwave thermal ablation (MWTA).</p> <p><strong>Methods: </strong>We retrospectively analyzed our experience performed during an 8-year period between January 2013 and December 2021 in patients treated for HCC, focusing on describing the impact on preoperative end-stage liver disease severity, oncologic staging, tumor characteristics, and surgical treatments. The Cox model was used to evaluate variables that could predict relapse risks. Relapse risk curves were calculated according to the Kaplan-Meier method, and the log-rank test was used to compare them.</p> <p><strong>Results: </strong>There were 557 HCC patients treated with a first-line approach of LR and/or LRTs (<em>n</em> = 335) or LT (<em>n</em> = 222). The median age at initial transplantation was 59 versus 68 for those whose first surgical approach was LR and/or LRT. In univariate analysis with the Cox model, nodule size was the single predictor of recurrence of HCC in the posttreatment setting (HR: 1.61, 95% CI: 1.05-2.47, <em>p</em> = 0.030). For the LRT group, we have enlightened the following clinical characteristics as significantly associated with RHCC: hepatitis B virus infection (which has a protective role with HR: 0.34, 95% CI: 0.13-0.94, <em>p</em> = 0.038), number of HCC nodules (HR: 1.54, 95% CI: 1.22-1.94, <em>p</em> < 0.001), size of the largest nodule (HR: 1.06, 95% CI: 1.01-1.12, <em>p</em> = 0.023), serum bilirubin (HR: 1.57, 95% CI: 1.03-2.40, <em>p</em> = 0.038), and international normalized ratio (HR: 16.40, 95% CI: 2.30-118.0, <em>p</em> = 0.006). Among the overall 111 patients with RHCC in the LRT group, 33 were iteratively treated with further curative treatment (12 were treated with LR, two with MWTA, three with a combined LR-MWTA treatment, and 16 underwent LT). Only one of 18 recurrent patients previously treated with LT underwent LR. For these RHCC patients, multivariable analysis showed the protective roles of LT for primary RHCC after IDLS (HR: 0.06, 95% CI: 0.01-0.36, <em>p</em> = 0.002), of the time relapsed between the first and second IDLS treatments (HR: 0.97, 95% CI: 0.94-0.99, <em>p</em> = 0.044), and the impact of previous minimally invasive treatment (HR: 0.28, 95% CI: 0.08-1.00, <em>p</em> = 0.051).</p> <p><strong>Conclusion: </strong>The coexistence of RHCC with underlying cirrhosis increases the complexity of assessing the net health benefit of ILDS before LT. Minimally invasive surgical therapies and time to HCC relapse should be considered an outcome in randomized clinical trials because they have a relevant impact on tumor-free survival.</p>
FIGURE 37. Aeshnidae with valve. Direct screen capture from 3D in COMPARATIVE ANATOMY OF THE INSECT TRACHEAL SYSTEM PART 1: INTRODUCTION, APTERYGOTES, PALEOPTERA, POLYNEOPTERA
FIGURE 37. Aeshnidae with valve. Direct screen capture from 3D Slicer.
Direct nanopore sequencing of human cytomegalovirus ge-nomes from high-titre clinical samples
<p>This archive contains the nanopore generated HCMV genomes from the urine and lung clinical samples. The illumina derived genome sequences have been uploaded to GenBank as they are of higher quality, the nanopore sequences are uploaded here to avoid duplication on GenBank. Raw FASTQ reads from the virus are uploaded to NCBI SRA. The full paper abstract is given below. Nanopore sequencing is becoming increasingly commonplace in clinical settings, particularly for diagnostics and outbreak investigations. Its portability, low cost and ability to operate in near real-time has propelled it to the forefront of the recent SARS-CoV-2 pandemic. Although high sequencing error rates initially hampered its wider implementation, improvements have continually been made with each iteration of the nanopore flow cells and base calling software. Here, we assess the feasibility of using nanopore sequencing to determine the complete genome of human cytomegalovirus (HCMV) present in high-titre clinical samples without viral DNA enrichment, PCR amplification or prior knowledge of the sequences. We utilised a hybrid bioinformatic approach that involved assembling the reads<em> de novo</em>, improving the <em>de novo</em> consensus through alignment of reads to the best-matching genome from a collated set of published genomes, and polishing the improved consensus. The final consensus genome sequences from a urine and a lung sample, the latter with an HCMV to human DNA load approximately 50 times lower than the former, achieved 99.97 and 99.93% identity, respectively, to the bench-mark consensuses obtained independently by Illumina sequencing. Thus, we demonstrate that nanopore sequencing is capable of determining HCMV genomes directly from high-titre clinical samples with high accuracy. </p>
EXPERIMENTAL GROWTH CONDITIONS AFFECT DIRECT AND INDIRECT DEFENCES IN TWO COTTON SPECIES
<p>The file "R code CHappuis et al. 2023.txt" contains the R code for all the analyses shown in the research article "EXPERIMENTAL GROWTH CONDITIONS AFFECT DIRECT AND INDIRECT DEFENCES IN TWO COTTON SPECIES". The other files contain the raw data used for the analyses.</p> <p> </p> <p> </p>
Plant growth strategy determines the magnitude and direction of drought-induced changes in root exudates in subtropical forests
<p><span>Root exudates are an important pathway for plant-microbial interactions and are highly sensitive to climate change.</span> <span>However, how extreme drought affects root exudates and the main components, as well as species-specific differences in response magnitude and direction, are poorly understood. In this study, root exudation rates of total carbon (C) and its components (e.g., sugar, organic acid, and amino acid) were measured under the control and extreme drought treatments (i.e., 70% throughfall reduction) by <em>in situ</em> collection of four tree species with different growth rates in a subtropical forest. We also quantified soil properties, root morphological traits, and mycorrhizal infection rates to examine the driving factors underlying variations in root exudation. Our results showed that extreme drought significantly decreased root exudation rates of total C, sugar, and amino acid by 17.8%, 30.8%, and 35.0%, respectively, but increased root exudation rate of organic acid by 38.6%, which were largely associated with drought-induced changes in tree growth rates, root morphological traits, and mycorrhizal infection rates. Specifically, trees with relatively high growth rates were more responsive to drought for root exudation rates compared to those with relatively low growth rates, which were closely related to root morphological traits and mycorrhizal infection rates. These findings highlight the importance of plant growth strategy in mediating drought-induced changes in root exudation rates. The co-ordinations among root exudation rates, root morphological traits, and mycorrhizal symbioses in response to drought could be incorporated into land surface models to improve the prediction of climate change impacts on rhizosphere C dynamics in forest ecosystems. </span></p>
Directly dating Plio-Pleistocene climate change in the terrestrial record
<p class="MsoNormal">This is the Supporting Information for Dröllner et al. "Directly dating Plio-Pleistocene climate change in the terrestrial record" published in Geophysical Research Letters. The data comes from a ferruginous induration in the arid landscapes of the Nullarbor Plain in southern Australia (30° 54' 33.84'' S, 132° 13' 5.88'' E). The data provides constraints on the timing of Plio-Pleistocene aridification in the continental realm and supports the use of ferruginous indurations as targets to obtain absolute ages on landscape evolution. The dataset includes chemical-mineralogical results, which suggest that the formation of ferruginous indurations was linked with a decline of the groundwater table. (U-Th)/He geochronology of goethite from ferruginous indurations provides age constraints that link the textural and chemical-mineralogical observations to a rapid climatic shift from humid Late Pliocene to arid Early Pleistocene conditions. Specifically, this Supporting Information includes a pdf file (available through Zenodo; <a href="https://doi.org/10.5281/zenodo.7739575" title="https://doi.org/10.5281/zenodo.7739575">https://doi.org/10.5281/zenodo.7739575</a>) with detailed analytical methods for X-ray powder diffraction (XRD, Text S1), energy-dispersive spectroscopy (Text S2), Raman spectroscopy (Text S3), and (U-Th)/He geochronology (Text S4). This pdf file also includes Supporting Figures S1 (sample material, and fragments used for dating) and S2 (XRD spectra), as well as Supporting Tables S1 (XRD bulk mineralogy), S2 ((U-Th)/He data), S3 (XRD instrument parameters), and the captions for Table S4 (Raman data) and Table S5 (XRD data). The latter two datasets are provided as separate files available through Dryad (this data).</p>
Bibliographic Information on PNAS Direct and Contributed Submissions
<p>This dataset contains observations of 46,391 articles published as "Direct" or "Contributed" submissions in PNAS. Only includes publications in the Biological, Physical and Social Sciences sections.</p> <p>Variables:</p> <ul> <li>extract_id: incremental ID</li> <li>topic: main section</li> <li>sub_label: labelled submission type</li> <li>pub_year: publication year</li> <li>review_time: number of days from the manuscript was received until it was accepted for publication</li> <li>ncs_full: The field normalised citation score, full counting</li> </ul> <p>-</p>
TIRF Microscopy Data Files. "Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides: Implications for target site search"
<p>TIRF-microscopy images and analysis data from single-molecule experiments assessing the direct transfer phenomenon in the TREX1 exonuclease. </p>
Setup of a 3D printed wind tunnel: application for calibrating bi-directional velocity probes used in Fire Engineering Applications
<p>The research presented here focuses on the development of a 3D printed wind tunnel and the relevant equipment to be used for calibrating bi-directional velocity probes (BDVP). BDVP are equipment to be used for measuring velocity flow by determining the pressure difference of hot gases generated during fires. The manufactured probes require calibration to determine the calibration factor to achieve precise measurement. The calibration is usually performed in wind tunnels which can be difficult to access due to costs, complexity and the various pieces of equipment required. The aim of the current study is to develop and assemble an inexpensive and easy-to-build bench-scale wind tunnel, with a data-logging system and fan control functionalities for fast and effective calibration of BDVP. A 3D printer with a PET-G filament is used, able to produce parts for the wind tunnel system which are durable and easy to handle and assemble. The system additionally includes an Arduino-based measuring unit with a hot-wire anemometer and temperature correction: Rev. P. This takes precise measurements; continuously logging data on a computer through a USB interface and capable of saving data on an SD card. This design provides users with parameters of velocity flow up to 4 m/s with standard deviation of 1.2 % and turbulence intensity of 1 %. The main advantages of this wind tunnel are its simplicity to build and portability.</p> <p>The dataset contains design files for 3D printing of the wind tunnel, BOM and wiring of electronic components.</p> <p>The project is prototype under development and authors are not responsible for any damages or injuries caused by inappropriate construction or operation. This source is distributed WITHOUT ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING OF MERCHANTABILITY, SATISFACTORY QUALITY AND FITNESS FOR A PARTICULAR PURPOSE.</p>
Tunable directional photon scattering from a pair of superconducting qubits
<p>This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.</p>
Policy and programmatic directions for the Lesotho tuberculosis programme: Findings of the national tuberculosis prevalence survey, 2019
<p><strong>Introduction</strong></p> <p>The Kingdom of Lesotho has one of the highest burdens of tuberculosis (TB) in the world. A national TB prevalence survey was conducted to estimate the prevalence of bacteriologically confirmed pulmonary TB disease among those ≥15 years of age in 2019.</p> <p><strong>Method</strong></p> <p>A multistage cluster-based cross-sectional survey where residents ≥15 years in 54 clusters sampled from across the country were eligible to participate. Survey participants were screened using a symptom screen questionnaire and digital chest X-ray (CXR). Respondents who acknowledged cough of any duration, fever, weight loss, night sweats and/or had any CXR abnormality in the lungs were asked to provide two spot sputum specimens. All sputum testing was conducted at the National TB Reference Laboratory (NTRL), where samples underwent Xpert MTB/RIF Ultra (1st sample) and MGIT culture (2nd sample). HIV counselling and testing was offered to all survey participants. TB cases were those with Mycobacterium tuberculosis complex-positive samples with culture; and where culture was not positive, Xpert MTB/RIF Ultra (Xpert Ultra) was positive with a CXR suggestive of active TB and no current or prior history of TB.</p> <p><strong>Result</strong></p> <p>A total of 39,902 individuals were enumerated, and of these, 26,857 (67.3%) were eligible to participate; 21,719 (80.9%) participated in the survey of which 8,599 (40%) were males and 13,120 (60%) were females. All 21,719 (100%) survey participants underwent symptom screening and a total of 21,344 participants (98.3%) had a CXR. Of the 7,584 (34.9%) participants who were eligible for sputum examination, 4,190 (55.2%) were eligible by CXR only, 1,455 (19.2%) by symptom screening, 1,630 by both, and 309 by CXR exemption. A total of 6,780 (89.4%) submitted two sputum specimens, and 311 (4.1%) submitted one sample only. From the 21,719 survey participants, HIV counseling and testing was offered to 17,048, and 3,915 (23.0%) were documented as HIV-positive. The survey identified 132 participants with bacteriologically confirmed pulmonary TB thus providing an estimated prevalence of 581 per 100,000 population (95% CI 466–696) for those ≥15 years in 2019. Using the survey results, TB incidence was re-estimated to be 654 per 100,000 (95% CI 406–959), which was comparable to the 2018 TB incidence rate of 611 per 100,000 (95% CI 395–872) reported by the World Health Organization (WHO). The highest TB burden was found in those ≥55 years and among men. The ratio of prevalence to case notification was estimated at 1.22. TB/HIV coinfection was identified in 39 (29.6%) participants. Out of the 1,825 participants who reported a cough, 50% of these participants, mostly men, did not seek care. Those who sought care predominantly went to the public health facilities.</p> <p><strong>Conclusion</strong></p> <p>The TB prevalence survey results confirmed that burden of TB and TB/HIV coinfection remains very high in Lesotho. Given that TB prevalence remains high, and there is a significant proportion of participants with confirmed TB that did not report TB suggestive symptoms. The National TB Programme will need to update its TB screening and treatment algorithms to achieve the End TB targets. A major focus will need to be placed on finding the "missing cases" i.e., undiagnosed or under-reported TB cases, or ensuring that not only TB symptomatic but also those who do not present with typical TB symptoms are promptly identified to reduce further onward transmission.</p>
Data from: Direct evidence of permeability evolution of Nanan granite after two cooling paths under different confining pressures: A comparative study
<p>Permeability decides the mass transfer behavior and plays a key role in the heat extraction of enhanced geothermal systems (EGSs), and the aim of the injection of cooling water is to enhance permeability within the geothermal reservoirs. Direct evidence of how cool water affecting permeability evolution is still limited. Therefore, we explored the permeability evolution of Nanan granite after air and water cooling under different confining pressures combined with optical microscopy and X-ray CT observation. We found that there are lots of microdefects observed in Nanan granite after two cooling paths, which dominantly drives the evolution of permeability from a microscopic scale. The permeabilities of granite under water-cooling condition are always larger than those under air-cooling condition, and water-cooling treatment further enhances the permeability of specimens. The permeabilities of granite specimens after two cooling paths decrease with confining stress. More microcracks and better connectivity among microcracks produce a larger permeability within the specimen after water cooling. The observed microcracks are regarded as the seepage channels and direct microscale evidence of permeability evolution of granite after two cooling paths. Our results may suggest that water injection is an efficient way for permeability enhancement due to thermal microcracks propagation in thermal simulation.</p>
2. Files with parameters of anisotropy of thermoremanent magnetization and file with modulus of TRM intensity recalculated into direction of remanent magnetization according to the shape of ATRM ellipsoid
<p>Files with parameters of anisotropy of thermoremanent magnetization and file with modulus of TRM intensity recalculated into direction of remanent magnetization according to the shape of ATRM ellipsoid</p> <p>Data supporting manuscript entitled “Archaeomagnetic studies of bricks from ancient buildings sampled in SE Poland (Central Europe)” by J. Nawrocki, K. Standzikowski, M. Chadima, T. Werner, M. Łanczont, J. Gancarski, Z. Gil submitted to Journal of Archaeological Science: Reports (JASREP-D-23-00078).</p>
Data for "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"
<p>This is the data associated with the following publication : "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"</p>
Time-Resolved XAS Provides Direct Evidence for Oxygen Activation on Cationic Iron in a Bimetallic Pt-FeOx/Al2O3 Catalyst
<p>Open data for "Time-Resolved XAS Provides Direct Evidence for Oxygen Activation on Cationic Iron in a Bimetallic Pt-FeOx/Al2O3 Catalyst" published in ACS Catal. 2021, 11, 11793−11805 <a href="https://doi.org/10.1021/acscatal.1c02795">https://doi.org/10.1021/acscatal.1c02795</a> </p>
Emulator of PR-DNS: Accelerating Dynamical Fields with Neural Operators in Particle-Resolved Direct Numerical Simulation
<p>The codes directory includes the various machine learning models, such as FNO, UNet and ResNet. R128_init1 and R128_init2 are the PR-DNS time step simulations at different initial conditions. R64_init2, R128_init2 and R256_init2 are the PR-DNS time step simulations at different resolutions. </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.