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opencc-by-4.0Mar 2022View details →

Data for "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection"

Once decompressed, the file contains a folder which contains: <ul> <li>The files "s100_Nth.fasta" (where "N" is 5, 6, 7 or 8), which are the output of the SELEX experiment described in the paper with DOI: <a href="https://doi.org/10.1002/cbic.201900265">10.1002/cbic.201900265</a>. They are standard fasta files, and the descriptor of each sequence is of the form "seqX-Y", where "X" is an increasing label, and "Y" is the number of times "seqX" has been obtained (number of counts of "seqX").</li> <li>The file "Aptamer_Exp_Results.csv", which contains the sequences tested experimentally for the paper "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection" (preprint available at https://doi.org/10.1101/2022.03.12.484094), with the following experimental results for each sequence: (i) whether the sequence was able to bind thrombin ('B' for binders, 'NB' for non-binders); (ii) the thrombin exosite used for binding ('I' for exosite I, 'II' for exosite II, 'n/a' for sequences not tested).</li> </ul> Examples of usage of the data are available at https://github.com/adigioacchino/RBMsForAptamers.

opencc-zeroMar 2022View details →

Supplemental material for: Clinical and neuroimaging outcomes of direct endovascular thrombectomy vs. bridging therapy in large vessel occlusion patients: a secondary analysis of SELECT cohort study

Objective: To evaluate the comparative safety and efficacy of direct endovascular thrombectomy(dEVT) compared to bridging therapy(BT:IV-tPA+EVT) and assess if BT potential benefit relates to stroke severity, size and initial presentation to EVT vs. non-EVT center. Methods: In a prospective multicenter cohort-study of imaging selection for endovascular thrombectomy[SELECT], anterior-circulation large vessel occlusion (LVO) patients presenting to EVT-capable centers within 4.5hours from last-known-well were stratified into BT vs. dEVT. The primary outcome was 90-day functional independence[modified Rankin Scale(mRS)=0-2]. Secondary outcomes included a shift across 90-day mRS grades, mortality, symptomatic intracranial hemorrhage. We also performed subgroup-analyses according to initial presentation to EVT-capable center (direct versus transfer), stroke severity and baseline infarct core volume. Results: We identified 226 LVOs (54%:men, mean age:65.6±14.6years, median NIHSS-score: 17, 28% received dEVT). Median time from arrival to groin-puncture did not differ in BT-patients when presenting directly[dEVT:1.43 (IQR=1.13-1.90) hours vs. BT:1.58(IQR=1.27-2.02)hours,p=0.40] or transferred to EVT-capable centers[dEVT:1.17 (IQR: 0.90-1.48) hours vs. BT:1.27 (IQR: 0.97-1.87) hours,p=0.24]. BT was associated with higher odds of 90-day functional independence (57% vs. 44%,aOR=2.02,95%CI:1.01-4.03,p=0.046) and functional improvement (adjusted cOR=2.06,95%CI:1.18-3.60,p=0.011), and lower likelihood of 90-day mortality (11% vs. 23%,aOR: 0.20,95%CI:0.07-0.58,p=0.003). No differences in any other outcomes were detected. In subgroup-analyses, BT patients with baseline NIHSS-scores<15 had higher functional independence likelihood compared to dEVT (aOR=4.87,95%CI:1.56-15.18,p=0.006); this association was not evident for patients with NIHSS-scores≥15 (aOR=1.05,95%CI:0.40-2.74,p=0.92). Similarly, functional outcomes improvements with BT were detected in patients with core volume strata (Ischemic core <50cc: aOR: 2.10, 95% CI:1.02-4.33, p=0.044 vs ischemic core ≥50cc: aOR: 0.41,95% CI:0.01-16.02,p=0.64) and transfer status (transferred: aOR: 2.21,95% CI:0.93-9.65,p=0.29 vs direct to EVT center: aOR:1.84,95%CI:0.80-4.23,p=0.15). Conclusions: Bridging therapy appears to be associated with better clinical outcomes, especially with milder NIHSS-scores, smaller presentation core volumes and those who were "dripped and shipped". Classification of Evidence: This study provides Class III evidence that for patients with ischemic stroke from anterior-circulation LVO within 4.5 hours from last-known-well, bridging therapy compared to direct endovascular thrombectomy leads to better 90-day functional outcomes.

openSep 2022View details →

Input data for Bayesian and information theoretic model selection and similarity analysis

This data serves as input to the codes found in the following repository https://github.com/MariaFMoralesOreamuno/Bayesian_Information_theoretic_model_selection.git

openmit-licenseSep 2022View details →

Blinded Predictions and Post-hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models

Training and test datasets and scripts for training models.

opencc-by-nc-nd-4.0May 2024View details →

Data from: D3.2. Multi-criteria decision analysis (MCDA) for selection and location of hybrid solutions

Open the record for dataset details and reuse information.

opencc-by-4.0Jun 2024View details →

Millennial-Scale Microbiome Analysis Reveals Ancient Antimicrobial Resistance Conserved Despite Modern Selection Pressures

This dataset contains metadata and profiled antibiotic resistance genes from ancient metagenome permafrost.

opennotspecifiedMay 2003View details →

text-fig. 52. wo selected reduced consensus trees from the analysis of the complete data set. a, after deletion of 'Chilantaisaurus' maortuensis. B, after deletion of Proceratosaurus and Xuanhanosaurus. in The interrelationships and evolution of basal theropod dinosaurs

text-fig. 52. wo selected reduced consensus trees from the analysis of the complete data set. a, after deletion of 'Chilantaisaurus' maortuensis. B, after deletion of Proceratosaurus and Xuanhanosaurus.

opennotspecifiedSep 2021View details →

FIG. 1. Colorado Pikeminnow and Razorback Sucker larvae for this study were selected from 2009 in Otolith Microstructure Analysis Elucidates Spawning and Early Life Histories of Federally Endangered Fishes in the San Juan River

FIG. 1. Colorado Pikeminnow and Razorback Sucker larvae for this study were selected from 2009 to 2017 larval fish collections made in the San Juan River between reach 6, near Farmington, NM, and reach 1, near the terminus of the San Juan River in Lake Powell.

FIGURE 5 in Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

FIGURE 5. Phylogenetic estimation on relationship of the marine unicellular cyanobacteria inferred by maximum likelihood analysis of 16S–23S ITS region. Number at nodes indicates the bootstrap values (1000 replicates) obtained from the analysis. Bootstrap values (≥50%) are indicated on the branches. The investigated strains are marked with a black triangle.

FIGURE 2. Transmission electron micrographs a, BDU 140431. b. BDU 100913. c. BDU 130052. d. BDHKU 35101 in Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

FIGURE 2. Transmission electron micrographs a, BDU 140431. b. BDU 100913. c. BDU 130052. d. BDHKU 35101. Thylakoid was denoted as T. Scale bar 200nm.

FIGURE 1 in Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

FIGURE 1. Bright field photomicrographs of a. BDU 10144. b. BDU 70542. c. BDU 140431. d. BDU 141741. e. BDHKU 20401. f. BDHKU 35301 g. BDU 130052. h. BDU 100913. i. BDU 130192. j. BDU 130911. k. BDHKU 35101. l. BDU 20121. Scale bar: 10μm.

FIGURE 4 in Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

FIGURE 4. Length of ITS region of the studied marine unicellular cyanobacteria —Spacer 1, —tRNAIle, —spacer2, —tRNAAla, —Spacer 3 and their GC content are presented within parenthesis.

FIGURE 3 in Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

FIGURE 3. Phylogenetic estimation on relationship of marine unicellular cyanobacteria inferred by maximum likelihood analysis of 16S rRNA gene sequences (~1386 bp). Number at nodes indicates the bootstrap values (1000 replicates) obtained from the analysis. Bootstrap values (≥ 50%) are indicated on the branches. The investigated strains are marked with a black triangle.

opencc-by-4.0Sep 2024View details →

Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants

This is all the source data associated with the manuscript which has the same title with this dataset. The abstract and the authors of the manuscripts are below: Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants   Víctor Sánchez de Medina Hernández1,2*, Marintia Mayola Nava García1,2*, Marion Clavel1,3, Ranjith K. Papareddy1, Veselin I. Andreev1, Varsha Mathur1, Azadeh Mohseni1,4, Marta García-León1, Peng Gao1, Juan Carlos de la Concepción1, Lorenzo Picchianti1, Nenad Grujic1, Roksolana Kobylinska1, Alibek Abdrakhmanov1,2, Héloïse Duvergé1, Gaurav Anand5, Nils Leibrock1,4, Anita Bianchi1, Margot Raffeiner6, Timothy Scott Crawford7, Luca Argirò1, Mateusz Matuszkiewicz1,8, Cheuk-Ling Wun1, Jakob Valdbjørn Kanne9, Anton Meinhart10, Elisabeth Roitinger1, Isabel Bäurle7, Byung Ho Kang11, Morten Petersen9, Suayib Üstün6, Yogesh Kulathu5, Tim Clausen10, Silvia Ramundo1, Yasin Dagdas1 1 Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria. 2 Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. 3 Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany. 4 Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, BOKU University, Vienna, Austria. 5 MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. 6 Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany. 7 Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany. 8 Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland. 9 Functional Genomic Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark. 10 Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. 11 School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.   *These authors contributed equally to this work   Correspondence: Yasin Dagdas, <a href="mailto:yasin.dagdas@gmi.oeaw.ac.at">yasin.dagdas@gmi.oeaw.ac.at</a>   Abstract Selective autophagy is a fundamental protein quality control pathway that safeguards proteostasis by degrading damaged or surplus cellular components, particularly under stress. This process is orchestrated by selective autophagy receptors (SARs) that direct specific cargo for degradation. While significant strides have been made in understanding the molecular framework of selective autophagy, the diversity of SAR repertoires across species remain largely unexplored. Through a comparative interactome analysis across five model organisms, we identified a suite of conserved and lineage-specific SAR candidates. Among these, we validated CESAR as a conserved SAR critical for proteostasis under proteotoxic stress. CESAR specifically facilitates the degradation of hydrophobic, ubiquitinated protein aggregates and is indispensable for heat stress tolerance. Our study offers a rich resource for SAR discovery and positions CESAR as a pivotal regulator of proteostasis, with broad implications for improving stress resilience in plants.

opencc-zeroDec 2015View details →

Data from: Characterizing wildlife behavioural responses to roads using integrated step selection analysis

Roads are a prevalent, ever-increasing form of human disturbance on the landscape. In many places in western North America, energy development has brought human and road disturbance into seasonal winter range areas for migratory elk. We sought to evaluate the predictions from the risk-disturbance hypothesis when studying elk response to roads during winter. Road proximity and crossing were used to evaluate these behaviours, which offered a rare comparison between two common measures of roads. We used integrated step selection analysis (iSSA) to evaluate four alternative hypotheses regarding the influence of roads on space-use behaviour across 175 elk-years of elk telemetry data, and we quantified both population-level and individual-level variations in responses. We demonstrated, for the first time, how iSSA can be used to combine movement analysis in a refined approach to habitat selection. Elk responded to roads as they would natural predation risk. Elk selected areas farther from roads at all times of day with avoidance being greatest during twilight. In addition, elk sought cover and moved more when in the vicinity of roads. Road crossings were generally avoided, but this avoidance was weakest during daytime when elk were both moving and closer to roads. Synthesis and applications. Energy development is transforming landscapes in western North America with the proliferation of roads, which we show is having substantial and multifaceted negative effects on elk movement and behaviour. These adverse effects can be mitigated by minimizing new road construction and by restricting traffic on roads as well as providing the protection of tree cover on elk winter ranges.

opencc-zeroDec 2014View details →

Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

opennotspecifiedJul 2021View details →

FIGURE 1 in Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

FIGURE 1 (cont'd). Maximum Likelihood phylogeny (-lnL: 26590.631) inferred in RAxML under the GTR + Gamma model of nucleotide substitution. Bootstrap proportions resulting from 1000 bootstrap replicates are displayed at tree nodes, with values under 50 omitted. Branch lengths are measured as substitutions per site. A) denotes Diogenidae Clade 1, with subdivisions 1a, 1b, 1c, and 1d. An asterisk (*) denotes the Paguristes tortugae complex. B) denotes Paguridae Clade 1. C) denotes Lithodidae. D) denotes Paguridae Clade 2. E) denotes Diogenidae Clade 2. F) denotes Coenobitidae. G) denotes Diogenidae Clade 3. H) denotes the family Parapaguridae. For branch labels, taxon name is followed by voucher catalog number and abbreviated collection locality (Table 1). Abbreviations: nwAtlantic = northwestern Atlantic; neCarib = northeastern Caribbean; nwCarib = northwestern Caribbean; seCarib = southeastern Caribbean; swCarib = southwestern Caribbean; neGMx = northeastern Gulf of Mexico; nwGMx = northwestern Gulf of Mexico; seGMx = southeastern Gulf of Mexico; swGMx = southwestern Gulf of Mexico; nePac = northeastern Pacific; wPac = western Pacific; nwPac = northwestern Pacific; sePac = southeastern Pacific; swPac = southwestern Pacific.

opennotspecifiedJul 2021View details →

FIGURE 1 in Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

FIGURE 1. Maximum Likelihood phylogeny (-lnL: 26590.631) inferred in RAxML under the GTR + Gamma model of nucleotide substitution. Bootstrap proportions resulting from 1000 bootstrap replicates are displayed at tree nodes, with values under 50 omitted. Branch lengths are measured as substitutions per site. A) denotes Diogenidae Clade 1, with subdivisions 1a, 1b, 1c, and 1d. An asterisk (*) denotes the Paguristes tortugae complex. B) denotes Paguridae Clade 1. C) denotes Lithodidae. D) denotes Paguridae Clade 2. E) denotes Diogenidae Clade 2. F) denotes Coenobitidae. G) denotes Diogenidae Clade 3. H) denotes the family Parapaguridae. For branch labels, taxon name is followed by voucher catalog number and abbreviated collection locality (Table 1). Abbreviations: nwAtlantic = northwestern Atlantic; neCarib = northeastern Caribbean; nwCarib = northwestern Caribbean; seCarib = southeastern Caribbean; swCarib = southwestern Caribbean; neGMx = northeastern Gulf of Mexico; nwGMx = northwestern Gulf of Mexico; seGMx = southeastern Gulf of Mexico; swGMx = southwestern Gulf of Mexico; nePac = northeastern Pacific; wPac = western Pacific; nwPac = northwestern Pacific; sePac = southeastern Pacific; swPac = southwestern Pacific.

opencc-zeroSep 2021View details →

Data from: Model selection analysis of temporal variation in benefit for an ant-tended treehopper

Recent studies of mutualism have emphasized both that the net benefit to participants depends on the ecological context and that the density‐dependent pattern of benefit is key to understanding the population dynamics of mutualism. Indeed, changes in the ecological context are likely to drive changes in both the magnitude of benefit and the density‐dependent pattern of benefit. Despite the close linkage between these two areas of research, however, few studies have addressed the factors underlying variation in the density‐dependent pattern of benefit. Here I use model selection to evaluate how variation in the benefits of a mutualism drives temporal variation in the density‐dependent pattern of net benefit for the ant‐tended treehopper Publilia concava. In the interaction between ants and treehoppers in the genus Publilia, ants collect the sugary excretions of treehoppers as a food resource, and treehoppers benefit both directly (e.g., by feeding facilitation) and indirectly (e.g., by predator protection). Results presented here show that temporal changes in the relative magnitude of direct and indirect benefit components of ant tending, especially the effectiveness of predator protection by ants, qualitatively change the overall pattern of density‐dependent benefit between years with maximum benefit shifting from treehoppers in small to large aggregations. These results emphasize the need for empirical studies that evaluate the long‐term dynamics of mutualism and theoretical studies that consider the population dynamics consequences of variation in the density‐dependent pattern of benefit.