cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5512994
title: A unified genealogy of modern and ancient genomes: Unified, inferred tree sequences of 1000 Genomes, Human Genome Diversity, and Simons Genome Diversity Projects with ancient samples

description: Unified, inferred tree sequences built from the 1000 Genomes phase 3, Human Genome Diversity, and Simons Genome Diversity Projects with high coverage sequenced ancient samples. The ancient samples are the Altai, Chagyrskaya, and Vindija Neanderthals, the Denisovan, and a high-coverage family of four from the Afanasievo Culture. Each tree sequence is the arm of an autosome (the short arm of acrocentric chromosomes are not included). Tree sequences were inferred with tsinfer version 0.2.1 and tsdate version 0.1.4, as described in Wohns et al. (2021). The files were compressed using tszip. All data is in GRCh38. The full data pipeline used to generate these tree sequences and associated metadata is available on GitHub. A description can be found in the Supplementary Material of Wohns et al. (2021). Tree sequences can be decompressed as follows: <pre><code>$ tsunzip hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees.tsz</code></pre> Once decompressed, trees files can be loaded and processed in Python using tskit. <pre><code>import tskit ts = tskit.load("hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees") # ts is an instance of tskit.TreeSequence print("The short arm of chromosome 1 contains {} trees".format(ts.num_trees))</code></pre> Accessing variant sites in the tree sequence provides the position and id of variants: <pre><code>import json site = ts.site(1000) site_metadata = json.loads(site.metadata) print("The position of site 1000 is {} and its ID is {}.".format(site.position, site_metadata["ID"]))</code></pre> Metadata associated with individuals and populations was derived from the original sources (TGP, HGDP, and SGDP) and converted to JSON form. For example, to access individual metadata we can use: <pre><code>ind = ts.individual(0) metadata_dict = json.loads(ind.metadata)</code></pre> The metadata_dict variable will now contain all the metadata for the individual with ID 0 as a dictionary. Metadata associated with populations can be found in a similar way. Population IDs are associated with individuals via their constituent nodes. For example, <pre><code>pop_metadata = [json.loads(pop.metadata) for pop in ts.populations()] ind_node = ts.node(ind.nodes[0]) ind_pop_metadata = pop_metadata[ind_node.population]</code></pre> After this, the ind_pop_metadata variable will contain the population level metadata for individual ID 0.
DOI: 10.5281/zenodo.5512993
title: A unified genealogy of modern and ancient genomes: Unified, inferred tree sequences of 1000 Genomes, Human Genome Diversity, and Simons Genome Diversity Projects with ancient samples

description: Unified, inferred tree sequences built from the 1000 Genomes phase 3, Human Genome Diversity, and Simons Genome Diversity Projects with high coverage sequenced ancient samples. The ancient samples are the Altai, Chagyrskaya, and Vindija Neanderthals, the Denisovan, and a high-coverage family of four from the Afanasievo Culture. Each tree sequence is the arm of an autosome (the short arm of acrocentric chromosomes are not included). Tree sequences were inferred with tsinfer version 0.2.1 and tsdate version 0.1.4, as described in Wohns et al. (2021). The files were compressed using tszip. All data is in GRCh38. The full data pipeline used to generate these tree sequences and associated metadata is available on GitHub. A description can be found in the Supplementary Material of Wohns et al. (2021). Tree sequences can be decompressed as follows: <pre><code>$ tsunzip hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees.tsz</code></pre> Once decompressed, trees files can be loaded and processed in Python using tskit. <pre><code>import tskit ts = tskit.load("hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees") # ts is an instance of tskit.TreeSequence print("The short arm of chromosome 1 contains {} trees".format(ts.num_trees))</code></pre> Accessing variant sites in the tree sequence provides the position and id of variants: <pre><code>import json site = ts.site(1000) site_metadata = json.loads(site.metadata) print("The position of site 1000 is {} and its ID is {}.".format(site.position, site_metadata["ID"]))</code></pre> Metadata associated with individuals and populations was derived from the original sources (TGP, HGDP, and SGDP) and converted to JSON form. For example, to access individual metadata we can use: <pre><code>ind = ts.individual(0) metadata_dict = json.loads(ind.metadata)</code></pre> The metadata_dict variable will now contain all the metadata for the individual with ID 0 as a dictionary. Metadata associated with populations can be found in a similar way. Population IDs are associated with individuals via their constituent nodes. For example, <pre><code>pop_metadata = [json.loads(pop.metadata) for pop in ts.populations()] ind_node = ts.node(ind.nodes[0]) ind_pop_metadata = pop_metadata[ind_node.population]</code></pre> After this, the ind_pop_metadata variable will contain the population level metadata for individual ID 0.
DOI: 10.6084/m9.figshare.14723988.v1
title: Impacts of the invasive European Starling on two neotropical woodpecker species: agonistic responses and reproductive interactions

description: The European Starling (<i>Sturnus vulgaris</i>) – hereafter ‘starling’ – has been introduced in many countries, and its South American population recently started expanding exponentially. This invasive species has a worldwide negative impact on the breeding performance of woodpeckers, competing for cavity use. Nevertheless, information is still lacking regarding southern temperate neotropical woodpeckers nest defence strategies and starling effects on woodpeckers’ breeding performance. We monitored Campo Flicker (<i>Colaptes campestris</i>) and Green-barred Woodpecker (<i>Colaptes melanochloros</i>) nests in a native southern temperate forest of central-eastern Argentina, to detect interactions with starlings and to assess the effect of starlings presence on woodpeckers’ breeding performance. We assessed whether woodpeckers perform defensive behaviours against the starlings by exposing taxidermied starling models to woodpecker breeding pairs. We detected interactions with starlings at 11% of the nests. These nests had a significantly higher probability of being abandoned during the early stages (until the third incubation day), compared to nests without interactions. Moreover, woodpeckers attacked and made distress calls more frequently in response to the presentation of the starling, compared to predator and non-competing species models. We also documented evidence of joint nesting, as four breeding pairs of woodpeckers shared their nest chamber with starlings. Our results indicate that neotropical woodpeckers are more likely to abandon their cavity when they interact with starlings. As the starling is expanding quickly in Argentina, this information points at the need to develop management programmes to control the impacts of this invasive species on the native fauna, especially on species with conservation concerns.
DOI: 10.6084/m9.figshare.16621522
title: List of species from Delayed fertilization facilitates flowering time diversity in Fagaceae

description: Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
DOI: 10.6084/m9.figshare.16621522.v2
title: List of species from Delayed fertilization facilitates flowering time diversity in Fagaceae

description: Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
DOI: 10.6084/m9.figshare.16621522.v1
title: List of species from Delayed fertilization facilitates flowering time diversity in Fagaceae

description: Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
DOI: 10.6084/m9.figshare.16586456.v1
title: MOFs-Based Nanoagent Enables Dual Mitochondrial Damage in Synergistic Antitumor via Oxidative Stress and Calcium Overload

description: Source data generated in this study for supplementart information have been provided as xls format.
DOI: 10.6084/m9.figshare.16586420.v2
title: MOFs-Based Nanoagent Enables Dual Mitochondrial Damage in Synergistic Antitumor Therapy via Oxidative Stress and Calcium Overload

description: Source data generated in this study for main text have been provided as xls format.<br>
DOI: 10.6084/m9.figshare.16586420.v1
title: MOFs-Based Nanoagent Enables Dual Mitochondrial Damage in Synergistic Antitumor via Oxidative Stress and Calcium Overload

description: Source data generated in this study for main text have been provided as xls format.<br>
DOI: 10.14457/mu.the.1997.484
title: การศึกษาปัจจัยคัดสรรที่มีผลต่อความเมื่อยล้าของหลังส่วนล่าง ในพนักงานที่ทำงานกับเครื่องวีดีที
DOI: 10.14457/mu.the.1997.485
title: คุณภาพชีวิตของสตรีวัยหมดประจำเดือน ในเขตบางกอกน้อย กรุงเทพมหานคร
DOI: 10.14457/mu.the.1997.486
title: การศึกษาพฤติกรรมการป้องกันและควบคุมการติดเชื้อในโรงพยาบาลของพยาบาลในจังหวัดสุราษฎร์ธานี
DOI: 10.14457/mu.the.1997.487
title: รูปแบบการดำเนินงานบริการผู้ป่วยอุบัติเหตุและฉุกเฉินของโรงพยาบาลทั่วไปขนาด 450 เตียง
DOI: 10.14457/mu.the.1997.488
title: การประยุกต์ทฤษฎีขั้นตอนการเปลี่ยนแปลงพฤติกรรมในการเลิกสูบบุหรี่ของนักเรียนชายระดับมัธยมศึกษาตอนต้น กรุงเทพมหานคร
DOI: 10.14457/mu.the.1997.489
title: การสื่อสารผ่านเครือข่ายสังคมเพื่อส่งเสริมพฤติกรรมการตรวจมะเร็งปากมดลูกของสตรีอำเภอบ้านนาสาร จังหวัดสุราษฎร์ธานี
DOI: 10.14457/mu.the.1997.490
title: รองเง็ง : ระบำและดนตรีพื้นบ้านภาคใต้ของประเทศไทย
DOI: 10.14457/mu.the.1997.491
title: บทบาทของสตรีในการมีส่วนร่วมจัดการทรัพยากรป่าไม้ของชุมชน
DOI: 10.14457/mu.the.1997.492
title: การวิเคราะห์เพลงแขกสี่เกลอเถา
DOI: 10.14457/mu.the.1997.493
title: การใช้หลักสูตรนาฏศิลป์ชั้นสูง พุทธศักราช 2527 กลุ่มวิชาชีพสาขาดุริยางค์ไทย
DOI: 10.14457/mu.the.1997.494
title: การประเมินเทคโนโลยีที่เหมาะสมเพื่อป้องกันและควบคุมโรคไข้เลือดออก : กรณีศึกษาจังหวัดตรัง
DOI: 10.14457/mu.the.1997.495
title: การเปรียบเทียบในเชิงวิศวกรรมระหว่างเรือไฟฟ้าชนิดผสมกับเรือหางยาวเครื่องยนต์ดีเซล กรณีศึกษาคลองผดุงกรุงเกษม
DOI: 10.14457/mu.the.1997.496
title: การเปรียบเทียบในเชิงเศรษฐศาสตร์ระหว่างเรือไฟฟ้าชนิดผสมกับเรือหางยาว เครื่องยนต์ดีเซลเพื่อประกอบการขนส่ง กรณีศึกษา คลองผดุงกรุงเกษม
DOI: 10.14457/mu.the.1997.497
title: การศึกษาแนวทางความร่วมมือพหุภาคีต่อการจัดการมูลฝอยของชุมชนท้องถิ่น กรณีศึกษา : ชุมชนสาคลี อำเภอเสนา จังหวัดพระนครศรีอยุธยา
DOI: 10.14457/mu.the.1997.498
title: การพัฒนาหลักสูตรฝึกอบรมการสร้างสวนไม้ผลสำหรับยุวเกษตรกรในชุมชนเขตภูเขาภาคเหนือตอนบน : กรณีศึกษาจังหวัดลำปาง
DOI: 10.25345/c53v7q
title: MassIVE MSV000088137 - GNPS U19_Wisconsin_MARS_Stool_Samples
title: Untargeted LC/MS metabolomics of stool samples collected as part of the U19.
DOI: 10.5281/zenodo.5520451
title: OSTEOPATHIC MANIPULATIVE TREATMENT IMPROVES OUTCOMES AFTER HEART SURGERY: A RANDOMIZED CONTROLLED TRIAL (dataset)

description: Dataset for reproducing figures 2,3 and 4
DOI: 10.5281/zenodo.5520450
title: OSTEOPATHIC MANIPULATIVE TREATMENT IMPROVES OUTCOMES AFTER HEART SURGERY: A RANDOMIZED CONTROLLED TRIAL (dataset)

description: Dataset for reproducing figures 2,3 and 4
DOI: 10.34740/kaggle/dsv/2574263
title: MRI Images 1_random_Pome
DOI: 10.5281/zenodo.3978345
title: Fusion-dependent formation of lipid nanoparticles containing macromolecular payloads

description: The success of Onpattro™ (patisiran) clearly demonstrates the utility of lipid nanoparticle (LNP) systems for enabling gene therapies. These systems are composed of ionizable cationic lipids, phospholipid, cholesterol, and polyethylene glycol (PEG)-lipids, and are produced through rapid-mixing of an ethanolic- lipid solution with an acidic aqueous solution followed by dialysis into neutralizing buffer. A detailed understanding of the mechanism of LNP formation is crucial to improving LNP design. Here we use cryogenic transmission electron microscopy and fluorescence techniques to further demonstrate that LNP are formed through the fusion of precursor, pH-sensitive liposomes into large electron-dense core structures as the pH is neutralized. Next, we show that the fusion process is limited by the accumulation of PEGlipid on the emerging particle. Finally, we show that the fusion-dependent mechanism of formation also applies to LNP containing macromolecular payloads including mRNA, DNA vectors, and gold nanoparticles.
DOI: 10.5281/zenodo.3978344
title: Fusion-dependent formation of lipid nanoparticles containing macromolecular payloads

description: The success of Onpattro™ (patisiran) clearly demonstrates the utility of lipid nanoparticle (LNP) systems for enabling gene therapies. These systems are composed of ionizable cationic lipids, phospholipid, cholesterol, and polyethylene glycol (PEG)-lipids, and are produced through rapid-mixing of an ethanolic- lipid solution with an acidic aqueous solution followed by dialysis into neutralizing buffer. A detailed understanding of the mechanism of LNP formation is crucial to improving LNP design. Here we use cryogenic transmission electron microscopy and fluorescence techniques to further demonstrate that LNP are formed through the fusion of precursor, pH-sensitive liposomes into large electron-dense core structures as the pH is neutralized. Next, we show that the fusion process is limited by the accumulation of PEGlipid on the emerging particle. Finally, we show that the fusion-dependent mechanism of formation also applies to LNP containing macromolecular payloads including mRNA, DNA vectors, and gold nanoparticles.
DOI: 10.5258/soton/d1843
title: Dataset for 'A Si Optical Modulator based on Fano-like Resonance'

description: This dataset supports the publication: H. Du, W. Zhang, W. Cao, D. J. Thomson, C. G. Littlejohns, X. Yan, D. T. Tran, M. Banakar, G. T. Reed (2021) 'A Si Optical Modulator based on Fano-like Resonance' published in IEEE Photonics Technology Letters In this work, we present an experimental demonstration of a carrier depletion type Si optical modulator using Fano-like resonance, which is the first of its kind in the literature. The Fano-like resonance is obtained by weak coupling between two optical resonators in the prototype device and the PN junction is designed for carrier-depletion type electro-refractive modulation. 20 Gb/s on-off keying (OOK) is obtained in experiments on the prototype device.
DOI: 10.5281/zenodo.5520533
title: Waliguan BC data

description: Waliguan BC data
DOI: 10.5281/zenodo.5520532
title: Waliguan BC data

description: Waliguan BC data
DOI: 10.6084/m9.figshare.16651879.v1
title: normalized_mouse_hackathon.h5ad

description: Preprocessed (QC + normalization) mouse intestinal data<br>
DOI: 10.6084/m9.figshare.16651879
title: normalized_mouse_hackathon.h5ad

description: Preprocessed (QC + normalization) mouse intestinal data<br>
DOI: 10.6084/m9.figshare.16656991.v2
title: endocrinogenesis_day15_hackathon

description: scvelo version of the pancreas dataset without normalization<br>https://scvelo.readthedocs.io/scvelo.datasets.pancreas/#scvelo.datasets.pancreas
DOI: 10.6084/m9.figshare.16656991.v1
title: endocrinogenesis_day15

description: scvelo version of the pancreas dataset without normalization<br>https://scvelo.readthedocs.io/scvelo.datasets.pancreas/#scvelo.datasets.pancreas
DOI: 10.6084/m9.figshare.16656982.v1
title: endocrinogenesis_day15_sctransform

description: The results of sctransfrom are stored in layers with the “SCT” prefix. SCT_normalized contains the residuals (normalized values), and is used directly as input to PCA. To assist with visualization and interpretation. we also convert Pearson residuals back to ‘corrected’ UMI counts. You can interpret these as the UMI counts we would expect to observe if all cells were sequenced to the same depth. The ‘corrected’ UMI counts are stored in <code>SCT_corrected_UMI</code>. We store log-normalized versions of these corrected counts in <code>SCT_lognorm_corrected_UMI</code>, which are very helpful for visualization.You can use the corrected log-normalized counts for differential expression and integration. However, in principle, it would be most optimal to perform these calculations directly on the residuals (stored in the <code>SCT_normalized</code> slot) themselves.
DOI: 10.6084/m9.figshare.16656982.v2
title: sctransform_endocrinogenesis_day15_hackathon

description: The results of sctransfrom are stored in layers with the “SCT” prefix. SCT_normalized contains the residuals (normalized values), and is used directly as input to PCA. To assist with visualization and interpretation. we also convert Pearson residuals back to ‘corrected’ UMI counts. You can interpret these as the UMI counts we would expect to observe if all cells were sequenced to the same depth. The ‘corrected’ UMI counts are stored in <code>SCT_corrected_UMI</code>. We store log-normalized versions of these corrected counts in <code>SCT_lognorm_corrected_UMI</code>, which are very helpful for visualization.You can use the corrected log-normalized counts for differential expression and integration. However, in principle, it would be most optimal to perform these calculations directly on the residuals (stored in the <code>SCT_normalized</code> slot) themselves.
DOI: 10.6084/m9.figshare.16656991
title: endocrinogenesis_day15.h5ad

description: scvelo version of the pancreas dataset without normalization<br>https://scvelo.readthedocs.io/scvelo.datasets.pancreas/#scvelo.datasets.pancreas
DOI: 10.6084/m9.figshare.16656991.v3
title: raw_pancreas_hackathon.h5ad

description: scvelo version of the pancreas dataset without normalization<br>https://scvelo.readthedocs.io/scvelo.datasets.pancreas/#scvelo.datasets.pancreas
DOI: 10.25345/c50554
title: MassIVE MSV000088138 - Tes 1 GNPS Testing sample Nudibranch and Achantostrongylophora
title: Massive data testing about molecular networking using GNPs website
DOI: 10.6084/m9.figshare.16657003
title: Pupuke composite palaeomagnetic record.txt

description: Composite Holocene geomagnetic palaeosecular variation record from sediments of Lake Pupuke, New Zealand. Supplementary datafile.
DOI: 10.15151/esrf-es-421765889
title: Cryo-electron microscopy EPN BAG
DOI: 10.6084/m9.figshare.16657037.v1
title: Microindentation experiments by VIckers from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: Based on the mean values of the diagonal of the idents, the value of microhardness of composite materials was calculated.
DOI: 10.6084/m9.figshare.16657037
title: Microindentation experiments by VIckers from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: Based on the mean values of the diagonal of the idents, the value of microhardness of composite materials was calculated.
DOI: 10.6084/m9.figshare.16657040
title: EDS particle analysis from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: EDS analysis gives information about which atoms are present in material and what percentage.
DOI: 10.6084/m9.figshare.16657040.v1
title: EDS particle analysis from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: EDS analysis gives information about which atoms are present in material and what percentage.
DOI: 10.6084/m9.figshare.16657043
title: XRD analysis from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: Determination of the phase composition of the obtained materials
DOI: 10.6084/m9.figshare.16657043.v1
title: XRD analysis from Inorganically modified particles FeAl-LDH@SiO2 as reinforcement in poly (methyl) methacrylate matrix composite

description: Determination of the phase composition of the obtained materials