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2,399 results for “fragmentation”
Data from 'Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection'
<p>This repository contains the data for the manuscript: Sustainability in the laboratory: evaluating the reuseability of microtiter plates for PCR and fragment detection.</p> <p>The script can be found here: https://github.com/AneLivB/SGP</p> <p><strong>Files: </strong></p> <p><strong>R15*_R*.csv</strong></p> <p>The processed data used for the script. All other files of the same name format contain the same elements!</p> <ul> <li> <p>Columns: Rack_location, ID, all loci</p> <ul> <li> <p>Rack_location: the location on the microwell plate the individual had in the wet lab</p> </li> <li> <p>ID: individual identification tag of the animal the DNA sample stems from</p> </li> <li> <p>_a and _b denotes the first and second allele of all loci</p> </li> </ul> </li> </ul> <p><strong>Mismatches</strong></p> <p>A dataframe created by the script and later used to calcualte per treatment single-locus genotype error rates.</p> <ul> <li> <p>Columns: Rack.1, Rack.2, Treatment, No..of.mistyped.alleles, No..of.mistyped.reactions, No..of.reactions, Allelic.error.rate, Genotype.error.rate</p> <ul> <li> <p>Rack.1: One of three racks (R154, R155, R156) from the standard protocol</p> </li> <li> <p>Rack.2: One of three racks (R154, R155, R156) from one of the other treatments (e.g. R154_R2, R154_R3, R154_R4)</p> </li> <li> <p>Treatment: One of three treatments (Internal control, Reused detection plate, Reused PCR plate)</p> </li> <li> <p>No..of.mistyped.alleles: Number of mismatched alleles within one treatment group, within a DNA plate</p> </li> <li> <p>No..of.mistyped.reactions: Number of mismatched single-locus genotypes within one treatment group, within a DNA plate</p> </li> <li> <p>No..of.reactions: Number of single-locus genotypes within one treatment group, within a DNA plate</p> </li> <li> <p>Allelic.error.rate: Error rate per allele</p> </li> <li> <p>Genotype.error.rate: Error rate per single-locus genotypes</p> </li> </ul> </li> </ul> <p><strong>model.mismatch.2.Rdata</strong></p> <p>RData file containing the model output.</p> <p> </p> <p><strong>Manuscript abstract: </strong></p> <p>Single-use plastics (SUPs) are indispensable in laboratory research, but their disposal contributes substantially to environmental pollution. Consequently, reusing common SUP items such as microtiter plates represents a promising strategy for improving laboratory sustainability. However, the key challenge lies in determining whether SUP reuse can be implemented without sacrificing data quality. To investigate this, we conducted a simple experiment to assess the impact of reusing microtiter plates on microsatellite genotyping accuracy. Plates previously used for PCR and fragment detection were cleaned using an environmentally friendly method and then reused. Our results indicate that, while reusing PCR plates significantly increases genotyping error rates due to residual DNA contamination, detection plates can be reused without compromising data quality. Our approach offers laboratories a practical and sustainable option for reducing SUP waste and costs while maintaining research integrity.</p>
Skull shape of a widely-distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations
<p>The biogeographical distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences – geometric morphometrics – to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behaviour, and phenotypic differentiation, allowing us to ask if populations can be distinguished and if patterns of variation indicate adaptability to changing environmental conditions. We analysed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using Principal Components Analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbour similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation - 76% - remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g. specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetics-based conservation studies.</p>
Conservation of birds in fragmented landscapes requires protected areas
<p class="MsoNoSpacing">For successful conservation of biodiversity, it is vital to know whether protected areas in increasingly fragmented landscapes effectively conserve species. However, how large habitat fragments must be and what level of protection is required to sustain species, remains poorly known. We compiled a global dataset on almost 2000 bird species in 741 forest fragments varying in size and protection status, and show that protection is associated with higher bird occurrence, especially for threatened species. Protection becomes increasingly important with increasing size of forest fragments. For forest fragments >50 ha our results show that strict protection (IUCN cat. I-IV) is strongly associated with higher bird occurrences, whereas fragments should be at least 175 ha to observe a positive effect of moderate protection (cat. V-VI). This meta-analysis quantifies the importance of fragment size, protection status, and their interaction for the conservation of bird species communities, and stresses that protection should not be limited to large pristine areas.</p>
Scholastic Theology [IO Bijapur 186] Glosses on شرح المواقف [fragments]
<ul> <li><strong>Scholastic Theology.</strong></li> <li><strong>This manuscript is now IO Bijapur 186 </strong><strong>in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 447 here with further notations and hyperlinks]</strong>.</li> </ul> <p>447.</p> <p>B 186. Size 10<sup>1/2</sup> in. by 6 in.; foll. 149. Twenty-four lines in a page.</p> <p>Various fragments of the <a href="http://doi.org/10.5281/zenodo.5101916">preceding Glosses</a>, extending from Book II. to Book VI.</p> <p>The first entire gloss is: (قوله) و هو تصریح باثبات الواسطة الخ; and the last gloss begins: (قوله) و الحسن البصری الی انه منافق الخ.</p> <p>Written in a small hand. Injured on the margin.</p> <p> </p> <p> </p>
Scholastic Theology [IO Bijapur 218] Annotations on شرح المواقف [fragments]
<ul> <li><strong>Scholastic Theology.</strong></li> <li><strong>This manuscript is now IO Bijapur 218 </strong><strong>in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 449 here with further notations and hyperlinks]</strong>.</li> </ul> <p>449.</p> <p>B 218, 219. Size 10<sup>1/2</sup> in. by 6<sup>1/4</sup> in.; foll. 275. Nineteen lines in a page.</p> <p>Two fragments of the Annotations on the شرح المواقف by ‘<a href="http://www.worldcat.org/identities/lccn-n86140758/">ABD AL-ḤAKÎM b. Shams al-dîn SIYÂLKÛTÎ</a>, (d. about A.H. 1060). Cf. Ḥ. Kh. vi. 241. The author wrote these annotations while reading the book with his son ‘Abdallah Labîb.<sup>2</sup></p> <p>The first fragment contains the commencement of the work, with the preface, which begins as follows:</p> <p>اللهم لک الحمد حمدا یوافی نعمک....و بعد فهذه فوائد بل فرائد علقتها علی شرح المواقف لسیّد المدققین و افضل المحققین عند قراءة قرة العین لهذا الغریب عبدالله الملقب باللبیب تذکرة للاحباب و تحفة للاصحاب و عدّة لیوم الحساب و انا الفقیر المتمسک بالحبل المتین عبد الحکیم بن شیخ شمس الدین الخ</p> <p>It breaks off on fol. 102<em>v</em>., soon after the commencement of Book (موقف) II.</p> <p>The second fragment begins with the words (fol. 103<em>v</em>.) الذهنی و اثبات احکامه, from the third مقصد of the first مرصد of Book II., and extends to the end of the same book.</p> <p>Well written in Nasta’liḳ. Injured by insects.</p> <p>Cat. 225, vii. 3.</p> <p> </p> <p><sup>1</sup> The statement of Ḥ. Kh. vi. 239 is incorrect.</p> <p><sup>2</sup> See above, nos. <a href="https://doi.org/10.5281/zenodo.4487411">113</a> and <a href="https://doi.org/10.5281/zenodo.4736773">327</a>.</p> <p>[Bijapur Collection]</p> <p> </p>
Immigration credit of temperate forest herbs in fragmented landscapes – implications for restoration of habitat connectivity
<p>1. In many agricultural landscapes, it is important to restore networks of forests to provide habitat and stepping stones for forest specialist taxa. More knowledge is, however, needed on how to facilitate the immigration of such taxa in restored forest patches. Here, we present the first chronosequence study to quantify the dynamics of immigration credits of forest specialist plants in post-arable forest patches.</p> <p>2. We studied the distribution of herbaceous forest specialist plant species in 54 post-arable broadleaved forest patches along gradients of age (20-140 years since forest establishment), distance from ancient forest (0-2600 m) and patch area (0.5-9.6 ha). With Linear Mixed Models we estimated the effects of these factors on species richness, patch means of four dispersal-related plant traits and with Generalized Linear Models on the occurrence of 20 individual species.</p> <p>3. Post-arable forest patch age and spatial isolation from ancient forest, but not patch size, were important predictors for species richness of forest specialists, suggesting that also small patches are valuable for habitat connectivity. Compared to species richness in ancient forest stands, the immigration credit was reduced by more than 90% after 80 years in post-arable forest patches contiguous to ancient forest compared to 40% after 80 years and 60% after 140 years in isolated patches (at least 100 m to next forest). Tall-growing species with adaptations to long-distance dispersal were faster colonizers while species with heavy diaspores and clonal growth were slower to colonize.</p> <p>4. Synthesis and applications: We show that post-arable oak plantations have a high potential for restoration of forest herb vegetation. Dispersal-related plant traits play a key role in explaining interspecific differences among forest specialists. To facilitate forest herb immigration across all functional groups in agricultural landscapes, we suggest to create clusters of relatively small new forest patches nearby older forest with source populations.</p>
Data for Ferretto et al, 2021 "Naturally-detached fragments of the endangered seagrass Posidonia australis collected by citizen scientists can be used to successfully restore fragmented meadows"
<p>Please find attached the data for the manuscript "Ferretto et al, 2021" and a brief description of each file.</p>
Fragmentation in trader preferences among multiple markets: Market coexistence versus single market dominance
<p>Technological advancement has lead to an increase in number and type of trading venues and diversification of goods traded. These changes have re-emphasized the importance of understanding the effects of market competition: does proliferation of trading venues and increased competition lead to dominance of a single market or coexistence of multiple markets? In this paper, we address these questions in a stylized model of Zero Intelligence traders who make repeated decisions at which of three available markets to trade. We analyse the model numerically and analytically and find that parameters that govern traders' decisions--memory length and intensity of choice, e.g. how strongly decisions are based on past success--make the key distinctions between consolidated and fragmented steady states of the population of traders. All three markets coexist with equal shares of traders only when either learning is too weak and traders choose randomly, or when markets are identical. In the latter case, the population of traders is fragmented across the markets. For the more general case of markets with different biases, we note that market dominance is the more typical scenario. These results are interesting because previously either strong differentiation of markets or heterogeneity in the needs of traders was found to be a necessary condition for market coexistence. We show that, in contrast, these states can emerge simply as a consequence of co-adaptation of an initially homogeneous population of traders.</p>
Figure 1 in Orchid bees (Hymenoptera, Apidae, Euglossini) are seasonal in Seasonal Semideciduous Forest fragments, southern Brazil
Figure 1. Orchid bee phenology in Seasonal Semideciduous Forest fragments, (A-C) Eufriesea violacea, (D-G) Euglossa cordata, (H-I) Eulaema nigrita.
Figure 1 in Ants (Hymenoptera: Formicidae) from an Amazonian fragmented landscape, Juara, Mato Grosso, Brazil, with new records of ant species
Figure 1. Map indicating the Modules (M) where the samples were collected in the municipality of Juara, north of Mato Grosso state, Brazil.The four points on the Arinos River represent samples taken on islands.
Text-fig. 5. Fragment of the musk-ox skull from Herne-Crange. GMM A5.53. Scale bar 5 cm. in Everything Is A Question Of Time - Age Of Important Quaternary Palaeontological Finds From Westphalia
Text-fig. 5. Fragment of the musk-ox skull from Herne-Crange. GMM A5.53. Scale bar 5 cm.
Text-fig. 4. Rib fragment inserted in the nasal cavity of canid skull fragment (10). in Consumption Of Canid Meat At The Gravettian Předmostí Site, The Czech Republic
Text-fig. 4. Rib fragment inserted in the nasal cavity of canid skull fragment (10).
FIGURE 1 in Fragmented host distribution and trombiculid parasitic load: Eutrombicula araucanensis and Liolaemus pictus in Chile
FIGURE 1: Sample sites of Liolaemus pictus. White triangles show the localities where none were recorded Eutrombicula araucanensis. 1. Altos de Lircay National Park (N. P.); 2. Las Trancas; 3. Curacautín; 4. Malalcahuello; 5. Villarrica N. P.; 6. Oncol Park; 7. Panguipulli; 8. Valdivia Reserve; 9. Alerce Costero; 10. Hueicolla; 11. San Juan de la Costa; 12. Puyehue N. P.; 13. Puyehue; 14. Osorno Vulcano; 15. Llanquihue National Reserve (N. R.); 16. Puerto Montt; 17. Río Puelo basin; 18. Ancud; 19. La Chacra; 20. Chonchi; 21. Tantauco Park; 22. ChaitØn; 23. Cisnes.
Rapid morphological change in a small mammal species after habitat fragmentation over the past half-century
<p><span><b>Study Aim:</b> To compare the rapid shifts in body size of mainland and island populations of a native rodent and examine the mechanisms underlying these changes.</span></p> <p><span><b>Location:</b> Thousand Island Lake, China, which was created in 1959 when the Xin'anjiang Dam was constructed for generating hydroelectricity.</span></p> <p><b>Taxon:</b> The Chinese white-bellied rat, <i>Niviventer confucianus</i>.</p> <p><span><b>Methods</b>: Field surveys were conducted from 2015 to 2018 to collect data on body size of the rodents from a set of islands and nearby mainland sites. We constructed multiple linear models to examine the relationships between body size (length and mass) of rodents and biological variables (predators, interspecific and intraspecific competitors, and food availability). We also conducted structural equation modeling (SEM) by constructing models via confirmatory path analysis.</span></p> <p><span><b>Results: </b>All island populations of <i>N. confucianus</i> had significantly larger body size (both body mass and body length) than their mainland counterparts. Moreover, populations on small and more isolated islands had larger body size than their relatives on big islands. The relative absence of predators (large-bodied mammals, snakes, and raptors) on islands was most strongly associated with shifts in the body size of rodents. The documented changes occurred after only a half-century of fragmentation.</span></p> <p><span><b>Main conclusions: </b>The observed rapid body enlargement of rodents after habitat fragmentation is consistent with a release from predation pressure. SEM indicated that island area, rather than island isolation, had positive effects on the richness of predators, interspecific competitors and food resources, which then had an indirect impact on body size of the rodents. In this study, we report a remarkably rapid case of mammal morphological shifts in a small mammal in response to habitat fragmentation. Given the omnipresence of dams and other anthropogenic disturbances, our findings suggest that a wave of rapid phenotypic shifts in terrestrial vertebrates is taking place in the Anthropocene.</span></p>
Dataset for "Binding energies of molecular solids from fragment and periodic approaches"
<p>Dataset containing many-body contributions to binding energies of molecular crystals as described in the article</p> <pre>"Binding energies of molecular solids from fragment and periodic approaches"</pre> <p>published in Electronic Structure, doi: 10.1088/2516-1075/ac25d6</p> <p> </p>
Insect RTUs from the degraded forest fragments in the Attappady and Anaikatti landscapes.
<p>Datasets were collected as part of the project titled "EVALUATING THE EFFICEINCY OF RESTORATION EFFORTS IN REVIVING TROPICAL FORESTS USING GROUND INSECTS AS INDICATORS."</p>
Supplementary Movies for the article "The fragmentation mechanism of gold nanoparticles in water under femtosecond laser irradiation"
<p>Supplementary movies for the publication "The fragmentation mechanism of gold nanoparticles in water under femtosecond laser irradiation", <a href="https://doi.org/10.1039/D1NA00406A">https://doi.org/10.1039/D1NA00406A</a>.</p> <p>The movies show gold nanoparticles in water under pulsed laser irradiation and are recorded with <em>in situ </em>liquid cell electron microscopy. The full description of every movie can be found in the "Supplementary Information" file at <a href="https://doi.org/10.1039/D1NA00406A">https://doi.org/10.1039/D1NA00406A</a>.</p>
Molecular Dynamics Simulation on the Effect of Transition Metal Binding to the N-Terminal Fragment of Amyloid-β
<p>Molecular dynamics trajectories in PDB format for 3x Cu-Aβ, 3x Zn-Aβ and 9x Fe-Aβ<strong> </strong>simulations.</p>
Data on the mineralised textile fragment A2A3_1 from Creney-près-Troyes – Le Paradis locality
<p>This dataset contains data regarding the mineralised textile fragment A2A3_1 from Creney-près-Troyes – Le Paradis locality:</p> <p>A2A3 1 1 back.001.tif: digital microscope image of the B side of the sample<br> A2A3 1 1.002.tif: digital microscope image of sample side A<br> Output_P5.tif: 5x magnification optical microscope image of the fibres on side A of the sample<br> A2A311_320mm_50ms_68kev_new_aligned_3420x3420x908.raw: concatenated 8 bit volume of sample A2A3_1<br> A3A311_back_layer1_3136x2640x114.raw: 8 bit volume of the B1 layer of the sample<br> A3A311_back_layer1__orientationXY_3136x2640x114.raw: volume of orientations of layer B1 of the sample<br> A3A311_back_layer2_3136x2640x121.raw: 8 bit volume of the sample layer B2<br> A3A311_back_layer2__orientationXY_3136x2640x121.raw: volume of orientations of the sample layer B2<br> A3A311_back_layer3_3136x2640x175.raw: 8 bit volume of the B3 layer of the sample<br> A3A311_back_layer3__orientationXY_3136x2640x175.raw: orientation volume of the B3 layer of the sample<br> A3A311_front_3016x2536x220.raw: 8 bit volume of the A layer of the sample<br> A3A311_front__orientationXY_3016x2536x220.raw: volume of the orientations of the A layer of the sample<br> mask_A3A311_back_layer1_3136x2640x114.raw: voxel mask of the B1 layer of the sample<br> mask_A3A311_back_layer2_3136x2640x121.raw: voxel mask of the B2 layer of the sample<br> mask_A3A311_back_layer3_3136x2640x175.raw: voxel mask of the B3 layer of the sample<br> mask_A3A311_front_3016x2536x220.raw: voxel mask of the A layer of the sample</p>
Data from: Eastern Whip-poor-wills have larger nonbreeding home ranges in areas with more agriculture and forest fragmentation
<p>Migratory bird populations can be limited by events in disparate parts of the world. Birds in tropical regions are facing rapid habitat loss, climate change, and intensive agricultural regimes, potentially contributing to population declines. However, an understanding of basic non-breeding ecology of species, such as habitat and space use, is critical for determining if this is the case. Populations of the nocturnal/crepuscular Eastern Whip-poor-will (<em>Antrostomus</em> <em>vociferus</em>) have declined by 70% since the 1960's, yet data on the species are sparse outside of the breeding season. We extracted data from 41 archival GPS tags deployed on whip-poor-wills and estimated non-breeding home ranges and land covers used. We used satellite imagery and stable carbon and nitrogen isotope values from claws grown during the non-breeding season to analyze how land cover and habitat moisture impacted home range size and relative trophic level. Forest was by far the most prevalent land cover used by whip-poor-wills, occurring in all home ranges and accounting for >80% of diurnal roosting points. We found that less forest, the presence of agriculture, and more edge (irrespective of land cover) were associated with larger home ranges. Stable isotope values differed by broadscale ecoregion but not local land cover characteristics in our study, indicating that regional idiosyncrasies or broadscale processes can be more important in determining stable isotope ratios. Our findings suggest that the loss, fragmentation, and replacement of forest by agriculture in the core of the whip-poor-will's non-breeding range may represent a threat to the species, as they rely heavily upon forest, and appear to alter space use in response to changes in forest cover.</p>
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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.