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2,399 results for “fragmenter”
Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
<p>Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.</p> <p><br> Here we publish the primary data of the biolayer-interferometry (BLI), STD-NMR, HSQC-NMR and mixed-solvent MD simulation results.<br> For BLI, the sensorgrams of 10 binding fragments identified in the screening are given. Measurements were conducted with the N-domain and the ND1-construct of p97. Additionaly, the measurements with ADP as positive control (n=6) are provided.<br> Four of the 10 fragments were selected as most promising hits for further investigation: TROLL2, TROLL7, TROLL8 and TROLL12. For these fragemnts, the STD-NMR build-up data, the HSQC-NMR spectra and the representative poses from the mixed solvent MD simulations used for CORCEMA predictions are provided. For TROLL2 the anomalous map of the bromine atom of the crystal structure (PDB entry: 7PUX) is given.</p>
Data for: Fluid fermionic fragments for optimizing quantum measurements of electronic Hamiltonians in the variational quantum eigensolver
<p>Data for publication: S. Choi, I. Loaiza, and A. F. Izmaylov, "Fluid fermionic fragments for optimizing quantum measurements of electronic Hamiltonians in the variational quantum eigensolver" arXiv:2208.14490 (2022).</p> <p> </p> <p> </p>
[IO Islamic 2556] Story fragment (كه نام او چيرمان)
<ul> <li><strong>Story.</strong></li> <li><strong>This manuscript is now IO Islamic 856 in the India Office collections.</strong></li> <li><strong>[metadata:</strong> <a href="https://en.wikipedia.org/wiki/Carl_Hermann_Eth%C3%A9"><strong>Hermann Ethé</strong></a><strong><em>, </em></strong><a href="http://doi.org/10.5281/zenodo.1323681"><strong><em>Catalogue of Persian Manuscripts in the Library of the India Office,</em></strong> </a><a href="http://doi.org/10.5281/zenodo.1323681"><strong>2 vols. (Oxford: India Office, 1903): volume 1,</strong></a> <strong>number 2556 here with notations and hyperlinks].</strong></li> </ul> <p>856</p> <p>A short fragment of a story of an Indian Râjah (كه نام او چيرمان) in Calicut ( كلى كوتَ), at the time of the prophet Muḥammad, Beginning:</p> <p>چنين روايت ميكنند كه در ايّام پيغمبر محمّد رسول الله كه در سرحد كلى كوتَ الخ</p> <p>Bibliotheca <a href="https://www.worldcat.org/identities/lccn-no91006101/">Leydeniana</a>.</p> <p>No. 2556, ff. 92-95, ll. 8; Nasta’lîḳ; size, 9<sup>1/4</sup> in. by 6<sup>5/8</sup> in.</p> <p> </p>
Code and data for "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape"
<p>Archive file containing all the code and data for producing results and the supplementary result of the MS entitled "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape". See README.txt for files descriptions.</p>
Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
<p>Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.</p>
Deep Learning Code Fragments for Code Clone Detection
<p>Paper: Deep Learning Code Fragments for Code Clone Detection</p> <p>Authors: White, M., Tufano, M., Vendome, C. and Poshyvanyk, D.</p> <p>Conference: 2016 31st IEEE/ACM International Conference on Automated Software Engineering (ASE)</p>
Fig. 2 in Variation in diet of frugivorous bats in fragments of Brazil's Atlantic Forest associated with vegetation density
Fig. 2.—Carbon and nitrogen isotopic ratios for each bat population presented as mean and standard deviation. Each panel represents one species–season pairing: Al-H is Artibeus lituratus in the Humid season; Cp-H is Carollia perspicillata in the Humid season; Cp-S is C. perspicillata in the super-humid season; Sl-S is Sturnira lilium in the super-humid season. Fragments and population designations correspond to fragments in Brazil's Atlantic Forest in Fig. 1. Shades correspond to fragment where the sample was collected ordered by area. Darker greens are largest fragments; darkest purple are smallest fragments.
Fig. 1 in Variation in diet of frugivorous bats in fragments of Brazil's Atlantic Forest associated with vegetation density
Fig. 1.—Map of study sites situated in Brazil's Atlantic Forest, Rio de Janeiro State, Brazil. Sites in Reserva Ecologica de Guapiacu ("REGUA") and fragments (F) adjacent to this area are indicated as points. Thirteen areas were sampled and allocated as REGUA, REGUA2, REGUA3 for those sampled in the reserve (considered repeated efforts sampling in the same fragment), and 10 fragments designated as F1 through F10. This figure was constructed using ESRI base maps and existing maps available through Instituto Brasileiro de Geografia (IBGE) (SOS Mata Atlântica (2009) (www.sosma.org). Used under commons licence). Figure is adapted from Teixeira (2019).
replica of figurine venus from mold fragments
<p>The mold is from the Museum of Ceramic Techniques collection in Koło, Poland. The mold fragments were brought to the Academy of Fine Arts in Warsaw, Poland, to recreate the figurine venus from the mold. The dataset was used for 3D printing the mold and recreating the figurine. Reverse engineering was done by combining both digital and manual technologies to manufacture the mold and make the figurine replica. The work has been presented at "Manufacturing of Ceramic Venus Figurine Replica from a Mold by Combining Traditional and Digital Technologies" (Heritage Science)</p>
Figure 1 in Natural regeneration in Atlantic Forest Fragments: using ants (Hymenoptera: Formicidae) for monitoring a conservation unit
Figure 1. Botujuru Private Natural Heritage Preserve location and the respective collecting sites.
The fragmentation-induced fluidization of pyroclastic density currents - dataset
<p>These are the data behind the study entitled "The Fragmentation-Induced Fluidization of Pyroclastic Density Currents".</p>
Negative effects of the spatial clumping of thermal resources on lizard thermoregulation in a fragmented habitat
<p>Abstract of the manuscript associated to this dataset:</p> <p>In ecosystems threatened by the expansion of croplands, habitat fragmentation and climate change, two of the main extinction drivers, may have thermoregulationmediated interacting effects on demographic trends of terrestrial ectotherms. We studied the thermal biology of a metapopulation of the widespread Mediterranean lacertid Psammodromus algirus in fragments of evergreen or deciduous oak forests interspersed among cereal fields. We obtained thermoregulation statistics (selected temperature range, body and operative temperatures, thermal quality of the habitat, and precision, accuracy, and effectiveness of thermoregulation) that could be compared among fragments and with conspecific populations living in unfragmented habitat. We also measured the selection (use vs. availability) and spatial distribution of sunlit and shaded patches used for behavioral thermoregulation in fragments, and we estimated operative temperatures and thermal habitat quality in the agricultural matrix surrounding the fragments. Variation of the thermal environment was much larger within fragments than among them, and thermoregulation was accurate, precise, and efficient throughout the fragmented landscape; its effectiveness was similar to that of previously studied unfragmented populations. The average distance between sunlit and shaded patches was shorter in deciduous than in evergreen fragments, producing a more clumped distribution of the mosaic of thermal resources. Consequently, in evergreen habitat the cost of thermoregulation was higher, because lizards were more selective in their choice of sunlit sites (they used sunlit patches closer to shade and refuge than expected at random, and the extent of such selection was larger than at deciduous habitat). Temperatures available in croplands were too high to allow lizard dispersal, at least in the post-breeding season. This result confirms the role of croplands as a thermal barrier that promotes inbreeding in isolated fragments, and it forecasts a dark future for populations of forest lizards in agricultural landscapes under the combined effects of habitat fragmentation and global warming.</p>
Video of the experimental setup for fragment impact loading using Fragment Simulating Projectiles
<p>The experiment is conducted using the launcher of the Accredited Ballistic Applications Laboratory (ABAL) in the department of ballistics at the Royal Military Academy. It allows to impact a target by a Fragment Simulating Projectile with a user-defined range of velocities. The different components of the experimental setup is shown in this video. </p> <p>Two FSP calibers are used for the different tests: 7.62mm and 12.7mm. They are accelerated up to 322m/s by means of a powder gun. The FSP dimensions are taken from STANAG-NATO. The aluminum plate specimens EN AW-1050A-H24 (average elastic properties: Young’s modulus of 62.5GPa and a Poisson’s ratio of 0.33) with dimensions of 400mm x 400mm x 2mm are fixed to a steel frame with dimensions of 1000mm x 1000mm x 15mm. They are positioned at a distance of 5m from the launcher. The central part of the aluminum specimens is painted by application of a white background and a black speckle pattern. </p> <p>During the experiments, the plate behavior is observed using a field of view of 300mm x 300mm. Two Photron Fastcam SA5 high speed cameras HSC (camera 2 and 3) are mounted in a stereoscopic configuration to record synchronized images during the impact process. The high speed cameras are placed behind a shield protector at a safe distance from the plate in order to avoid damage by the projectiles. Two light emitting diodes LEDs are used to increase the illumination of the aluminum plate. This was done to maintain adequate contrast throughout the experiment. During its flight, the FSP velocity is measured by a pair of light barriers (velocity gates). The FSP initial velocity is chosen to be higher than the plate’s ballistic limit velocity. This choice allows for the deformation to be limited to a small region around the impact point. The striking velocities are recorded using measurements by HSC1.</p>
FIGURE 1 in Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil
FIGURE 1. Location of the municipalities of the sampling sites in Paraná, Brazil. Light grey = Faxinal (FX), Black = Mauá da Serra (MS), Dark grey = Palmeira (PL)
Data for "The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges"
<p>The input and output data to the filtering pipeline described in "The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges"; code available from https://github.com/oxpig/fragment_network_merges. </p>
Critical transitions and evolutionary hysteresis in movement: Habitat fragmentation can cause abrupt shifts in dispersal that are difficult to revert
<p>Under habitat fragmentation, plant species' survival hinges on the ability of individuals to disperse from one habitat patch to another. While there is evidence that severe habitat fragmentation leads to evolution of reduced dispersal ability and that such decreased mobility is generally detrimental for species' survival, it is unknown whether species adapt via a gradual loss in dispersal ability or via a sudden shift from frequent to infrequent dispersal between patches (i.e., a critical transition). Using both a spatially explicit deterministic and individual-based stochastic model of hydrochorous seed dispersal, we show that a small increase in inter-patch distance can generate an abrupt shift in plant seed dispersal strategy from long to short distances. Most importantly, we found that a substantial increase in connectivity between habitat fragments is required to reverse this loss of long-distance dispersal, due to an evolutionary hysteresis effect. Our theory prompts for re-consideration of the eco-evolutionary consequences of habitat fragmentation as restoring habitat connectivity may require restoration of much higher connectivity levels than currently assumed.</p>
Fragments of the dataset of the research (Un)limited pleasure
<p>This publication contains seven fragments of a dataset for the research project (un)limited pleasure. The total dataset covers more than 20 hours of video and audio material. The research explores how wheelchair users negotiate their sexuality within the context of Dutch society, where they are often denied a sexual identity.</p>
ExtendedData Fig. 9 in Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds
ExtendedData Fig. 9 | Correlationbetweenseasonalityanddisturbance. At thelocallandscapelevel (a), seasonalityiscalculatedasthestandarddeviationof meanmonthlytemperaturevaluesthroughouttheyearatthelandscapecentroid (n = 31). Highdisturbancemeans 50% of thestudylandscapeareaoverlaps areasofhighnatural (forexamplestorms,glaciers,fires) orAnthropogenic (for exampleforestloss).Boxplotsshowmedian,interquartile range,andwhiskers toextremevalues (outliersaredatapoints>1.5x quartiles).Statisticsarefrom atwo-sided Wilcoxon test.Atthespecieslevel (b), communitymeanvalues (n = 31), arecalculatedusingspecies' distributionalseasonalityanddisturbance scores.Disturbanceiscalculatedastheproportionof thespeciesbreedingrange whichoverlapsareasofhighnatural (forexamplestorms,glaciers,fires) or anthropogenic (forexampleforestloss) disturbance.Seasonalityiscalculated asthestandarddeviationof meanmonthlytemperaturevaluesthroughoutthe year,averagedacrossallgridcellsinthespecies' breedingrange.Statisticsare fromalinearregressionwith Gaussianerrors;purplelineshowsmodelfit;shaded areais 95% confidenceintervals.
ExtendedData Fig. 8 in Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds
ExtendedData Fig. 8 | Relationshipbetweendispersallimitation (nHWI) anddiet. Datashownfor (a) 276 birdspeciessampledacross 18 temperate studylandscapes,and (b) 817 birdspeciessampledacross 13 tropicalstudy landscapes.Dietaryclasseswith <5 specieswereremovedfromtheanalysis.Diet classificationsarefrom Tobiasand Pigot110. F-statisticand P-valuearecalculated withatwo-way ANOVA.Boxplotsshowmedian,interquartile range,andwhiskers toextremevalues (outliersaredatapoints>1.5x quartiles).
ExtendedData Fig. 7 in Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds
ExtendedData Fig. 7 | Predictorsofdispersallimitationinbirds. Results shownareoutputsof phylogeneticleastsquaresmodelpredictingdispersal limitation (nHWI) acrossallbirdspeciessampled,includinglong-distance migrants (swallowimage,dark bars;n = 1034); onlyresidentspeciesandshort distance/partialmigrants (thrushimage,medium bars;n = 921); orresident speciesonly (pittaimage,palebars;n = 858). Panelspresentthreesetsofmodels withincreasingcomplexity:aunivariatemodelwithsinglepredictor (a,d), and multivariatemodelswithtwo (b,e) andthree (c,f) predictors.Eachpredictor iscalculatedatthespecieslevelbyaveragingacross landscapeswhereeach speciesispresent.Disturbance (red) iscalculatedastheproportionofspecies breedingrangewhichoverlapsareasofhigh natural (e.g. storms,glaciers,fires) oranthropogenic (e.g. forestloss) disturbance.Absolutelatitude (yellow) is calculatedasthecentroidlatitudeof thespeciesbreedingrange.Seasonality (blue) iscalculatedasthestandarddeviationof meanmonthlytemperature valuesthroughouttheyear,averagedacrossallgridcellsinthebreedingrange. a–c, EffectsiZeestimatesaregivenwith 95% confidenceintervals;anegative effectindicatesreduceddispersallimitation (thatisincreased dispersalability). R2 and AICvaluesarecalculatedforfullsamplemodelsonly.d–f, Proportion of independentvariationexplainedbyeachmodelcovariate,calculatedusing hierarchicalpartitioning.
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.