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1,355 results for “manipulation”
Data: The effects of glucose addition and water table manipulation on peat quality of drained peatland forests with different management practices
<p>The file contain data on peat chemical quality and peat decomposition. We studied how glucose addition, water table and forest harvesting affect the chemical composition of peat and decomposition rate (carbon dioxide fluxes) and soil water quality. Experiments and results are presented in:</p> <p>Aaltonen H., Zhu X., Khatun R., Laurén A., Palviainen M., Könönen M., Peltomaa E., Berninger F., Köster K., Ojala A., Pumpanen J. 2022. The effects of glucose addition and water table manipulation on peat quality of drained peatland forests with different management practices. Soil Science Society of America Journal 86:1625–1638. <a href="https://doi.org/10.1002/saj2.20419">https://doi.org/10.1002/saj2.20419</a></p> <p> </p>
An Exoskeleton System using a 3-UPU Spherical Parallel Manipulator for Rehabilitation in Stroke Patients
<p>One of the important branches of medical robotics is rehabilitation robotics. A 3-UPU spherical parallel manipulator is designed and controlled to perform wrist extension, flexion, radial deviation and ulnar deviation motions in stroke-affected patients. This exoskeleton robot produces spherical motion about a fixed center. In order to produce the rotational motion, the robot is designed based on certain geometric and structural conditions. Using the inverse kinematics solution the 3-UPU robot is controlled to perform rehabilitation task. The robot parts are manufactured using additive manufacturing technology. The manufacturing tolerance in universal joints have been identified. There is always a mystery behind the singularity of this robot, which describes the manner in which it will collapse in its home position. Thus, the robot is designed and developed in such a way that it can be effectively used at home position for hand rehabilitation.</p>
Bats generate lower affinity, but higher diversity antibody responses compared to mice, an effect that can be manipulated with diet
<p><span>Bats are reservoirs of many zoonotic viruses that are fatal in humans but do not cause disease in bats. Moreover, bats generate low neutralizing antibody titers in response to experimental viral infection, although more robust antibody responses have been observed in wild caught bats during times of food stress. Here we compared the antibody titers and B cell receptor (BCR) diversity of Jamaican fruit bats (<em>Artibeus jamaicensis</em>; JFB) and BALB/c mice generated in response to T-dependent and T-independent antigens. We then manipulated the diet of JFBs and challenged them with H18N11 influenza A-like virus or a replication incompetent Nipah virus VSV (Nipah-riVSV). Under standard housing conditions, JFBs generated a lower avidity antibody response and possessed more BCR mRNA diversity compared to BALB/c mice. However, withholding protein from JFBs improved serum neutralization in response to Nipah-riVSV and improved serum antibody titers specific to H18 but reduced BCR mRNA diversity. </span></p>
Bimanual Robot Arm Cloth Manipulation Dataset
<p>This dataset contains 945 trials of a bimanual robot arm setup, where one arm holds a piece of cloth (e.g., a towel) by one corner while the other arm, equipped with a wrist-mounted camera, captures images from approximately 180 different angles by making a half-circle motion around the cloth. Each trial includes images and the corresponding TCP (Tool Center Point) poses of the second arm. Additionally, the dataset provides annotated positions of the two corners adjacent to the held corner, which are critical for unfolding the cloth by grasping these points. This dataset is valuable for research in robotic manipulation, computer vision, and cloth handling tasks.</p>
Dataset of the study on field evidence for manipulation of mosquito host selection by the human malaria parasite
<p>This repository contains the dataset from host preferences assays to determine odour-mediated mosquito host preference as well as mosquito host selection determination through identification of the blood meal origin from indoor-resting blood-fed mosquito females in Burkina Faso.</p>
Dataset related to "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations"
<p>This is an accompanying dataset to the article with the title "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations" (DOI: <a href="https://doi.org/10.1162/netn_a_00429" target="_blank" rel="noopener">10.1162/netn_a_00429</a>). It contains the resulting data of the manipulated SSCx network model, such as benchmarks, fitted stochastic models, manipulated connectomes, structural validations, as well as simulation data and analysis results.</p> <p>The corresponding repository with code, configuration files, and detailed instructions for reproducing the results in this dataset as well as generating the results figures in the accompanying article is available here: <a href="https://github.com/BlueBrain/sscx-connectome-manipulations" target="_blank" rel="noopener">https://github.com/BlueBrain/sscx-connectome-manipulations</a></p> <p>The underlying <em>Connectome-Manipulator</em> software is available here: <a href="https://github.com/BlueBrain/connectome-manipulator" target="_blank" rel="noopener">https://github.com/BlueBrain/connectome-manipulator</a></p> <p>Additional requirement: Original SSCx network model (DOI: <a href="https://doi.org/10.5281/zenodo.8026353" target="_blank" rel="noopener">10.5281/zenodo.8026353</a>)</p> <p>ℹ️ Disclaimer: Some results may have been produced with an older version of <em>Connectome-Manipulator</em>, so slight differences might be possible when re-running with the latest version.</p> <p><strong>Update 25/09/2024 (v2):</strong> Added benchmark results for assessing strong and weak scaling behavior of connectome rewiring.</p> <blockquote> <p><strong><em>Funding</em></strong></p> <p><em>Funding provided by the Swiss government’s ETH Board to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL).</em></p> </blockquote>
Data from: Manipulation of habitat isolation and area implicates deterministic factors and limited neutrality in community assembly
Theory predicts deterministic and stochastic factors will contribute to community assembly in different ways: environmental filters should regulate those species that establish in a particular area resulting in the ecological requirements of species being the primary driver of species distributions, while chance and dispersal limitation should dictate the likelihood of species reaching certain areas with the ecology of species being largely neutral. These factors are specifically relevant for understanding how the area and isolation of different habitats or islands interact to affect community composition. Our review of the literature found few experimental studies have examined the interactive effect of habitat area and isolation on community assembly, and the results of those experiments have been mixed. We manipulated the area and isolation of rock 'islands' created de novo in a grassland matrix to experimentally test how deterministic and stochastic factors shape colonizing animal communities. Over 64 weeks, the experiment revealed the primacy of deterministic factors in community assembly, with habitat islands of the same size exhibiting remarkable consistency in community composition and diversity, irrespective of isolation. Nevertheless, tangible differences still existed in abundance inequality among taxa: large, near islands had consistently higher numbers of common taxa compared to all other island types. Dispersal limitation is often assumed to be negligible at small spatial scales, but our data shows this not to be the case. Furthermore, the dispersal limitation of a subset of species has potentially complex flow-on effects for dictating the type of deterministic factors affecting other colonising species.
Data from: Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)
Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented by Anatolia, Italy and Iberia. Understanding modern patterns of diversity depends on understanding these historical population dynamics. Traditionally, European fallow deer (Dama dama dama) are thought to have been restricted to refugia in Anatolia and possibly Sicily and the Balkans. However, the distribution of this species was also greatly influenced by human-mediated translocations. We focus on fallow deer to better understand the relative influence of these natural and anthropogenic processes. We compared modern fallow deer putative populations across a broad geographic range using microsatellite and mitochondrial DNA loci. The results revealed highly insular populations, depauperate of genetic variation and significantly differentiated from each other. This is consistent with the expectations of drift acting on populations founded by small numbers of individuals, and reflects known founder populations in the north. However, there was also evidence for differentiation among (but not within) physically isolated regions in the south, including Iberia. In those regions we find evidence for a stronger influence from natural processes than may be expected for a species with such strong, known anthropogenic influence.
Figure 1 in Two new species of Hymenoepimecis (Hymenoptera: Ichneumonidae: Pimplinae) with notes on their spider hosts and behaviour manipulation
Figure 1. (A–E) Hymenoepimecis japi sp. nov. (A) Female, dorsal view; (B) fore- and hind wings; (C) metasoma dorsal view; (D) sternite I, lateral view; (E) head. (F–L). Webs of Leucauge roseosignata. (F) Normal web; (G) egg of H. japi sp. nov. attached on the abdomen of a female; (H) third instar larva consuming the host; (I) third instar larva holding the threads of the web hub; (J) cocoon web; (K) fixation point of the axial threads of the cocoon web on vegetation; (L) hub of the cocoon web. Scale bars: (A, G, H) 5 mm; (B, C, I, K, L) 1 mm; (D, E) 0.5 mm; (F) 10 cm; (J) 1 cm.
Figure 3 in Two new species of Hymenoepimecis (Hymenoptera: Ichneumonidae: Pimplinae) with notes on their spider hosts and behaviour manipulation
Figure 3. Webs of Manogea porracea. (A) Normal web showing the positions occupied by the female and by the male. (B) Cocoon web showing the positions occupied by the male, the horizontal sheet of the female (arrow close to male), and the cocoon (arrow below). Scale bars: 1 cm.
Figure 2 in Two new species of Hymenoepimecis (Hymenoptera: Ichneumonidae: Pimplinae) with notes on their spider hosts and behaviour manipulation
Figure 2. (A–F) Hymenoepimecis sooretama sp. nov. (A) Male lateral view; (B) female lateral view; (C) fore- and hind wings; (D) metasoma dorsal view; (E) sternite I lateral view; (F) head. (G–I) Webs of Manogea porracea. (G) Parasitoid invading a web; (H) larva of H. sooretama sp. nov. attached on the abdomen of a host female; (I) cocoon. Scale bars: (A–D) 1 mm; (E) 0.5 mm; (F) 0.1 mm; (G–I) 5 mm.
Non-native species outperform natives in coastal marine ecosystems subjected to warming and freshening events - A meta-analysis of coastal marine native and non-native species responses to experimentally manipulated climatic events
<p><b>Aims</b>: Contemporary climate change and biological invasions are two main drivers of biodiversity redistribution. Interactive effects between these drivers have been reported in a number of study systems, yet results are conflicting. Some studies find that future climate change facilitates the spread and success of non-native species, especially those with broad physiological tolerances. Other studies conclude that non-natives are vulnerable to current and future changes in climatic conditions. Given that most studies have focused on terrestrial species, here we contribute to this debate by analysing responses of coastal native and non-native fauna and flora to key climate-related stressors namely increased temperature (warming) and decreased salinity (freshening).</p> <p><b>Location: </b>Global.</p> <p><b>Time period: </b>2002 – 2019.</p> <p><b>Major taxa studied: </b>Marine benthic<b> </b>macrophytes and invertebrates.</p> <p><b>Methods</b>: We conducted a meta-analysis of results from experiments investigating the performance (e.g., growth, survival and reproduction) of sessile and sedentary species from benthic marine communities to warming and freshening.</p> <p><b>Results</b>: We found evidence of positive responses to elevated temperature across a range of biological processes on non-native species, whereas the performance of native species declined. Similarly, decreased salinity negatively affected the biological processes of native species, but non-natives<span> showed no positive or negative overall response to freshening</span>.</p> <p><b>Main conclusions:</b> Our study showed that non-native species outperform natives under a wide variety of warming and freshening conditions. The growth and reproduction of non-natives are enhanced by warmer temperatures, and thus ocean warming is expected to facilitate future spread and success of non-native species. Increased freshening, however, <span>will likely have a negative impact in the future in both native and non-native species and thus is expected to be a driver of significant change in coastal marine ecosystems. Our</span> comprehensive literature search revealed the need of more <span>studies </span>focusing on s<span>alinity changes and highlighted the need to expand our understanding of climate change drivers beyond warming.</span></p>
Dataset for photothermally induced birefringence in an optical nanofiber for all-optical polarization manipulation
<p>Dataset for manuscript named as "photothermally induced birefringence in an optical nanofiber for all-optical polarization manipulation".</p>
Figure 3 in Regional Distribution Of A Brain-Encysting Parasite Provides Insight On Parasite-Induced Host Behavioral Manipulation
Figure 3. Correlation between the number of encysted Euhaplorchis californiensis metacercariae on the whole brain of California killifish (Fundulus parvipinnis) and the number of parasites on the diencephalon/ mesencephalon region in experimentally infected F. parvipinnis individuals. The correlation was checked using Spearman's rho (¼ 0.98).
Figure 1 in Regional Distribution Of A Brain-Encysting Parasite Provides Insight On Parasite-Induced Host Behavioral Manipulation
Figure 1. Figure displaying the number of Euhaplorchis californiensis parasites (A), weight (B), and mass parasite density (parasites/g body mass) (C) in experimentally infected and naturally infected fish. Different letters indicate differences in Tukey post-hoc test performed after a 1-way ANOVA; stars indicate significant difference in the Mann–Whitney Utest. On the y-axis, we show the number of parasites (A), body mass in + grams (B), and parasite density (parasites/g body mass) (C), and on the x- axis, we show the different treatment groups: low-infection treatment (n ¼ 8), high-infection treatment (n ¼ 8), experimentally infected (n ¼ 16), and naturally infected (n ¼ 25).
Figure 2 in Regional Distribution Of A Brain-Encysting Parasite Provides Insight On Parasite-Induced Host Behavioral Manipulation
Figure 2. Contrasting Euhaplorchis californiensis brain surface parasite density (A) and parasite numbers (B) in 3 brain regions in both high- and low-infection treatment groups. Different letters indicate the statistical difference between the different brain regions given by a Tukey post-hoc test, and the stars indicate a statistical difference between the 2 infection treatments (low and high). In all groups, n ¼ 8. Brain surface parasite density is defined as the number of parasites per square millimeter of brain surface area.
Data supporting "COMBI-Tweez: high-precision single-molecule mechanical manipulation and imaging for dynamic chiral biopolymers"
<p>Experimental data for our paper on COMBI-Tweez</p>
MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"
<p>Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model<br> protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it<br> an ideal candidate to understand protein function and protein evolution mechanisms. In this<br> study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim<br> (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior<br> performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP,<br> we first confirmed, both computationally and experimentally, that the relative binding free<br> energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the<br> characteristic differences to be kinetic rather than thermodynamic. We then employed an<br> interaction-based analysis by focusing first on the active site, then on the whole enzyme. We<br> confirmed that the polar modification in 4’-DTMP induces additional local interactions with<br> the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as<br> shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support<br> our analysis with network-based community analysis and show that segmentation of the loop<br> domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.</p>
Transmission of beneficial yeasts accompanies offspring production in Drosophila – an initial evolutionary stage of insect maternal care through manipulation of microbial load?
<p>Parent-to-offspring transmission of beneficial microorganisms is intimately interwoven with the evolution of social behaviors. Ancestral stages of complex sociality-microbe vectoring interrelationships may be characterized by high costs of intensive parental care and hence only a weak link between the transmission of microbial symbionts and offspring production. We investigate the relationship between yeast symbiont transmission and egg-laying, as well as some general factors thought to drive the 'farming' of microscopic fungi by the fruit fly <em>Drosophila</em> <em>melanogaster</em>, an insect with no obvious parental care but which is highly dependent on dietary microbes during offspring development. The process of transmitting microbes involves flies ingesting microbes from their previous environment, storing and vectoring them, and finally depositing them in a new environment. This study revealed that fecal materials of adult flies play a significant role in this process, as they contain viable yeast cells that support larval development. During single patch visits, egg-laying female flies transmitted more yeast cells than non-egg-laying females, suggesting that dietary symbiont transmission is not random, but linked to offspring production. The crop, an extension of the foregut, was identified as an organ capable of storing viable yeast cells during travel between egg-laying sites. However, the amount of yeast in the crop reduced rapidly during periods of starvation. Although females starved for 24 hours deposited a smaller amount of yeast than those starved for 6 hours, the yeast inoculum produced still promoted the development of larval offspring. The results of these experiments suggest that female <em>Drosophila</em> fruit flies have the ability to store and regulate the transfer of microorganisms beneficial to their offspring via the shedding of fecal material. We argue that our observation may represent an initial evolutionary stage of maternal care through the manipulation of microbial load, from which more specialized feedbacks of sociality and microbe management may evolve.</p>
Mechanical manipulation of cancer cell tumorigenicity via heat shock protein signaling
<p><span>Biophysical cues of rigid tumor matrix play a critical role in cancer cell malignancy. Herein, we report that stiffly confined cancer cells exhibit robust growth of spheroids in the stiff hydrogel that exerts substantial confining stress on the cells. The stressed condition activated Hsp (heat shock protein)-STAT3 signaling via the TRPV4-PI3K/Akt axis, thereby upregulating the expression of the stemness-related markers in cancer cells, whereas these signaling activities were suppressed in cancer cells cultured in softer hydrogels or stiff hydrogels with stress relief or Hsp70 knockdown/inhibition. This mechanopriming based on 3D culture enhanced cancer cell tumorigenicity and metastasis in animal models upon transplantation, and pharmaceutically inhibiting Hsp70 improved the anticancer efficacy of chemotherapy. Mechanistically, our study reveals the crucial role of Hsp70 in regulating cancer cell malignancy under mechanically stressed conditions and its impacts on cancer prognosis-related molecular pathways for cancer treatments. </span></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.