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1,183 results for “Insertion”
Participation of electrochemically inserted protons in the hydrogen evolution reaction on tungsten oxides
<p>Understanding the mechanisms by which electrodes undergo the hydrogen evolution reaction (HER) is<br>necessary to design better materials for aqueous energy storage and conversion. Here, we investigate<br>the HER mechanism on tungsten oxide electrodes, which are stable in acidic electrolytes and can<br>undergo proton-insertion coupled electron transfer concomitant with the HER. Electrochemical<br>characterization showed that anhydrous and hydrated tungsten oxides undergo changes in HER activity<br>coincident with changes in proton composition, with activity in the order HxWO3*H2O>HxWO3 ><br>HxWO3*2H2O. We used operando X-ray diffraction and density functional theory to understand the<br>structural and electronic changes in the materials at high states of proton insertion, when the oxides are<br>most active towards the HER. H0.69WO3*H2O and H0.65WO3 have similar proton composition, structural<br>symmetry, and electronic properties at the onset of the HER, yet exhibit different activity. We<br>hypothesize that the electrochemically inserted protons can diffuse in hydrogen bronzes and participate<br>in the HER. This would render the oxide volume, and not just the surface, as a proton and electron<br>reservoir at high overpotentials. HER activity is highest in HxWO3*H2O, which optimizes both the degree<br>of proton insertion and solid-state proton transport kinetics. Our results highlight the interplay between<br>the HER and proton insertion-coupled electron transfer on transition metal oxides, many of which are<br>non-blocking electrodes towards protons.</p>
Figure 1 in Differences in the soil seed bank of a mining area and its surroundings: a case study inserted in the Cerrado domain
Figure 1. Location of Vazante city and study area, northwest of Minas Gerais state, Brazil.
Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes
<p><span><span><span><span><span><span><span><span><span><span><span>Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remained elusive. Here, we aimed to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (<i>Amphilophus </i>spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic "dark morph", about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous "gold morph". Using a new haplotype-resolved long-read assembly we discovered an 8.2kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term <i>goldentouch</i> in reference to the Greek myth of King Midas. The gene <i>goldentouch</i> is differentially expressed between morphs, likely due to structural implications of inverted repeats in both DNA and RNA (cruciform and hairpin formation). The near-perfect association with the phenotype across several independent populations suggests that this insertion likely underlies this trans-specific, stable polymorphism.</span></span></span></span></span></span></span></span></span></span></span></p>
Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
<p>A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e., local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1,000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e clades separated by branches >0.3 CUs) with high support and identified rapid radiations (i.e., shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.</p>
Data for heat transfer characterisation of inserts of ASTEP thermal storage system
<p>Dataset for heat transfer characterisation of Honeycomb inserts and Y-Inserts considered in ASTEP project.</p>
Comprehensive characterisation of the genomic insertion site of a transgene in highly repetitive, centromeric region of Anopheles mosquitoes
<p>The availability of the genomic sequence of the malaria mosquito <em>Anopheles</em> <em>gambiae</em> has sparked in recent years the development of transgenic technologies with the potential to be used as novel tools for vector control. These technologies rely on genome editing that confers features able to affect vector capacity. This can be achieved by either reducing the mosquito population or by making mosquitoes refractory to the parasite infection. Although sophisticated molecular techniques such as those based on AttB/AttP site-specific recombination and CRISPR/Cas9 systems can lead to the integration of transgenes in specific sites of the genome, methods that allow semi-random integration are still in use due to their high efficiency; PiggyBac transposon-mediated integrations fall in this category. Characterization of the insertion site of transgenes in transgenic strains generated via PiggyBac integration can be hampered when the transgene is inserted in regions of the genome rich in repetitive sequences. Here we describe a number of techniques that were used to identify the genomic location of the transgene in a repetitive region in the <em>Anopheles gambiae</em> strain Ag(PMB)1 which was initially reported on Chromosome 3R 36D. Whilst Inverse PCR used in previous analysis was unable to distinguish between multiple genomic locations as potential insertion sites of the transgene, here we demonstrate that the use of FISH identifies clearly the integration of the transgene in a poorly annotated centromeric region of Chromosome 2R 19D. This study emphasises the need for accuracy in sequencing data for the genome of organisms of medical importance such as <em>Anopheles </em>mosquitoes. An effort to further improve reference genomes is of paramount importance to support and facilitate vector control interventions based on genome editing.</p>
Reunion of Australasian possums by shared SINE insertions
<p><span>Although first posited to be of a single origin, the two subfamilies of Phalangeriform marsupial possums (Phalangeroidea: cuscuses and brushtail possums and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. We reinvestigated these relationships by screening ~200,000 orthologous SINE loci across the newly available whole-genome sequences of Phalangeriform species and their relatives, and identified 106 highly reliable phylogenetic SINE markers. The presence/absence patterns of these SINE elements within the various Australasian possum genomes provide the first highly significant evidence for the reunification of Australasian possums into one monophyletic group.</span></p>
An Artificial Metalloenzyme Based on a Copper Heteroscorpionate Enables sp3 C–H Functionalization via Intramolecular Carbene Insertion
<p>Data underlying the figures in the publication: Rumo, C. <em>et al.</em> “An Artificial Metalloenzyme Based on a Copper Heteroscorpionate Enables Sp3 C–H Functionalization Via Intramolecular Carbene Insertion” <em>J. Am. Chem. Soc.</em> <strong>2022</strong>, <a href="https://doi.org/10.1021/jacs.2c03311">https://doi.org/10.1021/jacs.2c03311</a></p> <p>TOC</p> <ol> <li><strong>Table_1.xlsx</strong> Source data for <em>Table 1</em></li> <li><strong>Figure_2_Relative_contribution.xlsx</strong> Source data for <em>Figure 2</em></li> <li><strong>Figure_S6_CD_titration.xlsx</strong> Source data for <em>Figure S6</em></li> <li><strong>Table_S2_Double_saturation.xlsx</strong> Source data for <em>Table S2</em></li> <li><strong>Table_S3_Complementary_data_of_selected_Sav_mutants.xlsx</strong> Source data for <em>Table S3</em></li> <li><strong>Table_S4_Substrate_scope.xlsx</strong> Source data for <em>Table S4</em></li> </ol>
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
<p>Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.</p>
Rings Insertion Dataset for Determining Exception Context in Assembly Operations form Multimodal Data
<p>Rings Insertion Dataset used in Simonič, M.; Majcen Hrovat, M.; Džeroski, S.; Ude, A.; Nemec, B. Determining Exception Context in Assembly Operations from Multimodal Data. <em>Sensors</em> <strong>2022</strong>, <em>22</em>, 7962. https://doi.org/10.3390/s22207962</p> <p>The dataset consists of color images of different outcomes of the ring insertion task as well as the corresponding Cartesian pose of the robot end-effector and force torque data. Data is organized into four folders, representing one of the possible insertion slots. In each of the folders, data is further split into the following cases:<br> - error in insertion target position ranging from -3 to 3 mm in x direction in 1 mm steps,<br> - error in insertion target position ranging from -3 to 3 mm in y direction in 1 mm steps,<br> - no positional error,<br> - other unidentified error (bad insertion).</p> <p>Multiple attempts were made for each case.</p> <p>Each entry has unique date-time tag and comprises: RGB image (.jpg) and .mat file with <em>states </em>object that contains reference and measured target pose in Cartesian space (positions and quaternions) and raw force-torque sensor data and force-torque data transformed to the tool frame.</p> <p>The experiments were performed with Franka Emika Panda collaborative robot. For acquisition of image data an Intel Realsense D435 RGB-D camera has been utilized. </p>
Data set: methanol formation via oxygen insertion chemistry in ices
<p>This data set corresponds to the experiments appearing in the article "Methanol Formation via Oxygen Insertion Chemistry in Ices" (Bergner, Oberg, & Rajappan, The Astrophysical Journal, 2017, 845:29). Please refer to the article for experimental details & methods.</p> <p>The data set consists of infrared spectra from 600-4000 wavenumbers. Each file contains the spectra taken for a single experiment. The first column holds the spectrum wavenumber values, and all subsequent columns hold the IR absorbance values for spectra taken during ice irradiation. The first row lists column headings, including the time increments (in minutes) of the irradiation spectra. </p> <p>File names are formatted: "IR_N.txt" where N corresponds to the Experiment # listed in Table 1 of the corresponding article. All details about the experiment (irradiation temperature, ice composition) can be retrieved from Table 1.</p>
Fig. 1. Geographic distribution of bogidiellid amphipods. Large map: type localities of: 1, Bogidiella veneris n. sp.; 2, Bogidomma australis; 3, Xystriogidiella capricornea; and 4, Xystriogidiella juliani on the Australian continent (with kind permission of demis.nl). Insert map: global distribution of Bogidiellidae and several, possibly closely related taxa (modified after Koenemann and Holsinger, 1999).
Fig. 1. Geographic distribution of bogidiellid amphipods. Large map: type localities of: 1, Bogidiella veneris n. sp.; 2, Bogidomma australis; 3, Xystriogidiella capricornea; and 4, Xystriogidiella juliani on the Australian continent (with kind permission of demis.nl). Insert map: global distribution of Bogidiellidae and several, possibly closely related taxa (modified after Koenemann and Holsinger, 1999).
Dataset: Direct insertion of NASA Airborne Snow Observatory-derived snow depth time-series into the iSnobal energy balance snow model
<p>This dataset is a companion to the submitted WRR publication entitled ‘Direct insertion of NASA Airborne Snow Observatory-derived snow depth time-series into the iSnobal energy balance snow model’. The file structure is organized as follows:</p> <ul> <li><strong>ASO_50m_depth_surfaces</strong> - This folder contains the Airborne Snow Observatory lidar-derived snow depth products aggregated to 50m gridded spatial resolution. Each file is titled with a date such as ‘TB<em>YYYYMMDD</em>_SUPERsnow_depth.asc’. The coordinates are in UTM zone 11N and use the WGS84 coordinate system.</li> <li><strong>static_grids</strong> <ul> <li>Static grids are used in each of the subsequent folders and are not changed between years.</li> <li>init0000.ipw <ul> <li>Initialization file to begin the model run. Contains the digital elevation model in band 1, surface roughness raster in band 2, and zeroed images of snow properties in bands 3-7.</li> </ul> </li> <li>maxus.nc <ul> <li>netCDF file of 72 separate images of maximum upwind slope for all upwind directions from 0 (north) to 355 degrees in 5-degree increments. Derived using Adam Winstral’s Sx algorithm.</li> </ul> </li> <li>tuolx_dem_50m.ipw <ul> <li>Digital elevation model from ASO snow-free acquisition aggregated to 50m gridded spatial resolution. Same information as band 1 in the init0000.ipw file.</li> </ul> </li> <li>tuolx_hetchy_mask_50m.ipw <ul> <li>Basin mask of the Tuolumne River Basin above Hetch Hetchy Reservoir. Out-of-basin cells denoted as 0, and in-basin cells denoted as 1.</li> </ul> </li> <li>tuolx_vegheight_50m.ipw <ul> <li>Vegetation height raster in meters. Derived from NLCD dataset of vegetation type..</li> </ul> </li> <li>tuolx_vegk_50m.ipw <ul> <li>Emissivity of the vegetation canopy. Derived from NLCD dataset of vegetation type.</li> </ul> </li> <li>tuolx_vegnlcd_50m.ipw <ul> <li>Vegetation type from the National Land Cover Database.</li> </ul> </li> <li>tuolx_vegtau_50m.ipw <ul> <li>Fractional transmissivity of the vegetation canopy. Derived from NLCD dataset of vegetation type.</li> </ul> </li> </ul> </li> <li><strong>level1_raw_data</strong> <ul> <li>{Hourly data interpolated to nearest hour from downloaded raw data (CDEC/MesoWest)}</li> <li>air_temp_level1.csv</li> <li>precip_accum_level1.csv</li> <li>relative_humidity_level1.csv</li> <li>solar_radiation_level1.csv</li> <li>wind_direction_level1.csv</li> <li>wind_speed_level1.csv</li> </ul> </li> </ul> <p>The directories for each water year contain the configuration file for that year along with the vector meteorological data from measurement sites and site metadata in .csv format.</p> <ul> <li><strong>wy2013</strong></li> <li><strong>wy2014</strong></li> <li><strong>wy2015</strong></li> <li><strong>wy2016</strong> <ul> <li> <ul> <li>backup_config.ini {Initialization file used to distribute station data over a regular grid for each water year.}</li> <li>air_temp.csv</li> <li>cloud_factor.csv</li> <li>metadata.csv</li> <li>precip.csv</li> <li>vapor_pressure.csv</li> <li>wind_direction.csv</li> <li>wind_speed.csv</li> <li><strong>data/</strong> <ul> <li>[subdirectory containing all future created forcing grid files]</li> </ul> </li> <li><strong>runs/</strong> <ul> <li>[subdirectory containing all <em>iSnobal</em> output files in addition to reinitialization scripts for ASO snow depth updates]</li> </ul> </li> </ul> </li> </ul> </li> </ul>
Artificial sound mixes with event insertions
<p><strong>Contains artificial sound mixes and meta data that were created for the task of<br> sound event detection.</strong></p> <p>The mixes were created using background and event audio recordings<br> from Tampere University's Detection and Classification of Acoustic Scenes and<br> Events (DCASE) Community. More information on the source data can be found at<br> http://www.cs.tut.fi/sgn/arg/dcase2017/challenge/task-rare-sound-event-detection#audio-dataset.</p> <p>Source data credits: Diment, Aleksandr et al (2017, 2018)</p> <p><strong>Created artificial sound mixes are 10 seconds long and contain:</strong></p> <p>- background audio from diverse scenes from start to end<br> - 0 to 4 event insertions</p> <p>With this formula, two datasets were created separately: a training, and an<br> evaluation dataset. These were created separately so that the backgrounds and<br> event recordings used for the evaluation dataset were not used in any of the<br> training audio mixes. Thus, keeping them unseen by the system during development.</p> <p><strong>Audio data:</strong><br> <strong>mixes_train.zip</strong>: Contains the audio mixes created for training.<br> Audio format: .wav<br> Count: 1000 tracks</p> <p><strong>mixes_eval.zip</strong>: Contains the audio mixes created for evaluation.<br> Audio format: .wav<br> Count: 500 tracks</p> <p><strong>Meta-data:</strong><br> Meta-data was maintained documenting the source background, the overlaid source<br> events, and the time onset and offset of each sound event or confusing sound.</p> <p><strong>meta_track_info_train.csv and meta_track_info_eval.csv columns:</strong></p> <p>- trackID: the unique ID of a mix<br> - class_dummy: whether a mix contain a glas break event (other events can be<br> determined using meta_clip_insertions_train and meta_clip_insertions_eval)<br> - background_file: the unique file reference used for background sound to the<br> source data (i.e. DCASE original audio data set)<br> - background_t0: the second in the original background sound recording in which<br> the 10 second background starts.</p> <p><strong>meta_clip_insertions_train.csv and meta_clip_insertions_eval.csv columns:</strong></p> <p>- trackID: the unique ID of a mix<br> - event: the type of event insertion<br> - event_start: at which time in the mix the event start<br> - event_end: at which time in the mix the event ends<br> - event_file: the unique file_number of event reference to the<br> source data (i.e. DCASE original audio data set)<br> an event_file with value 345584_4.wav means the event comes from file<br> 345584.wav in the DCASE audio set and is the 4th event in that audio file.</p> <p>To see the project for which this data set was created visit the github<br> repository at https://github.com/reyvaz/sound-event-detection</p> <p><strong>References:</strong><br> Diment, Aleksandr, Mesaros, Annamaria, Heittola, Toni, & Virtanen, Tuomas. (2017).<br> TUT Rare sound events, Development dataset [Data set]. Zenodo.<br> http://doi.org/10.5281/zenodo.401395</p> <p>Aleksandr Diment, Annamaria Mesaros, Toni Heittola, & Tuomas Virtanen. (2018).<br> TUT Rare sound events, Evaluation dataset [Data set]. Zenodo.<br> http://doi.org/10.5281/zenodo.1160455<br> </p>
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival
<p>This dataset is related to "Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival" (Cajuso et al.).</p> <p><strong>Abstract:</strong></p> <p>Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are usually repressed, they become active in several human cancers, in particular those of the gastrointestinal tract. Here we characterize retrotransposon insertions in 202 colorectal tumor whole genomes and investigate their associations with molecular and clinical characteristics. We find highly variable retrotransposon activity among tumors and identify recurrent insertions in 15 known cancer genes. In approximately 1% of the cases we identify insertions in <em>APC</em>,<em> </em>likely to be tumor-initiating events. Insertions are positively associated with the CpG island methylator phenotype and the genomic fraction of allelic imbalance. Clinically, high number of insertions is independently associated with poor disease-specific survival.</p> <p><strong>Sample description: </strong></p> <p>A signed informed consent was obtained for as many human participants as possible. In cases without a signed informed consent, an authorization from the National Supervisory Authority for Welfare and Health (Dnro 421/04/044/06, Dnro 8048/06.01.03.01/2014, Dnro 358/32/300/05, Dnro 1476/06.01.03.01/2012) was obtained as stated in Finnish law. The study has been reviewed by the Ethics Committee of the Hospital district of Helsinki and Uusima (Dnro 133/E8/03, 408/13/03/03/2009). Permission to use patient information was obtained from the National Institute for Health and Welfare (Dnro 53/07/2000, Dnro THL/1071/5.05.00/2011, Dnro THL/151/5.05.00/2017). </p> <p><strong>RNA sequencing:</strong></p> <p>Total RNA from consecutive cryosections was extracted using RNeasy Mini Kit (Qiagen) from 34 tumors that displayed more than 50% of cancer cell percentage (HE staining of cryosections) and RNA integrity>6 (Agilent RNA 6000, Agilent 2100 Bioanalyzer). Paired-end RNA sequencing was performed on the Illumina Hiseq 2000. RNA-seq data was processed using Kallisto (version 0.43.0) software. Kallisto quantification was executed in paired-end mode and aligned against the Ensembl Human reference transcriptome (GRCh37_79). Quantification results from Kallisto were normalized and aggregated to gene-level utilizing sleuth (version 0.28.1) R package with default filtering settings.</p> <p> </p>
Comprehensive understanding of Tn5 insertion preference recovers expansive transcription regulatory lexicon
<p>This repository stores pre-calculated mappability files for BiasFreeATAC correction pipeline.</p>
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).
Data for: Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+, K+-ATPases
<p>The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino-acid substitutions in the H1-H2 extracellular loop of Na<sub>+</sub>, K<sub>+</sub>-ATPase (NKA). Previous work revealed that hystricognath rodents (e.g. chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino-acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino-acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.</p>
DATASET RELATED TO ARTICLE"SORL1 GENE MUTATION AND OCTAPEPTIDE REPEAT INSERTION IN PRNP GENE IN A CASE PRESENTING WITH RAPIDLY PROGRESSIVE DEMENTIA AND CEREBRAL AMYLOID ANGIOPATHY"
<p><strong>electropherogram of prnp octarepeat region</strong></p> <p><strong>ngs analysis of causal and risk genes associated to dementia</strong></p> <p><strong>prnp octarepeat region analysis by size discrimination of pcr amplicons</strong></p>
HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia
<p>Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ2 test with p-values < 0.05.</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
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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.
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