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Matlab scripts used to analyze data associated with the manuscript entitled "A single cell atlas of the human liver tumor microenvironment". *please used Matlab 2019b to run the following m files. Files: inputData.mat: mat contains all raw and preprocessed data used in the study Create_Interactions_Network.m: Matlab script used to calculate Ligand-Receptor interaction score between different cell types. The script creates panels of Figure 3 and Table S5. Hepatocytes_Reconstruction.m: Matlab script used to reconstruct human hepatocytes zonation along the lobule axis. The script creates panel 'c' of Figure 4, Figure S4, and Table S7. Cancer_Cells_Spatial_Analysis.m: Matlab script used to calculate differential gene expression between malignant cells found at different zones (malignant border, malignant core, and fibrotic zone) captured by laser microdissection. The script creates panel 'd' of Figure 4 helperFunctions.zip: This folder contains required functions used by the m files.
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  • Software/Code
Cambridge Butterfly Collection. Loreto, Peru Part 1 EN: This upload contains photographs taken by Eva van der Heijden at the Butterfly Genetics Group at the University of Cambridge, from a butterfly wing collection from Loreto, Peru, in collaboration with Green Gold Forestry. Individual sample names can be found in the information sheet. Further Information on individual samples from the Butterfly Genetics Group Collection can be found on the public database Earthcape (click here for the database, and here for FAQ). Please contact Chris Jiggins (c.jiggins[at]zoo.cam.ac.uk) or Gabriela Montejo-Kovacevich (gmontejokovacevich[at]gmail.com) for further information. ES: Este repositorio contiene fotografías tomadas por Eva van der Heijden en el Butterfly Genetics Group de la Universidad de Cambridge, de mariposas de Loreto (Peru), en colaboración con la compañía Green Gold Forestry. Puede encontrar información sobre muestras individuales de Butterfly Genetics Group Collection en la base de datos pública Earthcape (haga clic aquí para la base de datos, y aquí para preguntas frecuentes) Por favor, póngase en contacto con Chris Jiggins (c.jiggins [arroba] zoo.cam.ac.uk) o Gabriela Montejo-Kovacevich (gmontejokovacevich[at]gmail.com) con sus preguntas o peticiones.
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intronsf10k image
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# Installation conda create -n deep_texture python=3.6 source activate deep_texture conda install numpy pillow conda install keras-gpu conda install keras # if GPUs are not available pip install git+https://github.com/keras-team/keras-applications.git@d506dc82d0 # downgrade keras-application ## usage import deep_texture (prep, dnn) = deep_texture.setup_texture(arch = 'nasnet', layer = 'normal_concat_11', cbp_dir = '/tmp') dtr = deep_texture.calc_features_file("./test.png", prep, dnn)
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Integrating data from multiple sources with the aim to identify records that correspond to the same entity is required in many real-world applications including healthcare, national security, and businesses. However, privacy and confidentiality concerns impede the sharing of personal identifying values to conduct linkage across different organizations. Privacy-preserving record linkage (PPRL) techniques have been developed to tackle this problem by performing clustering based on the similarity between encoded record values, such that each cluster contains (similar) records corresponding to one single entity. When employing PPRL on databases from multiple parties, one major challenge is the prohibitively large number of similarity comparisons required for clustering, especially when the number and size of databases are large. While there have been several private blocking methods proposed to reduce the number of comparisons, they fall short in providing an efficient and effective solution for linking multiple large databases. Further, all of these methods are largely dependent on data. In this paper, we propose a novel private blocking method for efficiently linking multiple databases by exploiting the data characteristics in the form of probabilistic signatures and introduce a local blocking evaluation step for validating blocking methods without knowing the ground-truth. Experimental results show the efficacy of our method in comparison to several state-of-the-art methods.
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This code enables the mapping of single-molecule m6A methylations.
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  • Software/Code
Fig. 3: Maxillolabial complex of Opamyrma hungvuong worker, nontype (AKY05vii17-06, China, Guangxi). (A) Scanning electron microscope image of maxillolabial complex in ventral view, labrum removed; (B) right maxilla in outer view; (C) labium in lateral view; (D) labium in dorsal view. Abbreviations: Ams = anteromedian sclerite; Gcss = galeal crown's stout seta; Hyp = hypopharynx; Lbp = labial palp; Lcn = lacinia; Mxco = maxillary comb; Mxp = maxillary palp; Mxst = maxillary stipes; Prm = prementum; Sglb = subglossal brush.
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Fig. 8: Scanning electron microscope images of metasoma of Opamyrma hungvuong worker, nontype (AKY05vii17-06, China, Guangxi). (A) petiole in lateral view; (B) petiole in ventral view; (C) helcium in anterior view; (D) helcium in ventral view; (E) pretergite of abdominal segment IV in dorsal view; (F) gaster in lateral view; (G) gaster in ventral view. Abbreviations: Absg = abdominal segment; Prsn = presternite; Prtg = pretergite; Ptlt = petiolar laterotergite; Ptsn = petiolar sternite; Tss = tergosternal suture.
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Fig. 13: Male genitalia of Opamyrma hungvuong, nontype (Dai19iii2019-029, Son La, Vietnam). (A) genital capsule in dorsal view; (B) genital capsule in ventral view; (C) abdominal sternite IX in ventral view; (D) cupula in ventral view; (E) left paramere with basiventral part of right paramere and cupula, in unfolded outer view; (F) left volsella in lateral view; (G) left penisvalva in lateral view. Abbreviations: Bm = basimere; Cu = cupula; Cs = cuspis; Dg = digitus; Lp = lateral apodeme; Pv = penisvalva; Spl = spinescent lobe; Spc = spiculum; Tm = telomere; Va = valvura.
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Fig. 4: Tentorium of Opamyrma hungvuong worker, nontype (AKY05vii17-06, China, Guangxi). (A) anterior part of dorsal sclerite of cranium in dorsal view; (B) part of dorsal sclerite of cranium around right antennal socket with anterior part of tentorium, in inner ventral view; (C) part of ventral sclerite of cranium with posterior part of tentorium in inner dorsal view; (D) right half of tentorium in dorsal view (lacking posterior tentorial arm). Abbreviations: Ata = anterior tentorial arm; Atp = anterior tentorial pit; Ct = corpotendon; Dta = dorsal tentorial arm; Ep = external plate; Ip = internal plate; Lclp = lateral portion of clypeus; Mdb = mandible; Occ = occipital carina; Pgr = postgenal ridge; Pta = posterior tentorial arm; Ptg = peritorular groove; Ptp = posterior tentorial pit; Tb = tentorial bridge.
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