Contributors:Pacheco Andre G. C., Lima Gustavo R., Salomão Amanda S., Krohling Breno, Biral Igor P., Gabriel Giorisatto De Angelo, Alves Jr Fábio C. R. , Esgario José G. M., Simora Alana C. , Castro Pedro B. C. , Rodrigues Felipe B., Frasson Patricia H. L. , Krohling Renato A., Knidel Helder , Santos Maria C. S. , Espírito Santo Rachel B., Macedo Telma L. S. G., Canuto Tania R. P. , de Barros Luíz F. S.
- The PAD-UFES-20 dataset was collected along with the Dermatological and Surgical Assistance Program (in Portuguese: Programa de Assistência Dermatológica e Cirurgica - PAD) at the Federal University of Espírito Santo (UFES-Brazil), which is a nonprofit program that provides free skin lesion treatment, in particular, to low-income people who cannot afford private treatment.
- The dataset consists of 2,298 samples of six different types of skin lesions. Each sample consists of a clinical image and up to 22 clinical features including the patient's age, skin lesion location, Fitzpatrick skin type, and skin lesion diameter.
- The skin lesions are: Basal Cell Carcinoma (BCC), Squamous Cell Carcinoma (SCC), Actinic Keratosis (ACK), Seborrheic Keratosis (SEK), Bowen’s disease (BOD), Melanoma (MEL), and Nevus (NEV). As the Bowen’s disease is considered SCC in situ, we clustered them together, which results in six skin lesions in the dataset, three skin cancers (BCC, MEL, and SCC) and three skin disease (ACK, NEV, and SEK)
- All BCC, SCC, and MEL are biopsy-proven. The remaining ones may have clinical diagnosis according to a consensus of a group of dermatologists. In total, approximately 58% of the samples in this dataset are biopsy-proven. This information is described in the metadata.
- The images present in the dataset have different sizes because they are collected using different smartphone devices. All images are available in .png format.
- The metadata associated with each skin lesion is composed of up to 26 features. All features are available in a CSV document in which each line represents a skin lesion and each column a metadata feature.
- In total, there are 1,373 patients, 1,641 skin lesions, and 2,298 images present in the dataset. Each image/sample has a reference to the patient and the skin lesion in the metadata.
The dataset was collected along with the Dermatological and Surgical Assistance Program (PAD) of the Federal University of Espírito Santo. The program is managed by the Department of Specialized Medicine and was approved by the university ethics committee (nº 500002/478) and the Brazilian government through Plataforma Brasil (nº 4.007.097), the Brazilian agency responsible for research involving human beings. In addition, all data is collected under patient consent and the patient’s privacy is completely preserved.
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Here we study patterns of surround modulation in primary visual cortex (V1) and middle temporal complex (hMT+) utilizing a well-studied effect in motion perception, where human observers' ability to discriminate the drift direction of a grating improves as its size gets bigger if the grating has a low contrast, and deteriorates if it has a high contrast. We first replicated the findings in the literature with a behavioral experiment using small and large (1.67 and 8.05 degrees of visual angle) drifting gratings with either low (2%) or high (99%) contrast presented at the periphery. Next, using functional MRI, we found that in V1 with increasing size cortical responses increased at both contrast levels. Whereas in hMT+ with increasing size cortical responses remained unchanged or decreased at high contrast, and increased at low contrast, reflecting the perceptual effect.
3.1.3. Visual Stimuli & Experimental Design
Visual stimuli were drifting gratings. Two size (small: 1.67°, large: 8.05°) and two contrast levels (2% and 99%) were tested. Size (diameter) was defined as six times the standard deviation of the Gaussian envelope in the fMRI experiment. FMRI experimental code was written in Python using the built-in methods of the
Psychopy package, whereas the behavioral experiment was written using custom Java modules developed by us. Therefore the formulation
and implementation was slightly different in the behavioral experiment. Nevertheless, the stimuli were ensured to have same sizes in both experiments. Due to the limits of the visual display system, gratings were presented at ± 8.02 degrees of horizontal eccentricity (was 9.06° in the behavioral experiment), and drifted with a rate of 6°/s (was 4°/s in the behavioral experiment) either upward or downward for the duration of 12 s. Both gratings drifted in the same direction simultaneously, and alternated direction every 2 s to avoid motion adaptation. A functional run was composed of “active” and “control” blocks, each lasting for 12 s. In the active blocks, drifting gratings and a central fixation mark were presented, whilst in the control blocks, only the fixation mark remained visible. In alternating active blocks, small and large drifting gratings were shown, each repeated for 6 times in a run. Contrast level was kept constant within a run. Two experimental runs were conducted for each contrast level in a session. The runs started with an initial blank period of 24 s to allow hemodynamic response to reach a steady state. The total duration of a functional run was around 5 min.
Contributors:Mazzanti Valentina, Malagutti Lorenzo, Mollica Francesco
The first software quantifies the error amplification, the other one can be used by interested researchers for properly designing the testing setup (e.g. the most convenient choice for the capillary diameters). In order to use the programs, though, the material constants of the fluid that is intended to be characterized must be known at least approximately
Those additional supplemental data includes figures, raw image galleries, quantification tables and movie, which are complementary to the main-text figures 1-4 and supplemental figure S1-S4.
Validation of the E14TG2a mESC line used in this study. (A) Representative images of the mESC morphology and alkaline phosphatase (AP) staining when cultured in complete medium (CM) with LIF+2i. (B) Cells cultured in N2B27 medium with bFGF/ActivinA for five days show EpiSCs cell morphology and decreased AP staining. (C) Growth curve of mESCs and mEpiSCs, with cell doubling time indicated in the plot. Scale bar in (A) and (B): 100 um.
Expression of histone-Dendra2 fusion proteins have no apparent effect on the cell cycle progression of mESCs. (A) Western blot analysis of non-transgenic wild-type (WT) mESCs and transgenic mESCs expressing H3-Dendra2, H4-Dendra2, H2A-Dendra2, H2B-Dendra2 and H3.3-Dendra2, respectively. The sizes of histone proteins are ~15 KD, the sizes for Histone-Dendra2 fusion proteins are ~40 KD, as indicated in the panel. (B) The cell cycle profiles obtained using DNA content analysis (PI staining) with FACS (Fluorescence Activated Cell Sorting). (C) Growth curves of non-transgenic WT-mESCs and each histone-Dendra2 transgenic mESC lines, with cell doubling times indicated in the panel. (D) The percentage of EdU-positive cells with 30-minute EdU pulse labeling in H3-Dendra2, H4-Dendra2, H2A-Dendra2, H2B-Dendra2 and H3.3-Dendra2 transgenic mESCs. (E) The “stemness” identity of the mESC line carrying the H3-Dendra2 transgene, confirmed by immunofluorescent signals for ESC markers, including Nanog, Rex1, Oct4, Sox2 and SSEA-1. Scale bar in (E): 20 um.
Schematic depiction of a model for different histone distribution patterns with Wnt3a-induced ACD of mESCs. (A) With Wnt3a bead, non-overlapping histone H3 and H4 regions could be explained by regional conservative mode of nucleosome reassembly during DNA replication, shown as [Model (1) in (E)]. (B) The separable signals are lost in symmetrically dividing mESCs, which could be due to dispersive mode of nucleosome reassembly during DNA replication, shown as [Model (2) in (E)]. (C) The symmetric histone distribution patterns of H2A and H2B during ACD of mESCs. (D) DNA replication-independent model, which applies to H3.3. (E) Distinct nucleosome reassembly modes [(1) conservative versus (2) dispersive] during DNA replication could have regional specificities: the conservative model could occur at gene regions that need to be differentially expressed in the two daughter cells derived from Wnt3a-induced asymmetrically dividing mESCs, such as stemness genes, differentiation genes, or Wnt signaling pathway target genes. On the other hand, for those genes whose expression is similar between the two daughter cells, such as housekeeping genes and genes silenced in mESCs, the dispersive model could be applied to make sure the sister chromatids inherit the identical epigenetic information.
SARS-CoV-2 coinfection with other pathogens and their interactions is increasingly recognized in the literature as potential determinants of COVID-19 phenotypes. A direct implication of this concept is whether and which co-pathogens function synergistically on the transcriptomic level with SARS-CoV-2. Using a list of differentially expressed genes following SARS-CoV-2 infection extracted, gene set enrichment analysis revealed HSV1, EBV, HIV1, IAV and Strep. Pneumoniae, among other pathogens (FDR<0.05). These results provide insight into the synergism between SARS-CoV-2 and other pathogens.