scholarly journals Mistic: an open-source multiplexed image t-SNE viewer

2021 ◽  
Author(s):  
Sandhya Prabhakaran ◽  
Chandler Gatenbee ◽  
Mark Robertson-Tessi ◽  
Jeffrey West ◽  
Amer A Beg ◽  
...  
Keyword(s):  
Open Source ◽  
Tumor Tissue ◽  
Specific Expression ◽  
Temporal Relationships ◽  
Spatio Temporal ◽  
Specific Expression Pattern ◽  
Downstream Analysis ◽  
Immune Oncology ◽  
Entire Dataset ◽  
2D Images

Understanding the complex ecology of a tumor tissue and the spatio-temporal relationships between its cellular and microenvironment components is becoming a key component of translational research, especially in immune-oncology. The generation and analysis of multiplexed images from patient samples is of paramount importance to facilitate this understanding. In this work, we present Mistic, an open-source multiplexed image t-SNE viewer that enables the simultaneous viewing of multiple 2D images rendered using multiple layout options to provide an overall visual preview of the entire dataset. In particular, the positions of the images can be taken from t-SNE or UMAP coordinates. This grouped view of all the images further aids an exploratory understanding of the specific expression pattern of a given biomarker or collection of biomarkers across all images, helps to identify images expressing a particular phenotype or to select images for subsequent downstream analysis. Currently there is no freely available tool to generate such image t-SNEs. Mistic is open-source and can be downloaded at: https://github.com/MathOnco/Mistic.

scholarly journals atoh8 expression pattern in early zebrafish embryonic development

2021 ◽  
Author(s):  
Ninfa Fragale ◽  
Satya Srirama Karthik Divvela ◽  
Beate Brand-Saberi
Keyword(s):  
Expression Pattern ◽  
Developmental Stages ◽  
In Situ Hybridisation ◽  
Temporal Analysis ◽  
Paraxial Mesoderm ◽  
Specific Expression ◽  
Helix Loop Helix ◽  
Spatio Temporal ◽  
Specific Expression Pattern

AbstractAtonal homologue 8 (atoh8) is a basic helix-loop-helix transcription factor expressed in a variety of embryonic tissues. While several studies have implicated atoh8 in various developmental pathways in other species, its role in zebrafish development remains uncertain. So far, no studies have dealt with an in-depth in situ analysis of the tissue distribution of atoh8 in embryonic zebrafish. We set out to pinpoint the exact location of atoh8 expression in a detailed spatio-temporal analysis in zebrafish during the first 24 h of development (hpf). To our surprise, we observed transcription from pre-segmentation stages in the paraxial mesoderm and during the segmentation stages in the somitic sclerotome and not—as previously reported—in the myotome. With progressing maturation of the somites, the restriction of atoh8 to the sclerotomal compartment became evident. Double in situ hybridisation with atoh8 and myoD revealed that both genes are expressed in the somites at coinciding developmental stages; however, their domains do not spatially overlap. A second domain of atoh8 expression emerged in the embryonic brain in the developing cerebellum and hindbrain. Here, we observed a specific expression pattern which was again in contrast to the previously published suggestion of atoh8 transcription in neural crest cells. Our findings point towards a possible role of atoh8 in sclerotome, cerebellum and hindbrain development. More importantly, the results of this expression analysis provide new insights into early sclerotome development in zebrafish—a field of research in developmental biology which has not received much attention so far.

Identification and expression analysis of Dazl homologue in Cynops cyanurus

Zygote ◽  
2021 ◽  
pp. 1-6
Author(s):  
Yinjiao Zhao ◽  
Ya Du ◽  
Qinglan Ge ◽  
Fang Yan ◽  
Shu Wei
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Studies ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Specific Expression ◽  
Recognition Motif ◽  
Deleted In Azoospermia ◽  
Specific Expression Pattern

Summary The Dazl (deleted in azoospermia-like) gene encodes an RNA-binding protein containing an RNA recognition motif (RRM) and a DAZ motif. Dazl is essential for gametogenesis in vertebrates. In this study, we report the cloning of Dazl cDNA from Cynops cyanurus. Ccdazl mRNA showed a germline-specific expression pattern as expected. Ccdazl expression gradually decreased during oogenesis, suggesting that it may be involved in oocyte development. Phylogenetic analysis revealed that the Ccdazl protein shares conserved motifs/domains with Dazl proteins from other species. Cloning of Ccdazl provides a new tool to carry out comparative studies of germ cell development in amphibians.

scholarly journals Bootstrap joint prediction regions for sequences of missing values in spatio-temporal datasets

2021 ◽  
Author(s):  
Maria Lucia Parrella ◽  
Giuseppina Albano ◽  
Cira Perna ◽  
Michele La Rocca
Keyword(s):  
Missing Data ◽  
Missing Values ◽  
Sample Selection ◽  
Sample Path ◽  
Temporal Relationships ◽  
Empirical Performance ◽  
Spatio Temporal ◽  
Joint Prediction ◽  
Point Forecast ◽  
Prediction Regions

AbstractMissing data reconstruction is a critical step in the analysis and mining of spatio-temporal data. However, few studies comprehensively consider missing data patterns, sample selection and spatio-temporal relationships. To take into account the uncertainty in the point forecast, some prediction intervals may be of interest. In particular, for (possibly long) missing sequences of consecutive time points, joint prediction regions are desirable. In this paper we propose a bootstrap resampling scheme to construct joint prediction regions that approximately contain missing paths of a time components in a spatio-temporal framework, with global probability $$1-\alpha $$ 1 - α . In many applications, considering the coverage of the whole missing sample-path might appear too restrictive. To perceive more informative inference, we also derive smaller joint prediction regions that only contain all elements of missing paths up to a small number k of them with probability $$1-\alpha $$ 1 - α . A simulation experiment is performed to validate the empirical performance of the proposed joint bootstrap prediction and to compare it with some alternative procedures based on a simple nominal coverage correction, loosely inspired by the Bonferroni approach, which are expected to work well standard scenarios.

scholarly journals Neuroendocrine prostate cancer has distinctive, non-prostatic HOX code that is represented by the loss of HOXB13 expression

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Siyuan Cheng ◽  
Shu Yang ◽  
Yingli Shi ◽  
Runhua Shi ◽  
Yunshin Yeh ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Hox Genes ◽  
Human Cancer ◽  
Specific Expression ◽  
Hox Gene ◽  
Human Cancer Cell Lines ◽  
All Trans Retinoic Acid ◽  
Neuroendocrine Prostate Cancer ◽  
Hox Code ◽  
Specific Expression Pattern

AbstractHOX gene-encoded homeobox proteins control body patterning during embryonic development; the specific expression pattern of HOX genes may correspond to tissue identity. In this study, using RNAseq data of 1019 human cancer cell lines that originated from 24 different anatomic sites, we established HOX codes for various types of tissues. We applied these HOX codes to the transcriptomic profiles of prostate cancer (PCa) samples and found that the majority of prostate adenocarcinoma (AdPCa) samples sustained a prostate-specific HOX code whereas the majority of neuroendocrine prostate cancer (NEPCa) samples did not, which reflects the anaplastic nature of NEPCa. Also, our analysis showed that the NEPCa samples did not correlate well with the HOX codes of any other tissue types, indicating that NEPCa tumors lose their prostate identities but do not gain new tissue identities. Additionally, using immunohistochemical staining, we evaluated the prostatic expression of HOXB13, the most prominently changed HOX gene in NEPCa. We found that HOXB13 was expressed in both benign prostatic tissues and AdPCa but its expression was reduced or lost in NEPCa. Furthermore, we treated PCa cells with all trans retinoic acid (ATRA) and found that the reduced HOXB13 expression can be reverted. This suggests that ATRA is a potential therapeutic agent for the treatment of NEPCa tumors by reversing them to a more treatable AdPCa.

Patterns of Cognitive Test Performance As Functions of the Lateral Localization of Cerebral Abnormalities in the Temporal Lobe

1957 ◽  
Vol 103 (433) ◽  
pp. 758-772 ◽  
Author(s):  
Victor Meyer ◽  
H. Gwynne Jones
Keyword(s):  
Test Performance ◽  
Right Hemisphere ◽  
Cognitive Test ◽  
Temporal Relationships ◽  
Verbal Tasks ◽  
Specific Locus ◽  
Left And Right ◽  
Spatio Temporal ◽  
Cognitive Test Performance ◽  
Lateral Localization

Various investigations into the effects of brain injury on psychological test performance (Weisenburg and McBride, 1935; Patterson and Zangwill, 1944; Anderson, 1951; McFie and Piercy, 1952; Bauer and Becka, 1954; Milner, 1954) suggest the overall conclusion that patients with left hemisphere lesions are relatively poor at verbal tasks, while those with right-sided lesions do worst at practical tasks, particularly the manipulation of spatial or spatio-temporal relationships. Heilbfun's (1956) study confirmed that verbal deficits result from left-sided lesions but his left and right hemisphere groups produced almost identical scores on spatial tests. In so far as these workers paid attention to the specific sites of the lesions, their findings indicate that the pattern of test performance is a function of the hemisphere in which the lesion occurs rather than of its specific locus.

scholarly journals Tissue Distribution of ACE2 Protein in Syrian Golden Hamster (Mesocricetus auratus) and Its Possible Implications in SARS-CoV-2 Related Studies

2021 ◽  
Vol 11 ◽  
Author(s):  
Voddu Suresh ◽  
Deepti Parida ◽  
Aliva P. Minz ◽  
Manisha Sethi ◽  
Bhabani S. Sahoo ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Golden Hamster ◽  
Expression Patterns ◽  
Mesocricetus Auratus ◽  
Syrian Golden Hamster ◽  
Surface Epithelium ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Specific Expression Pattern

The Syrian golden hamster (Mesocricetus auratus) has recently been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. However, lack of knowledge about the tissue-specific expression pattern of various proteins in these animals and the unavailability of reagents like antibodies against this species hampers these models’ optimal use. The major objective of our current study was to analyze the tissue-specific expression pattern of angiotensin-converting enzyme 2, a proven functional receptor for SARS-CoV-2 in different organs of the hamster. Using two different antibodies (MA5-32307 and AF933), we have conducted immunoblotting, immunohistochemistry, and immunofluorescence analysis to evaluate the ACE2 expression in different tissues of the hamster. Further, at the mRNA level, the expression of Ace2 in tissues was evaluated through RT-qPCR analysis. Both the antibodies detected expression of ACE2 in kidney, small intestine, tongue, and liver. Epithelium of proximal tubules of kidney and surface epithelium of ileum expresses a very high amount of this protein. Surprisingly, analysis of stained tissue sections showed no detectable expression of ACE2 in the lung or tracheal epithelial cells. Similarly, all parts of the large intestine were negative for ACE2 expression. Analysis of tissues from different age groups and sex didn’t show any obvious difference in ACE2 expression pattern or level. Together, our findings corroborate some of the earlier reports related to ACE2 expression patterns in human tissues and contradict others. We believe that this study’s findings have provided evidence that demands further investigation to understand the predominant respiratory pathology of SARS-CoV-2 infection and disease.

scholarly journals Genome-wide analysis of CrRLK1L genes and their expression profiling during fiber development in cotton

2020 ◽  
Author(s):  
Dongyun Zuo ◽  
Javaria Ashraf ◽  
Hailiang Cheng ◽  
Shang Liu ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Plant Immunity ◽  
Fiber Development ◽  
The Other ◽  
Element Analysis ◽  
Specific Expression ◽  
Group Iii ◽  
Group I ◽  
Genome Wide ◽  
Specific Expression Pattern

Abstract Background: Catharanthus roseus receptor-like kinase 1-like (CrRLK1Ls) proteins play important roles in cell growth, plant morphogenesis, reproduction, hormone signaling, plant immunity and stress responses in Arabidopsis. However, not much information is available about their functions during cotton fiber development.Results: We identified a total of 125, 73 and 71 full-length putative CrRLK1L genes in G. hirsutum, G. arboreum and G. raimondii, which are much greater than that of the other plants. The phylogenetic and gene structure analysis divided the cotton CrRLK1L genes into six major groups, among which only group I and II contained AtCrRLK1Ls of Arabidopsis, suggesting that other groups (group III-VI) were expanded by gene duplication during cotton evolution. Genome collinearity analysis revealed that half of the At02 genes in G. hirsutum derived from A02 of G. arboreum, while the other half (GhCrRLK1L6 and GhCrRLK1L7) originated from Dt03 and Dt02 of G. raimondii, indicating segmental duplication between noncorresponding chromosomes during polyploidization of G. hirsutum. In addition, expression and cis-element analysis revealed that only 22 GhCrRLK1Ls showed specific expression pattern during fiber development which are mainly due to the presence of binding sites for NAC, MYB and WRKY transcription factors.Conclusions: This study provides a strong foundation to further explore the molecular mechanism of CrRLK1L genes during fiber development in upland cotton.

scholarly journals Neuropeptides in modulation of Drosophila behavior: how to get a grip on their pleiotropic actions

2019 ◽  
Author(s):  
Dick R Nässel ◽  
Dennis Pauls ◽  
Wolf Huetteroth
Keyword(s):  
Expression Pattern ◽  
Internal State ◽  
Neurosecretory Cells ◽  
Higher Order ◽  
Specific Expression ◽  
Specific Expression Pattern ◽  
Pleiotropic Functions ◽  
Pleiotropic Actions ◽  
The Brain ◽  
Different Levels

Neuropeptides constitute a large and diverse class of signaling molecules that are produced by many types of neurons, neurosecretory cells, endocrines and other cells. Many neuropeptides display pleiotropic actions either as neuromodulators, co-transmitters or circulating hormones, while some play these roles concurrently. Here, we highlight pleiotropic functions of neuropeptides and different levels of neuropeptide signaling in the brain, from context-dependent orchestrating signaling by higher order neurons, to local executive modulation in specific circuits. Additionally, orchestrating neurons receive peptidergic signals from neurons conveying organismal internal state cues and relay these to executive circuits. We exemplify these levels of signaling with four neuropeptides, SIFamide, short neuropeptide F, allatostatin-A and leucokinin, each with a specific expression pattern and level of complexity in signaling.

scholarly journals Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures

2016 ◽  
Author(s):  
Paolo Corti ◽  
Benjamin G Lewis ◽  
Athanasios Tom Kralidis ◽  
Ntabathia Jude Mwenda
Keyword(s):  
Open Source ◽  
Search Engine ◽  
Language Processing ◽  
Spatial Data ◽  
Spatial Information ◽  
National Endowment ◽  
Data Infrastructure ◽  
Advanced Search ◽  
Data Infrastructures ◽  
Spatio Temporal

A Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide an efficient and flexible way to use spatial information. One of the key software components of an SDI is the catalogue service which is needed to discover, query, and manage the metadata. Catalogue services in an SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard which defines common interfaces for accessing the metadata information. A search engine is a software system capable of supporting fast and reliable search, which may use “any means necessary” to get users to the resources they need quickly and efficiently. These techniques may include features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting, recommendations, feedback mechanisms based on log mining, usage statistic gathering, and many others. In this paper we will be focusing on improving geospatial search with a search engine platform that uses Lucene, a Java-based search library, at its core. In work funded by the National Endowment for the Humanities, the Centre for Geographic Analysis (CGA) at Harvard University is in the process of re-engineering the search component of its public domain SDI (WorldMap http://worldmap.harvard.edu ) which is based on the GeoNode platform. In the process the CGA has developed Harvard Hypermap (HHypermap), a map services registry and search platform independent from WorldMap. The goal of HHypermap is to provide a framework for building and maintaining a comprehensive registry of web map services, and because such a registry is expected to be large, the system supports the development of clients with modern search capabilities such as spatial and temporal faceting and instant previews via an open API. Behind the scenes HHypermap scalably harvests OGC and Esri service metadata from distributed servers, organizes that information, and pushes it to a search engine. The system monitors services for reliability and uses that to improve search. End users will be able to search the SDI metadata using standard interfaces provided by the internal CSW catalogue, and will benefit from the enhanced search possibilities provided by an advanced search engine. HHypermap is built on an open source software source stack.

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