scholarly journals Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sergio Marco Salas ◽  
Daniel Gyllborg ◽  
Christoffer Mattsson Langseth ◽  
Mats Nilsson
Keyword(s):  
De Novo ◽  
Comprehensive Analysis ◽  
Computational Techniques ◽  
Simple Analysis ◽  
Spatially Resolved ◽  
Coronal Section ◽  
User Friendly ◽  
Different Levels ◽  
Initial Exploration

Abstract Background A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computational techniques are developed to facilitate data analysis. There is also a need for versatile user friendly tools that can be used for a de novo exploration of datasets. Results Here we present MATLAB-based Analysis toolbox for in situ sequencing (ISS) expression maps (Matisse). We demonstrate Matisse by characterizing the 2-dimensional spatial expression of 119 genes profiled in a mouse coronal section, exploring different levels of complexity. Additionally, in a comprehensive analysis, we further analyzed expression maps from a second technology, osmFISH, targeting a similar mouse brain region. Conclusion Matisse proves to be a valuable tool for initial exploration of in situ sequencing datasets. The wide set of tools integrated allows for simple analysis, using the position of individual reads, up to more complex clustering and dimensional reduction approaches, taking cellular content into account. The toolbox can be used to analyze one or several samples at a time, even from different spatial technologies, and it includes different segmentation approaches that can be useful in the analysis of spatially resolved transcriptomic datasets.

FT-IR microspectroscopic analysis of diseased white matter brain tissues

1995 ◽  
Vol 53 ◽  
pp. 968-969
Author(s):  
Steven M. Le Vine ◽  
David L. Wetzel
Keyword(s):  
White Matter ◽  
Gray Matter ◽  
Twitcher Mouse ◽  
Grid Pattern ◽  
Marked Contrast ◽  
Spatially Resolved ◽  
Ft Ir ◽  
Ir Microspectroscopy ◽  
Chemical Evidence

In situ FT-IR microspectroscopy has allowed spatially resolved interrogation of different parts of brain tissue. In previous work the spectrrscopic features of normal barin tissue were characterized. The white matter, gray matter and basal ganglia were mapped from appropriate peak area measurements from spectra obtained in a grid pattern. Bands prevalent in white matter were mostly associated with the lipid. These included 2927 and 1469 cm-1 due to CH2 as well as carbonyl at 1740 cm-1. Also 1235 and 1085 cm-1 due to phospholipid and galactocerebroside, respectively (Figs 1and2). Localized chemical changes in the white matter as a result of white matter diseases have been studied. This involved the documentation of localized chemical evidence of demyelination in shiverer mice in which the spectra of white matter lacked the marked contrast between it and gray matter exhibited in the white matter of normal mice (Fig. 3).The twitcher mouse, a model of Krabbe’s desease, was also studied. The purpose in this case was to look for a localized build-up of psychosine in the white matter caused by deficiencies in the enzyme responsible for its breakdown under normal conditions.

Manifestations of the bias of an unreliable narrator in novel by V. Domontovich “Doctor Serafikus”

2018 ◽  
pp. 132-138
Author(s):  
М. І. Підодвірна
Keyword(s):  
Narrative Analysis ◽  
Focal Point ◽  
Comprehensive Analysis ◽  
The Novel ◽  
Personal Interest ◽  
Cognitive Approach ◽  
Personal Story ◽  
Unreliable Narrator ◽  
German Researcher ◽  
Different Levels

The results and achievements of the main schools and directions of naratology indicate the need to reread both well-known and recondite texts in order to spell out the meanings. We believe that the narrative analysis of prose by Victor Domontovich (the Ukrainian intellectual writer) is interesting and relevant. The article attempts to characterize the manifestations of the bias of an unreliable narato in the novel “Doctor Seraficus” based on the A. Nyuninga’s cognitive approach. A modern German researcher provides a set of tools that can supplemented for a multidimensional consideration of all ambiguities and contradictions in the text. An intelligent game that unfolds in the text manifests itself at different levels. V. Domontovych conducts the biggest game, the game with meaning through the pending authority of unreliable presenter. The text of the novel consists of abstract reflections, notes, dreams, illusions, fantasies, dreams and retrospective journeys. The main law of the text is the game. Irony and contradictions in the narrator’s words encourage the reader to feel dissonance, uncertainty. Therefore, in a narrative analysis, attention is focused on the speaker and who sees (the focal point). It was investigated that the artist Corvin is the narrator of the novel “Doctor Serafikus”, he tries to give as much as possible objectively the personal story. The motives for the unreliability narration based on the personal interest and bias of the character are determined. We identified the main symptoms of the unreliability of the narrator in the work, and the different levels at which the corresponding narrative is expressed, are highlighted. It is established that an unreliable narrative forces distancing itself from a narrator and takes everything that has been said with caution and detachment. Detailed narrative analysis of the work sheds light on the meanings, which for some reason masked, and allows you to establish artistic functions of an unreliable narrator. We believe that understanding this phenomenon makes it possible to make a comprehensive analysis of artistic text.

scholarly journals Spatially Resolved Experimental Modal Analysis on High-Speed Composite Rotors Using a Non-Contact, Non-Rotating Sensor

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4705
Author(s):  
Julian Lich ◽  
Tino Wollmann ◽  
Angelos Filippatos ◽  
Maik Gude ◽  
Juergen Czarske ◽  
...  
Keyword(s):  
High Speed ◽  
Natural Frequencies ◽  
Mode Shapes ◽  
Fiber Reinforced ◽  
Structural Dynamic ◽  
Spatially Resolved ◽  
Glass Fiber Reinforced ◽  
Vibration Responses ◽  
And Performance

Due to their lightweight properties, fiber-reinforced composites are well suited for large and fast rotating structures, such as fan blades in turbomachines. To investigate rotor safety and performance, in situ measurements of the structural dynamic behaviour must be performed during rotating conditions. An approach to measuring spatially resolved vibration responses of a rotating structure with a non-contact, non-rotating sensor is investigated here. The resulting spectra can be assigned to specific locations on the structure and have similar properties to the spectra measured with co-rotating sensors, such as strain gauges. The sampling frequency is increased by performing consecutive measurements with a constant excitation function and varying time delays. The method allows for a paradigm shift to unambiguous identification of natural frequencies and mode shapes with arbitrary rotor shapes and excitation functions without the need for co-rotating sensors. Deflection measurements on a glass fiber-reinforced polymer disk were performed with a diffraction grating-based sensor system at 40 measurement points with an uncertainty below 15 μrad and a commercial triangulation sensor at 200 measurement points at surface speeds up to 300 m/s. A rotation-induced increase of two natural frequencies was measured, and their mode shapes were derived at the corresponding rotational speeds. A strain gauge was used for validation.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

scholarly journals Associations between Amplification (1q) and Prior Cancer in a Real-World De Novo Myeloma Cohort

2021 ◽  
Author(s):  
Elizabeth B Lamont ◽  
Andrew J Yee ◽  
Stuart L Goldberg ◽  
David S Siegel ◽  
Andrew D Norden
Keyword(s):  
Real World ◽  
Fluorescent In Situ Hybridization ◽  
De Novo ◽  
Chromosome 1 ◽  
Second Malignancies ◽  
Cancer History ◽  
Screening Strategies ◽  
Cytogenetic Testing

Abstract Genomic biomarkers inform treatment in multiple myeloma (MM) making patient clinical data a potential window into MM biology. We evaluated de novo MM patients for associations between specific MM cytogenetic patterns and prior cancer history. Analyzing a MM real-world dataset (RWD), we identified a cohort of 1,769 patients with fluorescent in-situ hybridization (FISH) cytogenetic testing at diagnosis. Fully 241 patients (0.14) had histories of prior cancer(s). Amplification of the long arm of chromosome 1 [amp(1q)] varied by prior cancer history (0.31 with prior cancer vs 0.24 without; p = .02). No other MM translocations, amplifications, or deletions were associated with prior cancers. Amp(1q) and cancer history remained strongly associated in a logistic regression adjusting for patient demographic and disease attributes. The results merit follow-up regarding carcinogenic treatment effects and screening strategies for second malignancies. Broadly the findings suggest analyses of patient-level phenotypic-genomic RWD may accelerate cancer research through hypothesis generating studies.

scholarly journals Velody 2—Resilient High-Capacity MIDI Steganography for Organ and Harpsichord Music

2020 ◽  
Vol 11 (1) ◽  
pp. 39
Author(s):  
Eric Järpe ◽  
Mattias Weckstén
Keyword(s):  
Mean Absolute Error ◽  
Signal To Noise Ratio ◽  
High Capacity ◽  
Absolute Error ◽  
Music Technology ◽  
Alternative Methods ◽  
File Size ◽  
User Friendly ◽  
Different Levels ◽  
Better Than

A new method for musical steganography for the MIDI format is presented. The MIDI standard is a user-friendly music technology protocol that is frequently deployed by composers of different levels of ambition. There is to the author’s knowledge no fully implemented and rigorously specified, publicly available method for MIDI steganography. The goal of this study, however, is to investigate how a novel MIDI steganography algorithm can be implemented by manipulation of the velocity attribute subject to restrictions of capacity and security. Many of today’s MIDI steganography methods—less rigorously described in the literature—fail to be resilient to steganalysis. Traces (such as artefacts in the MIDI code which would not occur by the mere generation of MIDI music: MIDI file size inflation, radical changes in mean absolute error or peak signal-to-noise ratio of certain kinds of MIDI events or even audible effects in the stego MIDI file) that could catch the eye of a scrutinizing steganalyst are side-effects of many current methods described in the literature. This steganalysis resilience is an imperative property of the steganography method. However, by restricting the carrier MIDI files to classical organ and harpsichord pieces, the problem of velocities following the mood of the music can be avoided. The proposed method, called Velody 2, is found to be on par with or better than the cutting edge alternative methods regarding capacity and inflation while still possessing a better resilience against steganalysis. An audibility test was conducted to check that there are no signs of audible traces in the stego MIDI files.

scholarly journals Giant Cell Carcinosarcoma of the Parotid Gland With a PLAG 1 Translocation in Association With a Pleomorphic Adenoma With HMGA2 Translocation

2020 ◽  
Vol 154 (6) ◽  
pp. 811-815
Author(s):  
Levon Katsakhyan ◽  
Virginia A LiVolsi ◽  
Ara A Chalian ◽  
Paul J Zhang
Keyword(s):  
Salivary Gland ◽  
In Situ Hybridization ◽  
Parotid Gland ◽  
Giant Cell ◽  
Pleomorphic Adenoma ◽  
De Novo ◽  
Sarcomatous Component ◽  
Gland Tumor ◽  
Parotid Gland Tumor

Abstract Objectives Carcinosarcomas of the salivary gland are rare neoplasms and have been described arising de novo or in association with pleomorphic adenoma (PA). PLAG1 and HMGA2 translocations are known to occur in PAs and carcinomas ex PA but are mutually exclusive. Methods We report a case of a carcinosarcoma in the parotid gland of a 77-year-old man with unusual anaplastic sarcomatoid giant cell morphology. Results Microscopically, a small separate PA was found adjacent to the carcinosarcoma. By conventional notion, the PA and carcinosarcoma would be considered related, as carcinosarcomas are well known to arise from PAs (carcinosarcoma ex PA). However, fluorescence in situ hybridization (FISH) assay demonstrated PLAG1 translocation in the carcinosarcoma and HMGA2 translocation in the separate PA. Conclusions These findings support that the carcinosarcoma likely originated from another PA with a PLAG1 translocation or de novo but not from the coexisting PA harboring a different translocation. To our knowledge, the case is the first to demonstrate PLAG1 translocation by FISH in a sarcomatous component of any parotid gland tumor, which may help better classify these tumors. In addition, multiple PAs are commonly found in the salivary gland, and to our knowledge, our case is the first to demonstrate that the same parotid gland can host PAs and PA-related tumors with different translocations.

scholarly journals Airborne determination of the temporo-spatial distribution of benzene, toluene, nitrogen oxides and ozone in the boundary layer across Greater London, UK

2015 ◽  
Vol 15 (9) ◽  
pp. 5083-5097 ◽  
Author(s):  
M. D. Shaw ◽  
J. D. Lee ◽  
B. Davison ◽  
A. Vaughan ◽  
R. M. Purvis ◽  
...  
Keyword(s):  
Boundary Layer ◽  
Nitrogen Oxides ◽  
Linear Regression Analysis ◽  
Proton Transfer Reaction ◽  
Mixing Ratios ◽  
Spatially Resolved ◽  
Dual Channel ◽  
Benzene Toluene

Abstract. Highly spatially resolved mixing ratios of benzene and toluene, nitrogen oxides (NOx) and ozone (O3) were measured in the atmospheric boundary layer above Greater London during the period 24 June to 9 July 2013 using a Dornier 228 aircraft. Toluene and benzene were determined in situ using a proton transfer reaction mass spectrometer (PTR-MS), NOx by dual-channel NOx chemiluminescence and O3 mixing ratios by UV absorption. Average mixing ratios observed over inner London at 360 ± 10 m a.g.l. were 0.20 ± 0.05, 0.28 ± 0.07, 13.2 ± 8.6, 21.0 ± 7.3 and 34.3 ± 15.2 ppbv for benzene, toluene, NO, NO2 and NOx respectively. Linear regression analysis between NO2, benzene and toluene mixing ratios yields a strong covariance, indicating that these compounds predominantly share the same or co-located sources within the city. Average mixing ratios measured at 360 ± 10 m a.g.l. over outer London were always lower than over inner London. Where traffic densities were highest, the toluene / benzene (T / B) concentration ratios were highest (average of 1.8 ± 0.5 ppbv ppbv-1), indicative of strong local sources. Daytime maxima in NOx, benzene and toluene mixing ratios were observed in the morning (~ 40 ppbv NOx, ~ 350 pptv toluene and ~ 200 pptv benzene) and in the mid-afternoon for ozone (~ 40 ppbv O3), all at 360 ± 10 m a.g.l.

scholarly journals Ultrastructural Studies of Human Basophils and Mast Cells

2005 ◽  
Vol 53 (9) ◽  
pp. 1043-1070 ◽  
Author(s):  
Ann M. Dvorak
Keyword(s):  
Growth Factor ◽  
Mast Cells ◽  
Cord Blood ◽  
Blood Cells ◽  
De Novo ◽  
Ultrastructural Studies ◽  
Specific Growth Factor ◽  
Cord Blood Cells ◽  
Human Basophils

Ultrastructural studies of human mast cells (HMCs) and basophils (HBs) are reviewed. Sources of HMCs include biopsies of tissue sites and in situ study of excised diseased organs; isolated, partially purified samples from excised organs; and growth-factor-stimulated mast cells that develop de novo in cultures of cord blood cells. Sources of HBs for study include partially purified peripheral blood basophils, basophils in tissue biopsies, and specific growth factor-stimulated basophils arising de novo from cord blood cells. The ultrastructural studies reviewed deal with identity, secretion, vesicles, recovery, and synthesis issues related to the biology of these similar cells.

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