scholarly journals An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile

2017 ◽  
Vol 24 (3) ◽  
pp. 200-212 ◽  
Author(s):  
Celine Prakash ◽  
Arndt Von Haeseler
Keyword(s):  
Rna Sequencing ◽  
Enumerative Combinatorics ◽  
Starting Point ◽  
Fragmentation Patterns ◽  
Coverage Profile

scholarly journals Cross-Species analysis defines the conservation of anatomically-segregated VMH neuron populations

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alison H Affinati ◽  
Paul V Sabatini ◽  
Cadence True ◽  
Abigail J Tomlinson ◽  
Melissa Kirigiti ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Leptin Receptor ◽  
Affinity Purification ◽  
Species Conservation ◽  
Hypothalamic Nucleus ◽  
Ventromedial Hypothalamic Nucleus ◽  
Neuron Populations ◽  
Starting Point ◽  
Species Analysis ◽  
And Function

The ventromedial hypothalamic nucleus (VMH) controls diverse behaviors and physiologic functions, suggesting the existence of multiple VMH neural subtypes with distinct functions. Combing Translating Ribosome Affinity Purification with RNA sequencing (TRAP-seq) data with snRNA-seq data, we identified 24 mouse VMH neuron clusters. Further analysis, including snRNA-seq data from macaque tissue, defined a more tractable VMH parceling scheme consisting of 6 major genetically- and anatomically-differentiated VMH neuron classes with good cross-species conservation. In addition to two major ventrolateral classes, we identified three distinct classes of dorsomedial VMH neurons. Consistent with previously-suggested unique roles for leptin receptor (Lepr)-expressing VMH neurons, Lepr expression marked a single dorsomedial class. We also identified a class of glutamatergic VMH neurons that resides in the tuberal region, anterolateral to the neuroanatomical core of the VMH. This atlas of conserved VMH neuron populations provides an unbiased starting point for the analysis of VMH circuitry and function.

scholarly journals Analysis of single-cell RNA sequencing data based on autoencoders

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Andrea Tangherloni ◽  
Federico Ricciuti ◽  
Daniela Besozzi ◽  
Pietro Liò ◽  
Ana Cvejic
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Types ◽  
Batch Effect ◽  
Learning Approaches ◽  
Sequencing Data ◽  
Starting Point ◽  
Single Cell Rna Sequencing ◽  
Downstream Analysis ◽  
Low Dimensional

Abstract Background Single-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches. Results Autoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions. Conclusions scAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics.

Crystal structure images of large gold clusters and growing crystals by HRTEM

1984 ◽  
Vol 42 ◽  
pp. 428-429
Author(s):  
L.R. Wallenberg ◽  
J.-O. Bovin ◽  
G. Schmid
Keyword(s):  
Crystal Structure ◽  
Nucleation And Growth ◽  
Close Packing ◽  
Gold Clusters ◽  
Molecular Weight Determination ◽  
Growth Mechanisms ◽  
Starting Point ◽  
Different Types ◽  
Nucleation And Growth Mechanisms ◽  
Points Of View

Metallic clusters are interesting from various points of view, e.g. as a mean of spreading expensive catalysts on a support, or following heterogeneous and homogeneous catalytic events. It is also possible to study nucleation and growth mechanisms for crystals with the cluster as known starting point.Gold-clusters containing 55 atoms were manufactured by reducing (C6H5)3PAuCl with B2H6 in benzene. The chemical composition was found to be Au9.2[P(C6H5)3]2Cl. Molecular-weight determination by means of an ultracentrifuge gave the formula Au55[P(C6H5)3]Cl6 A model was proposed from Mössbauer spectra by Schmid et al. with cubic close-packing of the 55 gold atoms in a cubeoctahedron as shown in Fig 1. The cluster is almost completely isolated from the surroundings by the twelve triphenylphosphane groups situated in each corner, and the chlorine atoms on the centre of the 3x3 square surfaces. This gives four groups of gold atoms, depending on the different types of surrounding.

Two isoprenylated flavonoids from Dorstenia psilurus activate AMPK, stimulate glucose uptake, inhibit glucose production and lower glycemia

2019 ◽  
Vol 476 (24) ◽  
pp. 3687-3704 ◽  
Author(s):  
Aphrodite T. Choumessi ◽  
Manuel Johanns ◽  
Claire Beaufay ◽  
Marie-France Herent ◽  
Vincent Stroobant ◽  
...  
Keyword(s):  
Glucose Uptake ◽  
Human Cancer ◽  
Glucose Production ◽  
Liver Mitochondria ◽  
New Drugs ◽  
Structural Isomer ◽  
Rat Liver Mitochondria ◽  
Ionization Mass ◽  
Ampk Activation ◽  
Starting Point

Root extracts of a Cameroon medicinal plant, Dorstenia psilurus, were purified by screening for AMP-activated protein kinase (AMPK) activation in incubated mouse embryo fibroblasts (MEFs). Two isoprenylated flavones that activated AMPK were isolated. Compound 1 was identified as artelasticin by high-resolution electrospray ionization mass spectrometry and 2D-NMR while its structural isomer, compound 2, was isolated for the first time and differed only by the position of one double bond on one isoprenyl substituent. Treatment of MEFs with purified compound 1 or compound 2 led to rapid and robust AMPK activation at low micromolar concentrations and increased the intracellular AMP:ATP ratio. In oxygen consumption experiments on isolated rat liver mitochondria, compound 1 and compound 2 inhibited complex II of the electron transport chain and in freeze–thawed mitochondria succinate dehydrogenase was inhibited. In incubated rat skeletal muscles, both compounds activated AMPK and stimulated glucose uptake. Moreover, these effects were lost in muscles pre-incubated with AMPK inhibitor SBI-0206965, suggesting AMPK dependency. Incubation of mouse hepatocytes with compound 1 or compound 2 led to AMPK activation, but glucose production was decreased in hepatocytes from both wild-type and AMPKβ1−/− mice, suggesting that this effect was not AMPK-dependent. However, when administered intraperitoneally to high-fat diet-induced insulin-resistant mice, compound 1 and compound 2 had blood glucose-lowering effects. In addition, compound 1 and compound 2 reduced the viability of several human cancer cells in culture. The flavonoids we have identified could be a starting point for the development of new drugs to treat type 2 diabetes.

Overview of Current Approaches to Aural Rehabilitation for Adults With Cochlear Implants

2020 ◽  
Vol 5 (5) ◽  
pp. 1175-1187
Author(s):  
Rachel Glade ◽  
Erin Taylor ◽  
Deborah S. Culbertson ◽  
Christin Ray
Keyword(s):  
Health Care ◽  
Clinical Practice ◽  
Cochlear Implants ◽  
Practice Patterns ◽  
The United States ◽  
Care Providers ◽  
Aural Rehabilitation ◽  
Starting Point ◽  
Clinical Models ◽  
Hearing Health

Purpose This clinical focus article provides an overview of clinical models currently being used for the provision of comprehensive aural rehabilitation (AR) for adults with cochlear implants (CIs) in the Unites States. Method Clinical AR models utilized by hearing health care providers from nine clinics across the United States were discussed with regard to interprofessional AR practice patterns in the adult CI population. The clinical models were presented in the context of existing knowledge and gaps in the literature. Future directions were proposed for optimizing the provision of AR for the adult CI patient population. Findings/Conclusions There is a general agreement that AR is an integral part of hearing health care for adults with CIs. While the provision of AR is feasible in different clinical practice settings, service delivery models are variable across hearing health care professionals and settings. AR may include interprofessional collaboration among surgeons, audiologists, and speech-language pathologists with varying roles based on the characteristics of a particular setting. Despite various existing barriers, the clinical practice patterns identified here provide a starting point toward a more standard approach to comprehensive AR for adults with CIs.

Indirect Assessment of Attitudes with Response-Time-Based Measures

2006 ◽  
Vol 37 (3) ◽  
pp. 131-139 ◽  
Author(s):  
Juliane Degner ◽  
Dirk Wentura ◽  
Klaus Rothermund
Keyword(s):  
Social Cognitive ◽  
Incremental Validity ◽  
Self Report ◽  
Small Scale ◽  
Implicit Measures ◽  
Scale Theory ◽  
Starting Point ◽  
Self Reports ◽  
Predicting Behavior ◽  
Social Cognitive Theories

Abstract: We review research on response-latency based (“implicit”) measures of attitudes by examining what hopes and intentions researchers have associated with their usage. We identified the hopes of (1) gaining better measures of interindividual differences in attitudes as compared to self-report measures (quality hope); (2) better predicting behavior, or predicting other behaviors, as compared to self-reports (incremental validity hope); (3) linking social-cognitive theories more adequately to empirical research (theory-link hope). We argue that the third hope should be the starting point for using these measures. Any attempt to improve these measures should include the search for a small-scale theory that adequately explains the basic effects found with such a measure. To date, small-scale theories for different measures are not equally well developed.

The Solidarity of Distance1

2005 ◽  
Vol 36 (3) ◽  
pp. 103-115 ◽  
Author(s):  
Robert A. Wicklund
Keyword(s):  
Physical Contact ◽  
Emotional Distance ◽  
Starting Point ◽  
Shared Emotions ◽  
Common Goals ◽  
Full Interaction ◽  
The Individual ◽  
Social Incompetence

Abstract: Solidarity in the classic sense pertains to a cohesion among humans that entails physical contact, shared emotions, and common goals or projects. Characteristic cases are to be found among families, close friends, or co-workers. The present paper, in contrast, treats a phenomenon of the solidarity of distance, a solidarity based in fear of certain others and in incompetence to interact with them. The starting point for this analysis is the person who is motivated to interact with others who are unfamiliar or fear-provoking. Given that the fear and momentary social incompetence do not allow a full interaction to ensue, the individual will move toward solidarity with those others on a symbolic level. In this manner the motivation to approach the others is acted upon while physical and emotional distance is retained.

A Starting Point for Inquiry Into Inquiry

PsycCRITIQUES ◽  
2006 ◽  
Vol 51 (4) ◽  
Author(s):  
Joseph L. Polman
Keyword(s):  
Starting Point

Study interest in technology and psychology: The starting point.

1989 ◽  
Author(s):  
Bengt Jansson ◽  
Britt-Marie Drottz ◽  
Lennart Sjoeberg
Keyword(s):  
Starting Point ◽  
Interest In Technology
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