scholarly journals MotifBoost: k-mer based data-efficient immune repertoire classification method

2021 ◽  
Author(s):  
Yotaro Katayama ◽  
Tetsuya J Kobayashi
Keyword(s):  
Large Datasets ◽  
Sequence Motifs ◽  
Immune Repertoire ◽  
Complementary Information ◽  
Basic Task ◽  
Repertoire Analysis ◽  
Further Development ◽  
Clinical Problems ◽  
Generation Sequencing

The repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing. In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that the their performances are impaired catastrophically below critical sample sizes. To overcome this, we propose MotifBoost, which exploits the information of short motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of motifs as representation features of repertoires. Finally, by comparing predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.

A Taxonomy for Psycho-Oncological Intervention Techniques in an Acute Care Hospital in Germany

2021 ◽  
pp. 1-7
Author(s):  
Martina Madl ◽  
Marietta Lieb ◽  
Katharina Schieber ◽  
Tobias Hepp ◽  
Yesim Erim
Keyword(s):  
Acute Care ◽  
Interrater Reliability ◽  
Acute Care Hospital ◽  
Future Research ◽  
Systematic Research ◽  
Care Hospital ◽  
Certification System ◽  
Stepwise Procedure ◽  
Further Development

<b><i>Background:</i></b> Due to the establishment of a nationwide certification system for cancer centers in Germany, the availability of psycho-oncological services for cancer patients has increased substantially. However, little is known about the specific intervention techniques that are applied during sessions in an acute care hospital, since a standardized taxonomy is lacking. With this study, we aimed at the investigation of psycho-oncological intervention techniques and the development of a comprehensive and structured taxonomy thereof. <b><i>Methods:</i></b> In a stepwise procedure, a team of psycho-oncologists generated a data pool of interventions and definitions that were tested in clinical practice during a pilot phase. After an adaptation of intervention techniques, interrater reliability (IRR) was attained by rating 10 previously recorded psycho-oncological sessions. A classification of interventions into superordinate categories was performed, supported by cluster analysis. <b><i>Results:</i></b> Between April and June 2017, 980 psycho-oncological sessions took place. The experts agreed on a total number of 22 intervention techniques. An IRR of 89% for 2 independent psycho-oncological raters was reached. The 22 techniques were classified into 5 superordinate categories. <b><i>Discussion/Conclusion:</i></b> We developed a comprehensive and structured taxonomy of psycho-oncological intervention techniques in an acute care hospital that provides a standardized basis for systematic research and applied care. We expect our work to be continuously subjected to further development: future research should evaluate and expand our taxonomy to other contexts and care settings.

scholarly journals ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Anke Fähnrich ◽  
Moritz Krebbel ◽  
Normann Decker ◽  
Martin Leucker ◽  
Felix D. Lange ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis

scholarly journals System development for its disclosure of Portuguese digital type design

2016 ◽  
Author(s):  
Vítor Quelhas ◽  
Vasco Branco ◽  
Rui Mendonça
Keyword(s):  
Early Stage ◽  
System Development ◽  
Complete Agreement ◽  
Collaborative System ◽  
Test And Evaluation ◽  
Usability Tests ◽  
Type Design ◽  
Third Stage ◽  
Further Development

This study aims to cover the current development of a platform for the disclosure of the Portuguese type design community, since the beginning of the desktop revolution, until today. 
To deepen our understanding, interviews were made to a selected and representative group of type designers from our sample based on several criteria. The interview tested six dimensions: people, processes, products, uses, identity and platform. The results analyzed in the last dimension, through content analysis and quantitative data, lead to the development of an online digital collaborative system – one of our specific objectives. 
Our hypothesis – that the development of a online digital collaborative system would allow further development of knowledge between products, users and authors, as well as, processes and uses – was also corroborated by the interviewers. 
Reviews have been made to reference international online projects to identify their purposes, areas of activity, objectives, mechanisms of interaction, usability and accessibility. This previous research brought together a set of notes that would become essential in the definition and development of our concept. 

The classification of typefaces is a subject of study by researchers and designers, but it is certainly not a topic for complete agreement. Organizing and balancing the content for the database was our first challenge since we were expecting users with good knowledge on the field, but also beginners. Several diagrams were put into test during the early stage of information architecture to better define categories, filters, and sorting methods, as well as users role in the system. The items and categories chosen were redefined in a second stage, and in the third stage hi-fidelity wireframes were produced, to concentrate on design aspects and decisions, and put the system into test and evaluation. 

The current results on the platform development, with the improvements made through several user tests, evaluations and refinements undertaken in all phases of the project have been crucial. We are expecting to run some pilot tests, as well as usability tests prior to the full implementation to further improve the system and meet the expectations.DOI: http://dx.doi.org/10.4995/IFDP.2016.3351

scholarly journals Application of neuron networks of deep learning for exposures editing of digital phonograms

2020 ◽  
Vol 65 (4) ◽  
pp. 506-512
Author(s):  
V. I. Solovyov ◽  
O. V. Rybalskiy ◽  
V. V. Zhuravel ◽  
V. K. Zheleznyak
Keyword(s):  
Deep Learning ◽  
Binary Classification ◽  
Maximum Size ◽  
Maximum Efficiency ◽  
Correct Classification ◽  
Digital Audio ◽  
Neuron Networks ◽  
Effective System ◽  
Further Development

Possibility of creation of effective system, which is intended for exposure of tracks of editing in digital phonograms and is built on the basis of neuron networks of the deep learning, is experimentally proven. Sense of experiment consisted in research of ability of the systems on the basis of such networks to expose pauses with tracks of editing. The experimental array of data is created in a voice editor from phonograms written on the different apparatus of the digital audio recording (at frequency of discretisation 44,1 kHz). A preselection of pauses was produced from it, having duration from 100 мs to a few seconds. From 1000 selected pauses the array of fragments of pauses is formed in the automatic (computer) mode, from which the arrays of fragments of pauses of different duration are generated by a dimension about 100 000. For forming of array of fragments of pauses with editing, the chosen pauses were divided into casual character parts in arbitrary correlation. Afterwards, the new pauses were created from it with the fixed place of editing. The general array of all fragments of pauses was broken into training and test arrays. The maximum efficiency, achieved on a test array in the process of educating, was determined. In general case this efficiency is determined by the maximum size of probability of correct classification of fragments with editing and fragments without editing. Scientifically reasonable methodology of exposure of signs of editing in digital phonograms is offered on the basis of neuron networks of the deep learning. The conducted experiments showed that the construction of the effective system is possible for the exposure of such tracks. Further development of methodology must be directed to find the ways to increase the probability of correct binary classification of investigated pauses.

scholarly journals Advances in application of nanomaterials in remediation of heavy metal contaminated soil

2021 ◽  
Vol 261 ◽  
pp. 04027
Author(s):  
Na Ding ◽  
Mengxuan Han ◽  
Yao He ◽  
Xinshuai Wang ◽  
Yuxuan Pan ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Contaminated Soil ◽  
Environmental Problem ◽  
High Reactivity ◽  
Large Specific Surface Area ◽  
Remediation Technology ◽  
Strong Adsorption ◽  
Combination Technology ◽  
Further Development

Soil heavy metal pollution has become an environmental problem that has attracted worldwide attention. Nanomaterials have the advantages of large specific surface area, strong adsorption capacity and high reactivity, making nanomaterials remediation technology an excellent application prospect in contaminated soil remediation. This article introduces the main classification of nanomaterials, summarizes the mechanism of nanomaterials to remove heavy metals, and the combination technology of nanomaterials. It provides a scientific reference for the further development of this field.

scholarly journals Next-Generation Sequencing Mutational Landscape and Clinical Features of Chinese Adults with Myeloproliferative Neoplasms

2021 ◽  
Author(s):  
Shuna Luo ◽  
Zanzan Wang ◽  
Xiaofei Xu ◽  
Lan Zhang ◽  
Shengjie Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comprehensive Evaluation ◽  
Myeloproliferative Neoplasms ◽  
Primary Myelofibrosis ◽  
Next Generation ◽  
Chinese Adults ◽  
Leukocyte Counts ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background: Myeloproliferative neoplasms (MPNs) include three classical subtypes: polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Since prefibrotic primary myelofibrosis (pre-PMF) was recognized as a separate entity in the 2016 revised classification of MPN, it has been a subject of debate among experts due to its indefinite diagnosis. However, pre-PMF usually has a distinct outcome compared with either ET or overt PMF. In this study, we examined the clinical, haematologic, genetic, and prognostic differences among pre-PMF, ET, and overt PMF.Methods: We retrospectively reviewed the clinical parameters, haematologic information, and genetic mutations of patients who were diagnosed with pre-PMF, ET, and overt PMF according to the WHO 2016 criteria using next-generation sequencing (NGS).Results: Pre-PMF patients exhibited higher leukocyte counts, higher LDH values, a higher frequency of splenomegaly, and a higher incidence of hypertension than ET patients. On the other hand, pre-PMF patients had higher platelet counts and haemoglobin levels than overt PMF patients. Molecular analysis revealed that the frequency of EP300 mutations was significantly increased in pre-PMF patients compared with ET and overt PMF patients. In terms of outcome, male sex, along with symptoms including MPN-10, anaemia, thrombocytopenia, and KMT2A and CUX1 mutations, indicated a poor prognosis for PMF patients.Conclusion: The results of this study indicated that comprehensive evaluation of BM features, clinical phenotypes, haematologic parameters, and molecular profiles is needed for the accurate diagnosis and treatment of ET, pre-PMF, and overt PMF patients.

scholarly journals High-throughput immune repertoire analysis with IGoR

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Quentin Marcou ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
High Throughput ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis
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