Search results for "Toolbox"

Using mathematical morphology for unsupervised classification of functional data

2011

This paper is concerned with the unsupervised classification of functional data by using mathematical morphology. Different morphological operators are used to extract relevant structures of the functions (considered as sets through their subgraph representations). These operators can be considered as preprocessing tools whose outputs are also functional data. We explore some dissimilarity measures and clustering methods for the classification of the transformed data. Our approach is illustrated through a detailed analysis of two data sets. These techniques, which have mainly been used in image processing, provide a flexible and robust toolbox for improving the results in unsupervised funct…

NeoFox: annotating neoantigen candidates with neoantigen features

2020

Abstract Summary The detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features. Availability and implementation NeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox. Supplementary information Supplementary data are available at Bioinformatics online.

Integrative Gene Expression and Metabolic Analysis Tool IgemRNA

2022

ABSTRACTGenome scale metabolic modelling is widely used technique to research metabolism impacts on organism’s properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome…

Reactive Polymers: A Versatile Toolbox for the Immobilization of Functional Molecules on TiO2 Nanoparticles

2006

Teaching master's degree students to read research literature

2017

The skill to read research literature critically belongs in every university graduate’s toolbox. I have attempted to teach this skill in a master’s degree level course in programming languages over 15 years using, at various times, simulated conferences, voluntary reading exercises, evidence-based practice training, and a flipped classroom with mandatory reading assignments. I discuss my experience and analyze preliminary qualitative data on the use of evidence-based practice and a flipped classroom for this purpose. I present no firm conclusions, but expect that future work (by me or others) will be able to use my experience as a baseline for better teaching of research literature reading.…

Cortical networks show characteristic recruitment patterns after somatosensory stimulation by pneumatically evoked repetitive hand movements in newbo…

2022

Abstract Controlled assessment of functional cortical networks is an unmet need in the clinical research of noncooperative subjects, such as infants. We developed an automated, pneumatic stimulation method to actuate naturalistic movements of an infant’s hand, as well as an analysis pipeline for assessing the elicited electroencephalography (EEG) responses and related cortical networks. Twenty newborn infants with perinatal asphyxia were recruited, including 7 with mild-to-moderate hypoxic–ischemic encephalopathy (HIE). Statistically significant corticokinematic coherence (CKC) was observed between repetitive hand movements and EEG in all infants, peaking near the contralateral sensorimotor…

Crop Nitrogen Retrieval Methods for Simulated Sentinel-2 Data Using In-Field Spectrometer Data.

2021

Nitrogen (N) is one of the key nutrients supplied in agricultural production worldwide. Over-fertilization can have negative influences on the field and the regional level (e.g., agro-ecosystems). Remote sensing of the plant N of field crops presents a valuable tool for the monitoring of N flows in agro-ecosystems. Available data for validation of satellite-based remote sensing of N is scarce. Therefore, in this study, field spectrometer measurements were used to simulate data of the Sentinel-2 (S2) satellites developed for vegetation monitoring by the ESA. The prediction performance of normalized ratio indices (NRIs), random forest regression (RFR) and Gaussian processes regression (GPR) f…

Neural Mechanisms of Acceptance and Commitment Therapy for Chronic Pain: A Network-Based fMRI Approach

2021

AbstractOver 100 million Americans suffer from chronic pain (CP), which causes more disability than any other medical condition in the U.S. at a cost of $560-$635 billion per year (IOM, 2011). Opioid analgesics are frequently used to treat CP. However, long term use of opioids can cause brain changes such as opioid-induced hyperalgesia that, over time, increase pain sensation. Also, opioids fail to treat complex psychological factors that worsen pain-related disability, including beliefs about and emotional responses to pain. Cognitive behavioral therapy (CBT) can be efficacious for CP. However, CBT generally does not focus on important factors needed for long-term functional improvement, i…

An Emulator Toolbox to Approximate Radiative Transfer Models with Statistical Learning

2015

Physically-based radiative transfer models (RTMs) help in understanding the processes occurring on the Earth’s surface and their interactions with vegetation and atmosphere. When it comes to studying vegetation properties, RTMs allows us to study light interception by plant canopies and are used in the retrieval of biophysical variables through model inversion. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. Emulators are advantageous in real practice because…

Musiikillisen vuorovaikutuksen dynamiikkaa : tapaustutkimus musiikkiterapiassa soitetuista improvisaatioista

2012

Tässä kandidaatin tutkielmassa tutkitaan psykodynaamisen musiikkiterapiajakson aikana soitettuja improvisaatioita musiikkiterapeuttiseen käyttöön kehiteltyjen musiikkianalyysimenetelmin. Tutkimuksen tarkoituksena on tarkastella asiakkaan ja terapeutin välistä musiikillista vuorovaikutusta, musiikin dynamiikkaa ja siinä tapahtuvia muutoksia terapian kaaressa. Tutkimuksen aineisto on osa Jyväskylän yliopiston musiikin laitoksella tehtyä kansainvälistä Braintuning- tutkimusta, jossa selvitettiin improvisaatiolle pohjautuvan musiikkiterapian vaikutusta masennuksesta toipumiseen. Tämän tutkimuksen aineisto koostuu yhden asiakkaan musiikkiterapiassa soitettujen improvisaatioiden äänitteistä. Musi…