TY  - JOUR
A1  - Hake, Tim
A1  - Bodenberger, Bernhard
A1  - Groth, Detlef
T1  - In Python available: St. Nicolas House Algorithm (SNHA) with bootstrap support for improved performance in dense networks
JF  - Human biology and public health
N2  - The St. Nicolas House Algorithm (SNHA) finds association chains of direct dependent variables in a data set. The dependency is based on the correlation coefficient, which is visualized as an undirected graph. The network prediction is improved by a bootstrap routine. It enables the computation of the empirical p-value, which is used to evaluate the significance of the predicted edges. Synthetic data generated with the Monte Carlo method were used to firstly compare the Python package with the original R package, and secondly to evaluate the predicted network using the sensitivity, specificity, balanced classification rate and the Matthew's correlation coefficient (MCC). The Python implementation yields the same results as the R package. Hence, the algorithm was correctly ported into Python. The SNHA scores high specificity values for all tested graphs. For graphs with high edge densities, the other evaluation metrics decrease due to lower sensitivity, which could be partially improved by using bootstrap,while for graphs with low edge densities the algorithm achieves high evaluation scores. The empirical p-values indicated that the predicted edges indeed are significant.
KW  - Python
KW  - correlation
KW  - network reconstruction
KW  - bootstrap
KW  - St. Nicolas House Algorithm
Y1  - 2023
U6  - https://doi.org/10.52905/hbph2023.1.63
SN  - 2748-9957
VL  - 1
PB  - Universitätsverlag Potsdam
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Vi, Son Lang
A1  - Trost, Gerda
A1  - Lange, Peggy
A1  - Czesnick, Hjördis
A1  - Rao, Nishta
A1  - Lieber, Diana
A1  - Laux, Thomas
A1  - Gray, William M.
A1  - Manley, James L.
A1  - Groth, Detlef
A1  - Kappel, Christian
A1  - Lenhard, Michael
T1  - Target specificity among canonical nuclear poly(A) polymerases in plants
 modulates organ growth and pathogen response
JF  - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
 AMERICA
N2  - Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs.
Y1  - 2013
U6  - https://doi.org/10.1073/pnas.1303967110
SN  - 0027-8424
VL  - 110
IS  - 34
SP  - 13994
EP  - 13999
PB  - NATL ACAD SCIENCES
CY  - WASHINGTON
ER  - 
TY  - JOUR
A1  - Hoang, Yen
A1  - Gryzik, Stefanie
A1  - Hoppe, Ines
A1  - Rybak, Alexander
A1  - Schädlich, Martin
A1  - Kadner, Isabelle
A1  - Walther, Dirk
A1  - Vera, Julio
A1  - Radbruch, Andreas
A1  - Groth, Detlef
A1  - Baumgart, Sabine
A1  - Baumgrass, Ria
T1  - PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments
JF  - Frontiers in immunology
N2  - Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data.
KW  - multi-parametric analysis
KW  - re-analysis
KW  - combinatorial protein
KW  - expression
KW  - high-dimensional cytometry data
KW  - mass cytometry data
KW  - pattern perception
Y1  - 2022
U6  - https://doi.org/10.3389/fimmu.2022.849329
SN  - 1664-3224
VL  - 13
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Koziel, Slawomir
A1  - Scheffler, Christiane
A1  - Tutkuviene, Janina
A1  - Jakimaviciene, Egle Marija
A1  - Mumm, Rebekka
A1  - Barbieri, Davide
A1  - Godina, Elena
A1  - El-Shabrawi, Mortada
A1  - Elhusseini, Mona
A1  - Musalek, Martin
A1  - Pruszkowska-Przybylska, Paulina
A1  - El Dash, Hanaa H.
A1  - Safar, Hebatalla Hassan
A1  - Lehmann, Andreas
A1  - Swanson, James
A1  - Bogin, Barry
A1  - Liu, Yuk-Chien
A1  - Groth, Detlef
A1  - Kirchengast, Sylvia
A1  - Siniarska, Anna
A1  - Nieczuja-Dwojacka, Joanna
A1  - Kralik, Miroslav
A1  - Satake, Takashi
A1  - Harc, Tomasz
A1  - Roelants, Mathieu
A1  - Hermanussen, Michael
T1  - Meeting Report: Growth and social environment
BT  - Proceedings of the 25th Aschauer Soiree, held at Krobielowice, Poland, November 18th 2017
JF  - Pediatric Endocrinology Reviews
N2  - Twenty-two scientists met at Krobielowice, Poland, to discuss the impact of the social environment, spatial proximity, migration, poverty, but also psychological factors such as body perception and satisfaction, and social stressors such as elite sports, and teenage pregnancies, on child and adolescent growth. The data analysis included linear mixed effects models with different random effects, Monte Carlo analyses, and network simulations. The work stressed the importance of the peer group, but also included historic material, some considerations about body proportions, and growth in chronic liver, and congenital heart disease.
KW  - Body height
KW  - Social environment
KW  - Strategic growth adjustment
KW  - Competitive growth
KW  - Community effects on growth
Y1  - 2018
U6  - https://doi.org/10.17458/per.vol15.2018.ksh.mr.GrowthSocialEnvironment
SN  - 1565-4753
VL  - 15
IS  - 4
SP  - 319
EP  - 329
PB  - Medical Media
CY  - Netanya
ER  - 
TY  - GEN
A1  - Hermanussen, Michael
A1  - Ipsen, Josefin
A1  - Mumm, Rebekka
A1  - Assmann, Christian
A1  - Quitmann, Julia
A1  - Gomula, Aleksandra
A1  - Lehmann, Andreas
A1  - Jasch, Isabelle
A1  - Tassenaar, Vincent
A1  - Bogin, Barry
A1  - Satake, Takashi
A1  - Scheffler, Christiane
A1  - Nunez, Javier
A1  - Godina, Elena
A1  - Hardeland, Ruediger
A1  - Boldsen, Jesper L.
A1  - El-Shabrawi, Mortada
A1  - Elhusseini, Mona
A1  - Barbu, Carmen Gabriela
A1  - Pop, Ralucca
A1  - Soederhaell, Jani
A1  - Merker, Andrea
A1  - Swanson, James
A1  - Groth, Detlef
T1  - Stunted Growth. Proceedings of the 23rd Aschauer Soiree, Held at Aschauhof, Germany, November 7th 2015
T2  - Pediatric Endocrinology Reviews
N2  - Twenty-four scientists met at Aschauhof, Altenhof, Germany, to discuss the associations between child growth and development, and nutrition, health, environment and psychology. Meta-analyses of body height, height variability and household inequality, in historic and modern growth studies published since 1794, highlighting the enormously flexible patterns of child and adolescent height and weight increments throughout history which do not only depend on genetics, prenatal development, nutrition, health, and economic circumstances, but reflect social interactions. A Quality of Life in Short Stature Youth Questionnaire was presented to cross-culturally assess health-related quality of life in children. Changes of child body proportions in recent history, the relation between height and longevity in historic Dutch samples and also measures of body height in skeletal remains belonged to the topics of this meeting. Bayesian approaches and Monte Carlo simulations offer new statistical tools for the study of human growth.
KW  - Adolescent growth
KW  - Peer group
KW  - Growth hormone
KW  - Community effect
KW  - Body height
Y1  - 2016
SN  - 1565-4753
VL  - 13
SP  - 756
EP  - 767
PB  - Medical Media
CY  - Netanya
ER  -