Biology subjects

Gerber, D.

Publications and source records attributed to Gerber, D..

3 recordsLinked to original sources

bioRxiv2018

Inner Asian maternal genetic origin of the Avar period nomadic elite in the 7th century AD Carpathian Basin

After 568 AD the nomadic Avars settled in the Carpathian Basin and founded their empire, which was an important force in Central Europe until the beginning of the 9th century AD. The Avar elite was probably of Inner Asian origin; its identification with the Rourans (who ruled the region of todays Mongolia and North China in the 4th-6th centuries AD) is widely accepted in the historical research.\n\nHere, we study the whole mitochondrial genomes of twenty-three 7th century and two 8th century AD individuals from a well-characterised Avar elite group of burials excavated in Hungary. Most of them were buried with high value prestige artefacts and their skulls showed Mongoloid morphological traits.\n\nThe majority (64%) of the studied samples mitochondrial DNA variability belongs to Asian haplogroups (C, D, F, M, R, Y and Z). This Avar elite group shows affinities to several ancient and modern Inner Asian populations.\n\nThe genetic results verify the historical thesis on the Inner Asian origin of the Avar elite, as not only a military retinue consisting of armed men, but an endogamous group of families migrated. This correlates well with records on historical nomadic societies where maternal lineages were as important as paternal descent.

genomics↗

bioRxiv2018

Development and Validation of a Nomogram Prognostic Model for Small-Cell Lung Cancer Patients

BackgroundSmall-cell lung cancer (SCLC) accounts for almost 15% of lung cancer cases in the United States. Nomogram prognostic models could greatly facilitate risk stratification and treatment planning, as well as more refined enrollment criteria for clinical trials. We developed and validated a new nomogram prognostic model for SCLC patients using a large SCLC patient cohort from the National Cancer Database (NCDB).\n\nMethodsClinical data of 24,680 SCLC patients diagnosed from 2004 to 2011 were used to develop the nomogram prognostic model. The model was then validated using an independent cohort of 9,700 SCLC patients diagnosed from 2012 to 2013. The prognostic performance was evaluated using p value, concordance index and integrated Area Under the (time dependent Receiver Operating Characteristic) Curve.\n\nResultsThe following variables were contained in the final prognostic model: age, gender, race, ethnicity, Charlson/Deyo Score, TNM Stage (assigned according to the AJCC 8th edition), treatment type (combination of surgery, radiation therapy and chemotherapy), and laterality. The model was validated in an independent testing group with a concordance index of 0.722 {+/-} 0.004 and an integrated AUC of 0.79. The nomogram model has a significantly higher prognostic accuracy than previously developed models, including the AJCC 8th edition TNM-staging system. We implemented the proposed nomogram and two previously published nomograms in an online webserver.\n\nConclusionsWe developed a nomogram prognostic model for SCLC patients, and validated the model using an independent patient cohort. The nomogram performs better than earlier models, including AJCC staging.

cancer biology↗

bioRxiv2017

Multiple hidden processes complicate phylogenomic inference of deep Basidiomycota relationships

Resolving deep divergences in the fungal tree of life remains a challenging task even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts (Pucciniomycotina), smuts (Ustilaginomycotina) and mushroom forming fungi (Agaricomycotina) represent a particularly challenging situation that posed problems to both traditional multigene and genome-scale phylogenetic studies. Here, we address basal Basidiomycota relationships using three different phylogenomic datasets, concatenated and gene tree-based analyses and examine the contribution of several potential sources of uncertainty, including fast-evolving sites, putative long-branch taxa, model violation and missing data. We inferred conflicting results with different datasets and under different models. Fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and Astral analyses. The most conserved datasets grouped rusts with mushroom forming fungi, although this relationship proved labile, sensitive to model choice, different data subsets and missing data. Excluding putative long branch taxa, genes with the highest proportions of missing data and/or genes with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play too. Our analyses suggest that topologies uniting smuts with mushroom forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for rusts, smuts and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of the tree space that is difficult to access using both concatenation and gene tree based approaches. Thus, basal Basidiomycota relationships remain unresolved and might represent a phylogenetic problem that remains contentious even in the genomic era.

evolutionary biology↗