TY  - JOUR
A1  - Wagner, Ines
A1  - Volkmer, Michael
A1  - Sharan, Malvika
A1  - Villaveces, Jose M.
A1  - Oswald, Felix
A1  - Surendranath, Vineeth
A1  - Habermann, Bianca H.
T1  - morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring
JF  - BMC Bioinformatics
N2  - Background: Searching the orthologs of a given protein or DNA sequence is one of the most important and most commonly used Bioinformatics methods in Biology. Programs like BLAST or the orthology search engine Inparanoid can be used to find orthologs when the similarity between two sequences is sufficiently high. They however fail when the level of conservation is low. The detection of remotely conserved proteins oftentimes involves sophisticated manual intervention that is difficult to automate. 
Results: Here, we introduce morFeus, a search program to find remotely conserved orthologs. Based on relaxed sequence similarity searches, morFeus selects sequences based on the similarity of their alignments to the query, tests for orthology by iterative reciprocal BLAST searches and calculates a network score for the resulting network of orthologs that is a measure of orthology independent of the E-value. Detecting remotely conserved orthologs of a protein using morFeus thus requires no manual intervention. We demonstrate the performance of morFeus by comparing it to state-of-the-art orthology resources and methods. We provide an example of remotely conserved orthologs, which were experimentally shown to be functionally equivalent in the respective organisms and therefore meet the criteria of the orthology-function conjecture. 
Conclusions: Based on our results, we conclude that morFeus is a powerful and specific search method for detecting remotely conserved orthologs.
KW  - reciprocal best hit
KW  - finder using symmetrical best hits
KW  - sequences
KW  - annotation
KW  - identification
KW  - database
KW  - genomes
KW  - proteins
KW  - homologs
KW  - hidden markov-models
KW  - phylogenetic trees
KW  - PSI-blast
KW  - eigenvector centrality
KW  - meta-analysis based orthology
KW  - orthology
KW  - remote sequence conservation
KW  - alignment clustering
KW  - orthology network
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115590
VL  - 15
IS  - 263
ER  - 
TY  - JOUR
A1  - Herrmann, Johannes
A1  - Lotz, Christopher
A1  - Karagiannidis, Christian
A1  - Weber-Carstens, Steffen
A1  - Kluge, Stefan
A1  - Putensen, Christian
A1  - Wehrfritz, Andreas
A1  - Schmidt, Karsten
A1  - Ellerkmann, Richard K.
A1  - Oswald, Daniel
A1  - Lotz, Gösta
A1  - Zotzmann, Viviane
A1  - Moerer, Onnen
A1  - Kühn, Christian
A1  - Kochanek, Matthias
A1  - Muellenbach, Ralf
A1  - Gaertner, Matthias
A1  - Fichtner, Falk
A1  - Brettner, Florian
A1  - Findeisen, Michael
A1  - Heim, Markus
A1  - Lahmer, Tobias
A1  - Rosenow, Felix
A1  - Haake, Nils
A1  - Lepper, Philipp M.
A1  - Rosenberger, Peter
A1  - Braune, Stephan
A1  - Kohls, Mirjam
A1  - Heuschmann, Peter
A1  - Meybohm, Patrick
T1  - Key characteristics impacting survival of COVID-19 extracorporeal membrane oxygenation
JF  - Critical Care
N2  - Background
Severe COVID-19 induced acute respiratory distress syndrome (ARDS) often requires extracorporeal membrane oxygenation (ECMO). Recent German health insurance data revealed low ICU survival rates. Patient characteristics and experience of the ECMO center may determine intensive care unit (ICU) survival. The current study aimed to identify factors affecting ICU survival of COVID-19 ECMO patients.
Methods
673 COVID-19 ARDS ECMO patients treated in 26 centers between January 1st 2020 and March 22nd 2021 were included. Data on clinical characteristics, adjunct therapies, complications, and outcome were documented. Block wise logistic regression analysis was applied to identify variables associated with ICU-survival.
Results
Most patients were between 50 and 70 years of age. PaO\(_{2}\)/FiO\(_{2}\) ratio prior to ECMO was 72 mmHg (IQR: 58–99). ICU survival was 31.4%. Survival was significantly lower during the 2nd wave of the COVID-19 pandemic. A subgroup of 284 (42%) patients fulfilling modified EOLIA criteria had a higher survival (38%) (p = 0.0014, OR 0.64 (CI 0.41–0.99)). Survival differed between low, intermediate, and high-volume centers with 20%, 30%, and 38%, respectively (p = 0.0024). Treatment in high volume centers resulted in an odds ratio of 0.55 (CI 0.28–1.02) compared to low volume centers. Additional factors associated with survival were younger age, shorter time between intubation and ECMO initiation, BMI > 35 (compared to < 25), absence of renal replacement therapy or major bleeding/thromboembolic events.
Conclusions
Structural and patient-related factors, including age, comorbidities and ECMO case volume, determined the survival of COVID-19 ECMO. These factors combined with a more liberal ECMO indication during the 2nd wave may explain the reasonably overall low survival rate. Careful selection of patients and treatment in high volume ECMO centers was associated with higher odds of ICU survival.
KW  - Covid-19
KW  - extracorporeal membrane oxygenation (ECMO)
KW  - intensive care unit
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-299686
VL  - 26
IS  - 1
ER  -