TY  - JOUR
A1  - Jiang, Yuxiang
A1  - Oron, Tal Ronnen
A1  - Clark, Wyatt T.
A1  - Bankapur, Asma R.
A1  - D'Andrea, Daniel
A1  - Lepore, Rosalba
A1  - Funk, Christopher S.
A1  - Kahanda, Indika
A1  - Verspoor, Karin M.
A1  - Ben-Hur, Asa
A1  - Koo, Da Chen Emily
A1  - Penfold-Brown, Duncan
A1  - Shasha, Dennis
A1  - Youngs, Noah
A1  - Bonneau, Richard
A1  - Lin, Alexandra
A1  - Sahraeian, Sayed M. E.
A1  - Martelli, Pier Luigi
A1  - Profiti, Giuseppe
A1  - Casadio, Rita
A1  - Cao, Renzhi
A1  - Zhong, Zhaolong
A1  - Cheng, Jianlin
A1  - Altenhoff, Adrian
A1  - Skunca, Nives
A1  - Dessimoz, Christophe
A1  - Dogan, Tunca
A1  - Hakala, Kai
A1  - Kaewphan, Suwisa
A1  - Mehryary, Farrokh
A1  - Salakoski, Tapio
A1  - Ginter, Filip
A1  - Fang, Hai
A1  - Smithers, Ben
A1  - Oates, Matt
A1  - Gough, Julian
A1  - Törönen, Petri
A1  - Koskinen, Patrik
A1  - Holm, Liisa
A1  - Chen, Ching-Tai
A1  - Hsu, Wen-Lian
A1  - Bryson, Kevin
A1  - Cozzetto, Domenico
A1  - Minneci, Federico
A1  - Jones, David T.
A1  - Chapman, Samuel
A1  - BKC, Dukka
A1  - Khan, Ishita K.
A1  - Kihara, Daisuke
A1  - Ofer, Dan
A1  - Rappoport, Nadav
A1  - Stern, Amos
A1  - Cibrian-Uhalte, Elena
A1  - Denny, Paul
A1  - Foulger, Rebecca E.
A1  - Hieta, Reija
A1  - Legge, Duncan
A1  - Lovering, Ruth C.
A1  - Magrane, Michele
A1  - Melidoni, Anna N.
A1  - Mutowo-Meullenet, Prudence
A1  - Pichler, Klemens
A1  - Shypitsyna, Aleksandra
A1  - Li, Biao
A1  - Zakeri, Pooya
A1  - ElShal, Sarah
A1  - Tranchevent, Léon-Charles
A1  - Das, Sayoni
A1  - Dawson, Natalie L.
A1  - Lee, David
A1  - Lees, Jonathan G.
A1  - Sillitoe, Ian
A1  - Bhat, Prajwal
A1  - Nepusz, Tamás
A1  - Romero, Alfonso E.
A1  - Sasidharan, Rajkumar
A1  - Yang, Haixuan
A1  - Paccanaro, Alberto
A1  - Gillis, Jesse
A1  - Sedeño-Cortés, Adriana E.
A1  - Pavlidis, Paul
A1  - Feng, Shou
A1  - Cejuela, Juan M.
A1  - Goldberg, Tatyana
A1  - Hamp, Tobias
A1  - Richter, Lothar
A1  - Salamov, Asaf
A1  - Gabaldon, Toni
A1  - Marcet-Houben, Marina
A1  - Supek, Fran
A1  - Gong, Qingtian
A1  - Ning, Wei
A1  - Zhou, Yuanpeng
A1  - Tian, Weidong
A1  - Falda, Marco
A1  - Fontana, Paolo
A1  - Lavezzo, Enrico
A1  - Toppo, Stefano
A1  - Ferrari, Carlo
A1  - Giollo, Manuel
A1  - Piovesan, Damiano
A1  - Tosatto, Silvio C. E.
A1  - del Pozo, Angela
A1  - Fernández, José M.
A1  - Maietta, Paolo
A1  - Valencia, Alfonso
A1  - Tress, Michael L.
A1  - Benso, Alfredo
A1  - Di Carlo, Stefano
A1  - Politano, Gianfranco
A1  - Savino, Alessandro
A1  - Rehman, Hafeez Ur
A1  - Re, Matteo
A1  - Mesiti, Marco
A1  - Valentini, Giorgio
A1  - Bargsten, Joachim W.
A1  - van Dijk, Aalt D. J.
A1  - Gemovic, Branislava
A1  - Glisic, Sanja
A1  - Perovic, Vladmir
A1  - Veljkovic, Veljko
A1  - Almeida-e-Silva, Danillo C.
A1  - Vencio, Ricardo Z. N.
A1  - Sharan, Malvika
A1  - Vogel, Jörg
A1  - Kansakar, Lakesh
A1  - Zhang, Shanshan
A1  - Vucetic, Slobodan
A1  - Wang, Zheng
A1  - Sternberg, Michael J. E.
A1  - Wass, Mark N.
A1  - Huntley, Rachael P.
A1  - Martin, Maria J.
A1  - O'Donovan, Claire
A1  - Robinson, Peter N.
A1  - Moreau, Yves
A1  - Tramontano, Anna
A1  - Babbitt, Patricia C.
A1  - Brenner, Steven E.
A1  - Linial, Michal
A1  - Orengo, Christine A.
A1  - Rost, Burkhard
A1  - Greene, Casey S.
A1  - Mooney, Sean D.
A1  - Friedberg, Iddo
A1  - Radivojac, Predrag
A1  - Veljkovic, Nevena
T1  - An expanded evaluation of protein function prediction methods shows an improvement in accuracy
JF  - Genome Biology
N2  - Background
A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.

Results
We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.

Conclusions
The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
KW  - Protein function prediction
KW  - Disease gene prioritization
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166293
VL  - 17
IS  - 184
ER  - 
TY  - JOUR
A1  - Song, Ning-Ning
A1  - Jia, Yun-Fang
A1  - Zhang, Lei
A1  - Zhang, Qiong
A1  - Huang, Ying
A1  - Liu, Xiao-Zhen
A1  - Hu, Ling
A1  - Lan, Wei
A1  - Chen, Ling
A1  - Lesch, Klaus-Peter
A1  - Chen, Xiaoyan
A1  - Xu, Lin
A1  - Ding, Yu-Qiang
T1  - Reducing central serotonin in adulthood promotes hippocampal neurogenesis
JF  - Scientific Reports
N2  - Chronic administration of selective serotonin reuptake inhibitors (SSRIs), which up-regulates central serotonin (5-HT) system function, enhances adult hippocampal neurogenesis. However, the relationship between central 5-HT system and adult neurogenesis has not fully been understood. Here, we report that lowering 5-HT level in adulthood is also able to enhance adult hippocampal neurogenesis. We used tamoxifen (TM)-induced Cre in Pet1-CreER\(^{T2}\) mice to either deplete central serotonergic (5-HTergic) neurons or inactivate 5-HT synthesis in adulthood and explore the role of central 5-HT in adult hippocampal neurogenesis. A dramatic increase in hippocampal neurogenesis is present in these two central 5-HT-deficient mice and it is largely prevented by administration of agonist for 5-HTR2c receptor. In addition, the survival of new-born neurons in the hippocampus is enhanced. Furthermore, the adult 5-HT-deficient mice showed reduced depression-like behaviors but enhanced contextual fear memory. These findings demonstrate that lowering central 5-HT function in adulthood can also enhance adult hippocampal neurogenesis, thus revealing a new aspect of central 5-HT in regulating adult neurogenesis.
KW  - serotonin
KW  - SSRI
KW  - hippocampal neurogenesis
KW  - adulthood
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-168004
VL  - 6
IS  - 20338
ER  - 
TY  - JOUR
A1  - Tsai, Yu-Chen
A1  - Grimm, Stefan
A1  - Chao, Ju-Lan
A1  - Wang, Shih-Chin
A1  - Hofmeyer, Kerstin
A1  - Shen, Jie
A1  - Eichinger, Fred
A1  - Michalopoulou, Theoni
A1  - Yao, Chi-Kuang
A1  - Chang, Chih-Hsuan
A1  - Lin, Shih-Han
A1  - Sun, Y. Henry
A1  - Pflugfelder, Gert O.
T1  - Optomotor-blind negatively regulates Drosophila eye development by blocking Jak/STAT signaling
JF  - PLoS ONE
N2  - Organ formation requires a delicate balance of positive and negative regulators. In Drosophila eye development, wingless (wg) is expressed at the lateral margins of the eye disc and serves to block retinal development. The T-box gene optomotor-blind (omb) is expressed in a similar pattern and is regulated by Wg. Omb mediates part of Wg activity in blocking eye development. Omb exerts its function primarily by blocking cell proliferation. These effects occur predominantly in the ventral margin. Our results suggest that the primary effect of Omb is the blocking of Jak/STAT signaling by repressing transcription of upd which encodes the Jak receptor ligand Unpaired.
KW  - morphogenetic furrow progression
KW  - cell fate
KW  - compartment boundary
KW  - reporter gene
KW  - compound eye
KW  - gene expression
KW  - retinal differentiation
KW  - acts downstream
KW  - imaginal disk
KW  - glial cells
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143577
VL  - 10
IS  - 3
ER  - 
TY  - JOUR
A1  - Jiang, Fan
A1  - Chen, Lin
A1  - Belimov, Andrey A.
A1  - Shaposhnikov, Alexander I.
A1  - Gong, Fan
A1  - Meng, Xu
A1  - Hartung, Wolfram
A1  - Jeschke, Dieter W.
A1  - Davies, William J.
A1  - Dodd, Ian C.
T1  - Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum
JF  - Journal of Experimental Botany
N2  - Resolving the physiological mechanisms by which rhizobacteria enhance plant growth is difficult, since many such bacteria contain multiple plant growth-promoting properties. To understand further how the 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCd)-containing rhizobacterium Variovorax paradoxus 5C-2 affects plant growth, the flows and partitioning of mineral nutrients and abscisic acid (ABA) and ABA metabolism were studied in pea (Pisum sativum) plants following rhizosphere bacterial inoculation. Although root architecture was not affected, inoculation increased root and shoot biomass, and stomatal conductance, by 20, 15, and 24%, respectively, and increased N, P, K, Ca, and Mg uptake by 16, 81, 50, 46, and 58%, respectively. P deposition in inoculated plant roots was 4.9 times higher than that in uninoculated controls. Rhizobacterial inoculation increased root to shoot xylem flows and shoot to root phloem flows of K by 1.8- and 2.1-fold, respectively. In control plants, major sinks for K deposition were the roots and upper shoot (43% and 49% of total uptake, respectively), while rhizobacterial inoculation increased K distribution to the lower shoot at the expense of other compartments (xylem, phloem, and upper shoot). Despite being unable to metabolize ABA in vitro, V. paradoxus 5C-2 decreased root ABA concentrations and accumulation by 40–60%. Although inoculation decreased xylem ABA flows, phloem ABA flows increased. Whether bacterial ACCd attenuates root to shoot ABA signalling requires further investigation, since ABA is critical to maintain growth of droughted plants, and ACCd-containing organisms have been advocated as a means of minimizing growth inhibition of plants in drying soil.
KW  - Variovorax paradoxus
KW  - abscisic acid
KW  - ACC deaminase
KW  - hormone flow modelling
KW  - nutrient uptake
KW  - pea
KW  - plant–microbe interaction
KW  - rhizobacteria
Y1  - 2012
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-127011
VL  - 63
IS  - 18
ER  - 
TY  - RPRT
A1  - Angnide, Enarile
A1  - Bielitska, Iryna
A1  - Borchert, Leon
A1  - Braun, Louisa
A1  - Bühler, Pascal
A1  - Chen, Xinyue
A1  - Ho, Katherina
A1  - Hofmann, Lena
A1  - Kebekus, Melvin
A1  - Kubsch, Torbjörn
A1  - Li, Alexander
A1  - Lin, Simon
A1  - Mischer, Andreas
A1  - Mogus, Mateja
A1  - Schmid, Fabian
A1  - Schneidawind, Luisa
A1  - Voss, Manuela
A1  - Wilson, Claire
A1  - Wieteska, Filip
A1  - Yu, Linda
ED  - Lindner, Jonas
ED  - Fischer, Doris
T1  - Chinese Entanglements in Lower Franconian Business
BT  - A student research project by the Chair of China Business and Economics at the University of Würzburg
N2  - Using own survey data and interviews, this study analyzes how businesses in Lower Franconia (Unterfranken) are entangled with China. Starting with a bird's-eye-view of the current situation, the study goes on to provide valuable insights from five specific industries. The study shows that a majority of the analyzed firms have some sort of ties to China, be it through Chinese customers, import/export activities, or else.
KW  - China
KW  - Unterfranken
KW  - China
KW  - Lower Franconia
KW  - Unterfranken
KW  - business
KW  - entanglement
KW  - Handel
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-209876
ER  -