Update citations (#1293)

Co-authored-by: bgruening <[email protected]>

_bibliography/citations-eu.bib

@@ -5557,6 +5557,25 @@ @article{kandinov_mini-multilocus_2024
  year = {2024}
 }
 
+@article{karim_silico_2024,
+ abstract = {The rising antimicrobial resistance crisis has diminished the effectiveness of traditional antibiotics against pathogenic bacteria. This study addresses this urgent challenge by exploring the antibacterial potential of novel quinolone derivatives (1–33). Using computational in silico modeling to simulate biological interactions, we aimed to identify candidates with potent antibacterial activity. A total of 33 quinolone derivatives were assessed for their physicochemical properties and effectiveness against a range of clinically relevant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, Streptococcus pneumoniae, and Enterococcus faecalis. Molecular docking studies identified compounds 28, 29, 32, and 33 as having notable binding affinities, particularly against MRSA. Further molecular dynamics simulations of compound 29 confirmed its favorable stability and potential for disrupting MRSA, reinforcing the docking results and showing strong alignment with in vitro findings. These findings position compound 29 as a promising lead for developing alternative MRSA therapies and underscore the need for further in vivo studies to evaluate its therapeutic potential.},
+ author = {Karim, Tafsir and Almatarneh, Mansour H. and Rahman, Shofiur and Alodhayb, Abdullah N. and Albrithen, Hamad and Hossain, Md. Mainul and Kawsar, Sarkar M. A. and Poirier, Raymond A. and Uddin, Kabir M.},
+ copyright = {© 2024 Wiley-VCH GmbH},
+ doi = {10.1002/slct.202402780},
+ issn = {2365-6549},
+ journal = {ChemistrySelect},
+ keywords = {{\textgreater}UseGalaxy.eu, ADMET, DFT, MD simulation, Molecular docking, PCA calculations, Quinoline},
+ language = {en},
+ note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/slct.202402780},
+ number = {36},
+ pages = {e202402780},
+ title = {In {Silico} {Prediction} of {Antibacterial} {Activity} of {Quinolone} {Derivatives}},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/slct.202402780},
+ urldate = {2024-10-10},
+ volume = {9},
+ year = {2024}
+}
+
 @article{karthik_foremost_2023,
  abstract = {Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN\_CUL\_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN\_CUL\_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.},
  author = {Karthik, Kumaragurubaran and Anbazhagan, Subbaiyan and Ananda Chitra, Murugesan and Ramya, Rajendran and Sridhar, Ramaswamy and Dhinakar Raj, Gopal},
@@ -5704,7 +5723,7 @@ @article{kim_complete_2022
  year = {2022}
 }
 
-@article{kim_complete_2022,
+@article{kim_complete_2022-1,
  abstract = {Terrisporobacter glycolicus is an emerging obligate anaerobic pathogen. We report the 3.9-Mbp genome sequence of T. glycolicus strain WW3900, which was isolated from wastewater at a research center with laboratory animal facilities. The genome sequence predicted a biosynthetic gene cluster encoding an S-adenosylmethionine enzyme and other synthetic genes associated with potential antimicrobial producers.},
  author = {Kim, Sung Guk and Summage-West, Christine V. and Reyna, Mariela and Feye, Kristina M. and Foley, Steven L.},
  doi = {10.1128/mra.00859-22},
@@ -7031,6 +7050,29 @@ @article{martinez-fabregas_cdk8_2020
  year = {2020}
 }
 
+@article{martins_laminin-2_2024,
+ abstract = {LAMA2, coding for the laminin-α2 chain, is a crucial ECM component, particularly abundant in skeletal muscle. Mutations in LAMA2 trigger the often-lethal LAMA2-congenital muscular dystrophy (LAMA2-CMD). Various phenotypes have been linked to LAMA2-CMD; nevertheless, the precise mechanisms that malfunction during disease onset in utero remain unknown. We generated Lama2-deficient C2C12 cells and found that Lama2-deficient myoblasts display proliferation, differentiation, and fusion defects, DNA damage, oxidative stress, and mitochondrial dysfunction. Moreover, fetal myoblasts isolated from the dyW mouse model of LAMA2-CMD display impaired differentiation and fusion in vitro. We also showed that disease onset during fetal development is characterized by a significant down-regulation of gene expression in muscle fibers, causing pronounced effects on cytoskeletal organization, muscle differentiation, and altered DNA repair and oxidative stress responses. Together, our findings provide unique insights into the critical importance of the laminin-α2 chain for muscle differentiation and muscle cell homeostasis.
+Graphical Abstract
+{\textless}img class="highwire-fragment fragment-image" alt="Figure" src="https://www.life-science-alliance.org/content/lsa/7/12/e202402829/F1.medium.gif" width="440" height="427"/{\textgreater}Download figureOpen in new tabDownload PowerPoint},
+ author = {Martins, Susana G. and Ribeiro, Vanessa and Melo, Catarina and Paulino-Cavaco, Cláudia and Antonini, Dario and Naidu, Sharadha Dayalan and Murtinheira, Fernanda and Fonseca, Inês and Saget, Bérénice and Pita, Mafalda and Fernandes, Diogo R. and Santos, Pedro Gameiro dos and Rodrigues, Gabriela and Zilhão, Rita and Herrera, Federico and Dinkova-Kostova, Albena T. and Carlos, Ana Rita and Thorsteinsdóttir, Sólveig},
+ copyright = {© 2024 Martins et al.. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).},
+ doi = {10.26508/lsa.202402829},
+ issn = {2575-1077},
+ journal = {Life Science Alliance},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ language = {en},
+ month = {December},
+ note = {Publisher: Life Science Alliance
+Section: Research Articles},
+ number = {12},
+ pmid = {39379105},
+ title = {Laminin-α2 chain deficiency in skeletal muscle causes dysregulation of multiple cellular mechanisms},
+ url = {https://www.life-science-alliance.org/content/7/12/e202402829},
+ urldate = {2024-10-11},
+ volume = {7},
+ year = {2024}
+}
+
 @article{martins_rodrigues_dataplant_2021,
  author = {Martins Rodrigues, Cristina and von Suchodoletz, Dirk and Mühlhaus, Timo and Krüger, Jens and Usadel, Björn},
  copyright = {Creative Commons Attribution 4.0 International},