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UFGI Publication round-up week 6/22

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M.

Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. No abstract available.

PMID: 32381734

 

Prdm1 overexpression causes a photoreceptor fate-shift in nascent, but not mature, bipolar cells.

Goodson NB, Park KU, Silver JS, Chiodo VA, Hauswirth WW, Brzezinski JA 4th.

Dev Biol. 2020 Jun 17. pii: S0012-1606(20)30178-0. doi: 10.1016/j.ydbio.2020.06.003. [Epub ahead of print]

PMID: 32562755

 

Risk Factors for Recurrent Staphylococcus aureus Bacteremia.

Choi SH, Dagher M, Ruffin F, Park LP, Sharma-Kuinkel BK, Souli M, Morse AM, Eichenberger EM, Hale L, Kohler C, Warren B, Hansen B, Medie FM, McIntyre LM, Fowler VG.

Clin Infect Dis. 2020 Jun 21. pii: ciaa801. doi: 10.1093/cid/ciaa801. [Epub ahead of print]

PMID: 32564065

 

System dynamics modelling of urbanization under energy constraints in China.

Gu C, Ye X, Cao Q, Guan W, Peng C, Wu Y, Zhai W.

Sci Rep. 2020 Jun 19;10(1):9956. doi: 10.1038/s41598-020-66125-3.

PMID: 32561760

 

Evaluating the Use of rCBV as a Tumor Grade and Treatment Response Classifier Across NCI Quantitative Imaging Network Sites: Part II of the DSC-MRI Digital Reference Object (DRO) Challenge.

Bell LC, Semmineh N, An H, Eldeniz C, Wahl R, Schmainda KM, Prah MA, Erickson BJ, Korfiatis P, Wu C, Sorace AG, Yankeelov TE, Rutledge N, Chenevert TL, Malyarenko D, Liu Y, Brenner A, Hu LS, Zhou Y, Boxerman JL, Yen YF, Kalpathy-Cramer J, Beers AL, Muzi M, Madhuranthakam AJ, Pinho M, Johnson B, Quarles CC.

Tomography. 2020 Jun;6(2):203-208. doi: 10.18383/j.tom.2020.00012.

PMID: 32548297

 

Harmonization of quality metrics and power calculation in multi-omic studies.

Tarazona S, Balzano-Nogueira L, Gómez-Cabrero D, Schmidt A, Imhof A, Hankemeier T, Tegnér J, Westerhuis JA, Conesa A.

Nat Commun. 2020 Jun 18;11(1):3092. doi: 10.1038/s41467-020-16937-8.

PMID: 32555183

 

Decision analysis and reinforcement learning in surgical decision-making.

Loftus TJ, Filiberto AC, Li Y, Balch J, Cook AC, Tighe PJ, Efron PA, Upchurch GR Jr, Rashidi P, Li X, Bihorac A.

Surgery. 2020 Jun 13. pii: S0039-6060(20)30261-0. doi: 10.1016/j.surg.2020.04.049. [Epub ahead of print]

PMID: 32540036

Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology.

Mietzsch M, McKenna R, Väisänen E, Yu JC, Ilyas M, Hull JA, Kurian J, Smith JK, Chipman P, Lasanajak Y, Smith D, Söderlund-Venermo M, Agbandje-McKenna M.

Viruses. 2020 Jun 17;12(6). pii: E653. doi: 10.3390/v12060653.

PMID: 32560452

 

Genome Diversity and the Origin of the Arabian Horse.

Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, Brooks SA.

Sci Rep. 2020 Jun 16;10(1):9702. doi: 10.1038/s41598-020-66232-1.

PMID: 32546689

 

Extracellular Matrix Disparities in an Nkx2-5 Mutant Mouse Model of Congenital Heart Disease

Bousalis D, Lacko CS, Hlavac N, Alkassis F, Wachs RA, Mobini S, Schmidt CE, Kasahara H.

Front Cardiovasc Med. 2020 May 29;7:93. doi: 10.3389/fcvm.2020.00093. eCollection 2020.

PMID: 32548129

Remarkably Complex Microbial Community Composition in Bromeliad Tank Waters Revealed by eDNA Metabarcoding.

Simão TLL, Utz LRP, Dias R, Giongo A, Triplett EW, Eizirik E.

J Eukaryot Microbiol. 2020 Jun 20. doi: 10.1111/jeu.12814. [Epub ahead of print]

PMID: 32562451

 

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M.

Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. No abstract available.

PMID: 32381734

 

Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis.

Vujkovic M, Keaton JM, Lynch JA, Miller DR, Zhou J, Tcheandjieu C, Huffman JE, Assimes TL, Lorenz K, Zhu X, Hilliard AT, Judy RL, Huang J, Lee KM, Klarin D, Pyarajan S, Danesh J, Melander O, Rasheed A, Mallick NH, Hameed S, Qureshi IH, Afzal MN, Malik U, Jalal A, Abbas S, Sheng X, Gao L, Kaestner KH, Susztak K, Sun YV, DuVall SL, Cho K, Lee JS, Gaziano JM, Phillips LS, Meigs JB, Reaven PD, Wilson PW, Edwards TL, Rader DJ, Damrauer SM, O’Donnell CJ, Tsao PS; HPAP Consortium; Regeneron Genetics Center; VA Million Veteran Program, Chang KM, Voight BF, Saleheen D.

Nat Genet. 2020 Jun 15. doi: 10.1038/s41588-020-0637-y. [Epub ahead of print]

PMID: 32541925

 

Decision analysis and reinforcement learning in surgical decision-making.

Loftus TJ, Filiberto AC, Li Y, Balch J, Cook AC, Tighe PJ, Efron PA, Upchurch GR Jr, Rashidi P, Li X, Bihorac A.

Surgery. 2020 Jun 13. pii: S0039-6060(20)30261-0. doi: 10.1016/j.surg.2020.04.049.

PMID: 32540036

 

Genetic breakdown of a Tet-off conditional lethality system for insect population control.

Zhao Y, Schetelig MF, Handler AM.

Nat Commun. 2020 Jun 18;11(1):3095. doi: 10.1038/s41467-020-16807-3.

PMID: 32555259

 

Decision analysis and reinforcement learning in surgical decision-making.

Loftus TJ, Filiberto AC, Li Y, Balch J, Cook AC, Tighe PJ, Efron PA, Upchurch GR Jr, Rashidi P, Li X, Bihorac A.

Surgery. 2020 Jun 13. pii: S0039-6060(20)30261-0. doi: 10.1016/j.surg.2020.04.049.

PMID: 32540036

 

Neuroanesthesia Guidelines for Optimizing Transcranial Motor Evoked Potential Neuromonitoring During Deformity and Complex Spinal Surgery: A Delphi Consensus Study.

Walker CT, Kim HJ, Park P, Lenke LG, Weller MA, Smith JS, Nemergut EC, Sciubba DM, Wang MY, Shaffrey C, Deviren V, Mummaneni PV, Chang JM, Mummaneni VP, Than KD, Berjano P, Eastlack RK, Mundis GM Jr, Kanter AS, Okonkwo DO, Shin JH, Lewis JM, Koski T, Hoh DJ, Glassman SD, Vinci SB, Daniels AH, Clavijo CF, Turner JD, McLawhorn M, Uribe JS.

Spine (Phila Pa 1976). 2020 Jul 1;45(13):911-920. doi: 10.1097/BRS.0000000000003433.

PMID: 32539292

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