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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

pipeline programs

Parra G, Bradnam K.
GSID: 2zpwUxAouzoJ
G Parra, K Bradnam, I Korf - Bioinformatics, 2007 - academic.oup.com

… Recent developments that further exploit sequence similarity come from comparative gene prediction programs. Instead of comparing an anonymous genomic sequence to known coding sequences, a genomic sequence is compared to anonymous genomic sequences from …

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Parra, G., Bradnam, K., & Korf, I. (2007). CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23(9), 1061-1067.
Parra, Genis, Keith Bradnam, and Ian Korf. "CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes." Bioinformatics 23.9 (2007): 1061-1067.
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Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection.

Scientific reports

Feger BJ, Thompson JW, Dubois LG, Kommaddi RP, Foster MW, Mishra R, Shenoy SK, Shibata Y, Kidane YH, Moseley MA, Carnell LS, Bowles DE.
PMID: 27670941
Sci Rep. 2016 Sep 27;6:34091. doi: 10.1038/srep34091.

On Earth, biological systems have evolved in response to environmental stressors, interactions dictated by physical forces that include gravity. The absence of gravity is an extreme stressor and the impact of its absence on biological systems is ill-defined. Astronauts...

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Feger BJ, Thompson JW, Dubois LG, et al. Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Sci Rep. 2016;6:34091doi: 10.1038/srep34091.
Feger, B. J., Thompson, J. W., Dubois, L. G., Kommaddi, R. P., Foster, M. W., Mishra, R., Shenoy, S. K., Shibata, Y., Kidane, Y. H., Moseley, M. A., Carnell, L. S., & Bowles, D. E. (2016). Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Scientific reports, 634091. https://doi.org/10.1038/srep34091
Feger, Bryan J, et al. "Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection." Scientific reports vol. 6 (2016): 34091. doi: https://doi.org/10.1038/srep34091
Feger BJ, Thompson JW, Dubois LG, Kommaddi RP, Foster MW, Mishra R, Shenoy SK, Shibata Y, Kidane YH, Moseley MA, Carnell LS, Bowles DE. Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Sci Rep. 2016 Sep 27;6:34091. doi: 10.1038/srep34091. PMID: 27670941; PMCID: PMC5037457.
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The effect of a single session of whole-body vibration training in recreationally active men on the excitability of the central and peripheral nervous system.

Journal of human kinetics

Chmielewska D, Piecha M, Błaszczak E, Król P, Smykla A, Juras G.
PMID: 25114735
J Hum Kinet. 2014 Jul 08;41:89-98. doi: 10.2478/hukin-2014-0036. eCollection 2014 Jun 28.

Vibration training has become a popular method used in professional sports and recreation. In this study, we examined the effect of whole-body vibration training on the central nervous system and muscle excitability in a group of 28 active men....

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Chmielewska D, Piecha M, Błaszczak E, et al. The effect of a single session of whole-body vibration training in recreationally active men on the excitability of the central and peripheral nervous system. J Hum Kinet. 2014;41:89-98doi: 10.2478/hukin-2014-0036.
Chmielewska, D., Piecha, M., Błaszczak, E., Król, P., Smykla, A., & Juras, G. (2014). The effect of a single session of whole-body vibration training in recreationally active men on the excitability of the central and peripheral nervous system. Journal of human kinetics, 4189-98. https://doi.org/10.2478/hukin-2014-0036
Chmielewska, Daria, et al. "The effect of a single session of whole-body vibration training in recreationally active men on the excitability of the central and peripheral nervous system." Journal of human kinetics vol. 41 (2014): 89-98. doi: https://doi.org/10.2478/hukin-2014-0036
Chmielewska D, Piecha M, Błaszczak E, Król P, Smykla A, Juras G. The effect of a single session of whole-body vibration training in recreationally active men on the excitability of the central and peripheral nervous system. J Hum Kinet. 2014 Jul 08;41:89-98. doi: 10.2478/hukin-2014-0036. eCollection 2014 Jun 28. PMID: 25114735; PMCID: PMC4120468.
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Adherence and Dosage Contributions to Parenting Program Quality.

Journal of the Society for Social Work and Research

Gross TJ, Mason WA, Parra G, Oats R, Ringle J, Haggerty KP.
PMID: 26726301
J Soc Social Work Res. 2015 Dec;6(4):467-489. doi: 10.1086/684108.

OBJECTIVE: The 3 most frequently examined elements of treatment fidelity are adherence, dosage, and quality. The relationships between these fidelity elements are complex, and additional research is needed to provide clarity. Improving clarity may be especially relevant to parenting...

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Gross TJ, Mason WA, Parra G, et al. Adherence and Dosage Contributions to Parenting Program Quality. J Soc Social Work Res. 2015;6(4):467-489doi: 10.1086/684108.
Gross, T. J., Mason, W. A., Parra, G., Oats, R., Ringle, J., & Haggerty, K. P. (2015). Adherence and Dosage Contributions to Parenting Program Quality. Journal of the Society for Social Work and Research, 6(4), 467-489. https://doi.org/10.1086/684108
Gross, Thomas J, et al. "Adherence and Dosage Contributions to Parenting Program Quality." Journal of the Society for Social Work and Research vol. 6,4 (2015): 467-489. doi: https://doi.org/10.1086/684108
Gross TJ, Mason WA, Parra G, Oats R, Ringle J, Haggerty KP. Adherence and Dosage Contributions to Parenting Program Quality. J Soc Social Work Res. 2015 Dec;6(4):467-489. doi: 10.1086/684108. PMID: 26726301; PMCID: PMC4697741.
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Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor.

Frontiers in endocrinology

Slater PG, Gutierrez-Maldonado SE, Gysling K, Lagos CF.
PMID: 29515519
Front Endocrinol (Lausanne). 2018 Feb 20;9:43. doi: 10.3389/fendo.2018.00043. eCollection 2018.

The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with...

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Slater PG, Gutierrez-Maldonado SE, Gysling K, et al. Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor. Front Endocrinol (Lausanne). 2018;9:43doi: 10.3389/fendo.2018.00043.
Slater, P. G., Gutierrez-Maldonado, S. E., Gysling, K., & Lagos, C. F. (2018). Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor. Frontiers in endocrinology, 943. https://doi.org/10.3389/fendo.2018.00043
Slater, Paula G, et al. "Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor." Frontiers in endocrinology vol. 9 (2018): 43. doi: https://doi.org/10.3389/fendo.2018.00043
Slater PG, Gutierrez-Maldonado SE, Gysling K, Lagos CF. Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor. Front Endocrinol (Lausanne). 2018 Feb 20;9:43. doi: 10.3389/fendo.2018.00043. eCollection 2018. PMID: 29515519; PMCID: PMC5826306.
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The effect of the training with the different combinations of frequency and peak-to-peak vibration displacement of whole-body vibration on the strength of knee flexors and extensors.

Biology of sport

Stania M, Król P, Sobota G, Polak A, Bacik B, Juras G.
PMID: 28566806
Biol Sport. 2017 Jun;34(2):127-136. doi: 10.5114/biolsport.2017.64586. Epub 2017 Jan 01.

Whole-body vibration training has become a popular method used in sports and physiotherapy. The study aimed to evaluate the effect of different vibration frequency and peak-to-peak displacement combinations on men knee flexors and extensors strength in isokinetic conditions. The...

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Stania M, Król P, Sobota G, et al. The effect of the training with the different combinations of frequency and peak-to-peak vibration displacement of whole-body vibration on the strength of knee flexors and extensors. Biol Sport. 2017;34(2):127-136doi: 10.5114/biolsport.2017.64586.
Stania, M., Król, P., Sobota, G., Polak, A., Bacik, B., & Juras, G. (2017). The effect of the training with the different combinations of frequency and peak-to-peak vibration displacement of whole-body vibration on the strength of knee flexors and extensors. Biology of sport, 34(2), 127-136. https://doi.org/10.5114/biolsport.2017.64586
Stania, M, et al. "The effect of the training with the different combinations of frequency and peak-to-peak vibration displacement of whole-body vibration on the strength of knee flexors and extensors." Biology of sport vol. 34,2 (2017): 127-136. doi: https://doi.org/10.5114/biolsport.2017.64586
Stania M, Król P, Sobota G, Polak A, Bacik B, Juras G. The effect of the training with the different combinations of frequency and peak-to-peak vibration displacement of whole-body vibration on the strength of knee flexors and extensors. Biol Sport. 2017 Jun;34(2):127-136. doi: 10.5114/biolsport.2017.64586. Epub 2017 Jan 01. PMID: 28566806; PMCID: PMC5424452.
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An Evaluation of the Decision-Making Capacity Assessment Model.

Canadian geriatrics journal : CGJ

Brémault-Phillips SC, Parmar J, Friesen S, Rogers LG, Pike A, Sluggett B.
PMID: 27729947
Can Geriatr J. 2016 Sep 30;19(3):83-96. doi: 10.5770/cgj.19.222. eCollection 2016 Sep.

BACKGROUND: The Decision-Making Capacity Assessment (DMCA) Model includes a best-practice process and tools to assess DMCA, and implementation strategies at the organizational and assessor levels to support provision of DMCAs across the care continuum. A Developmental Evaluation of the...

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Brémault-Phillips SC, Parmar J, Friesen S, et al. An Evaluation of the Decision-Making Capacity Assessment Model. Can Geriatr J. 2016;19(3):83-96doi: 10.5770/cgj.19.222.
Brémault-Phillips, S. C., Parmar, J., Friesen, S., Rogers, L. G., Pike, A., & Sluggett, B. (2016). An Evaluation of the Decision-Making Capacity Assessment Model. Canadian geriatrics journal : CGJ, 19(3), 83-96. https://doi.org/10.5770/cgj.19.222
Brémault-Phillips, Suzette C, et al. "An Evaluation of the Decision-Making Capacity Assessment Model." Canadian geriatrics journal : CGJ vol. 19,3 (2016): 83-96. doi: https://doi.org/10.5770/cgj.19.222
Brémault-Phillips SC, Parmar J, Friesen S, Rogers LG, Pike A, Sluggett B. An Evaluation of the Decision-Making Capacity Assessment Model. Can Geriatr J. 2016 Sep 30;19(3):83-96. doi: 10.5770/cgj.19.222. eCollection 2016 Sep. PMID: 27729947; PMCID: PMC5038930.
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Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil.

Anais da Academia Brasileira de Ciencias

Silva PG, Klein AH, González M, Gutierrez O, Espejo A.
PMID: 25993356
An Acad Bras Cienc. 2015 Apr-Jun;87(2):623-34. doi: 10.1590/0001-3765201520140329. Epub 2015 May 08.

This work presents a validation of wave parameters from the new sixty years Downscaled Ocean Waves (DOW) reanalysis database. This study compares quantiles of the Gumbel distribution of Hs (significant wave height) and Tp (peak period) from simulated data...

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Silva PG, Klein AH, González M, et al. Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil. An Acad Bras Cienc. 2015;87(2):623-34doi: 10.1590/0001-3765201520140329.
Silva, P. G., Klein, A. H., González, M., Gutierrez, O., & Espejo, A. (2015). Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil. Anais da Academia Brasileira de Ciencias, 87(2), 623-34. https://doi.org/10.1590/0001-3765201520140329
Silva, Paula G, et al. "Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil." Anais da Academia Brasileira de Ciencias vol. 87,2 (2015): 623-34. doi: https://doi.org/10.1590/0001-3765201520140329
Silva PG, Klein AH, González M, Gutierrez O, Espejo A. Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil. An Acad Bras Cienc. 2015 Apr-Jun;87(2):623-34. doi: 10.1590/0001-3765201520140329. Epub 2015 May 08. PMID: 25993356.
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Induction Chemotherapy for p16 Positive Oropharyngeal Squamous Cell Carcinoma.

Laryngoscope investigative otolaryngology

Saito Y, Ando M, Omura G, Yasuhara K, Yoshida M, Takahashi W, Yamasoba T.
PMID: 28894801
Laryngoscope Investig Otolaryngol. 2016 Mar 29;1(2):28-32. doi: 10.1002/lio2.18. eCollection 2016 Apr.

OBJECTIVES/HYPOTHESIS: We aimed to determine the effectiveness of induction chemotherapy for treating p16-positive oropharyngeal cancer in our department.STUDY DESIGN: This was a retrospective case series to assess treatment effectiveness.METHODS: We administered induction chemotherapy to patients with stage III to...

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Saito Y, Ando M, Omura G, et al. Induction Chemotherapy for p16 Positive Oropharyngeal Squamous Cell Carcinoma. Laryngoscope Investig Otolaryngol. 2016;1(2):28-32doi: 10.1002/lio2.18.
Saito, Y., Ando, M., Omura, G., Yasuhara, K., Yoshida, M., Takahashi, W., & Yamasoba, T. (2016). Induction Chemotherapy for p16 Positive Oropharyngeal Squamous Cell Carcinoma. Laryngoscope investigative otolaryngology, 1(2), 28-32. https://doi.org/10.1002/lio2.18
Saito, Yuki, et al. "Induction Chemotherapy for p16 Positive Oropharyngeal Squamous Cell Carcinoma." Laryngoscope investigative otolaryngology vol. 1,2 (2016): 28-32. doi: https://doi.org/10.1002/lio2.18
Saito Y, Ando M, Omura G, Yasuhara K, Yoshida M, Takahashi W, Yamasoba T. Induction Chemotherapy for p16 Positive Oropharyngeal Squamous Cell Carcinoma. Laryngoscope Investig Otolaryngol. 2016 Mar 29;1(2):28-32. doi: 10.1002/lio2.18. eCollection 2016 Apr. PMID: 28894801; PMCID: PMC5527349.
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mRNA secondary structure optimization using a correlated stem-loop prediction.

Nucleic acids research

Gaspar P, Moura G, Santos MA, Oliveira JL.
PMID: 26917014
Nucleic Acids Res. 2016 Jun 20;44(11):5490. doi: 10.1093/nar/gkw127. Epub 2016 Feb 24.

No abstract available.

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Gaspar P, Moura G, Santos MA, et al. mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res. 2016;44(11):5490doi: 10.1093/nar/gkw127.
Gaspar, P., Moura, G., Santos, M. A., & Oliveira, J. L. (2016). mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic acids research, 44(11), 5490. https://doi.org/10.1093/nar/gkw127
Gaspar, Paulo, et al. "mRNA secondary structure optimization using a correlated stem-loop prediction." Nucleic acids research vol. 44,11 (2016): 5490. doi: https://doi.org/10.1093/nar/gkw127
Gaspar P, Moura G, Santos MA, Oliveira JL. mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res. 2016 Jun 20;44(11):5490. doi: 10.1093/nar/gkw127. Epub 2016 Feb 24. PMID: 26917014; PMCID: PMC4914086.
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The Association between Early Artificial Amniotomy and Chorioamnionitis in Nulliparous Induction of Labor.

International scholarly research notices

Cooney LG, Bastek JA.
PMID: 27379338
Int Sch Res Notices. 2014 Dec 16;2014:628452. doi: 10.1155/2014/628452. eCollection 2014.

Objectives. To investigate whether early artificial amniotomy (AROM)

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Cooney LG, Bastek JA. The Association between Early Artificial Amniotomy and Chorioamnionitis in Nulliparous Induction of Labor. Int Sch Res Notices. 2014;2014:628452doi: 10.1155/2014/628452.
Cooney, L. G., & Bastek, J. A. (2014). The Association between Early Artificial Amniotomy and Chorioamnionitis in Nulliparous Induction of Labor. International scholarly research notices, 2014628452. https://doi.org/10.1155/2014/628452
Cooney, Laura G, and Bastek, Jamie A. "The Association between Early Artificial Amniotomy and Chorioamnionitis in Nulliparous Induction of Labor." International scholarly research notices vol. 2014 (2014): 628452. doi: https://doi.org/10.1155/2014/628452
Cooney LG, Bastek JA. The Association between Early Artificial Amniotomy and Chorioamnionitis in Nulliparous Induction of Labor. Int Sch Res Notices. 2014 Dec 16;2014:628452. doi: 10.1155/2014/628452. eCollection 2014. PMID: 27379338; PMCID: PMC4897382.
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Math anxiety and its relationship with basic arithmetic skills among primary school children.

The British journal of educational psychology

Sorvo R, Koponen T, Viholainen H, Aro T, Räikkönen E, Peura P, Dowker A, Aro M.
PMID: 28258597
Br J Educ Psychol. 2017 Sep;87(3):309-327. doi: 10.1111/bjep.12151. Epub 2017 Mar 03.

BACKGROUND: Children have been found to report and demonstrate math anxiety as early as the first grade. However, previous results concerning the relationship between math anxiety and performance are contradictory, with some studies establishing a correlation between them while...

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Sorvo R, Koponen T, Viholainen H, et al. Math anxiety and its relationship with basic arithmetic skills among primary school children. Br J Educ Psychol. 2017;87(3):309-327doi: 10.1111/bjep.12151.
Sorvo, R., Koponen, T., Viholainen, H., Aro, T., Räikkönen, E., Peura, P., Dowker, A., & Aro, M. (2017). Math anxiety and its relationship with basic arithmetic skills among primary school children. The British journal of educational psychology, 87(3), 309-327. https://doi.org/10.1111/bjep.12151
Sorvo, Riikka, et al. "Math anxiety and its relationship with basic arithmetic skills among primary school children." The British journal of educational psychology vol. 87,3 (2017): 309-327. doi: https://doi.org/10.1111/bjep.12151
Sorvo R, Koponen T, Viholainen H, Aro T, Räikkönen E, Peura P, Dowker A, Aro M. Math anxiety and its relationship with basic arithmetic skills among primary school children. Br J Educ Psychol. 2017 Sep;87(3):309-327. doi: 10.1111/bjep.12151. Epub 2017 Mar 03. PMID: 28258597.
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