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Embedding open and reproducible science into teaching: A bank of lesson plans and resources

lesson plans

Pownall M, Azevedo F, Aldoh A, Elsherif M.
GSID: jKJl-pEEYasJ
M Pownall, F Azevedo, A Aldoh, M Elsherif… - … of Teaching and …, 2021 - psycnet.apa.org

… In this article, we describe and openly share a bank of teaching resources and lesson plans on the broad topics of open scholarship, open science, replication, and reproducibility that can be integrated into taught courses to support educators...

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Pownall, M., Azevedo, F., Aldoh, A., Elsherif, M., Vasilev, M., Pennington, C. R., ... & Parsons, S. (2021). Embedding open and reproducible science into teaching: A bank of lesson plans and resources. Scholarship of Teaching and Learning in Psychology.
Pownall, Madeleine, et al. "Embedding open and reproducible science into teaching: A bank of lesson plans and resources." Scholarship of Teaching and Learning in Psychology (2021).
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Genome Sequences of Two .

Genome announcements

Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR.
PMID: 28254974
Genome Announc. 2017 Mar 02;5(9). doi: 10.1128/genomeA.01687-16.

No abstract available.

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Viana MV, Wattam AR, Govil Batra D, et al. Genome Sequences of Two . Genome Announc. 2017;5(9)doi: 10.1128/genomeA.01687-16.
Viana, M. V., Wattam, A. R., Govil Batra, D., Boisvert, S., Brettin, T. S., Frace, M., Xia, F., Azevedo, V., Tiller, R., & Hoffmaster, A. R. (2017). Genome Sequences of Two . Genome announcements, 5(9), . https://doi.org/10.1128/genomeA.01687-16
Viana, Marcus Vinicius Canário, et al. "Genome Sequences of Two ." Genome announcements vol. 5,9 (2017). doi: https://doi.org/10.1128/genomeA.01687-16
Viana MV, Wattam AR, Govil Batra D, Boisvert S, Brettin TS, Frace M, Xia F, Azevedo V, Tiller R, Hoffmaster AR. Genome Sequences of Two . Genome Announc. 2017 Mar 02;5(9). doi: 10.1128/genomeA.01687-16. PMID: 28254974; PMCID: PMC5334581.
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Magnitude and frequency variations of vector-borne infection outbreaks using the Ross-Macdonald model: explaining and predicting outbreaks of dengue fever.

Epidemiology and infection

Amaku M, Azevedo F, Burattini MN, Coelho GE, Coutinho FAB, Greenhalgh D, Lopez LF, Motitsuki RS, Wilder-Smith A, Massad E.
PMID: 27538702
Epidemiol Infect. 2016 Dec;144(16):3435-3450. doi: 10.1017/S0950268816001448. Epub 2016 Aug 19.

The classical Ross-Macdonald model is often utilized to model vector-borne infections; however, this model fails on several fronts. First, using measured (or estimated) parameters, which values are accepted from the literature, the model predicts a much greater number of...

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Amaku M, Azevedo F, Burattini MN, et al. Magnitude and frequency variations of vector-borne infection outbreaks using the Ross-Macdonald model: explaining and predicting outbreaks of dengue fever. Epidemiol Infect. 2016;144(16):3435-3450doi: 10.1017/S0950268816001448.
Amaku, M., Azevedo, F., Burattini, M. N., Coelho, G. E., Coutinho, F. A. B., Greenhalgh, D., Lopez, L. F., Motitsuki, R. S., Wilder-Smith, A., & Massad, E. (2016). Magnitude and frequency variations of vector-borne infection outbreaks using the Ross-Macdonald model: explaining and predicting outbreaks of dengue fever. Epidemiology and infection, 144(16), 3435-3450. https://doi.org/10.1017/S0950268816001448
Amaku, M, et al. "Magnitude and frequency variations of vector-borne infection outbreaks using the Ross-Macdonald model: explaining and predicting outbreaks of dengue fever." Epidemiology and infection vol. 144,16 (2016): 3435-3450. doi: https://doi.org/10.1017/S0950268816001448
Amaku M, Azevedo F, Burattini MN, Coelho GE, Coutinho FAB, Greenhalgh D, Lopez LF, Motitsuki RS, Wilder-Smith A, Massad E. Magnitude and frequency variations of vector-borne infection outbreaks using the Ross-Macdonald model: explaining and predicting outbreaks of dengue fever. Epidemiol Infect. 2016 Dec;144(16):3435-3450. doi: 10.1017/S0950268816001448. Epub 2016 Aug 19. PMID: 27538702.
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Persistent Type I Endoleak after Endovascular Treatment with Chimney Technique.

Frontiers in cardiovascular medicine

Azevedo AI, Braga P, Rodrigues A, Ferreira N, Fonseca M, Dias A, Gama Ribeiro V.
PMID: 27703967
Front Cardiovasc Med. 2016 Sep 20;3:32. doi: 10.3389/fcvm.2016.00032. eCollection 2016.

Thoracic endovascular aortic repair (TEVAR) is increasingly used in the treatment of acute type B aortic dissection. Type Ia endoleaks are a common complication of the procedure, but its clinical significance and the best treatment strategy remain poorly defined....

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Azevedo AI, Braga P, Rodrigues A, et al. Persistent Type I Endoleak after Endovascular Treatment with Chimney Technique. Front Cardiovasc Med. 2016;3:32doi: 10.3389/fcvm.2016.00032.
Azevedo, A. I., Braga, P., Rodrigues, A., Ferreira, N., Fonseca, M., Dias, A., & Gama Ribeiro, V. (2016). Persistent Type I Endoleak after Endovascular Treatment with Chimney Technique. Frontiers in cardiovascular medicine, 332. https://doi.org/10.3389/fcvm.2016.00032
Azevedo, Ana Isabel, et al. "Persistent Type I Endoleak after Endovascular Treatment with Chimney Technique." Frontiers in cardiovascular medicine vol. 3 (2016): 32. doi: https://doi.org/10.3389/fcvm.2016.00032
Azevedo AI, Braga P, Rodrigues A, Ferreira N, Fonseca M, Dias A, Gama Ribeiro V. Persistent Type I Endoleak after Endovascular Treatment with Chimney Technique. Front Cardiovasc Med. 2016 Sep 20;3:32. doi: 10.3389/fcvm.2016.00032. eCollection 2016. PMID: 27703967; PMCID: PMC5028720.
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Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France.

Genome announcements

Guimarães LC, Viana MV, Benevides LJ, Mariano DC, Veras AA, Sá PH, Rocha FS, Vilas Boas PC, Soares SC, Barbosa MS, Guiso N, Badell E, Carneiro AR, Azevedo V, Ramos RT, Silva A.
PMID: 27034487
Genome Announc. 2016 Mar 31;4(2). doi: 10.1128/genomeA.00172-16.

Here, we present the draft genome of toxigenicCorynebacterium ulceransstrain 04-7514. The draft genome has 2,497,845 bp, 2,059 coding sequences, 12 rRNA genes, 46 tRNA genes, 150 pseudogenes, 1 clustered regularly interspaced short palindromic repeat (CRISPR) array, and a G+C...

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Guimarães LC, Viana MV, Benevides LJ, et al. Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France. Genome Announc. 2016;4(2)doi: 10.1128/genomeA.00172-16.
Guimarães, L. C., Viana, M. V., Benevides, L. J., Mariano, D. C., Veras, A. A., Sá, P. H., Rocha, F. S., Vilas Boas, P. C., Soares, S. C., Barbosa, M. S., Guiso, N., Badell, E., Carneiro, A. R., Azevedo, V., Ramos, R. T., & Silva, A. (2016). Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France. Genome announcements, 4(2), . https://doi.org/10.1128/genomeA.00172-16
Guimarães, Luis C, et al. "Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France." Genome announcements vol. 4,2 (2016). doi: https://doi.org/10.1128/genomeA.00172-16
Guimarães LC, Viana MV, Benevides LJ, Mariano DC, Veras AA, Sá PH, Rocha FS, Vilas Boas PC, Soares SC, Barbosa MS, Guiso N, Badell E, Carneiro AR, Azevedo V, Ramos RT, Silva A. Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France. Genome Announc. 2016 Mar 31;4(2). doi: 10.1128/genomeA.00172-16. PMID: 27034487; PMCID: PMC4816615.
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Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen.

Genome announcements

Azevedo AC, Bento CB, Ruiz JC, Queiroz MV, Mantovani HC.
PMID: 25745007
Genome Announc. 2015 Mar 05;3(2). doi: 10.1128/genomeA.00085-15.

Streptococcus equinus (Streptococcus bovis) HC5 is a bacteriocinogenic lactic acid bacterium with simple growth requirements. The draft genome sequence of S. equinus HC5 consists of 1,846,241 bp, with a G+C content of 37.04%. In silico analysis indicated that S....

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Azevedo AC, Bento CB, Ruiz JC, et al. Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen. Genome Announc. 2015;3(2)doi: 10.1128/genomeA.00085-15.
Azevedo, A. C., Bento, C. B., Ruiz, J. C., Queiroz, M. V., & Mantovani, H. C. (2015). Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen. Genome announcements, 3(2), . https://doi.org/10.1128/genomeA.00085-15
Azevedo, Analice C, et al. "Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen." Genome announcements vol. 3,2 (2015). doi: https://doi.org/10.1128/genomeA.00085-15
Azevedo AC, Bento CB, Ruiz JC, Queiroz MV, Mantovani HC. Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen. Genome Announc. 2015 Mar 05;3(2). doi: 10.1128/genomeA.00085-15. PMID: 25745007; PMCID: PMC4358394.
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Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview.

Frontiers in microbiology

Tiwari S, Jamal SB, Hassan SS, Carvalho PVSD, Almeida S, Barh D, Ghosh P, Silva A, Castro TLP, Azevedo V.
PMID: 29067003
Front Microbiol. 2017 Oct 10;8:1878. doi: 10.3389/fmicb.2017.01878. eCollection 2017.

The bacterial communities in a wide range of environmental niches sense and respond to numerous external stimuli for their survival. Primarily, a source they require to follow up this communication is the two-component signal transduction system (TCS), which typically...

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Tiwari S, Jamal SB, Hassan SS, et al. Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview. Front Microbiol. 2017;8:1878doi: 10.3389/fmicb.2017.01878.
Tiwari, S., Jamal, S. B., Hassan, S. S., Carvalho, P. V. S. D., Almeida, S., Barh, D., Ghosh, P., Silva, A., Castro, T. L. P., & Azevedo, V. (2017). Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview. Frontiers in microbiology, 81878. https://doi.org/10.3389/fmicb.2017.01878
Tiwari, Sandeep, et al. "Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview." Frontiers in microbiology vol. 8 (2017): 1878. doi: https://doi.org/10.3389/fmicb.2017.01878
Tiwari S, Jamal SB, Hassan SS, Carvalho PVSD, Almeida S, Barh D, Ghosh P, Silva A, Castro TLP, Azevedo V. Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview. Front Microbiol. 2017 Oct 10;8:1878. doi: 10.3389/fmicb.2017.01878. eCollection 2017. PMID: 29067003; PMCID: PMC5641358.
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pH-responsive hydrogels to protect IgY from gastric conditions: in vitro evaluation.

Journal of food science and technology

Bellingeri RV, Picco NY, Alustiza FE, Canova JV, Molina MA, Acevedo DF, Barbero C, Vivas AB.
PMID: 25892818
J Food Sci Technol. 2015 May;52(5):3117-22. doi: 10.1007/s13197-014-1337-3. Epub 2014 Apr 10.

Oral administration of specific egg yolk immunoglobulin (IgY) is effective against a number of gastrointestinal pathogens. However, the activity of orally administered IgY is reduced rapidly, since IgY is sensitive to pepsin and low pH. In this study, hydrogels...

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Bellingeri RV, Picco NY, Alustiza FE, et al. pH-responsive hydrogels to protect IgY from gastric conditions: in vitro evaluation. J Food Sci Technol. 2014;52(5):3117-22doi: 10.1007/s13197-014-1337-3.
Bellingeri, R. V., Picco, N. Y., Alustiza, F. E., Canova, J. V., Molina, M. A., Acevedo, D. F., Barbero, C., & Vivas, A. B. (2015). pH-responsive hydrogels to protect IgY from gastric conditions: in vitro evaluation. Journal of food science and technology, 52(5), 3117-22. https://doi.org/10.1007/s13197-014-1337-3
Bellingeri, R V, et al. "pH-responsive hydrogels to protect IgY from gastric conditions: in vitro evaluation." Journal of food science and technology vol. 52,5 (2015): 3117-22. doi: https://doi.org/10.1007/s13197-014-1337-3
Bellingeri RV, Picco NY, Alustiza FE, Canova JV, Molina MA, Acevedo DF, Barbero C, Vivas AB. pH-responsive hydrogels to protect IgY from gastric conditions: in vitro evaluation. J Food Sci Technol. 2015 May;52(5):3117-22. doi: 10.1007/s13197-014-1337-3. Epub 2014 Apr 10. PMID: 25892818; PMCID: PMC4397343.
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Cooperation between CD4+ T Cells and Humoral Immunity Is Critical for Protection against Dengue Using a DNA Vaccine Based on the NS1 Antigen.

PLoS neglected tropical diseases

Gonçalves AJ, Oliveira ER, Costa SM, Paes MV, Silva JF, Azevedo AS, Mantuano-Barradas M, Nogueira AC, Almeida CJ, Alves AM.
PMID: 26650916
PLoS Negl Trop Dis. 2015 Dec 09;9(12):e0004277. doi: 10.1371/journal.pntd.0004277. eCollection 2015 Dec.

Dengue virus (DENV) is spread through most tropical and subtropical areas of the world and represents a serious public health problem. At present, the control of dengue disease is mainly hampered by the absence of antivirals or a vaccine,...

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Gonçalves AJ, Oliveira ER, Costa SM, et al. Cooperation between CD4+ T Cells and Humoral Immunity Is Critical for Protection against Dengue Using a DNA Vaccine Based on the NS1 Antigen. PLoS Negl Trop Dis. 2015;9(12):e0004277doi: 10.1371/journal.pntd.0004277.
Gonçalves, A. J., Oliveira, E. R., Costa, S. M., Paes, M. V., Silva, J. F., Azevedo, A. S., Mantuano-Barradas, M., Nogueira, A. C., Almeida, C. J., & Alves, A. M. (2015). Cooperation between CD4+ T Cells and Humoral Immunity Is Critical for Protection against Dengue Using a DNA Vaccine Based on the NS1 Antigen. PLoS neglected tropical diseases, 9(12), e0004277. https://doi.org/10.1371/journal.pntd.0004277
Gonçalves, Antônio J S, et al. "Cooperation between CD4+ T Cells and Humoral Immunity Is Critical for Protection against Dengue Using a DNA Vaccine Based on the NS1 Antigen." PLoS neglected tropical diseases vol. 9,12 (2015): e0004277. doi: https://doi.org/10.1371/journal.pntd.0004277
Gonçalves AJ, Oliveira ER, Costa SM, Paes MV, Silva JF, Azevedo AS, Mantuano-Barradas M, Nogueira AC, Almeida CJ, Alves AM. Cooperation between CD4+ T Cells and Humoral Immunity Is Critical for Protection against Dengue Using a DNA Vaccine Based on the NS1 Antigen. PLoS Negl Trop Dis. 2015 Dec 09;9(12):e0004277. doi: 10.1371/journal.pntd.0004277. eCollection 2015 Dec. PMID: 26650916; PMCID: PMC4674122.
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Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California.

Genome announcements

Dias LM, Alves JT, Veras AA, Baraúna RA, Sá PH, Spier S, Edman JM, Guimarães LC, Rocha FS, Ramos RT, Azevedo V, Silva A, Carneiro AR.
PMID: 26950327
Genome Announc. 2016 Feb 25;4(1). doi: 10.1128/genomeA.00038-16.

Corynebacterium pseudotuberculosis is the etiological agent of a caseous lymphadenitis disease. Herein, we present the first complete genome sequencing of C. pseudotuberculosis strain 226, isolated from an abscess of the sub-iliac lymph node of a goat from California (USA)....

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Dias LM, Alves JT, Veras AA, et al. Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California. Genome Announc. 2016;4(1)doi: 10.1128/genomeA.00038-16.
Dias, L. M., Alves, J. T., Veras, A. A., Baraúna, R. A., Sá, P. H., Spier, S., Edman, J. M., Guimarães, L. C., Rocha, F. S., Ramos, R. T., Azevedo, V., Silva, A., & Carneiro, A. R. (2016). Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California. Genome announcements, 4(1), . https://doi.org/10.1128/genomeA.00038-16
Dias, Larissa M, et al. "Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California." Genome announcements vol. 4,1 (2016). doi: https://doi.org/10.1128/genomeA.00038-16
Dias LM, Alves JT, Veras AA, Baraúna RA, Sá PH, Spier S, Edman JM, Guimarães LC, Rocha FS, Ramos RT, Azevedo V, Silva A, Carneiro AR. Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California. Genome Announc. 2016 Feb 25;4(1). doi: 10.1128/genomeA.00038-16. PMID: 26950327; PMCID: PMC4767917.
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Medication adherence in patients with juvenile idiopathic arthritis.

Revista brasileira de reumatologia

Adriano LS, Fonteles MM, Azevedo MF, Beserra MP, Romero NR.
PMID: 27012520
Rev Bras Reumatol. 2016 Mar 08; doi: 10.1016/j.rbr.2015.11.004. Epub 2016 Mar 08.

OBJECTIVE: The aim of this study was to investigate pharmacological treatment adherence of patients with juvenile idiopathic arthritis, attended in an outpatient pharmacy at a tertiary hospital in northeastern Brazil.METHODS: The analysis of adherence was performed along with caregivers,...

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Adriano LS, Fonteles MM, Azevedo MF, et al. Adesão ao tratamento farmacológico em pacientes com artrite idiopática juvenil por meio de questionários. Medication adherence in patients with juvenile idiopathic arthritis. Rev Bras Reumatol. 2016;doi: 10.1016/j.rbr.2015.11.004.
Adriano, L. S., Fonteles, M. M., Azevedo, M. F., Beserra, M. P., & Romero, N. R. (2016). Adesão ao tratamento farmacológico em pacientes com artrite idiopática juvenil por meio de questionários. Medication adherence in patients with juvenile idiopathic arthritis. Revista brasileira de reumatologia, . https://doi.org/10.1016/j.rbr.2015.11.004
Adriano, Liana Silveira, et al. "Adesão ao tratamento farmacológico em pacientes com artrite idiopática juvenil por meio de questionários." Medication adherence in patients with juvenile idiopathic arthritis. Revista brasileira de reumatologia vol. (2016). doi: https://doi.org/10.1016/j.rbr.2015.11.004
Adriano LS, Fonteles MM, Azevedo MF, Beserra MP, Romero NR. Adesão ao tratamento farmacológico em pacientes com artrite idiopática juvenil por meio de questionários. Medication adherence in patients with juvenile idiopathic arthritis. Rev Bras Reumatol. 2016 Mar 08; doi: 10.1016/j.rbr.2015.11.004. Epub 2016 Mar 08. Portuguese. PMID: 27012520.
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Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.

Genome announcements

Loureiro D, Portela RW, Sousa TJ, Rocha F, Pereira FL, Dorella FA, Carvalho AF, Menezes N, Macedo ES, Moura-Costa LF, Meyer R, Leal CA, Figueiredo HC, Azevedo V.
PMID: 26823597
Genome Announc. 2016 Jan 28;4(1). doi: 10.1128/genomeA.01673-15.

We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The sequencing was performed with the Ion Torrent Personal Genome Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C content of 52.85%, and a...

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Loureiro D, Portela RW, Sousa TJ, et al. Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1. Genome Announc. 2016;4(1)doi: 10.1128/genomeA.01673-15.
Loureiro, D., Portela, R. W., Sousa, T. J., Rocha, F., Pereira, F. L., Dorella, F. A., Carvalho, A. F., Menezes, N., Macedo, E. S., Moura-Costa, L. F., Meyer, R., Leal, C. A., Figueiredo, H. C., & Azevedo, V. (2016). Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1. Genome announcements, 4(1), . https://doi.org/10.1128/genomeA.01673-15
Loureiro, Dan, et al. "Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1." Genome announcements vol. 4,1 (2016). doi: https://doi.org/10.1128/genomeA.01673-15
Loureiro D, Portela RW, Sousa TJ, Rocha F, Pereira FL, Dorella FA, Carvalho AF, Menezes N, Macedo ES, Moura-Costa LF, Meyer R, Leal CA, Figueiredo HC, Azevedo V. Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1. Genome Announc. 2016 Jan 28;4(1). doi: 10.1128/genomeA.01673-15. PMID: 26823597; PMCID: PMC4732350.
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