Helen Hardy, Lisa French, Josh Humphries, Sabine von Mering, Peter Giere, Frederik Berger, Anne Koivunen, Jonas Grieb, Martin Vipp, Vincent Smith
As a highly decentralised research infrastructure, the Distributed System of Scientific Collections (DiSSCo) will need to develop cross-institutional teams, adopting work practices where individual staff are intensively working collectively on common tasks in a distributed environment. These flexible and distributed working practices will be essential to the delivery of the research infrastructure across a wide range of delivery partners and a geographically dispersed set of scarce resources and skills, particularly in more technical roles. Since work to consider secondment and distributed working in DiSSCo was first envisaged, there has been a step change in distributed working owing to the Covid-19 pandemic and lockdowns or other restrictions to where work could take place. This report examines distributed team working practices and how they have changed, through interviews with a range of key roles across DiSSCo Prepare institutions. It briefly examines key project management and technical team delivery techniques. It documents how some of these approaches have been piloted within DiSSCo Prepare for the development, testing and delivery of DiSSCo Policy and Digital Maturity tools. Finally, bringing this together with previous work on secondment policies and practices for DiSSCo, we make recommendations about how secondment and distributed team working can be approached to enhance DiSSCo capabilities and the likelihood of successful implementation of the research infrastructure.
{"title":"Distributed Team Working - Approaches for DiSSCo","authors":"Helen Hardy, Lisa French, Josh Humphries, Sabine von Mering, Peter Giere, Frederik Berger, Anne Koivunen, Jonas Grieb, Martin Vipp, Vincent Smith","doi":"10.3897/rio.9.e115454","DOIUrl":"https://doi.org/10.3897/rio.9.e115454","url":null,"abstract":"As a highly decentralised research infrastructure, the Distributed System of Scientific Collections (DiSSCo) will need to develop cross-institutional teams, adopting work practices where individual staff are intensively working collectively on common tasks in a distributed environment. These flexible and distributed working practices will be essential to the delivery of the research infrastructure across a wide range of delivery partners and a geographically dispersed set of scarce resources and skills, particularly in more technical roles. Since work to consider secondment and distributed working in DiSSCo was first envisaged, there has been a step change in distributed working owing to the Covid-19 pandemic and lockdowns or other restrictions to where work could take place. This report examines distributed team working practices and how they have changed, through interviews with a range of key roles across DiSSCo Prepare institutions. It briefly examines key project management and technical team delivery techniques. It documents how some of these approaches have been piloted within DiSSCo Prepare for the development, testing and delivery of DiSSCo Policy and Digital Maturity tools. Finally, bringing this together with previous work on secondment policies and practices for DiSSCo, we make recommendations about how secondment and distributed team working can be approached to enhance DiSSCo capabilities and the likelihood of successful implementation of the research infrastructure.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"55 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139256729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Charlene da Silva, T. Samaai, S. Kerwath, Luther Adams, Katie M Watson, Anthony Bernard, Grant van der Heever, Andrea Angel, Stefan Schoombie, Guilherme Frainer, Mari-Lisa Franken, Adam Rees, Angus Paterson
The inaugural Computer Vision for Marine Scientists workshop was held at the 17th South African Marine Science Symposium, with the primary goal of establishing a community of practice for computer vision (CV) in marine sciences in South Africa. The one-day hybrid event, attended by 97 people, covered the principles of artificial intelligence (AI) techniques required for evaluating video and photographic imagery through presentations, practical demonstrations and interactive discussions. The recordings of the workshop sessions are available online, providing an opportunity to reach marine researchers both regionally and globally. The workshop highlighted that many scientists have begun to incorporate CV and AI into their research activities; however, there is little national coordination and the extent of research is lagging behind international trends. To support image-based AI research in South Africa, it is critical to maintain and expand the network established during the workshop. This would enable a more collaborative and successful approach to incorporating CV technology in the country's marine research initiatives, ultimately leading to ground-breaking discoveries and advancements in the field.
{"title":"Leaping into the future: Current application and future direction of computer vision and artificial intelligence in marine sciences in South Africa","authors":"Charlene da Silva, T. Samaai, S. Kerwath, Luther Adams, Katie M Watson, Anthony Bernard, Grant van der Heever, Andrea Angel, Stefan Schoombie, Guilherme Frainer, Mari-Lisa Franken, Adam Rees, Angus Paterson","doi":"10.3897/rio.9.e112231","DOIUrl":"https://doi.org/10.3897/rio.9.e112231","url":null,"abstract":"The inaugural Computer Vision for Marine Scientists workshop was held at the 17th South African Marine Science Symposium, with the primary goal of establishing a community of practice for computer vision (CV) in marine sciences in South Africa. The one-day hybrid event, attended by 97 people, covered the principles of artificial intelligence (AI) techniques required for evaluating video and photographic imagery through presentations, practical demonstrations and interactive discussions. The recordings of the workshop sessions are available online, providing an opportunity to reach marine researchers both regionally and globally. The workshop highlighted that many scientists have begun to incorporate CV and AI into their research activities; however, there is little national coordination and the extent of research is lagging behind international trends. To support image-based AI research in South Africa, it is critical to maintain and expand the network established during the workshop. This would enable a more collaborative and successful approach to incorporating CV technology in the country's marine research initiatives, ultimately leading to ground-breaking discoveries and advancements in the field.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139267179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Dynamic Laser Speckle (DLS) is a photonic phenomenon transformed into a technique to monitor tiny changes in many materials, particularly in biological ones (Biospeckle Laser – BSL). Its high sensitivity is key to monitor tiny changes in the tissues that can characterise biological features in medical and in agricultural samples. This work aimed to develop an environment at the world-wide-web to share raw data of BSL and to offer access to an interactively online analysis with tutorials. The gateway designed was implemented using PHP and JavaScript tools solving the challenges of managing data (images) and online interactive use. The result was an easy-to-use environment boosting the BSL research. The early results presented thousands of accesses and of more than one hundred different users from all around the world.
{"title":"Biospeckle Laser On Clouds, a digital gateway aiming at collaborative research improvement","authors":"Roberto Braga, Robson Godinho","doi":"10.3897/rio.9.e114736","DOIUrl":"https://doi.org/10.3897/rio.9.e114736","url":null,"abstract":"The Dynamic Laser Speckle (DLS) is a photonic phenomenon transformed into a technique to monitor tiny changes in many materials, particularly in biological ones (Biospeckle Laser – BSL). Its high sensitivity is key to monitor tiny changes in the tissues that can characterise biological features in medical and in agricultural samples. This work aimed to develop an environment at the world-wide-web to share raw data of BSL and to offer access to an interactively online analysis with tutorials. The gateway designed was implemented using PHP and JavaScript tools solving the challenges of managing data (images) and online interactive use. The result was an easy-to-use environment boosting the BSL research. The early results presented thousands of accesses and of more than one hundred different users from all around the world.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"28 11","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135868771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Louise Ahl, Luca Bellucci, Philippa Brewer, Pierre-Yves Gagnier, Elspeth Haston, Laurence Livermore, Sofie De Smedt, Helen Hardy, Henrik Enghoff
There are approximately 1.5 billion specimens kept in European Natural History Collections. The mission for the Distributed System of Scientific Collections (DiSSCo) is to unite all these specimens into a one-stop e-science infrastructure of digital specimens. This is a monumental digitisation task and criteria for how to prioritise this effort are, therefore, crucial for the success of the project. In this report, we have reviewed the literature and designed and conducted surveys of the digitisation plans and criteria used by DiSSCo Partners to understand the prioritisation criteria used in the digitisation of natural history collections. As an attempt to provide some guidance for the digitisation of specimens, we suggest that an organisation (e.g. DiSSCo or an individual institution) that is planning to digitise natural history collections considers four categories of prioritisation criteria: Relevance, Data quality, Cost and Feasibility.
{"title":"Digitisation of natural history collections: criteria for prioritisation","authors":"Louise Ahl, Luca Bellucci, Philippa Brewer, Pierre-Yves Gagnier, Elspeth Haston, Laurence Livermore, Sofie De Smedt, Helen Hardy, Henrik Enghoff","doi":"10.3897/rio.9.e114548","DOIUrl":"https://doi.org/10.3897/rio.9.e114548","url":null,"abstract":"There are approximately 1.5 billion specimens kept in European Natural History Collections. The mission for the Distributed System of Scientific Collections (DiSSCo) is to unite all these specimens into a one-stop e-science infrastructure of digital specimens. This is a monumental digitisation task and criteria for how to prioritise this effort are, therefore, crucial for the success of the project. In this report, we have reviewed the literature and designed and conducted surveys of the digitisation plans and criteria used by DiSSCo Partners to understand the prioritisation criteria used in the digitisation of natural history collections. As an attempt to provide some guidance for the digitisation of specimens, we suggest that an organisation (e.g. DiSSCo or an individual institution) that is planning to digitise natural history collections considers four categories of prioritisation criteria: Relevance, Data quality, Cost and Feasibility.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"14 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135934108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer.
{"title":"The Nekton Maldives taxonomic workshop: Exploring the biodiversity of shallow, mesophotic and deep-sea communities in Maldives","authors":"Mohamed Ahusan, Nuria Rico-Seijo, Farah Amjad, Erika Gress, Shafiya Naeem, Toufiek Samaai, Kaveh Samimi-Namin, Lucy Woodall, Paris Stefanoudis","doi":"10.3897/rio.9.e114370","DOIUrl":"https://doi.org/10.3897/rio.9.e114370","url":null,"abstract":"The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"29 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135272567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Based on the notion of a FAIR Digital Object (FDO) record, which consists of key-value pairs as attributes that are precisely defined in a Data Type Registry and selected in a profile, we show three examples of FDOs from different viewpoints how FDO records can be implemented as Handle PID records. As references to the attribute definitions, the keys determine the value space of the attribute. In the first two examples, the profiles enable human-readable keys and legacy digital objects to be integrated into FDO records. How legacy metadata from IANA media types that can be transformed into structured metadata of appropriate attribute definitions that then can be applied in profiles and FDO records, is described in the third example.
{"title":"How FDO attributes can support machine- and human-readability? - a description along three examples","authors":"Ulrich Schwardmann, Tibor Kálmán","doi":"10.3897/rio.9.e108737","DOIUrl":"https://doi.org/10.3897/rio.9.e108737","url":null,"abstract":"Based on the notion of a FAIR Digital Object (FDO) record, which consists of key-value pairs as attributes that are precisely defined in a Data Type Registry and selected in a profile, we show three examples of FDOs from different viewpoints how FDO records can be implemented as Handle PID records. As references to the attribute definitions, the keys determine the value space of the attribute. In the first two examples, the profiles enable human-readable keys and legacy digital objects to be integrated into FDO records. How legacy metadata from IANA media types that can be transformed into structured metadata of appropriate attribute definitions that then can be applied in profiles and FDO records, is described in the third example.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"67 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136067399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rebecca Dikow, Corey DiPietro, Michael Trizna, Hanna BredenbeckCorp, Madeline Bursell, Jenna Ekwealor, Richard Hodel, Nilda Lopez, William Mattingly, Jeremy Munro, Richard Naples, Candace Oubre, Drew Robarge, Sara Snyder, Jennifer Spillane, Melinda Jane Tomerlin, Luis Villanueva, Alexander White
Applications of artificial intelligence (AI) and machine learning (ML) have become pervasive in our everyday lives. These applications range from the mundane (asking ChatGPT to write a thank you note) to high-end science (predicting future weather patterns in the face of climate change), but, because they rely on human-generated or mediated data, they also have the potential to perpetuate systemic oppression and racism. For museums and other cultural heritage institutions, there is great interest in automating the kinds of applications at which AI and ML can excel, for example, tasks in computer vision including image segmentation, object recognition (labelling or identifying objects in an image) and natural language processing (e.g. named-entity recognition, topic modelling, generation of word and sentence embeddings) in order to make digital collections and archives discoverable, searchable and appropriately tagged. A coalition of staff, Fellows and interns working in digital spaces at the Smithsonian Institution, who are either engaged with research using AI or ML tools or working closely with digital data in other ways, came together to discuss the promise and potential perils of applying AI and ML at scale and this work results from those conversations. Here, we present the process that has led to the development of an AI Values Statement and an implementation plan, including the release of datasets with accompanying documentation to enable these data to be used with improved context and reproducibility (dataset cards). We plan to continue releasing dataset cards and for AI and ML applications, model cards, in order to enable informed usage of Smithsonian data and research products.
{"title":"Developing responsible AI practices at the Smithsonian Institution","authors":"Rebecca Dikow, Corey DiPietro, Michael Trizna, Hanna BredenbeckCorp, Madeline Bursell, Jenna Ekwealor, Richard Hodel, Nilda Lopez, William Mattingly, Jeremy Munro, Richard Naples, Candace Oubre, Drew Robarge, Sara Snyder, Jennifer Spillane, Melinda Jane Tomerlin, Luis Villanueva, Alexander White","doi":"10.3897/rio.9.e113334","DOIUrl":"https://doi.org/10.3897/rio.9.e113334","url":null,"abstract":"Applications of artificial intelligence (AI) and machine learning (ML) have become pervasive in our everyday lives. These applications range from the mundane (asking ChatGPT to write a thank you note) to high-end science (predicting future weather patterns in the face of climate change), but, because they rely on human-generated or mediated data, they also have the potential to perpetuate systemic oppression and racism. For museums and other cultural heritage institutions, there is great interest in automating the kinds of applications at which AI and ML can excel, for example, tasks in computer vision including image segmentation, object recognition (labelling or identifying objects in an image) and natural language processing (e.g. named-entity recognition, topic modelling, generation of word and sentence embeddings) in order to make digital collections and archives discoverable, searchable and appropriately tagged. A coalition of staff, Fellows and interns working in digital spaces at the Smithsonian Institution, who are either engaged with research using AI or ML tools or working closely with digital data in other ways, came together to discuss the promise and potential perils of applying AI and ML at scale and this work results from those conversations. Here, we present the process that has led to the development of an AI Values Statement and an implementation plan, including the release of datasets with accompanying documentation to enable these data to be used with improved context and reproducibility (dataset cards). We plan to continue releasing dataset cards and for AI and ML applications, model cards, in order to enable informed usage of Smithsonian data and research products.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"32 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gabriela Ioana-Toroimac, Gabriela Moroșanu, Dana Constantin, Cătălina Stoica, Ionuț Șandor
In the context of the requirements of the Water Framework Directive to reinstate a river’s good ecological status after being severely altered by human pressures, river restoration became a major topic in the last decade in the EU and the number of projects implemented especially on hydromorphology increased. However, it is still uncertain whether these restoration measures have positive cumulative effects, i.e. hydromorphological effectiveness, when compared to reference conditions and expectations of stakeholders, because of inconsistent methodologies. Therefore, the goal of our project is to develop a methodology to evaluate the hydromorphological effectiveness of river restoration, based on standardised indicators, at various spatial scales, appropriate for implemented measures and for restored river types, weighting the expectations of actors and adapted to case studies in Romania. This methodological protocol could become also a useful tool to create a strategy and make decisions in the practice of river restoration. Moreover, this kind of analysis could contribute to clarifying the issue of standards in environmental projects.
{"title":"Methodology to evaluate the effectiveness of hydromorphological restoration of rivers in Romania","authors":"Gabriela Ioana-Toroimac, Gabriela Moroșanu, Dana Constantin, Cătălina Stoica, Ionuț Șandor","doi":"10.3897/rio.9.e113991","DOIUrl":"https://doi.org/10.3897/rio.9.e113991","url":null,"abstract":"In the context of the requirements of the Water Framework Directive to reinstate a river’s good ecological status after being severely altered by human pressures, river restoration became a major topic in the last decade in the EU and the number of projects implemented especially on hydromorphology increased. However, it is still uncertain whether these restoration measures have positive cumulative effects, i.e. hydromorphological effectiveness, when compared to reference conditions and expectations of stakeholders, because of inconsistent methodologies. Therefore, the goal of our project is to develop a methodology to evaluate the hydromorphological effectiveness of river restoration, based on standardised indicators, at various spatial scales, appropriate for implemented measures and for restored river types, weighting the expectations of actors and adapted to case studies in Romania. This methodological protocol could become also a useful tool to create a strategy and make decisions in the practice of river restoration. Moreover, this kind of analysis could contribute to clarifying the issue of standards in environmental projects.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135219601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raphael Abban, Sarpong Kwabena, Samuel Duodu, Lydia Mosi, Isawumi Abiola
Urinary tract infections (UTIs) are frequent hospital-acquired infection, with Escherichia coli and Proteus mirabilis accounting for 90% of complicated UTIs. Emergence of multidrug-resistant (MDR) bacteria have complicated the treatment UTIs. P. mirabilis related UTIs has been associated with the production of urinary stones and long-term infections in patients with catheters. P. mirabilis and other uropathogens constitute a largely unexplored pathogen group. The pathogen is resistant to most antibiotics as a result of its impermeable outer membrane (OM). The β-barrel assemble machinery folds and inserts outer membrane proteins; however, there are no antibiotics targeting the OM assemble in clinical use currently. Therefore, this study seeks to identify drugs that will inhibit the activity of P. mirabilis B complex proteins and also determine their effects on P. mirabilis OM biogenesis. This would be achieved by screening approved drugs against the P. mirabilis Bam complex using computer-based in silico screening and cellular-based assays. First, the binding effects of drugs on P. mirabilis B complex proteins will be determined using docking algorithms. The antimicrobial and antivirulence activity of selected drugs from in silico analysis will be screened against MDR P. mirabilis . Finally, the effect of active drug(s) on the OM biogenesis of wild-type P. mirabilis and mutant P. mirabilis will be determined using peptide nucleic acids (PNA). Western lot analysis will be used to determine the abundance of proteins involved in OM biogenesis. Successful completion of this study will lead to the identification of novel antibiotics against MDR P. mirabilis and associated mechanisms while providing the foundation for future research endeavours on other uropathogens.
{"title":"Targeting Proteus mirabilis BAM Complex Proteins for Development of Novel Antibiotics","authors":"Raphael Abban, Sarpong Kwabena, Samuel Duodu, Lydia Mosi, Isawumi Abiola","doi":"10.3897/rio.9.e106849","DOIUrl":"https://doi.org/10.3897/rio.9.e106849","url":null,"abstract":"Urinary tract infections (UTIs) are frequent hospital-acquired infection, with Escherichia coli and Proteus mirabilis accounting for 90% of complicated UTIs. Emergence of multidrug-resistant (MDR) bacteria have complicated the treatment UTIs. P. mirabilis related UTIs has been associated with the production of urinary stones and long-term infections in patients with catheters. P. mirabilis and other uropathogens constitute a largely unexplored pathogen group. The pathogen is resistant to most antibiotics as a result of its impermeable outer membrane (OM). The β-barrel assemble machinery folds and inserts outer membrane proteins; however, there are no antibiotics targeting the OM assemble in clinical use currently. Therefore, this study seeks to identify drugs that will inhibit the activity of P. mirabilis B complex proteins and also determine their effects on P. mirabilis OM biogenesis. This would be achieved by screening approved drugs against the P. mirabilis Bam complex using computer-based in silico screening and cellular-based assays. First, the binding effects of drugs on P. mirabilis B complex proteins will be determined using docking algorithms. The antimicrobial and antivirulence activity of selected drugs from in silico analysis will be screened against MDR P. mirabilis . Finally, the effect of active drug(s) on the OM biogenesis of wild-type P. mirabilis and mutant P. mirabilis will be determined using peptide nucleic acids (PNA). Western lot analysis will be used to determine the abundance of proteins involved in OM biogenesis. Successful completion of this study will lead to the identification of novel antibiotics against MDR P. mirabilis and associated mechanisms while providing the foundation for future research endeavours on other uropathogens.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135730344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shortwave and microwave diathermy devices are commonly used in physical therapy as heating treatment. The rise in temperature occurs due to the flow of electric current in the treated area. Ions are evenly distributed in a predicted pattern from skin to deeper tissues. We hypothesise that the diathermy physiotherapy devices (DPDs) can be repurposed as a means of neutralisation of the Rabies virus (RABV) by exploiting the generated electric charges. In order to minimise the ohmic heating of the tissue, the pulsed output of the diathermy devices is preferred where the ‘on’ time of active energy emission is considerably shorter than the ‘off’ time. RABV proteins mediating cell invasion, cytoplasmic replication and budding, contain polar components that can be adversely affected by non-thermal electric phenomena. Repurposed DPDs can replace the Rabies immunoglobulin (RIG) by targeting the site of inoculation i.e. the area of the animal bite, provided that the delivered electric charges can reduce pathogenicity by altering key viral proteins. The modality is advantageous compared to conventional RIG since it can theoretically neutralise all Lyssavirus species, is not limited by the compartment syndrome, can intercept RABV even after it gains access to the peripheral neural network where conventional post-exposure prophylaxis is ineffective and is cost-effective in the long term. The principle of physical alteration of vulnerable proteins by electricity delivered by electromagnetic radiation is not limited to RABV, but may be applied to a spectrum of viral pathogens.
{"title":"Electromagnetic radiation as antiviral treatment with a focus on Rabies post-exposure prophylaxis","authors":"Georgios Dougas","doi":"10.3897/rio.9.e107227","DOIUrl":"https://doi.org/10.3897/rio.9.e107227","url":null,"abstract":"Shortwave and microwave diathermy devices are commonly used in physical therapy as heating treatment. The rise in temperature occurs due to the flow of electric current in the treated area. Ions are evenly distributed in a predicted pattern from skin to deeper tissues. We hypothesise that the diathermy physiotherapy devices (DPDs) can be repurposed as a means of neutralisation of the Rabies virus (RABV) by exploiting the generated electric charges. In order to minimise the ohmic heating of the tissue, the pulsed output of the diathermy devices is preferred where the ‘on’ time of active energy emission is considerably shorter than the ‘off’ time. RABV proteins mediating cell invasion, cytoplasmic replication and budding, contain polar components that can be adversely affected by non-thermal electric phenomena. Repurposed DPDs can replace the Rabies immunoglobulin (RIG) by targeting the site of inoculation i.e. the area of the animal bite, provided that the delivered electric charges can reduce pathogenicity by altering key viral proteins. The modality is advantageous compared to conventional RIG since it can theoretically neutralise all Lyssavirus species, is not limited by the compartment syndrome, can intercept RABV even after it gains access to the peripheral neural network where conventional post-exposure prophylaxis is ineffective and is cost-effective in the long term. The principle of physical alteration of vulnerable proteins by electricity delivered by electromagnetic radiation is not limited to RABV, but may be applied to a spectrum of viral pathogens.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"73 12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136114096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：