scholarly journals A framework for implementing metaheuristic algorithms using intercellular communication

2020 ◽  
Author(s):  
Martín Gutiérrez ◽  
Yerko Ortiz ◽  
Javier Carrión

ABSTRACTMetaheuristic procedures (MH) have been a trend driving Artificial Intelligence (AI) researchers for the past 50 years. A variety of tools and applications (not only in Computer Science) stem from these techniques. Also, MH frequently rely on evolution, a trademark process involved in cell colony growth. Generally, MH are used to approximate the solution to difficult problems but require a large amount of computational resources. Cell colonies harboring synthetic distributed circuits using intercell communication offer a direction for tackling this problem, as they process information in a massively parallel fashion. In this work, we propose a framework that maps MH elements to synthetic circuits in growing cell colonies. The framework relies on cell-cell communication mechanisms such as quorum sensing (QS) and bacterial conjugation. As a proof-of-concept, we also implemented the workflow associated to the framework, and tested the execution of two specific MH (Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits on the gro simulator. Furthermore, we show an example of how our framework can be extended by implementing another kind of computational model: The Cellular Automaton. This work seeks to lay the foundations of mappings for implementing AI algorithms in a general manner using Synthetic Biology constructs in cell colonies.

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 245 ◽  
Author(s):  
Gary Hardiman

A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]


Author(s):  
Yerko Ortiz ◽  
Javier Carrión ◽  
Rafael Lahoz-Beltrá ◽  
Martín Gutiérrez

Metaheuristics (MH) are Artificial Intelligence procedures that frequently rely on evolution. MH approximate difficult problem solutions, but are computationally costly as they explore large solution spaces. This work pursues to lay the foundations of general mappings for implementing MH using Synthetic Biology constructs in cell colonies. Two advantages of this approach are: harnessing large scale parallelism capability of cell colonies and, using existing cell processes to implement basic dynamics defined in computational versions. We propose a framework that maps MH elements to synthetic circuits in growing cell colonies to replicate MH behavior in cell colonies. Cell-cell communication mechanisms such as quorum sensing (QS), bacterial conjugation, and environmental signals map to evolution operators in MH techniques to adapt to growing colonies. As a proof-of-concept, we implemented the workflow associated to the framework: automated MH simulation generators for the gro simulator and two classes of algorithms (Simple Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits. Implementation tests show that synthetic counterparts mimicking MH are automatically produced, but also that cell colony parallelism speeds up the execution in terms of generations. Furthermore, we show an example of how our framework is extended by implementing a different computational model: The Cellular Automaton.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 14-15
Author(s):  
Austin Kulasekararaj ◽  
Jacques Le Roux Malherbe ◽  
Andrew McDonald ◽  
Melanie Cornpropst ◽  
Phil Collis ◽  
...  

INTRODUCTION: PNH, a rare, chronic, life-threatening disease, is characterized by hemolytic anemia due to uncontrolled activity of the complement alternative pathway (AP), bone marrow failure, and thrombosis. Inhibition of C5 by intravenously administered eculizumab and ravulizumab reduces intravascular hemolysis, but PNH red blood cells (RBCs) become opsonized and susceptible to extravascular hemolysis (Risitano et al, Blood 2009). Only approximately half of PNH patients become transfusion independent with eculizumab treatment (Hillmen et al, NEJM 2006). BCX9930 is a potent, selective, orally administered inhibitor of complement factor D. Inhibition of factor D may prevent both intravascular and extravascular hemolysis in PNH. In healthy subjects, BCX9930 showed linear pharmacokinetics and dose-related AP suppression, and was safe and generally well-tolerated over a wide dose range. Here we describe safety and laboratory data establishing proof-of-concept for BCX9930 monotherapy in PNH patients in Study BCX9930-101 (NCT04330534). METHODS: Ongoing Study BCX9930-101 includes an open-label, dose-ranging evaluation of BCX9930 in PNH subjects who may either be naïve to C5 inhibitors (and receive BCX9930 as monotherapy) or have an incomplete treatment response to eculizumab or ravulizumab (with BCX9930 added to existing treatment). Up to 4 sequential cohorts each use a forced titration design for the first 28 days (Figure 1). Subjects enrolled in South Africa can participate in an individualized 48-week extension if they derive benefit at Day 28. Clinical benefit from BCX9930 is evaluated using laboratory monitoring and symptom assessment. Safety and tolerability are evaluated via clinical and laboratory monitoring, causality of adverse events is assessed by investigators, and the study is overseen by an independent Data Monitoring Committee. Data from Cohort 1 through 28 days is reported; data from the extension and subsequent cohorts will be subsequently summarized as available. RESULTS: To date, four C5 inhibitor naïve PNH subjects in South Africa have enrolled in Cohort 1. These subjects had PNH for a median of 4.5 years; 2 subjects had a history of transfusions in the past year; 1 subject each had a history of aplastic anemia or major thrombosis. Pre-treatment lactate dehydrogenase (LDH), total bilirubin, hemoglobin (Hb), reticulocyte count, and RBC PNH Type III clone size ranged from 3.7-11.1 × ULN, 0.61-3.3 mg/dL, 6.1-11.6 g/dL, 0.13-0.29 × 106/µL, and 41.4%-88.6% respectively. Treatment over 28 days with 50 mg twice daily (BID; Days 1-14) and 100 mg BID (Days 15-28) of BCX9930 produced dose-dependent, clinically meaningful improvements across hemolysis biomarkers (Figure 2). Decreases were observed in LDH (4/4), reticulocytes (4/4), and total bilirubin (2/2 subjects with elevated pre-treatment values). Increases were observed in Hb (3/4) and PNH RBC clone size (4/4). One subject showed an initial response to BCX9930 50 mg BID, followed by worsening indicators of hemolysis temporally associated with an upper respiratory tract infection (URTI; onset on Day 7). With an increase in dose to 100 mg BID and resolution of the URTI, LDH and reticulocytes fell and Hb rose. All four subjects reported one or more PNH-associated symptoms, including hemoglobinuria, jaundice, fatigue, erectile dysfunction, headache and abdominal pain, prior to enrollment. With the exception of one subject with persistent hemoglobinuria, all symptoms resolved by Day 28 on BCX9930. Three subjects experienced moderate headache that resolved in < 3 days after initiating BCX9930. One subject developed a rash during treatment with amoxicillin for an URTI; the rash resolved while continuing BCX9930 dosing. One subject on concomitant chronic corticosteroids and azathioprine had an unrelated fatal serious adverse event of disseminated varicella during the study extension. Based on review of safety data, Cohort 2 opened at doses of 200 mg BID and 400 mg BID and, in the 3 subjects who continued into the extension, the dose was titrated to ≥ 200 mg BID. CONCLUSIONS: Oral BCX9930 elicited rapid changes in laboratory parameters indicative of reduced hemolysis and clinical benefit and was safe and generally well-tolerated over a 28-day dosing interval. These interim results establish proof of concept for monotherapy with BCX9930 in the treatment of C5-inhibitor naïve PNH patients and support evaluation of higher doses. Disclosures Kulasekararaj: Alexion:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Ra Pharma:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;BioCryst Pharmaceuticals, Inc.:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees;Apellis:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Roche:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Novartis:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau;Celgene:Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel grants, Speakers Bureau.Malherbe:Key Oncologics:Honoraria, Other: Conference sponsor;Novartis:Other: Conference sponsor;Astellas:Honoraria, Other: Conference sponsor;Takeda:Consultancy;Acino:Honoraria;Shire:Other: Conference sponsor;BioCryst Pharmaceuticals, Inc.:Consultancy;Janssen:Consultancy, Honoraria, Other: Conference sponsor;Roche:Honoraria, Other: Conference sponsor.McDonald:venetoclax advisory board in South Africa (in CLL context):Consultancy;Alberts Cellular Therapy:Current Employment.Cornpropst:BioCryst Pharmaceuticals, Inc.:Current Employment.Collis:BioCryst Pharmaceuticals, Inc.:Current Employment.Davidson:BioCryst Pharmaceuticals, Inc.:Current Employment.Chen:BioCryst Pharmaceuticals, Inc.:Current Employment.Tower:BioCryst Pharmaceuticals, Inc.:Current Employment.Gesty-Palmer:BioCryst Pharmaceuticals, Inc.:Current equity holder in publicly-traded company, Ended employment in the past 24 months.Sheridan:BioCryst Pharmaceuticals, Inc.:Current Employment.Risitano:Alexion:Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau;Alnylam:Research Funding;Novartis:Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau;Pfizer:Speakers Bureau;Achillion:Membership on an entity's Board of Directors or advisory committees;Apellis:Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Biocryst:Membership on an entity's Board of Directors or advisory committees;RA pharma:Research Funding;Amyndas:Consultancy;Samsung:Membership on an entity's Board of Directors or advisory committees;Roche:Membership on an entity's Board of Directors or advisory committees;Jazz:Speakers Bureau.


2021 ◽  
Author(s):  
Dawsyn Borland

This project presents the idea that historic house museums (HHMs) can use Augmented Reality (AR) and physical interactive space to bring stories and characters of the past back to life. Designed to foster self-directed discovery and informal learning of the space and story, this project uses a historically factual AR character to reanimate the sense of human presence within the space. Rather than disrupting the traditional narratives of HHMs, this mixed media storytelling experience extends historical stories by making them more personal and relatable. Using tangible stories, multisensory interactions, and an AR experience to extend the historical narrative, this form of museological work creates more opportunities for empathic character-driven storytelling. Lastly, I identify that this proof of concept could be used in multiple applications, as both a storytelling medium and a communication tool.


2021 ◽  
Author(s):  
jorge cabrera Alvargonzalez ◽  
Ana Larranaga Janeiro ◽  
Sonia Perez ◽  
Javier Martinez Torres ◽  
Lucia martinez lamas ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been and remains one of the major challenges humanity has faced thus far. Over the past few months, large amounts of information have been collected that are only now beginning to be assimilated. In the present work, the existence of residual information in the massive numbers of rRT-PCRs that tested positive out of the almost half a million tests that were performed during the pandemic is investigated. This residual information is believed to be highly related to a pattern in the number of cycles that are necessary to detect positive samples as such. Thus, a database of more than 20,000 positive samples was collected, and two supervised classification algorithms (a support vector machine and a neural network) were trained to temporally locate each sample based solely and exclusively on the number of cycles determined in the rRT-PCR of each individual. Finally, the results obtained from the classification show how the appearance of each wave is coincident with the surge of each of the variants present in the region of Galicia (Spain) during the development of the SARS-CoV-2 pandemic and clearly identified with the classification algorithm.


2015 ◽  
Vol 6 (1) ◽  
pp. 34-43
Author(s):  
Mark Bruce Freeman

There has been a dramatic shift in the interaction methods of mobile devices over the past decade. From devices simply being able to make phone calls to being able to handle complex tasks traditionally performed on personal computers (PCs); this change has led to new interaction issues that need to be understood during the application development process, particularly as these devices now commonly incorporate a touch-screen as their primary source of input. Currently, the methods of conducting software user experience testing of these devices employs techniques that were developed for PCs, however mobile devices are used within different contexts of use. This research initially reviews the current methods for user experience testing of applications running on mobile devices and then presents, through a proof-of-concept approach, an innovative method for conducting user experience testing employing actual devices.


Author(s):  
Vibeke Strand ◽  
Jeremy Sokolove ◽  
Alvina D. Chu

Development of new therapies for rheumatic diseases requires a series of randomized controlled trials (RCTs) progressing from phase 1, ’first-in-human’ to generate initial safety, pharmacokinetic (PK) and pharmacodynamic (PD) data; to phase 2, proof of concept for efficacy with safety and PK/PD data; and phase 3, designed to demonstrate definitive efficacy and safety to support regulatory approval. Important aspects of RCT designs include sample size estimations, treatment allocation, rescue, blinding, and statistical analyses of prespecified endpoints to preserve trial integrity. Over the past 15 years, significant progress has been made in the design of RCTs in rheumatoid arthritis (RA). Similarly, development and validation of composite outcome measures in psoriatic arthritis, ankylosing spondylitis, gout, and osteoarthritis have furthered trial design and treatment approvals. RCTs in systemic lupus erythematosus and other multisystem, heterogeneous diseases pose more challenges. Trial design will continue to evolve as promising therapies are introduced into the clinic.


Author(s):  
Vibeke Strand ◽  
Jeremy Sokolove ◽  
Alvina D. Chu

Development of new therapies for rheumatic diseases requires a series of randomized controlled trials (RCTs) progressing from phase 1, 'first-in-human' to generate initial safety, pharmacokinetic (PK) and pharmacodynamic (PD) data; to phase 2, proof of concept for efficacy with safety and PK/PD data; and phase 3, designed to demonstrate definitive efficacy and safety to support regulatory approval. Important aspects of RCT designs include sample size estimations, treatment allocation, rescue, blinding, and statistical analyses of prespecified endpoints to preserve trial integrity. Over the past 15 years, significant progress has been made in the design of RCTs in rheumatoid arthritis (RA). Similarly, development and validation of composite outcome measures in psoriatic arthritis, ankylosing spondylitis, gout, and osteoarthritis have furthered trial design and treatment approvals. RCTs in systemic lupus erythematosus and other multisystem, heterogeneous diseases pose more challenges. Trial design will continue to evolve as promising therapies are introduced into the clinic.


2020 ◽  
Vol 12 (572) ◽  
pp. eaaz2253
Author(s):  
James P. K. Armstrong ◽  
Timothy J. Keane ◽  
Anne C. Roques ◽  
P. Stephen Patrick ◽  
Claire M. Mooney ◽  
...  

The past few decades have produced a large number of proof-of-concept studies in regenerative medicine. However, the route to clinical adoption is fraught with technical and translational obstacles that frequently consign promising academic solutions to the so-called “valley of death.” Here, we present a proposed blueprint for translational regenerative medicine. We offer principles to help guide the selection of cells and materials, present key in vivo imaging modalities, and argue that the host immune response should be considered throughout design and development. Last, we suggest a pathway to navigate the often complex regulatory and manufacturing landscape of translational regenerative medicine.


2017 ◽  
Vol 373 (1737) ◽  
pp. 20160479 ◽  
Author(s):  
Mercedes Tkach ◽  
Joanna Kowal ◽  
Clotilde Théry

In the past decade, cell-to-cell communication mediated by exosomes has attracted growing attention from biomedical scientists and physicians, leading to several recent publications in top-tier journals. Exosomes are generally defined as secreted membrane vesicles, or extracellular vesicles (EVs), corresponding to the intraluminal vesicles of late endosomal compartments, which are secreted upon fusion of multi-vesicular endosomes with the cell's plasma membrane. Cells, however, were shown to release other types of EVs, for instance, by direct budding off their plasma membrane. Some of these EVs share with exosomes major biophysical and biochemical characteristics, such as size, density and membrane orientation, which impose difficulties in their efficient separation. Despite frequent claims in the literature, whether exosomes really display more important patho/physiological functions, or are endowed with higher potential as diagnostic or therapeutic tools than other EVs, is not yet convincingly demonstrated. In this opinion article, we describe reasons for this lack of precision knowledge in the current stage of the EV field, we review recently described approaches to overcome these caveats, and we propose ways to improve our knowledge on the respective functions of distinct EVs, which will be crucial for future development of well-designed EV-based clinical applications. This article is part of the discussion meeting issue ‘Extracellular vesicles and the tumour microenvironment’.


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