DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning.

BackgroundMeasuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target for diseases like cancer. In recent years, the detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method to supersede existing single-molecule methods such as DNA fibre analysis: ONT sequencing yields long reads with high throughput, and sequenced molecules can be mapped to the genome using standard sequence alignment software.ResultsThis paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-nucleotide resolution. DNAscent v2 also comes equipped with an autoencoder that interprets the pattern of BrdU incorporation on each ONT-sequenced molecule into replication fork direction to call the location of replication origins termination sites. DNAscent v2 surpasses previous versions of DNAscent in BrdU calling accuracy, origin calling accuracy, speed, and versatility across different experimental protocols. Unlike NanoMod, DNAscent v2 positively identifies BrdU without the need for sequencing unmodified DNA. Unlike RepNano, DNAscent v2 calls BrdU with single-nucleotide resolution and detects more origins than RepNano from the same sequencing data. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent .ConclusionsThis paper shows that DNAscent v2 is the new state-of-the-art in the high-throughput, single-molecule detection of replication fork dynamics. These improvements in DNAscent v2 mark an important step towards measuring DNA replication dynamics in large genomes with single-molecule resolution. Looking forward, the increase in accuracy in single-nucleotide resolution BrdU calls will also allow DNAscent v2 to branch out into other areas of genome stability research, particularly the detection of DNA repair

DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning

Abstract: Background: Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be used as a therapeutic target for diseases like cancer. In recent years, the detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method to supersede existing single-molecule methods such as DNA fibre analysis: ONT sequencing yields long reads with high throughput, and sequenced molecules can be mapped to the genome using standard sequence alignment software. Results: This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-nucleotide resolution. DNAscent v2 also comes equipped with an autoencoder that interprets the pattern of BrdU incorporation on each ONT-sequenced molecule into replication fork direction to call the location of replication origins termination sites. DNAscent v2 surpasses previous versions of DNAscent in BrdU calling accuracy, origin calling accuracy, speed, and versatility across different experimental protocols. Unlike NanoMod, DNAscent v2 positively identifies BrdU without the need for sequencing unmodified DNA. Unlike RepNano, DNAscent v2 calls BrdU with single-nucleotide resolution and detects more origins than RepNano from the same sequencing data. DNAscent v2 is open-source and available at https://github.com/MBoemo/DNAscent. Conclusions: This paper shows that DNAscent v2 is the new state-of-the-art in the high-throughput, single-molecule detection of replication fork dynamics. These improvements in DNAscent v2 mark an important step towards measuring DNA replication dynamics in large genomes with single-molecule resolution. Looking forward, the increase in accuracy in single-nucleotide resolution BrdU calls will also allow DNAscent v2 to branch out into other areas of genome stability research, particularly the detection of DNA repair

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.

Biological systems are made up of components that change their actions (and interactions) over time and coordinate with other components nearby. Together with a large state space, the complexity of this behaviour can make it difficult to create concise mathematical models that can be easily extended or modified. This paper introduces the Beacon Calculus, a process algebra designed to simplify the task of modelling interacting biological components. Its breadth is demonstrated by creating models of DNA replication dynamics, the gene expression dynamics in response to DNA methylation damage, and a multisite phosphorylation switch. The flexibility of these models is shown by adapting the DNA replication model to further include two topics of interest from the literature: cooperative origin firing and replication fork barriers. The Beacon Calculus is supported with the open-source simulator bcs (https://github.com/MBoemo/bcs.git) to allow users to develop and simulate their own models

The Formal Language and Design Principles of Autonomous DNA Walker Circuits.

Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses

Watermarking strategies for IP protection of micro-processor cores

L. Parrilla, E. Castillo, U. Meyer-Bäse, A. García, D. González, E. Todorovich, E. Boemo, A. Lloris, "Watermarking strategies for IP protection of micro-processor cores", Proceedings of SPIE 7703, Independent Component Analyses, Wavelets, Neural Networks, Biosystems, and Nanoengineering VIII, 77030L (2010). Copyright 2010 Society of Photo‑Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.Reuse-based design has emerged as one of the most important methodologies for integrated circuit design, with reusable Intellectual Property (IP) cores enabling the optimization of company resources due to reduced development time and costs. This is of special interest in the Field-Programmable Logic (FPL) domain, which mainly relies on automatic synthesis tools. However, this design methodology has brought to light the intellectual property protection (IPP) of those modules, with most forms of protection in the EDA industry being difficult to translate to this domain. However, IP core watermarking has emerged as a tool for IP core protection. Although watermarks may be inserted at different levels of the design flow, watermarking Hardware Description Language (HDL) descriptions has been proved to be a robust and secure option. In this paper, a new framework for the protection of μP cores is presented. The protection scheme is derived from the IPP@HDL procedure and it has been adapted to the singularities of μP cores, overcoming the problems for the digital signature extraction in such systems. Additionally, the feature of hardware activation has been introduced, allowing the distribution of μP cores in a "demo" mode and a later activation that can be easily performed by the customer executing a simple program. Application examples show that the additional hardware introduced for protection and/or activation has no effect over the performance, and showing an assumable area increase.This work was partially funded by project TEC2007-68074-C02-01/MIC (Plan Nacional I+D+I, Spain). CAD tools and supporting material were provided by Altera Corp. trough University Program agreements. Any opinions, findings, and conclusions or recommendations expressed in this paper are those of the authors and do not necessarily reflect the views of the sponsors

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git

Minimally invasive urologic surgery is safe during COVID-19: experience from two high-volume centers in Italy

Potential risks of COVID-19 spread during minimally invasive procedures caused several concerns among surgeons, despite the lack of high-level evidence. Urological robotic and laparoscopic surgery is performed in elective setting in almost all occasions, thus allowing adequate planning and stratification. Two high-volume urological centers in Italy performed 77 robotic and laparoscopic surgeries during the \u201clockdown\u201d period and adopted various strategies to prevent contamination. First of all, all patients were tested negative with nasopharyngeal swab before the surgical intervention. Patients and personnel were provided adequate personal protective equipment and intraoperative strategies to prevent smoke formation and pneumoperitoneum spread were adopted. No patients nor staff members tested positive for COVID-19 during a 15-day follow-up period. In conclusion, minimally invasive urologic surgery can be safely performed during the pandemic period with adequate planning. We believe that renouncing the benefits of it would be counterproductive, especially in a scenario of long-lasting cohabitation with the virus

Pilot Study on the Efficiency of the Biostimulation with Autologous Plasma Rich in Platelet Growth Factors in Otorhinolaryngology: Otologic Surgery (Tympanoplasty Type I)

When otologic procedures that involve tympanic membrane repairs are performed, biomaterials or biological tissues as normal as grafts are used. At the moment, biological material from the own patient is used with varying success rates. The procedure used and the patient's tissue repair capabilities tend to determine the outcome. We present a preliminary study on tympanic membrane perforation repairs using an autograft obtained by manipulating platelet degranulation and the coagulation cascade and reinforced with a seal using platelet growth factors. We present three cases in which we used this procedure. The results will be valued based on the tympanic perforation closure index. With this study, we want to assess the effectiveness of tympanic perforation repairs with this technically simple method. If this method was objectively proved to be effective, it would lead to lower patient morbidity and sanitary costs

Chemometric modeling for spatiotemporal characterization and self-depuration monitoring of surface water assessing the pollution sources impact of northern Argentina rivers

In Argentina, both surface and ground water are used for a diverse priority purposes, such as drinking and basic hygiene, but they are also utilized as receivers of different types of industrial and urban and suburban effluents that affect their natural composition. This activity accompanied by the increase of the population and climate changes have activated the alarms of organism water management forced to implement strict quality controls previous to its use. In this work, a systematic evaluation of a set of physicochemical and biological parameters measured in 19 sampling sites during the period 2017–2019 is presented. Principal component analysis (PCA) and matrix augmentation-PCA (MA-PCA) were applied as exploratory analysis tools to visualize and interpret the information contained in the dataset. Both studies allowed to detect the relevant variables and to differentiate the samples based on pollution areas. These models led to similar conclusions; nonetheless, MA-PCA provided a more straightforward overview of the spatiotemporal variation of the samples in comparison to classical PCA. Finally, a significant and sensitive discriminant model (93% non-error rate) was developed to analyze and predict the self-depuration of the rivers. The excellent predictive ability achieved by this model makes its application suitable for the monitoring of the water quality.Fil: Jurado Zavaleta, Marcelo A.. Universidad Nacional de Salta; ArgentinaFil: Alcaraz, Mirta Raquel. Universidad Nacional del Litoral; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Peñaloza, Lidia Guadalupe. Universidad Nacional de Salta; ArgentinaFil: Boemo, Analía. Universidad Nacional de Salta; ArgentinaFil: Cardozo, Ana. No especifíca;Fil: Tarcaya, Gerardo. No especifíca;Fil: Azcarate, Silvana Mariela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Goicoechea, Hector Casimiro. Universidad Nacional del Litoral; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin