The NTD Nanoscope: potential applications and implementations

<p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.</p> <p>Results</p> <p>The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.</p> <p>Conclusions</p> <p>SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.</p

Validity of Landauer's principle in the quantum regime

We demonstrate the validity of Landauer's erasure principle in the strong coupling quantum regime by treating the system-reservoir interaction in a consistent way. We show that the initial coupling to the reservoir modifies both energy and entropy of the system and provide explicit expressions for the latter in the case of a damped quantum harmonic oscillator. These contributions are related to the Hamiltonian of mean force and dominate in the strong damping limit. They need therefore to be fully taken into account in any low-temperature thermodynamic analysis of quantum systems.Comment: 4 pages, 2 figure

Analyzing Declarative Deployment Code with Large Language Models

In the cloud-native era, developers have at their disposal an unprecedented landscape of services to build scalable distributed systems. The DevOps paradigm emerged as a response to the increasing necessity of better automations, capable of dealing with the complexity of modern cloud systems. For instance, Infrastructure-as-Code tools provide a declarative way to define, track, and automate changes to the infrastructure underlying a cloud application. Assuring the quality of this part of a code base is of utmost importance. However, learning to produce robust deployment specifications is not an easy feat, and for the domain experts it is time-consuming to conduct code-reviews and transfer the appropriate knowledge to novice members of the team. Given the abundance of data generated throughout the DevOps cycle, machine learning (ML) techniques seem a promising way to tackle this problem. In this work, we propose an approach based on Large Language Models to analyze declarative deployment code and automatically provide QA-related recommendations to developers, such that they can benefit of established best practices and design patterns. We developed a prototype of our proposed ML pipeline, and empirically evaluated our approach on a collection of Kubernetes manifests exported from a repository of internal projects at Nokia Bell Labs

Recent Advances on Iron Oxide Magnetic Nanoparticles as Sorbents of Organic Pollutants in Water and Wastewater Treatment

The constant growth in population worldwide over the past decades continues to put forward the need to provide access to safe, clean water to meet human needs. There is a need for cost-effective technologies for water and wastewater treatment that can meet the global demands and the rigorous water quality standards and at the same maximizing pollutant efficiency removal. Current remediation technologies have failed in keeping up with these factors without becoming cost-prohibitive. Most recently, nanotechnology has been sought as the best alternative to increase access to water supplies by remediating those already contaminated and offering ways to access unconventional sources. The use of iron oxide magnetic nanoparticles as nanoadsorbents has led way to a new class of magnetic separation strategies for water treatment. This review focuses on highlighting some of the most recent advances in core-shell iron oxide magnetic nanoparticles and nanocomposites containing iron oxide nanoparticles currently being developed for water and wastewater treatment of organic pollutants. We discuss the novelty of these novel materials and the insight gained from their advances that can help develop cost-effective reusable technologies for scale-up and commercial use

Boom‐bust dynamics in biological invasions: towards an improved application of the concept

Boom‐bust dynamics – the rise of a population to outbreak levels, followed by a dramatic decline – have been associated with biological invasions and offered as a reason not to manage troublesome invaders. However, boom‐bust dynamics rarely have been critically defined, analyzed, or interpreted. Here, we define boom‐bust dynamics and provide specific suggestions for improving the application of the boom‐bust concept. Boom‐bust dynamics can arise from many causes, some closely associated with invasions, but others occurring across a wide range of ecological settings, especially when environmental conditions are changing rapidly. As a result, it is difficult to infer cause or predict future trajectories merely by observing the dynamic. We use tests with simulated data to show that a common metric for detecting and describing boom‐bust dynamics, decline from an observed peak to a subsequent trough, tends to severely overestimate the frequency and severity of busts, and should be used cautiously if at all. We review and test other metrics that are better suited to describe boom‐bust dynamics. Understanding the frequency and importance of boom‐bust dynamics requires empirical studies of large, representative, long‐term data sets that use clear definitions of boom‐bust, appropriate analytical methods, and careful interpretations

Décision motrice et contrôle modulaire d'un système hyper-redondant

This thesis is aimed at better understanding how the Central Nervous System (CNS) plans and controls voluntary movements. When moving, humans must overcome intrinsic (e.g. choosing which muscles to activate) and extrinsic (e.g. choosing where to reach an object) redundancy, requiring selecting one motor solution among several potential ones. To better understand this process, we studied in parallel two important motor control theories: muscular synergies and motor decision. In a first part, we focused on intrinsic redundancy by testing the muscular synergies hypothesis. According to it, the CNS simplifies the control of muscles, in using a limited set of building blocks whose linear combinations allow the performance of virtually any motor task. In this study, we challenge the modular motor control hypothesis by combining a) the design of a highly comprehensive experiment with b) the use of a unifying modularity model to describe single-trial EMG activity in space and time and c) a module evaluation process that assesses the modular decomposition not only in input space (EMG data reconstruction) but also in task space (task discrimination). Our rationale is that an effective modular control implementation would allow not only the formation of a wide variety of muscle patterns but also the achievement of a large set of tasks. The main theoretical result is the existence of few spatial and temporal modules that not onlygive a concise representation of muscle patterns but also carry nearly all task-relevant information of EMG signals. In a second part, we studied the decisional process that underlies all voluntary movement. In daily life, human movement is guided by objective external constraints (e.g. an object to reach), potential external cost/benefits (e.g. monetary reward) and internal cost/benefits associated with each movement (e.g. energy expenditure). Here,we aimed at investigating internal variables orienting action selection when facing the complexity of human-environment interactions. To this aim, we designed an experimental protocol reducing external constraints: no predetermined endpoint (e.g. salient target) and no explicit reward (e.g. money). Subjects had to perform whole body reaching movements towards a uniform surface (no pre-determined endpoint). Our results illustrate the presence of idiosyncratic values guiding posture and movement coordination that can be combined in a flexible manner as a function of context and subject. A first value takes into account the energy expenditure and articular jerk, while the other favored stable dynamic equilibrium but requires larger energy expenditure and articular jerk. In conclusion of this work, we suggest that motor control can be viewed as a decision process evaluating internal values to elaborate the most efficient control in function of context. In addition, this control can be simplified by the use of functional modules allowing CNS to generate rapidly a large set of whole body movements.Ces travaux de thèse ont pour objectif de mieux comprendre comment le système nerveux central (SNC) planifie et contrôle les mouvements volontaires. Tout mouvement nécessite la résolution de deux types de redondance : interne (complexité du corps) et externe (interactions avec l’environnement), qui rendent difficile la sélection d’une action. Pour mieux comprendre ce contrôle, nous avons étudié en parallèle deux hypothèses importantes dans le domaine du contrôle moteur : les synergies musculaires et la décision motrice. Selon l’hypothèse des synergies musculaires, le contrôle des muscles par le SNC serait simplifié par l’utilisation de groupements invariants d’activations coordonnées de différents muscles, dont la combinaison sous-tendrait la réalisation de mouvements complexes. Le but de cette étude était de mettre à l’épreuve l’hypothèse des synergies musculaires en étudiant simultanément : a) un protocole spécifiant un grand nombre de mouvements variés, b) un nouveau modèle mathématiques tenant compte, pour l’extraction des synergies, de la modularité spatiale et temporelle, c) une double-évaluation de la qualité de la décomposition en synergies : au niveau musculaire (métrique VAF) et fonctionnel (performance de décodage). Notre idée directrice était que l’utilisation de synergies musculaires par le SNC n’est plausible que si elles permettent de rendre compte des activations musculaires d’un grand nombre de mouvements différents, et possèdent chacune un rôle fonctionnel spécifique. Les résultats de cette première étude montrent l'existence d'un petit ensemble de synergies dont la combinaison reconstruit les activations musculaires, et code efficacement toutes les tâches testées. La sélection d’une action, vue comme une prise de décision, peut être guidée par les contraintes extérieures objectives (e.g. la position de l’objet à attraper), les coûts/bénéfices explicites potentiels (e.g. une récompense monétaire), et les coûts/bénéfices internes associés à chaque mouvement (e.g. dépense d’énergie). Au quotidien, les actes sont rarement associés à des récompenses explicites. De plus, la redondance extrinsèque est toujours présente, la saisie d'une pomme par exemple ne définit pas une position finale précise de la main, contrairement au protocole souvent étudié de pointage d'une cible saillante. Les valeurs internes guidant le mouvement auraient donc une importance particulière dans le processus de décision motrice. Afin de les étudier, nous avons construit un protocole limitant les influences décisionnelles externes décrites ci-dessus. Les résultats de cette deuxième étude montrent des comportements différents entre les sujets, et mettent en avant en particulier l'existence de deux valeurs internes guidant la coordination entre posture et mouvement En conclusion, nous suggérons que le contrôle du mouvement peut être vu comme un processus de décision évaluant des valeurs internes pour produire la solution motrice la plus pertinente pour le contexte présent. De plus, ce contrôle serait simplifié par l'utilisation complémentaire de modules fonctionnels stockés dans le SNC

Differences in gaze anticipation for locomotion with and without vision

International audiencePrevious experimental studies have shown a spontaneous anticipation of locomotor trajectory by the head and gaze direction during human locomotion. This anticipatory behavior could serve several functions: an optimal selection of visual information, for instance through landmarks and optic flow, as well as trajectory planning and motor control. This would imply that anticipation remains in darkness but with different characteristics. We asked 10 participants to walk along two predefined complex trajectories (limaçon and figure eight) without any cue on the trajectory to follow. Two visual conditions were used: (i) in light and (ii) in complete darkness with eyes open. The whole body kinematics were recorded by motion capture, along with the participant's right eye movements. We showed that in darkness and in light, horizontal gaze anticipates the orientation of the head which itself anticipates the trajectory direction. However, the horizontal angular anticipation decreases by a half in darkness for both gaze and head. In both visual conditions we observed an eye nystagmus with similar properties (frequency and amplitude). The main difference comes from the fact that in light, there is a shift of the orientations of the eye nystagmus and the head in the direction of the trajectory. These results suggest that a fundamental function of gaze is to represent self motion, stabilize the perception of space during locomotion, and to simulate the future trajectory, regardless of the vision condition