Direct Perturbation Research Articles

Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits.

We present an enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits. Best-in-class vectors were curated for accessing major striatal neuron populations including medium spiny neurons (MSNs), direct and indirect pathway MSNs, as well as Sst-Chodl, Pvalb-Pthlh, and cholinergic interneurons. Specificity was evaluated by multiple modes of molecular validation, three different routes of virus delivery, and with diverse transgene cargos. Importantly, we provide detailed information necessary to achieve reliable cell type specific labeling under different experimental contexts. We demonstrate direct pathway circuit-selective optogenetic perturbation of behavior and multiplex labeling of striatal interneuron types for targeted analysis of cellular features. Lastly, we show conserved in vivo activity for exemplary MSN enhancers in rat and macaque. This collection of striatal enhancer AAVs offers greater versatility compared to available transgenic lines and can readily be applied for cell type and circuit studies in diverse mammalian species beyond the mouse model.

Unexpectedly high wet mercury deposition observed in the Yarlung Tsangpo Grand canyon

Situated in the south edge of the Tibetan Plateau, the Himalayas is expected to receive direct anthropogenic Hg perturbations from South Asia, yet the measurements of atmospheric Hg deposition in the Himalayan region remain scarce. Here we report wet Hg deposition measured in the Yarlung Tsangpo Grand Canyon of the Eastern Himalayas, which is the deepest and longest canyon on earth. The precipitation Hg concentration (56.3 ng L−1) and wet Hg deposition flux (84.7 μg m−2 yr−1) from the Motuo station were observed among the highest ever reported for the Tibetan Plateau. Together with analysis of principal component suggesting Hg was mainly clustered with anthropogenic ions and backward trajectories indicating 88.8% of air masses came from South Asia, our results show that transboudary pollution influences from South Asia could be largely responsible for the unexpectedly high levels of wet Hg deposition. Moreover, the wet Hg flux measurements (84.7 μg m−2 yr−1) are found an order of magnitude (∼13 times) higher than the GEOS-Chem estimates (6.8 μg m−2 yr−1), most likely due to the underestimation of transboundary Hg pollution influence by this model. Our study has important implications for better understanding Hg dynamics and verifying atmospheric Hg models in the Tibetan Plateau and Himalayas region.

Human organoids with an autologous tissue-resident immune compartment

The intimate relationship between the epithelium and immune system is crucial for maintaining tissue homeostasis, with perturbations therein linked to autoimmune disease and cancer1–3. Whereas stem cell-derived organoids are powerful models of epithelial function4, they lack tissue-resident immune cells that are essential for capturing organ-level processes. We describe human intestinal immuno-organoids (IIOs), formed through self-organization of epithelial organoids and autologous tissue-resident memory T (TRM) cells, a portion of which integrate within the epithelium and continuously survey the barrier. TRM cell migration and interaction with epithelial cells was orchestrated by TRM cell-enriched transcriptomic programs governing cell motility and adhesion. We combined IIOs and single-cell transcriptomics to investigate intestinal inflammation triggered by cancer-targeting biologics in patients. Inflammation was associated with the emergence of an activated population of CD8+ T cells that progressively acquired intraepithelial and cytotoxic features. The appearance of this effector population was preceded and potentiated by a T helper-1-like CD4+ population, which initially produced cytokines and subsequently became cytotoxic itself. As a system amenable to direct perturbation, IIOs allowed us to identify the Rho pathway as a new target for mitigation of immunotherapy-associated intestinal inflammation. Given that they recapitulate both the phenotypic outcomes and underlying interlineage immune interactions, IIOs can be used to study tissue-resident immune responses in the context of tumorigenesis and infectious and autoimmune diseases.

Torque-ratio-adjustable ankle-foot exoskeleton for resisting perturbation in forward direction within fan-shaped region of pelvis horizontal plane.

Introduction: The ankle-foot exoskeleton has been demonstrated to help users resist anterior perturbation in the horizontal pelvis plane. However, its effects on perturbations in other directions remain unclear. This paper focuses on how the ankle-foot exoskeleton helps people resist perturbations coming from forward directions within the fan-shaped region in the pelvis horizontal plane. Methods: Firstly, we proposed and validated a hypothesis that the human torque ratio of inversion to plantar flexion torque would change with the perturbation directions of anterior (dir0) and 45° deviating from anterior to left (dir45). Subsequently, based on the regulation demand, we developed an ankle-foot exoskeleton that can adjust the torque ratio delivered to the human body by controlling the forces on two cross-arranged cables. Finally, we evaluated and compared the assistance performance of three powered assistive modes (NM, medBD, and latBD) with the unpowered one (UN) by setting different force pairs in two cables. Results: The results showed that, with the assistance, the margin of stability was increased and the standard deviations of ankle-foot segmental movements were decreased. Meanwhile, the biological inversion torque has a significant difference among the three assistive modes. Compared to the UN, the latBD was shown to reduce the biological inversion torque by 15.8 and 13.7 in response to the dir0 and dir45 perturbations, respectively, while the reductions for the NM and medBD were smaller. It was also observed that the torque ratios, generated by the human and the exoskeleton in latBD mode, differed by about 0.1 under dir0 and 0.08 under dir45, while the physiologically similarity of the exoskeleton torque ratio in NM and medBD modes were smaller. Based on the above results, we found that the more physiologically similar the exoskeleton torque ratio, the better the assistive performance. Discussion: The findings demonstrated that the torque-ratio-adjustable exoskeleton could support human resistance to perturbations coming from forward directions within a fan-shaped region in the pelvis horizontal plane and indicated that the exoskeleton's torque ratio should be carefully modulated to match the ratio of the human under various environmental conditions for better assistive performance.

Nonlinear coupled vibration of an arch-beam structural system

Nonlinear dynamic analysis of a shallow arch coupled with a cantilever beam (resting on Winkler foundation) is investigated by direct perturbation method. Two key parameters, (beam over arch) density ratio and height of beam, recharacterize coupling intensity between arch and beam. Nonlinear dynamic responses of arch-beam coupled model are predicted by asymptotic analysis, which include hardening and softening cases. After numerical verification of arch-beam coupled model, the uncoupled model (i.e., skipping beam-arch coupling) is also investigated for comparison. Besides, two more related but degenerately coupled models, e.g., arch-oscillator coupled model [1] and arch-rigid body coupled model [2] are both compared with the current arch-beam coupled model, revealing one key coupling characteristic of elastic support/foundation, which is however overlooked in previous models, e.g., only partial mass is involved with dynamic coupling.

Time-Dependent Effective Hamiltonians for Light-Matter Interactions.

In this paper, we present a systematic approach to building useful time-dependent effective Hamiltonians in molecular quantum electrodynamics. The method is based on considering part of the system as an open quantum system and choosing a convenient unitary transformation based on the evolution operator. We illustrate our formalism by obtaining four Hamiltonians, each suitable to a different class of applications. We show that we may treat several effects of molecular quantum electrodynamics with a direct first-order perturbation theory. In addition, our effective Hamiltonians shed light on interesting physical aspects that are not explicit when employing more standard approaches. As applications, we discuss three examples: two-photon spontaneous emission, resonance energy transfer, and dispersion interactions.

SSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis

sSNAPPY: an R/Bioconductor package for single-sample directional pathway perturbation analysis

Frequency Domain Channel-Wise Attack to CNN Classifiers in Motor Imagery Brain-Computer Interfaces.

Convolutional neural network (CNN), a classical structure in deep learning, has been commonly deployed in the motor imagery brain-computer interface (MIBCI). Many methods have been proposed to evaluate the vulnerability of such CNN models, primarily by attacking them using direct temporal perturbations. In this work, we propose a novel attacking approach based on perturbations in the frequency domain instead. For a given natural MI trial in the frequency domain, the proposed approach, called frequency domain channel-wise attack (FDCA), generates perturbations at each channel one after another to fool the CNN classifiers. The advances of this strategy are two-fold. First, instead of focusing on the temporal domain, perturbations are generated in the frequency domain where discriminative patterns can be extracted for motor imagery (MI) classification tasks. Second, the perturbing optimization is performed based on differential evolution algorithm in a black-box scenario where detailed model knowledge is not required. Experimental results demonstrate the effectiveness of the proposed FDCA which achieves a significantly higher success rate than the baselines and existing methods in attacking three major CNN classifiers on four public MI benchmarks. Perturbations generated in the frequency domain yield highly competitive results in attacking MIBCI deployed by CNN models even in a black-box setting, where the model information is well-protected. To our best knowledge, existing MIBCI attack approaches are all gradient-based methods and require details about the victim model, e.g., the parameters and objective function. We provide a more flexible strategy that does not require model details but still produces an effective attack outcome.

Implementation and Testing of Generalized Perturbation Theory Capabilities in TRIPOLI-4®

In this paper, we describe the implementation, verification, and numerical validation of Generalized Perturbation Theory (GPT) capabilities in the TRIPOLI4® Monte Carlo code. The GPT is applied to reaction rate ratios (linear forms) and effective kinetics parameters (bilinear forms). For these latter, we focus in particular on the effective neutron generation time Λ eff , the effective prompt lifetime ℓ eff , and the effective delayed neutron fraction β eff . Verification is achieved comparing the results obtained using TRIPOLI-4® to benchmarks where analytical solutions are available. Numerical validation is performed with respect to independent Monte Carlo calculations using the SCALE 6.2.4 and SERPENT 2.2 codes, to published results, and to direct perturbations. Finally, a comparison with respect to the APOLLO3® deterministic code is performed for the EPICURE experimental configuration of the water-moderated EOLE reactor core, formerly operated at CEA.

ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates’ biomineralizing cells, yet, little is known on ROCK’s role in invertebrates’ biomineralization. Here, we reveal that ROCK controls the formation, growth, and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces the spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.

ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates’ biomineralizing cells, yet, little is known on ROCK’s role in invertebrates’ biomineralization. Here, we reveal that ROCK controls the formation, growth, and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces the spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.

Iterated local search with ejection chains for the space-free multi-row facility layout problem

This paper presents an iterated local search algorithm based on ejection chains to solve the space-free multi-row facility layout problem. The aim of this problem is to find a non-overlapping layout of facilities on a given number of rows such that there is no space between two adjacent facilities. In addition, the left-most facility of the arrangement must have zero abscissa. Our algorithm looks for a local optimal solution by continuously alternating ejection moves and trial moves to form an ejection chain. Since the ejection chain can compound simple moves to create more complex and powerful moves, it has a greater chance to discover better solutions. Additionally, we propose a directional perturbation strategy to produce a solution of both high quality and good diversity. The idea is to calculate the score of each facility based on the location concentration of facilities in the elite solution set and the historical perturbation times of facilities in the search process, and to select the facility with the highest score for perturbation. Experimental results on four benchmark sets containing a total of 290 instances reveal that the proposed algorithm performs better for 131 (45.2%) instances in terms of best solution values and for 196 (80.0%) instances in terms of average solution values than a recently reported state-of-the-art algorithm.

Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell

The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of C. elegans anchor cell (AC) invasion into the vulval epithelium. The AC is a terminally differentiated uterine cell that normally exits the cell cycle and enters a post-mitotic state before initiating contact between the uterus and vulva through a cell invasion event. Here, we set out to identify the set of negative cell cycle regulators that maintain the AC in this post-mitotic, invasive state. Our findings revealed a critical role for CKI-1 (p21CIP1/p27KIP1) in redundantly maintaining the post-mitotic state of the AC, as loss of CKI-1 in combination with other negative cell cycle regulators—including CKI-2 (p21CIP1/p27KIP1), LIN-35 (pRb/p107/p130), FZR-1 (Cdh1/Hct1), and LIN-23 (β-TrCP)—resulted in proliferating ACs. Remarkably, time-lapse imaging revealed that these ACs retain their ability to invade. Upon examination of a node in the gene regulatory network controlling AC invasion, we determined that proliferating, invasive ACs do so by maintaining aspects of pro-invasive gene expression. We therefore report that the requirement for a post-mitotic state for invasive cell behavior can be bypassed following direct cell cycle perturbation.

Cellular Mechanisms Associated with Neurodevelopmental Alterations Produced by General Anesthetics

: There is concern about neurodevelopmental disturbances associated with exposure to general anesthesia during early childhood. In 2016, the U.S. Food and Drug Administration released a safety alert regarding the use of gamma-aminobutyric acid (GABA) agonists and N-methyl-D-aspartate (NMDA) receptor antagonists in pediatric anesthesia, warning about the risks of their use during the last trimester of pregnancy and in children under 3 years for neurodevelopment. Animal and in vitro studies demonstrate worrisome morphological and functional alterations in young neurons and glia induced by different anesthetic drugs. These drugs can induce changes in various neuronal transmission systems, alter dendritic growth and brain connectivity, and initiate processes leading to cell demise, such as aberrant cell cycle reentry, mitochondrial dysfunction, excitotoxicity, neuroapoptosis, disruption of cytoskeletal assembly, and dysregulation of brain-derived neurotrophic factor (BNDF). Additionally, they can generate epigenetic changes that can be transmitted intergenerationally. These effects are related to age, dose, number of anesthetics received, and duration of exposure to said drugs and can be reversible or permanent, caused by direct or indirect perturbations on neurons. These disturbances may manifest as neurodevelopmental disorders later in life. This work aimed to review the cellular mechanisms involved in these alterations.

Dynamical evolution of exciton-polariton Bose-Einstein condensate under coupled interaction

Abstract We studied the exciton-polariton Bose-Einstein condensation (BEC) under light field manipulation by considering the coupled interaction of the system between exciton-polariton and light. Based on the coupled Gross-Pitaevskii equation (GPE) model and with modified variational method, we analytically derived the solutions of the excitonic system under the polar angle direction perturbation and system rotation. We identified that for different rotational angular velocities and different coupled strengths, the system evolves from a meta-stable oscillation state to monotonically decaying state, with potential for the study of quantum vortex identification for such kind of coupled systems. Our theoretical results can be used to guide the study of the evolution mode of the exciton-polariton system involving coupled interaction.

Dynamic response characteristics and economic analyses of two solar-assisted multi-generation systems

Efficient use of solar energy can alleviate the depletion of fossil energy and global warming. In this paper, two solar-aided combined cooling, heating and power systems are proposed and dynamically modeled. The main difference between the two systems is whether the solar energy is stored. A rotor speed-temperature-fuel control system is established, which is suitable for both systems. A control system for solar heat collection process is developed. Energy, exergy and techno-economic analyses are carried out to evaluate the thermodynamic and economic performances. The dynamic responses under direct normal irradiation perturbation and load perturbation are also investigated. The result shows that compared with the system without energy storage, the system with energy storage has higher primary energy utilization rate, exergy efficiency and fuel saving rate, but the economic performance is poorer. The rotor speed-temperature-fuel control system can guarantee a short equilibrium time and a small overshoot for power generation process. When electrical load disturbance occurs, the stabilization times of the output power, cooling energy supply and thermal energy supply are 30 s, 675 s and 770 s, respectively. Under the regulation of the solar heat collection control system, the maximum overshoot of the outlet thermal oil temperature of the parabolic trough solar collector is 2.6 % with a stabilization time of 83 s when the direct normal irradiation step disturbance occurs.

Use of correlations for neutron induced fission yields in DARWIN/PEPIN2 Uncertainty Quantification

Uncertainty quantification on Decay Heat is of utmost importance for the safety evaluations linked to nuclear waste management. International nuclear data libraries like JEFF, ENDF/B or JENDL provide evaluations on independent fission yields, but generally no correlations between those fission yields. With those data, independent fission yields can be considered as the most important contributor to the Decay Heat uncertainty. Nevertheless, other data are available, like correlation matrices for some fissile systems, or the use of fission yields by mass. Complete correlation matrices appear in nuclear data libraries, like JEFF-4, but are still very scares as only the most prominent fissile systems for nuclear reactor applications have been added. Another approach is to consider the use of the fission yields by mass, which uncertainty is smaller than those of independent fission yields, and adding a constraint when propagating uncertainties. In the work, we show the impact of considering the fission yields by mass, as it was implemented in DARWIN/PEPIN2.4.8. We compare DARWIN/PEPIN2.4.8 results, obtained on a first order direct perturbation approach, with a random sampling method through the use of an URANIE/MENDEL scheme.

Development of an Adjoint Flux Calculation Technique for Exact Perturbation Theory in Monte Carlo Code MCS

A calculation technique computing the adjoint flux of perturbed system is developed for the exact perturbation theory in Monte Carlo transport. By using a correlated sampling and iterated fission probability methods together, the adjoint flux of perturbed system is calculated during a forward Mote Carlo simulation of an unperturbed system. In the method, no additional particle simulation is required to compute the adjoint flux of perturbed system. The exact perturbation method is implemented in the Monte Carlo code MCS. The results of perturbation method for k-eigenvalue change are compared against differential operator sampling, adjoint-weighted perturbation, and direct perturbation methods for the Godiva benchmark and PLUS7 fuel assembly.

Interareal Synaptic Inputs Underlying Whisking-Related Activity in the Primary Somatosensory Barrel Cortex.

Body movements influence brain-wide neuronal activities. In the sensory cortex, thalamocortical bottom-up inputs and motor-sensory top-down inputs are thought to affect the dynamics of membrane potentials (Vm ) of neurons and change their processing of sensory information during movements. However, direct perturbation of the axons projecting to the sensory cortex from other remote areas during movements has remained unassessed, and therefore the interareal circuits generating motor-related signals in sensory cortices remain unclear. Using a Gi/o -coupled opsin, eOPN3, we here inhibited interareal signals incoming to the whisker primary somatosensory barrel cortex (wS1) of awake male mice and tested their effects on whisking-related changes in neuronal activities in wS1. Spontaneous whisking in air induced the changes in spike rates of a subset of wS1 neurons, which were accompanied by depolarization and substantial reduction of slow-wave oscillatory fluctuations of Vm Despite an extensive innervation, inhibition of inputs from the whisker primary motor cortex (wM1) to wS1 did not alter the spike rates and Vm dynamics of wS1 neurons during whisking. In contrast, inhibition of axons from the whisker-related thalamus (wTLM) and the whisker secondary somatosensory cortex (wS2) to wS1 largely attenuated the whisking-related supra- and sub-threshold Vm dynamics of wS1 neurons. Notably, silencing inputs from wTLM markedly decreased the modulation depth of whisking phase-tuned neurons in wS1, while inhibiting wS2 inputs did not impact the whisking variable tuning of wS1 neurons. Thus, sensorimotor integration in wS1 during spontaneous whisking is predominantly facilitated by direct synaptic inputs from wTLM and wS2 rather than from wM1.

“From shadows to shores”-quantitative analysis of CuO nanoparticle-induced apoptosis and DNA damage in fish erythrocytes: A multimodal approach combining experimental, image-based quantification, docking and molecular dynamics

The usage of copper (II) oxide nanoparticles (CuO NPs) has significantly expanded across industries and biomedical fields. However, the potential toxic effects on non-target organisms and humans lack comprehensive understanding due to limited research on molecular mechanisms. With this study, by combining the 96 h in vivo exposure of crucian carp fish, Carassius carassius, to sub-lethal CuO NPs doses (0.5 and 1 mg/dL) with image-based quantification, and docking and molecular dynamics approaches, we aimed to understand the mechanism of CuO NPs-induced cyto-genotoxicity in the fish erythrocytes. The results revealed that both doses of copper NPs used were toxic to erythrocytes causing oxidative stress response and serious red blood cell morphological abnormalities, and genotoxicity. Docking and 10-ns molecular dynamics confirmed favorable interactions (ΔG = −2.07 kcal mol−1) and structural stability of Band3-CuO NP complex, mainly through formation of H-bonds, implying the potential of CuO NPs to induce mitotic nuclear abnormalities in C. carassius erythrocytes via Band3 inhibition. Moreover, conventional and multiple ligand simultaneous docking with DNA revealed that single, double and triple CuO NPs bind preferentially to AT-rich regions consistently in the minor grooves of DNA. Of note, the DNA-binding strength subtantially increased (ΔG = −2.13 kcal mol−1, ΔG = −4.08 kcal mol−1, and ΔG = −6.03 kcal mol−1, respectively) with an increasing number of docked CuO NPs, suggesting that direct structural perturbation on DNA could also count for the molecular basis of in-vivo induced DNA damage in C. carassius erythrocytes. This study introduces the novel term “erythrotope” to describe comprehensive red blood cell morphological abnormalities. It proves to be a reliable and cost-effective biomarker for evaluating allostatic erythrocyte load in response to metallic nanoparticle exposure, serving as a distinctive fingerprint to assess fish erythrocyte health and physiological fitness.