Cortical Layer-Dependent Signaling in Cognition: Three Computational Modes of the Canonical Circuit.

The cerebral cortex performs computations via numerous six-layer modules. The operational dynamics of these modules were studied primarily in early sensory cortices using bottom-up computation for response selectivity as a model, which has been recently revolutionized by genetic approaches in mice. However, cognitive processes such as recall and imagery require top-down generative computation. The question of whether the layered module operates similarly in top-down generative processing as in bottom-up sensory processing has become testable by advances in the layer identification of recorded neurons in behaving monkeys. This review examines recent advances in laminar signaling in these two computations, using predictive coding computation as a common reference, and shows that each of these computations recruits distinct laminar circuits, particularly in layer 5, depending on the cognitive demands. These findings highlight many open questions, including how different interareal feedback pathways, originating from and terminating at different layers, convey distinct functional signals.

Heatwave-induced functional shifts in zooplankton communities result in weaker top-down control on phytoplankton.

Freshwater ecosystems are increasingly affected by rising annual mean temperatures and heatwaves. While heatwaves are expected to have more immediate effects than mean temperature increases on local communities, comparative experimental studies are largely lacking. We conducted a 1-month mesocosm experiment to test the effect of different warming treatments, constantly raised temperatures (+3°C) and recurring heatwaves (+6°C), on plankton communities. We specifically tested how shifts in zooplankton trait composition and functional groups are reflected in ecosystem function (top-down control on primary producers). We found that heatwaves had a stronger and more immediate effect on zooplankton trait composition (specifically on body length and body mass) and functional groups. Heatwaves led to the decrease of small-bodied grazers (i.e., Rotifera) and the dominance of larger omnivorous Copepoda, and these shifts resulted in weaker top-down control, leading to elevated phytoplankton biomass. Altogether, our results highlight the importance of the indirect effects of heatwaves via inducing shifts in zooplankton functional groups and trait composition, which may lead to algal blooms.

Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry.

Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods─namely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation─in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns.

Bioinspired Molecular Scalpel for Two-Dimensional Metal-Organic Nanosheet: Design Strategies and Recent Progress.

Ultrathin two-dimensional (2D) metal-organic nanosheets (MONs) have attracted continued attention in the field of advanced functional materials. Their nanoscale thickness, high surface-to-volume ratio, and abundant accessible active sites, are superior advantages compared with their 3D bulk counterparts. Bioinspired molecular scalpel strategy is a promising method for the creation of 2D MONs, and may solve the current shortcomings of MONs synthesis. This review aims to provide a state-of-the-art overview of molecular scalpel strategies and share the results of current development to provide a better solution for MONs synthesis. Different types of molecular scalpel strategies have been systematically summarized. Both mechanisms, advantages and limitations of multiform molecular scalpel strategies have been discussed. Besides, the challenges to be overcome and the question to be solved are also introduced.

Rethinking Nanoparticle Synthesis: A Sustainable Approach vs. Traditional Methods.

This review portrays a comparison between green protocols and conventional nanoparticle (NP) synthesis strategies, highlighting each method's advantages and limitations. Various top-down and bottom-up methods in NP synthesis are described in detail. The green chemistry principles are emphasized for designing safe processes for nanomaterial synthesis. Among the green biogenic sources plant extracts, vitamins, enzymes, polysaccharides, fungi (Molds and mushrooms), bacteria, yeast, algae, and lichens are discussed. Limitations in the reproducibility of green protocols in terms of availability of raw material, variation in synthetic protocol, and selection of material due to geographical differences are elaborated. Finally, a conclusion is drawn utilizing green chemical principles, & a circular economy strategy to minimize waste generation, offering a promising framework for the synthesis of NPs emphasizing sustainability.

Scent-driven Selective Attention on Gambling Outcome: Implications for Responsible Gambling.

Many casinos diffuse a pleasant ambient scent into their facilities as a customer experience management practice, but the ethics of this scenting process is questionable. Although the effect of a pleasant scent on cognitive, emotional, and behavioral responses has been well-documented, its effect on attention during gambling has yet to be explored. Grounded in the tenets of the top-down control of attention and cross-modal correspondence between vision and olfaction, we conduct two eye-tracking experiments that involve different electronic casino games including video slots and live Cussec. The findings consistently show that pleasant ambient scent prolongs attention and induces more frequent attention to the win/loss areas on the video screen. The findings add to the implications related to responsible gambling by inspiring the stakeholders to consider the use of ambient scent in the gambling environment. Theoretically, the findings offer insights into scent as the catalyst that directs attention to goal-related information, while scent and goal do not need to be congruent in traits.

Impacts of coyote colonization on coastal mammalian predators.

Extreme ecosystem modification by humans has caused drastic reductions in populations and ranges of top mammalian predators, while simultaneously allowing synanthropic mesopredator species to expand. These conditions often result in inflated local densities of highly adaptable mesopredators that disrupt trophic dynamics and place unsustainable predation pressure on native prey populations. Colonization of a dominant predator may lead to top-down control of mesopredators and restore trophic balance. Coyotes are a novel colonizer of some coastal barrier islands of eastern North America, offering an opportunity to test how the addition of an apex predator impacts an established guild of mesopredators. To assess their trophic impact, we conducted 75,576 camera trapping hours over an 18-month study period, capturing > 1.5 million images across 108 coastal camera sites. Using two-species occupancy and habitat use models, we found sizeable effects of coyote habitat use on that of red foxes and free-ranging domestic cats, suggesting that coyotes function as apex predators in barrier island ecosystems. In fact, the only factor that determined the spatial pattern of highly ubiquitous red foxes was the sympatric habitat use of the largest carnivore in the food web-coyotes. That 'novel' apex predators can become established in coastal food webs illustrates the highly dynamic nature of conservation challenges for habitats and species at the edge of the sea.

Biogeographic and seasonal differences in consumer pressure underlie strong predation in the tropics.

Biotic interactions play a critical role in shaping patterns of global biodiversity. While several macroecological studies provide evidence for stronger predation in tropical regions compared with higher latitudes, results are variable even within the tropics, and the drivers of this variability are not well understood. We conducted two complementary standardized experiments on communities of sessile marine invertebrate prey and their associated predators to test for spatial and seasonal differences in predation across the tropical Atlantic and Pacific coastlines of Panama. We further tested the prediction that higher predator diversity contributes to stronger impacts of predation, using both direct observations of predators and data from extensive reef surveys. Our results revealed substantially higher predation rates and stronger effects of predators on prey in the Pacific than in the Atlantic, demonstrating striking variation within tropical regions. While regional predator diversity was high in the Atlantic, functional diversity at local scales was markedly low. Peak predation strength in the Pacific occurred during the wet, non-upwelling season when ocean temperatures were warmer and predator communities were more functionally diverse. Our results highlight the importance of regional biotic and abiotic drivers that shape interaction strength and the maintenance of tropical communities, which are experiencing rapid environmental change.

Enhanced Declustering Enables Native Top-Down Analysis of Membrane Protein Complexes using Ion-Mobility Time-Aligned Fragmentation.

Native mass spectrometry (MS) is proving to be a disruptive technique for studying the interactions of proteins, necessary for understanding the functional roles of these biomolecules. Recent research is expanding the application of native MS towards membrane proteins directly from isolated membrane preparations or from purified detergent micelles. The former results in complex spectra comprising several heterogeneous protein complexes; the latter enables therapeutic protein targets to be screened against multiplexed preparations of compound libraries. In both cases, the resulting spectra are increasingly complex to assign/interpret, and the key to these new directions of native MS research is the ability to perform native top-down analysis, which allows unambiguous peak assignment. To achieve this, detergent removal is necessary prior to MS analyzers, which allow selection of specific m/z values, representing the parent ion for downstream activation. Here, we describe a novel, enhanced declustering (ED) device installed into the first pumping region of a cyclic IMS-enabled mass spectrometry platform. The device enables declustering of ions prior to the quadrupole by imparting collisional activation through an oscillating electric field applied between two parallel plates. The positioning of the device enables liberation of membrane protein ions from detergent micelles. Quadrupole selection can now be utilized to isolate protein-ligand complexes, and downstream collision cells enable the dissociation and identification of binding partners. We demonstrate that ion mobility (IM) significantly aids in the assignment of top-down spectra, aligning fragments to their corresponding parent ions by means of IM drift time. Using this approach, we were able to confidently assign and identify a novel hit compound against PfMATE, obtained from multiplexed ligand libraries.

The interaction of top-down and bottom-up attention in visual working memory.

Understanding the interplay between top-down and bottom-up attention in visual working memory (VWM) is crucial, although the specific challenges arising from this interaction remain ambiguous. In this study, we address this complexity by examining how cue informativeness and probe status of the salient items influence this interaction. Through three experiments, we manipulated top-down attention by varying probe frequencies using pre-cues and bottom-up attention by varying the visual salience of memory items. Experiment 1 explored cue informativeness at 100% and 50%, while Experiments 2 and 3 maintained cue informativeness at 80% and 50%. Additionally, Experiment 1 tested a few of the salient items, Experiment 2 excluded them, and Experiment 3 tested half of them in each cue condition. Across all experiments, we consistently observed cueing benefits for cue-directed items, albeit with costs to non-cued items. Furthermore, cue informativeness and the probe status of salient items emerged as critical factors influencing the interaction between top-down and bottom-up attention in VWM. These findings underscore the pivotal roles of cue informativeness and salient item relevance in shaping the dynamics of top-down and bottom-up attention within VWM.

Combining Native Mass Spectrometry and Proteomics to Differentiate and Map the Metalloform Landscape in Metallothioneins.

Within the intricate landscape of the proteome, approximately 30% of all proteins bind metal ions. This repertoire is even larger when considering all the different forms of a protein, known as proteoforms. Here, we propose the term "metalloforms" to refer to different structural or functional variations of a protein resulting from the binding of various hetero- or homogeneous metal ions. Using human Cu(I)/Zn(II)-metallothionein-3 as a representative model, we developed a chemical proteomics strategy to simultaneously differentiate and map Zn(II) and Cu(I) metal binding sites. In the first labeling step, N-ethylmaleimide reacts with Cysteine (Cys), resulting in the dissociation of all Zn(II) ions while Cu(I) remains bound to the protein. In the second labeling step, iodoacetamide is utilized to label Cu(I)-bound Cys residues. Native mass spectrometry (MS) was used to determine the metal/labeling protein stoichiometries, while bottom-up/top-down MS was used to map the Cys-labeled residues. Next, we used a developed methodology to interrogate an isolated rabbit liver metallothionein fraction containing three metallothionein-2 isoforms and multiple Cd(II)/Zn(II) metalloforms. The approach detailed in this study thus holds the potential to decode the metalloproteoform diversity within other proteins.

An OpenSim thoracolumbar spine model applying a bottom-up modelling approach is similar to a top-down approach.

The kinetic demands of the spine can be assessed using a top-down (TD) or bottom-up (BU) approach, which start calculations from the either the hands or from the feet, respectively. Biomechanists have traditionally favored a BU approach, though existing modeling approaches encourage a TD approach. Regardless of the approach the demands should be similar, provided the external forces and linked segment parameters are equivalently measured and modeled. Demonstrating a level of agreement between the two approaches can help evaluate a model. Further, having both approaches can be advantageous when data is inaccurate or unavailable for one. The purpose of this study was to compare the internal moments and forces at multiple lumbar and thoracic intervertebral joint (IVJ) levels during lifting tasks from an established OpenSim thoracolumbar spine model that applies a TD approach and a similar model modified to adopt a BU approach. Kinematics and external forces were recorded from twelve participants during sagittal and lateral lifts of different lifting speeds and crate masses. For both approaches IVJ kinetics were estimated using a standard OpenSim modeling pipeline. The BU and TD approach IVJ joint moments generally agreed both temporally (R2 = .94 ± .17) and in magnitude (RMSE=6.2 ± 3.5 Nm) of the primary planes of movement. There were however some temporal fit exceptions for off axes moments with low magnitudes (i.e., < 10 Nm). Bland-Altman plots also indicated acceptable agreement for IVJ peak forces (BU-TD difference of 12 ± 111 and 8 ± 31 N in compression and resultant shear, respectfully). These results support the application of the BU approach and the assigned linked segment parameters of the model. The new BU model is available on the SimTK site (https://simtk.org/projects/spine_ribcage).

The relevance of top-down self-regulation for children's and adolescents' developmental outcomes.

A popular topic in developmental science is self-regulation, an aspect of functioning viewed as contributing to optimal development. Of particular theoretical importance is top-down (frontal cortically based) self-regulation (TDSR). This article briefly reviews recent research on TDSR's relation to four areas of development: maladjustment, social competence, prosocial development, and academic development. Recent studies on the topic often involve sophisticated methods and designs; moreover, several relevant meta-analyses have been published in the recent past. In general, a higher level of TDSR has been associated with better adjustment, social competence, prosociality, and success in the school setting. Limitations in the research and extant meta-analyses are briefly noted.

Orbitofrontal cortex modulates auditory cortical sensitivity and sound perception in Mongolian gerbils.

Sensory perception is dynamic, quickly adapting to sudden shifts in environmental or behavioral context. Although decades of work have established that these dynamics are mediated by rapid fluctuations in sensory cortical activity, we have a limited understanding of the brain regions and pathways that orchestrate these changes. Neurons in the orbitofrontal cortex (OFC) encode contextual information, and recent data suggest that some of these signals are transmitted to sensory cortices. Whether and how these signals shape sensory encoding and perceptual sensitivity remain uncertain. Here, we asked whether the OFC mediates context-dependent changes in auditory cortical sensitivity and sound perception by monitoring and manipulating OFC activity in freely moving Mongolian gerbils of both sexes under two behavioral contexts: passive sound exposure and engagement in an amplitude modulation (AM) detection task. We found that the majority of OFC neurons, including the specific subset that innervates the auditory cortex, were strongly modulated by task engagement. Pharmacological inactivation of the OFC prevented rapid context-dependent changes in auditory cortical firing and significantly impaired behavioral AM detection. Our findings suggest that contextual information from the OFC mediates rapid plasticity in the auditory cortex and facilitates the perception of behaviorally relevant sounds.

A grazing crab drives saltmarsh carbon storage and recovery.

Consumers can directly (e.g., consumption) and indirectly (e.g., trophic cascades) influence carbon cycling in blue carbon ecosystems. Previous work found that large grazers have nuanced effects on carbon stocks, yet, small, bioturbating-grazers, which remove plant biomass and alter sediment properties, remain an understudied driver of carbon cycling. We used field-derived and remote sensing data to quantify how the purple marsh crab, Sesarma reticulatum, influenced carbon stocks, flux, and recovery in salt marshes. Sesarma caused a 40%-70% loss in carbon stocks as fronts propagated inland (i.e., ungrazed to recovered transition), with front migration rates accelerating over time. Despite latitudinal differences, front migration rate had no effect on carbon stocks, flux, or time to replacement. When we included Sesarma disturbance in carbon flux calculations, we found it may take 5-100 years for marshes to replace lost carbon, if at all. Combined, we show that small grazers cause a net loss in carbon stocks as they move through the landscape, and irrespective of migration rate, these grazer-driven impacts persist for decades. This work showcases the significant role of consumers in carbon storage and flux, challenging the classic paradigm of plant-sediment feedbacks as the primary ecogeomorphic driver of carbon cycling in blue carbon ecosystems.

Determining KRAS4B-Targeting Compound Specificity by Top-Down Mass Spectrometry.

We present a novel method to determine engagement and specificity of KRAS4B-targeting compounds in vitro. By employing top-down mass spectrometry (MS), which analyzes intact and modified protein molecules (proteoforms), we can directly visualize and confidently characterize each KRAS4B species within compound-treated samples. Moreover, by employing targeted MS2 fragmentation, we can precisely localize each compound molecule to a specific residue on a given KRAS4B proteoform. This method allows us to comprehensively evaluate compound specificity, clearly detect nonspecific binding events, and determine the order and frequency with which they occur. We provide two proof-of-concept examples of our method employing publicly available compounds, along with detailed protocols for sample preparation, top-down MS data acquisition, targeted proteoform MS2 fragmentation, and analysis of the resulting data. Our results demonstrate the concentration dependence of KRAS4B-compound engagement and highlight the ability of top-down MS to directly map compound binding location(s) without disrupting the KRAS4B primary structure. Our hope is that this novel method may help accelerate the identification of new successful targeted inhibitors for KRAS4B and other RAS isoforms.

Increases in Global and East Asian Nitrogen Trifluoride (NF3) Emissions Inferred from Atmospheric Observations.

Nitrogen trifluoride (NF3) is a potent and long-lived greenhouse gas that is widely used in the manufacture of semiconductors, photovoltaic cells, and flat panel displays. Using atmospheric observations from eight monitoring stations from the Advanced Global Atmospheric Gases Experiment (AGAGE) and inverse modeling with a global 3-D atmospheric chemical transport model (GEOS-Chem), we quantify global and regional NF3 emission from 2015 to 2021. We find that global emissions have grown from 1.93 ± 0.58 Gg yr-1 (± one standard deviation) in 2015 to 3.38 ± 0.61 Gg yr-1 in 2021, with an average annual increase of 10% yr-1. The available observations allow us to attribute significant emissions to China (0.93 ± 0.15 Gg yr-1 in 2015 and 1.53 ± 0.20 Gg yr-1 in 2021) and South Korea (0.38 ± 0.07 Gg yr-1 to 0.65 ± 0.10 Gg yr-1). East Asia contributes around 73% of the global NF3 emission increase from 2015 to 2021: approximately 41% of the increase is from emissions from China (with Taiwan included), 19% from South Korea, and 13% from Japan. For Japan, which is the only one of these three countries to submit annual NF3 emissions to UNFCCC, our bottom-up and top-down estimates are higher than reported. With increasing demand for electronics, especially flat panel displays, emissions are expected to further increase in the future.

The modulation of task relevance on emotion-induced blindness depends on whether targets and distractors belong to the same category.

Previous research on emotion-induced blindness (EIB) argues emotional distractors capture attention in a bottom-up manner due to their physical and emotional salience. However, recent research has shown it is controversial whether EIB will be modulated by top-down factors. The present study further investigated whether the magnitude of EIB would be modulated by top-down factors, specifically the emotional relevance between tasks and distractors. Participants were divided into two groups having the same targets except for different task instructions. The orientation judgment group was asked to judge the orientation of the target (an emotionally irrelevant task), and the emotion judgment group was required to judge the emotional valence of the target (an emotionally relevant task). It was found the emotional relevance between tasks and distractors has no modulation on the magnitudes of EIB in two groups when targets and distractors are from different categories (Experiment 1), but a modulation when they are from the same category (Experiment 2). Consequently, we contend top-down task relevance modulates the EIB effect and distractors' priority is regulated by the emotional relevance between tasks and distractors. The current study holds attentional capture by stimulus-driven is unconditional in EIB, while attentional capture by goal-driven requires certain conditions.

Combining SDS-PAGE to capillary zone electrophoresis-tandem mass spectrometry for high-resolution top-down proteomics analysis of intact histone proteoforms.

Mass spectrometry (MS)-based top-down proteomics (TDP) analysis of histone proteoforms provides critical information about combinatorial post-translational modifications (PTMs), which is vital for pursuing a better understanding of epigenetic regulation of gene expression. It requires high-resolution separations of histone proteoforms before MS and tandem MS (MS/MS) analysis. In this work, for the first time, we combined SDS-PAGE-based protein fractionation (passively eluting proteins from polyacrylamide gels as intact species for mass spectrometry, PEPPI-MS) with capillary zone electrophoresis (CZE)-MS/MS for high-resolution characterization of histone proteoforms. We systematically studied the histone proteoform extraction from SDS-PAGE gel and follow-up cleanup as well as CZE-MS/MS, to determine an optimal procedure. The optimal procedure showed reproducible and high-resolution separation and characterization of histone proteoforms. SDS-PAGE separated histone proteins (H1, H2, H3, and H4) based on their molecular weight and CZE provided additional separations of proteoforms of each histone protein based on their electrophoretic mobility, which was affected by PTMs, for example, acetylation and phosphorylation. Using the technique, we identified over 200 histone proteoforms from a commercial calf thymus histone sample with good reproducibility. The orthogonal and high-resolution separations of SDS-PAGE and CZE made our technique attractive for the delineation of histone proteoforms extracted from complex biological systems.

Erratum: Resting state functional connectivity of the rat claustrum.

[This corrects the article DOI: 10.3389/fnana.2019.00022.].