A bottom-up agricultural emissions inventory and its analysis via CMAQ and IASI-NH3.

The global increase in population has led to higher emissions from livestock and synthetic fertilizers. This study investigates the impact of agricultural ammonia emissions on NH3 concentrations and provides insights into PM2.5 levels and their components in agriculturally intensified areas. We developed a bottom-up emission inventory focused on fertilizer application over croplands and livestock, instead of relying on the EMEP database. This approach utilized an improved spatial and temporal distribution of these emissions. We compared annual total NH3 emissions from livestock and fertilizer, estimated at 598.5 kt and 187.2 kt in the EMEP inventory (Base case), and 245.2 kt and 536 kt in the bottom-up inventory (Scenario case). Using the CMAQ modelling framework, we estimated atmospheric concentrations for both cases and evaluated the model results by comparing them with IASI-NH3 satellite retrievals. This comparison revealed significant differences in column concentrations between the Base and Scenario cases, with the Scenario case showing substantial improvement. Over a period of seven months, which contributed 80 % of the annual agricultural emissions for the Scenario case, the domain averages of NH3 were 3.02 × 1015, 4.15 × 1015, and 4.17 × 1015 molecules/cm2 for the Base and Scenario cases and IASI-NH3, respectively. The Scenario case closely matched IASI measurements, indicating a more accurate representation of NH3 emissions and concentrations. This enhanced reliability underscores the effectiveness of the bottom-up inventory approach. Additionally, using the CMAQ model, we found that in the IASI hotspots, the averages were 1.67 µg/m3 for sulfate, 0.57 µg/m3 for nitrate, and 0.62 µg/m3 for ammonium, with a total PM2.5 mean of 10.45 µg/m3.

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.

Heterometallic-organic cages with customized cavities: constructed by bottom-up step-wise coordination-driven self-assembly.

accurately synthesizing coordination-driven metal-organic cages with customized shape and cavity remain a great challenge for chemists. In this work, a bottom-up step-wise coordination-driven self-assembly approach was put forward. Employing this strategy, three terpyridyl heterometallic-organic truncated tetrahedral cages with different sizes and cavity were precisely synthesized. Firstly, the coordination of tripodal organic ligands with Ru2+ afforded dendritic metal-organic ligands L1-L3. Then the Ru building blocks complexed with Fe2+ and shrunk to form the desired heterometallic-organic cages (C1-C3). These discrete heterometallic-organic supramolecular cages were fully characterized and displayed the large and open cavities varied from 7205 Å3 to 9384 Å3. Notably, these cages could not be directly constructed by single-step assembly process using initial organic ligands or dimeric metal-organic ligands, indicative of the irreplaceability of a bottom-up step-wise assembly strategy for size-customized architectures. This work paves a new way for precisely constructing metal-organic cages with well-defined cavities.

Template Selection Strategy for Synthesis of One-Dimensional CrSbSe3 Ferromagnetic Semiconductor Nanoribbons.

CrSbSe3─the only experimentally validated one-dimensional (1D) ferromagnetic semiconductor─has recently attracted significant attention. However, all reported synthesis methods for CrSbSe3 nanocrystals are based on top-down methods. Here we report a template selection strategy for the bottom-up synthesis of CrSbSe3 nanoribbons. This strategy relies on comparing the formation energies of potential binary templates to the ternary target product. It enables us to select Sb2Se3 with the highest formation energy, along with its 1D crystal structure, as the template instead of Cr2Se3 with the lowest formation energy, thereby facilitating the transformation from Sb2Se3 to CrSbSe3 by replacing half of the Sb atoms in Sb2Se3 with Cr atoms. The as-prepared CrSbSe3 nanoribbons exhibit a length of approximately 5 µm, a width ranging from 80 to 120 nm, and a thickness of about 5 nm. The single CrSbSe3 nanoribbon presents typical semiconductor behavior and ferromagnetism, confirming the intrinsic ferromagnetism in the 1D CrSbSe3 semiconductor.

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.

Sex-specific variation in species interactions matters in ecological communities.

Understanding how natural communities and ecosystems are structured and respond to anthropogenic pressures in a rapidly changing world is key to successful management and conservation. A fundamental but often overlooked biological characteristic of organisms is sex. Sex-based responses are often considered when conducting studies at organismal and population levels, but are rarely investigated in community ecology. Focusing on kelp forests as a model system, and through a review of other marine and terrestrial ecosystems, we found evidence of widespread sex-based variation in species interactions. Sex-based variation in species interactions is expected to affect ecosystem structure and functioning via multiple trophic and nontrophic pathways. Understanding the drivers and consequences of sex-based variation in species interactions can inform more effective management and restoration.

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.

Co-creating community wellbeing initiatives: what is the evidence and how do they work?

BACKGROUND: Addressing wellbeing at the community level, using a public health approach may build wellbeing and protective factors for all. A collaborative, community-owned approach can bring together experience, networks, local knowledge, and other resources to form a locally-driven, place-based initiative that can address complex issues effectively. Research on community empowerment, coalition functioning, health interventions and the use of local data provide evidence about what can be achieved in communities. There is less understanding about how communities can collaborate to bring about change, especially for mental health and wellbeing. METHOD: A comprehensive literature search was undertaken to identify community wellbeing initiatives that address mental health. After screening 8,972 titles, 745 abstracts and 188 full-texts, 12 exemplar initiatives were identified (39 related papers). RESULTS: Eight key principles allowed these initiatives to become established and operate successfully. These principles related to implementation and outcome lessons that allowed these initiatives to contribute to the goal of increasing community mental health and wellbeing. A framework for community wellbeing initiatives addressing principles, development, implementation and sustainability was derived from this analysis, with processes mapped therein. CONCLUSION: This framework provides evidence for communities seeking to address community wellbeing and avoid the pitfalls experienced by many well-meaning but short-lived initiatives.

Insulated π-Conjugated Azido Scaffolds for Stepwise Functionalization via Huisgen Cycloaddition on Metal Oxide Surfaces.

In organic-inorganic hybrid devices, fine interfacial controls by organic components directly affect the device performance. However, fabrication of uniformed interfaces using π-conjugated molecules remains challenging due to facile aggregation by their strong π-π interaction. In this report, a π-conjugated scaffold insulated by covalently linked permethylated α-cyclodextrin moiety with an azido group is synthesized for surface Huisgen cycloaddition on metal oxides. Fourier-transformed infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy confirm the successful immobilization of the insulated azido scaffold on ZnO nanowire array surfaces. Owing to the highly independent immobilization, the scaffold allows rapid and complete conversion of the surface azido group in Huisgen cycloaddition reactions with ethynyl-terminated molecules, as confirmed by FT-IR spectroscopy monitoring. Cyclic voltammetry analysis of modified indium tin oxide substrates shows the positive effects of cyclic insulation toward suppression of intermolecular interaction between molecules introduced by the surface Huisgen cycloaddition reactions. The utility of the scaffold for heterogeneous catalysis is demonstrated in electrocatalytic selective O2 reduction to H2O2 with cobalt(II) chlorin modified fluorine doped tin oxide electrode and photocatalytic H2 generation with iridium(III) dye-sensitized Pt-loaded TiO2 nanoparticle. These results highlight the potential of the insulated azido scaffold for a stepwise functionalization process, enabling precise and well-defined hybrid interfaces.

Identification of RVFV Host Factors Using Quantitative Interaction Proteomics.

Affinity enrichment coupled with liquid chromatography-tandem mass spectrometry (AE-LC-MS/MS) enables a comprehensive study of virus-host protein-protein interactions in cells and tissues infected with Rift Valley fever virus (RVFV) or ectopically expressing RVFV proteins. Depending on the research question, different experimental setups with carefully chosen controls are needed. Here, we describe the detailed workflow of sample preparation, processing, and cleanup, while also outlining critical points to consider when designing and performing AE-LC-MS/MS experiments.

Recent advance for animal-derived polysaccharides in nanomaterials.

Inspired by the structure characteristics of natural products, the size and morphology of particles are carefully controlled using a bottom-up approach to construct nanomaterials with specific spatial unit distribution. Animal polysaccharide nanomaterials, such as chitosan and chondroitin sulfate nanomaterials, exhibit excellent biocompatibility, degradability, customizable surface properties, and novel physical and chemical properties. These nanomaterials hold great potential for development in achieving a sustainable bio-economy. This paper provides a summary of the latest research results on the preparation of nanomaterials from animal polysaccharides. The mechanism for preparing nanomaterials through the bottom-up method from different sources of animal polysaccharides is introduced. Furthermore, this paper discusses the potential hazards posed by industrial applications to the environment and human health, as well as the challenges and future prospects associated with using animal polysaccharides in nanomaterials.

The bottom-up approach in multigenerational family therapy: The child as the family guide.

In therapy, the child is mainly seen as a problem to be labeled or as a victim of various forms of abuse. The idea of the child as a therapeutic resource is the central point of my article where children's symptoms are quickly reframed and get a relational meaning in the family. Once the relational competence of the child is appreciated and his voice is heard, the child becomes a special guide to explore the emotional world of his family, and the genogram can provide a wonderful platform to start this therapeutic journey. Using a multigenerational lens, I describe how to explore family development with a "bottom-up approach." Intergenerational questions can be asked to the child and with his help relevant family events can emerge and broken bonds repaired. The therapeutic results I expect are the resolution of children's problems and family transformation.

Cell-Free Protein Expression by a Reconstituted Transcription-Translation System Energized by Sugar Catabolism.

Cooperation between catabolism and anabolism is crucial for maintaining homeostasis in living cells. The most fundamental systems for catabolism and anabolism are the glycolysis of sugars and the transcription-translation (TX-TL) of DNA, respectively. Despite their importance in living cells, the in vitro reconstitution of their cooperation through purified factors has not been achieved, which hinders the elucidation of the design principle in living cells. Here, we reconstituted glycolysis using sugars and integrated it with the PURE system, a commercial in vitro TX-TL kit composed of purified factors. By optimizing key parameters, such as glucokinase and initial phosphate concentrations, we determined suitable conditions for their cooperation. The optimized system showed protein synthesis at up to 33% of that of the original PURE system. We observed that ATP consumption in upstream glycolysis inhibits TX-TL and that this inhibition can be alleviated by the co-addition of glycolytic intermediates, such as glyceraldehyde 3-phosphate, with glucose. Moreover, the system developed here simultaneously synthesizes a subset of its own enzymes, that is, glycolytic enzymes, in a single test tube, which is a necessary step toward self-replication. As glycolysis and TX-TL provide building blocks for constructing cells, the integrated system can be a fundamental material for reconstituting living cells from purified factors.

Heavy metal exposure reduces larval gut microbiota diversity of the rice striped stem borer, Chilo suppressalis.

Cadmium (Cd), a widely distributed environmental pollutant in agroecosystems, causes negative effects on crops and herbivores through bottom-up processes. The gut microbial community of an insect can play a critical role in response to metal stress. To understand how microbiota affect the stress responses of organisms to heavy metals in agroecosystems, we initially used 16S rRNA sequencing to characterize the larval gut microbiota of Chilo suppressalis, an important agricultural pest, exposed to a diet containing Cd. The species richness, diversity, and composition of the gut microbial community was then analyzed. Results revealed that while the richness (Chao1 and ACE) of gut microbiota in larvae exposed to Cd was not significantly affected, diversity (Shannon and Simpson) was reduced due to changes in species distribution and relative abundance. Overall, the most abundant genus was Enterococcus, while the abundance of the genera Micrococcaceae and Faecalibaculum in the control significantly superior to that in Cd-exposed pests. Phylogenetic investigation of microbial communities by the reconstruction of unobserved states (PICRUSt) showed that the intestinal microorganisms appear to participate in 34 pathways, especially those used in environmental information processing and the metabolism of the organism. This study suggests that the gut microbiota of C. suppressalis are significantly impacted by Cd exposure and highlights the importance of the gut microbiome in host stress responses and negative effects of Cd pollution in agroecosystems.

The cost of delivering COVID-19 vaccines in Vietnam.

BACKGROUND: The COVID-19 pandemic affected hundreds of millions of people and lives, and vaccination was the safest and most effective strategy to prevent and mitigate the burden of this disease. The implementation of COVID-19 vaccination in Vietnam in 2021 was unprecedentedly challenging in scale and complexity, yet economic evidence on the cost of delivery vaccines thought the program was lacking. METHODS: This retrospective costing study utilized a bottom-up, ingredient-based approach to estimate the cost of delivering COVID-19 vaccines in Vietnam in 2021, from a payer perspective. The study included 38 study sites across all administrative and implementation level, including three geographic areas and two delivery strategies, in two provinces, Hanoi and Dak Lak. The study findings were complemented with qualitative interviews with health staff and stakeholders. RESULTS: The economic cost to deliver one COVID-19 vaccine dose was $1.73, mostly comprised of opportunity costs ($1.14 per dose) which were driven by labor costs ($1.12 per dose). The delivery cost in urban areas was the highest ($2.02), followed by peri-urban areas ($1.45) and remote areas ($1.37). Delivery costs were higher at temporary sites ($1.78) when compared to facility-based delivery ($1.63). Comparing low-volume and high-volume periods showed that the delivery cost decreased significantly as volume increased, from $5.24 per dose to $1.65 per dose. CONCLUSIONS: The study estimates the cost of delivering COVID-19 vaccines in Vietnam in 2021. Enabling factors and challenges during the implementation of the program were explored. Study limitations may lead to underestimation of results and reduce generalizability.

Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package.

Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker's implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.

Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders.

Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

Impact of Surfactants on Cumulative Trypsin Activity in Bottom-Up Proteome Analysis.

Trypsin digestion plays a pivotal role in successful bottom-up peptide characterization and quantitation. While denaturants are often incorporated to enhance protein solubility, surfactants are recognized to inhibit enzyme activity. However, several reports have suggested that incorporating surfactants or other solvent additives may enhance digestion and MS detection. Here, we assess the impacts of ionic surfactants on cumulative trypsin activity and subsequently evaluate the total digestion efficiency of a proteome mixture by quantitative MS. Although low surfactant concentrations, such as 0.01% SDS or 0.2% SDC, significantly enhanced the initial trypsin activity (by 14 or 42%, respectively), time course assays revealed accelerated enzyme deactivation, evident by 10- or 40-fold reductions in trypsin activity half-life at these respective surfactant concentrations. Despite enhanced initial tryptic activity, quantitative MS analysis of a common liver proteome extract, digested with various surfactants (0.01 or 0.1% SDS, 0.5% SDC), consistently revealed decreased peptide counts and signal intensity, indicative of a lower digestion efficiency compared to a nonsurfactant control. Furthermore, including detergents for digestion did not improve the detection of membrane proteins, nor hydrophobic peptides. These results stress the importance of assessing cumulative enzyme activity when optimizing the digestion of a proteome mixture, particularly in the presence of denaturants.

Phytochemical drivers of insect herbivory: a functional toolbox to support agroecological diversification.

Plant metabolism is a key feature of biodiversity that remains underexploited in functional frameworks used in agroecology. Here, we study how phytochemical diversity considered at three organizational levels can promote pest control. In a factorial field experiment, we manipulated plant diversity in three monocultures and three mixed crops of oilseed rape to explore how intra- and interspecific phytochemical diversity affects pest infestation. We combined recent progress in metabolomics with classic metrics used in ecology to test a box of hypotheses grounded in plant defence theory. According to the hypothesis of 'phytochemically mediated coevolution', our study stresses the relationships between herbivore infestation and particular classes of specialized metabolites like glucosinolates. Among 178 significant relationships between metabolites and herbivory rates, only 20% were negative. At the plant level, phytochemical abundance and richness had poor predictive power on pest regulation. This challenges the hypothesis of 'synergistic effects'. At the crop cover level, in line with the hypothesis of 'associational resistance', the phytochemical dissimilarity between neighbouring plants limited pest infestation. We discuss the intricate links between associational resistance and bottom-up pest control. Bridging different levels of organization in agroecosystems helps to dissect the multi-scale relationships between phytochemistry and insect herbivory.

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.