Abstract Protein engineering increasingly relies on machine learning models to computationally pre-screen variants to identify those that meet the target requirements. Although machine learning approaches have proven effective, their performance on prospective screening data has room for improvement. Prediction accuracy can vary greatly from one variant to the next. So far, it is unclear what characterizes variants that are associated with large model error. We designed and generated a dataset that can be stratified based on four structural characteristics (buriedness, number of contact residues, proximity to the active site and presence of secondary structure), to answer this question. We found that variants with multiple mutations that are buried, closely connected with other residues or close to the active site, which we call challenging mutations, are harder to model than their counterparts (i.e. exposed, loosely connected, far from the active site). This effect emerges only for variants with multiple challenging mutations, since single mutations at these sites were not harder to model. Our findings indicate that variants with challenging mutations are appropriate benchmarking targets for assessing model quality and that stratified dataset design can be leveraged to highlight areas of improvement for machine learning guided protein engineering.

The article raises the problem of using Earth remote sensing data to collect evidence of damages caused by the military actions of the Russian army in Ukraine. The core data set obtained by deciphering aerial photographs reflects the general current and operational situation in the affected area, reducing the subjectivity and uncertainty of damage characteristics on the ground. Earth remote sensing data visualize visible damage to the environment, which can be recognized and assessed using images of different spectral bands with appropriate resolution. Among the damage caused to the environment as a result of hostilities, according to the Earth remote sensing data, it is possible to study: degradation of land resources, destruction of natural ecosystems by fires, destruction of structures (buildings) and structures. Satellite images with a very high resolution (≤ 1 m) make it possible to quantify the degree of damage to the soil surface due to shell explosions: the amount of metal fragments and chemicals that have entered the soil, damage to the biological cover, etc. Images with a resolution of less than 30 meters in the short-wave infrared (SWIR) range allow to depict the devastating effects of forest and steppe fires caused by military actions. Using two different time frames, one before the fire and one after, will ensure the accuracy, objectivity and reliability of the evidence collected. These very high resolution Earth remote sensing images are used to investigate the destruction of structures (buildings) and constructions. The analysis of satellite images guarantees the diagnosis of the condition of the building in three degrees of destruction: completely destroyed, partially destroyed or not destroyed. In order to ensure the storage, quick search, analysis and visualization of all useful information obtained from the data of Earth remote sensing, it is necessary to use geoinformation systems.The proposed methodology for assessing military destruction is characterized by simplicity, accuracy and versatility, and does not require the use of expensive equipment.

AbstractCapsicum(pepper) is among the most economically important species worldwide, the fruit accumulates specialized metabolites with essential roles in plant environmental interaction and potential health benefits. However, the underlying genetic basis of their biosynthesis remains largely unknown. In this study, we developed and assessed both wild genetic variance and a bespoke mapping population to determine the genetic architecture of the pepper metabolome. The genetic analysis provided over 30 metabolic quantitative trait loci (mQTL) for over 1100 metabolites. We identified 92 candidate genes involved in various mQTL. Among the identified loci, we described and validated by transient overexpression a domestication gene cluster of eleven UDP-glycosyltransferases involved in monomeric capsianoside biosynthesis. We additionally constructed the biosynthetic reactions and annotated the genes involved in capsianoside biosynthesis in pepper. Given that differential glycosylation of acyclic diterpenoid glycosides contributes to plant resistance and acts as anticancer agents in humans, our data provide new insight, and resources for better understanding the biosynthesis of beneficial natural compounds to improve human health.

Ports are major air pollution sources impacting downwind communities with emissions from port activities, nearby energy and other heavy industries, truck, train, and vessel traffic, and commuting traffic. The Ports of Los Angeles/Long Beach, denoted Ports, are the western hemisphere's largest, with plans for port electrification to reduce air pollution. The covid19 shutdown impacted the Ports, providing a real-world experiment on the effects of electrification on exposure to neighboring communities.Eight in situ surveys with a mobile air quality laboratory (14 trace gases, aerosols, and meteorology) were conducted spanning the covid19 shutdown to characterize the resultant air quality changes. These data were combed with time series (2015-) from six Port area air quality stations and TROPOMI satellite nitrogen dioxide NO2 column XNO2.In situ surveys showed dramatic NO2 decreases from Jul. 2019 to May 2020 (during the shutdown), with NO2 only returning towards pre-covid levels by Jul. 2022. Lesser covid19 NO2 decreases were observed by the air quality station data and satellite XNO2 for the Los Angeles Basin; both showed NO2 decrease during the shutdown and an extended time for recovery to more normal concentration (and underlying economic activity) - until 2022 - far longer than the shutdown. Overall, ozone, O3 increased, signifying that O3, formation is volatile organic hydrocarbons, VOH, limited, with the strongest O3 source(s) arriving from offshore. This finding suggests efforts to purely address air quality by electrification without addressing area VOH emissions could potentially lessen, perhaps significantly, the expected air quality and health improvements in downwind communities. The Ports’ area industrial sites were identified as driving these VOHs, as the inverse relationship between NO2 and O3 persisted during the shutdown when non-industrial VOH sources would have decreased.

Patient and public involvement is an idea whose time has firmly come. It is the views of these Guest Editors that it is the right thing to do morally and improves research quality and applicability.

Fragile X syndrome (FXS), resulting from a mutation in the Fmr1 gene, is the most common monogenic cause of autism and inherited intellectual disability. Fmr1 encodes the Fragile X Messenger Ribonucleoprotein (FMRP), and its absence leads to cognitive, emotional, and social deficits compatible with the nucleus accumbens (NAc) dysfunction. This structure is pivotal in social behavior control, consisting mainly of spiny projection neurons (SPNs), distinguished by dopamine D1 or D2 receptor expression, connectivity, and associated behavioral functions. This study aims to examine how FMRP absence differentially affects SPN cellular properties, which is crucial for categorizing FXS cellular endophenotypes. We utilized a novel Fmr1-/y::Drd1a-tdTomato mouse model, which allows in-situ identification of SPN subtypes in FXS mice. Using RNA-sequencing, RNAScope and ex-vivo patch-clamp in adult male mice NAc, we comprehensively compared the intrinsic passive and active properties of SPN subtypes. Fmr1 transcripts and their gene product, FMRP, were found in both SPNs subtypes, indicating potential cell-specific functions for Fmr1. The study found that the distinguishing membrane properties and action potential kinetics typically separating D1- from D2-SPNs in wild-type mice were either reversed or abolished in Fmr1-/y::Drd1a-tdTomato mice. Interestingly, multivariate analysis highlighted the compound effects of Fmr1 ablation by disclosing how the phenotypic traits distinguishing each cell type in wild-type mice were altered in FXS. Our results suggest that the absence of FMRP disrupts the standard dichotomy characterizing NAc D1- and D2-SPNs, resulting in a homogenous phenotype. This shift in cellular properties could potentially underpin select aspects of the pathology observed in FXS. Therefore, understanding the nuanced effects of FMRP absence on SPN subtypes can offer valuable insights into the pathophysiology of FXS, opening avenues for potential therapeutic strategies.

Abstract Background Jackfruit (Artocarpus heterophyllus), is an economically valuable fruit tree. Despite its potential, the production of jackfruit in Uganda is currently low, and may face further reduction due to deforestation. As a result, genetic erosion of the tree resource is predicted, before its documentation and exploitation for possible crop improvement and sustainable conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers. Results The results from the morphological analysis showed variation in the tree height, diameter at breast height (DBH), and crown diameter traits, with coefficients of variation (CV) values of 20%, 41%, and 33% respectively. Except for taste, various forms of the 13 assessed qualitative traits were observed. Genotyping showed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90, and totalling to 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57 respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from further analysis using ‘Partitioning Around Medoids’ (PAM), Principal Coordinate Analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the A. heterophyllus populations. In addition, the Mantel test revealed no significant correlation between the genetic and geographic distances, and the morphological and geographic distances, and a negligible correlation between the morphological and genetic distances. Discussion Diversity was observed in the assessed A. heterophyllus because the crop is crossly pollinated. However, there was no differentiation of the jackfruit populations probably because of continuous gene flow in the adjacently located districts. Morphological resemblance did not imply genetic similarity probably because morphology is influenced by the environment. Conclusions Both morphological and genetic analyses revealed variation of jackfruit within a single interbreeding population. The observed diversity can be exploited to establish breeding and conservation strategies to increase production of jackfruit. However, selecting germplasm depending on morphological assessment alone may be misleading.

Patient and public involvement (PPI) in every aspect of research will add valuable insights from patients’ experiences, help to explore barriers and facilitators to their compliance/adherence to assessment and treatment methods, bring meaningful outcomes that could meet their expectations, needs and preferences, reduce health care costs, and improve dissemination of research findings. It is essential to ensure competence of the research team by capacity building with available resources on PPI. This review summarizes practical resources for PPI in various stages of research projects—conception, co-creation, design (including qualitative or mixed methods), execution, implementation, feedback, authorship, acknowledgement and remuneration of patient research partners, and dissemination and communication of research findings with PPI. We have briefly summarized the recommendations and checklists, amongst others, for PPI in rheumatic and musculoskeletal research (e.g. the European Alliance of Associations for Rheumatology (EULAR) recommendations, the Core Outcome Measures in Effectiveness Trials (COMET) checklist and the Guidance for Reporting Involvement of Patients and the Public (GRIPP) checklist). Various tools that could be used to facilitate participation, communication and co-creation of research projects with PPI are highlighted in the review. We shed light on the opportunities and challenges for young investigators involving PPI in their research projects, and have summarized various resources that could be used to enhance PPI in various phases/aspects of research. A summary of web links to various tools and resources for PPI in various stages of research is provided in Additional file 1.

Highly aged asphalt binder in RAP is a potential source of inferior performance, especially the cracking resistance of HMA. Use of rejuvenators is a suitable way to incorporate more RAP by offsetting the stiffness of the aged binder. In this study, bio-based and petroleum-based rejuvenators were evaluated based on cracking susceptibility of the hot mix asphalt prepared with low (15%) and high (30%) RAP content. Less amount of plant-based rejuvenator (15% by weight of RAP binder) was required to lower the RAP binder grade to a certain level in comparison to petroleum-based one (35%). Cracking susceptibility of the mix was determined by semi-circular bend test performed at intermediate and low temperature as well as by overlay test. It was observed that use of rejuvenator can successfully restore the cracking resistance of the mix with low RAP content from 93% to even 112% of the control mix. For mix with high RAP content the cracking potential cannot always be restored at the level similar to the control mix but can be improved from 56% to 144% of control mix properties. Petroleum-based rejuvenator is less susceptible to aging and performed significantly better to resist cracking for long-term aged mix in all the test performed in this study. However, use of maximum amount of rejuvenator should be limited because it can adversely affect the rutting as well as cracking resistance of the mix.

The greenhouse gas, methane, budget has significant uncertainty for many sources, including natural geological emissions. A major uncertainty of geological methane emissions, including onshore and offshore hydrocarbon seepage from subsurface hydrocarbon reservoirs is the gas emissions’ temporal variability. Current atmospheric methane budget models assume seepage is constant; nevertheless, available data and seepage conceptual models suggest gas seepage can vary considerably on timescales from second to century. The assumption of steady-seepage is used because long-term datasets to characterize these variabilities are lacking. A 30-year air quality dataset downwind of the Coal Oil Point seep field, offshore California found methane, CH4, concentrations downwind of the seep field increased from a 1995 minimum to a 2008 peak, decreasing exponentially afterward with a 10.2-year timescale (R2 = 0.91). Atmospheric emissions, EA, were derived by a time-resolved Gaussian plume inversion model of the concentration anomaly using observed winds and gridded sonar source location maps. EA increased from 27,200 to 161,000 m3 day−1 (corresponding to 6.5–38 Gg CH4 year−1 for 91% CH4 content) for 1995–2009, respectively, with 15% uncertainty, then decreased exponentially from 2009 to 2015 before rising above the trend. 2015 corresponded to the cessation of oil and gas production, which affects the western seep field. EA varied sinusoidally with a 26.3-year period (R2 = 0.89) that largely tracked the Pacific Decadal Oscillation (PDO), which is driven on these timescales by an 18.6-year earth-tidal cycle (27.9-year beat). A similar controlling factor may underlie both, specifically varying compressional stresses on migration pathways. This also suggests the seep atmospheric budget may exhibit multi-decadal trends.