Long-term trends of black carbon and particle number concentrations and their vehicle emission factors in Stockholm.

Black carbon (BC) and particle number (PN) concentrations are usually high in cities due to traffic emissions. European mitigation policies, including Euro emission standards, have been implemented to curb these emissions. We analyzed BC and PN (particle diameter Dp > 4 nm) concentrations in Stockholm spanning the years 2013-2019 (BC) and 2009-2019 (PN) measured at street canyon and rooftop sites to assess the effectiveness of the implemented policies. Combining these data with inverse dispersion modeling, we estimated BC and PN emission factors (EFBC and EFPN) for the mixed fleet, reflecting real-world driving conditions. The pollutants showed decreasing trends at both sites, but PN concentrations remained high at the canyon site considering the World Health Organization (WHO) recommendations. BC concentrations declined more rapidly than PN concentrations, showing a -9.4% and -4.9% annual decrease at the canyon and -7.2% and -0.5% at the rooftop site in the years 2013-2019. The EFBC and EFPN trends showed that the mitigation strategies for reducing particulate emissions for on-road vehicles were successful over the study period. However, the introduction of biofuels in the vehicle fleet -ethanol and later rapeseed methyl ester (RME)- increased the concentrations of particles with Dp < 10 nm before the adoption of particulate filters in the exhausts. Stricter Euro emission regulations, especially with diesel particulate filters (DPF) in Euro 5, 6, and VI vehicles, led to 66% decrease in EFBC and 55% in EFPN. Real-world EFBC surpassed HBEFA (Handbook Emission Factors for Road Transport) database values by 2.4-4.8 times; however, direct comparisons between real-world and HBEFA EFPN are difficult due to differences in lower cut-off sizes and measurement techniques. Our results underscore the necessity for revising the HBEFA database, updating laboratory testing methods and portable emission measuring systems (PEMS) measurements to account for liquid condensate contributions to PN measurements.

Inter-annual trends of ultrafine particles in urban Europe.

Ultrafine particles (UFP, those with diameters ≤ 100 nm), have been reported to potentially penetrate deeply into the respiratory system, translocate through the alveoli, and affect various organs, potentially correlating with increased mortality. The aim of this study is to assess long-term trends (5-11 years) in mostly urban UFP concentrations based on measurements of particle number size distributions (PNSD). Additionally, concentrations of other pollutants and meteorological variables were evaluated to support the interpretations. PNSD datasets from 12 urban background (UB), 5 traffic (TR), 3 suburban background (SUB) and 1 regional background (RB) sites in 15 European cities and 1 in the USA were evaluated. The non-parametric Theil-Sen's method was used to detect monotonic trends. Meta-analyses were carried out to assess the overall trends and those for different environments. The results showed significant decreases in NO, NO2, BC, CO, and particle concentrations in the Aitken (25-100 nm) and the Accumulation (100-800 nm) modes, suggesting a positive impact of the implementation of EURO 5/V and 6/VI vehicle standards on European air quality. The growing use of Diesel Particle Filters (DPFs) might also have clearly reduced exhaust emissions of BC, PM, and the Aitken and Accumulation mode particles. However, as reported by prior studies, there remains an issue of poor control of Nucleation mode particles (smaller than 25 nm), which are not fully reduced with current DPFs, without emission controls for semi-volatile organic compounds, and might have different origins than road traffic. Thus, contrasting trends for Nucleation mode particles were obtained across the cities studied. This mode also affected the UFP and total PNC trends because of the high proportion of Nucleation mode particles in both concentration ranges. It was also found that the urban temperature increasing trends might have also influenced those of PNC, Nucleation and Aitken modes.

Sr65: a widely effective gene for stem rust resistance in wheat.

KEY MESSAGE: Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.

Wheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery.

BACKGROUND: Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection. RESULTS: YR63 exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS_YR63 and sunCS_67, positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63 locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63 is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63 within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63 and validated on a panel of Australian bread wheat, durum and triticale cultivars. CONCLUSIONS: This study highlights YR63 as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63 into elite cultivars through marker-assisted selection. The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.

Is Methotrexate Ototoxic? Investigating the Ototoxic Late Effects of Pediatric Cancer Treatment.

PURPOSE: Pediatric cancer survivors often experience long-term adverse health conditions or late effects, including hearing loss, that are attributable to cancer therapy. Ototoxic late effects have been documented in patients with cancer treated with cisplatin-based chemotherapy and/or radiation. This study evaluated the late effects of methotrexate as compared to cisplatin and other cancer therapy agents on pediatric cancer survivors at the Children's Hospital of New Orleans in Louisiana (CHNOLA) and patients currently undergoing cancer treatment at Our Lady of the Lake (OLOL) Hospital in Baton Rouge, Louisiana. METHOD: A retrospective chart review was conducted of medical records from the CHNOLA Audiology Clinic and the Treatment After Cancer Late Effects clinic, which followed patients 2-19 years after cancer treatment completion and current patients with pediatric cancer at OLOL. This study identified pediatric cancer survivors between 2 and 24 years of age with treatment protocol information and audiological evaluations. Association studies were performed to calculate p values using an exact chi-square test. RESULTS: More than 44% of late-effects patients had significant hearing loss; mild-to-profound hearing loss was observed in 37.5% of patients who received methotrexate treatment without cisplatin or irradiation. Eighty-three percent of the patients who received cisplatin had late-effect hearing loss. In patients currently receiving cancer treatment, 12% had significant hearing loss. CONCLUSIONS: The results from this study suggest that children who receive therapies not clinically established as ototoxic (i.e., methotrexate) may still be at a high risk of developing long-term hearing loss as a late effect. Due to the high incidence rate of hearing loss among patients with pediatric cancer, we recommend that audiologists be part of the late-effects care team. This study also demonstrates that patients with pediatric cancer treated with methotrexate should receive routine long-term auditory monitoring as part of their standard of care to detect and manage hearing loss early, minimizing adverse outcomes.

The variability of mass concentrations and source apportionment analysis of equivalent black carbon across urban Europe.

This study analyzed the variability of equivalent black carbon (eBC) mass concentrations and their sources in urban Europe to provide insights into the use of eBC as an advanced air quality (AQ) parameter for AQ standards. This study compiled eBC mass concentration datasets covering the period between 2006 and 2022 from 50 measurement stations, including 23 urban background (UB), 18 traffic (TR), 7 suburban (SUB), and 2 regional background (RB) sites. The results highlighted the need for the harmonization of eBC measurements to allow for direct comparisons between eBC mass concentrations measured across urban Europe. The eBC mass concentrations exhibited a decreasing trend as follows: TR > UB > SUB > RB. Furthermore, a clear decreasing trend in eBC concentrations was observed in the UB sites moving from Southern to Northern Europe. The eBC mass concentrations exhibited significant spatiotemporal heterogeneity, including marked differences in eBC mass concentration and variable contributions of pollution sources to bulk eBC between different cities. Seasonal patterns in eBC concentrations were also evident, with higher winter concentrations observed in a large proportion of cities, especially at UB and SUB sites. The contribution of eBC from fossil fuel combustion, mostly traffic (eBCT) was higher than that of residential and commercial sources (eBCRC) in all European sites studied. Nevertheless, eBCRC still had a substantial contribution to total eBC mass concentrations at a majority of the sites. eBC trend analysis revealed decreasing trends for eBCT over the last decade, while eBCRC remained relatively constant or even increased slightly in some cities.

Ambient air particulate total lung deposited surface area (LDSA) levels in urban Europe.

This study aims to picture the phenomenology of urban ambient total lung deposited surface area (LDSA) (including head/throat (HA), tracheobronchial (TB), and alveolar (ALV) regions) based on multiple path particle dosimetry (MPPD) model during 2017-2019 period collected from urban background (UB, n = 15), traffic (TR, n = 6), suburban background (SUB, n = 4), and regional background (RB, n = 1) monitoring sites in Europe (25) and USA (1). Briefly, the spatial-temporal distribution characteristics of the deposition of LDSA, including diel, weekly, and seasonal patterns, were analyzed. Then, the relationship between LDSA and other air quality metrics at each monitoring site was investigated. The result showed that the peak concentrations of LDSA at UB and TR sites are commonly observed in the morning (06:00-8:00 UTC) and late evening (19:00-22:00 UTC), coinciding with traffic rush hours, biomass burning, and atmospheric stagnation periods. The only LDSA night-time peaks are observed on weekends. Due to the variability of emission sources and meteorology, the seasonal variability of the LDSA concentration revealed significant differences (p = 0.01) between the four seasons at all monitoring sites. Meanwhile, the correlations of LDSA with other pollutant metrics suggested that Aitken and accumulation mode particles play a significant role in the total LDSA concentration. The results also indicated that the main proportion of total LDSA is attributed to the ALV fraction (50 %), followed by the TB (34 %) and HA (16 %). Overall, this study provides valuable information of LDSA as a predictor in epidemiological studies and for the first time presenting total LDSA in a variety of European urban environments.

The Keys to Controlling Wheat Rusts: Identification and Deployment of Genetic Resistance.

Rust diseases are among the major constraints for wheat production worldwide due to the emergence and spread of highly destructive races of Puccinia. The most common approach to minimize yield losses due to rust is to use cultivars that are genetically resistant. Modern wheat cultivars, landraces, and wild relatives can contain undiscovered resistance genes, which typically encode kinase or nucleotide-binding site leucine rich repeat (NLR) domain containing receptor proteins. Recent research has shown that these genes can provide either resistance in all growth stages (all-stage resistance; ASR) or specially in later growth stages (adult-plant resistance; APR). ASR genes are pathogen and race-specific, meaning can function against selected races of the Puccinia fungus due to the necessity to recognize specific avirulence molecules in the pathogen. APR genes are either pathogen-specific or multipathogen resistant but often race-nonspecific. Prediction of resistance genes through rust infection screening alone remains complex when more than one resistance gene is present. However, breakthroughs during the past half century such as the single-nucleotide polymorphism-based genotyping techniques and resistance gene isolation strategies like mutagenesis, resistance gene enrichment, and sequencing (MutRenSeq), mutagenesis and chromosome sequencing (MutChromSeq), and association genetics combined with RenSeq (AgRenSeq) enables rapid transfer of resistance from source to modern cultivars. There is a strong need for combining multiple genes for better efficacy and longer-lasting resistance. Hence, techniques like gene cassette creation speeds up the gene combination process, but their widespread adoption and commercial use is limited due to their transgenic nature.

Tunable superconductivity and its origin at KTaO3 interfaces.

What causes Cooper pairs to form in unconventional superconductors is often elusive because experimental signatures that connect to a specific pairing mechanism are rare. Here, we observe distinct dependences of the superconducting transition temperature Tc on carrier density n2D for electron gases formed at KTaO3 (111), (001) and (110) interfaces. For the (111) interface, a remarkable linear dependence of Tc on n2D is observed over a range of nearly one order of magnitude. Further, our study of the dependence of superconductivity on gate electric fields reveals the role of the interface in mediating superconductivity. We find that the extreme sensitivity of superconductivity to crystallographic orientation can be explained by pairing via inter-orbital interactions induced by an inversion-breaking transverse optical phonon and quantum confinement. This mechanism is also consistent with the dependence of Tc on n2D. Our study may shed light on the pairing mechanism in other superconducting quantum paraelectrics.

Primary splenic diffuse large B-cell lymphoma presenting as a splenic abscess.

Diffuse large B-cell lymphoma (DLBCL) arising in the spleen, also known as primary splenic DLBCL (PS-DLBCL), is a rare form of malignant lymphoma. It is defined as a lymphoma confined to the spleen or involving splenic hilar lymph nodes. Here we report a case of PS-DLBCL with CD30. The patient was a 62-year-old who presented with 2 weeks of left flank pain, chills, and abdominal distension. Computed tomography identified an 8-cm splenic mass with central necrosis interpreted as an abscess. A drain was placed, yielding purulent necrotic material; cytologically, only neutrophils were identified. However, purulent drainage continued for 28 days without resolution, prompting splenectomy. Pathological dissection revealed a multinodular mass with central necrosis. Microscopic examination revealed extensive karyorrhexis, abundant ghosts of large cells, and scattered large cells with pleomorphic, multilobated, and vesicular nuclei with moderately abundant cytoplasm. Immunohistochemical staining revealed large, atypical cells positive for CD20, CD30, CD45, PAX5, MYC (>40%), MUM1 (>30%), and p53 (focally). The large cells were negative for CD3 (polyclonal), CD4, CD5, CD8, CD10, CD15, CD34, BCL2, BCL6, AE1/AE3, S100, HHV8, and ALK. The Ki-67 proliferation rate was approximately 80% in large cells. Notably, this PS-DLBCL was positive for CD30, an unusual finding among non-Hodgkin B-cell lymphomas, which, coupled with the Reed-Sternberg-like morphology, raised the possibility of classic Hodgkin lymphoma. Therefore, we reviewed the literature to confirm the unique features of this large B-cell lymphoma, its abscess-like appearance, and its expression of CD30.

A Cysteine Pair Controls Flavin Reduction by Extracellular Cytochromes during Anoxic/Oxic Environmental Transitions.

Many bacteria of the genus Shewanella are facultative anaerobes able to reduce a broad range of soluble and insoluble substrates, including Fe(III) mineral oxides. Under anoxic conditions, the bacterium Shewanella oneidensis MR-1 uses a porin-cytochrome complex (Mtr) to mediate extracellular electron transfer (EET) across the outer membrane to extracellular substrates. However, it is unclear how EET prevents generating harmful reactive oxygen species (ROS) when exposed to oxic environments. The Mtr complex is expressed under anoxic and oxygen-limited conditions and contains an extracellular MtrC subunit. This has a conserved CX8C motif that inhibits aerobic growth when removed. This inhibition is caused by an increase in ROS that kills the majority of S. oneidensis cells in culture. To better understand this effect, soluble MtrC isoforms with modified CX8C were isolated. These isoforms produced increased concentrations of H2O2 in the presence of flavin mononucleotide (FMN) and greatly increased the affinity between MtrC and FMN. X-ray crystallography revealed that the molecular structure of MtrC isoforms was largely unchanged, while small-angle X-ray scattering suggested that a change in flexibility was responsible for controlling FMN binding. Together, these results reveal that FMN reduction in S. oneidensis MR-1 is controlled by the redox-active disulfide on the cytochrome surface. In the presence of oxygen, the disulfide forms, lowering the affinity for FMN and decreasing the rate of peroxide formation. This cysteine pair consequently allows the cell to respond to changes in oxygen level and survive in a rapidly transitioning environment. IMPORTANCE Bacteria that live at the oxic/anoxic interface have to rapidly adapt to changes in oxygen levels within their environment. The facultative anaerobe Shewanella oneidensis MR-1 can use EET to respire in the absence of oxygen, but on exposure to oxygen, EET could directly reduce extracellular oxygen and generate harmful reactive oxygen species that damage the bacterium. By modifying an extracellular cytochrome called MtrC, we show how preventing a redox-active disulfide from forming causes the production of cytotoxic concentrations of peroxide. The disulfide affects the affinity of MtrC for the redox-active flavin mononucleotide, which is part of the EET pathway. Our results demonstrate how a cysteine pair exposed on the surface controls the path of electron transfer, allowing facultative anaerobic bacteria to rapidly adapt to changes in oxygen concentration at the oxic/anoxic interface.

Immuno-engineered mRNA combined with cell adhesive niche for synergistic modulation of the MSC secretome.

In vitro transcribed (IVT-)mRNA has entered center stage for vaccine development due to its immune co-stimulating properties. Given the widely demonstrated safety of IVT-mRNA-based vaccines, we aimed to adopt IVT-mRNA encoding VEGF for secretory phenotype modulation of therapeutic cells. However, we observed that the immunogenicity of IVT-mRNA impairs the endogenous secretion of pro-angiogenic mediators from transfected mesenchymal stromal cells, instead inducing anti-angiogenic chemokines. This inflammatory secretome modulation limits the application potential of unmodified IVT-mRNA for cell therapy manufacturing, pro-angiogenic therapy and regenerative medicine. To uncouple immunogenicity from the protein expression functionality, we immuno-engineered IVT-mRNA with different chemically modified ribonucleotides. 5-Methoxy-uridine-modification of IVT-mRNA rescued the endogenous secretome pattern of transfected cells and prolonged secretion of IVT-mRNA-encoded VEGF. We found that high secretion of IVT-mRNA-encoded protein further depends on optimized cell adhesion. Cell encapsulation in a collagen-hyaluronic acid hydrogel increased secretion of IVT-mRNA-encoded VEGF and augmented the endogenous secretion of supporting pro-angiogenic mediators, such as HGF. Integrating minimally immunogenic mRNA technology with predesigned matrix-derived cues allows for the synergistic combination of multiple dimensions of cell manipulation and opens routes for biomaterial-based delivery of mRNA-engineered cell products. Such multimodal systems could present a more biologically relevant way to therapeutically address complex multifactorial processes such as tissue ischemia, angiogenesis, and regeneration.

RGD density along with substrate stiffness regulate hPSC hepatocyte functionality through YAP signalling.

Human pluripotent stem cell-derived hepatocytes (hPSC-Heps) may be suitable for treating liver diseases, but differentiation protocols often fail to yield adult-like cells. We hypothesised that replicating healthy liver niche biochemical and biophysical cues would produce hepatocytes with desired metabolic functionality. Using 2D synthetic hydrogels which independently control mechanical properties and biochemical cues, we found that culturing hPSC-Heps on surfaces matching the stiffness of fibrotic liver tissue upregulated expression of genes for RGD-binding integrins, and increased expression of YAP/TAZ and their transcriptional targets. Alternatively, culture on soft, healthy liver-like substrates drove increases in cytochrome p450 activity and ureagenesis. Knockdown of ITGB1 or reducing RGD-motif-containing peptide concentration in stiff hydrogels reduced YAP activity and improved metabolic functionality; however, on soft substrates, reducing RGD concentration had the opposite effect. Furthermore, targeting YAP activity with verteporfin or forskolin increased cytochrome p450 activity, with forskolin dramatically enhancing urea synthesis. hPSC-Heps could also be successfully encapsulated within RGD peptide-containing hydrogels without negatively impacting hepatic functionality, and compared to 2D cultures, 3D cultured hPSC-Heps secreted significantly less fetal liver-associated alpha-fetoprotein, suggesting furthered differentiation. Our platform overcomes technical hurdles in replicating the liver niche, and allowed us to identify a role for YAP/TAZ-mediated mechanosensing in hPSC-Hep differentiation.

Phenomenology of ultrafine particle concentrations and size distribution across urban Europe.

The 2017-2019 hourly particle number size distributions (PNSD) from 26 sites in Europe and 1 in the US were evaluated focusing on 16 urban background (UB) and 6 traffic (TR) sites in the framework of Research Infrastructures services reinforcing air quality monitoring capacities in European URBAN & industrial areaS (RI-URBANS) project. The main objective was to describe the phenomenology of urban ultrafine particles (UFP) in Europe with a significant air quality focus. The varying lower size detection limits made it difficult to compare PN concentrations (PNC), particularly PN10-25, from different cities. PNCs follow a TR > UB > Suburban (SUB) order. PNC and Black Carbon (BC) progressively increase from Northern Europe to Southern Europe and from Western to Eastern Europe. At the UB sites, typical traffic rush hour PNC peaks are evident, many also showing midday-morning PNC peaks anti-correlated with BC. These peaks result from increased PN10-25, suggesting significant PNC contributions from nucleation, fumigation and shipping. Site types to be identified by daily and seasonal PNC and BC patterns are: (i) PNC mainly driven by traffic emissions, with marked correlations with BC on different time scales; (ii) marked midday/morning PNC peaks and a seasonal anti-correlation with PNC/BC; (iii) both traffic peaks and midday peaks without marked seasonal patterns. Groups (ii) and (iii) included cities with high insolation. PNC, especially PN25-800, was positively correlated with BC, NO2, CO and PM for several sites. The variable correlation of PNSD with different urban pollutants demonstrates that these do not reflect the variability of UFP in urban environments. Specific monitoring of PNSD is needed if nanoparticles and their associated health impacts are to be assessed. Implementation of the CEN-ACTRIS recommendations for PNSD measurements would provide comparable measurements, and measurements of <10 nm PNC are needed for full evaluation of the health effects of this size fraction.

ß-heavy-spectrin stabilizes the constricting contractile ring during cytokinesis.

Cytokinesis requires the constriction of an actomyosin-based contractile ring and involves multiple F-actin crosslinkers. We show that partial depletion of the C. elegans cytokinetic formin generates contractile rings with low F-actin levels that constrict but are structurally fragile, and we use this background to investigate the roles of the crosslinkers plastin/PLST-1 and ß-heavy-spectrin/SMA-1 during ring constriction. We show that the removal of PLST-1 or SMA-1 has opposite effects on the structural integrity of fragile rings. PLST-1 loss reduces cortical tension that resists ring constriction and makes fragile rings less prone to ruptures and regressions, whereas SMA-1 loss exacerbates structural defects, leading to frequent ruptures and cytokinesis failure. Fragile rings without SMA-1 or containing a shorter SMA-1, repeatedly rupture at the same site, and SMA-1::GFP accumulates at repair sites in fragile rings and in rings cut by laser microsurgery. These results establish that ß-heavy-spectrin stabilizes the constricting ring and reveals the importance of ß-heavy-spectrin size for network connectivity at low F-actin density.

Harnessing interpretable and unsupervised machine learning to address big data from modern X-ray diffraction.

The information content of crystalline materials becomes astronomical when collective electronic behavior and their fluctuations are taken into account. In the past decade, improvements in source brightness and detector technology at modern X-ray facilities have allowed a dramatically increased fraction of this information to be captured. Now, the primary challenge is to understand and discover scientific principles from big datasets when a comprehensive analysis is beyond human reach. We report the development of an unsupervised machine learning approach, X-ray diffraction (XRD) temperature clustering (X-TEC), that can automatically extract charge density wave order parameters and detect intraunit cell ordering and its fluctuations from a series of high-volume X-ray diffraction measurements taken at multiple temperatures. We benchmark X-TEC with diffraction data on a quasi-skutterudite family of materials, (CaxSr[Formula: see text])3Rh4Sn13, where a quantum critical point is observed as a function of Ca concentration. We apply X-TEC to XRD data on the pyrochlore metal, Cd2Re2O7, to investigate its two much-debated structural phase transitions and uncover the Goldstone mode accompanying them. We demonstrate how unprecedented atomic-scale knowledge can be gained when human researchers connect the X-TEC results to physical principles. Specifically, we extract from the X-TEC-revealed selection rules that the Cd and Re displacements are approximately equal in amplitude but out of phase. This discovery reveals a previously unknown involvement of [Formula: see text] Re, supporting the idea of an electronic origin to the structural order. Our approach can radically transform XRD experiments by allowing in operando data analysis and enabling researchers to refine experiments by discovering interesting regions of phase space on the fly.

Involving society in science: Reflections on meaningful and impactful stakeholder engagement in fundamental research.

Open Science calls for transparent science and involvement of various stakeholders. Here are examples of and advice for meaningful stakeholder engagement.

Plastin and spectrin cooperate to stabilize the actomyosin cortex during cytokinesis.

Cytokinesis, the process that partitions the mother cell into two daughter cells, requires the assembly and constriction of an equatorial actomyosin network. Different types of non-motor F-actin crosslinkers localize to the network, but their functional contribution remains poorly understood. Here, we describe a synergy between the small rigid crosslinker plastin and the large flexible crosslinker spectrin in the C. elegans one-cell embryo. In contrast to single inhibitions, co-inhibition of plastin and the ßH-spectrin (SMA-1) results in cytokinesis failure due to progressive disorganization and eventual collapse of the equatorial actomyosin network. Cortical localization dynamics of non-muscle myosin II in co-inhibited embryos mimic those observed after drug-induced F-actin depolymerization, suggesting that the combined action of plastin and spectrin stabilizes F-actin in the contractile ring. An in silico model predicts that spectrin is more efficient than plastin at stabilizing the ring and that ring formation is relatively insensitive to ßH-spectrin length, which is confirmed in vivo with a sma-1 mutant that lacks 11 of its 29 spectrin repeats. Our findings provide the first evidence that spectrin contributes to cytokinesis and highlight the importance of crosslinker interplay for actomyosin network integrity.

Selectively Cross-Linked Tetra-PEG Hydrogels Provide Control over Mechanical Strength with Minimal Impact on Diffusivity.

Synthetic hydrogels formed from poly(ethylene glycol) (PEG) are widely used to study how cells interact with their extracellular matrix. These in vivo-like 3D environments provide a basis for tissue engineering and cell therapies but also for research into fundamental biological questions and disease modeling. The physical properties of PEG hydrogels can be modulated to provide mechanical cues to encapsulated cells; however, the impact of changing hydrogel stiffness on the diffusivity of solutes to and from encapsulated cells has received only limited attention. This is particularly true in selectively cross-linked "tetra-PEG" hydrogels, whose design limits network inhomogeneities. Here, we used a combination of theoretical calculations, predictive modeling, and experimental measurements of hydrogel swelling, rheological behavior, and diffusion kinetics to characterize tetra-PEG hydrogels' permissiveness to the diffusion of molecules of biologically relevant size as we changed polymer concentration, and thus hydrogel mechanical strength. Our models predict that hydrogel mesh size has little effect on the diffusivity of model molecules and instead predicts that diffusion rates are more highly dependent on solute size. Indeed, our model predicts that changes in hydrogel mesh size only begin to have a non-negligible impact on the concentration of a solute that diffuses out of hydrogels for the smallest mesh sizes and largest diffusing solutes. Experimental measurements characterizing the diffusion of fluorescein isothiocyanate (FITC)-labeled dextran molecules of known size aligned well with modeling predictions and suggest that doubling the polymer concentration from 2.5% (w/v) to 5% produces stiffer gels with faster gelling kinetics without affecting the diffusivity of solutes of biologically relevant size but that 10% hydrogels can slow their diffusion. Our findings provide confidence that the stiffness of tetra-PEG hydrogels can be modulated over a physiological range without significantly impacting the transport rates of solutes to and from encapsulated cells.

Measuring the elastic modulus of soft culture surfaces and three-dimensional hydrogels using atomic force microscopy.

Growing interest in exploring mechanically mediated biological phenomena has resulted in cell culture substrates and 3D matrices with variable stiffnesses becoming standard tools in biology labs. However, correlating stiffness with biological outcomes and comparing results between research groups is hampered by variability in the methods used to determine Young's (elastic) modulus, E, and by the inaccessibility of relevant mechanical engineering protocols to most biology labs. Here, we describe a protocol for measuring E of soft 2D surfaces and 3D hydrogels using atomic force microscopy (AFM) force spectroscopy. We provide instructions for preparing hydrogels with and without encapsulated live cells, and provide a method for mounting samples within the AFM. We also provide details on how to calibrate the instrument, and give step-by-step instructions for collecting force-displacement curves in both manual and automatic modes (stiffness mapping). We then provide details on how to apply either the Hertz or the Oliver-Pharr model to calculate E, and give additional instructions to aid the user in plotting data distributions and carrying out statistical analyses. We also provide instructions for inferring differential matrix remodeling activity in hydrogels containing encapsulated single cells or organoids. Our protocol is suitable for probing a range of synthetic and naturally derived polymeric hydrogels such as polyethylene glycol, polyacrylamide, hyaluronic acid, collagen, or Matrigel. Although sample preparation timings will vary, a user with introductory training to AFM will be able to use this protocol to characterize the mechanical properties of two to six soft surfaces or 3D hydrogels in a single day.