X-Ray Multibeam Ptychography at up to 20 keV: Nano-Lithography Enhances X-Ray Nano-Imaging.

Hard X-rays are needed for non-destructive nano-imaging of solid matter. Synchrotron radiation facilities (SRF) provide the highest-quality images with single-digit nm resolution using advanced techniques such as X-ray ptychography. However, the resolution or field of view is ultimately constrained by the available coherent flux. To address this, the beam's incoherent fraction can be exploited using multiple parallel beams in an X-ray multibeam ptychography (MBP) approach. This expands the domain of X-ray ptychography to larger samples or more rapid measurements. Both qualities favor the study of complex composite or functional samples, such as catalysts, energy materials, or electronic devices. The challenge of performing ptychography at high energy and with many parallel beams must be overcome to extract the full advantages for extended samples while minimizing beam attenuation. Here, that challenge is overcome by creating a lens array using cutting-edge laser printing technology and applying it to perform scanning with MBP with up to 12 beams and at photon energies of 13 and 20 keV. This exceeds the measurement limits of conventional hard X-ray ptychography without compromising image quality for various samples: Siemens star test pattern, Ni/Al2O3 catalyst, microchip, and gold nano-crystal clusters.

Fluorescence Switching and Photoisomerization of a Spiropyran Molecular Photoswitch through Confined Spaces Regulation in Crystals.

Spiropyran (SP) and its derivatives are highly attractive owing to their distinctive merits in high contrast and fast response read-out systems. However, the realization of photoswitching properties of SP is hindered in the aggregate state, particularly in crystals owing to the dense packing of molecules leading to insufficient study of the relationship between the molecular structure/stacking mode and photoswitching behavior. Herein, we report three SP derivatives: different flexible chains (carboxyl group for SP-0 and ester group for SP-1) are attached to the indoline moiety, while the ester group is attached to the chromene moiety for SP-2. SP-1 exhibits fluorescent photoswitching properties in crystals due to the weak intermolecular interactions resulting in enough free space for the photoisomerization. The presence of hydrogen bonds in SP-0 enhances the molecular interactions to restrict the photoisomerization, and the ester group of SP-2 impacts the thermodynamic properties, thereby limiting the realization of photoswitching of SP-2.

Ensemble learning for integrative prediction of genetic values with genomic variants.

BACKGROUND: Whole genome variants offer sufficient information for genetic prediction of human disease risk, and prediction of animal and plant breeding values. Many sophisticated statistical methods have been developed for enhancing the predictive ability. However, each method has its own advantages and disadvantages, so far, no one method can beat others. RESULTS: We herein propose an Ensemble Learning method for Prediction of Genetic Values (ELPGV), which assembles predictions from several basic methods such as GBLUP, BayesA, BayesB and BayesCπ, to produce more accurate predictions. We validated ELPGV with a variety of well-known datasets and a serious of simulated datasets. All revealed that ELPGV was able to significantly enhance the predictive ability than any basic methods, for instance, the comparison p-value of ELPGV over basic methods were varied from 4.853E-118 to 9.640E-20 for WTCCC dataset. CONCLUSIONS: ELPGV is able to integrate the merit of each method together to produce significantly higher predictive ability than any basic methods and it is simple to implement, fast to run, without using genotype data. is promising for wide application in genetic predictions.

[Promoting fucoxanthin accumulation in Phaeodactylum tricornutum by multiple nitrogen supplementation and blue light enhancement].

The aim of this study was to promote fucoxanthin accumulation in Phaeodactylum tricornutum by photo-fermentation through optimizing the mode of multiple nitrogen supplementation and blue light enhancement. The results showed that the mixed nitrogen source (tryptone: urea=1:1, N mol/N mol; total nitrogen concentration at 0.02 mol/L) added to the culture system by six times was the best mode in shake flasks. Two-phase culture with light adjustment was then carried out in 5 L photo-fermenter with an enhanced blue light (R: G: B=67.1:16.7:16.3) in the second phase, leading to improved cell density (1.12×108 cells/mL), biomass productivity (330 mg/(d·L)), fucoxanthin content (19.62 mg/g), titer (69.71 mg/L) and productivity (6.97 mg/(d·L)). Compared with one-phase culture under red/blue (R: G: B=70.9:18.3:10.9) light and six-times nitrogen supplementation, the fucoxanthin content was significantly increased by 7.68% (P < 0.05) but the productivity did not change significantly (P > 0.05). Compared with one-phase culture under red/blue (R: G: B=70.9:18.3:10.9) light and one-time nitrogen supplementation, the content and productivity of fucoxanthin were significantly increased by 45.98% and 48.30% (P < 0.05), respectively. This study developed a two-phase culture mode with multiple nitrogen supplementation and blue light enhancement, which effectively promoted the accumulation of fucoxanthin and improved the efficiency of nitrogen source utilization, thus providing a new approach for fucoxanthin accumulation in P. tricornutum by photo-fermentation.

Low-Pressure Sensitive Piezochromic Fluorescence Switching of Tetraphenylethylene-Anthraquinone.

Invited for the cover of this issue are Prof. Wenjing Tian and co-workers at Jilin University. The image depicts the highly sensitive piezochromic fluorescence switching of tetraphenylethylene-anthraquinone under low-pressure regimes (∼60 kPa). Read the full text of the article at 10.1002/chem.202301070.

Low-Pressure Sensitive Piezochromic Fluorescence Switching of Tetraphenylethylene-Anthraquinone.

Sensing of low-pressure signals is of great importance for cutting-edge technologies. Organic piezochromic molecules offer a promising library of pressure sensitive materials which can be tailor-designed toward specific requirements. However, very few examples of low-pressure sensitive piezochromic fluorescent molecules have been obtained till date, and the underlying mechanisms are still in its infancy. Herein, we report highly sensitive piezochromic fluorescent switching under low-pressure regimes (∼60 kPa) of tetraphenylethylene-anthraquinone (TPE-AQ) based on the controlled molecular design and polymorphic phase strategy. The influence of both intramolecular conformation effect and variations of intermolecular stacking modes on the piezochromic property of TPE-AQ is investigated. The underlying mechanism of the low-pressure sensitive piezochromic fluorescence switching is demonstrated to be closely related to the loosely packed molecular orientation, as confirmed by X-ray diffraction measurements combined with simulations. This work provides a way to design highly efficient pressure sensors based on organic molecular systems.

[Enhancing fucoxanthin production in Phaeodactylum tricornutum by photo-fermentation].

The aim of this study was to develop a technical system for high-efficient production of fucoxanthin by photo-fermentation of Phaeodactylum tricornutum. In a 5 L photo-fermentation tank, the effects of initial light intensity, nitrogen source and concentration as well as light quality on biomass concentration and fucoxanthin accumulation in P. tricornutum were investigated systematically under mixotrophic condition. The results showed that the biomass concentration, fucoxanthin content and productivity reached the highest level of 3.80 g/L, 13.44 mg/g and 4.70 mg/(L·d) under the optimal conditions of initial light intensity of 100 µmol/(m2·s), 0.02 mol TN/L of tryptone: urea (1:1, N mol/N mol) as mixed nitrogen source, and a mixed red/blue (R: B=6:1) light, 1.41, 1.33 and 2.05-fold higher than that before optimization, respectively. This study developed a key technology for enhancing the production of fucoxanthin by photo-fermentation of P. tricornutum, facilitating the development of marine natural products.

Gene-Based Genome-Wide Association Study Identified Genes for Agronomic Traits in Maize.

A gene integrates the effects of all SNPs in its sequence span, which benefits the genome-wide association study. To explore gene-level variations affecting economic traits in maize, we extended the SNP-based GWAS analysis software Single-RunKing developed by our team to gene-based GWAS, which used the FaST-LMM algorithm to convert the linear mixed model into simple linear model association analysis. An F-test statistic was formulated to test and identify candidate genes. We compared the statistical efficiency of using 80% principal components (EPC), the first principal component (FPC), and all SNP markers (ALLSNP) as independent variables, which predecessors commonly used to integrate SNPs and represent genes. With a Huazhong Agricultural University (HAU) genomic dataset of 2.65M SNPs from 540 maize plants, 34,774 genes were annotated across the whole genome. Genome-wide association studies with 20 agronomic traits were performed using the software developed here. Another maize dataset from the Ames panel (AP) was also analyzed. The EPC method fits the model well and has good statistical efficiency. It not only overcomes the false negative problem when using all SNP markers for analysis (ALLSNP) but also solves the false positive problem of its corresponding simple linear model method EPCLM. Compared with FPC, the EPC method has higher statistical efficiency. A total of 132 quantitative trait genes (QTG) were identified for the 20 traits from HAU maize dataset and one trait of AP maize.

Cost-Effectiveness of Poly ADP-Ribose Polymerase Inhibitors in Cancer Treatment: A Systematic Review.

Background: PARP inhibitors have shown significant improvement in progression-free survival, but their costs cast a considerable financial burden. In line with value-based oncology, it is important to evaluate whether drug prices justify the outcomes. Objectives: The aim of the study was to systematically evaluate PARP inhibitors on 1) cost-effectiveness against the standard care, 2) impact on cost-effectiveness upon stratification for genetic characteristics, and 3) identify factors determining their cost-effectiveness, in four cancer types. Methods: We systematically searched PubMed, EMBASE, Web of Science, and Cochrane Library using designated search terms, updated to 31 August 2021. Trial-based or modeling cost-effectiveness analyses of four FDA-approved PARP inhibitors were eligible. Other studies known to authors were included. Reference lists of selected articles were screened. Eligible studies were assessed for methodological and reporting quality before review. Results: A total of 20 original articles proceeded to final review. PARP inhibitors were not cost-effective as recurrence maintenance in advanced ovarian cancer despite improved performance upon genetic stratification. Cost-effectiveness was achieved when moved to upfront maintenance in a new diagnosis setting. Limited evidence indicated non-cost-effectiveness in metastatic breast cancer, mixed conclusions in metastatic pancreatic cancer, and cost-effectiveness in metastatic prostate cancer. Stratification by genetic testing displayed an effect on cost-effectiveness, given the plummeting ICER values when compared to the "treat-all" strategy. Drug cost was a strong determinant for cost-effectiveness in most models. Conclusions: In advanced ovarian cancer, drug use should be prioritized for upfront maintenance and for patients with BRCA mutation or BRCAness at recurrence. Additional economic evaluations are anticipated for novel indications.

Canonical transformation for multivariate mixed model association analyses.

KEY MESSAGE: In extension of Single-RunKing to analyze multiple correlated traits, mvRunKing not only enlarged number of the analyzed phenotypes with canonical transformation, but also improved statistical power to detect pleiotropic QTNs through joint association analysis. Based on genomic variance-covariance matrices, we simplified multivariate mixed model association analysis to multiple univariate ones by using canonical transformation, and then individually implemented univariate association tests in the Single-RunKing. which enlarged number of the analyzed phenotypes. With canonical transformation back to the original scale, the association results would be biologically interpretable. Especially, we rapidly estimated genomic variance-covariance matrices with multivariate GEMMA and optimized separately the polygenic variances (or heritabilities) for only the markers that had large effects or higher significance levels in univariate mixed models, greatly improving computing efficiency for multiple univariate association tests. Beyond one test at once, joint association analysis for quantitative trait nucleotide (QTN) candidates can significantly increase statistical powers to detect QTNs. A user-friendly mvRunKing software was developed to efficiently implement multivariate mixed model association analyses.

Reversible Three-Color Fluorescence Switching of an Organic Molecule in the Solid State via "Pump-Trigger" Optical Manipulation.

In photoswitches that undergo fluorescence switching upon ultraviolet irradiation, photoluminescence and photoisomerization often occur simultaneously, leading to unstable fluorescence properties. Here, we successfully demonstrated reversible solid-state triple fluorescence switching through "Pump-Trigger" multiphoton manipulation. A novel fluorescence photoswitch, BOSA-SP, achieved green, yellow, and red fluorescence under excitation by pump light and isomerization induced by trigger light. The energy ranges of photoexcitation and photoisomerization did not overlap, enabling appropriate selection of the multiphoton light for "pump" and "trigger" photoswitching, respectively. Additionally, the large free volume of the spiropyran (SP) moiety in the solid state promoted reversible photoisomerization. Switching between "pump" and "trigger" light is useful for three-color tunable switching cell imaging, which can be exploited in programmable fluorescence switching. Furthermore, we exploited reversible dual-fluorescence switching in a single molecular system to successfully achieve two-color super-resolution imaging.

Optimizing genomic control in mixed model associations with binary diseases.

Complex computation and approximate solution hinder the application of generalized linear mixed models (GLMM) into genome-wide association studies. We extended GRAMMAR to handle binary diseases by considering genomic breeding values (GBVs) estimated in advance as a known predictor in genomic logit regression, and then reduced polygenic effects by regulating downward genomic heritability to control false negative errors produced in the association tests. Using simulations and case analyses, we showed in optimizing GRAMMAR, polygenic effects and genomic controls could be evaluated using the fewer sampling markers, which extremely simplified GLMM-based association analysis in large-scale data. Further, joint association analysis for quantitative trait nucleotide (QTN) candidates chosen by multiple testing offered significant improved statistical power to detect QTNs over existing methods.

Genome-wide hierarchical mixed model association analysis.

In genome-wide mixed model association analysis, we stratified the genomic mixed model into two hierarchies to estimate genomic breeding values (GBVs) using the genomic best linear unbiased prediction and statistically infer the association of GBVs with each SNP using the generalized least square. The hierarchical mixed model (Hi-LMM) can correct confounders effectively with polygenic effects as residuals for association tests, preventing potential false-negative errors produced with genome-wide rapid association using mixed model and regression or an efficient mixed-model association expedited (EMMAX). Meanwhile, the Hi-LMM performs the same statistical power as the exact mixed model association and the same computing efficiency as EMMAX. When the GBVs have been estimated precisely, the Hi-LMM can detect more quantitative trait nucleotides (QTNs) than existing methods. Especially under the Hi-LMM framework, joint association analysis can be made straightforward to improve the statistical power of detecting QTNs.

Knowledge, Attitudes, and Practices Related to COVID-19 Among Malawi Adults: A Community-Based Survey.

INTRODUCTION: It is well-recognized that containing COVID-19 successfully is determined by people's prevention measures which are related to their knowledge, attitudes, and practices (KAP). This perception has attracted attention in low- and middle-income countries (LMIC) due to their fragile health systems and economies. The objective of this study was to understand how residents in Malawi perceived COVID-19, to determine the factors related to KAP. METHODS: A semi-structured questionnaire was used for the data collection. A field-based survey was conducted among adult residents in Lilongwe, Malawi. Descriptive statistic, linear regression, the Chi-square test, and Pearson's correlation statistics were used for data analysis. RESULTS: A total of 580 questionnaires were involved. The mean knowledge, attitude, and practice (KAP) scores were 10 (SD = ±3, range: 3-19), 16 (SD = ±4, range: 5-25), and 2 (SD = ±1, range: 0-5), respectively. Lack of money and resources (39%) was the biggest challenge for people who practice prevention measures. Among the participants, the radio (70%) and friends/family (56%) were the main sources of information. A higher economic status was associated with better KAP. CONCLUSIONS: A low level of KAP was detected among the population. The people faced challenges regarding a lack of necessary preventive resources and formal information channels. The situation was worse considering vulnerable population who had low economic status. Further all-round health education is urgently needed along with providing adequate health supplies and ensuring proper information management.

Hierarchical mixed-model expedites genome-wide longitudinal association analysis.

A hierarchical random regression model (Hi-RRM) was extended into a genome-wide association analysis for longitudinal data, which significantly reduced the dimensionality of repeated measurements. The Hi-RRM first modeled the phenotypic trajectory of each individual using a RRM and then associated phenotypic regressions with genetic markers using a multivariate mixed model (mvLMM). By spectral decomposition of genomic relationship and regression covariance matrices, the mvLMM was transformed into a multiple linear regression, which improved computing efficiency while implementing mvLMM associations in efficient mixed-model association expedited (EMMAX). Compared with the existing RRM-based association analyses, the statistical utility of Hi-RRM was demonstrated by simulation experiments. The method proposed here was also applied to find the quantitative trait nucleotides controlling the growth pattern of egg weights in poultry data.

Genetic Association Analysis for Relative Growths of Body Compositions and Metabolic Traits to Body Weights in Broilers.

In animal breeding, body components and metabolic traits always fall behind body weights in genetic improvement, which leads to the decline in standards and qualities of animal products. Phenotypically, the relative growth of multiple body components and metabolic traits relative to body weights are characterized by using joint allometric scaling models, and then random regression models (RRMs) are constructed to map quantitative trait loci (QTLs) for relative grwoth allometries of body compositions and metabolic traits in chicken. Referred to as real joint allometric scaling models, statistical utility of the so-called LASSO-RRM mapping method is given a demonstration by computer simulation analysis. Using the F2 population by crossing broiler × Fayoumi, we formulated optimal joint allometric scaling models of fat, shank weight (shank-w) and liver as well as thyroxine (T4) and glucose (GLC) to body weights. For body compositions, a total of 9 QTLs, including 4 additive and 5 dominant QTLs, were detected to control the allometric scalings of fat, shank-w, and liver to body weights; while a total of 10 QTLs of which 6 were dominant, were mapped to govern the allometries of T4 and GLC to body weights. We characterized relative growths of body compositions and metabolic traits to body weights in broilers with joint allometric scaling models and detected QTLs for the allometry scalings of the relative growths by using RRMs. The identified QTLs, including their highly linked genetic markers, could be used to order relative growths of the body components or metabolic traits to body weights in marker-assisted breeding programs for improving the standard and quality of broiler meat products.

Solid-State Reversible Dual Fluorescent Switches for Multimodality Optical Memory.

Fluorescent photoswitches are highly attractive, because they hold great promises for photonic devices and imaging. However, a limited number of reversible switches with a response to light have been achieved in the solid state. Here, we report reversible dual fluorescent photoswitching characteristics in the solid state of spiropyran (SP)-functionalized tetraphenylethene (TPE) derivatives. These photoswitches exhibit two distinct and selectively addressable states, a cyan fluorescence and a red fluorescence, which can be conveyed into each other in a reversible feature upon irradiation with alternating UV and visible light. Detailed spectroscopic and theoretical studies suggest that the nonplanar molecular conformation of TPE moieties leads to large free volumes, which facilitates the reversible photoisomerization of SP. The excellent reversibility and high-contrast fluorescence of solid-state photoswitches enable great applications in multimodality anticounterfeiting and optical writing and erasing fluorescent devices.

The deubiquitinase CYLD controls protective immunity against helminth infection by regulation of Treg cell plasticity.

BACKGROUND: Type 2 immunity can be modulated by regulatory T (Treg) cell activity. It has been suggested that the deubiquitinase cylindromatosis (CYLD) plays a role in the development or function of Treg cells, implying that it could be important for normal protective immunity, where type 2 responses are prevalent. OBJECTIVE: We sought to investigate the role of CYLD in Treg cell function and TH2 cell immune responses under steady-state conditions and during helminth infection. METHODS: Foxp3-restricted CYLD conditional knockout (KO) mice were examined in mouse models of allergen-induced airway inflammation and Nippostrongylus brasiliensis infection. We performed multiplex magnetic bead assays, flow cytometry, and quantitative PCR to understand how a lack of CYLD affected cytokine production, homing, and suppression in Treg cells. Target genes regulated by CYLD were identified and validated by microarray analysis, coimmunoprecipitation, short hairpin RNA knockdown, and transfection assays. RESULTS: Treg cell-specific CYLD KO mice showed severe spontaneous pulmonary inflammation with increased migration of Treg cells into the lung. CYLD-deficient Treg cells furthermore produced high levels of IL-4 and failed to suppress allergen-induced lung inflammation. Supporting this, the conditional KO mice displayed enhanced protection against N brasiliensis infection by contributing to type 2 immunity. Treg cell conversion into IL-4-producing cells was due to augmented mitogen-activated protein kinase and nuclear factor κB signaling. Moreover, Scinderin, a member of the actin-binding gelsolin family, was highly upregulated in CYLD-deficient Treg cells, and controlled IL-4 production through forming complexes with mitogen-activated protein kinase kinase/extracellular receptor kinase. Correspondingly, both excessive IL-4 production in vivo and the protective role of CYLD-deficient Treg cells against N brasiliensis were reversed by Scinderin ablation. CONCLUSIONS: Our findings indicate that CYLD controls type 2 immune responses by regulating Treg cell conversion into TH2 cell-like effector cells, which potentiates parasite resistance.

Improving Fucoxanthin Production in Mixotrophic Culture of Marine Diatom Phaeodactylum tricornutum by LED Light Shift and Nitrogen Supplementation.

Fucoxanthin (Fx), a kind of primary carotenoids in brown seaweeds and diatoms, has attractive efficacy in human's healthcare including loss weight, the prevention of diabetes and Alzheimer's disease. Marine diatom Phaeodactylum tricornutum is now realized as a promising producer for commercial Fx production due to its higher content of Fx than brown seaweeds with easily artificial cultivation and Fx extraction. In the present study, to improve Fx production in P. tricornutum, the mixotrophic cultures were applied to optimize initial cell density, light intensity, light regime and nitrogen supplementation. The results showed that the higher initial cell density (1 × 107 cells mL-1) and lower light intensity (20 µmol m-2 s-1) were favorable for biomass production and Fx accumulation. The maximal Fx content [16.28 mg g-1 dry weight (DW)] could be achieved under blue light (BL), but the highest biomass concentration (5.53 g L-1) could be attained under red: blue light (R: B, 6:1) in the batch culture. A novel two-phase culture approach was developed to increase the biomass concentration to the highest value (6.52 g L-1) with the maximal productivity of Fx (8.22 mg L-1 d-1) through light shift from R:B ratio (6:1) in phase 1 to R:B ratio (5:1) by enhancing BL and tryptone addition in phase 2. The content and intracellular amount of Fx were also increased 8% and 12% in phase 2 compared to phase 1. The expression levels analysis revealed that genes encoding phytoene synthase (PSY), zeaxanthin epoxidase (ZEP), and fucoxanthin-chlorophyll-protein b (FCPb) were upregulated significantly, with downregulation of the gene encoding violaxanthin de-epoxidase (VDE), leading to the improvement of Fx in phase 2. The present study demonstrated the two-phase culture strategy could promote Fx productivity through enhancing biomass production and increasing Fx content, indicating that strengthening BL coupled with adding tryptone were effective to facilitate Fx production by mixotrophic cultivation of marine diatom P. tricornutum.

Diatoms as cell factories for high-value products: chrysolaminarin, eicosapentaenoic acid, and fucoxanthin.

Diatoms are unicellular photosynthetic microalgae existing ubiquitously in marine and freshwater environments. This review focuses on high-value compounds produced from diatoms, including chrysolaminarin (Chrl), eicosapentaenoic acid (EPA), and fucoxanthin (Fx), which can be applied in aquaculture, human health foods, pharmaceuticals, and cosmetics. In addition, this review provides an overview of their biosynthesis in diatoms and technologies for production. EPA and Fx typically accumulate synergistically in diatoms, while Chrl competes with EPA and Fx for carbon precursors. Several diatom strains have been employed that simultaneously accumulate these three compounds, but limitations and challenges still exist during commercialization. To address the bottleneck in biomass and high-value compound production, the optimization of cultivation parameters, the trophic mode, elicitor- or bacteria-assisted stimulations, and genetic modifications via mutant breeding, adaptive evolution engineering, and metabolic engineering have been developed in diatoms to establish improved technologies. Currently, large-scale cultivation of diatoms occurs mostly in open ponds and photobioreactors in autotrophic mode. Mixotrophic cultivation and coextraction approaches for multiple products represent novel strategies for economically enhancing the future production of biomass and high-value compounds on an industrial scale.