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Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by up to an order of magnitude and improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300 kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved. Tomographic reconstructions of cryopreserved specimens enable in-situ structural studies. Here, the authors present the beam image-shift electron cryo-tomography (BISECT) approach that accelerates data collection speed and improves the map resolution compared to earlier approaches and present the in vitro structure of a 300 kDa protein complex that was solved at 3.6 Å resolution as a test case.

Stress wave tomography technology uses instruments to collect stress wave velocity data via sensors, visualizes those velocity data, and reconstructs an image of internal defects using estimated velocity distribution. This technology can be used to detect the size, position, and shape of internal defects in hardwood, and it has increasingly attracted the attention of researchers. In order to obtain enough stress wave signals, 12 sensors are usually equidistantly positioned around the cross-section of trunks like a clock. Although this strategy is reasonable and convenient, it is obviously not the optimal signal acquisition strategy for all defects. In this paper, a novel sensor position’s optimization method for high-quality stress wave tomography is proposed. The relationship between the shape of defects and the planar distribution of sensors is established by taking the ray penetration ratio and degree of equidistant distribution of sensors as indicators. Through the construction of the fitness function and optimization conditions, the optimal strategy for the planar distribution of sensors was determined using the Genetic Algorithm. Seven samples containing simulated defects and real tree trunks were used to test the proposed algorithm, and the comparison results show that the image of internal defects in hardwood can be reconstructed with high accuracy after optimizing the sensor positions.

In order to detect the size and shape of defects inside wood, an image reconstruction method based on segmented propagation rays of stress waves is proposed. The method uses sensors to obtain the stress wave velocity data by hanging around the timber equally, visualizes those data, and reconstructs the image of internal defects with the visualized propagation rays. The basis of the algorithm is precisely segmenting the rays to benefit the spatial interpolation. First, a ray segmentation algorithm using the elliptical neighborhood technique is proposed, which can be used to segment the rays and estimate the velocity values of segmented rays by the nearby original rays using elliptical zones. Second, a spatial interpolation algorithm utilizing a segmented ellipse according to the segmented rays is also proposed, which can be used to estimate the velocity value of a grid cell by the segmented ellipses corresponding to the nearby segmented rays. Then, the image of the internal defect inside the wood is reconstructed. Both simulation and experimental data were used to evaluate the proposed method, and the area and shape of the imaging results were analyzed. The comparison results show that the proposed method can produce high quality reconstructions with clear edges and high accuracy.

Background Childhood asthma presents a multifaceted immune-driven pathology shaped by genetic, epigenetic, and immune regulatory interactions. Despite extensive genome-wide analyses pinpointing multiple susceptibility loci, the precise functional contributors to asthma pathogenesis remain elusive. This study employs a comprehensive multi-omics framework and Mendelian randomization (MR) analysis to systematically identify and validate key genetic determinants implicated in childhood asthma. Methods A genome-wide screening of over 19,000 human genes was performed to identify cis-eQTL-regulated genes associated with childhood asthma. Two-sample MR was conducted to assess causality, followed by Summary-based Mendelian Randomization (SMR) to validate findings in independent datasets. Colocalization analysis determined whether gene expression and asthma GWAS signals share a common causal variant. Protein quantitative trait loci (pQTL) analysis further validated gene associations at the protein level. DNA methylation quantitative trait loci (mQTL) MR and mediation analysis explored epigenetic regulatory mechanisms, while linkage disequilibrium score regression (LDSC) quantified genome-wide genetic correlations. Immune cell mediation analysis examined potential immune-driven effects, and Phenome-Wide Association Study (PheWAS) evaluated pleiotropy and therapeutic safety. Results Following systematic screening, STX4 emerged as a strong candidate gene for childhood asthma. MR and SMR analyses confirmed its causal role, while colocalization analysis provided robust genetic evidence supporting STX4’s regulatory influence on childhood asthma susceptibility. pQTL validation confirmed that STX4’s effects extend to the protein level, strengthening its biological relevance. DNA methylation analysis revealed key CpG (Cytosine-phosphate-Guanine) sites regulating STX4 expression, with higher methylation levels reducing childhood asthma risk. Immune cell mediation analysis demonstrated that STX4 influences childhood asthma risk via CD4+ and CD8+ T cell subsets. LDSC analysis reinforced a significant genetic correlation between STX4 and childhood asthma, while PheWAS detected no major pleiotropy, suggesting that STX4 is a specific and promising therapeutic target. Conclusions This study systematically identifies and validates STX4 as a key genetic regulator in childhood asthma by integrating large-scale genetic, epigenetic, and immune regulatory data. These findings provide strong evidence for STX4’s role in childhood asthma pathogenesis, highlighting STX4 as a potential target for future precision therapies in childhood asthma.

To address the imbalance in the supply of grass resources caused by seasonality and regional factors, it is crucial to efficiently store and transport alfalfa. Exploring suitable grass feed processing techniques contributes to the stable transportation of grass blocks and long-term storage of nutritional components. The Central Composite Design response surface design was used to design experiments, with moisture content and compressive force as the test factors. Based on the experimental results, it was found that lower moisture content and a certain compressive force were beneficial for the stability, high density, and protein storage of alfalfa blocks. The microscopic examination of alfalfa particles revealed that a certain moisture content (15%) facilitates the formation of solid bridges between particles, leading to more stable alfalfa blocks. The final optimized process parameters were moisture content of 14.3% and compressive force of 34.8 kN. Under these conditions, the density of the molded alfalfa block was 1001 kg/m3, with R-CP at 96.96%, R-EE at 67.23%, and R-CF at 114.13%.

Fragment-based approaches offer rapid screening of chemical space and have become a mainstay in drug discovery. This manuscript provides a recent example that highlights the initial and intermediate stages involved in the fragment-based discovery of an allosteric inhibitor of the malarial aspartate transcarbamoylase (ATCase), subsequently shown to be a potential novel anti-malarial. The initial availability of high-resolution diffracting crystals allowed the collection of a number of protein fragment complexes, which were then assessed for inhibitory activity in an in vitro assay, and binding was assessed using biophysical techniques. Elaboration of these compounds in cycles of structure-based drug design improved activity and selectivity between the malarial and human ATCases. A key element in this process was the use of multicomponent reaction chemistry as a multicomponent compatible fragment library, which allowed the rapid generation of elaborated compounds, the rapid construction of a large (70 member) chemical library, and thereby efficient exploration of chemical space around the fragment hits. This review article details the steps along the pathway of the development of this library, highlighting potential limitations of the approach and serving as an example of the power of combining multicomponent reaction chemistry with fragment-based approaches.

Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 – a potent, yet unselective, antimalarial – is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.

Individual tree crown detection and morphological parameter estimation can be used to quantify the social, ecological, and landscape value of urban trees, which play increasingly important roles in densely built cities. In this study, a novel architecture based on deep learning was developed to automatically detect tree crowns and estimate crown sizes and tree heights from a set of red-green-blue (RGB) images. The feasibility of the architecture was verified based on high-resolution unmanned aerial vehicle (UAV) images using a neural network called FPN-Faster R-CNN, which is a unified network combining a feature pyramid network (FPN) and a faster region-based convolutional neural network (Faster R-CNN). Among more than 400 tree crowns, including 213 crowns of Ginkgo biloba, in 7 complex test scenes, 174 ginkgo tree crowns were correctly identified, yielding a recall level of 0.82. The precision and F-score were 0.96 and 0.88, respectively. The mean absolute error (MAE) and mean absolute percentage error (MAPE) of crown width estimation were 0.37 m and 8.71%, respectively. The MAE and MAPE of tree height estimation were 0.68 m and 7.33%, respectively. The results showed that the architecture is practical and can be applied to many complex urban scenes to meet the needs of urban green space inventory management.

Numerous prior analyses have highlighted a potential link between androgen suppression therapy (AST) and bladder cancer (BCa). However, there is a notable gap in research specifically examining the influence of finasteride on BCa risk and clinical outcomes. This study aimed to evaluate preventive and therapeutic value of finasteride for BCa patients. This meta-analysis adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Guidelines. The PubMed, Embase, Cochrane Library, and Web of Science databases were searched up to 20 December 2024, to identify studies that examined the intake of finasteride and its impact on the incidence and clinical prognosis of patients with BCa. Data was extracted for further analysis by two different reviewers who independently examined the titles and abstracts of the included articles. Subgroup analyses and leave-one-out sensitivity analyses, were applied to mitigate the potential confounding factors associated with heterogeneity. Our investigation revealed that finasteride markedly decreased the likelihood of developing BCa (hazard ratio [HR]: 0.75, 95% confidence interval [CI]: 0.63-0.88). Subgroup analyses indicated that the preventive effect of finasteride in BCa incidence were generally consistent, regardless of study region, types of research. Furthermore, no notable disparities were observed in OS, CSS, or RFS between the finasteride group and the control group. Finasteride plays a protective role against the progression of BCa, nevertheless, its effects on prognostic outcomes, including OS, CSS, and RFS, remain inconclusive. Additional multi-center prospective studies with long-term follow-up are required to further validate prophylactic role of finasteride on bladder cancer. https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=525046, identifier CRD42024525046.

A series of propargylamides containing an electron-rich benzene ring was prepared through the Ugi reaction of 3,5-dimethoxyaniline with various propiolic acids, aldehydes and isocyanides. Subjecting these adducts to a gold-catalyzed intramolecular alkyne hydroarylation process allowed to efficiently construct the 2-quinolone core bearing a branched substituent on the nitrogen atom.