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Abstract The quantitative characterization and prediction of localized severe weather events that emerge as coherences generated by the highly non-linear interacting multivariate dynamics of global weather systems poses a significant challenge whose solution is increasingly important in the face of climate change where weather extremes are on the rise. As weather measurement systems (multiband satellite, radar, etc) continue to dramatically improve, increasingly complex time-dependent multivariate 3D datasets offer the potential to inform such problems but pose an increasingly daunting computational challenge. Here we describe the application to global weather systems of a novel computational method called the Entropy Field Decomposition (EFD) capable of efficiently characterizing coherent spatiotemporal structures in non-linear multivariate interacting physical systems. Using the EFD derived system configurations, we demonstrate the application of a second novel computational method called Space-Time Information Trajectories (STITs) that reveal how spatiotemporal coherences are dynamically connected. The method is demonstrated on the specific phenomenon known as atmospheric rivers (ARs) which are a prime example of a highly coherent, in both space and time, severe weather phenomenon whose generation and persistence are influenced by weather dynamics on a wide range of spatial and temporal scales. The EFD reveals how the interacting wind vector field and humidity scalar field couple to produce ARs, while the resulting STITS reveal the linkage between ARs and large-scale planetary circulations. The focus on ARs is also motivated by their devastating social and economic effects that have made them the subject of increasing scientific investigation to which the EFD may offer new insights. The application of EFD and STITs to the broader range of severe weather events is discussed.

Currently, heterosis is an effective method for achieving high crop quality and yield worldwide. Owing to the challenges of breeding and the high cost of the F1 generation, the F2 generation is considered the more desirable hybrid offspring for agricultural production. The use of OJIP fluorescence provides rapid insights into various photosynthetic mechanisms. However, OJIP fluorescence has not been previously studied as an indicator of the rate of heterosis. Consequently, we investigated the relationship between photosynthetic characteristics and growth and developmental parameters in hybrid cotton cultivars. The findings showed a gradual decline in the photosynthetic performance of hybrid cotton as the number of generations increased. In comparison to the F3 generation, both the F1 and F2 generations showed minimal variations in parameters, thus maintaining hybrid dominant and emphasizing the agricultural production potential of the F2 generation. The JIP-test revealed significant differences in the relationship between ψEo and ϕEo parameters, as well as variations in the connections between the photo-response center and electron transfer efficiency, and between cotton yield and fiber quality in the hybrid progeny. These variations can serve as indicators for predicting the extent of hybrid dominance in cotton. The results indicated significant differences in the light and dark responses of the hybrid offspring. By using parents with similar photosynthetic performance as genetic resources for crossbreeding, the photosynthetic capacity of the hybrid progeny can be enhanced to facilitate the efficient absorption and conversion of light energy in crops.

Abstract Cuproptosis is an emerging cell death pathway that depends on the intracellular Cu ions. Elesclomol (ES) as an efficient Cu ionophore can specifically transport Cu into mitochondria and trigger cuproptosis. However, ES can be rapidly removed and metabolized during intravenous administration, leading to a short half‐life and limited tumor accumulation, which hampers its clinical application. Here, the study develops a reactive oxygen species (ROS)‐responsive polymer (PCP) based on cinnamaldehyde (CA) and polyethylene glycol (PEG) to encapsulate ES‐Cu compound (EC), forming ECPCP. ECPCP significantly prolongs the systemic circulation of EC and enhances its tumor accumulation. After cellular internalization, the PCP coating stimulatingly dissociates exposing to the high‐level ROS, and releases ES and Cu, thereby triggering cell death via cuproptosis. Meanwhile, Cu2+‐stimulated Fenton‐like reaction together with CA‐stimulated ROS production simultaneously breaks the redox homeostasis, which compensates for the insufficient oxidative stress treated with ES alone, in turn inducing immunogenic cell death of tumor cells, achieving simultaneous cuproptosis and immunotherapy. Furthermore, the excessive ROS accelerates the stimuli‐dissociation of ECPCP, forming a positive feedback therapy loop against tumor self‐alleviation. Therefore, ECPCP as a nanoplatform for cuproptosis and immunotherapy improves the dual antitumor mechanism of ES and provides a potential optimization for ES clinical application.

Background: The TGF-β gene is a gemcitabine (GEM) resistance gene; however, the mechanism by which it regulates GEM resistance in pancreatic cancer remains unclear. Methods: The PANC-1 cell line was treated with GEM and then stimulated with TGF-β. Subsequently, we constructed GEM-resistant pancreatic cancer cell lines, knocked down TGF-β in these cell lines, and detected changes in the proliferation and apoptosis of drug-resistant cancer cells. In addition, the protein expression levels of KLF-4, GFI-1, and ZEB-1 were determined. The xenograft tumor models of nude mice were constructed by subcutaneously injecting GEM-resistant PANC-1 cells into mouse axilla. The tumors were removed, dissected, and weighed after 6 weeks. The protein levels of KLF-4, GFI-1, and ZEB-1 in tumor tissues were quantified. In addition, the percentage of M2 macrophages in tumor tissues was determined using flow cytometry. Results: The protein levels of TGF-β in pancreatic cancer cells were significantly decreased after GEM treatment. The protein expression of KLF-4 was downregulated, whereas the expressions of GFI-1 and ZEB-1 were upregulated after TGF-β stimulation. Apoptosis increased and proliferation decreased after TGF-β knockdown in GEM-resistant pancreatic cancer cells, moreover, silencing TGF-β promoted the expression of Caspase 3 and Cleaved caspase 3. In addition, the protein expression of KLF-4 was upregulated, whereas the expressions of GFI-1 and ZEB-1 were downregulated. Further, the volume and weight of the transplanted tumor decreased after TGF-β knockdown. The protein expression of KLF-4 was upregulated, whereas the expressions of GFI-1 and ZEB-1 were downregulated in tumor tissues. In addition, the percentage of M2 macrophages decreased in tumor tissues after TGF-β knockdown. Conclusions: The knockdown of TGF-β inhibits epithelial-to-mesenchymal transition, suppresses the proliferation and promotes the apoptosis of drug-resistant cancer cells, and decreases the macrophage polarization to the M2 phenotype, consequently ameliorating GEM resistance in pancreatic cancer.

Abstract Food digestion requires the cooperation of different digestive organs. The differentiation of digestive organs is crucial for larvae to start feeding. Therefore, during digestive organogenesis, cell identity and the tissue morphogenesis must be tightly coordinated but how this is accomplished is poorly understood. Here, we demonstrate that WD repeat domain 5 (Wdr5)-mediated H3K4 tri-methylation (H3K4me3) coordinately regulates cell differentiation, proliferation and apoptosis in zebrafish organogenesis of three major digestive organs including intestine, liver, and exocrine pancreas. During zebrafish digestive organogenesis, some of cells in these organ primordia usually undergo differentiation without apoptotic activity and gradually reduce their proliferation capacity. In contrast, cells in the three digestive organs of wdr5 −/− mutant embryos retain progenitor-like status with high proliferation rates, and undergo apoptosis. Wdr5 is a core member of COMPASS complex to implement H3K4me3 and its expression is enriched in digestive organs from 2 days post-fertilization (dpf). Further analysis reveals that lack of differentiation gene expression is due to significant decreases of H3K4me3 around the transcriptional start sites of these genes; this histone modification also reduces the proliferation capacity in differentiated cells by increasing the expression of apc to promote the degradation of β-Catenin; in addition, H3K4me3 promotes the expression of anti-apoptotic genes such as xiap-like, which modulates p53 activity to guarantee differentiated cell survival. Thus, our findings have discovered a common molecular mechanism for cell fate determination in different digestive organs during organogenesis, and also provided insights to understand mechanistic basis of human diseases in these digestive organs.

Yearly epidemics of seasonal influenza cause an enormous disease burden around the globe. An understanding of the rules behind the immune response with repeated vaccination still presents a significant challenge, which would be helpful for optimizing the vaccination strategy. In this study, 34 healthy volunteers with 16 vaccinated were recruited, and the dynamics of the BCR repertoire for consecutive vaccinations in two seasons were tracked. In terms of diversity, length, network, V and J gene segments usage, somatic hypermutation (SHM) rate and isotype, it was found that the overall changes were stronger in the acute phase of the first vaccination than the second vaccination. However, the V gene segments of IGHV4-39, IGHV3-9, IGHV3-7 and IGHV1-69 were amplified in the acute phase of the first vaccination, with IGHV3-7 dominant. On the other hand, for the second vaccination, the changes were dominated by IGHV1-69, with potential for coding broad neutralizing antibody. Additional analysis indicates that the application of V gene segment for IGHV3-7 in the acute phase of the first vaccination was due to the elevated usage of isotypes IgM and IgG3. While for IGHV1-69 in the second vaccination, it was contributed by isotypes IgG1 and IgG2. Finally, 41 public BCR clusters were identified in the vaccine group, with both IGHV3-7 and IGHV1-69 were involved and representative complementarity determining region 3 (CDR3) motifs were characterized. This study provides insights into the immune response dynamics following repeated influenza vaccination in humans and can inform universal vaccine design and vaccine strategies in the future.

AbstractD-alpha-tocopheryl polyethylene glycol 1000 succinate (TPGS) is a commonly used nonionic surfactant used as a pharmaceutical carrier in different drug delivery systems. TPGS can reverse P-glycoprotein (P-gp)-mediated multidrug resistance (MDR) and also has anticancer activities. It suggests that when designing antitumor drug preparation, it’s necessary to take into account the antitumor activity of TPGS. Our in vivo studies showed that TPGS exerted the strongest cytotoxicity in MCF-7-ADR cells when compared with seven other tumor cell lines. The further study revealed TPGS caused apoptosis and blocked MCF-7 cell growth in G2/M phase. Mechanistic insights suggested that TPGS increased intracellular calcium ion concentrations, leading to apoptosis via the mitochondrial pathway. Furthermore, two in vivo experiments were performed. One was TPGS, and DOX solution was administered by tail vein injection on MCF-7-ADR tumor bearing nude mice. The other was temperature sensitive TPGS gel (TPGS-TG) was administered by intratumoral injection on MCF-7-ADR tumor bearing nude mice combined with paclitaxel albumin nanoparticles (Abraxane®) administered by tail vein injection. The findings confirmed that TPGS could play its role in anti-tumor to reduce the toxicity of chemotherapeutic drugs and improve the efficiency of drug-resistant tumors, thereby enhancing the development of safe oncology therapeutics.

Chronic diabetic wound remains a critical challenge suffering from the complicated negative microenvironments, such as high-glucose, excessive reactive oxygen species (ROS), hypoxia and malnutrition. Unfortunately, few strategies have been developed to ameliorate the multiple microenvironments simultaneously. In this study, Chlorella sp. (Chlorella) hydrogels were prepared against diabetic wounds. In vitro experiments demonstrated that living Chlorella could produce dissolved oxygen by photosynthesis, actively consume glucose and deplete ROS with the inherent antioxidants, during the daytime. At night, Chlorella was inactivated in situ by chlorine dioxide with human-body harmless concentration to utilize its abundant contents. It was verified in vitro that the inactivated-Chlorella could supply nutrition, relieve inflammation and terminate the oxygen-consumption of Chlorella-respiration. The advantages of living Chlorella and its contents were integrated ingeniously. The abovementioned functions were proven to accelerate cell proliferation, migration and angiogenesis in vitro. Then, streptozotocin-induced diabetic mice were employed for further validation. The in vivo outcomes confirmed that Chlorella could ameliorate the undesirable microenvironments, including hypoxia, high-glucose, excessive-ROS and chronic inflammation, thereby synergistically promoting tissue regeneration. Given the results above, Chlorella is considered as a tailor-made therapeutic strategy for diabetic wound healing.

Abstract Background Hepatoma is a serious public health concern. New attempts are urgently needed to solve this problem. Melittin, a host defense peptide derived from the venom of honeybees, has noteworthy hemolysis and non-specific cytotoxicity in clinical applications. Here, the self-assembly of melittin and vitamin E-succinic acid-(glutamate)12 (VG) was fabricated via noncovalent π-stacking and hydrogen bonding interactions using an environment-friendly method without “toxic” solvents. Results As expected, the designed self-assembly (denoted as M/VG nanoparticles) exhibits a uniform morphology with a particle size of approximately 60 nm and a zeta potential of approximately − 26.8 mV. Furthermore, added VG significantly decreased hemolytic activity, increased tumor-targeted effects, and accelerated apoptosis. Conclusion Our research provides a promising strategy for the development of natural self-assembled biological peptides for clinical application, particularly for transforming toxic peptides into safe therapeutic systems. Graphical Abstract

Abstract Background Combination of chemotherapy and immune checkpoint inhibitor therapy has greatly improved the anticancer effect on multiple malignancies. However, the efficiency on triple-negative breast cancer (TNBC) is limited, since most patients bear “cold” tumors with low tumor immunogenicity. Doxorubicin (DOX), one of the most effective chemotherapy agents, can induce immunogenic cell death (ICD) and thus initiating immune response. Methods In this study, to maximize the ICD effect induced by DOX, chitosan and cell-penetrating peptide (R6F3)-modified nanoparticles (PNPs) loaded with ginsenoside Rg3 (Rg3) were fabricated using the self-assembly technique, followed by co-encapsulation with DOX based on thermo-sensitive hydrogel. Orthotopic tumor model and contralateral tumor model were established to observe the antitumor efficacy of the thermo-sensitive hydrogel combined with anti-PD-L1 immunotherapy, besides, the biocompatibility was also evaluated by histopathological. Results Rg3-PNPs strengthened the immunogenic cell death (ICD) effect induced by DOX. Moreover, the hydrogel co-loading Rg3-PNPs and DOX provoked stronger immune response in originally nonimmunogenic 4T1 tumors than DOX monotherapy. Following combination with PD-L1 blocking, substantial antitumor effect was achieved due to the recruitment of memory T cells and the decline of adaptive PD-L1 enrichment. Conclusion The hydrogel encapsulating DOX and highly permeable Rg3-PNPs provided an efficient strategy for remodeling immunosuppressive tumor microenvironment and converting immune “cold” 4T1 into “hot” tumors.

Integrated positioning methods in the high-velocity train control system require auxiliary equipment leading to more construction and maintenance costs. This paper proposes a BDS/LTE-R (Beidou Navigation Satellite System/Long Term Evolution-Railway) integrated positioning system based on deep learning and establishes a 7L-CNNSeven-layer convolutional neural network) an enhanced model of BDS/LTE-R data fusion positioning. Firstly, the positioning principles of the BDS and LTE-R system are analyzed to construct a data space second order autocorrelation matrix of the results from each single positioning system, which serves as the input of the 7L-CNN model. The positioning data are output after the depth feature extraction and feature fusion. In a test based on field data, the 7L-CNN model obtains fusion results with the second-order autocorrelation matrix of positioning data space as the input. Compared with the results obtained from the early fusion algorithm and CNN (convolutional neural network) fusion positioning model with the input of the original positioning data, the 7L-CNN enhanced algorithm can bring better convergence accuracy for both solving velocity and positioning results according to the velocity and position errors in the east and north directions. When a satellite is out of the lock, the 7L-CNN algorithm also has a good correction effect on the single LTE-R positioning, which can meet the requirements for high-precision and continuous real-time positioning of a train.

Introduction: It is urgent to make a rapid screening of infants at the highest risk for bronchopulmonary dysplasia (BPD) via some succinct postnatal biomarkers, such as Ureaplasma Urealyticum (UU) infection and chest radiograph images. Methods: A retrospective study was performed. Moderate to severe BPD or death was set as the main outcome. The association between putative variables and the main outcome were assessed by bivariate analyses and logistic regression. Results: A total of 134 infants were enrolled. Bivariate analyses showed the gestational age, birth weight, appearances of diffuse opacities or grid shadows/interstitial opacities or mass opacities or cystic lucencies on chest radiographic images, a ductal diameter ≥1.5 mm and whether UU infection was associated with BPD. After adjustment by logistic regression, the risk of BPD with gestational age, sex and specific chest-radiographic manifestations remained significant. Conclusions: Chest radiograph images (appearance of diffuse opacities or grid shadows/interstitial opacities or mass opacities or cystic lucencies) could provide a quick prediction of developing BPD in clinical practice, in addition to gestational age and sex. UU infection was not an independent risk factor for BPD.

Cholangiocarcinoma (CCA) is the second most common primary tumor of the hepatobiliary system. At present, the therapeutic efficiency of cholangiocarcinoma is fairly low and the prognosis is poor. The root cause is that the molecular mechanism of the occurrence and development of CCA is largely unclear. This work intended to clarify the role of DEP domain-containing protein 1B (DEPDC1B) in the progress of CCA through cellular biology research strategies and further clarify the molecular mechanism of CCA. Clinical tissue-related detection showed that the expression level of DEPDC1B in tumor tissues was significantly higher than that in normal tissues and was positively correlated with tumor grade. Knockdown of the endogenous DEPDC1B of CCA cells can significantly inhibit cell proliferation and migration, while promoting cell apoptosis and blocking the cell cycle. DEPDC1B overexpression induced the opposite effects. Studies in animal models also showed that the downregulation of DEPDC1B can reduce the tumorigenicity of CCA cells. In addition, through gene profiling analysis and molecular biology studies, we found that CDK1 may be an important downstream mediator of DEPDC1B, the protein stability of which was significantly decreased through the ubiquitin–proteasome system in DEPDC1B knockdown cells. Moreover, knockdown of CDK1 can weaken the promotion of CCA caused by DEPDC1B overexpression. In summary, our research showed that DEPDC1B plays an important role in the development of CCA and its targeted inhibition may become one of the important methods to inhibit the progress of CCA.

Abstract Background Bronchopulmonary dysplasia (BPD) infants present an increased incidence of metabolic bone disease (MBD), but it is unknown which factors contribute to this. The aim of this study was to determine the risk factors for developing MBD in BPD infants. Methods A retrospective review of the medical records of BPD infants admitted to the Neonatal intensive care unit at Zhangzhou Hospital between Jun 2016 and May 2020 was performed. BPD infants with MBD were identified, two contemporaneous without MBD matched by gestational age and gender were randomly selected as controls for each case of MBD. The association between putative risk factors and MBD was estimated with ORs and 95% CIs. A P-value threshold ≤0.2 was used in univariate analysis for inclusion into a multivariate (adjusted) model with a P-value of 2 weeks) diuretics application (OR 5.45, 95% CI, 1.25–23.84) were found to be statistically significant risk factors for MBD in BPD infants. Conclusion In BPD infants of homogeneous gestational age, fetal growth restriction, extremely low birth weight, feeding volume

The receiver integrity monitoring of a satellite navigation system directly affects positioning accuracy and train safety. The GPS/BDS (Global Positioning System/BeiDou Navigation System) integrated navigation system can meet the requirements of RAIM (Receiver Autonomous Integrity Monitoring) for the minimum number of visible satellites. However, the probability of multiple satellite simultaneous failures increases in the GPS/BDS integrated navigation system so that when the failures occur, the RAIM algorithm cannot meet the requirements of safety for the receiver when positioning trains. In response to the problem, this paper applies the CIPSO-FCM (Chaotic Immune-vaccine Particle Swarm Optimization_ Fuzzy C-means) algorithm to RAIM to establish a new algorithm. It can predict the HPL (Horizontal Protection Level) value of the GPS/BDS integrated navigation system to verify RAIM availability. It also uses the parity space vector to obtain cluster samples through a pseudo-range observation matrix. The CIPSO algorithm obtains the initial cluster centers by iteration to prevent the FCM algorithm from falling into the local optimum, leading to inconsistent classification. A test based on actual field data shows that the CIPSO-FCM-based RAIM algorithm achieves a probability of 99.98% for detecting and identifying multiple satellite failures with a gross error of 28m, which can meet the safety requirements for the receiver when positioning trains.

Abstract The SARS‐CoV‐2 Delta (B.1.617.2) strain is a variant of concern (VOC) that has become the dominant strain worldwide in 2021. Its transmission capacity is approximately twice that of the original strain, with a shorter incubation period and higher viral load during infection. Importantly, the breakthrough infections of the Delta variant have continued to emerge in the first‐generation vaccine recipients. There is thus an urgent need to develop a novel vaccine with SARS‐CoV‐2 variants as the major target. Here, receptor binding domain (RBD)‐conjugated nanoparticle vaccines targeting the Delta variant, as well as the early and Beta/Gamma strains, are developed. Under both a single‐dose and a prime‐boost strategy, these RBD‐conjugated nanoparticle vaccines induce the abundant neutralizing antibodies (NAbs) and significantly protect hACE2 mice from infection by the authentic SARS‐CoV‐2 Delta strain, as well as the early and Beta strains. Furthermore, the elicitation of the robust production of broader cross‐protective NAbs against almost all the notable SARS‐CoV‐2 variants including the Omicron variant in rhesus macaques by the third re‐boost with trivalent vaccines is found. These results suggest that RBD‐based monovalent or multivalent nanoparticle vaccines provide a promising second‐generation vaccine strategy for SARS‐CoV‐2 variants.

Abstract Background Epigenetic regulation is essential in regulating gene expression across a variety of biological processes. Many high-throughput sequencing technologies have been widely used to generate epigenetic data, such as histone modification, transcription factor binding sites, DNA modifications, chromatin accessibility, and etc. A large scale of epigenetic data is stored in NCBI Gene Expression Omnibus (GEO). However, it is a great challenge to reanalyze these large scale and complex data, especially for researchers who do not specialize in bioinformatics skills or do not have access to expensive computational infrastructure. Results GsmPlot can simply accept GSM IDs to automatically download NCBI data or can accept user’s private bigwig files as input to plot the concerned data on promoters, exons or any other user-defined genome locations and generate UCSC visualization tracks. By linking public data repository and private data, GsmPlot can spark data-driven ideas and hence promote the epigenetic research. Conclusions GsmPlot web server allows convenient visualization and efficient exploration of any NCBI epigenetic data in any genomic region without need of any bioinformatics skills or special computing resources. GsmPlot is freely available at https://gsmplot.deqiangsun.org/.

ABSTRACTThe Zika virus (ZIKV) is a mosquito-borne flavivirus that causes neonatal abnormalities and other disorders. Antibodies to the ZIKV envelope (E) protein can block infection. In this study, next-generation sequencing (NGS) of immunoglobulin heavy chain (IgH) mRNA transcripts was combined with single-cell PCR cloning of E-binding monoclonal antibodies for analysing antibody response in a patient from the early stages of infection to more than one year after the clearance of the virus. The patient's IgH repertoire 14 and 64 days after symptom onset showed dramatic dominant clonal expansion but low clonal diversity. IgH repertoire 6 months after disease-free status had few dominant clones but increased diversity. E-binding antibodies appeared abundantly in the repertoire during the early stages of infection but quickly declined after clearance of the virus. Certain VH genes such as VH5-10-1 and VH4-39 appeared to be preferentially enlisted for a rapid antibody response to ZIKV infection. Most of these antibodies require relatively few somatic hypermutations to acquire the ability to bind to the E protein, pointing to a possible mechanism for rapid defence against ZIKV infection. This study provides a unique and holistic view of the dynamic changes and characteristics of the antibody response to ZIKV infection.

In order to alleviate the conflict at intersections in a networked environment between trams in a semi-exclusive right-of-way mode and social vehicles, the running characteristics of these trams and vehicles and their coupling characteristics with the intersection signal are analyzed. The positive and negative effects of the special priority signal on the intersection are considered, and a guidance optimization model that combines urban rails and roads is constructed. With the aim of creating an unplanned delay adjustment scenario for trams, an online collaborative optimization algorithm is proposed, which takes the energy consumption, passenger travel time and comfort of both trams and connected vehicles as optimization objectives in order to realize integrated adjustment of the running trajectories and signal timing, and the population is evolved by using an adaptive elitist genetic algorithm. The study is based on the actual traffic information and timing scheme of an intersection on the T1 line of the Sanya Tram. By comparing with conventional trajectories, the optimized trajectories reduce the total transit time by about 17.1%, the total energy consumption by about 34.7% and the passenger discomfort degree by about 27.8%. The contradiction of the right-of-way distribution at the intersection is alleviated, effectively safeguarding the interests of different users and enterprises. The experimental results show that the model has excellent applicability for different proportions of passenger numbers.

Many visual SLAM systems are generally solved using natural landmarks or optical flow. However, due to textureless areas, illumination change or motion blur, they often acquire poor camera poses or even fail to track. Additionally, they cannot obtain camera poses with a metric scale in the monocular case. In some cases (such as when calibrating the extrinsic parameters of camera-IMU), we prefer to sacrifice the flexibility of such methods to improve accuracy and robustness by using artificial landmarks. This paper proposes enhancements to the traditional SPM-SLAM, which is a system that aims to build a map of markers and simultaneously localize the camera pose. By placing the markers in the surrounding environment, the system can run stably and obtain accurate camera poses. To improve robustness and accuracy in the case of rotational movements, we improve the initialization, keyframes insertion and relocalization. Additionally, we propose a novel method to estimate marker poses from a set of images to solve the problem of planar-marker pose ambiguity. Compared with the state-of-art, the experiments show that our system achieves better accuracy in most public sequences and is more robust than SPM-SLAM under rotational movements. Finally, the open-source code is publicly available and can be found at GitHub.

Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel allele candidates (NACs) using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the NACs detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.

Avermectin (AVM), as a biological insecticide, is widely used in agriculture and forestry production globally. However, inhalation of AVM may pose a risk, and the lung is the direct target, but the cytotoxicity of AVM on human lung cells is still unclear. Here, we attempted to elucidate the cytotoxic effect and molecular mechanism of AVM on human lung A549 cells. The results indicated that AVM inhibits cell proliferation, and enhances programmed cell death (apoptosis and autophagy). In addition, we found the AVM-treated cells showed an obvious drop in mitochondrial membrane potential and LC3-I/II, increased ROS production, DNA double-strand breaks, caspase-3/9 activated, PARP cleaved, cytochrome c and Bax/Bcl-2 content rise. The results showed that AVM induced mitochondria-related apoptosis and autophagy in lung A549 cells. These results indicate that AVM can pose a potential threat to human health by inducing DNA damage and programmed cell death.

A dual parallel factor (PARAFAC)-based approach to jointly estimating the two-dimensional direction of arrival (2-D DOA) and Doppler is proposed in this paper, where an L-shaped array consisting of acoustic vector-sensor is used. First, we apply the PARAFAC decomposition to the data model formed by concatenating the outputs of multi-level delays of the observations, and we get the parameter matrix H, which accomplish the 2-D DOA estimation and pairing automatically, then the dual PARAFAC decomposition is applied to the achieved composite steering matrix from the first PARAFAC decomposition, and thus, the same permutation matrices link the estimates of steering matrices and delay matrices from X-subarray and Y-subarray, respectively. Following this, the Doppler and 2-D DOA matching information are obtained via triple matching implementation, e.g. 2-D DOA and frequency matching. Finally, Doppler is estimated by delay matrices. The proposed algorithm is computationally effective for both uniform and non-uniform L-shaped array as SNR exceeds 15dB, and its performance outperforms the joint angle and Doppler shift ESPRIT (JAD-ESPRIT) algorithm and the joint angle and Doppler shift PM (JAD-PM) algorithm. The simulation results justified the effectiveness of the proposed algorithm.

Knowledge about subsurface geological characteristics and a geothermic genetic model plays an essential role in geothermal exploration and resource assessment. To solve the problem in the Shunping area along eastern Taihang Mountain, geothermal geological conditions were analyzed by geophysical, geochemical, and geological methods, such as magnetotelluric, gas geochemistry, and structural analysis. The geothermic genetic model was developed by analyzing the characteristics of the heat source, water source, migration channel, reservoir, and cap rock of the geothermal geological conditions. Favorable deep thermal conduction conditions and sufficient atmospheric precipitation in the study area provide an original heat source and water supply for geothermal formation. The faults and unconformities of different scales have become effective channels for the migration of underground hot water. The thermal reservoir formed by marine carbonate rocks with karst fissure development provides suitable space for the storage of underground hot water. Although the Cenozoic strata have good thermal insulation and water insulation function, the thermal insulation and water insulation effect is not ideal because of the shallow coverage in the Shunping area and the damage by tectonic action, which affected thermal insulation and water insulation to some extent, restricting the practical preservation of underground heat energy in the Shunping area. The bedrock geothermal resource in the Shunping area is original from the combined action of multiple indexes of source, transport, reservoir, and cap. The geothermal geologic conditions of source and reservoir in the Shunping area are very similar to those in the Xiongan new area, and have obvious advantages in hydrodynamic conditions. Although limited by the cap’s effectiveness, the geothermal resources in the Shunping area can provide some clean energy support for local production and life, thereby satisfying economic development conditions and encouraging further geological exploration.

Evidence for reduced expression of cyclin G associated kinase (GAK) in glomeruli of patients with chronic kidney disease was observed in the Nephroseq human database, and GAK was found to be associated with the decline in kidney function. To examine the role of GAK, a protein that functions to uncoat clathrin during endocytosis, we generated podocyte-specific Gak-knockout mice (Gak-KO), which developed progressive proteinuria and kidney failure with global glomerulosclerosis. We isolated glomeruli from the mice carrying the mutation to perform messenger RNA profiling and unearthed evidence for dysregulated podocyte calpain protease activity as an important contributor to progressive podocyte damage. Treatment with calpain inhibitor III specifically inhibited calpain-1/-2 activities, mitigated the degree of proteinuria and glomerulosclerosis, and led to a striking increase in survival in the Gak-KO mice. Podocyte-specific deletion of Capns1, essential for calpain-1 and calpain-2 activities, also improved proteinuria and glomerulosclerosis in Gak-KO mice. Increased podocyte calpain activity–mediated proteolysis of IκBα resulted in increased NF-κB p65–induced expression of growth arrest and DNA-damage-inducible 45 beta in the Gak-KO mice. Our results suggest that loss of podocyte-associated Gak induces glomerular injury secondary to calcium dysregulation and aberrant calpain activation, which when inhibited, can provide a protective role.

Background: MicroRNAs (miRNAs) are small non-coding molecules that exhibit important regulatory roles in various biological or cellular functions, including tumor metastasis. However, the detailed mechanisms of the expression and functions of miRNAs in hepatocellular carcinoma (HCC) have not yet been completely investigated. Methods: In this study, the levels of miR-148b in HCC cells and patient specimens were determined using qPCR assays. MiR-148b-overexpressing HCC cells were used to investigate the effect of miR-148b in vitro and in vivo. The relationship between the expression of miR-148b and colony stimulating factor-1 (CSF1) in HCC patients and the infiltration of macrophages into the tumor microenvironment were assessed by immunohistochemical staining. Results: MiR-148b expression was decreased in metastatic HCC cells. A positive association between downregulated miR-148b expression and several clinical parameters, including recurrence, metastasis, and poor prognosis, was observed in patients with HCC. The results of bio-functional experiments indicated that the biological characteristics of HCC cells were not affected by miR-148b deficiency in vitro. However, miR-148b deficiency significantly enhanced the progression and metastasis of HCC in nude mice. By analyzing the gene expression profiles, we demonstrated that CSF1 was regulated by miR-148b and that miR-148b deficiency promoted HCC growth and metastasis through CSF1/CSF1 receptor (CSF1R)-mediated tumor-associated macrophage (TAM) infiltration. These results were supported by the negative relationship between miR-148b and CSF1 expression and TAM infiltration in HCC patients. Moreover, HCC patients with low miR-148b levels and high TAM infiltration were associated with poorer prognosis. Conclusion: MiR-148b-CSF1 signaling-induced TAM infiltration promotes HCC metastasis. Therefore, miR-148b plays a suppressor role in HCC and might be a potential prognostic factor and therapeutic candidate for HCC.

Polymer nanoparticles modified with collagen peptides (CPs) are an attractive strategy for the oral delivery of active ingredients from Chinese medicine. Thus, in the present study, collagen cationic CPs were simply separated using ion-exchange resin from bovine CPs, to modify mixed nanomicelles (MMs) on the surface to improve the oral bioavailability of Cucurbitacin B (CuB). The physicochemical property of micelles was characterized, which confirmed the successful modification of the nanomicelles. CPs-modified nanomicelles in vitro were found to significantly increase cellular uptake and transportation. Compared to unmodified micelles, the quantity of CPs-modified micelles internalized by Caco-2 cells were 3.74 times greater and the cumulative transportation flux (AP-BL) was 2.81 times greater. The membrane transportation process of CuB-MMs-CPs was found to be associated with energy consumption and clathrin- and caveolin-mediated endocytosis. In vivo studies performed on rats indicated that in comparison to CuB and CuB-MMs, the relative bioavailability of CuB-MMs-CPs increased by 3.43 times and 2.14 times, respectively. In addition, the tumor inhibition caused by CuB-MMs-CPs was increased significantly. Therefore, the nanomicelles co-modified with isolated CPs could act as attractive carriers for oral delivery of CuB.

This paper summarized the research status, imaging model, systems calibration, distortion correction, and panoramic expansion of panoramic vision systems, pointed out the existing problems and put forward the prospect of future research. According to the research status of panoramic vision systems, a panoramic vision system with single viewpoint of refraction and reflection is designed. The systems had the characteristics of fast acquisition, low manufacturing cost, fixed single-view imaging, integrated imaging, and automatic switching depth of field. Based on these systems, an improved nonlinear optimization polynomial fitting method is proposed to calibrate the monocular HOVS, and the binocular HOVS is calibrated with the Aruco label. This method not only improves the robustness of the calibration results, but also simplifies the calibration process. Finally, a real-time method of panoramic map of multi-function vehicle based on vcam is proposed.

Baohuoside I is an effective but a poorly soluble antitumor drug. In this study, we prepared baohuoside I-loaded mixed micelles with didecyldimethylammonium bromide (DDAB) and d-a-tocopheryl polyethylene glycol succinate (TPGS) (DTBM) and active targeting mixed micelles (HDTBM) with hyaluronic acid (HA) as the targeting ligand on the surface of the mixed micelles. We performed a systematic comparative evaluation of the antiproliferative effect, cellular uptake, antitumor efficacy, and in vivo tumor targeting of these micelles using A549 cells. HDTBM showed improved cellular uptake and had a greater hypersensitizing effect on A549 cell lines than baohuoside I; half-maximal inhibitory concentration (IC50) was 8.86 versus 20.42 μg/mL, respectively. Results of the antitumor efficacy study and the imaging study for in vivo targeting showed that the mixed-micelle formulation had higher antitumor efficacy and achieved effective and targeted drug delivery. Therefore, our results indicate that HA/baohuoside I-M may be used as a potential antitumor formulation.

We address the two-dimensional direction-of-arrival (2-D DOA) estimation problem for L-shaped uniform linear array (ULA) using two kinds of approaches represented by the subspace-like method and the sparse reconstruction method. Particular interest emphasizes on exploiting the generalized conjugate symmetry property of L-shaped ULA to maximize the virtual array aperture for two kinds of approaches. The subspace-like method develops the rotational invariance property of the full virtual received data model by introducing two azimuths and two elevation selection matrices. As a consequence, the problem to estimate azimuths represented by an eigenvalue matrix can be first solved by applying the eigenvalue decomposition (EVD) to a known nonsingular matrix, and the angles pairing is automatically implemented via the associate eigenvector. For the sparse reconstruction method, first, we give a lemma to verify that the received data model is equivalent to its dictionary-based sparse representation under certain mild conditions, and the uniqueness of solutions is guaranteed by assuming azimuth and elevation indices to lie on different rows and columns of sparse signal cross-correlation matrix; we then derive two kinds of data models to reconstruct sparse 2-D DOA via M-FOCUSS with and without compressive sensing (CS) involvements; finally, the numerical simulations validate the proposed approaches outperform the existing methods at a low or moderate complexity cost.

Distributed acoustic sensing based on phase-sensitive optical time-domain reflectometry (Φ-OTDR) has been widely used in many fields. Phase demodulation of the Φ-OTDR signal is essential for undistorted acoustic measurement. Digital coherent detection is a universal method to implement phase demodulation, but it may cause severe computational burden. In this paper, analog I/Q demodulation is introduced into the Φ-OTDR based DAS system to solve this problem, which can directly obtain the I and Q components of the beat signal without any digital processing, meaning that the computational cost can be sharply reduced. Besides, the sampling frequency of the data acquisition card can theoretically be lower than the beat frequency as the spectrum aliasing would not affect the demodulation results, thus further reducing the data volume of the system. Experimental results show that the proposed DAS system can demodulate the phase signal with good linearity and wide frequency response range. It can also adequately recover the sound signal sensed by the optical fiber, indicating that it can be a promising solution for computational-cost-sensitive distributed acoustic sensing applications.

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, leading to a proliferation of software tools for processing and annotating this data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intra-donor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic birthday trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.

Galactose-deficient IgA1 was evaluated in patients with IgA nephropathy(IgAN) and controls in order to determine the predictive value of galactose-deficient IgA1 in cases of IgA nephropathy.PubMed, EMBASE, Cochrane central register of controlled trials, CNKI, CBM disc, and VIP database were searched to identify eligible studies that evaluated a difference in aberrant IgA1 glycosylation in IgAN patients compared with controls. A meta-analysis was conducted to evaluate the impact of galactose-deficient IgA1(Gd-IgA1) levels in different groups.A total of 22 studies (n = 1657) met inclusion criteria. The mean Newcastle-Ottawa Scale (NOS) score was 7.2 and ranged from 6 to 8. The standard mean difference(SMD) in the meta-analysis of 20 studies of the level of Gd-IgA1 in the serum and/or supernatant of cultured cells was higher in the IgAN group compared with healthy controls as well as in those with other renal diseases (SMD = 1.76, 95% CI = 1.18-2.34, P

This study focuses on the preparation and enzymic hydrolysis of an icariin/β-cyclodextrin inclusion complex to efficiently generate icaritin. The physical characteristics of the inclusion complex were evaluated by differential scanning calorimetry (DSC). Enzymatic hydrolysis was optimized for the conversion of icariin/β-cyclodextrin complex to icaritin by Box–Behnken statistical design. The inclusion complex formulation increased the solubility of icariin approximately 17-fold, from 29.2 to 513.5 μg/mL at 60 °C. The optimum conditions were predicted by Box–Behnken statistical design as follows: 60 °C, pH 7.0, the ratio of enzyme/substrate (1:1.1) and reaction time 7 h. Under the optimal conditions the conversion of icariin was 97.91% and the reaction time was decreased by 68% compared with that without β-CD inclusion. Product analysis by melting point, ESI-MS, UV, IR, 1H NMR and 13C NMR confirmed the authenticity of icaritin with a purity of 99.3% and a yield of 473 mg of icaritin from 1.1 g icariin.

The main purpose of this study was to evaluate the intestinal absorption and the antineoplastic effect of the poorly water-soluble drug celastrol when liposomes were used as oral drug delivery system. Liposomes were prepared by the ethanol-injection method. An optimized liposome formulation composed of phospholipid, cholesterol and Tween-80 resulted in favorable encapsulation efficiency at 98.06 ± 0.94%. Homogeneous and stable particle size of 89.6 ± 7.3 nm and zeta potential of −(87.7 ± 5.8) mV were determined by laser particle size analyzer. Subsequently, the four-site perfusion rat intestinal model revealed that celastrol-loaded liposomes had improved effective permeability compared to the free drug in four intestinal segments (p < 0.05). Moreover, celastrol-loaded liposomes could also inhibit the tumor growth in C57BL/6 mice. These results suggest that liposomes could be a promising perioral carrier for celastrol.

Location error and false alarm are noticeable problems in fiber distributed acoustic sensing systems based on phase-sensitive optical time-domain reflectometry (Φ-OTDR). A novel method based on signal kurtosis is proposed to locate and discriminate perturbations in Φ-OTDR systems. The spatial kurtosis (SK) along the fiber is firstly obtained by calculating the kurtosis of acoustic signals at each position of the fiber in a short time period. After the moving average on the spatial dimension, the spatial average kurtosis (SAK) is then obtained, whose peak can accurately locate the center of the vibration segment. By comparing the SAK value with a certain threshold, we may to some degree discriminate the instantaneous destructive perturbations from the system noise and certain ambient environmental interferences. The experimental results show that, comparing with the average of the previous localization methods, the SAK method improves the pencil-break and digging locating signal-to-noise ratio (SNR) by 16.6 dB and 17.3 dB, respectively; and decreases the location standard deviation by 7.3 m and 9.1 m, respectively. For the instantaneous destructive perturbation (pencil-break and digging) detection, the false alarm rate can be as low as 1.02%, while the detection probability is maintained as high as 95.57%. In addition, the time consumption of the SAK method is adequate for a real-time Φ-OTDR system.

Meat quality is determined by properties such as carcass color, tenderness and drip loss. These properties are closely associated with meat composition, which includes the types of muscle fiber and content of intramuscular fat (IMF). Muscle fibers are the main contributors to meat mass, while IMF not only contributes to the sensory properties but also to the plethora of physical, chemical and technological properties of meat. However, little is known about the molecular mechanisms that determine meat composition in different pig breeds. In this report we show that Jinhua pigs, a Chinese breed, contains much higher levels of IMF than do Landrace pigs, a Danish breed. We analyzed global gene expression profiles in the longissimus dorsi muscles in Jinhua and Landrace breeds at the ages of 30, 90 and 150 days. Cross-comparison analysis revealed that genes that regulate fatty acid biosynthesis (e.g., fatty acid synthase and stearoyl-CoA desaturase) are expressed at higher levels in Jinhua pigs whereas those that regulate myogenesis (e.g., myogenic factor 6 and forkhead box O1) are expressed at higher levels in Landrace pigs. Among those genes which are highly expressed in Jinhua pigs at 90 days (d90), we identified a novel gene porcine FLJ36031 (pFLJ), which functions as a positive regulator of fat deposition in cultured intramuscular adipocytes. In summary, our data showed that the up-regulation of fatty acid biosynthesis regulatory genes such as pFLJ and myogenesis inhibitory genes such as myostatin in the longissimus dorsi muscles of Jinhua pigs could explain why this local breed produces meat with high levels of IMF.

Both multiple sequence alignment and phylogenetic analysis are problematic in the "twilight zone" of sequence similarity (≤ 25% amino acid identity). Herein we explore the accuracy of phylogenetic inference at extreme sequence divergence using a variety of simulated data sets. We evaluate four leading multiple sequence alignment (MSA) methods (MAFFT, T-COFFEE, CLUSTAL, and MUSCLE) and six commonly used programs of tree estimation (Distance-based: Neighbor-Joining; Character-based: PhyML, RAxML, GARLI, Maximum Parsimony, and Bayesian) against a novel MSA-independent method (PHYRN) described here. Strikingly, at "midnight zone" genetic distances (~7% pairwise identity and 4.0 gaps per position), PHYRN returns high-resolution phylogenies that outperform traditional approaches. We reason this is due to PHRYN's capability to amplify informative positions, even at the most extreme levels of sequence divergence. We also assess the applicability of the PHYRN algorithm for inferring deep evolutionary relationships in the divergent DANGER protein superfamily, for which PHYRN infers a more robust tree compared to MSA-based approaches. Taken together, these results demonstrate that PHYRN represents a powerful mechanism for mapping uncharted frontiers in highly divergent protein sequence data sets.

Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.

H2Av is a versatile histone variant that plays both positive and negative roles in transcription, DNA repair, and chromatin structure in Drosophila. H2Av, and its broader homolog H2A.Z, tend to be enriched toward 5' ends of genes, and exist in both euchromatin and heterochromatin. Its organization around euchromatin genes and other features have been described in many eukaryotic model organisms. However, less is known about H2Av nucleosome organization in heterochromatin. Here we report the properties and organization of individual H2Av nucleosomes around genes and transposable elements located in Drosophila heterochromatic regions. We compare the similarity and differences with that found in euchromatic regions. Our analyses suggest that nucleosomes are intrinsically positioned on inverted repeats of DNA transposable elements such as those related to the "1360" element, but are not intrinsically positioned on retrotransposon-related elements.

Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid sequences of highly divergent proteins. This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL. Results from our experiments demonstrate that FSL perform well in recognizing folds from the "twilight-zone" SABmark dataset. Further, this method is capable of accurate fold prediction in newly determined structures. We suggest that by building complete PSSM libraries for all unique folds within the Protein Database (PDB), FSL can be used to rapidly and reliably annotate a large subset of protein folds at proteomic level. The related programs and fold-specific PSSMs for our FSL are publicly available at: http://ccp.psu.edu/download/FSLv1.0/.

BACKGROUND: The fish medaka is the first vertebrate capable of full spermatogenesis in vitro from self-renewing spermatogonial stem cells to motile test-tube sperm. Precise staging and molecular dissection of this process has been hampered by the lack of suitable molecular markers. METHODOLOGY AND PRINCIPAL FINDINGS: We have generated a normalized medaka testis cDNA library and obtained 7040 high quality sequences representing 3641 unique gene clusters. Among these, 1197 unique clusters are homologous to known genes, and 2444 appear to be novel genes. Ontology analysis shows that the 1197 gene products are implicated in diverse molecular and cellular processes. These genes include markers for all major types of testicular somatic and germ cells. Furthermore, markers were identified for major spermatogenic stages ranging from spermatogonial stem cell self-renewal to meiosis entry, progression and completion. Intriguingly, the medaka testis expresses at least 13 homologs of the 33 mouse X-chromosomal genes that are enriched in the testis. More importantly, we show that key components of several signaling pathways known to be important for testicular function in mammals are well represented in the medaka testicular EST collection. CONCLUSIONS/SIGNIFICANCE: Medaka exhibits a considerable similarity in testicular gene expression to mammals. The medaka testicular EST collection we obtained has wide range coverage and will not only consolidate our knowledge on the comparative analysis of known genes' functions in the testis but also provide a rich resource to dissect molecular events and mechanism of spermatogenesis in vivo and in vitro in medaka as an excellent vertebrate model.