Shell thickness-induced thermal dependence: highly sensitive core-shell CdSe/ZnS/POSS-based temperature probes.

Fluorescence nanothermometry based on quantum dots is a current research hotspot for novel non-contact temperature monitoring, and is of vital significance for the modulation and design of the sensing properties of sensors. Herein, a design strategy to modulate the temperature-sensing characteristics of quantum dots based on the thickness of a shell is proposed. In this study, CdSe/ZnS quantum dot/POSS-based temperature probe films with varying fluorescence characteristics were developed, and the influence of the ZnS shell on temperature sensing was examined by varying the thickness of the ZnS shell. The temperature dependency, linearity, range of applications, and reversibility of quantum dot thin film probes were all considerably regulated by the ZnS shell, according to research on quantum dot/POSS-based films coated with various shell thicknesses. The CdSe/ZnS temperature probe with 4 monolayers (MLs) stood out among the rest due to its strong thermal stability (at least 5 cycles), large usable temperature range (20-80 °C), and excellent temperature sensitivity (R2 > 0.994). The results demonstrated that the temperature sensing performance of quantum dots was the consequence of the combined effect of multiple temperature response properties induced by the thickness of the shell, and the shell control of quantum dots to optimize the temperature sensing performance was an essential approach for the design of temperature probes. This work demonstrates the great potential of the shell in tuning the temperature sensing performance of quantum dots and provides a viable approach for the design of quantum dot temperature probes.

Does integrated health management within a county medical consortium improve rural type 2 diabetic patients' self-management behavior and quality of life? An empirical analysis from Eastern China.

BACKGROUND: Levels of self-management behaviors (SMB) and quality of life (QoL) are suboptimal in Chinese adults with type 2 diabetes (T2D), especially in rural China. Integrated health management within a county medical consortium, featuring multi-level teams of doctors, nurses, and other professionals offering follow-up services such as check-ups, assessments, treatment, and health education, is promising in improving this. This study aimed to assess the effect of integrated health management within a county medical consortium on the SMB and QoL of rural T2D patients in China. METHODS: Based on a survey conducted on the county medical consortium in Eastern China, this study initially employed propensity score matching (PSM), a nonparametric technique, to precisely estimate the average treatment effect on the treated (ATT) of integrated health management on SMB and QoL in rural T2D patients. Subsequently, quantile regression was also performed to estimate the relationship between the implementation of integrated health management, sociodemographic factors, follow-up services (offered during integrated health management) and both SMB and QoL. RESULTS: The ATT values for SMB and QoL, representing the net effect of integrated health management within a county medical consortium on SMB and QoL, were significantly positive. They ranged from 4.34 to 4.67 for SMB and from 0.89 to 1.06 for QoL, respectively, based on the four different PSM modalities. The results of quantile regression also revealed a statistically significant positive association between the implementation of integrated health management and both SMB (coef. = 4.15) and QoL (coef. = 1.54). These findings suggest that integrated health management within a county medical consortium can effectively improve SMB and QoL in rural T2D patients. Furthermore, frequency of follow-up service and health behavior guidance were positively associated with SMB and QoL. Conversely, on-call follow-up services, medication guidance and follow-up services at medical institutions were negatively correlated with SMB or QoL. CONCLUSIONS: The study highlights the effectiveness of integrated health management within a county medical consortium in improving SMB and QoL among individuals with T2D in rural China. The findings offer invaluable insights for the advancement of chronic disease management in rural areas of developing countries.

Integrative analysis of transcriptomic and metabolomic profiles reveals enhanced arginine metabolism in androgen-independent prostate cancer cells.

BACKGROUND: Prostate cancer is a common solid tumor that affects a significant number of men worldwide. Conventional androgen deprivation therapy (ADT) increases the risk of developing castration-resistant prostate cancer (CRPC). Effective clinical management of patients with CRPC is challenging due to the limited understanding. METHODS: In this study, transcriptomic and metabolomic profiles of androgen-dependent prostate cancer cell line LNCaP and the androgen-independent cells developed from LNCaP cells (LNCaP-ADR) were investigated using RNA-sequencing and LC-MS/MS, respectively. The differentially expressed genes and metabolites were analyzed, and integrative analysis of transcriptomic and metabolomic data was further conducted to obtain a comprehensive understanding of the metabolic characteristics in LNCaP-ADR cells. Quantitative real-time PCR (QPCR) was employed to ascertain the mRNA expression levels of the selected differentially expressed genes. RESULTS: The arginine and proline metabolism pathway was identified as a commonly altered pathway at both the transcriptional and metabolic levels. In the LNCaP-ADR cells, significant upregulation was observed for metabolites including 5-Aminopentanoic acid, L-Arginine, L-Glutamic acid, N-Acetyl-L-alanine, and Pyrrole-2-carboxylic acid at the metabolic level. At the transcriptional level, MAOA, ALDH3A2, ALDH2, ARG1, CKMT2, and CNDP1 were found to be significantly upregulated in the LNCaP-ADR cells. Gene set enrichment analysis (GSEA) identified various enriched gene sets in the LNCaP-ADR cells, encompassing inflammatory response, 9plus2 motile cilium, motile cilium, ciliary plasm, cilium or flagellum-dependent cell motility, cilium movement, cilium, response to endoplasmic reticulum stress, PTEN DN.V1 DN, SRC UP.V1 UP, IL15 UP.V1 DN, RB DN.V1 DN, AKT UP MTOR DN.V1 UP, VEGF A UP.V1 UP, and KRAS.LUNG.BREAST UP.V1 UP. CONCLUSIONS: These findings highlight the substantial association between the arginine and proline metabolism pathway and CRPC, emphasizing the need to prioritize strategies that target dysregulated metabolites and differentially expressed genes as essential interventions in the clinical management of CRPC.

Hydrophobic Carbon Dots Derived from Organic Pollutants and Applications in NIR Anticounterfeiting and Bioimaging.

In an effort to fulfill the strategy of sustainable development, Rhodamine B, a common and toxic organic pollutant in the textile industry, was reported for the first time as a single precursor to develop a kind of novel hydrophobic nitrogen-doped carbon dot (HNCD) through a green and facile one-pot solvothermal method. The HNCDs with an average size of 3.6 nm possess left and right water contact angles of 109.56° and 110.34°, respectively. The HNCDs manifest excitation wavelength-tunable and upconverted fluorescence from the ultraviolet (UV) to the near-infrared (NIR) range. Furthermore, the PEGylation of HNCDs enables them to be used as an optical marker for cell and in vivo imaging. Notably, the HNCDs with solvent-dependent fluorescence can be used for invisible inks with a wide range of light responses from UV-vis-NIR spectra. This work not only provides an innovative way to recycle chemical waste but also expands the potential application of HNCDs in NIR security printing and bioimaging.

Hippo/YAP signaling pathway protects against neomycin-induced hair cell damage in the mouse cochlea.

The Hippo/Yes-associated protein (YAP) signaling pathway has been shown to be able to maintain organ size and homeostasis by regulating cell proliferation, differentiation, and apoptosis. The abuse of aminoglycosides is one of the main causes of sensorineural hearing loss (SSNHL). However, the role of the Hippo/YAP signaling pathway in cochlear hair cell (HC) damage protection in the auditory field is still unclear. In this study, we used the YAP agonist XMU-MP-1 (XMU) and the inhibitor Verteporfin (VP) to regulate the Hippo/YAP signaling pathway in vitro. We showed that YAP overexpression reduced neomycin-induced HC loss, while downregulated YAP expression increased HC vulnerability after neomycin exposure in vitro. We next found that activation of YAP expression inhibited C-Abl-mediated cell apoptosis, which led to reduced HC loss. Many previous studies have reported that the level of reactive oxygen species (ROS) is significantly increased in cochlear HCs after neomycin exposure. In our study, we also found that YAP overexpression significantly decreased ROS accumulation, while downregulation of YAP expression increased ROS accumulation. In summary, our results demonstrate that the Hippo/YAP signaling pathway plays an important role in reducing HC injury and maintaining auditory function after aminoglycoside exposure. YAP overexpression could protect against neomycin-induced HC loss by inhibiting C-Abl-mediated cell apoptosis and decreasing ROS accumulation, suggesting that YAP could be a novel therapeutic target for aminoglycosides-induced sensorineural hearing loss in the clinic.

Correlation Between ICU Admission Time and Long-Term Mortality in Elderly Critically Ill Patients.

Objective: The the intensive care unit (ICU), also known as intensive care medicine department and intensive intensive care unit, is a medical place for centralized treatment of critical diseases and continuous monitoring and treatment. To investigate the relationship between the length of intensive care unit (ICU) admission and long-term mortality in elderly critically ill patients. Methods: A total of 2694 critically ill ICU patients admitted to Xianning First People's Hospital from April 2017 to April 2021 were selected. Inclusion criteria including: age ≥ 60 years; meet the diagnostic criteria for critical illness; admission to ICU ≥ 24h. According to admission time, patients were divided into 1684 patients admitted during working hours and 1010 patients admitted during non-working hours. The relationship between the admission time of ICU patients and long-term mortality was taken as the dependent variable. The evaluation was performed using the Acute Physiology and Chronic Health Status Assessment Scale (APACHE II score). Epidemiological questionnaire was used to investigate the status of time to hospital and mortality, and the independent risk factors affecting time to hospital and mortality were analyzed by univariate and multivariate analysis. SPSS 26.0 statistical software was used for analysis and processing. Results: Among 2694 critically ill patients in ICU, 1010 patients were hospitalized during non-working hours, with an admission rate of 37.49%. The acute physiology and chronic health evaluation (APACHE) II score of non-working hours was 19.91±6.62, which is significantly higher than that of working hours (18.21±6.42) (P < .05). The mortality rates of ICU patients hospitalized during non-working hours and during working hours accounted for 30.10 % and 19.71% of all patients, respectively, with statistical significance (P < .05). Comparing the mortality rates of the two groups at different time periods, there was a significant difference between the two groups (P < .05). In order to influence the independent variables of ICU mortality (non-occurrence = 0, occurrence = 1), the significant factors of univariate analysis were included in the logistic regression equation. Time of admission, combined cardiopulmonary disease, APACHE II score, nurse workload and other factors were independent risk factors for ICU mortality. Conclusion: Out-of-hours admission is associated with an increased risk of death and is associated with changes in ICU organizational structure. Therefore, sending patients to ICU in time migh help improve their life.

The Roles of Histone Deacetylases in the Regulation of Ovarian Cancer Metastasis.

Ovarian cancer is the most lethal gynecologic malignancy, and metastasis is the major cause of death in patients with ovarian cancer, which is regulated by the coordinated interplay of genetic and epigenetic mechanisms. Histone deacetylases (HDACs) are enzymes that can catalyze the deacetylation of histone and some non-histone proteins and that are involved in the regulation of a variety of biological processes via the regulation of gene transcription and the functions of non-histone proteins such as transcription factors and enzymes. Aberrant expressions of HDACs are common in ovarian cancer. Many studies have found that HDACs are involved in regulating a variety of events associated with ovarian cancer metastasis, including cell migration, invasion, and the epithelial-mesenchymal transformation. Herein, we provide a brief overview of ovarian cancer metastasis and the dysregulated expression of HDACs in ovarian cancer. In addition, we discuss the roles of HDACs in the regulation of ovarian cancer metastasis. Finally, we discuss the development of compounds that target HDACs and highlight their importance in the future of ovarian cancer therapy.

Driving forces and recovery potential of the macrophyte decline in East Taihu Lake.

Macrophytes are of key importance to the structure and ecological services of shallow lakes and are sensitive to anthropogenic and natural perturbations. Ongoing eutrophication and hydrological regime change affect macrophytes through changes in water transparency and water level, which lead to a dramatic decrease in bottom light availability. Here an integrated dataset (2005-2021) of multiple environmental factors is used to demonstrate the driving forces and recovery potential of the macrophyte decline in East Taihu Lake by using a critical indicator, which is the ratio of the Secchi disk depth to the water depth (SD/WD). The macrophyte distribution area showed a remarkable decrease from 136.1 ± 9.7 km2 (2005-2014) to 66.1 ± 6.5 km2 (2015-2021). The macrophyte coverage in the lake and in the buffer zone decreased by 51.4% and 82.8%, respectively. The structural equation model and correlation analysis showed that the distribution and coverage of macrophytes decreased with the decrease in the SD/WD over time. Moreover, an extensive hydrological regime change, which caused a sharp decrease in SD and an increase in the water level, is likely to be the driving force that brought about the decline of macrophytes in this lake. The proposed recovery potential model shows that the SD/WD has been low in recent years (2015-2021), and that this SD/WD cannot ensure the growth of submerged macrophytes and is unlikely to ensure the growth of floating-leaved macrophytes, especially in the buffer zone. The approach developed in the present study provides a basis for the assessment of macrophyte recovery potential and the management of ecosystems in shallow lakes that suffer from macrophyte loss.

Hollow Cuprous Oxide@Nitrogen-Doped Carbon Nanocapsules for Cascade Chemodynamic Therapy.

Cuprous-based nanozymes have demonstrated great potential for cascade chemodynamic therapy (CDT) due to their higher catalytic efficiency and simple reaction conditions. Here, hollow cuprous oxide@nitrogen-doped carbon (HCONC) dual-shell structures are designed as nanozymes for CDT oncotherapy. This HCONC with a size distribution of 130 nm is synthesized by a one-step hydrothermal method using cupric nitrate and dimethyl formamide as precursors. The thin-layer carbon (1.88 nm) of HCONC enhances the water-stability and reduces the systemic toxicity of cuprous oxide nanocrystals. The dissolved Cu+ of HCONC in acid solution induces a Fenton-like reaction and exhibits a fast reaction rate for catalyzing H2 O2 into highly toxic hydroxyl radicals (·OH). Meanwhile, the formed Cu+ consumes oversaturated glutathione (GSH) to avoid its destruction of ROS at the intracellular level. In general, both cellular and animal experiments show that HCONC demonstrates excellent antitumor ability without causing significant systemic toxicity, which may present tremendous potential for clinical cancer therapy.

Clinical efficacy and safety of MP-AzeFlu for the treatment of allergic rhinitis: a meta-analysis.

OBJECTIVE: MP-AzeFlu is a novel option for therapy of allergic rhinitis (AR). The purpose of our study was to assess the safety and efficacy of MP-AzeFlu for the treatment of allergic rhinitis, compared to placebo and azelastine monotherapy. METHODS: The PubMed, MEDLINE, EMBASE and Cochrane databases were comprehensively searched for all published randomized controlled trials (RCTs) of using MP-AzeFlu nasal spray on July 26, 2019. In these studies, we selected patients with clinical symptom scores. The heterogeneity of the included studies was assessed by I2. RESULTS: Among the 336 citations retrieved, 6 articles with over 6000 patients were finally included in the meta-analysis. The results of meta-analysis revealed that MP-AzeFlu was superior to placebo ( - 2.43 [95%CI,  - 2.73 to  - 2.14], P < 0.00001) and azelastine ( - 1.27 [95% CI,  - 1.57 to  - 0.97], P < 0.00001) in reflective total nasal symptom score. In the MP-AzeFlu group, the instantaneous total nasal symptom score ( - 2.56 [95% CI,  - 3.02 to  - 2.10], P < 0.00001) and the reflective total ocular symptom score ( - 1.22 [95% CI,  - 1.57 to  - 0.87], P < 0.00001) were significantly reduced compared to the placebo group. CONCLUSION: MP-AzeFlu is as safe and mild as placebo and azelastine, which also is associated with symptom relief and the improvement of quality of life in AR patients. MP-AzeFlu can provide better clinical benefits than two currently available first-line intranasal therapies. It is an ideal therapy for AR patients.

Use of Ferulic Acid in the Management of Diabetes Mellitus and Its Complications.

Diabetes mellitus, a metabolic disease mainly characterized by hyperglycemia, is becoming a serious social health problem worldwide with growing prevalence. Many natural compounds have been found to be effective in the prevention and treatment of diabetes, with negligible toxic effects. Ferulic acid (FA), a phenolic compound commonly found in medicinal herbs and the daily diet, was proved to have several pharmacological effects such as antihyperglycemic, antihyperlipidemic and antioxidant actions, which are beneficial to the management of diabetes and its complications. Data from PubMed, EM-BASE, Web of Science and CNKI were searched with the keywords ferulic acid and diabetes mellitus. Finally, 28 articles were identified after literature screening, and the research progress of FA for the management of DM and its complications was summarized in the review, in order to provide references for further research and medical applications of FA.

Factors influencing attitudes toward cyber-counseling among China's Generation Z: A structural equation model.

Information technology developments have combined traditional face-to-face counseling with online- or cyber-counseling. As digital natives, Generation Z has easy access to cyber-counseling. However, their attitudes toward cyber-counseling remain unknown. This study explored these attitudes and relevant influencing factors among 1216 Chinese adolescents using self-report questionnaires. Descriptive analyses and structural equation modeling were used for data analysis. The model explained 27.7 % of the total variance, attitudes toward psychological help was the most influential, followed by attitudes toward the Internet and perceived behavioral control. The model was effective in explaining attitudes toward cyber-counseling, emphasizing the influence of attitudes toward psychological help.

A cyclic nano-reactor achieving enhanced photodynamic tumor therapy by reversing multiple resistances.

BACKGROUND: Photodynamic therapy (PDT) is a clinically implemented modality to combat malignant tumor, while its efficacy is largely limited by several resistance factors from tumor microenvironment (TME), such as hypoxia, anti-oxidant systems, and ATP-dependent tumor adaptive resistances. The aim of this work is to construct a multifunctional nanoplatform to remodel multiple resistant TME for enhanced PDT. RESULTS: Here, a targeting nano-reactor was facilely constructed to reverse the multiple resistances of PDT by incorporating glucose oxidase (GOx) and chlorin e6 (Ce6) into poly (D, L-lactic-co-glycolic acid) (PLGA)/ metal-organic framework (MOF) core-shell nanoassembly, with surface deposition of hyaluronic acid (HA) stabilized MnO2. The nano-reactor could selectively target tumor cells by virtue of surface HA modification, and once internalization, a few reactions were initiated to modulate TME. Glucose was consumed by GOx to inhibit ATP generation, and the produced H2O2 was catalyzed by MnO2 to generate O2 for tumor hypoxia alleviation and photodynamic sensitization, and glutathione (GSH) was also effectively depleted by MnO2 to suppress the tumor antioxidant defense. Consequently, the nano-reactor achieved robust PDT with amplified tumor therapy via intravenous injection. CONCLUSIONS: This nano-reactor offers a multifunctional nanoplatform to sensitize TME-limited tumor treatment means via reversing multiple resistances.

Transport of imidazolium-based ionic liquids with different anion/cation species in sand/soil columns.

Ionic liquids (ILs) have been widely used as environmentally friendly solvents to replace volatile organic solvents in the chemistry industries. They have a high water solubility and potential risk to organisms in the soil-water environment. At present, most studies focused on the batch sorption of ILs in soil and neglected the investigation of IL transports in soil, which results in a lack of understanding of the structure-dependent mobility of ILs in the environment. Laboratory-scale sand/soil column experiments were performed to study the transport of imidazolium-based ILs, such as [C4mim][OTF], [C4mim][TOS], [C4mim][MeSO3], [C4mim][BF4], [C2mim][BF4], and [C6mim][BF4] including different counteranions and alkyl chain lengths of IL cations. Batch experiments were also carried out to compare the difference of sorption distribution coefficient (Kd) between the batch and column experiments. A one-dimensional convective-dispersive model using CXTFIT code was created based on the measured breakthrough curves (BTCs) to estimate the column transport parameters. For the anion, [BF4-], the Kd of ILs in both batch and column experiments increased with increasing alkyl chain lengths of the IL cation. In batch tests, counteranions showed no influence on the Kd of [C4mim][OTF], [C4mim][TOS], [C4mim][MeSO3], [C4mim][BF4], [C2mim][BF4], and [C6mim][BF4]. However, in column tests, the BTCs of 1-butyl-3-methylimidazolium-based ILs were anion dependent as evidenced by the change of retardation factor (R) for different counteranions. Furthermore, the effects of transport distance (11cm, 15cm, 19cm, and 24cm) on the mobility of ILs were estimated. The longer distances signified an increase in the contact time and more binding sites for ILs and therefore, the smoother shapes of BTCs in column experiments.

Microwave ablation combined with OK-432 induces Th1-type response and specific antitumor immunity in a murine model of breast cancer.

BACKGROUND: Minimally invasive therapies, such as microwave ablation (MWA), are widely used for the treatment of solid tumors. Previous studies suggest that MWA is feasible for the treatment of small breast cancer, and thermal ablation may induce adaptive antitumor immunity. However, the induced immune responses are mostly weak, and the immunomodulation effects of MWA in breast cancer are unclear. Immunostimulant OK-432 can induce tumor-specific T-cell responses and may augment the immunity induced by MWA. METHODS: We treated 4T1 breast cancer bearing BALB/c mice with MWA, OK-432, MWA plus OK-432, or left without treatment. Survival time was evaluated with the Kaplan-Meyer method comparing survival curves by log-rank test. On day 25 after ablation, surviving mice received tumor rechallenge, and the rechallenged tumor volumes were calculated every 5 days. Immunohistochemistry and flow cytometry were used to evaluate the T-cell immune responses in ablated tissues and spleens. The tumor-specific immunity was assessed by enzyme-linked immunospot assays. Besides, the cytokine patterns were identified from enzyme-linked immunosorbent assay. RESULTS: Microwave ablation plus OK-432 resulted in longer survival than single treatment and protect most surviving mice from tumor rechallenge. Both local and systemic T-cell responses were induced by MWA and were further enhanced by subsequent administration of OK-432. Moreover, the combination of MWA and OK-432 induced stronger tumor-specific immune responses than MWA alone. In addition, OK-432 and MWA synergistically promoted the production of Th1-type but not Th2-type cytokines, and polarized T-cell responses to Th1-dominant state. CONCLUSIONS: The T-cell immune responses were activated by MWA in breast cancer. Furthermore, the combination of MWA and OK-432 induced Th1-type response and elicited specific antitumor immunity.

Differential expression and miRNA regulation of the GSTP1 gene in the regenerating liver of Chiloscyllium plagiosum.

Liver regeneration is a complicated process, and understanding the regulatory mechanism will be helpful in the treatment of diseases associated with liver. In this study, the one-third liver resection model was established in Chiloscyllium plagiosum, and the whole transcriptome of the C. plagiosum was generated using the Illumina-Solexa sequencing platform. Differentially expressed genes were analyzed using bioinformatics methods and verified using quantitative real-time PCR (qRT-PCR). Using miRanda and TargetScan, we screened the microRNA library for miRNAs that target the glutathione S-transferase P1(GSTP1) gene. Dual-luciferase reporter assays were used to confirm binding between the miRNA and GSTP1. Finally, we used western blotting analysis to determine expression of the GSTP1 protein. As a result, 65,356 unigenes were obtained in normal and damaged liver tissues, with mean length of 955 bp. A total of 359 differentially expressed genes were acquired; 217 of which were upregulated, and 142 were downregulated, including the GSTP1 gene, following liver resection. The presence of the GSTP1 protein in C. plagiosum was shown for the first time. Luciferase reporter assay revealed that GSTP1 messenger RNA was targeted by ipu-miR-143. The discovery and differential expression analysis of GSTP1 in C. plagiosum will be a valuable resource to explain the molecular mechanism of GSTP1 regulation of liver repair.

InDel marker detection by integration of multiple softwares using machine learning techniques.

BACKGROUND: In the biological experiments of soybean species, molecular markers are widely used to verify the soybean genome or construct its genetic map. Among a variety of molecular markers, insertions and deletions (InDels) are preferred with the advantages of wide distribution and high density at the whole-genome level. Hence, the problem of detecting InDels based on next-generation sequencing data is of great importance for the design of InDel markers. To tackle it, this paper integrated machine learning techniques with existing software and developed two algorithms for InDel detection, one is the best F-score method (BF-M) and the other is the Support Vector Machine (SVM) method (SVM-M), which is based on the classical SVM model. RESULTS: The experimental results show that the performance of BF-M was promising as indicated by the high precision and recall scores, whereas SVM-M yielded the best performance in terms of recall and F-score. Moreover, based on the InDel markers detected by SVM-M from soybeans that were collected from 56 different regions, highly polymorphic loci were selected to construct an InDel marker database for soybean. CONCLUSIONS: Compared to existing software tools, the two algorithms proposed in this work produced substantially higher precision and recall scores, and remained stable in various types of genomic regions. Moreover, based on SVM-M, we have constructed a database for soybean InDel markers and published it for academic research.

QTLMiner: QTL database curation by mining tables in literature.

MOTIVATION: Figures and tables in biomedical literature record vast amounts of important experiment results. In scientific papers, for example, quantitative trait locus (QTL) information is usually presented in tables. However, most of the popular text-mining methods focus on extracting knowledge from unstructured free text. As far as we know, there are no published works on mining tables in biomedical literature. In this article, we propose a method to extract QTL information from tables and plain text found in literature. Heterogeneous and complex tables were converted into a structured database, combined with information extracted from plain text. Our method could greatly reduce labor burdens involved with database curation. RESULTS: We applied our method on a soybean QTL database curation, from which 2278 records were extracted from 228 papers with a precision rate of 96.9% and a recall rate of 83.3%, F value for the method is 89.6%.

PopGeV: a web-based large-scale population genome browser.

MOTIVATION: The development of high-throughput sequencing technology has made it possible for more and more researchers to use population sequencing data to mine genes associated with specific traits. However, the massive amounts of sequencing data have also brought new challenges to the researchers. The question of how to browse population genomic data in an easy and intuitive manner must be addressed. Web-based genome browsers allow user to conveniently view the results of genomic analyses, but heavy usage can reduce the response speed of the webpage, which limits its usefulness in the display of large-scale genome data. IndexedDB technology is a good solution to this problem; it supports web browsers and so creates local databases. In this way, data can be read from the local storage, achieving a smooth display of population genomic data. RESULTS: PopGeV has the following characteristics. First, it uses a new encoding method for compression of population SNP and INDEL data. IndexedDB technology is used to download the results to local storage so that users can browse the results smoothly even when the network traffic is heavy. Second, PopGeV identify similar genomic regions between two individuals based on SNP data. Population diversity indexes are calculated when comparing two populations. Third, user defined annotation information can be integrated for user-friendly mining of gene functions. Simulation shows that PopGeV can smoothly display analysis results of population genome containing over 500 individuals with 2 millions SNP data. AVAILABILITY AND IMPLEMENTATION: PopGeV is available at www.soyomics.com/popgev/ CONTACT: yuanxh@iga.ac.cn.

A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog.

FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.