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[This corrects the article DOI: 10.1371/journal.pone.0060860.].

Due to the high suitability of semi-supervised learning for medical image segmentation, a plethora of valuable research has been conducted and has achieved noteworthy success in this field. However, many approaches tend to confine their focus to a singular semi-supervised framework, thereby overlooking the potential enhancements in segmentation performance offered by integrating several frameworks. In this paper, we propose a novel semi-supervised framework named Pesudo-Label Mean Teacher (PLMT), which synergizes the self-training pipeline with pseudo-labeling and consistency regularization techniques. In particular, we integrate the student-teacher structure with consistency loss into the self-training pipeline to facilitate a mutually beneficial enhancement between the two methods. This structure not only generates remarkably accurate pseudo-labels for the self-training pipeline but also furnishes additional pseudo-label supervision for the student-teacher framework. Moreover, to explore the impact of different semi-supervised losses on the segmentation performance of the PLMT framework, we introduce adaptive loss weights. The PLMT could dynamically adjust the weights of different semi-supervised losses during the training process. Extension experiments on three public datasets demonstrate that our framework achieves the best performance and outperforms the other five semi-supervised methods. The PLMT is an initial exploration of the framework that melds the self-training pipeline with consistency regularization and offers a comparatively innovative perspective in semi-supervised image segmentation.

Automatic and accurate segmentation of medical images plays an essential role in disease diagnosis and treatment planning. Convolution neural networks have achieved remarkable results in medical image segmentation in the past decade. Meanwhile, deep learning models based on Transformer architecture also succeeded tremendously in this domain. However, due to the ambiguity of the medical image boundary and the high complexity of physical organization structures, implementing effective structure extraction and accurate segmentation remains a problem requiring a solution. In this paper, we propose a novel Dual Encoder Network named DECTNet to alleviate this problem. Specifically, the DECTNet embraces four components, which are a convolution-based encoder, a Transformer-based encoder, a feature fusion decoder, and a deep supervision module. The convolutional structure encoder can extract fine spatial contextual details in images. Meanwhile, the Transformer structure encoder is designed using a hierarchical Swin Transformer architecture to model global contextual information. The novel feature fusion decoder integrates the multi-scale representation from two encoders and selects features that focus on segmentation tasks by channel attention mechanism. Further, a deep supervision module is used to accelerate the convergence of the proposed method. Extensive experiments demonstrate that, compared to the other seven models, the proposed method achieves state-of-the-art results on four segmentation tasks: skin lesion segmentation, polyp segmentation, Covid-19 lesion segmentation, and MRI cardiac segmentation.

MotivationOur study aimed to identify biologically relevant transcription factors (TFs) that control the expression of a set of co-expressed or co-regulated genes.ResultsWe developed a fully automated pipeline, Motif Over Representation Analysis (MORA), to detect enrichment of known TF binding motifs in any query sequences. MORA performed better than or comparable to five other TF-prediction tools as evaluated using hundreds of differentially expressed gene sets and ChIP-seq datasets derived from known TFs. Additionally, we developed EnsembleTFpredictor to harness the power of multiple TF-prediction tools to provide a list of functional TFs ranked by prediction confidence. When applied to the test datasets, EnsembleTFpredictor not only identified the target TF but also revealed many TFs known to cooperate with the target TF in the corresponding biological systems. MORA and EnsembleTFpredictor have been used in two publications, demonstrating their power in guiding experimental design and in revealing novel biological insights.

As more attention is given to green and sustainable industries, an analysis of the industrial impacts on all aspects of life, including inclusive affluence, is gradually developing. Idle rural residential land is a valuable resource and an important factor in promoting sustainable development. Balanced urban and rural development contributes to inclusive prosperity, so understanding the relationship between industry and the balanced development of urban and rural can significantly impact social development. In China, achieving the balanced development requires narrowing the urban-rural income gap. This paper analyzed the impact of reallocating idle rural residential land on promoting the balanced development. The study found that industry development has a positive impact on the balanced development, with a regression coefficient of 1.478. Regions with higher industry indices in counties had better outcomes regarding the balanced development. When the development of rural industry derived from idle residential land was in good condition, the effect increased by 3.326 percentage. The results showed heterogeneity, with the regression coefficient of industry development on the balanced development in county-level cities being 0.498 larger than in urban areas. In summary, the reallocation of idle residential land can promote sustainable development, increase residents' income, and improve overall regional economic development. The results are applicable to the comprehensive reallocation of rural land resources.

Background This study was performed to explore the causal association between asthma and chronic obstructive pulmonary disease(COPD). Methods We obtained summary statistics for asthma from 408,442 Europeans in an open genome-wide association study (GWAS) from the UK Biobank to select strongly associated single nucleotide polymorphisms that could serve as instrumental variables for asthma (P < 5×10−8). Additional summary statistics for COPD were obtained from 193,638 individuals of European ancestry in the GWAS published by FinnGen. Univariable Mendelian randomization(UVMR) analysis was performed using inverse variance weighted (IVW) as the primary method of analysis. The reliability of the results was verified by multivariable MR(MVMR), reverse and replication MR analysis, and sensitivity analysis. Results In the UVMR analysis, asthma increased the risk of COPD, with an odds ratio (OR) of 1.27 (95% confidence interval (CI) = 1.16–1.39, P = 5.44×10−7). Estimates were consistent in MVMR analyses by the adjustments of smoking initiation, age of smoking initiation, cigarettes per day, PM 2.5, and the combination of the above factors. In the reverse MR analysis, there was no evidence of a causal effect of COPD on asthma risk(OR = 1.02, 95% CI = 0.97–1.07, P = 0.3643). In the replication MR analysis, asthma still increased the risk of COPD. Sensitivity analyses validated the robustness of the above associations. Conclusions We found that genetically predicted asthma was positively associated with the risk of COPD. Additionally, there was no evidence that COPD increases the risk of asthma. Further clarification of this link and underlying mechanisms is needed to identify feasible measures to promote COPD prevention.

IntroductionThe vertical dimensional arrangement of space is primarily influenced by the reachable range of human fingertips. Currently, this dimensional layout analysis concentrates solely on static body dimensions based on Farley's principle. However, the joint mobility of the elderly population has diminished, necessitating the identification of the factors influencing the age-friendly spatial vertical dimension layout through experimentation.MethodsA random sample of 62 adults and 62 elderly individuals were selected to measure the joint mobility of 8 groups with varying comfort levels. The measurement results were analyzed using an independent sample t-test with SPSS software.ResultsThe joint mobility of the elderly group exhibited a notable difference from that of the adult group across distinct comfort gradients. A significant reduction in the range of motion of all joints in the elderly was observed. The findings suggest that the reachable range of the upper limbs of the elderly should be considered in conjunction with joint mobility. We propose a vertical dimensional layout method for residential spaces that accommodates the joint mobility of elderly users.ConclusionThe joint mobility of the elderly is significantly deteriorating, and the traditional vertical spatial layout method cannot adequately support the daily life of the elderly. It is essential to integrate the joint mobility factor into the vertical dimensional layout design process. In this paper, we propose an elderly-friendly vertical spatial dimension layout method. It offers a reference for subsequent planning of elderly-friendly vertical dimension layout.

Atrial fibrillation (AF) is a typical category of arrhythmia. Clinical diagnosis of AF is based on the detection of abnormal R-R intervals (RRIs) with an electrocardiogram (ECG). Previous studies considered this detection problem as a classification problem and focused on extracting a number of features. In this study we demonstrate that instead of using any specific numerical characteristic as the input feature, the probability density of RRIs from ECG conserves comprehensive statistical information; hence, is a natural and efficient input feature for AF detection. Incorporated with a support vector machine as the classifier, results on the MIT-BIH database indicates that the proposed method is a simple and accurate approach for AF detection in terms of accuracy, sensitivity, and specificity.

Effective and adequate anesthesia is conducive to better restrain for pigs during surgical or diagnostic procedures This study aimed to evaluate cardiorespiratory and anesthetic effects of ketamine-midazolam-xylazine-sufentanil or tiletamine-zolazepam-xylazine as general anesthetics in miniature pigs. In phase 1, one of the combinations was administered intramuscularly to miniature pigs. The KMXS protocol combined 10 mg kg-1 ketamine, 0.5 mg kg-1 midazolam, and 2 mg kg-1 xylazine with 2 μg kg-1 sufentanil. The TZX protocol combined 2.2 mg kg-1 tiletamine, 2.2 mg kg-1 zolazepam, and 1.4 mg kg-1 xylazine. After treatment, the mean arterial pressure, systolic arterial pressure, diastolic arterial pressure, heart rate, respiratory rate, peripheral hemoglobin oxygen saturation, rectal temperature, and anesthesia quality were recorded. In phase 2, the feasibility of KMXS and TZX as general anesthetics were evaluated for pig castration. In phase 1, both drug combinations provided smooth induction with similar anesthetic effects. The KMXS protocol provided moderate anesthesia for 60-70 minutes in pigs, while the TZX protocol provided 30-45 minutes. In phase 2, castration was completed smoothly in all pigs with little fluctuation in physiological variables. The KMXS protocol is better for medium-term anesthesia, while the TZX protocol is preferable for short-term anesthesia in pigs.

High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.

This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.

Medicago falcata is one of the leguminous forage crops, which grows well in arid and semiarid region. To fully investigate the mechanism of drought resistance response in M. falcata, we challenged the M. falcata plants with 30% PEG-6000, and performed physiological and transcriptome analyses. It was found that, the activities of antioxidant enzymes (eg. SOD, POD, and CAT) and soluble sugar content were all increased in the PEG-treated group, as compared to the control group. Transcriptome results showed that a total of 706 genes were differentially expressed in the PEG-treated plants in comparison with the control. Gene enrichment analyses on differentially expressed genes revealed that a number of genes in various pathway were significantly enriched, including the phenylpropanoid biosynthesis (ko00940) and glycolysis/gluconeogenesis (ko00010), indicating the involvement of these key pathways in drought response. Furthermore, the expression levels of seven differentially expressed genes were verified to be involved in drought response in M. falcata by qPCR. Taken together, these results will provide valuable information related to drought response in M. falcata and lay a foundation for molecular studies and genetic breeding of legume crops in future research.

Reducing floor eggs in cage-free (CF) housing systems is among primary concerns for egg producers. The objective of this research was to evaluate the effects of ground robot manipulation on reduction of floor eggs. In addition, the effects of ground robot manipulation on production performance, stress response, bone quality, and behavior were also investigated. Two successive flocks of 180 Hy-Line Brown hens at 34 weeks of this age were used. The treatment structure for each flock consisted of six pens with three treatments (without robot running, with one-week robot running, and with two-weeks robot running), resulting in two replicates per treatment per flock and four replicates per treatment with two flocks. Two phases were involved with each flock. Phase 1 (weeks 35-38) mimicked the normal scenario, and phase 2 (weeks 40-43) mimicked a scenario after inadvertent restriction to nest box access. Results indicate that the floor egg reduction rate in the first two weeks of phase 1 was 11.0% without the robot treatment, 18.9% with the one-week robot treatment, and 34.0% with the two-week robot treatment. The effect of robot operation on floor egg production was not significant when the two phases of data were included in the analysis. Other tested parameters were similar among the treatments, including hen-day egg production, feed intake, feed conversion ratio, live body weight, plasma corticosterone concentration, bone breaking force, ash percentage, and time spent in nest boxes. In conclusion, ground robot operation in CF settings may help to reduce floor egg production to a certain degree for a short period right after being introduced. Additionally, robot operation does not seem to negatively affect hen production performance and well-being.

At the beginning of 2020, the COVID-19 pandemic was able to spread quickly in Wuhan and in the province of Hubei due to a lack of experience with this novel virus. Additionally, authories had no proven experience with applying insufficient medical, communication and crisis management tools. For a considerable period of time, the actual number of people infected was unknown. There were great uncertainties regarding the dynamics and spread of the Covid-19 virus infection. In this paper, we develop a system dynamics model for the three connected regions (Wuhan, Hubei excl. Wuhan, China excl. Hubei) to understand the infection and spread dynamics of the virus and provide a more accurate estimate of the number of infected people in Wuhan and discuss the necessity and effectivity of protective measures against this epidemic, such as the quarantines imposed throughout China. We use the statistics of confirmed cases of China excl. Hubei. Also the daily data on travel activity within China was utilized, in order to determine the actual numerical development of the infected people in Wuhan City and Hubei Province. We used a multivariate Monte Carlo optimization to parameterize the model to match the official statistics. In particular, we used the model to calculate the infections, which had already broken out, but were not diagnosed for various reasons.

Contrary to the common expectation that the reference evapotranspiration (ETo), which is an indicator of the atmospheric evaporation capability, increases in warming climate, the decline of the ETo has been reported worldwide, and this contradiction between the expected increasing ETo and the observed decreasing one is now termed the "evaporation paradox". Based on the updated meteorological data (1960-2019), we separately detected the spatiotemporal characteristics and the causes of the "evaporation paradox" in three subregions, namely Huaibei, Jianghuai, and Sunan, and throughout the entire province of Jiangsu in southeastern China. Different from the reported continuous unidirectional variations in the ETo, in the province of Jiangsu, it generally showed a decreasing trend before 1990 but followed an increasing trend from 1990 to 2019, which led to the different characteristics of the "evaporation paradox" in the periods from 1960 to 1989, from 1990 to 2019, and from 1960 to 2019. In the first 30 years, the reduction of the wind speed (WS) was the main reason for the decreased ETo, which consequently gave rise to the "evaporation paradox" in spring and winter in the Huaibei region and only in winter in the two other subregions and throughout the entire province. We noticed that the "evaporation paradox" in spring in the Sunan region was expressed by the decreased daily mean air temperature (Tmean) and the increased ETo which was chiefly induced by the decreased relative humidity (RH) and the increased vapor pressure deficit (VPD). After 1990, the decreased WS also dominated the decreased ETo and resulted in the "evaporation paradox" in winter in the Jianghuai region. Furthermore, the decreased sunshine hour (SH) was the main factor influencing the decreased ETo, thereby inducing the "evaporation paradox" in summer and autumn in the Jianghuai region and only in autumn in the Huaibei region and throughout the whole province from 1990 to 2019. In the whole study period from 1960 to 2019, the decreased SH was also found to be responsible for the decreased ETo and for the "evaporation paradox" in summer in all the subregions and throughout the whole province. However, regarding the "evaporation paradox" in autumn, in winter, and in the entire year in the Huaibei region and throughout the whole province, the observed decreased ETo was largely due to the reduced WS from 1960 to 2019. In summary, in addition to the air temperature, the ETo has shifted due to the other meteorological variables (especially the WS, the SH, and the VPD) and shaped the unique spatiotemporal characteristics of the "evaporation paradox" in the province of Jiangsu in southeastern China. Moreover, future studies and simulations addressing the regional climate change and hydrological cycles should take account of the changeable key meteorological variables in different subregions and seasons of the province of Jiangsu.

Cumulative evidence has been found for the associations between personality traits and stress experiences in adulthood. However, less is known about the moderating mechanisms underlying these associations. The present study tested whether the stress sensitization and stress inoculation hypotheses could be applied to the relationship between early adversity and personality in adulthood. Specifically, we tested the linear and curvilinear relations between early adversity (measured retrospectively) and adulthood personality traits, as well as the linear and curvilinear moderating effects of early adversity on the associations between adulthood stress and personality traits. Samples of older adults from the Health and Retirement Study (HRS; N = 6098) and middle-aged adults from the Midlife in the United States Survey (MIDUS; N = 6186) were used. Across the two samples, positive linear associations were found between retrospective early adversity and neuroticism. The results also suggested significant linear effects of early adversity on the association between ongoing chronic stressors and neuroticism such that individuals with moderate exposure to early adversity showed stronger associations between ongoing chronic stressors and neuroticism. Results from the current research were more in line with the stress sensitization model. No support was found for the stress inoculation effects on personality.

Spent mushroom substrate is made from the waste remaining after the harvest of mushrooms. Here, we evaluated the potential of five spent edible fungi (Auricularia cornea, Lentinus edodes, Pleurotus eryngii, P. citrinopileatus and P. ostreatus) substrates as feed sources for Tenebrio molitor larvae. Young larvae did not survive on any substrate except the spent L. edodes substrate (36.7%). The survival rates in young larvae were similar among the different diets in which wheat bran or rice bran was replaced with 0, 20, 30, 40, 50, or 60% spent L. edodes substrate. The weights of the surviving larvae were decreased only when 70% of wheat bran and > 40% of rice bran was replaced with spent L. edodes substrate. In addition, the middle-aged larvae fed wheat bran only were significantly larger than those fed diets with 30~60% spent L. edodes substrate in dry feed, but the larvae of all treatments failed to pupate. Whereas the green feed was added in dry feed, there were no significant differences in pupal weight, pupation rate, pupal duration, adult emergence, or deformed adults among the three treatments in middle-aged larvae that were fed on diets containing 0, 30, or 40% spent L. edodes substrate. Collectively, these results suggest that spent L. edodes substrate has considerable potential to be used as a partial replacement (< 40%) of conventional feed for T. molitor, and spent mushroom substrate waste may be recycled as feed material for resource insects.

Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae for which different sexes have separate medicinal uses. In order to study the genes related to sex determination, transcriptome sequencing was performed on flower buds of male and female plants using the high-throughput sequencing technology. A total of 145,975 unigenes and 7110 DEGs were obtained. There were 6776 DEGs annotated to 1234 GO terms and enriched to 18 functional groups, including five biological processes related to sugar metabolism. KEGG pathway analysis indicated genes involved in hormone transduction, hormone synthesis and carbohydrate metabolism. Many DEGs of TK are involved in reproductive organ formation, hormone signal transduction and regulatory networks. Combining the results of GO, KEGG and qRT-PCR, 11 sex determining candidate genes of TK were selected, including MYB80, MYB108, CER1, CBL9, ABCB19, SERK1, HSP81-3, ACS9, SEP3, AUX1 and YUC6. The results provide a foundation for the study of sex differentiation in TK.

ObjectiveTo reconstruct the transmission trajectory of SARS-CoV-2 and analyze the effects of control measures in China.MethodsPython 3.7.1 was used to write a SEIR class to model the epidemic procedure and proportional estimation method to estimate the initial true infected number. The epidemic area in China was divided into three parts, Wuhan city, Hubei province (except Wuhan) and China (except Hubei) based on the different transmission pattern. A testing capacity limitation factor for medical resources was imposed to model the number of infected but not quarantined individuals. Baidu migration data were used to assess the number of infected individuals who migrated from Wuhan to other areas.ResultsBasic reproduction number, R0, was 3.6 before the city was lockdown on Jan 23, 2020. The actual infected number the model predicted was 4508 in Wuhan before Jan 23, 2020. By January 22 2020, it was estimated that 1764 infected cases migrated from Wuhan to other cities in Hubei province. Effective reproductive number, R, gradually decreased from 3.6 (Wuhan), 3.4 (Hubei except Wuhan,) and 3.3 (China except Hubei) in stage 1 (from Dec 08, 2019 to Jan 22, 2020) to 0.67 (Wuhan), 0.59 (Hubei except Wuhan) and 0.63 (China except Hubei) respectively. Especially after January 23, 2020 when Wuhan City was closed, the infected number showed a turning point in Wuhan. By early April, there would be 42073 (95% confidence interval, 41673 to 42475), 21342 (95% confidence interval, 21057 to 21629) and 13384 (95% confidence interval, 13158 to 13612) infected cases in Wuhan, Hubei (except Wuhan) and China (except Hubei), respectively.ConclusionA series of control measures in China have effectively prevented the spread of COVID-19, and the epidemic should be under control in early April with very few new cases occasionally reported.

ObjectiveTo estimate the prevalence of disability and anxiety in Covid-19 survivors at discharge from hospital and analyze relative risk by exposures.DesignMulti-center retrospective cohort study.SettingTwenty-eight hospitals located in eight provinces of China.MethodsA total of 432 survivors with laboratory-confirmed SARS CoV-2 infection participated in this study. At discharge, we assessed instrumental activities of daily living (IADL) with Lawton's IADL scale, dependence in activities of daily living (ADL) with the Barthel Index, and anxiety with Zung's self-reported anxiety scale. Exposures included comorbidity, smoking, setting (Hubei vs. others), disease severity, symptoms, and length of hospital stay. Other risk factors considered were age, gender, and ethnicity (Han vs. Tibetan).ResultsPrevalence of at least one IADL problem was 36.81% (95% CI: 32.39-41.46). ADL dependence was present in 16.44% (95% CI: 13.23-20.23) and 28.70% (95% CI: 24.63-33.15) were screened positive for clinical anxiety. Adjusted risk ratio (RR) of IADL limitations (RR 2.48, 95% CI: 1.80-3.40), ADL dependence (RR 2.07, 95% CI 1.15-3.76), and probable clinical anxiety (RR 2.53, 95% CI 1.69-3.79) were consistently elevated in survivors with severe Covid-19. Age was an additional independent risk factor for IADL limitations and ADL dependence; and setting (Hubei) for IADL limitations and anxiety. Tibetan ethnicity was a protective factor for anxiety but a risk factor for IADL limitations.ConclusionA significant proportion of Covid-19 survivors had disability and anxiety at discharge from hospital. Health systems need to be prepared for an additional burden resulting from rehabilitation needs of Covid-19 survivors.

Expansin is a type of cell wall elongation and stress relaxation protein involved in various developmental processes and stress resistances in plant. In this study, we identified 36 potato (Solanum tuberosum L.) genes belonging to the expansin (StEXP) gene family from the genome reference. These genes included 24 α-expansins (StEXPAs), five β-expansins (StEXPBs), one expansin-like A (StEXLA) and six expansin-like B (StEXLBs). The RNA-Seq analysis conducted from a variety of tissue types showed 34 expansins differentially expressed among tissues, some of which only expressed in specific tissues. Most of the StEXPAs and StEXPB2 transcripts were more abundant in young tuber compared with other tissues, suggesting they likely play a role in tuber development. There were 31 genes, especially StEXLB6, showed differential expression under the treatments of ABA, IAA and GA3, as well as under the drought and heat stresses, indicating they were likely involved in potato stress resistance. In addition, the gene co-expression analysis indicated the StEXLBs likely contribute to a wider range of stress resistances compared with other genes. We found the StEXLA and six StEXLBs expressed differently under a range of abiotic stresses (salt, alkaline, heavy metals, drought, heat, and cold stresses), which likely participated in the associated signaling pathways. Comparing with the control group, potato growing under the drought or heat stresses exhibited up-regulation of the all six StEXLB genes in leaves, whereas, the StEXLB3, StEXLB4, StEXLB5 and StEXLB6 showed relatively higher expression levels in roots. This suggested these genes likely played a role in the drought and heat tolerance. Overall, this study has shown the potential role of the StEXP genes in potato growth and stress tolerance, and provided fundamental resources for the future studies in potato breeding.

Among various approaches to the repeated measures analysis in crossover clinical trials, the general linear models (GLMs) with correlated errors attract substantial attention due to their simplicity in model specification, implementation, and interpretation. The goal of this research note is to conduct simulation studies to numerically investigate the impact of model misspecification in the GLMs with correlated errors in the analysis of crossover trials. A series of synthetic two-treatment and three-treatment crossover trials were designed, and simulation studies were conducted to assess how treatment effect estimation, type I error rates, and power can be affected by misspecified period effects, carryover effects, and variance-covariance structures in the GLMs. Numerical studies confirm that (i) the GLMs with terms for both carryover and period effects and with an unstructured variance-covariance matrix can provide unbiased treatment effect estimates and control of Type I error rates and that (ii) misspecification in either period effects, carryover effects, or covariance structures in the GLMs can induce inflated type I error, declined power, or biased treatment effect estimates. Although methodologic contribution of this research note is minimal, we provide practical recommendations and advice to pharmaceutical sponsors and other investigational drugs and device applicants in designing and analyzing crossover trials using the GLMs with correlated errors.

Dendrobium, an important medicinal plant, is a source of widely used herbal medicine to nourish the stomach and treat throat inflammation. The present study is aimed at distinguishing and evaluating three major Dendrobium species by comparing physiochemical characteristics and understanding differences between different growth years in the Ta-pieh Mountains. Polysaccharides and total alkaloids of Dendrobium were determined, and the amino acids and trace elements were determined by UPLC (Ultra High-Performance Liquid Chromatography) and ICP-MS (Inductively coupled plasma mass spectrometry). It can be seen from the results that the polysaccharide content of these three kinds of Dendrobium in different growth years ranges from 249.31 mg·g-1 to 547.66 mg·g-1, and the highest content is in the 3-year-old Dendrobium huoshanense. The total alkaloid content ranges from 0.21 mg·g-1 to 0.54 mg·g-1, and the highest content is also the 3-year-old Dendrobium huoshanense. We determined the amino acid content of these three Dendrobium in different growth years, and we can see that each of the three kinds of Dendrobium contain seven kinds of amino acids required by the human body. We conducted a safety evaluation of the essential trace elements of Dendrobium, and the results showed that the dosage of 12g·d-1 Dendrobium prescribed in China Pharmacopoeia is in accordance with the recommended daily intake of trace elements recommended by the Food and Drug Administration of the United States, and will not cause trace element poisoning. Linear discriminant analysis was carried out on the basis of amino acids and trace elements and confirmed the applicability of multi-elemental analysis for identifying different Dendrobium species.

Shift work and jet lag, characterized by circadian misalignment, can disrupt several physiological activities, but whether they affect the rhythm of glucose uptake and insulin sensitivity remain unclear. In the present study, female C57BL/6J mice were maintained for four weeks under the condition of 8-hour phase advance and delay every 3-4 days to mimic shift work. Intraperitoneal glucose tolerance test (IPGTT) and intraperitoneal insulin tolerance test (IPITT) were performed repeatedly at Zeitgeber time (ZT) 0, ZT6, ZT12, and ZT18. Glucose-stimulated insulin secretion (GSIS) test was performed at ZT6. We found that the average level of daily glucose tolerance did not decrease but the phase of glucose tolerance advanced by 2.27 hours and the amplitude attenuated by 20.4% in shift work mice. At ZT6, IPITT showed blood glucose at 30 min after insulin injection decreased faster in shift work mice (-3.50±0.74mmol/L, -61.58±7.89%) than that in control mice (-2.11±1.10mmol/L, -33.72±17.24%), but IPGTT and GSIS test showed no significant difference between the two groups. Food intake monitor showed that the feeding time of shift work mice continued to advance. Restricting feed to a fixed 12-hour period alleviated the increase of insulin sensitivity induced by shift-work. We also observed that an increase of blood glucose and liver glycogen at ZT0, as well as a phase advance of liver clock genes and some glucose metabolism-related genes such as forkhead box O1 (Foxo1) and peroxisome proliferator activated receptor alpha (Pparα) in shift work mice. Our results showed that light change-simulated shift work altered insulin sensitivity during the light phase and shifted glucose tolerance rhythms in female mice, suggesting a causal association between long-term shift work and type 2 diabetes.

Human Multipotent Stromal Cells (MSCs) are a valuable resource for regenerative medicine and are widely studied. They can be isolated from a variety of tissues and differentiate into multiple cell types (multi-potent). Many reports have been published using human MSCs and to be able to compare outcome, or be able to identify differences between MSCs, several cell surface markers have been proposed. Nevertheless, still many differences remain. Gene expression is known to be different between cell stage and origin. Furthermore, cells cultured on a culture dish (2D) show different gene expression profiles as compared to cells grown on scaffolds (3D). Even the RNA extraction method and the selection of genes used for normalisation have a role in gene expression profiling. To be able to compare gene expression data from samples cultured in different dimensions and RNA extracted using a variety of protocols we set out to define a set of reference genes suitable to normalise qPCR data from a very heterogeneous sample set. Hereto, Trizol was used to extract RNA from human MSCs cultured in 3D and 2D to validate newly designed and previously published primer sets. Subsequently, RNA from fresh human MSC samples and samples stored in RLT-buffer, Trizol or RNAlater was extracted using RNeasy and Trizol methods. All samples have been used to rank the candidate reference genes according to their stability after qPCR enabling identification of the most suitable reference gene(s) for normalisation of a heterogeneous sample set. The most stably expressed reference genes indicated superior normalisation of MSC marker gene expression over the least stable reference genes.

Worldwide tree mortality as induced by climate change presents a challenge to forest managers. To successfully manage vulnerable forests requires the capacity of regeneration to compensate for losses from tree mortality. We observed rapid regeneration and the growth release of young trees after warming-induced mortality in a David aspen-dominated (Populus davidiana) broad-leaved forest in Inner Mongolia, China, as based on individual tree measurements taken in 2012 and 2015 from a 6-ha permanent plot. Warming and drought stress killed large trees 10-15 m tall with a total number of 2881 trees during 2011-2012, and also thinned the upper crowns. David aspen recruitment increased 2 times during 2012-2015 and resulted in a high transition probability of David aspen replacing the same or other species, whereas the recruitment of Mongolian oak (Quercus mongolica) was much lower: it decreased from 2012 to 2015, indicating that rapid regeneration represented a regrowth phase for David aspen, and not succession to Mongolian oak. Further, we found that the recruitment density increased with canopy openness, thus implying that warming-induced mortality enhanced regeneration. Our results suggest that David aspen has a high regrowth ability to offset individual losses from warming-induced mortality. This important insight has implications for managing this vulnerable forest in the semi-arid region of northern China.

Landmark studies showed that partial clinical remission in new-onset type 1 diabetes is associated with reduced prevalence of long-term complications, but early clinical indicators of this favorable outcome are poorly characterized.To determine if there were any differences in lipid parameters, especially LDL-cholesterol, between remitters and non-remitters 4 to 5 years after the diagnosis of type 1 diabetes after controlling for hemoglobin A1c, body mass index, and pubertal status.A longitudinal retrospective cohort study of 123 subjects of mean age 11.9 ± 2.9 years, [male 11.7 ± 2.9 years, (n = 55); female 12.0 ± 2.9 years, (n = 68), p = 0.60] with type 1 diabetes of 4-5 years duration. Anthropometric and biochemical data were collected at the 4th or 5th year after diagnosis in line with the American Diabetes Association recommendation to initiate screening for complications in children either at the beginning of puberty or 4-5 years after diagnosis. Puberty was defined by Tanner stages II-V. Partial clinical remission was defined by the gold-standard insulin-dose adjusted hemoglobin A1c (IDAA1c) of ≤9.There were 44 (35.8%) remitters (age 13.0 ± 2.5y; male 52.3%). Both the total cholesterol and LDL-cholesterol were significantly lower in remitters compared to non-remitters: LDL-C: 78.8 ± 28.7 mg/dL vs. 91.6 ± 26.5 mg/dL, p = 0.023; and total cholesterol: 151.5 ± 32.6 mg/dL vs. 167.0 ± 29.6 mg/dL, p = 0.015. Other lipid fractions were similar between the groups. There were no differences between the groups for glycemic control, body mass index z score, thyroid function, celiac disease occurrence, or vitamin D status. A greater number of remitters were in puberty compared to non-remitters (86.4% vs. 60.8%, p = 0.006). LDL-C concentration was similar in prepubertal remitters vs. non-remitters (p = 0.93), but was significantly lower in remitters in puberty compared to non-remitters in puberty (p = 0.018) after adjusting for age and duration of diabetes.Children with type 1 diabetes who underwent a honeymoon phase had significantly lower LDL cholesterol 5 years after diagnosis. This early divergence in lipidemia may explain the dichotomy in the prevalence of long-term complication in type 1 diabetes between remitters and non-remitters. It also offers a pathway for targeted lipid monitoring in type 1 diabetes, by establishing non-remission as a non-modifiable risk factor for vascular complication in type 1 diabetes.

This study aimed to evaluate the associations between types of night shift work and different indices of obesity using the baseline information from a prospective cohort study of night shift workers in China.A total of 3,871 workers from five companies were recruited from the baseline survey. A structured self-administered questionnaire was employed to collect the participants' demographic information, lifetime working history, and lifestyle habits. Participants were grouped into rotating, permanent and irregular night shift work groups. Anthropometric parameters were assessed by healthcare professionals. Multiple logistic regression models were used to evaluate the associations between night shift work and different indices of obesity.Night shift workers had increased risk of overweight and obesity, and odds ratios (ORs) were 1.17 (95% CI, 0.97-1.41) and 1.27 (95% CI, 0.74-2.18), respectively. Abdominal obesity had a significant but marginal association with night shift work (OR = 1.20, 95% CI, 1.01-1.43). A positive gradient between the number of years of night shift work and overweight or abdominal obesity was observed. Permanent night shift work showed the highest odds of being overweight (OR = 3.94, 95% CI, 1.40-11.03) and having increased abdominal obesity (OR = 3.34, 95% CI, 1.19-9.37). Irregular night shift work was also significantly associated with overweight (OR = 1.56, 95% CI, 1.13-2.14), but its association with abdominal obesity was borderline (OR = 1.26, 95% CI, 0.94-1.69). By contrast, the association between rotating night shift work and these parameters was not significant.Permanent and irregular night shift work were more likely to be associated with overweight or abdominal obesity than rotating night shift work. These associations need to be verified in prospective cohort studies.

This article presents and investigates performance of a series of robust multivariate nonparametric tests for detection of location shift between two multivariate samples in randomized controlled trials. The tests are built upon robust estimators of distribution locations (medians, Hodges-Lehmann estimators, and an extended U statistic) with both unscaled and scaled versions. The nonparametric tests are robust to outliers and do not assume that the two samples are drawn from multivariate normal distributions. Bootstrap and permutation approaches are introduced for determining the p-values of the proposed test statistics. Simulation studies are conducted and numerical results are reported to examine performance of the proposed statistical tests. The numerical results demonstrate that the robust multivariate nonparametric tests constructed from the Hodges-Lehmann estimators are more efficient than those based on medians and the extended U statistic. The permutation approach can provide a more stringent control of Type I error and is generally more powerful than the bootstrap procedure. The proposed robust nonparametric tests are applied to detect multivariate distributional difference between the intervention and control groups in the Thai Healthy Choices study and examine the intervention effect of a four-session motivational interviewing-based intervention developed in the study to reduce risk behaviors among youth living with HIV.

Nanobubbles (NBs) opened a new field of ultrasound imaging. There is still no practical method to control the diameter of bubbles. In this study, we developed a new method to control the size by incorporating of silicon hybrid lipids into the bubble membrane. The range of particle size of resulting NBs is between 523.02 ± 46.45 to 857.18 ± 82.90, smaller than the conventional microbubbles. The size of resulting NBs increased with the decrease in amount of silicon hybrid lipids, indicating the diameter of NBs can be regulated through modulating the ratio of silicon hybrid lipids in the bubble shell. Typical harmonic signals could be detected. The in vitro and in vivo ultrasound imaging experiments demonstrated these silicon-modified NBs had significantly improved ultrasound contrast enhancement abilities. Cytotoxicity assays revealed that these NBs had no obvious cytotoxicity to the 293 cell line at the tested bubble concentration. Our results showed that the novel NBs could use as nanoscale ultrasound contrast agents, providing the foundation for NBs in future applications including contrast-enhanced imaging and drug/gene delivery.

To report calculated crystalline lens power and describe the distribution of ocular biometry and its association with refractive error in older Chinese adults.Random clustering sampling was used to identify adults aged 50 years and above in Xuhui and Baoshan districts of Shanghai. Refraction was determined by subjective refraction that achieved the best corrected vision based on monocular measurement. Ocular biometry was measured by IOL Master. The crystalline lens power of right eyes was calculated using modified Bennett-Rabbetts formula.We analyzed 6099 normal phakic right eyes. The mean crystalline lens power was 20.34 ± 2.24D (range: 13.40-36.08). Lens power, spherical equivalent, and anterior chamber depth changed linearly with age; however, axial length, corneal power and AL/CR ratio did not vary with age. The overall prevalence of hyperopia, myopia, and high myopia was 48.48% (95% CI: 47.23%-49.74%), 22.82% (95% CI: 21.77%-23.88%), and 4.57% (95% CI: 4.05-5.10), respectively. The prevalence of hyperopia increased linearly with age while lens power decreased with age. In multivariate models, refractive error was strongly correlated with axial length, lens power, corneal power, and anterior chamber depth; refractive error was slightly correlated with best corrected visual acuity, age and sex.Lens power, hyperopia, and spherical equivalent changed linearly with age; Moreover, the continuous loss of lens power produced hyperopic shifts in refraction in subjects aged more than 50 years.

OBJECTIVE:To assess whether neoadjuvant chemotherapy (NACT) is superior to primary debulking surgery (PDS) with regard to optimal cytoreduction, peri-operative morbidity, mortality, and quality of life (QOL) in advanced epithelial ovarian cancer (EOC). METHODS:We searched the PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science, Registers of Clinical Trials for randomized controlled trials (RCTs) comparing NACT to PDS in women with Federation of International Gynaecologists and Obstetricians stage Ⅲ-Ⅳ EOC. RevMan 5.3 software was utilized for statistical analysis. RESULTS:Four RCTs involving 1,607 women with advanced EOC were included. Compared with PDS, NACT provided a higher rate of complete cytoreduction (risk ratio [RR], 1.95; 95% confidence interval [CI], 1.33 to 2.87), optimal cytoreduction (RR: 1.61 [95%CI: 1.05 to 2.47]), but there was no significant difference in residual disease 0-1 cm (p = 0.49). NACT was associated with lower peri-operative morbidity with respect to infection (RR: 0.30 [95% CI: 0.16 to 0.56]), gastrointestinal fistula (RR: 0.24 [95% CI: 0.06 to 0.95]), any grade 3 or 4 adverse event (RR: 0.29 [95% CI: 0.11 to 0.78]), and less post-surgical death within 28 days (RR: 0.14 [95% CI: 0.04 to 0.49]). NACT provided better QOL in terms of fatigue (weight mean difference [WMD], -3.28; [95% CI: -3.99 to -2.57]), role functioning (WMD: 5.29 [95% CI: 4.44 to 6.14]), emotional functioning (WMD: 6.19 [95% CI: 5.57 to 6.82]), and cognitive functioning (WMD: 1.02 [95% CI: 0.43 to 1.61]) at 6-month follow-up compared with PDS. CONCLUSIONS:NACT is associated with superior optimal cytoreduction, lower peri-operative morbidity as well as post-surgical mortality, and better QOL compared to initial surgery in patients with advanced EOC. Future research should focus on improving the efficacy of NACT.

The developmental neurotoxicity caused by environmental pollutants has received great concern; however, there were still barely known about the underlying toxic mechanisms, especially the influence of varieties of regulatory factors such as microRNA (miRNA). A representative flame retardant, 2,2',4,4'-tetrabromodiphenyl ether (BDE47), was found to disrupt zebrafish development in visual perception and bone formation in previous study, thus here we investigated its effects on miRNA expression profiling of 6 days post fertilization (dpf) zebrafish larvae by deep sequencing. To overcome the shortage of zebrafish miRNA annotation, multiple data processing approaches, especially constructed network based on the interactions between miRNAs and enrichment terms, were adopted and helped us acquire several validated zebrafish miRNAs and two novel miRNAs in BDE47-induced effects, and identify corresponding biological processes of the miRNAs. Among them, miR-735 was supposed to play essential roles in larval sensory development according to analysis results. Our study also provided an effective strategy for analyzing biological effects on non-mammalian miRNAs with limited basic information.

Zao5241 is an elite soybean [Glycine max (L.) Merr.] line and backbone parent. In this study, we employed iTRAQ to analyze the proteomes and protein expression profiles of Zao5241 during leaf development. We identified 1,245 proteins in all experiments, of which only 45 had been previously annotated. Among overlapping proteins between three biological replicates, 598 proteins with 2 unique peptides identified were reliably quantified. The protein datasets were classified into 36 GO functional terms, and the photosynthesis term was most significantly enriched. A total of 113 proteins were defined as being differentially expressed during leaf development; 41 proteins were found to be differently expressed between two and four week old leaves, and 84 proteins were found to be differently expressed between two and six week old leaves, respectively. Cluster analysis of the data revealed dynamic proteomes. Proteins annotated as electron carrier activity were greatly enriched in the peak expression profiles, and photosynthesis proteins were negatively modulated along the whole time course. This dataset will serve as the foundation for a systems biology approach to understanding photosynthetic development.

The human ether-a-go-go-related gene (hERG) potassium channel conducts rapid delayed rectifier potassium currents (IKr) and contributes to phase III cardiac action potential repolarization. Drugs inhibit hERG channels by binding to aromatic residues in hERG helixes. Berberine (BBR) has multiple actions, and its hydrogenated derivative dihydroberberine (DHB) is a potential candidate for developing new drugs. Previous studies have demonstrated that BBR blocks hERG channels and prolongs action potential duration (APD). Our present study aimed to investigate the effects and mechanism of DHB on hERG channels. Protein expression and the hERG current were analyzed using western blotting and patch-clamp, respectively. DHB inhibited the hERG current concentration-dependently after instantaneous perfusion, accelerated channel inactivation by directly binding tyrosine (Tyr652) and phenylalanine (Phe656), and decreased mature (155-kDa) and simultaneously increased immature (135-kDa) hERG expression, respectively. This suggests disruption of forward trafficking of hERG channels. Besides, DHB remarkably reduced heat shock protein 90 (Hsp90) expression and its interaction with hERG, indicating that DHB disrupted hERG trafficking by impairing channel folding. Meanwhie, DHB enhanced the expression of cleaved activating transcription factor-6 (ATF-6), a biomarker of unfolded protein response (UPR). Expression of calnexin and calreticulin, chaperones activated by ATF-6 to facilitate channel folding, were also increased, which indicating UPR activation. Additionally, the degradation rate of mature 155-kDa hERG increased following DHB exposure. In conclusion, we demonstrated that DHB acutely blocked hERG channels by binding the aromatic Tyr652 and Phe656. DHB may decrease hERG plasma membrane expression through two pathways involving disruption of forward trafficking of immature hERG channels and enhanced degradation of mature hERG channels. Furthermore, forward trafficking was disrupted by impaired channel folding associated with altered interactions between hERG proteins and chaperones. Finally, trafficking inhibition activated UPR, and mature hERG channel degradation was increased by DHB.

Electrocardiogram (ECG) data analysis is of great significance to the diagnosis of cardiovascular disease. ECG compression should be processed in real time, and the data should be based on lossless compression and have high predictability. In terms of the real time aspect, short-time Fourier transformation is applied to the processing of signal wave for reducing computational time. For the lossless compression requirement, wavelet-transformation that is a coding algorithm can be used to avoid loss of data. In practice, compression is required to avoid storing redundant recording data that are not useful in the diagnosis platform. The obtained data can be preprocessed to remove noise by using wavelet transform, and then a multi-objective optimize neural network model is used to extract feature information. Compared with the existing traditional methods such as direct data processing method and transform method, our proposed compression model has self-learning ability to achieve high data compression ratio at 1:19 without losing important ECG information and compromising quality. Upon testing, we demonstrated that the proposed ECG data compression method based on multi-objective optimization neural network is effective and efficient in clinical practice.

[This corrects the article DOI: 10.1371/journal.pone.0141138.].

Human hemochromatosis protein (HFE) is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM). However, the effect of other single nucleotide variation (SNV) in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA) GBM (Caucasian only) database. We found 9 SNVs with increased frequency in blood normal of TCGA GBM patients compared to the 1000Genome. Among 9 SNVs, 7 SNVs were located in the intron and 2 SNVs (i.e., H63D, C282Y) in the exon of HFE gene. The statistical analysis demonstrated that blood normal samples of TCGA GBM have more H63D (p = 0.0002, 95% Confidence interval (CI): 0.2119-0.3223) or C282Y (p = 0.0129, 95% CI: 0.0474-0.1159) HFE polymorphisms than 1000Genome. The Kaplan-Meier survival curve for the 264 GBM samples revealed no difference between wild type (WT) HFE and H63D, and WT HFE and C282Y GBM patients. In addition, there was no difference in the survival of male/female GBM patients based on HFE genotype. There was no correlation between HFE expression and survival. In conclusion, the current results suggest that somatic HFE polymorphisms do not impact GBM patients' survival in the TCGA data set of GBM.

Blue aleurone is a useful and interesting trait in common wheat that was derived from related species. Here, transcriptomes of blue and white aleurone were compared for isolating Blue aleurone 1 (Ba1) transferred from Thinopyrum ponticum. In the genes involved in anthocyanin biosynthesis, only a basic helix-loop-helix (bHLH) transcription factor, ThMYC4E, had a higher transcript level in blue aleurone phenotype, and was homologous to the genes on chromosome 4 of Triticum aestivum. ThMYC4E carried the characteristic domains (bHLH-MYC_N, HLH and ACT-like) of a bHLH transcription factor, and clustered with genes regulating anthocyanin biosynthesis upon phylogenetic analysis. The over-expression of ThMYC4E regulated anthocyanin biosynthesis with the coexpression of the MYB transcription factor ZmC1 from maize. ThMYC4E existed in the genomes of the addition, substitution and near isogenic lines with the blue aleurone trait derived from Th. ponticum, and could not be detected in any germplasm of T. urartu, T. monococcum, T. turgidum, Aegilops tauschii or T. aestivum, with white aleurone. These results suggested that ThMYC4E was candidate Ba1 gene controlling the blue aleurone trait in T. aestivum genotypes carrying Th. ponticum introgression. The ThMYC4E isolation aids in better understanding the genetic mechanisms of the blue aleurone trait and in its more effective use during wheat breeding.

[This corrects the article DOI: 10.1371/journal.pone.0166260.].

A key requirement for three-dimensional printing (3-DP) at room temperature of medical implants depends on the availability of printable and biocompatible binder-powder systems. Different concentration polyvinyl alcohol (PVA) and phosphoric acid solutions were chosen as the binders to make the artificial stent biocompatible with sufficient compressive strength. In order to achieve an optimum balance between the bioceramic powder and binder solution, the biocompatibility and mechanical properties of these artificial stent samples were tested using two kinds of binder solutions. This study demonstrated the printable binder formulation at room temperature for the 3D artificial bone scaffolds. 0.6 wt% PVA solution was ejected easily via inkjet printing, with a supplementation of 0.25 wt% Tween 80 to reduce the surface tension of the polyvinyl alcohol solution. Compared with the polyvinyl alcohol scaffolds, the phosphoric acid scaffolds had better mechanical properties. Though both scaffolds supported the cell proliferation, the absorbance of the polyvinyl alcohol scaffolds was higher than that of the phosphoric acid scaffolds. The artificial stents with a hydroxyapatite/beta-tricalcium phosphate (HA/β-TCP) weight ratios of 60:40 depicted good biocompatibility for both scaffolds. Considering the scaffolds' mechanical and biocompatible properties, the phosphoric acid scaffolds with a HA/β-TCP weight ratio of 60:40 may be the best combination for bone tissue engineering applications.

Phytophthora sojae, an oomycete pathogen of soybean, causes stem and root rot, resulting in annual economic loss up to $2 billion worldwide. Varieties with P. sojae resistance are environmental friendly to effectively reduce disease damages. In order to improve the resistance of P. sojae and broaden the genetic diversity in Southern soybean cultivars and germplasm in the U.S., we established a P. sojae resistance gene pool that has high genetic diversity, and explored genomic regions underlying the host resistance to P. sojae races 1, 3, 7, 17 and 25. A soybean germplasm panel from maturity groups (MGs) IV and V including 189 accessions originated from 10 countries were used in this study. The panel had a high genetic diversity compared to the 6,749 accessions from MGs IV and V in USDA Soybean Germplasm Collection. Based on disease evaluation dataset of these accessions inoculated with P. sojae races 1, 3, 7, 17 and 25, which are publically available, five accessions in this panel were resistant to all races. Genome-wide association analysis identified a total of 32 significant SNPs, which were clustered in resistance-associated genomic regions, among those, ss715619920 was only 3kb away from the gene Glyma.14g087500, a subtilisin protease. Gene expression analysis showed that the gene was down-regulated more than 4 fold (log2 fold > 2.2) in response to P. sojae infection. The identified molecular markers and genomic regions that are associated with the disease resistance in this gene pool will greatly assist the U.S. Southern soybean breeders in developing elite varieties with broad genetic background and P. sojae resistance.

OBJECTIVES:(i) To provide baseline knowledge of gene expression in macroscopically normal articular cartilage, (ii) to test the hypothesis that age, body-mass-index (BMI), and sex are associated with cartilage RNA transcriptome, and (iii) to predict individuals at potential risk for developing "pre-osteoarthritis" (OA) based on screening of genetic risk-alleles associated with OA and gene transcripts differentially expressed between normal and OA cartilage. DESIGN:Healthy-appearing cartilage was obtained from the medial femoral notch of 12 knees with a meniscus tear undergoing arthroscopic partial meniscectomy. Cartilage had no radiographic, magnetic-resonance-imaging or arthroscopic evidence for degeneration. RNA was subjected to Affymetrix microarrays followed by validation of selected transcripts by microfluidic digital polymerase-chain-reaction. The underlying biological processes were explored computationally. Transcriptome-wide gene expression was probed for association with known OA genetic risk-alleles assembled from published literature and for comparison with gene transcripts differentially expressed between healthy and OA cartilage from other studies. RESULTS:We generated a list of 27,641 gene transcripts in healthy cartilage. Several gene transcripts representing numerous biological processes were correlated with age and BMI and differentially expressed by sex. Based on disease-specific Ingenuity Pathways Analysis, gene transcripts associated with aging were enriched for bone/cartilage disease while the gene expression profile associated with BMI was enriched for growth-plate calcification and OA. When segregated by genetic risk-alleles, two clusters of study patients emerged, one cluster containing transcripts predicted by risk studies. When segregated by OA-associated gene transcripts, three clusters of study patients emerged, one of which is remarkably similar to gene expression pattern in OA. CONCLUSIONS:Our study provides a list of gene transcripts in healthy-appearing cartilage. Preliminary analysis into groupings based on OA risk-alleles and OA-associated gene transcripts reveals a subset of patients expressing OA transcripts. Prospective studies in larger cohorts are needed to assess whether these patterns are predictive for OA.

Various feeder layers have been extensively applied to support the prolonged growth of human pluripotent stem cells (hPSCs) for in vitro cultures. Among them, mouse embryonic fibroblast (MEF) and mouse fibroblast cell line (SNL) are most commonly used feeder cells for hPSCs culture. However, these feeder layers from animal usually cause immunogenic contaminations, which compromises the potential of hPSCs in clinical applications. In the present study, we tested human umbilical cord mesenchymal stem cells (hUC-MSCs) as a potent xeno-free feeder system for maintaining human induced pluripotent stem cells (hiPSCs). The hUC-MSCs showed characteristics of MSCs in xeno-free culture condition. On the mitomycin-treated hUC-MSCs feeder, hiPSCs maintained the features of undifferentiated human embryonic stem cells (hESCs), such as low efficiency of spontaneous differentiation, stable expression of stemness markers, maintenance of normal karyotypes, in vitro pluripotency and in vivo ability to form teratomas, even after a prolonged culture of more than 30 passages. Our study indicates that the xeno-free culture system may be a good candidate for growth and expansion of hiPSCs as the stepping stone for stem cell research to further develop better and safer stem cells.

Wheat (Triticum aestivum L.) cultivars possessing purple grain arethought to be more nutritious because of high anthocyanin contents in the pericarp. Comparative transcriptome analysis of purple (cv Gy115) and white pericarps was carried out using next-generation sequencing technology. There were 23,642 unigenes significantly differentially expressed in the purple and white pericarps, including 9945 up-regulated and 13,697 down-regulated. The differentially expressed unigenes were mainly involved in encoding components of metabolic pathways, The flavonoid biosynthesis pathway was the most represented in metabolic pathways. In the transcriptome of purple pericarp in Gy115, most structural and regulatory genes biosynthesizing anthocyanin were identified, and had higher expression levels than in white pericarp. The largestunigene of anthocyanin biosynthesis in Gy115 was longer than the reference genes, which implies that high-throughput sequencing could isolate the genes of anthocyanin biosynthesis in tissues or organs with high anthocyanin content. Based on present and previous results, three unigenes of MYB gene on chromosome 7BL and three unigenes of MYC on chromosome 2AL were predicted as candidate genes for the purple grain trait. This article was the first to provide a systematic overview comparing the transcriptomes of purple and white pericarps in common wheat, which should be very valuable for identifying the key genes for the purple pericarp trait.

Exendin-4, a glucagon-like protein-1 (GLP-1) receptor agonist, is an excellent therapeutic peptide drug for type 2 diabetes due to longer lasting biological activity compared to GLP-1. This study explored the feasibility of using probiotic Lactobacillus paracasei as an oral vector for recombinant exendin-4 peptide delivery, an alternative to costly chemical synthesis and inconvenient administration by injection. L. paracasei transformed with a plasmid encoding the exendin-4 gene (L. paracasei L14/pMG76e-exendin-4) with a constitutive promotor was successfully constructed and showed efficient secretion of exendin-4. The secreted exendin-4 significantly enhanced insulin secretion of INS-1 β-cells, along with an increment in their proliferation and inhibition of their apoptosis, corresponding to the effect of GLP-1 on these cells. The transcription level of the pancreatic duodenal homeobox-1 gene (PDX-1), a key transcription factor for cellular insulin synthesis and secretion, was upregulated by the treatment with secreted exendin-4, paralleling the upregulation of insulin gene expression. Caco-2 cell monolayer permeability assay showed a 34-fold increase in the transport of exendin-4 delivered by L. paracasei vs. that of free exendin-4 (control), suggesting effective facilitation of exendin-4 transport across the intestinal barrier by this delivery system. This study demonstrates that the probiotic Lactobacillus can be engineered to secrete bioactive exendin-4 and facilitate its transport through the intestinal barrier, providing a novel strategy for oral exendin-4 delivery using this lactic acid bacterium.

BACKGROUND:Increased plasma fibrinogen is thought to contribute to tumor progression and metastasis. The association of plasma fibrinogen with clinicopathological characteristics, and the optimal cutoff with an ideal predictive value has not been fully determined in patients with upper tract urothelial carcinoma (UTUC). We aimed to investigate the clinical significance of this parameter in a Chinese cohort of patients with UTUC. METHODS:A retrospective study was conducted to analyze the clinical data of 184 operable UTUC patients in a Chinese cohort with a high incidence of chronic kidney disease (CKD). An optimal cutoff was set for further analysis according to validated web-based software. The associations of plasma fibrinogen with clinicopathological characteristics and survival were assessed. Multivariate analyses were performed to determine the independent prognostic factors. RESULTS:Elevated plasma fibrinogen was significantly associated with tumor necrosis, lymph node involvement, and a higher preoperative CKD stage, pathological tumor stage and grade (all P < 0.05). Kaplan-Meier analysis showed that plasma fibrinogen ≥ 3.54 g/L predicted a poorer overall and cancer-specific survival than < 3.54 g/L (P < 0.001 for both). Multivariate analyses revealed that elevated preoperative plasma fibrinogen was an independent negative prognostic factor for overall survival (HR = 2.026; 95% CI: 1.226-3.349; P = 0.006) and cancer-specific survival (HR = 1.886; 95% CI: 1.019-3.490; P = 0.043). CONCLUSIONS:Increased plasma fibrinogen was an independent prognostic risk factor for poor outcomes in UTUC. This parameter may serve as an effective biomarker with easy accessibility for evaluating prognosis for patients with UTUC.

Glucose, xylose and arabinose are the three most abundant monosaccharide found in lignocellulosic biomass. Effectively and simultaneously utilization of these sugars by microorganisms for production of the biofuels and bio-chemicals is essential toward directly fermentation of the lignocellulosic biomass. In our previous study, the recombinant Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain was already shown to efficiently utilize xylose for production of acetoin, with a yield of 0.36 g/g xylose. In the current study, the Bacillus subtilis168ARSRCPΔacoAΔbdhA strain was further engineered to produce acetoin from a glucose, xylose, and arabinose mixtures. To accomplish this, the endogenous xylose transport protein AraE, the exogenous xylose isomerase gene xylA and the xylulokinase gene xylB from E. coli were co-overexpressed in the Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain, which enabled the resulting strain, denoted ZB02, to simultaneously utilize glucose and xylose. Unexpectedly, the ZB02 strain could simultaneously utilize glucose and arabinose also. Further results indicated that the transcriptional inhibition of the arabinose transport protein gene araE was the main limiting factor for arabinose utilization in the presence of glucose. Additionally, the arabinose operon in B. subtilis could be activated by the addition of arabinose, even in the presence of glucose. Through fed-batch fermentation, strain ZB02 could simultaneously utilize glucose, xylose, and arabinose, with an average sugar consumption rate of 3.00 g/l/h and an average production of 62.2 g/l acetoin at a rate of 0.864 g/l/h. Finally, the strain produced 11.2 g/l acetoin from lignocellulosic hydrolysate (containing 20.6g/l glucose, 12.1 g/l xylose and 0.45 g/l arabinose) in flask cultivation, with an acetoin yield of 0.34 g/g total sugar. The result demonstrates that this strain has good potential for the utilization of lignocellulosic hydrolysate for production of acetoin.

Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.