EXSCLAIM!: Harnessing materials science literature for self-labeled microscopy datasets.

This work introduces the EXSCLAIM! toolkit for the automatic extraction, separation, and caption-based natural language annotation of images from scientific literature. EXSCLAIM! is used to show how rule-based natural language processing and image recognition can be leveraged to construct an electron microscopy dataset containing thousands of keyword-annotated nanostructure images. Moreover, it is demonstrated how a combination of statistical topic modeling and semantic word similarity comparisons can be used to increase the number and variety of keyword annotations on top of the standard annotations from EXSCLAIM! With large-scale imaging datasets constructed from scientific literature, users are well positioned to train neural networks for classification and recognition tasks specific to microscopy-tasks often otherwise inhibited by a lack of sufficient annotated training data.

Long-term exercise preserves pancreatic islet structure and ß-cell mass through attenuation of islet inflammation and fibrosis.

Islet fibrosis is associated with the disruption of islet structure and contributes to ß-cell dysfunction, playing an essential role in the pathogenesis of type 2 diabetes. Physical exercise has been shown to attenuate fibrosis in various organs; however, the effect of exercise on islet fibrosis has not been defined. Male Sprague-Dawley rats were divided into four groups: normal diet sedentary [N-Sed], normal diet + exercise [N-Ex], high-fat diet sedentary [H-Sed], and high-fat diet + exercise [H-Ex]. After 60 weeks of exercise, 4452 islets from Masson-stained slides were analyzed. Exercise led to a 68% and 45% reduction in islet fibrosis in the normal and high-fat diet groups and was correlated with a lower serum blood glucose. Fibrotic islets were characterized by irregular shapes and substantial loss of ß-cell mass, which were significantly reduced in the exercise groups. Remarkably, the islets from exercised rats at week 60 were morphologically comparable to those of sedentary rats at 26 weeks. In addition, the protein and RNA levels of collagen and fibronectin, and the protein levels of hydroxyproline in the islets were also attenuated by exercise. This was accompanied by a significant reduction in inflammatory markers in the circulation Interleukin-1 beta (IL-1ß)] and pancreas [IL-1ß, Tumor Necrosis Factor-alpha, Transforming Growth Factor-ß, and Phosphorylated Nuclear Factor Kappa-B p65 subunit], lower macrophage infiltration, and stellate cell activation in the islets of exercised rats. In conclusion, we have demonstrated that long-term exercise preserves pancreatic islet structure and ß-cell mass through anti-inflammatory and anti-fibrotic actions, suggesting additional rationales for the success of exercise training in the prevention and treatment of type 2 diabetes that should be further explored.

Effects of Elevated Aluminum Concentration and Distribution on Root Damage, Cell Wall Polysaccharides, and Nutrient Uptake in Different Tolerant Eucalyptus Clones.

Aluminized acidic soil can damage Eucalyptus roots and limit tree growth, hindering the productivity of Eucalyptus plantations. At present, the negative impacts of elevated aluminum (Al) on the cell morphology and cell wall properties of Eucalyptus root tip are still unclear. In order to investigate the responses of two different tolerant clones, Eucalyptus urophylla (G4) and Eucalyptus grandis × Eucalyptus urophylla (G9), to Al toxicity, seedling roots were treated hydroponically with an Al solution, and the polysaccharide content in the root tip cell wall and the characteristics of programmed cell death were studied. The results show that the distribution of Al was similar in both clones, although G9 was found to be more tolerant to Al toxicity than G4. The Al3+ uptake of pectin in root tip cell walls was significantly higher in G4 than in G9. The root tip in G4 was obviously damaged, enlarged, thickened, and shorter; the root crown cells were cracked and fluffy; and the cell elongation area was squeezed. The lower cell wall polysaccharide content and PME activity may result in fewer carboxylic groups in the root tip cell wall to serve as Al-binding sites, which may explain the stronger Al resistance of G9 than G4. The uptake of nitrogen and potassium in G4 was significantly reduced after aluminum application and was lower than in G9. Al-resistant Eucalyptus clones may have synergistic pleiotropic effects in resisting high aluminum-low phosphorus stress, and maintaining higher nitrogen and potassium levels in roots may be an important mechanism for effectively alleviating Al toxicity.

Genome survey and development of 13 SSR markers in Eucalyptus cloeziana by NGS.

Eucalyptus cloeziana is a valuable timber tree species for its high durability and excellent sawmilling qualities. However, there is lack of complete genomic information for this plant, which severely constrains its genetic improvement. This study aim to survey the genome of E. cloeziana and determine the large-scale sequencing scheme of this species. Next-generation sequencing based on Illumina Hi- Seq X Ten platform was used to survey the E. cloeziana genome and its SSR markers development. We estimated the genome size to be 491.91 Mb and the heterozygosity rate to be 1.23%, with repetitive sequences accounting for 40.74%. The clean reads of E. cloeziana were assembled into 995,093 scaffolds (556,992,952 bp) with a N50 value of 2297 bp. In the GO database, the 10,172 genes annotated were matched to 50 functional gene groups in three categories of cell component, biological function and molecular function, respectively. Through KEGG pathways analysis, 10,802 genes were successfully annotated and 133 metabolic pathways were detected with the most abundant metabolism-related genes. Meanwhile, a total of 58,832 simple-sequence repeat (SSR) loci were identified in the E. cloeziana genome, and among them, dinucleotide repeats were the most abundant class. AG/CT, AT/AT, AAG/CTT were the three most frequent primitive types. Of the 50 genomic SSR primer pairs randomly selected for screening test, 13 showed polymorphism (PIC = 0.625). Three to nine alleles per locus (mean = 6.23) were observed, with the observed and expected heterozygosity at 0.317-1.000 and 0.276-0.838 across all the 44 E. cloeziana germplasms, respectively. Here, we report the genome information of E. cloeziana, and the novel 13 genomic SSR markers that were developed can be used as powerful tools for evaluating genetic diversity and population structure, and thus contribute to molecular breeding studies of E. cloeziana and other eucalypts.

Female Colon Cancer Metastasis Pattern and Prognosis: A SEER-Based Study.

The purpose of this study was to compare the metastatic pattern and prognosis of female colon cancer (FCC) to that of male colon cancer (MCC) to ascertain the independent factors impacting the prognosis of patients with FCC. The data of the present study population were retrieved from the Surveillance, Epidemiology, and End Results (SEER) database. Descriptive analysis, the Kaplan-Meier method, and the Cox regression were used to evaluated FCC characteristics and factors associated with prognosis. There were 56,442 patients diagnosed with FCC, of whom 8,817 had distant metastases. Compared to patients with nonmetastatic FCC, a greater proportion of metastatic FCC patients was less than 60 years of age, black race, and grade III-IV. The primary sites were mainly located on the left side and have more possibility to receive chemotherapy and radiotherapy. Compared to metastatic MCC, a higher proportion of metastatic FCC patients ranged over 60 years of age, black race, treated without chemotherapy, and insurance, while the primary site was located on the right side. Liver and lung were the two most common sites of solitary metastases in CC, and among patients with solitary metastases in CC, patients who had lung metastases had a better prognosis than those who developed other types of metastasizes. Patients with FCC with metastases of the liver had a worse prognosis than their MCC counterparts. Cox multivariate regression analysis showed that the risk ratio was higher in metastatic FCC patients compared to those without metastases. We report the survival comparison of metastatic FCC with nonmetastatic FCC through the SEER database. Our results suggest that it has unique clinicopathological features and differs from metastatic MCC. Furthermore, patients with liver metastatic FCC have a worse prognosis than those with MCC. Emphasis on screening for colon cancer in women and additional clinical care should be paid for, especially for patients with FCC with metastatic liver cancer.

Comprehensive Evaluation of the Metabolism of Genipin-1-ß-d-gentiobioside in Vitro and in Vivo by Using HPLC-Q-TOF.

To examine the metabolism of genipin-1-ß-d-gentiobioside (GG), its distribution and biotransformation in vivo and in vitro were investigated. Urine, plasma, feces, and various organs were collected after oral administration of GG to normal rats and pseudo-germ-free rats to evaluate GG metabolism in vivo. GG was incubated with intestinal flora and primary hepatocytes in vitro to investigate microbial and hepatic metabolism. Using HPLC-Q-TOF-LC/MS, 11 metabolites of GG were absolutely or tentatively identified in terms possible elemental compositions, retention times, and characteristics of fragmentation patterns corresponding to eight biotransformations: deglycosylation, hydroxylation, sulfate conjugation, glucuronidation, hydrogenation, demethylation, glycosylation, and dehydration. Fewer metabolites were detected in pseudo-germ-free rats than in conventional rats. Moreover, geniposide and genipin were generated by the deglycoslation of intestinal bacteria. Geniposidic acid was detected in rat primary-hepatocyte incubation. This study first explores the metabolism of GG in vivo and in vitro. The results can aid the elucidation of PK profiles and clinical usage of gardenia fruit.

Self-learning based Fourier ptychographic microscopy.

Fourier Ptychographic Microscopy (FPM) is a newly proposed computational imaging method aimed at reconstructing a high-resolution wide-field image from a sequence of low-resolution images. These low-resolution images are captured under varied illumination angles and the FPM recovery routine then stitches them together in the Fourier domain iteratively. Although FPM has achieved success with static sample reconstructions, the long acquisition time inhibits real-time application. To address this problem, we propose here a self-learning based FPM which accelerates the acquisition and reconstruction procedure. We first capture a single image under normally incident illumination, and then use it to simulate the corresponding low-resolution images under other illumination angles. The simulation is based on the relationship between the illumination angles and the shift of the sample's spectrum. We analyze the importance of the simulated low-resolution images in order to devise a selection scheme which only collects the ones with higher importance. The measurements are then captured with the selection scheme and employed to perform the FPM reconstruction. Since only measurements of high importance are captured, the time requirements of data collection as well as image reconstruction can be greatly reduced. We validate the effectiveness of the proposed method with simulation and experimental results showing that the reduction ratio of data size requirements can reach over 70%, without sacrificing image reconstruction quality.

Effect of Low pH and Aluminum Toxicity on the Photosynthetic Characteristics of Different Fast-Growing Eucalyptus Vegetatively Propagated Clones.

Knowing how acid soils and aluminum in soils may limit the growth of Eucalyptus trees in plantations is important because these plantations grow in many tropical and subtropical regions. Seedlings of four vegetatively propagated Eucalyptus clones, E. grandis × E. urophylla 'GLGU9'(G9), E. grandis × E. urophylla 'GLGU12' (G12), E. urophylla × E. camaldulensis 'GLUC3' (G3) and E. urophylla 'GLU4'(G4), were subjected to liquid culture with Hoagland nutrient solution for 40 days, then treated with four different treatments of acid and aluminum for 1 day. The four treatments used either pH 3.0 or 4.0 with or without added aluminum (4.4 mM) in all possible combinations; a control used no added aluminum at pH 4.8. Subsequently, the photosynthetic parameters and morphology of leaves from eucalypt seedlings were determined and observed. The results showed that the tested chlorophyll content, net photosynthetic rate, transpiration rate and water use efficiency were apparently inhibited by aluminum. Under uniform Al concentration (4.4 mM), the Al-induced limitation to photosynthetic parameters increased with pH, indicating acid stimulation to Al toxicity. Among all treatments, the most significant reduction was found in the combination of pH 3.0 and 4.4 mM Al. The photosynthetic and transpiration rates showed similar trends with G9 > G12 > G3 > G4, suggesting that G9 and G12 had higher Al-tolerance than other two clones. Microscopic observation revealed changes in leaf morphology when exposed to Al stress; for example, a reduced thickness of leaf epidermis and palisade tissue, the descendant palisade tissue/spongy tissue ratio and leaf tissue looseness. Overall, the acid and aluminum stress exerted negative effects on the photosynthetic activity of eucalypt seedlings, but the differences in tolerance to Al toxicity between the clones were favorable, offering potential to improve Eucalyptus plantation productivity by selecting Al tolerant clones.

Changes in Physicochemical, Structural, and Sensory Properties of Irradiated Brown Japonica Rice during Storage.

Brown japonica rice was treated with (60)Co γ irradiation at doses of 0, 0.2, 0.5, 1.0, and 2.0 kGy immediately after harvesting. The effects of irradiation on physicochemical, structural, and sensory properties during long-term storage (18 months) were investigated. The study revealed that the pasting properties, including peak, through, breakdown, final, and setback viscosities, decrease considerably in a dose-dependent manner and vary differently during 18 months of storage. Irradiation reduced the free fatty acid (FFA) content in comparison with unirradiated brown rice with long-term storage (from 12 to 18 months). Scanning electron microscope (SEM) observation showed that the mean range and shape of starch granules did not vary significantly. However, dark spots developed among starch granules and the narrow cracks became wider with increasing irradiation dose and storage time. During sensory evaluation, extremely low scores for odor and overall acceptability were obtained for medium-dose irradiated rice (1.0 and 2.0 kGy); however, no significant difference was found in acceptability between low-dose irradiated rice (0.2 and 0.5 kGy) and the control rice (0 kGy). Overall, low-dose (0.5 kGy or below) irradiation seems to be a promising alternative treatment to increase brown rice shelf life, without affecting the physicochemical and structural characteristics and sensory acceptability.

Nonlinear optimization approach for Fourier ptychographic microscopy.

Fourier ptychographic microscopy (FPM) is recently proposed as a computational imaging method to bypass the limitation of the space-bandwidth product of the traditional optical system. It employs a sequence of low-resolution images captured under angularly varying illumination and applies the phase retrieval algorithm to iteratively reconstruct a wide-field, high-resolution image. In current FPM imaging system, system uncertainties, such as the pupil aberration of the employed optics, may significantly degrade the quality of the reconstruction. In this paper, we develop and test a nonlinear optimization algorithm to improve the robustness of the FPM imaging system by simultaneously considering the reconstruction and the system imperfections. Analytical expressions for the gradient of a squared-error metric with respect to the object and illumination allow joint optimization of the object and system parameters. The algorithm achieves superior reconstructions when the system parameters are inaccurately known or in the presence of noise and corrects the pupil aberrations simultaneously. Experiments on both synthetic and real captured data validate the effectiveness of the proposed method.

Cytotoxic activities of chemical constituents from rhizomes of Anemarrhena asphodeloides and their analogues.

Seven steroidal saponins (1-7) and two xanthones (8, 9) were isolated from the rhizomes of Anemarrhena asphodeloides. Then in order to discover more analogues, which may possess good biological activity, the structural modifications of 2 and 9 were performed by acid hydrolysis and acetylation. Consequently, one novel steroidal saponin (2d, timosaponin BII-d), three compounds (2c, 2e and 2f) which were also the new products prepared by the diluted acid hydrolysis of 3 by our group previously, and four known compounds (2a, 2b, 9a and 9b) were obtained. The structures were elucidated by analyses of NMR and MS data. All the compounds were evaluated for their cytotoxicities against BEL-7402, HT-29, HeLa and MDA-MB-468 cell lines in vitro by Sulforhodamine protein coloration method. Compounds 1, 2, 2b, 4-6, 9a and 9b showed certain anti-proliferative activities against the four cell lines, in which compounds 2, 4 and 9b exhibited especially more potent activities. The structure-activity relationships of these compounds were simply discussed.

Anti-depressive activities and biotransformation of timosaponin B-III and its derivatives.

Timosaponin B-III (TB-III) is a steroidal saponin isolated from the rhizome of Anemarrhenae asphodeloides (Liliaceae). The biotransformation of TB-III by ß-glucosidase was investigated. Three biotransformation products were isolated and their structures were identified as timosaponin B-III-a (M1), (20R,25S)-5ß-spirostane-3ß-ol-3-O-ß-D-glucopyranosyl-(1 → 2)-ß-D-galacopyanoside (M2) and timosaponin AIII (M3). Then the four compounds were evaluated for their anti-depressive activity in mice by the open field test, tail suspension test and forced swimming test. As a result, TB-III, M1 and M3 exhibited modest anti-depressive activity. Structure-activity relationships were investigated and the preliminary conclusions are summarised as follows: the glycosyl at C-3 and C-26 can increase the activity, the double bond between C-20 and C-22 might be important for the anti-depressive activity, the R-configuration at C-22 and S-configuration at C-20 are necessary for its anti-depressive activity.

Development of polymorphic microsatellite markers for Phyllostachys edulis (Poaceae), an important bamboo species in China.

PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for Phyllostachys edulis (Poaceae), an ecologically and economically important bamboo species in China, to evaluate the genetic diversity and population genetic structure of P. edulis and other Phyllostachys species. • METHODS AND RESULTS: Twenty microsatellite markers were developed and their polymorphisms were tested on 71 samples from three geographically disparate populations. Each locus exhibited between two and 10 alleles with an average of five alleles. Excluding monomorphic loci, observed and expected heterozygosity ranged from zero to one and from 0.041 to 0.676, respectively. • CONCLUSIONS: These 20 polymorphic microsatellite loci will be useful for studies on the molecular ecology, population genetics, and conservation of P. edulis.

Characterization of multiple absorbed constituents in rats after oral administration of Paederia scandens decoction.

Paederia scandens (Lour.) Merri. (Jishiteng in Chinese) is a Chinese traditional medicine widely used in treating various diseases. However, its active components have remained unknown. In the present study, a rapid and sensitive method by high-performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-MSn) techniques was employed to investigate the absorbed constituents in rats after oral administration of Paederia scandens decoction. By comparing their MS data with those of authentic compounds and published data, a total of six compounds (paederosid, 1; paederosidic acid, 2; paederosidic acid methyl ester, 3; 6-hydroxy geniposide, 4; asperuloside, 5; and deacetyl asperuloside, 6) were identified in the P. scandens decoction samples. In addition, a total of seven compounds, including three iridoid glucosides and four of their metabolites, were identified in rat urine samples after administration. In addition, six compounds, including four iridoid glucosides and two of their metabolites, were identified in rat serum samples after administration. Our results significantly narrow the range of potentially active compounds in P. scandens decoction, and build a solid foundation for future research on its mechanism.

[Hepatoprotective effects of Gentiana scabra on the acute liver injuries in mice].

OBJECTIVE: To study the hepatoprotective effect of the aerial parts and the roots of G. scabra on cute liver injury models. METHOD: Acute liver injury models were induced by CCl4, TAA and D-GlanN in mice, and the levels of serum enzyme ALT, AST and AKP on acute liver injury mice with extracts of theaerial parts and the roots of G. scabra were determined. RESULT: Different dosages of theaerial part extract could significantly reduce the levels of serum enzyme ALT, AST and AKP (P < 0.05) on CCl4 and TAA model mice, but the serum enzymes reduction of D-GlanN model mice was not remarkably. CONCLUSION: The methanolic extracts of the aerial parts and the roots of G. scabra both have certain hepatoprotective effects on acute liver injury models, and so the aerial parts of G. scabra can be used as the succedaneumm of G. scabra roots.