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There are rich oil and gas resources in Alberta oil sand mining area in Canada. Since the 1960s, the Canadian government decided to increase the mining intensity. However, the exploitation will bring many adverse effects. In recent years, more people pay attention to the environmental protection and ecological restoration of mining area, such as issues related with changes of vegetated lands. Thus, the authors used the Landsat-5 TM and Landsat-8 OLI remote sensing images as the basic data sources, and obtained the land cover classification maps from 1995 to 2020 by ENVI. Based on the NDVI, NDMI and RVI, three images in each period are processed and output to explore the long-term impact of exploitation. The results show that from 1995 to 2020, the proportion of vegetation around mining areas decreased sharply, the scale of construction land in the mining area increased, and the vegetated land was changed to land types such as tailings pond, oil sand mine and other land types. In addition, three vegetation indexes decreased from 1995 to 2020. Although the exploitation of oil sand mining area brings great economic benefits, the environmental protection (especially vegetation) in oil sand mining areas should be paid more attention.

PDF file - 114K, Supplemental Figure 5 Cellular distribution of HIF-2alpha under normal oxygen conditions. (a) Representative confocal microscopy images (magnification 400x) showing HIF-2α or Nox4 immunofluorescense, DAPI nuclear staining, or merged images. b) Control (NS) or Nox4 shRNA (KD) cells were imaged following exposure to TEMPOL (0.25 mM), DTT (1mM). c) 786-0 NS cells imaged following transduction with Ad-GFP or Ad-MnSOD. d) 786-0 cells expressing pcDNA-Nox4 imaged with or without treatment with TEMPOL (0.25 mM).

PDF file - 376K, Supplemental Figure 2. Characterization of 786-0 cells stably transfected with the human, full-length Nox4 cDNA. (a) Morphology of 786-0 cells following exogenous expression of Nox4 reveals smaller, denser, more-rounded appearance relative to parental 786-0 cells. (b) Cell viability assay. Equal numbers of untransfected cells or 786-0 Nox4 cells were plated in 96-well plates. After attachment, assay reagent was added, incubated at 37{degree sign}C, and the fluorescent signal read at 590 nm.

PDF file - 224K, Supplemental Figure 1. Quantitative RT-PCR (a) and semi-quantitative RT-PCR (b) for detection of Nox1 in 786-0, RCC4 or LNCaP prostate cancer cells using two published primer pairs(14, 17),. Error bar represents +/- SE.

PDF file - 183K, Supplemental Figure 4. Cytotoxicity was measured by CellTiter-Blue (Promega, Madison, WI). 786-0 NS cells were plated at 1 x 104 cells per well in 96-well plates. After 24 hours, dithiothreitol was added as indicated in 5 replicate wells. 20 �l of the CellTiter-Blue reagent was added to each well and viability quantitated by spectrofluorometer (Spectra Max Plus384, Molecular Devices) and expressed as percentage of viability of media-only controls. Error bars indicate +/- S.E. mean.

Most sporadically occurring renal tumors include a functional loss of the tumor suppressor von Hippel Lindau (VHL). Development of VHL-deficient renal cell carcinoma (RCC) relies upon activation of the hypoxia-inducible factor-2α (HIF2α), a master transcriptional regulator of genes that drive diverse processes, including angiogenesis, proliferation, and anaerobic metabolism. In determining the critical functions for HIF2α expression in RCC cells, the NADPH oxidase NOX4 has been identified, but the pathogenic contributions of NOX4 to RCC have not been evaluated directly. Here, we report that NOX4 silencing in VHL-deficient RCC cells abrogates cell branching, invasion, colony formation, and growth in a murine xenograft model RCC. These alterations were phenocopied by treatment of the superoxide scavenger, TEMPOL, or by overexpression of manganese superoxide dismutase or catalase. Notably, NOX4 silencing or superoxide scavenging was sufficient to block nuclear accumulation of HIF2α in RCC cells. Our results offer direct evidence that NOX4 is critical for renal tumorigenesis and they show how NOX4 suppression and VHL re-expression in VHL-deficient RCC cells are genetically synonymous, supporting development of therapeutic regimens aimed at NOX4 blockade. Cancer Res; 74(13); 3501–11. ©2014 AACR.

PDF file - 98K, Supplemental Figure 3. Lucigenin chemiluminescence assay for superoxide detection performed as described in materials and methods on a) isolated membrane fractions from parental 786-0, RCC4 and Caki-1 cells or isolated cell fractions from 786-0 (b) or RCC4 (c) cells. RLU: relative light units.

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PDF file - 446K, Supplemental Figure 6 Immunohistochemistry for Nox4 and HIF-2alpha in 786-0 NS and KD xenograft explants confirms re-expression of Nox4 in KD tumors with corresponding elevated HIF-2alpha expression. Magnification 200X.

s: Purpose: As COVID-19 spreads globally and affects people's health, there are concerns that the pandemic and control policies may have psychological effects on young people (age from 17 to 35 years). This psychological impact might vary in different countries, and thus we compared the prevalence of self-reported psychological distress, loneliness and posttraumatic stress symptoms (PTSS) among young people in the United Kingdom (UK) and China at the beginning of the COVID-19 pandemic. Methods: Data of this study came from two sources. One source was the first wave of COVID-19 study in Understanding Society, a special wave of the UK household longitudinal study, which provided the high-quality, national-wide representative panel data. The sample comprised 1054 young people. The other source was an online survey on the mental health of 1003 young people from Shanghai, a highly developed area in China. The questionnaire included questions on the prevalence of common mental disorders (cut-off score ≥ 4), loneliness and potential PTSS (cut-off ≥ 33). Univariable analyses were conducted to test the differences in the self-reported prevalence of psychological distress and loneliness between the two groups. Multivariable logistic regression analyses were run to explore the predictors of psychological distress and loneliness among all the young people from England and Shanghai. Results: Among the samples with self-reported psychological distress, the UK sample accounted for 34.4% (n=1054) and the Chinese sample accounted for 14.1% (n=1003). The difference between the two groups was statistically significant (p

The enhanced photocatalytic hydrogen evolution performance of g-C3N4–Co3O4 2D–1D Z-scheme heterojunctions was achieved by employing the cobalt ion redox and conductive polymers (polyaniline, PANi) for the first time. Specifically, a Co3O4 1D nanobelt acting as the Z-scheme heterostructure component could promote the separation of photo-excited charge carriers and increased the redox capacity, and the conductive PANi brought about the boosted transport efficiency of the charge carriers. Notably, cobalt ions were adopted as the intermediate of the electron transfer between two components for boosting the carrier transport and utilization efficiency. Consequently, the Co3O4 nanobelt, PANi and cobalt ions exhibited a synergistic effect on facilitating the photocatalytic HER performance of the g-C3N4-based heterostructure, and the optimal ternary heterostructure (g-C3N4–PANi–Co3O4) exhibited a photocatalytic H2-evolution rate of 4.61 μmol h−1 under visible light, which further increased to 9.95 μmol h−1 by adding Co2+ solution owing to the further facilitated transport of charge carriers through the redox reaction of cobalt ions. Moreover, even in the absence of sacrificial agents, this Z-scheme system exhibited a photocatalytic hydrogen production activity of 3.35 μmol h−1 in the Co2+ aqueous solution under UV-visible light.

The phosphomolybdic acid hydrate (PMo12)-based g-C3N4-PANI-MoS2 with the conductive polyaniline mediator and the nanosized MoS2 cocatalyst were designed and in situ fabricated onto earth-abundant a...

Overweight and obesity are associated with many chronic diseases. This study aimed to clarify the possible effects of consuming golden kiwifruit as daily fruit intake on body composition, lipid metabolism and inflammatory responses. METHODS We recruited twenty-two overweight and obese subjects and they were asked to consume two golden kiwifruit every day during the 6-wk experimental period. At the baseline and end of the study, fasting blood samples were collected and anthropometric and blood pressure measurement were conducted. RESULTS During the experimental period, no adverse effect and dropout were reported. At the end of the study, a significant decrease in body fat and circulatory tumor necrosis factor (TNF)-α concentration were found. In addition, there was a reduction of angiotensin II (AgII) concentration and systolic blood pressure in subjects with baseline systolic blood pressure (SBP) ≥125 mmHg. CONCLUSION Our results suggested that daily golden kiwifruit intake can reduce body fat mass, improve blood pressure and regulating inflammatory responses in overweight and obese young adults.

A rational design of the morphology and configuration of the photocatalyst heterostructure is of great importance for solar energy conversion. This work reported the uniform distribution of CdS nanoparticles over the MOF-derived porous NiO skeleton, thanks to the PVP surface modification, with the residual carbon acting as a conductive medium of charge carriers. The formation of CdS-porous NiO exhibited an excellent photocatalytic hydrogen evolution activity of 7.12 mmol h−1 g−1, and was further improved to 14.25 mmol h−1 g−1 after the PVP surface modification. Impressively, even in the absence of a sacrificial agent, the well-dispersed CdS–NiO heterostructure exhibited a photocatalytic hydrogen production activity of 29.92 and 6.83 μmol h−1 g−1 with the production of a considerable amount of H2O2 under UV-visible and visible light irradiation, respectively.

The development of earth-abundant cocatalysts with confined size on suitable conductive supports is of high importance for facilitating solar energy conversion using semiconductors. In this work, a green redox relay reaction between FeCl3 and a pyrrole (Py) monomer was developed for the synthesis of g-C3N4–PPy–FeP, in which FeCl3 realized the formation of PPy over graphitic carbon nitride, and the as-formed PPy confined and tightly supported Fe ions, which were then transformed into the nanosized FeP of diameter less than 5 nm. A highly porous morphology was obtained by inserting well-dispersed g-C3N4 into PPy, accompanied by conductive PPy and nanosized FeP acting as a mediator of charge carriers and high-performance cocatalyst, respectively. Consequently, optimal g-C3N4–PPy–FeP demonstrated a photocatalytic hydrogen evolution activity 6 and 20 times larger than that of g-C3N4 singly loaded separately with PPy and FeP, respectively, under visible light irradiation.

The g-C3N4-MoS2-M(OH)x ternary heterostructures were designed and fabricated for the first time. The embedding of noble-metal-free MoS2-M(OH)x dual cocatalysts over g-C3N4 nanosheets led to obvious synergistic effect for improving the transport as well as utilization efficiency of photo-generated charge carriers. Consequently, the optimal ternary heterostructure (g-C3N4-MoS2-Ni(OH)2) exhibited photocatalytic hydrogen production activity 4.5 times larger than the sum of the photocatalytic HER activity of g-C3N4-MoS2 and g-C3N4-Ni(OH)2. More significantly, even in the absence of the sacrificial agent, the g-C3N4-MoS2-Ni(OH)2 ternary heterostructure exhibited a photocatalytic HER activity of 0.3 mmol h-1 g-1 with considerable H2O2 production under UV-visible light.

Single-molecule magnets (SMMs) with higher nuclearity provide opportunity for understanding the inherent nature of magnetic dynamics that are not limited to mononuclear SMMs. Herein, centrosymmetric [Dy2(L)2(9-AC)4(MeOH)2]·2CH2Cl2·2H2O (1, where 9-AC = anthracene-9-carboxylate) and equilateral triangular [Dy3(OH)(OMe)(L)3(dbm)3](OH)·3CH2Cl2·7H2O (2, where dbm = dibenzoylmethane anion) were isolated using the Schiff-base ligand 4-(anthracen-9-yl)-2-((quinolin-8-ylimino)methyl)phenol (HL). Static and dynamic magnetic measurements reveal that 1 and 2 display slow magnetic relaxation under zero and applied dc field, respectively. The magnetization relaxation for 1 is dominated by a Raman process due to its non-negligible transverse anisotropy. Complex 2 exhibits field-induced SMM behavior with a reversal barrier of 56 cm-1. By means of ab initio calculations and magnetic measurements, the multiple relaxation regime in 2 was investigated. We suggest that Orbach and Raman mechanisms dominate in the high/low temperature domains, respectively.

Glucose-derived porous activated carbon materials (AGC-600-4 and AGC-180-x) are prepared using ZnCl2 as the etching agent via impregnation treatment and hydrothermal method followed by the calcination process. The analytic results indicate that the obtained materials exhibit higher specific surface area and superior double-layer capacitive behavior than the corresponding pristine carbon (GC-600 and GC-180) when used as electrode materials for supercapacitors. Moreover, compared with the AGC-600-4 nanosheets, the optimal AGC-180-4 microspheres have a high specific surface area of 1713 m2 g−1 and a maximum specific capacitance of 235.9 F g−1 at a current density of 1.0 A g−1 in the three-electrode system. Meanwhile, AGC-180-4 also exhibits better capacitive properties than AGC-600-4 in the two-electrode system, showing an excellent cyclic stability with a high energy density of 24.63 Wh kg−1 at the power density of 949.5 W kg−1. It is thus demonstrated that AGC-180-4 could be ideal electrode materials for supercapacitor due to its unique etched spherical structure and excellent electrochemical properties.

Background The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. Results We tested symbiont cell proliferation and life stage changes in vitro in response to different nutrient-limiting conditions to determine the key nutrients and to compare the respective symbiont transcriptomic profiles to cells in hospite. We then examined the effects of nutrient repletion on symbiont proliferation in coral hosts and quantified life stage transitions in vitro using time-lapse confocal imaging. Here, we show that symbionts in hospite share gene expression and pathway activation profiles with free-living cells under nitrogen-limited conditions, strongly suggesting that symbiont proliferation in symbiosis is limited by nitrogen availability. Conclusions We demonstrate that nitrogen limitation not only suppresses cell proliferation but also life stage transition to maintain symbionts in the immobile coccoid stage. Nutrient repletion experiments in corals further confirmed that nitrogen availability is the major factor limiting symbiont density in hospite. Our study emphasizes the importance of nitrogen in coral-algae interactions and, more importantly, sheds light on the crucial role of nitrogen in symbiont life history regulation.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)—an established ecological model for studying the phenotypic effects of natural and artificial selection—and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32–1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ∼23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

We herein develop a selective phosphoranation of alkynes with phosphonium cation, which directs a concise approach to isoquinolines from unactivated alkyne and nitrile feedstocks in a single step. Mechanistic studies suggest that the annulation reaction is initiated by the unprecedented phosphoranation of alkynes, thus representing a unique reaction pattern of phosphonium salts and distinguishing it from existing protocols that largely rely on the utilization of highly functionalized imines/oximes and/or highly polarized alkynes.

The characteristics of the built environment and the configuration of public facilities can affect the health and well-being of older adults. Recognizing the range of daily activities and understanding the utilization of public facilities among older adults has become essential in planning age-friendly communities. However, traditional methods are unable to provide large-scale objective measures of older adults’ travel behaviors. To address this issue, we used the smartphone-based global positioning system (GPS) trajectory to explore the activity spaces of 76 older adults in a high-density urban community in Shanghai for 102 consecutive days. We found that activity spaces are centered around older adults’ living communities, with 46.3% within a 1.5 km distance. The older adults’ daily activities are within a 15 min walking distance, and accessibility is the most important factor when making a travel choice to parks and public facilities. We also found that the travel range and spatial distribution of points of interest are different between age and gender groups. In addition, we found that using a concave hull with Alpha shape algorithm is more applicable and robust than the traditional convex hull algorithm. This is a unique case study in a high-density urban area with objective measures for assessing the activity spaces of older adults, thus providing empirical evidence for promoting healthy aging in cities.

Laser-induced breakdown spectroscopy (LIBS) is a rapid, no-sample preparation, remote detection method that has been applied widely in the area of heavy metal detection in the soil. However, the promotion of LIBS is limited by its disadvantages, such as low precision analysis, a high detection limit, and so on. In recent years, many studies have been conducted to improve the LIBS spectral intensity. The double-pulse LIBS (DP-LIBS) is a representative technology in this area. Most of the research work focuses on the analytical methods of DP-LIBS, including the spatial configuration, the inter-pulse time, and the effect of signal enhancement of the DP-LIBS. However, there are few reports about the effect of the energy proportion of the two lasers and the contribution of different laser energies on the signal enhancement, and the inter-pulse time under the conditions of different laser energies. Moreover, DP-LIBS is mostly evaluated by the enhancement factor of the spectral signal, and there are few reports on the quantitative analysis of double-pulse LIBS. This study, which mainly detects Cu, Ni, and Pb in the soil, focuses on the contribution of the signal enhancement by adjusting the energy ratio of the two lasers and the best inter-pulse time under the conditions of different laser energies. Then, quantitative analysis of spectral signals obtained by single-pulse LIBS (SP-LIBS) and DP-LIBS are performed based on the random forest (RF) model. The results demonstrate that DP-LIBS shows better analytical performance than SP-LIBS, the coefficients of determination (R2) of the test have great improvement, the root-mean-squared error (RMSE) is much decreased and the relative error is much improved. Thus, this study shows that DP-LIBS is an effective method for the quantitative analysis of heavy metals in the soil.

Near infrared (NIR) dyes are useful for in vivo optical imaging. Liposomes have been used extensively for delivery of diverse cargos, including hydrophilic cargos which are passively loaded in the aqueous core. However, most currently available NIR dyes are only slightly soluble in water, making passive entrapment in liposomes challenging for achieving high optical contrast. Methods: We modified a commercially-available NIR dye (IR-820) via one-step Suzuki coupling with dicarboxyphenylboronic acid, generating a disulfonated heptamethine; dicarboxyphenyl cyanine (DCP-Cy). DCP-Cy was loaded in liposomes and used for optical imaging. Results: Owing to increased charge in mildly basic aqueous solution, DCP-Cy had substantially higher water solubility than indocyanine green (by an order of magnitude), resulting in higher NIR absorption. Unexpectedly, DCP-Cy tended to form J-aggregates with pronounced spectral red-shifting to 934 nm (from 789 nm in monomeric form). J-aggregate formation was dependent on salt and DCP-Cy concentration. Dissolved at 20 mg/mL, DCP-Cy J-aggregates could be entrapped in liposomes. Full width at half maximum absorption of the liposome-entrapped dye was just 25 nm. The entrapped DCP-Cy was readily detectable by fluorescence and photoacoustic NIR imaging. Upon intravenous administration to mice, liposomal DCP-Cy circulated substantially longer than the free dye. Accumulation was largely in the spleen, which was visualized with fluorescence and photoacoustic imaging. Conclusions: DCP-Cy is simple to synthesize and exhibits high aqueous solubility and red-shifted absorption from J-aggregate formation. Liposomal dye entrapment is possible, which facilitates in vivo photoacoustic and fluorescence imaging around 930 nm.

The design of highly effective noble metal-free cocatalysts plays an extremely important role in improving the photocatalytic solar energy conversion. Herein, we designed and synthesized a novel heterostructure form of MoS2–transition metals (Fe, Co, and Ni) on g-C3N4 nanosheets for obtaining a significant enhancement in the photocatalytic activity for hydrogen production and pollutant disposal. The electrochemical characterization and time-resolved photoluminescence results indicated that the unique tunable feature of the MoS2–transition metals greatly reduced the hydrogen evolution reaction (HER) overpotential, increased the separation, transport and utilization efficiency of the photo-generated charge carriers, and displayed a synergistic effect in improving the electrocatalytic and photocatalytic HER performances. The ternary g-C3N4–MoS2–metals exhibited extremely high photocatalytic HER rates of 1.7, 4.1, and 5.12 mmol h−1 g−1 for g-C3N4–MoS2–Fe, g-C3N4–MoS2–Co and g-C3N4–MoS2–Ni, respectively, which were 2.7, 4.7 and 5.3 times larger than the sum of the photocatalytic HER activities of g-C3N4–MoS2 and the corresponding g-C3N4–metals. This work provides a facile and effective strategy for improving photocatalytic energy conversion using only earth-abundant non-noble cocatalyst heterostructures.

Rationally designing a photocatalytic system is of significance for effectively converting infinite solar energy into clean hydrogen energy. This study revealed that bulk modification of ZnCdS–CdS heterojunction via phosphorus doping and surface modulation by adopting the novel VS2 as the cocatalyst exhibited synergistic effects for improving the photocatalytic activity of the heterojunction. Notably, the photocatalytic hydrogen evolution rate of the pristine ZnCdS–CdS heterostructure raised from 25.46 to 72.82 and 52.82 μmol h−1 using only 5 mg photocatalyst with the bulk and surface modification alone, respectively, while the hydrogen evolution rate increased to 192.28 μmol h−1 with both bulk phosphorus doping and surface adoption of VS2, opening a new method for the improving the photocatalytic activity by both bulk and surface modulation.

Switched Reluctance Motor (SRM) is a new type of high technology motor used in the most advanced warplanes. This paper combines the principle of SRM and takes the typical SRM power generation system of modern warplanes as an example to analyze the functions and power generation process of each part of the system, as well as its effective power generation conditions.

Glutathione is overexpressed in tumor cells and regulates cancer growth, metastasis, and drug resistance. Therefore, detecting glutathione levels may greatly facilitate cancer diagnosis and treatment response monitoring. Photoacoustic (PA) imaging is a noninvasive modality for high-sensitivity, high-resolution, deep-tissue optical imaging. Switchable PA probes that offer signal on/off responses to tumor targets would further improve the detection sensitivity and signal-to-noise ratio of PA imaging. Here, we explore the use of MnO2 nanotubes as a switchable and biodegradable PA probe for dynamic imaging of glutathione in cancer. Glutathione reduces black MnO2 nanotubes into colorless Mn2+ ions, leading to decreased and signal off PA amplitude. In phantoms, we observed a linear response of reduced PA signals of MnO2 nanotubes to increased glutathione concentrations. Using melanoma as the disease model, we demonstrated that MnO2 nanotube-based PA imaging of glutathione successfully distinguished B16F10 melan...

Background Intestinal barrier dysfunction is a significant clinical problem, commonly developing in a variety of acute or chronic pathological conditions. Herein, we evaluate the effect of microRNA-31 (miR-31) on intestinal barrier dysfunction through NF-κB/HIF-1α pathway by targeting HMOX1 in rats with sepsis. Methods Male Sprague-Dawley rats were collected and divided into the sham group, and the cecum ligation and perforation group which was subdivided after CACO-2 cell transfection of different mimic, inhibitor, or siRNA. Levels of serum D-lactic acid, diamine oxidase and fluorescence isothiocyanate dextran, FITC-DX concentration, and bacterial translocation were detected. Superoxidedismutase (SOD) activity and malondialdehyde (MDA) content were evaluated using the colorimetric method and an automatic microplate reader, respectively. Additionally, the levels of tumor necrosis factor, interleukin (IL)-6, and IL-10 were tested using enzyme-linked immunosorbent assay. The expression of miR-31, HMOX1, NF-κB, HIF-1α, IκB, ZO-1 and Occludin were assessed by reverse transcription quantitative polymerase chain reaction and Western blot analysis. Results Inhibition of miR-31 decreased intestinal mucosal permeability and intestinal barrier function. The increased levels of miR-31 could cause oxidative damage and affect the expression of inflammatory factors in intestinal tissue of rats. HMOX1 was confirmed as a target gene of miR-31. MiR-31 affected intestinal mucosal permeability and intestinal barrier function, as well as oxidative damage and inflammation level by regulating HMOX1. Down-regulation of miR-31 inhibited NF-κB/HIF-1α pathway related genes by regulating HMOX1 expression. Furthermore, inhibition of miR-31 increased survival rates of rats. Conclusion Overall, the current study found that inhibition of miR-31 protects against intestinal barrier dysfunction through suppression of the NF-κB/HIF-1α pathway by targeting HMOX1 in rats with sepsis.

Structural variants can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of structural variants in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify structural variants in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of non-coding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel 3D chromatin structural domains. Our results indicate that non-coding structural variations may be underappreciated mutational drivers in cancer genomes.

Bimetallic zeolite-imidazole frameworks with controllable flat band position, band gap and hydrogen evolution reaction characteristics were adopted as a photocatalytic hydrogen production catalyst. Furthermore, the g-C3N4–MoS2 2D–2D surface heterostructure was introduced to the ZnM-ZIF to facilitate the separation as well as utilization efficiency of the photo-exited charge carriers in the ZnM-ZIFs. On the other hand, the ZnM-ZIFs not only inhibited the aggregation of the g-C3N4–MoS2 heterostructure, but also improved the separation and transport efficiency of charge carriers in g-C3N4–MoS2. Consequently, the optimal g-C3N4–MoS2–ZnNi-ZIF exhibited an extraordinary photocatalytic hydrogen evolution activity 214.4, 37.5, and 3.7 times larger than that of the pristine g-C3N4, g-C3N4–ZnNi-ZIF and g-C3N4–MoS2, respectively, and exhibited a H2-evolution performance of 77.8 μmol h−1 g−1 under UV-Vis light irradiation coupled with oxidation of H2O into H2O2. This work will furnish a new MOF candidate for photocatalysis and provide insight into better utilization of porous MOF-based heterostructures for hydrogen production from pure water.

Dinoflagellates are main primary producers in the oceans, the cause of algal blooms and endosymbionts of marine invertebrates. Much remains to be understood about their biology, including their peculiar crystalline chromosomes. We assembled 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum and analyzed their organization. Genes are enriched towards the ends of chromosomes and are arranged in alternating unidirectional blocks. Some chromosomes are enriched for genes involved in specific biological processes. The chromosomes fold as linear rods and each is composed of a series of structural domains separated by boundaries. Domain boundaries are positioned at sites where transcription of two gene blocks converges and disappear when cells are treated with chemicals that block transcription, indicating correlations between gene orientation, transcription and chromosome folding. The description of the genetic and spatial organization of the S. microadriaticum genome provides a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes., Genome assembly of the coral endosymbiont Symbiodinium microadriaticum shows that genes are arranged in alternating unidirectional blocks and are enriched at the ends of chromosomes. Chromosomes are composed of structural domains separated by boundaries that disappear when transcription is blocked.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

Type 1 diabetes (T1D) is an incurable disease that affects 1. 25 million Americans. Diabetic patients typically rely on subcutaneous insulin infusions to regulate their glucose levels. A major contributor to their blood glucose levels is the amount of sugar intake, which cannot be easily tracked. While ultrasound imaging has been used to investigate the relationship between food characteristics and tongue movement, the technique utilized a bulky transducer array that cannot be translated into daily monitoring. Capitalizing on advanced electronics and data processing technologies, we developed a portable system that utilizes only a single ceramic disk to quantify the tongue movement in response to various levels of sweetness. After acquiring 32 subject datasets, we found a significant correlation between food sweetness and tongue movement. Our system can potentially be miniaturized into a wearable device for monitoring sugar intake, which will ultimately help T1D patients to better monitor and control their blood glucose levels and balance their diets accordingly.

Dinoflagellates are major primary producers in the world’s oceans, the cause of harmful algal blooms, and endosymbionts of marine invertebrates. Much remains to be understood about their biology including their peculiar crystalline chromosomes. Here we used Hi-C to order short read-based sub-scaffolds into 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum. Hi-C data show that chromosomes are folded as linear rods within which loci separated by up to several Mb are highly packed. Each chromosome is composed of a series of structural domains separated by boundaries. Genes are enriched towards the ends of chromosomes and are arranged in unidirectional blocks that alternate between top and bottom strands. Strikingly, the boundaries of chromosomal domains are positioned at sites where transcription of two gene blocks converges, indicating a correlation between gene orientation, transcription and chromosome folding. Some chromosomes are enriched for genes involved in specific biological processes (e.g., photosynthesis, and nitrogen-cycling), and functionally related genes tend to co-occur at adjacent sites in the genome. All chromosomes contain several repeated segments that are enriched in mobile elements. The assembly of the S. microadriaticum genome and initial description of its genetic and spatial organization provide a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.

Functional intestinal imaging holds importance for the diagnosis and evaluation of treatment of gastrointestinal diseases. Currently, preclinical imaging of intestinal motility in animal models is performed either invasively with excised intestines or noninvasively under anesthesia, and cannot reveal intestinal dynamics in the awake condition. Capitalizing on near-infrared optics and a high-absorbing contrast agent, we report the Trans-illumination Intestine Projection (TIP) imaging system for free-moving mice. After a complete system evaluation, we performed in vivo studies, and obtained peristalsis and segmentation motor patterns of free-moving mice. We show the in vivo typical segmentation motor pattern, that was previously shown in ex vivo studies to be controlled by intestinal pacemaker cells. We also show the effects of anesthesia on motor patterns, highlighting the possibility to study the role of the extrinsic nervous system in controlling motor patterns, which requires unanesthetized live animals. Combining with light-field technologies, we further demonstrated 3D imaging of intestine in vivo (3D-TIP). Importantly, the added depth information allows us to extract intestines located away from the abdominal wall, and to quantify intestinal motor patterns along different directions. The TIP system should open up avenues for functional imaging of the GI tract in conscious animals in natural physiological states., Current preclinical imaging of intestine in animal models cannot reveal intestinal dynamics in awake condition. Here the authors report a Transillumination Intestine Projection (TIP) imaging system for free-moving mice, and showed the intestine dynamics in conscious animal in natural physiological states.

Xist represents a paradigm for the function of long non-coding RNA in epigenetic regulation, although how it mediates X-chromosome inactivation (XCI) remains largely unexplained. Several proteins that bind to Xist RNA have recently been identified, including the transcriptional repressor SPEN1-3, the loss of which has been associated with deficient XCI at multiple loci2-6. Here we show in mice that SPEN is a key orchestrator of XCI in vivo and we elucidate its mechanism of action. We show that SPEN is essential for initiating gene silencing on the X chromosome in preimplantation mouse embryos and in embryonic stem cells. SPEN is dispensable for maintenance of XCI in neural progenitors, although it significantly decreases the expression of genes that escape XCI. We show that SPEN is immediately recruited to the X chromosome upon the upregulation of Xist, and is targeted to enhancers and promoters of active genes. SPEN rapidly disengages from chromatin upon gene silencing, suggesting that active transcription is required to tether SPEN to chromatin. We define the SPOC domain as a major effector of the gene-silencing function of SPEN, and show that tethering SPOC to Xist RNA is sufficient to mediate gene silencing. We identify the protein partners of SPOC, including NCoR/SMRT, the m6A RNA methylation machinery, the NuRD complex, RNA polymerase II and factors involved in the regulation of transcription initiation and elongation. We propose that SPEN acts as a molecular integrator for the initiation of XCI, bridging Xist RNA with the transcription machinery-as well as with nucleosome remodellers and histone deacetylases-at active enhancers and promoters.

Liver vessels provide lots of important information for liver-disease diagnosis and liver surgery. This paper presents an effective liver vessel segmentation method from abdominal computer tomography angiography (CTA) images. The proposed method applies two techniques including centerline constraint and intensity model for effective detection of liver vessels, in which the former aims at generating the position and distance restraints for the detection of thin vessels by the offset medialness filter and height ridge traversal algorithm, while the latter is mainly used to extract intensity feature for the detection of thick vessels based on Kernel Fuzzy C-Means (KFCM). And then, the centerline constraint and intensity model are integrated into graph cuts for ultimate liver vessel segmentation. The proposed method does not require any manual selection of the initial vessel regions, and is capable of dealing with complex liver vessel systems. The experimental results on clinical CTA data sets give an average accuracy, sensitivity, and specificity of 97.4%, 83.0%, and 98.1%, respectively, which show the efficiency of the proposed method on liver vessel segmentation.

Segmenting liver tumors from computed tomography (CT) images plays a very important role in computer-aided diagnosis, surgical planning, and treatment monitoring. However, accurate and robust segmentation of the tumors remains a challenging issue, due to low contrast and vague boundaries between the tumors and surrounding tissues as well as the wide variations of the tumors in intensity, shape, and location across patients. In this paper, we developed an effective method for liver tumor segmentation with adaptive region growing and graph cuts. First, initial segmentation results for liver tumors and the regions of interest (ROIs) that contain the tumors are extracted by adaptive region growing with a manual selected seed specified for each tumor region. Then, the ROIs are enhanced by Gaussian fitting based nonlinear mapping according to the intensity distributions of the initially segmented tumor regions. Finally, the enhanced information combined with gradient information is integrated into graph cuts to extract the tumors from the ROIs effectively and accurately. The method is non-sensitive to noise and does not involve a pre-segmentation of liver or a complicated and tedious procedure of training. Results on 3Dircadb dataset demonstrate that the method achieves much better comprehensive performance on liver tumor segmentation compared with many art-of-state methods and has a huge advantage in segmenting the tumors with low contrast, small size, and weak boundaries.

In computer vision, superpixel segmentation has been widely used as a very important preprocessing to reduce the number of image primitives for subsequent image processing tasks. To improve the segmentation accuracy and the robustness to noise, a hierarchical multi-level segmentation framework is developed in this paper. First, original image is initially segmented by a local information based simple liner iterative clustering (LI-SLIC) method. Then, the initial generated superpixels are further segmented hierarchically by LI-SLIC to ensure that all pixels contained within each superpixel belong to a same object. Finally, to eliminate over-segmentation and reduce the number of superpixels, adjacent superpixels belonging to a same object are merged based on the probability distribution similarity. The proposed method does not require setting the seeds or number of the superpixels to be generated in advance, which can segment image into an appropriate number of superpixels without under- or over- segmentation automatically according to its content. Experiments are conducted on two public datasets Berkeley and 3Dircadb, and the results demonstrate that our method is more effective and accurate than many existing superpixel methods and shows a great advantage in dealing with images corrupted by various noises.

Density-peak clustering is used to segment initial slice automatically.The pixel-, patch-based and inter-slice based features are used for segmentation.A novel automatic vessel compensation method is proposed based on border marching.Our method can segment livers with low contrast, varying shapes and intensities.Our method outperforms many existing methods on liver segmentation. Background and ObjectiveIdentifying liver regions from abdominal computed tomography (CT) volumes is an important task for computer-aided liver disease diagnosis and surgical planning. This paper presents a fully automatic method for liver segmentation from CT volumes based on graph cuts and border marching. MethodsAn initial slice is segmented by density peak clustering. Based on pixel- and patch-wise features, an intensity model and a PCA-based regional appearance model are developed to enhance the contrast between liver and background. Then, these models as well as the location constraint estimated iteratively are integrated into graph cuts in order to segment the liver in each slice automatically. Finally, a vessel compensation method based on the border marching is used to increase the segmentation accuracy. ResultsExperiments are conducted on a clinical data set we created and also on the MICCAI2007 Grand Challenge liver data. The results show that the proposed intensity, appearance models, and the location constraint are significantly effective for liver recognition, and the undersegmented vessels can be compensated by the border marching based method. The segmentation performances in terms of VOE, RVD, ASD, RMSD, and MSD as well as the average running time achieved by our method on the SLIVER07 public database are 5.83.2%, -0.14.1%, 1.00.5mm, 2.01.2mm, 21.29.3mm, and 4.7 minutes, respectively, which are superior to those of existing methods. ConclusionsThe proposed method does not require time-consuming training process and statistical model construction, and is capable of dealing with complicated shapes and intensity variations successfully.

Metal-organic framework-templated g-C3N4-NiCoP2-porous carbon (PC) ternary hybrid nanomaterials were designed by taking full advantage of the metal-organic framework (MOF) derivative in the photocatalytic reaction for the first time. The MOF-templated porous structure could prevent the stacking of the carbon nitride nanosheet, and the carefully designed NiCoP2, possessing low electrocatalytic hydrogen evolution reaction (HER) overpotential and flat-band potential, could improve the separation as well as the utilization efficiency of photogenerated electron-hole pairs. Moreover, the ligand-templated porous carbon, acting as an interface mediator between g-C3N4 and the NiCoP2 cocatalyst, could boost the charge carrier transport. Consequently, the optimal ternary g-C3N4-NiCoP2-PC heterostructure exhibited enhanced photocatalytic HER performance and considerable H2 evolution performance of 5.8 μmol/h/g under UV-visible light with stoichiometric H2O2 production even in pure water. This work took full advantage of the MOF derivative for improving the photocatalytic reaction activity and provided a method that can hopefully help in designing a novel high-performance catalyst for solar conversion.

Background Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Results Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments. Conclusions In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community. Electronic supplementary material The online version of this article (10.1186/s13059-019-1658-7) contains supplementary material, which is available to authorized users.

Glutathione is overexpressed in tumor cells and regulates cancer growth, metastasis, and drug resistance. Therefore, detecting glutathione levels may greatly facilitate cancer diagnosis and treatment response monitoring. Photoacoustic (PA) imaging is a noninvasive modality for high-sensitivity, high-resolution, deep-tissue optical imaging. Switchable PA probes that offer signal on/off responses to tumor targets would further improve the detection sensitivity and signal-to-noise ratio of PA imaging. Here, we explore the use of MnO