Search

Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including commensal, probiotic, pathogenic, and industrial bacteria, with >50% of target gene knockdown achieved in 12 bacterial species. For medical applications, virulence factors in Staphylococcus epidermidis and Klebsiella pneumoniae are knocked down to mitigate their virulence-associated phenotypes. For metabolic engineering applications, high performance Corynebacterium glutamicum strains capable of producing valerolactam (bulk chemical) and methyl anthranilate (fine chemical) are developed by combinatorial knockdown of target genes. A genome-scale sRNA library covering 2959 C. glutamicum genes is constructed for high-throughput colorimetric screening of indigoidine (natural colorant) overproducers. The BHR-sRNA platform will expedite engineering of diverse bacteria of both industrial and medical interest.

Days alive and out of hospital (DAOH) is a simple estimator based on the number of days not in hospital within a defined period. In cases of mortality within the period, DAOH is regarded as zero. It has not been validated solely in off-pump coronary artery bypass grafting (OPCAB). This study aimed to demonstrate a correlation between DAOH and outcome of OPCAB. We identified 2211 OPCAB performed from January 2010 to August 2016. We calculated DAOH at 30 and 60 days. We generated a receiver-operating curve and compared outcomes. The median duration of hospital stay after OPCAB was 6 days. The median DAOH values at 30 and 60 days were 24 and 54 days. The estimated thresholds for 3-year mortality for DAOH at 30 and 60 days were 20 and 50 days. Three-year mortality was higher for short DAOH (1.2% vs. 5.7% and 1.1% vs. 5.6% DAOH at 30 and 60 days). After adjustment, the short DAOH 30 group showed significantly higher mortality during 3-year follow-up (hazard ratio 3.07; 95% confidence interval 1.45–6.52; p = 0.004). DAOH at 30 days after OPCAB showed a correlation with 3-year outcomes. DAOH 30 might be a reliable long-term outcome measure that can be obtained within 30 days after surgery.

International audience; The Gram-negative, oxidase-negative, catalase-positive, rod-shaped strain Arafor3T was isolated from forest soil (France). Comparative 16S rRNA gene analysis and phylogenetic analysis based on (1) multilocus sequence analysis (MLSA) with four housekeeping genes (atpD, gyrB, infB and rpoB) and (2) genomes indicated that strain Arafor3T shared 98.83% 16S rRNA gene sequence similarity with the type strain of Serratia fonticola DSM 4576T and was closely related to this same strain in the MLSA and in the phylogenomic tree reconstruction. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons of strain Arafor3T with its nearest neighbor S. fonticola DSM 4576T showed 93.5% identity and 55.7% sequence similarity, respectively, and were lower than the 96% and 70% species-level cut-off values relating to these analyses (Logan et al. in Int J Syst Evol Microbiol 59:2114–21, 2009, https://doi.org/10.1099/ijs.0.013649-0). The strain differed from S. fonticola in that it was urease and arginine dihydrolase negative. The major fatty acids of strain Arafor3T are C16:0, C16:1 ω7c/C16:1 ω6c, C14:0, C14:0 3-OH/16:1 isoI, and C18:1 ω7c. The major respiratory quinone is Q8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and 6 unknown lipids. The mol G + C% content of the genomic DNA of strain Arafor3T was 53.49%. Hence, Arafor3T represents a novel species within the genus Serratia, for which the name Serratia silvae sp. nov. is proposed. The type strain is Arafor3T (=LMG 32338T = CIP 111939T).

BACKGROUND AND AIMS Some hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients show undetectable serum HBV DNA levels at HCC diagnosis. The risk of HBV reactivation and its impact on clinical outcomes are not well-unknown. METHODS This retrospective cohort study included a total of 985 HBV-related HCC patients with undetectable serum HBV DNA levels (

Loss-of-function variant in the gene encoding the KCNQ4 potassium channel causes autosomal dominant nonsyndromic hearing loss (DFNA2), and no effective pharmacotherapeutics have been developed to reverse channel activity impairment. Phosphatidylinositol 4,5-bisphosphate (PIP2), an obligatory phospholipid for maintaining KCNQ channel activity, confers differential pharmacological sensitivity of channels to KCNQ openers. Through whole-exome sequencing of DFNA2 families, we identified three novel KCNQ4 variants related to diverse auditory phenotypes in the proximal C-terminus (p.Arg331Gln), the C-terminus of the S6 segment (p.Gly319Asp), and the pore region (p.Ala271_Asp272del). Potassium currents in HEK293T cells expressing each KCNQ4 variant were recorded by patch-clamp, and functional recovery by PIP2 expression or KCNQ openers was examined. In the homomeric expression setting, the three novel KCNQ4 mutant proteins lost conductance and were unresponsive to KCNQ openers or PIP2 expression. Loss of p.Arg331Gln conductance was slightly restored by a tandem concatemer channel (WT-p.R331Q), and increased PIP2 expression further increased the concatemer current to the level of the WT channel. Strikingly, an impaired homomeric p.Gly319Asp channel exhibited hyperactivity when a concatemer (WT-p.G319D), with a negative shift in the voltage dependence of activation. Correspondingly, a KCNQ inhibitor and chelation of PIP2 effectively downregulated the hyperactive WT-p.G319D concatemer channel. Conversely, the pore-region variant (p.Ala271_Asp272del) was nonrescuable under any condition. Collectively, these novel KCNQ4 variants may constitute therapeutic targets that can be manipulated by the PIP2 level and KCNQ-regulating drugs under the physiological context of heterozygous expression. Our research contributes to the establishment of a genotype/mechanism-based therapeutic portfolio for DFNA2., Hearing loss: genetically tailored treatment strategy for congenital deafness People with a certain type of inherited hearing loss may stand to benefit from a personalized, genetically tailored treatment strategy. A research team from South Korea led by Byung Yoon Choi from Seoul National University College of Medicine identified three new mutations in KCNQ4, a gene that encodes a potassium channel protein found in the inner ear, that can cause congenital deafness. Strikingly, the authors identified the first hyperactive KCNQ4 variant. They inserted these gene variants into human cells in culture, and found that drugs known to affect the activity of this channel protein had different effects on different mutations. Impairments caused by two of the variants were prevented by drug treatment; the third variant proved resistant to the same therapeutic approach. The authors propose further validating the therapeutic responsiveness of different KCNQ4 variants in genetically engineered mice.

This study was conducted to provide basic data for chemical accident response by assessing the health risks of residents living near a chemical accident site due to long-term exposure. The study considered the temporal concentration changes of the leaked chemical (i.e., its behavior in the environment and dilution) until its extinction. A virtual chemical accident was assumed, in which 40 t of formaldehyde was accidentally discharged for 1 h in Ulsan Metropolitan City, Korea. Formaldehyde concentrations over time in each environmental medium after the accident were calculated using a multimedia environmental dynamics model. Exposure subjects divided into four age groups were considered. Carcinogenic risks due to respiration and non-carcinogenic risks due to soil intake were assessed. For all the age groups, the excess cancer risk did not exceed 1.0 × 10-6, indicating that no harmful health impact was caused by inhalation exposure to formaldehyde. The hazard index exceeded 1 for all the age groups, confirming that harmful health impacts were caused by exposure to soil containing the formaldehyde. This study is the first to assess chronic health risks by reflecting long-term residual and temporal concentration changes of a pollutant released in a chemical accident in each environmental medium until its extinction. This work is also significant in that it reflects the exposure characteristics of the toxic chemical.

Metal–organic frameworks (MOFs)1–3 are known for their specific interactions with gas molecules4,5; this, combined with their rich and ordered porosity, makes them promising candidates for the photocatalytic conversion of gas molecules to useful products6. However, attempts to use MOFs or MOF-based composites for CO2 photoreduction6–13 usually result in far lower CO2 conversion efficiency than that obtained from state-of-the-art solid-state or molecular catalysts14–18, even when facilitated by sacrificial reagents. Here we create ‘molecular compartments’ inside MOF crystals by growing TiO2 inside different pores of a chromium terephthalate-based MOF (MIL-101) and its derivatives. This allows for synergy between the light-absorbing/electron-generating TiO2 units and the catalytic metal clusters in the backbones of MOFs, and therefore facilitates photocatalytic CO2 reduction, concurrent with production of O2. An apparent quantum efficiency for CO2 photoreduction of 11.3 per cent at a wavelength of 350 nanometres is observed in a composite that consists of 42 per cent TiO2 in a MIL-101 derivative, namely, 42%-TiO2-in-MIL-101-Cr-NO2. TiO2 units in one type of compartment in this composite are estimated to be 44 times more active than those in the other type, underlining the role of precise positioning of TiO2 in this system. Investigation of a chromium-based metal–organic framework shows that the location of added TiO2 inside specific mesopores strongly affects the ability of the material to catalyse photoreduction of CO2.

We investigated the expression profiles of immune genes in patients with triple-negative breast cancer (TNBC) to identify the prognostic value of immune genes and their clinical implications. NanoString nCounter Analysis of 770 immune-related genes was used to measure immune gene expression in patients with TNBC who underwent curative surgery followed by adjuvant chemotherapy at Samsung Medical Center between 2000 and 2004. Statistical analyses were conducted to identify the associations between gene expression and distant recurrence-free survival (DRFS). Of 1189 patients who underwent curative BC surgery, 200 TNBC patients were included and stage was the only clinical factor predictive of DRFS. In terms of immune genes, 155 of 770 genes were associated with DRFS (p

Propagation of gametophytes and sporophytes using mechanical fragmentation has been considered a suitable method for mass production of ferns. This study aimed to develop a practical propagation method for Lemmaphyllum microphyllum C. Presl, which is a fern of significant ornamental and medicinal value. Gametophytes were obtained through in vitro spore germination and used for propagation experiments. The gametophyte was mechanically fragmented using a scalpel into small fragments, which were then used to investigate gametophyte proliferation. In addition, the gametophyte was fragmented using a blender and then used to study sporophyte formation. Optimal proliferation conditions of the gametophyte were determined using Murashige and Skoog (MS) basal medium (double-, full-, half-, quarter-strength), Knop medium, and medium components (sucrose, nitrogen sources, activated charcoal), at various concentrations. The fresh weight of the gametophyte was 14-fold higher than that of gametophytes (300 mg) used as culture material, when cultured on double-strength MS. Moreover, 1 g of the gametophyte fragmented in 25 mL of distilled water formed more than 430 sporophytes in a soil mixture in an area of 7.5 cm2. The sporophytes were successfully cultivated in the greenhouse after acclimation. A large-scale production method for L. microphyllum that can be easily implemented in a fern production farm is outlined.

Background Liquid suspension culture efficiently proliferates plant cells and can be applied to ferns because it rapidly increases the fresh weight of gametophytes. This study assessed gametophyte proliferation and sporophyte production of Pteridium aquilinum var. latiusculum using a suspension culture method. Results The growth curve linear phase of gametophyte cells was confirmed between 9 and 18 days of culture, and the subculture cycle was determined to be 2 weeks. A double-strength MS medium (fresh weight, 18.0 g) containing 2% sucrose and NH4+:NO3− (120 mM, 40:80) was found to be the optimal liquid medium. Gametophytes obtained after suspension culture for 18 days did not normally form sporophytes in an ex vitro soil environment. However, this issue was resolved after changing the culture type or extending the culture period to 6 weeks. A short suspension culture period increased the fresh weight of fragmented and homogenized gametophytes but yielded numerous relatively immature gametophytes (globular forms of branching gametophytes, BG). Furthermore, differences in gametophyte morphogenesis and development were indicated by changes in endogenous phytohormone content. BG with immature development exhibited high accumulation of zeatin, jasmonic acid, and salicylic acid, and relatively low levels of abscisic acid and indole-3-acetic acid. The immature development of gametophytes directly affected sporophyte formation. Conclusions This study maximized the advantages of liquid suspension culture using eastern bracken gametophytes and provides data to resolve any associated issues, thus facilitating efficient bracken production.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome. ispartof: NATURE MICROBIOLOGY vol:4 issue:10 pages:1727-1736 ispartof: location:England status: published

Tissue culture methods using gametophytes are considered the easiest ways to mass-produce fern sporophytes. The aim of this study was to develop a practical propagation method for the ornamental fern, Athyrium sheareri. The gametophytes obtained from in vitro spore germination were used as experimental materials. We used the chopping method to investigate the culturing conditions for proliferating gametophytes and the blending method for evaluating the mass production of sporophytes in mixed soil. Gametophyte proliferation was determined via Knop medium, various concentrations of Murashige and Skoog (MS) basal medium (1, 1/2, 1/4), and media components (sucrose, nitrogen source, and activated charcoal). The fresh weight of the gametophytes increased by more than 24-fold in 1/2 MS medium. In addition, 1 g of gametophyte could produce a maximum of 255.3 sporophytes in a mixed soil of 7.5 cm2 area. Treating gametophytes with exogenous plant growth regulators promoted the formation and growth of sporophytes. The cultivated young sporophytes were acclimated and successfully grown in greenhouses. We developed a mass production protocol for A. sheareri sporophytes suitable for field application, which is expected to have commercial value.

Cheilanthes argentea (S.G. Gmel.) Kunze is a highly valued indigenous/endemic Korean bracken species used for ornamental purposes. In this study, we developed a practical proliferation method for mass production of C. argentea plants using tissue culture. The gametophyte proliferation using the chopping method produced gametophytes that were morphologically identical to those obtained from in vitro spore germination. This new method increased plant fresh weight by more than 40-fold, from 300 mg to 12.7 g, in Murashige and Skoog medium. A blending method was used to produce 74.3 sporophytes in 7.5-cm2 plastic pots using 1 g of gametophytes. Furthermore, addition of exogenous gibberellin promoted sporophyte development and growth, suggesting the possibility of controlling the number of sporophytes formed. However, further studies are needed to explain the effect of exogenous gibberellin, which is closely related to the sex-determining hormone antheridiogen, on the number of sporophytes and its mechanism of action. Our new tissue culture system is capable of mass proliferation of C. argentea gametophytes in vitro and the formation of sporophytes by ex vitro preparation using the generated gametophytes.

Wear debris-induced osteolysis leads to periprosthetic loosening and subsequent prosthetic failure. Since excessive osteoclast formation is closely implicated in periprosthetic osteolysis, identification of agents to suppress osteoclast formation and/or function is crucial for the treatment and prevention of wear particle-induced bone destruction. In this study, we examined the potential effect of pentamidine treatment on titanium (Ti) particle-induced osteolysis, and receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclastogenesis. The effect of pentamidine treatment on bone destruction was examined in Ti particle-induced osteolysis mouse model. Ti particles were implanted onto mouse calvaria, and vehicle or pentamidine was administered for 10 days. Then, calvarial bone tissue was analyzed using micro-computed tomography and histology. We performed in vitro osteoclastogenesis assay using bone marrow-derived macrophages (BMMs) to determine the effect of pentamidine on osteoclast formation. BMMs were treated with 20 ng/mL RANKL and 10 ng/mL macrophage colony-stimulating factor in the presence or absence of pentamidine. Osteoclast differentiation was determined by tartrate-resistant acid phosphatase staining, real-time polymerase chain reaction, and immunofluorescence staining. Pentamidine administration decreased Ti particle-induced osteoclast formation significantly and prevented bone destruction compared to the Ti particle group in vivo. Pentamidine also suppressed RANKL-induced osteoclast differentiation and actin ring formation markedly, and inhibited the expression of nuclear factor of activated T cell c1 and osteoclast-specific genes in vitro. Additionally, pentamidine also attenuated RANKL-mediated phosphorylation of IκBα in BMMs. These results indicate that pentamidine is effective in inhibiting osteoclast formation and significantly attenuates wear debris-induced bone loss in mice.

Nowadays, due to escalating the demands of the direct purchase of e-commerce with many kinds of item, the demand for e-commerce is exploding. The recommender system finds items for customer easily and targets in customers for the e-commerce firms easily by an automated recommending process. And also, association rules are often used to facilitate product sales in marketing pattern analysis through recommender systems in e-commerce. This paper takes aim at a new recommending service in e-commerce using periodicity analysis of weighted sequential pattern. In e-commerce, we need the FRAT segmentation method based on the various items purchased by the customer, to reflect the weights and perform the pre-processing tasks using sequential patterns for period analysis. We apply an effective incremental sequential data mining method that adds incremental purchasing data as a change of the four season changes. As a result, we suggest a recommendation service for micro-marketing of e-commerce based on big data analysis for promoting e-commerce purchasing, which satisfies customer’s taste with various products of e-commerce. To check the performance of the proposal, we tested the data set with the same conditions as before. As a result, the proposed system is more efficient than the other systems in the results of system evaluation.

Production of industrial chemicals using renewable biomass feedstock is becoming increasingly important to address limited fossil resources, climate change and other environmental problems. To develop high-performance microbial cell factories, equivalent to chemical plants, microorganisms undergo systematic metabolic engineering to efficiently convert biomass-derived carbon sources into target chemicals. Over the past two decades, many engineered microorganisms capable of producing natural and non-natural chemicals have been developed. This Review details the current status of representative industrial chemicals that are produced through biological and/or chemical reactions. We present a comprehensive bio-based chemicals map that highlights the strategies and pathways of single or multiple biological reactions, chemical reactions and combinations thereof towards production of particular chemicals of interest. Future challenges are also discussed to enable production of even more diverse chemicals and more efficient production of chemicals from renewable feedstocks.

Aging is associated with widespread physiological changes, including skeletal muscle weakening, neuron system degeneration, hair loss, and skin wrinkling. Previous studies have identified numerous molecular biomarkers involved in these changes, but their regulatory mechanisms and functional repercussions remain elusive. In this study, we conducted next-generation sequencing of DNA methylation and RNA sequencing of blood samples from 51 healthy adults between 20 and 74 years of age and identified aging-related epigenetic and transcriptomic biomarkers. We also identified candidate molecular targets that can reversely regulate the transcriptomic biomarkers of aging by reconstructing a gene regulatory network model and performing signal flow analysis. For validation, we screened public experimental data including gene expression profiles in response to thousands of chemical perturbagens. Despite insufficient data on the binding targets of perturbagens and their modes of action, curcumin, which reversely regulated the biomarkers in the experimental dataset, was found to bind and inhibit JUN, which was identified as a candidate target via signal flow analysis. Collectively, our results demonstrate the utility of a network model for integrative analysis of omics data, which can help elucidate inter-omics regulatory mechanisms and develop therapeutic strategies against aging.

Inter-joint coordination and gait variability in knee osteoarthritis (KOA) has not been well investigated. Hip-knee cyclograms can visualize the relationship between the hip and knee joint simultaneously. The aim of this study was to elucidate differences in inter-joint coordination and gait variability with respect to KOA severity using hip-knee cyclograms. Fifty participants with KOA (early KOA, n = 20; advanced KOA, n = 30) and 26 participants (≥ 50 years) without KOA were recruited. We analyzed inter-joint coordination by hip-knee cyclogram parameters including range of motion (RoM), center of mass (CoM), perimeter, and area. Gait variability was assessed by the coefficient of variance (CV) of hip-knee cyclogram parameters. Knee RoM was significantly reduced and total perimeter tended to be decreased with KOA progression. KOA patients (both early and advanced) had reduced stance phase perimeter, swing phase area, and total area than controls. Reduced knee CoM and swing phase perimeter were observed only in advanced KOA. Both KOA groups had a greater CV for CoM, knee RoM, perimeter (stance phase, swing phase and total) and swing phase area than the controls. Increased CV of hip RoM was only observed in advanced KOA. These results demonstrate that hip-knee cyclograms can provide insights into KOA patient gait.

Dryopteris erythrosora (D. C. Eaton) Kuntze is used as an ornamental horticultural crop and landscaping plant, and it is a plant with high development value as an herbal medicine, but there are few studies to proliferate a large amount of plants. This study aimed to determine a suitable method for spore germination, gametophyte proliferation, sporophyte formation, and seedling production in D. erythrosora. Spore germination rate was highest in 1/2 × Murashige and Skoog (MS) medium (92.8%). A suitable medium for prothallus proliferation was selected based on gametophytes produced from germinated spores. A 1 × MS medium was most effective for gametophyte proliferation and active organ formation; moreover, 1 × MS medium containing 1% sucrose without activated charcoal was the most effective growth condition for inducing gametophyte growth and development. The suitable culture soil composition for sporophyte formation was investigated by varying the ratio of horticultural substrate, peat moss, perlite, and decomposed granite. We found that a 2:1 (v:v) mixture of horticultural substrate and perlite accelerated sporophyte formation (155 units). Furthermore, suitable seedlings and transplants for sporophyte seedling growth were determined by varying the ratio of horticultural substrate and decomposed granite, as well as plug tray cell size. For sporophyte seedlings, the greatest growth in root length (92.9 mm) and the most aerial and underground fresh weight (234.1 and 40.3 g, respectively) were observed in a mixture of horticultural substrate and decomposed granite at a 1:2 (v:v) ratio. Our results using tissue culture technology will be provided as a mass production method for substantial industrialization of D. erythrosora plants.

This study discussed application of a machine learning approach (Support vector machine, SVM) for the automatic cognition of gait changes due to scoliosis using gait measures: kinematic based on gait phase segmentation. The gaits of 18 controls and 24 scoliosis patients were recorded and analyzed using inertial measurement unit (IMU)-based systems during normal walking. Altogether, 72 gait features were extracted for developing gait recognition models. Cross-validation test results indicated that the performance of SVM was 90.5% to recognize scoliosis patients and controls gait patterns. When features were optimally selected, a feature selection algorithm could effectively distinguish the age groups with 95.2% accuracy. Applying the method that the previous test used, the severity of scoliosis was classified after clinician labeled the severity based on the Cobb angle. Test results indicated an accuracy of 81.0% by the SVM to recognize scoliosis severity gait patterns. Optimal selected features could effectively distinguish the scoliosis severity with 85.7% accuracy. When the measured features are ranked in order of high contribution, the abduction and adduction of left hip joint in the single support phase is most important in gait of patients with scoliosis. These results demonstrate considerable potential in applying SVMs in gait classification for medical applications.

Cornus kousa (kousa dogwood), used as a landscape tree and a source of food and medicine, is difficult to propagate from seeds owing to dormancy. The present study was conducted to develop an effective method of seed propagation and identify the seed dormancy type. Kousa dogwood seeds were classified as presenting physical dormancy (PY) and physiological dormancy (PD) from an immature embryo. Seeds were contained within an impermeable endocarp that conferred PY and had an undifferentiated embryo that grew and differentiated after scarification and cold moist stratification, leading to improved germination. To break PY + PD, four replicates of 50 seeds (3200 in total) for each treatment were prepared by scarification and cold moist stratification. These methods combined improved moisture absorption and germination more than either treatment alone. In particular, the addition of cold moist stratification treatment to scarified seeds could effectively induce embryo development. By contrast, untreated seeds showed low germination rate of less than 1% at 30 °C with continuous light. Sulfuric acid (H2SO4) at different concentrations and durations was used to uniformly wound the endocarp of seeds. Treatment with 80% H2SO4 for 10 min resulted in the highest germination rate (68.6%) and moisture content (65.7%), which were higher than those following polishing with a brushing machine for 5–40 min. Longer treatment with high concentrations of H2SO4 (80 and 100%) caused the acid to infiltrate the seed and inhibit germination by damaging internal tissues, while low concentrations (40 and 60%) did not affect germination rates even after treatment for more than 10 min. To obtain maximum germination, concentration and treatment duration of sulfuric acid should be carefully controlled.

The calculation of thermophysical properties of stainless steel castings and its application to casting simulation is discussed. It is considered that accurate thermophysical properties of the casting alloys are necessary for the valid simulation of the casting processes. Although previous thermophysical calculation software requires a specific knowledge of thermodynamics, the calculation method proposed in the present study does not require any special knowledge of thermodynamics, but only the information of compositions of the alloy. The proposed calculator is based on the CALPHAD approach for modeling of multi-component alloys, especially in stainless steels. The calculator proposed in the present study can calculate thermophysical properties of eight-component systems on an iron base alloy (Fe-C-Si-Cr-Mn-Ni-Cu-Mo), and several Korean standard stainless steel alloys were calculated and discussed. The calculator can evaluate the thermophysical properties of the alloys such as density, heat capacity, enthalpy, latent heat, etc, based on full Gibbs energy for each phase. It is expected the proposed method can help casting experts to devise the casting design and its process easily in the field of not only stainless steels but also other alloy systems such as aluminum, copper, zinc, etc.

BackgroundBirds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day, and owls (Strigiformes) hunting by night.ResultsHere, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops-owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identified common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems (e.g., loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems) that are probably convergent with other nocturnal avian orders. Additionally, we found that a suite of genes associated with vision and circadian rhythm were differentially expressed between nocturnal and diurnal raptors, indicating adaptive expression change during the transition to nocturnality.ConclusionsOverall, raptor genomes showed genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators.

Background Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura’s jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. Results We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura’s jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). Conclusions Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators. Electronic supplementary material The online version of this article (10.1186/s12915-019-0643-7) contains supplementary material, which is available to authorized users.

Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation., No structural data have been available for RNA polymerase holoenzymes or transcription initiation complexes that contain extracytoplasmic σ factors. Here the authors report the crystal structures of transcription initiation complexes comprising Mycobacterium tuberculosis RNA polymerase, extracytoplasmic σ factor σL and promoter DNA.

Recently, number of studies delved into the application of Support Vector Machine (SVM) which is used in various fields to remote sensing has been rapidly increasing. The SVM was originally designed for purposes of binary classification and thus it needs to be extended to be applied to the multi-class classification. However, the SVM multi-class classifier extended for this purpose, may accompany problems in selecting items for the classification with varying accuracy of the results of classification to be depending upon classifiers and kernel functions to be employed for. Therefore, general criteria to select applicable algorithm are also needed for the practical application of the results of such multi-class classification. This study was designed to compare and find the most suitable multi-class classifier for the satellite land cover image classification in a high resolution KOMPSAT 2 image around the Expo-Science Park placed in Yuseong-gu, South Korea. The results of the study found the multi-class classifier of Crammer and Singer appeared to be superior to other classifiers in the study area. And results of the application of 4 kernel functions to such multiclass classifiers revealed the best performance of the RBF kernel function followed by those of the Polynomial and Linear ones while the Sigmoid function was lagging behind other ones.

Glasgow Prognostic Score (GPS) has been reported to predict oncologic outcomes in various type of cancer. However, their prognostic value in patients with renal cell carcinoma (RCC) is unclear. In this meta-analysis, we evaluated the prognostic significance of GPS in RCC patients. We performed comprehensive searches of electronic databases to identify studies that evaluated the prognostic impact of pretreatment GPS in RCC patients. The end points were cancer-specific survival (CSS), recurrence-free/disease-free survival (RFS/DFS). Meta-analysis using random-effects models was performed to calculate hazard ratios (HRs) or odds ratios with 95 % confidence intervals (CIs). Nine retrospective, observational, cohort studies involving 2096 patients were included. Seven studies evaluated CSS, and three evaluated RFS. Our results showed that higher GPS (0 vs. 1 vs. 2) was significantly predictive of poorer CSS (HR 3.68, 95 % CI 2.52–5.40, p

For environmental reason, buildings increasingly install smart windows, which can dim incoming daylight based on active electrochromic devices (ECDs). In this work, multi-layered graphene (MLG) was investigated as an ECD window electrode, to minimize carbon dioxide (CO2) emissions by decreasing the electricity consumption for building space cooling and heating and as an alternative to the transparent conductor tin-doped indium oxide (ITO) in order to decrease dependence on it. Various MLG electrodes with different numbers of graphene layers were prepared with environmentally friendly poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS) to produce ECD cells. Tests demonstrated the reproducibility and uniformity in optical performance, as well as the flexibility of the ECD fabrication. With the optimized MLG electrode, the ECD cells exhibited a very fast switching response for optical changes from transparent to dark states of a few hundred msec.

The effect of cloudy apple juice on fecal microbiota of type 2 diabetics was studied. Five volunteers consumed apple juice while 5 control volunteers received an isocaloric control beverage daily for 4 weeks. DGGE profile analysis showed high diversity between volunteers that did not change over the intervention period using primers for Firmicutes, Bacteroidetes, bifidobacteria, enterococci, and enterobacteria. An exception was observed using lactobacilli primers, perhaps as the result of the dietary influence. Consumption of apple juice was not correlated with changes in DGGE profiles. Quantitative PCR was used to investigate the effect of apple juice on bacterial counts in different subgroups. Apple juice did not lead to significantly (p>0.05) different numbers of total bacteria, enterobacteria, bifidobacteria, lactobacilli, or Bacteroidetes, but caused a significant (p

Metal-organic frameworks (MOFs) have a high internal surface area and widely tunable composition, which make them useful for applications involving adsorption, such as hydrogen, methane or carbon dioxide storage. The selectivity and uptake capacity of the adsorption process are determined by interactions involving the adsorbates and their porous host materials. But, although the interactions of adsorbate molecules with the internal MOF surface and also amongst themselves within individual pores have been extensively studied, adsorbate-adsorbate interactions across pore walls have not been explored. Here we show that local strain in the MOF, induced by pore filling, can give rise to collective and long-range adsorbate-adsorbate interactions and the formation of adsorbate superlattices that extend beyond an original MOF unit cell. Specifically, we use in situ small-angle X-ray scattering to track and map the distribution and ordering of adsorbate molecules in five members of the mesoporous MOF-74 series along entire adsorption-desorption isotherms. We find in all cases that the capillary condensation that fills the pores gives rise to the formation of 'extra adsorption domains'-that is, domains spanning several neighbouring pores, which have a higher adsorbate density than non-domain pores. In the case of one MOF, IRMOF-74-V-hex, these domains form a superlattice structure that is difficult to reconcile with the prevailing view of pore-filling as a stochastic process. The visualization of the adsorption process provided by our data, with clear evidence for initial adsorbate aggregation in distinct domains and ordering before an even distribution is finally reached, should help to improve our understanding of this process and may thereby improve our ability to exploit it practically.

In the power steering system of an automobile, the balanced and fixed displacement type vane pump is principally applied to the main power source. It is driven by a pulley that is attached to the shaft of the vehicle's engine, and the pulley ratio is about 1:1. The vane pump continuously discharges an outlet flow rate proportional to the rotating speed of the engine. In a vane pump without the flow control valve, an increase in the discharge flow rate means a linear increase in the actuator speed. At high speed when the driver rotates the steering wheel by even a small amount, there is a high risk of an accident due to the quick rotation of the tire joined to the actuator and links. We designed a flow control valve of the fixed displacement and pressure balanced type vane pump for power steering is designed and simulated using AMESim software. Its theoretical flow characteristics with respect to the rotating speed of the engine are compared and validated with experimental data. The results show that the design parameters, such as the flow area, the underlap length, the spool clearance, the main spring stiffness and the spring initial force, largely affect the flow control characteristics.

Numerous studies have been conducted on hydraulic systems operating under high pressure. However, such systems are difficult to realize because of mechanical limitations as a result of tribological problems between relative sliding parts. Design techniques, manufacturing techniques, and tribological characteristics must be improved or innovated to operate such systems under increased pressure. The stress distributions and optimum design factors needed to satisfy these requirements under maximum pressure are determined by analyzing the stress on the valve plate of a hydraulic axial piston pump. This pump is among the most important relative sliding parts. As per the result of the analysis conducted using an orthogonal array, the extent of the influence of the design factors on maximum stress value is ordered as follows: [z > M > h > r]. Moreover, the maximum stress value of the optimum model is 13.3% lower than that of the standard model. Results also show that the stress characteristic of the optimum model is more stable than that of the standard model.

The performance of a reciprocating compressor in refrigeration and air-conditioning systems is influenced by the lubrication characteristics of the critical sliding components. Improvements in design and performance of reciprocating compressors therefore depend in part upon the lubrication characteristics between the crankshaft and journal bearing. Current studies have explored experimental and theoretical methods, yet difficulties arise when applying these results to practical designs in the field. The present study seeks to enhance the energy efficiency ratio, and to improve the reliability of the reciprocating compressor for refrigeration and air conditioning systems by studying the influence of boundary conditions on the lubrication characteristics between the crankshaft and journal bearing. The results demonstrate that appropriate boundary conditions, when applied to theoretical analysis, improve both the speed and ease of the design process.

Background: Transposable elements (TEs) comprise similar to 10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for similar to 1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago. Results: We identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5' and 3' LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker. Conclusions: GGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification.

The effect of a daily intake of the probiotic strain Lactobacillus casei Shirota (LcS) on the colonisation of pathogens, specifically streptococci and Staphylococcus aureus, in the nose and throat of healthy human volunteers with low natural killer cell activity, was investigated in a randomised and controlled intervention study. The study consisted of a 2-week run-in phase, followed by a 4-week intervention phase. The probiotic treatment group received a fermented milk drink with LcS, while the placebo group received an equally composed milk drink without the probiotic additive. To isolate potential pathogenic streptococci and Staph. aureus, samples from the pharynx, as well as of both middle nasal meati, were taken, once after the run-in phase and once at the end of the intervention phase. Isolated bacteria were identified as either Staph. aureus and α- or β-haemolytic streptococci in a polyphasic taxonomical approach based on phenotypic tests, amplified ribosomal DNA restriction analysis genotyping, and 16S rRNA gene sequencing of representative strains. Salivary secretory immunoglobulin A (SIgA) was used as marker of protective mucosal immunity to evaluate whether LcS treatment influenced SIgA production. No statistically significant effect could be determined for intervention with LcS on the incidence of Staph. aureus in the nasal space, Staph. aureus in the pharyngeal space or for β-haemolytic streptococci and Streptococcus pneumoniae in the pharyngeal space. Thus, the intervention did not influence the nasopharyngeal colonisation with Gram-positive potential pathogens. Production of salivary SIgA as a potential means of microbiota modulation was also not affected.

The performance of a reciprocating compressor in refrigeration and air-conditioning systems is influenced by the lubrication characteristics of the critical sliding components. Thus, the lubrication characteristics between the crankshaft and journal bearing have to be researched in order to improve the design and performance of a reciprocating compressor. Therefore, in this study, to enhance the EER (energy efficiency ratio) to reduce power consumption, and to improve the reliability of a reciprocating compressor for refrigeration and air conditioning systems, theoretical analysis of the friction characteristics between the crankshaft and journal bearing in a reciprocating compressor is studied. The results demonstrate that frictional characteristics are significantly influenced by the clearance between the crankshaft and journal bearing and the viscosity of the lubricating oil.

To improve the performance of a bent-axis type axial piston pump driven by tapered pistons, it is necessary to know the pressure ripple characteristics. The purpose of this paper is to understand the effect on the pressure ripple characteristics, and to predict by comparing experimental and theoretical analysis results. The simulation model of a bent-axis type axial piston pump is developed in the AMESim environment using the geometrical dimension, and the driving mechanism of the piston pump, such as the stroke of pump, the velocity of piston, the instantaneous volumetric flow, the overlap area of valve plate opening to cylinder bore, the angle of notch, and so on. The results show that theoretical analysis results of the bent-axis type axial piston pump by using the AMESim approximate the pressure ripple characteristic of the test pump, and through this, simulations can be obtained that predict the performance characteristics of a bentaxis type axial piston pump.

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. The utility of a universal reference sequence for human genome comparisons is dependent on the ethnic origins of the individuals being sequenced. Here the authors report a Korean reference genome and consensus variome, and show that an ethnically-relevant reference can improve variant detection.

It is proposed that lead concentrations in the blood are related to intracellular glutathione and lead might be conjugated with glutathione non-enzymatically or enzymatically via glutathione S-transferase (GST). Essential hypertension is a complex, multifactorial and polygenic disease in which the underlying genetic components remain unknown. This study was aimed to investigate GST-mu1 (GSTM1) and GST-theta1 (GSTT1) gene polymorphisms in lead-exposed workers and their relationship with blood lead levels and leadrelated hypertension. To address the possible association, GSTM1 and GSTT1 (homozygous deletion vs. non-deleted) polymorphisms in 755 lead-exposed male workers were analyzed. GSTM1 and GSTT1 polymorphisms were determined using a Multiplex PCR. We observed significant association in positive alleles of GSTT1 (OR=1.593, 95% CI=1.157–2.194). However, no significant association in GSTM1 was observed with lead-related hypertension. For combined analysis with GSTM1 and GSTT1, both positive type (+/+) and GSTT1 positive (−/+) group showed significant differences between groups. These data suggest that the GSTT1 positive type polymorphism might be associated with lead-related hypertension in the lead-exposed male workers.

Two putative adhesion genes of the potentially probiotic strain Lactobacillus plantarum BFE 5092, i.e., a gene with similarity to an aggregation-promoting factor gene apf5092, and the mucin-binding protein gene mub5092, were investigated in this study. The gene encoding apf5092 encoded a protein bearing a predicted 26 amino acid signal peptide and a LysM domain putatively involved in binding to peptidoglycan. Moreover, the deduced protein also showed an amino acid sequence characteristic of an aggregation-promoting factor. The genes were tested for expression under different environmental conditions, and transcriptional studies on apf5092 showed that the expression could be influenced by low temperature and pH within 30 min. The aggregation behavior of the cells also changed at the low pH condition, but less noticeably at low temperature. To further investigate the role of apf5092 in aggregation, it was cloned and expressed in E. coli. The transformed strain showed higher co-aggregation ability with Gram-positive bacteria. Transcription studies on mub5092 revealed that it could be induced by mucin when added to the growth medium within 30 min. The data suggested that L. plantarum BFE 5092 can quickly adapt to changing environmental conditions and that enhanced aggregation may be important to survive low pH conditions, e.g., of the stomach or of fermented foods, and may thus be an important colonization factor.

Atom transfer radical polymerization was used to synthesize a well-defined poly(ethylene glycol)-b-poly(mercapto ethylacrylamide) (PEG-b-PMEAAm) diblock copolymer. Poly(ethylene glycol)-b-poly[N-(acryloxysuccinimide)](PEG-b-PNAS) was synthesized at 80 °C using methoxy-poly(ethylene glycol)-2-bromo propanoate (PEG-Br) and CuBr/2,2′-bipyridine as a macroinitiator and catalyst, respectively. The monomer conversion was determined by 1H nuclear magnetic resonance (NMR) spectroscopy. The resulting PEG-b-PNAS diblock copolymer was characterized by gel permeation chromatography, Fourier transform infrared (FT-IR), and 1H NMR spectroscopy. Disulfide groups were introduced by a simple reaction through the N-acryloxysuccinimide (NAS) moieties of the PEG-b-PNAS diblock copolymer with cystamine dihydrochloride in the presence of triethylamine. FT-IR spectroscopy was used to confirm the introduction of disulfide moieties into the polymer repeating units. Subsequently, a thiol-functionalized block copolymer was prepared using DL-dithiothreitol (DTT) as the reducing agent and the reduction step was monitored by 1H NMR spectroscopy. This thiol group was transformed easily to a disulfide bond using FeCl3 as an oxidizing agent. The transformation into disulfide could be visualized easily as insoluble polymeric particles formed from a clear solution of PEG-b-PMEAAm after oxidation.

To develop a stabilized formulation of amorphous raloxifene hydrochloride (RXF), solid dispersion granules (SDG) of amorphous RXF were prepared by fluidized bed granulation with non-pareil beads, compressed and filmcoated to produce solid dispersion tablets (SDT). Polymorphic changes in RXF were inhibited by SDG formulation. Drug content, impurity, and dissolution profile of SDT revealed that the SDT meets the acceptance criteria, and the content of RXF was maintained over 95% for 5 months at accelerated conditions of 40 °C and 75% R.H. In comparative dissolution study of reference tablet (Evista®) and SDT, the similarity factor (f2) provided evidence for similar dissolution profiles between two formulations. Therefore, we suggest the usefulness of SDT for the development of generic pharmaceuticals containing amorphous RXF.

The bent-axis type of piston pump driven by the piston rod works by the piston rod driving the cylinder block; because of this the taper angle of the piston rod and the swivel angle between the cylinder block and the shaft are important design factors. If these factors cannot satisfy the conditions for optimum design, the friction loss between the cylinder bore and the piston increases, and the pump can fail to work under conditions of severe friction and wear. Since the piston reciprocates in the cylinder bore with high velocity, at the same time rotating on its own axis and revolving on the center of the cylinder block, a decrease of the volume efficiency is generated because of the leakage between the cylinder bore and the piston. Therefore, to prevent this, the piston ring is designed to be at the end of the piston, and the friction characteristics between the piston ring and the cylinder bore require further research due to their great influence on the performance of the piston pump. Thus, in this paper, the elastohydrodynamic lubrication (EHL) analysis of the film thickness, the pressure distribution, and the friction force, have been studied between the piston ring and the cylinder bore in the bent-axis type of piston pump. The analyzed results show that the friction force is influenced by the rotating speed and the discharge pressure.

The rolling piston type rotary compressor has been widely used for refrigeration and air-conditioning systems due to its compactness and high-speed characteristics. However, it is necessary to develop alternative refrigerants that can guarantee environmental protection. In addition, advanced refrigerant compressors must be further developed to overcome the compatibility problems inherent in refrigeration and air-conditioning systems. The refrigerant compressor is the most important mechanical component, which determines the performances of refrigeration and air-conditioning systems. Therefore, we theoretically investigated the lubrication characteristics of the rotary compressor currently used in both refrigeration and air-conditioning systems with an alternative refrigerant. In the theoretical investigation, the Runge-Kutta method is used to analyze the behavior of a rolling piston in the rotary compressor. Subsequently, the Newton-Raphson method is used, which provided good performance in the analysis of the elastohydrodynamic lubrication of the line contacts between a rolling piston and a vane in the rotary compressor. The results demonstrate that the alternative refrigerants influence the friction force and the energy loss between the vane and the rolling piston.