bluuebunny/crossref_metadata_2025_split huggingface dataset:
HilD and PhoP independently regulate the expression of grhD1, a novel gene required for Salmonella Typhimurium invasion of host cells
Authors: Banda María M. , López Carolina , Manzo Rubiceli , Rico-Pérez Gadea , García Pablo , Rosales-Reyes Roberto , De la Cruz Miguel A. , Soncini Fernando C. , García-del Portillo Francisco , Bustamante Víctor H. 
Published: March 2018

AbstractWhen Salmonella is grown in the nutrient-rich lysogeny broth (LB), the AraC-like transcriptional regulator HilD positively controls the expression of genes required for Salmonella invasion of host cells, such as the Salmonella pathogenicity island 1 (SPI-1) genes. However, in minimal media, the two-component system PhoP/Q activates the expression of genes necessary for Salmonella replication inside host cells, such as the SPI-2 genes. Recently, we found that the SL1344_1872 hypothetical gene, located in a S. Typhimurium genomic island, is co-expressed with the SPI-1 genes. In this study we demonstrate that HilD induces indirectly the expression of SL1344_1872 when S. Typhimurium is grown in LB; therefore, we named SL1344_1872 as grhD1 for gene regulated by HilD. Furthermore, we found that PhoP positively controls the expression of grhD1, independently of HilD, when S. Typhimurium is grown in LB or N-minimal medium. Moreover, we demonstrate that the grhD1 gene is required for the invasion of S. Typhimurium into epithelial cells, macrophages and fibroblasts, as well as for the intestinal inflammatory response caused by S. Typhimurium in mice. Thus, our results reveal a novel virulence factor of Salmonella, whose expression is positively and independently controlled by the HilD and PhoP transcriptional regulators.
Comparison of CPI and GAP models in patients with idiopathic pulmonary fibrosis: a nationwide cohort study
Authors: Lee Sang Hoon , Park Jong Sun , Kim Song Yee , Kim Dong Soon , Kim Young Whan , Chung Man Pyo , Uh Soo Taek , Park Choon Sik , Park Sung Woo , Jeong Sung Hwan , Park Yong Bum , Lee Hong Lyeol , Shin Jong Wook , Lee Eun Joo , Lee Jin Hwa , Jegal Yangin , Lee Hyun Kyung , Kim Yong Hyun , Song Jin Woo , Park Moo Suk 
Published: March 2018

AbstractThe clinical course of idiopathic pulmonary fibrosis (IPF) is difficult to predict, partly owing to its heterogeneity. Composite physiologic index (CPI) and gender-age-physiology (GAP) models are easy-to-use predictors of IPF progression. This study aimed to compare the predictive values of these two models. From 2003 to 2007, the Korean Interstitial Lung Disease (ILD) Study Group surveyed ILD patients using the 2002 ATS/ERS criteria. A total of 832 patients with IPF were enrolled in this study. CPI was calculated as follows: 91.0 − (0.65 × %DLCO) − [0.53 × %FVC + [0.34 × %FEV1. GAP stage was calculated based on gender (0–1 points), age (0–2 points), and two physiologic lung function parameters (0–5 points). The two models had similar significant predictive values for patients with IPF (p < 0.001). The area under the curve (AUC) was higher for CPI than GAP for prediction of 1-, 2-, and 3-year mortality in this study. The AUC was higher for surgically diagnosed IPF patients than for clinically diagnosed patients. However, neither CPI nor GAP yielded good predictions of outcomes; the AUC was approximately 0.61~0.65. Although both CPI and GAP stage are significantly useful predictors for IPF, they have limited capability to accurately predict outcomes.
The role of gel-phase domains in electroporation of vesicles
Authors: Perrier Dayinta L. , Rems Lea , Kreutzer Michiel T. , Boukany Pouyan E. 
Published: March 2018

AbstractTransient permeabilisation of the cell membrane is a critical step to introduce drugs or DNA into living cells, yet challenging for both biological research and therapeutic applications. To achieve this, electroporation (or electropermeabilisation) has become a widely used method due to its simplicity to deliver almost any biomolecule to any cell type. Although this method demonstrates promise in the field of drug/gene delivery, the underlying physical mechanisms of the response of the heterogeneous cell membrane to strong electric pulses is still unknown. In this study, we have investigated the role of gel-phase lipids in the electroporation of binary giant unilamellar vesicles (GUVs), composed from DPPC (gel-phase) and DPhPC (fluid-phase) lipids (molar ratio 8:2 and 2:8). We have observed that the exposure to electric pulses leads to expel of fluid-phase lipids and concomitant decrease in GUV size, whereas the gel-phase domains become buckled. Based on experiments on pure fluid-phase and gel-phase GUVs, we have found that fluid-phase lipids can be expelled by electrical forces and the highly viscous gel-phase lipids cannot. Moreover, our analyses suggest that pore formation occurs primarily in fluid-phase domains and that the pore size is similar in all GUVs containing fluid-phase lipids, irrespective of the gel-phase percentage.
Label-free photoacoustic microscopy for in-vivo tendon imaging using a fiber-based pulse laser
Authors: Lee Hwi Don , Shin Jun Geun , Hyun Hoon , Yu Bong-Ahn , Eom Tae Joong 
Published: March 2018

AbstractTendons are tough, flexible, and ubiquitous tissues that connect muscle to bone. Tendon injuries are a common musculoskeletal injury, which affect 7% of all patients and are involved in up to 50% of sports-related injuries in the United States. Various imaging modalities are used to evaluate tendons, and both magnetic resonance imaging and sonography are used clinically to evaluate tendons with non-invasive and non-ionizing radiation. However, these modalities cannot provide 3-dimensional (3D) structural images and are limited by angle dependency. In addition, anisotropy is an artifact that is unique to the musculoskeletal system. Thus, great care should be taken during tendon imaging. The present study evaluated a functional photoacoustic microscopy system for in-vivo tendon imaging without labeling. Tendons have a higher density of type 1 collagen in a cross-linked triple-helical formation (65–80% dry-weight collagen and 1–2% elastin in a proteoglycan-water matrix) than other tissues, which provides clear endogenous absorption contrast in the near-infrared spectrum. Therefore, photoacoustic imaging with a high sensitivity to absorption contrast is a powerful tool for label-free imaging of tendons. A pulsed near-infrared fiber-based laser with a centered wavelength of 780 nm was used for the imaging, and this system successfully provided a 3D image of mouse tendons with a wide field of view (5 × 5 mm2).
Baseline mRNA expression differs widely between common laboratory strains of zebrafish
Authors: Holden Lindsay A. , Brown Kim H. 
Published: March 2018

AbstractCommon strains of wildtype zebrafish (Danio rerio) have unique genomic features including SNPs and CNV, but strain information often goes unreported in the literature. As a result, the confounding effects of interstrain variation makes repetition of studies in zebrafish challenging. Here we analyze hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen (TU), and WIK) using Agilent 4 × 44 K gene expression microarrays to establish baseline mRNA expression across strains and between sexes. We observed wide variation in sex-specific gene expression within AB and WIK strains (141 genes in AB and 67 genes in WIK), but no significant variation between sexes within TU. After partitioning the dataset into male and female subsets, we detected 421 unique mRNA transcripts with statistically significant differential expression; 269 mRNA transcripts varied between males, 212 mRNA transcripts varied between females, and 59 mRNA transcripts varied across the three strains, regardless of sex. It is not surprising that mRNA expression profiles differ between sexes and strains, but it is imperative to characterize the differences. These results highlight the complexity of variation within zebrafish and underscore the value of this model system as a valid representation of normal variation present in other species, including humans.
Contribution of transformation products towards the total herbicide toxicity to tropical marine organisms
Authors: Mercurio Philip , Eaglesham Geoff , Parks Stephen , Kenway Matt , Beltran Victor , Flores Florita , Mueller Jochen F. , Negri Andrew P. 
Published: March 2018

AbstractThe toxicity of herbicide degradation (transformation) products is rarely taken into account, even though these are commonly detected in the marine environment, sometimes at concentrations higher than the parent compounds. Here we assessed the potential contribution of toxicity by transformation products of five photosystem II herbicides to coral symbionts (Symbiodinium sp.), the green algae Dunaliella sp., and prawn (Penaeus monodon) larvae. Concentration-dependent inhibition of photosynthetic efficiency (∆F/F
m
′) was observed for all herbicides in both microalgal species. The toxicity of solutions of aged diuron solutions containing transformation products to Symbiodinium sp. and Dunaliella sp. was greater than could be explained by the concentrations of diuron measured, indicating transformation products contributed to the inhibition of ∆F/F
m
′. However, the toxicity of aged atrazine, simazine, hexazinone, and ametryn solutions could be explained by the concentration of parent herbicide, indicating no contribution by transformation products. Prawn larval metamorphosis was not sensitive to the herbicides, but preliminary results indicated some toxicity of the transformation products of atrazine and diuron. Risk assessments should take into account the contribution of herbicide transformation products; however, further studies are clearly needed to test the toxicity of a far wider range of transformation products to a representative diversity of relevant taxa.
Integrated Modelling of Cell Responses after Irradiation for DNA-Targeted Effects and Non-Targeted Effects
Authors: Matsuya Yusuke , Sasaki Kohei , Yoshii Yuji , Okuyama Go , Date Hiroyuki 
Published: March 2018

AbstractIntercellular communication after ionizing radiation exposure, so-called non-targeted effects (NTEs), reduces cell survival. Here we describe an integrated cell-killing model considering NTEs and DNA damage along radiation particle tracks, known as DNA-targeted effects (TEs) based on repair kinetics of DNA damage. The proposed model was applied to a series of experimental data, i.e., signal concentration, DNA damage kinetics, cell survival curve and medium transfer bystander effects (MTBEs). To reproduce the experimental data, the model considers the following assumptions: (i) the linear-quadratic (LQ) function as absorbed dose to express the hit probability to emit cell-killing signals, (ii) the potentially repair of DNA lesions induced by NTEs, and (iii) lower efficiency of repair for the damage in NTEs than that in TEs. By comparing the model results with experimental data, we found that signal-induced DNA damage and lower repair efficiency in non-hit cells are responsible for NTE-related repair kinetics of DNA damage, cell survival curve with low-dose hyper-radiosensitivity (HRS) and MTBEs. From the standpoint of modelling, the integrated cell-killing model with the LQ relation and a different repair function for NTEs provide a reasonable signal-emission probability and a new estimation of low-dose HRS linked to DNA repair efficiency.
Efficient and synergistic removal of tetracycline and Cu(II) using novel magnetic multi-amine resins
Authors: Zhu Zengyin , Zhang Mancheng , Wang Wei , Zhou Qing , Liu Fuqiang 
Published: March 2018

AbstractA series of magnetic multi-amine resins (MMARs, named E1D9-E9D1) was proposed for the removal of tetracycline (TC) and Cu(II) in sole and binary solutions. Results showed that the N content of the resins increased sharply from 1.7% to 15.49%, and the BET surface areas decreased from 1433.4 m2/g to 8.9 m2/g with methyl acrylate ratio increasing from E1D9 to E9D1. Their adsorption capacities for TC and Cu(II) could reach 0.243 and 0.453 mmol/g, respectively. The adsorption isotherms of TC onto MMARs transformed from heterogeneous adsorption to monolayer-type adsorption with DVB monomer ratio in resin matrix decrease, suggesting the dominant physical adsorption between TC and benzene rings. TC adsorption capacity onto E9D1 was higher than that onto E7D3 when the equilibrium concentration of TC exceeded 0.043 mmol/L because the electrostatic interaction between negatively charged groups of TC and protonated amines of adsorbents could compensate for the capacity loss resulting from BET surface area decrease. In the binary system, the electrostatic interaction between negatively charged TC-Cu(II) complex and protonated amines of adsorbents was responsible for the synergistic adsorption onto E7D3 and E9D1. The XPS spectra of magnetic resins before and after adsorption were characterized to prove the probable adsorption mechanisms. This work provides alternative adsorbent for the efficient treatment of multiple pollution with different concentrations of organic micropollutants and heavy metal ions.
Iso-α-acids, bitter components of beer, prevent obesity-induced cognitive decline
Authors: Ayabe Tatsuhiro , Ohya Rena , Kondo Keiji , Ano Yasuhisa 
Published: March 2018

AbstractDementia and cognitive decline have become worldwide public health problems, and it was recently reported that life-style related diseases and obesity are key risk factors in dementia. Iso-α-acids, hop-derived bitter components of beer, have been reported to have various physiological functions via activation of peroxisome proliferator-activated receptor γ. In this report, we demonstrated that daily intake of iso-α-acids suppresses inflammations in the hippocampus and improves cognitive decline induced by high fat diet (HFD). Body weight, epididymal fat weight, and plasma triglyceride levels were increased in HFD-fed mice, and significantly decreased in iso-α-acids supplemented HFD-fed mice. HFD feeding enhances the production of inflammatory cytokines and chemokines, such as TNF-α, which was significantly suppressed by iso-α-acids administration. HFD-induced neuroinflammation caused lipid peroxidation, neuronal loss, and atrophy in hippocampus, and those were not observed in iso-α-acids-treated mice. Furthermore, iso-α-acids intake significantly improved cognitive decline induced by HFD-feeding. Iso-α-acids are food derived components that suppressing both lipid accumulation and brain inflammation, thus iso-α-acids might be beneficial for the risk of dementia increased by obesity and lifestyle-related diseases.
TiO2 nanoparticles induce omphalocele in chicken embryo by disrupting Wnt signaling pathway
Authors: Patel Shweta , Jana Sarmita , Chetty Rajlakshmi , Thakore Sonal , Singh Man , Devkar Ranjitsinh 
Published: March 2018

AbstractTitanium dioxide nanoparticles (TiO2 NPs) are among abundantly used metal oxide NPs but their interactions with biomolecules and subsequent embryonic toxicity in higher vertebrates is not extensively reported. Physicochemical interactions of TiO2 NPs with egg albumen reveals that lower doses of TiO2 NPs (10 and 25 µg/ml) accounted for higher friccohesity and activation energy but an increment in molecular radii was recorded at higher doses (50 and 100 µg/ml). FTIR analysis revealed conformational changes in secondary structure of egg albumen as a result of electrostratic interactions between egg albumen and TiO2 NPs. The morphometric data of chicken embryo recorded a reduction at all the doses of TiO2 NPs, but toxicity and developmental deformity (omphalocele and flexed limbs) were recorded at lower doses only. Inductively coupled plasma optical emission spectrometry (ICP-OES) confirmed presence of Ti in chicken embryos. mRNA levels of genes involved in canonical and non-canonical Wnt signaling were lowered following TiO2 NPs treatment resulting in free radical mediated disruption of lateral plate mesoderm and somite myogenesis. Conformational changes in egg albumen and subsequent developmental deformity in chicken embryo following TiO2 NPs treatment warrants detailed studies of NP toxicity at lower doses prior to their biomedical applications.
Nucleotide-mediated SPDEF modulates TFF3-mediated wound healing and intestinal barrier function during the weaning process
Authors: Lee Sang In , Kim In Ho 
Published: March 2018

AbstractMost alterations during weaning involve physiological changes in intestinal structure and function. Here, we evaluated the molecular mechanisms regulating the effects of nucleotides on weaning. Nucleotide treatment induced Trefoil factor 3 (TFF3) expression and IPEC-J2 cell growth and reduced wound width. Treatment with nucleosides and TFF3 in lipopolysaccharide-challenged IPEC-J2 cells increased intestinal transepithelial electrical resistance and decreased intestinal permeability. Additionally, nucleosides improved intestinal barrier function through induction of TFF3-mediated phosphatidylinositol 3-kinase/Akt, extracellular signal-regulated kinase 1/2, p38, and Janus kinase/signal transducer and activator of transcription signaling pathways. Among selected differentially expressed genes, SAM pointed domain containing ETS transcription factor (SPDEF) expression was elevated by nucleotides in a concentration-dependent manner. Moreover, SPDEF directly regulated TFF3 expression via binding to the promoter. In vivo, nucleotide supplementation improved growth performance, serum stress levels, and intestinal morphology. Our findings provide insights into the molecular mechanisms of intestinal development during weaning in pigs.
Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion
Authors: Zhao Shanrong , Zhang Ying , Gamini Ramya , Zhang Baohong , von Schack David 
Published: March 2018

AbstractTo allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.
High-performance inertial impaction filters for particulate matter removal
Authors: Zhang Xiaowei , Zhang Wei , Yi Mingqiang , Wang Yingjie , Wang Pengjun , Xu Jun , Niu Fenglei , Lin Feng 
Published: March 2018

AbstractAirborne particulate matter (PM) is causing more and more serious air pollution and threatening the public health. However, existing air filter technologies with the easy-to-block manner can rarely meet the requirements of high-performance PM filters. Here we propose a conceptually new type of inertial impaction filters for rapidly high-efficiency PM removal. Under the airflow velocity of 8.0 m/s, the real inertial impaction filters show high PM removal efficiencies of up to 97.77 ± 1.53% and 99.47 ± 0.45% for PM2.5 and PM10, respectively. Compared with the traditional air filters reported previously, the inertia impaction filters exhibit extremely low pressure drop of 5–10 Pa and high quality factor (QF) values of 0.380 Pa−1 and 0.524 Pa−1 for PM2.5 and PM10, respectively. These greatly improved QF values are achieved through a series of inertial separation processes. The feature dimension of filtration channel is dozens of times larger than PM average size, which greatly decreases airflow resistance. Particularly, this inertial structure can be made of various types of materials, which shows great potential for low-cost fabrication of large-area devices. As a stand-alone device or incorporated with the existing PM air filter, this inertial impaction filter will bring great benefits to the public health.
Radionuclide uptake by colloidal and particulate humic acids obtained from 14 soils collected worldwide
Authors: Lin Peng , Xu Chen , Xing Wei , Sun Luni , Kaplan Daniel I. , Fujitake Nobuhide , Yeager Chris M. , Schwehr Kathleen A. , Santschi Peter H. 
Published: March 2018

AbstractUptake of six particle-reactive and/or redox-sensitive radionuclides (210Pb, 234Th, 7Be, 59Fe, 237Np and 233Pa) by 14 humic acids (HAs) was investigated in artificial groundwater under mildly acidic conditions (pH~5.5). In HA-groundwater slurry, Pb, Be, Fe and Pa bound strongly to particulate HA (>0.45 µm), supporting their application as tracers of soil erosion. Th bound strongly to the colloidal HA (3 kDa-0.45 µm) and as such, would not be a good candidate as a tracer for monitoring soil erosion. HAs likely reduced the oxidized neptunyl form (Np(V)O4+) to Np(IV) based on its enhanced particle-reactivity and Np uptake by particulate HAs, partially retarding the movement of anthropogenic 237Np in field polluted environments. Particulate/colloidal carbonyl/O-aryl (likely through hydroquinone/quinone) functionalities in the HA correlated to Np and Pa uptake, but only particulate O-aryl functionalities was responsible for Fe uptake. The carboxylate- and carbonyl/O-aryl-containing organic functionalities in the HA correlated strongly with Th uptake. In contrast, no significant correlations between organic parameters and Pb or Be uptake implied their predominance of uniform surface adsorption onto particles. This study provides novel insight into the binding of six radionuclides with different organic functionalities of three size fractions, as well as its possible impact on their application in the soil-tracing research.
Synthesis of C-coordinated O-carboxymethyl chitosan metal complexes and evaluation of their antifungal activity
Authors: Liu Weixiang , Qin Yukun , Liu Song , Xing Ronge , Yu Huahua , Chen Xiaolin , Li Kecheng , Li Pengcheng 
Published: March 2018

AbstractBased on a condensation reaction, a chitosan-derivative-bearing amino pyridine group was prepared and subsequently followed by coordination with cupric ions, zinc ions and nickel ions to synthesize chitosan metal complexes. The calculations using the density functional theory (DFT) show that the copper ions and nickel ions underwent dsp2 hybridization, the zinc ions underwent sp3 hybridization, and they all formed a coordination bond with the carbon atom in the p-π conjugate group. The antifungal properties of O-CSPX-M against Phytophthora capsici (P. capsici), Verticillium alboatrum (V. alboatrum), Botrytis cinerea (B. cinerea) and Rhizoctonia solani (R. solani) were also assayed. Apparently, chitosan metal complexes showed enhanced antifungal activity against four fungi at the tested concentrations compared to that of chitosan. It was shown that Cu complexes can inhibit the growth of P. capsici 100%, and Ni complexes can inhibit the growth of B. cinerea 77.1% at a concentration of 0.4 mg/mL and 0.2 mg/mL, respectively. The pot experiment also verified the result. In addition, the phytotoxicity experiment showed that O-CSPX-M had no obvious toxicity on wheat leaves. This kind of complexes may represent as an attractive direction for chemical modifications of metal fungicides.