bluuebunny/crossref_metadata_2025_split huggingface dataset:
UV radiation enhanced oxygen vacancy formation caused by the PLD plasma plume
Authors: Hensling F. V. E. , Keeble D. J. , Zhu J. , Brose S. , Xu C. , Gunkel F. , Danylyuk S. , Nonnenmann S. S. , Egger W. , Dittmann R. 
Published: June 2018

AbstractPulsed Laser Deposition is a commonly used non-equilibrium physical deposition technique for the growth of complex oxide thin films. A wide range of parameters is known to influence the properties of the used samples and thin films, especially the oxygen-vacancy concentration. One parameter has up to this point been neglected due to the challenges of separating its influence from the influence of the impinging species during growth: the UV-radiation of the plasma plume. We here present experiments enabled by a specially designed holder to allow a separation of these two influences. The influence of the UV-irradiation during pulsed laser deposition on the formation of oxygen-vacancies is investigated for the perovskite model material SrTiO3. The carrier concentration of UV-irradiated samples is nearly constant with depth and time. By contrast samples not exposed to the radiation of the plume show a depth dependence and a decrease in concentration over time. We reveal an increase in Ti-vacancy–oxygen-vacancy-complexes for UV irradiated samples, consistent with the different carrier concentrations. We find a UV enhanced oxygen-vacancy incorporation rate as responsible mechanism. We provide a complete picture of another influence parameter to be considered during pulsed laser depositions and unravel the mechanism behind persistent-photo-conductivity in SrTiO3.
Anti-inflammatory role of 15-lipoxygenase contributes to the maintenance of skin integrity in mice
Authors: Kim Sang-Nam , Akindehin Seun , Kwon Hyun-Jung , Son Yeon-Ho , Saha Abhirup , Jung Young-Suk , Seong Je-Kyung , Lim Kyung-Min , Sung Jong-Hyuk , Maddipati Krishna Rao , Lee Yun-Hee 
Published: June 2018

Abstract15-lipoxygenase is involved in the generation of specialized pro-resolving lipid mediators that play essential roles in resolution and inflammatory responses. Here, we investigated anti-inflammatory role of Alox15 in skin homeostasis. We demonstrated that knockout (KO) of Alox15 led to hair loss and disrupted the structural integrity of the dorsal skin. Alox15 KO resulted in loss of hair follicle stem cells and abnormal transition of dermal adipocytes into fibroblasts. Alox15 deficiency increased infiltration of proinflammatory macrophages and upregulated proinflammatory and necroptotic signaling in dermal adipose tissue in the dorsal skin. Lipidomic analysis revealed severe loss of resolvin D2 in the dorsal skin of Alox15 KO mice compared to wild type controls. Treatment with resolvin D2 reduced skin inflammation in Alox15 KO mice. Collectively, these results indicate that Alox15-mediated production of resolvin D2 is required to maintain skin integrity by suppressing dermal inflammation.
The intrinsically disordered E-domains regulate the IGF-1 prohormones stability, subcellular localisation and secretion
Authors: Annibalini Giosuè , Contarelli Serena , De Santi Mauro , Saltarelli Roberta , Di Patria Laura , Guescini Michele , Villarini Anna , Brandi Giorgio , Stocchi Vilberto , Barbieri Elena 
Published: June 2018

AbstractInsulin-like growth factor-1 (IGF-1) is synthesised as a prohormone (proIGF-1) requiring enzymatic activity to yield the mature IGF-1. Three proIGF-1s are encoded by alternatively spliced IGF-1 mRNAs: proIGF-1Ea, proIGF-1Eb and proIGF-1Ec. These proIGF-1s have a common IGF-1 mature sequence but different E-domains. The structure of the E-domains has not been resolved, and their molecular functions are still unclear. Here, we show that E-domains are Intrinsically Disordered Regions that have distinct regulatory functions on proIGF-1s production. In particular, we identified a highly conserved N-glycosylation site in the Ea-domain, which regulated intracellular proIGF-1Ea level preventing its proteasome-mediated degradation. The inhibition of N-glycosylation by tunicamycin or glucose starvation markedly reduced proIGF-1Ea and mature IGF-1 production. Interestingly, 2-deoxyglucose, a glucose and mannose analogue, increased proIGF-1Ea and mature IGF-1 levels, probably leading to an accumulation of an under-glycosylated proIGF-1Ea that was still stable and efficiently secreted. The proIGF-1Eb and proIGF-1Ec were devoid of N-glycosylation sites, and hence their production was unaffected by N-glycosylation inhibitors. Moreover, we demonstrated that alternative Eb- and Ec-domains controlled the subcellular localisation of proIGF-1s, leading to the nuclear accumulation of both proIGF-1Eb and proIGF-1Ec. Our results demonstrated that E-domains are regulatory elements that control IGF-1 production and secretion.
Super-resolution CT Image Reconstruction Based on Dictionary Learning and Sparse Representation
Authors: Jiang Changhui , Zhang Qiyang , Fan Rui , Hu Zhanli 
Published: June 2018

AbstractIn this paper, a single-computed tomography (CT) image super-resolution (SR) reconstruction scheme is proposed. This SR reconstruction scheme is based on sparse representation theory and dictionary learning of low- and high-resolution image patch pairs to improve the poor quality of low-resolution CT images obtained in clinical practice using low-dose CT technology. The proposed strategy is based on the idea that image patches can be well represented by sparse coding of elements from an overcomplete dictionary. To obtain similarity of the sparse representations, two dictionaries of low- and high-resolution image patches are jointly trained. Then, sparse representation coefficients extracted from the low-resolution input patches are used to reconstruct the high-resolution output. Sparse representation is used such that the trained dictionary pair can reduce computational costs. Combined with several appropriate iteration operations, the reconstructed high-resolution image can attain better image quality. The effectiveness of the proposed method is demonstrated using both clinical CT data and simulation image data. Image quality evaluation indexes (root mean squared error (RMSE) and peak signal-to-noise ratio (PSNR)) indicate that the proposed method can effectively improve the resolution of a single CT image.
NtLTP4, a lipid transfer protein that enhances salt and drought stresses tolerance in Nicotiana tabacum
Authors: Xu Yang , Zheng Xinxin , Song Yunzhi , Zhu Lifei , Yu Zipeng , Gan Liming , Zhou Shumei , Liu Hongmei , Wen Fujiang , Zhu Changxiang 
Published: June 2018

AbstractLipid transfer proteins (LTPs), a class of small, ubiquitous proteins, play critical roles in various environmental stresses. However, their precise biological functions remain unknown. Here we isolated an extracellular matrix-localised LTP, NtLTP4, from Nicotiana tabacum. The overexpression of NtLTP4 in N. tabacum enhanced resistance to salt and drought stresses. Upon exposure to high salinity, NtLTP4-overexpressing lines (OE lines) accumulated low Na+ levels. Salt-responsive genes, including Na+/H+ exchangers (NHX1) and high-affinity K+ transporter1 (HKT1), were dramatically higher in OE lines than in wild-type lines. NtLTP4 might regulate transcription levels of NHX1 and HKT1 to alleviate the toxicity of Na+. Interestingly, OE lines enhanced the tolerance of N. tabacum to drought stress by reducing the transpiration rate. Moreover, NtLTP4 could increase reactive oxygen species (ROS)-scavenging enzyme activity and expression levels to scavenge excess ROS under drought and high salinity conditions. We used a two-hybrid yeast system and screened seven putative proteins that interact with NtLTP4 in tobacco. An MAPK member, wound-induced protein kinase, was confirmed to interact with NtLTP4 via co-immunoprecipitation and a firefly luciferase complementation imaging assay. Taken together, this is the first functional analysis of NtLTP4, and proves that NtLTP4 positively regulates salt and drought stresses in N. tabacum.
Brain Cell Type Specific Gene Expression and Co-expression Network Architectures
Authors: McKenzie Andrew T. , Wang Minghui , Hauberg Mads E. , Fullard John F. , Kozlenkov Alexey , Keenan Alexandra , Hurd Yasmin L. , Dracheva Stella , Casaccia Patrizia , Roussos Panos , Zhang Bin 
Published: June 2018

AbstractElucidating brain cell type specific gene expression patterns is critical towards a better understanding of how cell-cell communications may influence brain functions and dysfunctions. We set out to compare and contrast five human and murine cell type-specific transcriptome-wide RNA expression data sets that were generated within the past several years. We defined three measures of brain cell type-relative expression including specificity, enrichment, and absolute expression and identified corresponding consensus brain cell “signatures,” which were well conserved across data sets. We validated that the relative expression of top cell type markers are associated with proxies for cell type proportions in bulk RNA expression data from postmortem human brain samples. We further validated novel marker genes using an orthogonal ATAC-seq dataset. We performed multiscale coexpression network analysis of the single cell data sets and identified robust cell-specific gene modules. To facilitate the use of the cell type-specific genes for cell type proportion estimation and deconvolution from bulk brain gene expression data, we developed an R package, BRETIGEA. In summary, we identified a set of novel brain cell consensus signatures and robust networks from the integration of multiple datasets and therefore transcend limitations related to technical issues characteristic of each individual study.
Optimization of Assembly Pipeline may Improve the Sequence of the Chloroplast Genome in Quercus spinosa
Authors: Zhang Xiangzhou , Hu Yong , Liu Mei , Lang Tiange 
Published: June 2018

AbstractObtaining chloroplast (cp) genome sequence is necessary for studying physiological roles in plants. However, it is difficult to use traditional sequencing methods to get cp genome sequences because of the complex procedures of preparing templates. With the advent of next-generation sequencing technology, massive genome sequences can be produced. Thus, a good pipeline to assemble next-generation sequence reads with optimized k-mer length is essential to get whole cp genome sequences. Moreover, adjustment of other parameters is also very important, especially for the assembly of the cp genome. In this study, we developed a pipeline to generate the cp genome for Quercus spinosa. When Quercus rubra was used as a reference, we achieved coverage of 97.75% after optimizing k-mer length as well as other parameters. The efficiency of the pipeline makes it a useful method for cp genome construction in plants. It also provides great perspective on the analysis of cp genome characteristics and evolution.
NF-кB increases LPS-mediated procalcitonin production in human hepatocytes
Authors: Bai Yongfeng , Lu Jun , Cheng Ying , Zhang Feng , Fan Xueyu , Weng Yuanyuan , Zhu Jin 
Published: June 2018

AbstractFor years, procalcitonin (PCT) has been employed as a diagnostic biomarker for the severity of sepsis and septic shock, as well as for guiding the application of antibiotics. However, the molecular/cellular basis for the regulation of PCT production is not fully understood. In this study, we identified the signalling pathway by which the expression of PCT was induced by lipopolysaccharide in human hepatocytes at the mRNA and protein levels. This expression was dependent on nuclear transcription factor κB (NF-κB), as indicated by a NF-κB binding site (nt −53 to −44) found in the PCT promoter region. We also showed that microRNA-513b (miR-513b) was also able to bind to the 3′-untranslated region (UTR) of the PCT promoter sequence. Meanwhile, the activation of NF-κB down-regulated the expression of miR-513b. In conclusion, we suggest that NF-κB is capable of enhancing the expression of PCT by either directly activating the transcription of the PCT gene or indirectly modulating the expression of its regulatory component, miR-513b. Our results indicate a molecular mechanism responsible for the regulation of PCT production.
Mathematical Modeling of the Function of Warburg Effect in Tumor Microenvironment
Authors: Shamsi Milad , Saghafian Mohsen , Dejam Morteza , Sanati-Nezhad Amir 
Published: June 2018

AbstractTumor cells are known for their increased glucose uptake rates even in the presence of abundant oxygen. This altered metabolic shift towards aerobic glycolysis is known as the Warburg effect. Despite an enormous number of studies conducted on the causes and consequences of this phenomenon, little is known about how the Warburg effect affects tumor growth and progression. We developed a multi-scale computational model to explore the detailed effects of glucose metabolism of cancer cells on tumorigenesis behavior in a tumor microenvironment. Despite glycolytic tumors, the growth of non-glycolytic tumor is dependent on a congruous morphology without markedly interfering with glucose and acid concentrations of the tumor microenvironment. Upregulated glucose metabolism helped to retain oxygen levels above the hypoxic limit during early tumor growth, and thus obviated the need for neo-vasculature recruitment. Importantly, simulating growth of tumors within a range of glucose uptake rates showed that there exists a spectrum of glucose uptake rates within which the tumor is most aggressive, i.e. it can exert maximal acidic stress on its microenvironment and most efficiently compete for glucose supplies. Moreover, within the same spectrum, the tumor could grow to invasive morphologies while its size did not markedly shrink.
Optimization of Culture Conditions for Enhanced Growth, Lipid and Docosahexaenoic Acid (DHA) Production of Aurantiochytrium SW1 by Response Surface Methodology
Authors: Nazir Yusuf , Shuib Shuwahida , Kalil Mohd Sahaid , Song Yuanda , Hamid Aidil Abdul 
Published: June 2018

AbstractIn this study, optimization of growth, lipid and DHA production of Aurantiochytrium SW1 was carried out using response surface methodology (RSM) in optimizing initial fructose concentration, agitation speed and monosodium glutamate (MSG) concentration. Central composite design was applied as the experimental design and analysis of variance (ANOVA) was used to analyze the data. ANOVA analysis revealed that the process which adequately represented by quadratic model was significant (p < 0.0001) for all the response. All the three factors were significant (p < 0.005) in influencing the biomass and lipid data while only two factors (agitation speed and MSG) gave significant effect on DHA production (p < 0.005). The estimated optimal conditions for enhanced growth, lipid and DHA production were 70 g/L fructose, 250 rpm agitation speed and 10 g/L MSG. Consequently, the quadratic model was validated by applying the estimated optimum conditions, which confirmed the model validity where 19.0 g/L biomass, 9.13 g/L lipid and 4.75 g/L of DHA were produced. The growth, lipid and DHA were 28, 36 and 35% respectively higher than that produced in the original medium prior to optimization.
Treatment Response to a Double Administration of Constraint-Induced Language Therapy in Chronic Aphasia
Authors: Mozeiko Jennifer , Myers Emily B. , Coelho Carl A. 
Published: June 2018

Purpose
This study investigated changes in oral–verbal expressive language associated with improvements following 2 treatment periods of constraint-induced language therapy in 4 participants with stroke-induced chronic aphasia. Generalization of treatment to untrained materials and to discourse production was also analyzed, as was the durability of the treatment effect.

Method
Participants with aphasia were assessed using standardized measures and discourse tasks at 3 to 4 time points to document behavioral changes throughout each of two 30-hr treatment periods of constraint-induced language therapy. Daily probes of trained and untrained materials were also administered.

Results
Despite participant heterogeneity, behavioral results for each person with aphasia indicated a positive response to treatment following each treatment period indicated by performance on standardized tests, trained materials, or both. Treatment effects generalized to some degree to untrained stimuli and to discourse measures and were generally maintained at follow-up testing.

Conclusions
Data support the utility of a 2nd treatment period. Results are relevant to rehabilitation in chronic aphasia, confirming that significant language gains continue well past the point of spontaneous recovery and can occur in a relatively short time period. Importantly, changes are not confined to a single treatment period, suggesting that people with aphasia may benefit from multiple doses of high-intensity treatment.
Abundance of zinc in the red giants of Galactic globular cluster 47 Tucanae
Authors: Černiauskas A. , Kučinskas A. , Klevas J. , Bonifacio P. , Ludwig H.-G. , Caffau E. , Steffen M. 
Published: June 2018

Aims. We investigate possible relations between the abundances of zinc and the light elements sodium, magnesium, and potassium in the atmospheres of red giant branch (RGB) stars of the Galactic globular cluster 47 Tuc and study connections between the chemical composition and dynamical properties of the cluster RGB stars.
Methods. The abundance of zinc was determined in 27 RGB stars of 47 Tuc using 1D local thermal equilibrium (LTE) synthetic line profile fitting to the high-resolution 2dF/HERMES spectra obtained with the Anglo-Australian Telescope (AAT). Synthetic spectra used in the fitting procedure were computed with the SYNTHE code and 1D ATLAS9 stellar model atmospheres.
Results. The average 1D LTE zinc-to-iron abundance ratio and its RMS variations due to star-to-star abundance spread determined in the sample of 27 RGB stars is 〈[Zn/Fe]〉1D LTE = 0.11 ± 0.09. We did not detect any statistically significant relations between the abundances of zinc and those of light elements. Neither did we find any significant correlation or anticorrelation between the zinc abundance in individual stars and their projected distance from the cluster center. Finally, no statistically significant relation between the absolute radial velocities of individual stars and the abundance of zinc in their atmospheres was detected. The obtained average [Zn/Fe]1DLTE ratio agrees well with those determined in this cluster in earlier studies and nearly coincides with that of Galactic field stars at this metallicity. All these results suggest that nucleosynthesis of zinc and light elements proceeded in separate, unrelated pathways in 47 Tuc.
Management of HCV-Related Liver Disease in Hemophilia and Thalassemia
Authors: Di Marco Vito , Rumi Maria Grazia , Colombo Massimo 
Published: June 2018

AbstractChronic infection with the hepatitis C virus (HCV) has long been the dominant complication of substitution therapy in patients with inherited blood disorders and the cause of anticipated death due to end-stage liver disease. In hemophilia, transmission of HCV with clotting factors concentrates started to be curbed in the mid-1980s following the adoption of procedures of virus inactivation of concentrates based on heat, whereas in the 1990s treatment of HCV infection with interferon monotherapy was attempted, however, with little success. The advent of combination therapy of interferon with ribavirin led to a substantial improvement of treatment outcome (40% rate of cure), that however was still of limited efficacy in patients with advanced liver disease, those with high load of HCV genotype 1, and patients coinfected with the human immunodeficiency virus. In this latter population, while the course of hepatitis C was accelerated as a consequence of immunodeficiency, the advent of highly active antiretroviral therapy led acquired immunodeficiency syndrome (AIDS) to decline and hepatitis C to progressively emerge as a dominant cause of mortality, in parallel. In patients with thalassemia, transfusion-related transmission of HCV was efficiently interrupted in 1992 with the advent of sensitive screening tests for testing donors for HCV, whereas treatment with interferon and ribavirin of infected thalassemics was constrained by an increased risk of anemia due to the hemolytic properties of ribavirin coupled with interferon-induced bone marrow suppression. The advent of safe and potent regimens based on the oral administration of direct antiviral agents has revolutionized therapy of HCV in patients with congenital blood diseases, providing substantial clinical benefits and making elimination of infection in these populations, possible.
A Primer on Systematic Reviews and Meta-Analyses
Authors: Nguyen Nghia H. , Singh Siddharth 
Published: June 2018

AbstractWith the rapid growth of biomedical literature, there is increasing need to make meaningful inferences from a comprehensive and complex body of evidence. Systematic reviews with or without meta-analyses offer an objective and summative approach to synthesize knowledge and critically appraise evidence to inform clinical practice. Systematic reviews also help identify key knowledge gaps for future investigation. In this review, the authors provide a step-by-step approach to conducting a systematic review. These include: (1) formulating a focused and clinically-relevant question; (2) designing a detailed review protocol with explicit inclusion and exclusion criteria; (3) performing a systematic literature search of multiple databases and unpublished data, in consultation with a medical librarian, to identify relevant studies; (4) meticulous data abstraction by at least two sets of investigators independently; (5) assessing risk of bias in individual studies; (6) quantitative synthesis with meta-analysis; and (7) critically and transparently ascertaining quality of evidence.
A Study of the Separation of Fibrinogen and Antihemophilic Factor (AHF) in Canine, Porcine, and Human Plasmas
Authors: Wagner Robert H. , Richardson Bobby A. , Brinkhous K. M 
Published: June 2018

Summary1. Studies are reported on attempts to separate antihemophilic factor (AHF) from fibrinogen in plasma by selective adsorption with fuller’s earth, aluminum hydroxide gel, and Seitz filtration.2. Fuller’s earth adsorption of canine plasma resulted in almost complete removal of fibrinogen without loss of AHF. By the use of this procedure as part of the fractionation procedure, potent AHF fractions free of fibrinogen have been obtained.3. Al(OH)3 adsorption of fibrinogen from bovine, canine, and human plasmas is greater than the adsorption of AHF. Al(OH)3 adsorption offers promise for the preparation of fibrinogen-poor AHF fractions of human or bovine plasma.4. Seitz filtration of plasma causes loss of AHF with little or no loss of fibrinogen.
Coagulation studies on „Reptilase”, an extract of the venom from Bothrops jararaca
Authors: Blombäck Birger , Blombäck Margareta , Nilsson Inga Marie 
Published: June 2018

SummaryReptilase — the clot-promoting extract of the venom of Bothrops jararaca — was found to have a thrombin-like activity. No effect could be demonstrated in the first phase of coagulation. Unlike bovine thrombin it was not inactivated by heparin + heparin-cofactor or by the antithrombin of normal plasma. Analyses of N-terminal aminoacids in the fibrin formed by Reptilase revealed the same aminoacids as in the fibrin formed by bovine thrombin. Quantitative differences found may reflect different specificity of the two enzymes.It is concluded that the use of Reptilase as a haemostaticum is unwarranted.We wish to thank Professor Erik Jorpes for valuable advice and support in this investigation.