bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient communication dynamics on macro-connectome, and the propagation speed
Authors: Shimono Masanori , Hatano Naomichi 
Published: January 2018

AbstractGlobal communication dynamics in the brain can be captured using fMRI, MEG, or electrocorticography (ECoG), and the global slow dynamics often represent anatomical constraints. Complementary single-/multi-unit recordings have described local fast temporal dynamics. However, global fast temporal dynamics remain incompletely understood with considering of anatomical constraints. Therefore, we compared temporal aspects of cross-area propagations of single-unit recordings and ECoG, and investigated their anatomical bases. First, we demonstrated how both evoked and spontaneous ECoGs can accurately predict latencies of single-unit recordings. Next, we estimated the propagation velocity (1.0–1.5 m/s) from brain-wide data and found that it was fairly stable among different conscious levels. We also found that the shortest paths in anatomical topology strongly predicted the latencies. Finally, we demonstrated that Communicability, a novel graph-theoretic measure, is able to quantify that more than 90% of paths should use shortest paths and the remaining are non-shortest walks. These results revealed that macro-connectome is efficiently wired for detailed communication dynamics in the brain.
Double blind microarray-based polysaccharide profiling enables parallel identification of uncharacterized polysaccharides and carbohydrate-binding proteins with unknown specificities
Authors: Salmeán Armando A. , Guillouzo Alexia , Duffieux Delphine , Jam Murielle , Matard-Mann Maria , Larocque Robert , Pedersen Henriette L. , Michel Gurvan , Czjzek Mirjam , Willats William G. T. , Hervé Cécile 
Published: January 2018

AbstractMarine algae are one of the largest sources of carbon on the planet. The microbial degradation of algal polysaccharides to their constitutive sugars is a cornerstone in the global carbon cycle in oceans. Marine polysaccharides are highly complex and heterogeneous, and poorly understood. This is also true for marine microbial proteins that specifically degrade these substrates and when characterized, they are frequently ascribed to new protein families. Marine (meta)genomic datasets contain large numbers of genes with functions putatively assigned to carbohydrate processing, but for which empirical biochemical activity is lacking. There is a paucity of knowledge on both sides of this protein/carbohydrate relationship. Addressing this ‘double blind’ problem requires high throughput strategies that allow large scale screening of protein activities, and polysaccharide occurrence. Glycan microarrays, in particular the Comprehensive Microarray Polymer Profiling (CoMPP) method, are powerful in screening large collections of glycans and we described the integration of this technology to a medium throughput protein expression system focused on marine genes. This methodology (Double Blind CoMPP or DB-CoMPP) enables us to characterize novel polysaccharide-binding proteins and to relate their ligands to algal clades. This data further indicate the potential of the DB-CoMPP technique to accommodate samples of all biological sources.
Structural, microstructural and magnetic evolution in cryo milled carbon doped MnAl
Authors: Fang Hailiang , Cedervall Johan , Hedlund Daniel , Shafeie Samrand , Deledda Stefano , Olsson Fredrik , von Fieandt Linus , Bednarcik Jozef , Svedlindh Peter , Gunnarsson Klas , Sahlberg Martin 
Published: January 2018

AbstractThe low cost, rare earth free τ-phase of MnAl has high potential to partially replace bonded Nd2Fe14B rare earth permanent magnets. However, the τ-phase is metastable and it is experimentally difficult to obtain powders suitable for the permanent magnet alignment process, which requires the fine powders to have an appropriate microstructure and high τ-phase purity. In this work, a new method to make high purity τ-phase fine powders is presented. A high purity τ-phase Mn0.55Al0.45C0.02 alloy was synthesized by the drop synthesis method. The drop synthesized material was subjected to cryo milling and followed by a flash heating process. The crystal structure and microstructure of the drop synthesized, cryo milled and flash heated samples were studied by X-ray in situ powder diffraction, scanning electron microscopy, X-ray energy dispersive spectroscopy and electron backscatter diffraction. Magnetic properties and magnetic structure of the drop synthesized, cryo milled, flash heated samples were characterized by magnetometry and neutron powder diffraction, respectively. The results reveal that the 2 and 4 hours cryo milled and flash heated samples both exhibit high τ-phase purity and micron-sized round particle shapes. Moreover, the flash heated samples display high saturation magnetization as well as increased coercivity.
The FDA-approved anti-cancer drugs, streptozotocin and floxuridine, reduce the virulence of Staphylococcus aureus
Authors: Yeo Won-Sik , Arya Rekha , Kim Kyeong Kyu , Jeong Hyunyoung , Cho Kyu Hong , Bae Taeok 
Published: January 2018

AbstractIn Staphylococcus aureus, an important Gram-positive human pathogen, the SaeRS two-component system is essential for the virulence and a good target for the development of anti-virulence drugs. In this study, we screened 12,200 small molecules for Sae inhibitors and identified two anti-cancer drugs, streptozotocin (STZ) and floxuridine (FU), as lead candidates for anti-virulence drug development against staphylococcal infections. As compared with STZ, FU was more efficient in repressing Sae-regulated promoters and protecting human neutrophils from S. aureus-mediated killing. FU inhibited S. aureus growth effectively whereas STZ did not. Intriguingly, RNA-seq analysis suggests that both compounds inhibit other virulence-regulatory systems such as Agr, ArlRS, and SarA more efficiently than they inhibit the Sae system. Both compounds induced prophages from S. aureus, indicating that they cause DNA damages. Surprisingly, a single administration of the drugs was sufficient to protect mice from staphylococcal intraperitoneal infection. Both compounds showed in vivo efficacy in a murine model of blood infection too. Finally, at the experimental dosage, neither compound showed any noticeable side effects on blood glucose level or blood cell counts. Based on these results, we concluded that STZ and FU are promising candidates for anti-virulence drug development against S. aureus infection.
Quantitative Magnetization Transfer in Monitoring Glioblastoma (GBM) Response to Therapy
Authors: Mehrabian Hatef , Myrehaug Sten , Soliman Hany , Sahgal Arjun , Stanisz Greg J. 
Published: January 2018

AbstractQuantitative magnetization transfer (qMT) was used as a biomarker to monitor glioblastoma (GBM) response to chemo-radiation and identify the earliest time-point qMT could differentiate progressors from non-progressors. Nineteen GBM patients were recruited and MRI-scanned before (Day0), two weeks (Day14), and four weeks (Day28) into the treatment, and one month after the end of the treatment (Day70). Comprehensive qMT data was acquired, and a two-pool MT model was fit to the data. Response was determined at 3–8 months following the end of chemo-radiation. The amount of magnetization transfer ($${\bf{R}}{{\bf{M}}}_{{\bf{0b}}}/{{\bf{R}}}_{{\bf{a}}}$$
R

M

0b

/

R

a

) was significantly lower in GBM compared to normal appearing white matter (p < 0.001). Statistically significant difference was observed in $${\bf{R}}{{\bf{M}}}_{{\bf{0b}}}/{{\bf{R}}}_{{\bf{a}}}$$

R

M

0b

/

R

a

at Day0 between non-progressors (1.06 ± 0.24) and progressors (1.64 ± 0.48), with p = 0.006. Changes in several qMT parameters between Day14 and Day0 were able to differentiate the two cohorts with $${\bf{R}}{{\bf{M}}}_{{\bf{0b}}}/{{\bf{R}}}_{{\bf{a}}}$$

R

M

0b

/

R

a

providing the best separation (relative $${\bf{R}}{{\bf{M}}}_{{\bf{0b}}}/{{\bf{R}}}_{{\bf{a}},{\bf{Non}}-{\bf{progressor}}}$$

R

M

0b

/

R

a
,
Non
−
progressor

= 1.34 ± 0.21, relative $${\bf{R}}{{\bf{M}}}_{{\bf{0b}}}/{{\bf{R}}}_{{\bf{a}},{\bf{progressor}}}$$

R

M

0b

/

R

a
,
progressor

= 1.07 ± 0.08, p = 0.031). Thus, qMT characteristics of GBM are more sensitive to treatment effects compared to clinically used metrics. qMT could assess tumor aggressiveness and identify early progressors even before the treatment. Changes in qMT parameters within the first 14 days of the treatment were capable of separating early progressors from non-progressors, making qMT a promising biomarker to guide adaptive radiotherapy for GBM.
Escaping the Ashby limit for mechanical damping/stiffness trade-off using a constrained high internal friction interfacial layer
Authors: Unwin A. P. , Hine P. J. , Ward I. M. , Fujita M. , Tanaka E. , Gusev A. A. 
Published: January 2018

AbstractThe development of new materials with reduced noise and vibration levels is an active area of research due to concerns in various aspects of environmental noise pollution and its effects on health. Excessive vibrations also reduce the service live of the structures and limit the fields of their utilization. In oscillations, the viscoelastic moduli of a material are complex and it is their loss part – the product of the stiffness part and loss tangent – that is commonly viewed as a figure of merit in noise and vibration damping applications. The stiffness modulus and loss tangent are usually mutually exclusive properties so it is a technological challenge to develop materials that simultaneously combine high stiffness and high loss. Here we achieve this rare balance of properties by filling a solid polymer matrix with rigid inorganic spheres coated by a sub-micron layer of a viscoelastic material with a high level of internal friction. We demonstrate that this combination can be experimentally realised and that the analytically predicted behaviour is closely reproduced, thereby escaping the often termed ‘Ashby’ limit for mechanical stiffness/damping trade-off and offering a new route for manufacturing advanced composite structures with markedly reduced noise and vibration levels.
Realization of a thermal cloak–concentrator using a metamaterial transformer
Authors: Liu Ding-Peng , Chen Po-Jung , Huang Hsin-Haou 
Published: January 2018

AbstractBy combining rotating squares with auxetic properties, we developed a metamaterial transformer capable of realizing metamaterials with tunable functionalities. We investigated the use of a metamaterial transformer-based thermal cloak–concentrator that can change from a cloak to a concentrator when the device configuration is transformed. We established that the proposed dual-functional metamaterial can either thermally protect a region (cloak) or focus heat flux in a small region (concentrator). The dual functionality was verified by finite element simulations and validated by experiments with a specimen composed of copper, epoxy, and rotating squares. This work provides an effective and efficient method for controlling the gradient of heat, in addition to providing a reference for other thermal metamaterials to possess such controllable functionalities by adapting the concept of a metamaterial transformer.
Effect of nanopatterning on mechanical properties of Lithium anode
Authors: Campbell Colin , Lee Yong Min , Cho Kuk Young , Lee Young-Gi , Lee Byeongdu , Phatak Charudatta , Hong Seungbum 
Published: January 2018

AbstractOne of the challenges in developing Lithium anodes for Lithium ion batteries (LIB) is controlling the formation of Li dendrites during cycling of the battery. Nanostructuring and nanopatterning of electrodes shows a promising way to suppress the growth of Li dendrites. However, in order to control this behavior, a fundamental understanding of the effect of nanopatterning on the electro-mechanical properties of Li metal is necessary. In this paper, we have investigated the mechanical and wear properties of Li metal using Atomic Force Microscopy (AFM) in an airtight cell. By using different load regimes, we determined the mechanical properties of Li metal. We show that as a result of nanopatterning, Li metal surface underwent work hardening due to residual compressive stress. The presence of such stresses can help to improve cycle lifetime of LIBs with Li anodes and obtain very high energy densities. Keywords: Nanopatterning, mechanical properties, Li anode, Lithium ion batteries
Anti-adipogenic effects of KD025 (SLx-2119), a ROCK2-specific inhibitor, in 3T3-L1 cells
Authors: Diep Duy Trong Vien , Hong Kyungki , Khun Triyeng , Zheng Mei , ul-Haq Asad , Jun Hee-Sook , Kim Young-Bum , Chun Kwang-Hoon 
Published: January 2018

AbstractAdipose tissue is a specialized organ that synthesizes and stores fat. During adipogenesis, Rho and Rho-associated kinase (ROCK) 2 are inactivated, which enhances the expression of pro-adipogenic genes and induces the loss of actin stress fibers. Furthermore, pan ROCK inhibitors enhance adipogenesis in 3T3-L1 cells. Here, we show that KD025 (formerly known as SLx-2119), a ROCK2-specific inhibitor, suppresses adipogenesis in 3T3-L1 cells partially through a ROCK2-independent mechanism. KD025 downregulated the expression of key adipogenic transcription factors PPARγ and C/EBPα during adipogenesis in addition to lipogenic factors FABP4 and Glut4. Interestingly, adipogenesis was blocked by KD025 during days 1~3 of differentiation; after differentiation terminated, lipid accumulation was unaffected. Clonal expansion occurred normally in KD025-treated cells. These results suggest that KD025 could function during the intermediate stage after clonal expansion. Data from depletion of ROCKs showed that KD025 suppressed cell differentiation partially independent of ROCK’s activity. Furthermore, no further loss of actin stress fibers emerged in KD025-treated cells during and after differentiation compared to control cells. These results indicate that in contrast to the pro-adipogenic effect of pan-inhibitors, KD025 suppresses adipogenesis in 3T3-L1 cells by regulating key pro-adipogenic factors. This outcome further implies that KD025 could be a potential anti-adipogenic/obesity agent.
Heme interaction of the intrinsically disordered N-terminal peptide segment of human cystathionine-β-synthase
Authors: Kumar Amit , Wißbrock Amelie , Goradia Nishit , Bellstedt Peter , Ramachandran Ramadurai , Imhof Diana , Ohlenschläger Oliver 
Published: January 2018

AbstractCystathionine-β-synthase (CBS) belongs to a large family of pyridoxal 5’-phosphate (PLP)-dependent enzymes, responsible for the sulfur metabolism. The heme-dependent protein CBS is part of regulatory pathways also involving the gasotransmitter hydrogen sulfide. Malfunction of CBS can lead to pathologic conditions like cancer, cardiovascular and neurodegenerative disorders. Truncation of residues 1–40, absent in X-ray structures of CBS, reduces but does not abolish the activity of the enzyme. Here we report the NMR resonance assignment and heme interaction studies for the N-terminal peptide stretch of CBS. We present NMR-spectral evidence that residues 1–40 constitute an intrinsically disordered region in CBS and interact with heme via a cysteine-proline based motif.
Knockdown of SPRY4 and SPRY4-IT1 inhibits cell growth and phosphorylation of Akt in human testicular germ cell tumours
Authors: Das Mrinal K. , Furu Kari , Evensen Herman F. , Haugen Øyvind P. , Haugen Trine B. 
Published: January 2018

AbstractTesticular germ cell tumour (TGCT) is the most common cancer in young men in large parts of the world, but the aetiology is mainly unknown. Genome-wide association studies have so far identified about 50 susceptibility loci associated with TGCT, including SPRY4. SPRY4 has shown tumour suppressor activity in several cancer cells, such as lung and prostate, while it was found to act as an oncogene in ovarian cancer. An intronic region within the SPRY4 gene produces a long non-coding RNA, SPRY4-IT1, which has been reported to act as an oncogene in melanoma, breast cancer, and colorectal cancer, and as a tumour suppressor in lung cancer. The roles of SPRY4 and SPRY4-IT1 in TGCT development are yet unknown. We found higher expression levels of SPRY4, both mRNA and protein, and of SPRY4-IT1 in human TGCT than in normal adult testis. Small-interfering RNA (siRNA)-mediated transient knockdown of SPRY4 and SPRY4-IT1 in two TGCT cell lines 833 K and NT2-D1 resulted in decreased cell growth, migration, and invasion. Knockdown of SPRY4 and SPRY4-IT1 also led to a significant reduction in the phosphorylation of Akt. Our findings indicate that SPRY4 and SPRY4-IT1 may act as oncogenes in TGCTs via activation of the PI3K / Akt signalling pathway.
Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade
Authors: López M. , Rueda A. , Florido J. P. , Blasco L. , Fernández-García L. , Trastoy R. , Fernández-Cuenca F. , Martínez-Martínez L. , Vila J. , Pascual A. , Bou G. , Tomas M. 
Published: January 2018

AbstractIn this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for blaOXA 24/40 ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.
Virtual acoustics in inhomogeneous media with single-sided access
Authors: Wapenaar Kees , Brackenhoff Joeri , Thorbecke Jan , van der Neut Joost , Slob Evert , Verschuur Eric 
Published: January 2018

AbstractA virtual acoustic source inside a medium can be created by emitting a time-reversed point-source response from the enclosing boundary into the medium. However, in many practical situations the medium can be accessed from one side only. In those cases the time-reversal approach is not exact. Here, we demonstrate the experimental design and use of complex focusing functions to create virtual acoustic sources and virtual receivers inside an inhomogeneous medium with single-sided access. The retrieved virtual acoustic responses between those sources and receivers mimic the complex propagation and multiple scattering paths of waves that would be ignited by physical sources and recorded by physical receivers inside the medium. The possibility to predict complex virtual acoustic responses between any two points inside an inhomogeneous medium, without needing a detailed model of the medium, has large potential for holographic imaging and monitoring of objects with single-sided access, ranging from photoacoustic medical imaging to the monitoring of induced-earthquake waves all the way from the source to the earth’s surface.
Impact of mid-season sulphur deficiency on wheat nitrogen metabolism and biosynthesis of grain protein
Authors: Yu Zitong , Juhasz Angela , Islam Shahidul , Diepeveen Dean , Zhang Jingjuan , Wang Penghao , Ma Wujun 
Published: January 2018

AbstractWheat (Triticum aestivum) quality is mainly determined by grain storage protein compositions. Sulphur availability is essential for the biosynthesis of the main wheat storage proteins. In this study, the impact of different sulphur fertilizer regimes on a range of agronomically important traits and associated gene networks was studied. High-performance liquid chromatography was used to analyse the protein compositions of grains grown under four different sulphur treatments. Results revealed that sulphur supplementation had a significant effect on grain yield, harvest index, and storage protein compositions. Consequently, two comparative sulphur fertilizer treatments (0 and 30 kg ha−1 sulphur, with 50 kg ha−1 nitrogen) at seven days post-anthesis were selected for a transcriptomics analysis to screen for differentially expressed genes (DEGs) involved in the regulation of sulphur metabolic pathways. The International Wheat Genome Sequencing Consortium chromosome survey sequence was used as reference. Higher sulphur supply led to one up-regulated DEG and sixty-three down-regulated DEGs. Gene ontology enrichment showed that four down-regulated DEGs were significantly enriched in nitrogen metabolic pathway related annotation, three of which were annotated as glutamine synthetase. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment identified three significantly enriched pathways involved in nitrogen and amino acid metabolism.
Spheroid-cultured human umbilical cord-derived mesenchymal stem cells attenuate hepatic ischemia-reperfusion injury in rats
Authors: Sun Yi , Wang Yang , Zhou Liang , Zou Yizhou , Huang Gengwen , Gao Ge , Ting Shi , Lei Xiong , Ding Xiang 
Published: January 2018

AbstractMesenchymal stem cell (MSC) transplantation is a promising treatment for ischemia-reperfusion injury (IRI). However, its effects on hepatic IRI were not consistent in the previous studies. 3D spheroid-cultured MSCs enhance their production of trophic and anti-inflammatory properties, but their effects on hepatic IRI remain unclear. In this study, we compared the 3D spheroid-cultured human umbilical derived MSCs (3D UC-MSCs) with 2D-cultured UC-MSCs (2D UC-MSCs) on treating hepatic IRI. The RNA sequencing data showed that suppression of cell mitosis, response to hypoxia, inflammation, and angiogenesis were the top genetic changes in 3D UC-MSCs compared with 2D UC-MSCs. Although both pro-inflammatory and anti-inflammatory genes were upregulated in the 3D UC-MSCs, the mRNA and protein of an RNase (ZC3H12A), which turnovers the mRNA of pro-inflammatory genes at the post-transcript level, were significantly upregulated in 3D UC-MSCs. 3D UC-MSCs reduced the secretion of many chemokines and growth factors, but increased the secretion of vascular endothelial growth factor. Compared with the vehicle and 2D UC-MSCs, 3D UC-MSCs significantly reduced hepatic IRI in rats, based on the plasma aminotransferase levels, liver damage scores, neutrophil infiltration, hepatocyte apoptosis and expression of inflammation-associated genes. These findings suggest that 3D UC-MSCs therapy is a promising treatment for hepatic IRI.