bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)
Authors: Zhang Meng , Huang Wenyang , Xia Zijun , Liu Jiahui , Xie Jiankun , Zhang Fantao 
Published: July 2017

AbstractDongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.
Metabonomics Approach to Assessing the Modulatory Effects of Kisspeptin-10 on Liver Injury Induced by Heat Stress in Rats
Authors: Hou Yuanlong , Wang Xiaoyan , Ping Jihui , Lei Zhihai , Gao Yingdong , Ma Zhiyu , Jia Cuicui , Zhang Zheng , Li Xiang , Jin Mengmeng , Li Xiaoliang , Suo Chuan , Zhang Ying , Su Juan 
Published: July 2017

AbstractThe protective effects of Kisspeptin on heat-induced oxidative stress in rats were investigated by using a combination of biochemical parameters and metabonomics. Metabonomic analyses were performed using gas chromatography/mass spectrometry in conjunction with multivariate and univariate statistical analyses. At the end point of the heat stress experiment, histological observation, ultrastructural analysis and biochemical parameters were measured. Metabonomic analysis of liver tissue revealed that Kisspeptin mainly attenuated the alteration of purine metabolism and fatty acid metabolism pathways. Futhermore, Kisspeptin also increased the levels of GSH, T-AOC as well as SOD activities, and upregulated MDA levels. These results provide important mechanistic insights into the protective effects of Kisspeptin against heat-induced oxidative stress.
Contrast-Enhanced Ultrasound Imaging Quantification of Adventitial Vasa Vasorum in a Rabbit Model of Varying Degrees of Atherosclerosis
Authors: Li Xiaoying , Zhang Ruyou , Li Zongmin , Ning Chunping , Wang Zhenzhen , Dang Meizheng , Peng Yanqing , Han Xuesong , Sun Litao , Tian Jiawei 
Published: July 2017

AbstractThis study used an atherosclerotic rabbit model to investigate the feasibility of quantifying adventitial vasa vasorum (VV) via contrast-enhanced ultrasound (CEUS) imaging to identify early atherosclerosis. Recent evidence has linked adventitial VV with atherosclerotic plaque progression and vulnerability. A growth in VV density has been detected preceding intimal thickening and even endothelial dysfunction. In our study, carotid atherosclerosis rabbit models were used, and animals underwent CEUS imaging at the end of the atherosclerotic induction period. Normalized maximal video-intensity enhancement (MVE) was calculated to quantify VV density. After CEUS imaging, animals were euthanized, and their carotids were processed for histopathological analysis following staining for CD31 and VEGF. Adventitial normalized MVE increased as atherosclerosis progressed (p < 0.001), and normalized MVE also progressed, demonstrating a linear correlation with histological findings (r = 0.634, p < 0.001 for VEGF-positive; r = 0.538, p < 0.001 for CD31-positive). Thus, we histologically validated that CEUS imaging can be used to quantify the development of adventitial VV associated with atherosclerosis progression. This method can be used for monitoring the VV to detect early atherosclerosis.
Greenhouse gas emissions as a result of spectators travelling to football in England
Authors: Dosumu Adekunle , Colbeck Ian , Bragg Rachel 
Published: July 2017

AbstractTransport remains a critical avenue in the attempt to reduce greenhouse gas (GHG) emissions and any significant effort to reduce travel GHG emissions will need to encourage a movement towards more fuel-efficient, less polluting behaviours. The aim of this paper is to calculate GHG emissions arising from the travel of spectators to and from football games within eight football tiers (3 to 10) in England, and to extrapolate this to a national level. The study comprised of 1649 participants with an average age of 42 years (M = 42.63, SD = 17.10). Participants travelled to and from games by walking, cycling, car, bus, train or taxi. The average distance travelled to and from games was 41.5 km. A Kruskal-Wallis test was conducted to evaluate differences in travel related GHG emissions between the eight football tiers during the 2012/13 season. The results indicate significant differences between football tiers’ GHG emissions, H(7) = 46.474, p < 0.001. The annual GHG emission of spectators from the 8 tiers for the 2012/13 season was estimated at 56,237 tonnes of CO2e, accounting for less than 0.05% of transport emissions in England. Football authorities should have robust travel plans and educate spectators to employ more sustainable travel plans to games.
Evaluation of realistic layouts for next generation on-scalp MEG: spatial information density maps
Authors: Riaz Bushra , Pfeiffer Christoph , Schneiderman Justin F. 
Published: July 2017

AbstractWhile commercial magnetoencephalography (MEG) systems are the functional neuroimaging state-of-the-art in terms of spatio-temporal resolution, MEG sensors have not changed significantly since the 1990s. Interest in newer sensors that operate at less extreme temperatures, e.g., high critical temperature (high-Tc) SQUIDs, optically-pumped magnetometers, etc., is growing because they enable significant reductions in head-to-sensor standoff (on-scalp MEG). Various metrics quantify the advantages of on-scalp MEG, but a single straightforward one is lacking. Previous works have furthermore been limited to arbitrary and/or unrealistic sensor layouts. We introduce spatial information density (SID) maps for quantitative and qualitative evaluations of sensor arrays. SID-maps present the spatial distribution of information a sensor array extracts from a source space while accounting for relevant source and sensor parameters. We use it in a systematic comparison of three practical on-scalp MEG sensor array layouts (based on high-Tc SQUIDs) and the standard Elekta Neuromag TRIUX magnetometer array. Results strengthen the case for on-scalp and specifically high-Tc SQUID-based MEG while providing a path for the practical design of future MEG systems. SID-maps are furthermore general to arbitrary magnetic sensor technologies and source spaces and can thus be used for design and evaluation of sensor arrays for magnetocardiography, magnetic particle imaging, etc.
Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube
Authors: Kaul-Strehlow Sabrina , Urata Makoto , Praher Daniela , Wanninger Andreas 
Published: July 2017

AbstractA tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.
Simultaneous determination of hydrophilic and lipophilic constituents in herbal medicines using directly-coupled reversed-phase and hydrophilic interaction liquid chromatography-tandem mass spectrometry
Authors: Sun Wan-Yang , Lu Qin-Wei , Gao Hao , Tong Ling , Li Dong-Xiang , Zhou Zheng-Qun , Jiang Zheng-Jin , Sun Henry , Bi Kai-Shun 
Published: July 2017

AbstractLimitations in the separation ability of conventional liquid chromatography system remains a challenge in developing a versatile method for simultaneously determining both hydrophilic and lipophilic constituents in herbal medicines (HMs). To measure compounds covering a broad polarity span in HMs, we developed a directly-coupled reversed-phase and hydrophilic interaction liquid chromatography-tandem mass spectrometry system. Samples were firstly separated according to lipophilicity by using a C18 column. Utilizing a T-piece as connector, the eluent was then pumped into an amide column to get further separation that mainly based on the hydrogen bonding effects. Dan-Qi pair, an extensively used herb-combined prescription in China, was selected to test the practicability and performance of the established system. A total of 27 components, containing 9 hydrophilic and 18 lipophilic constituents, were simultaneously determined using a schedule multiple reaction monitoring method in 15 min. Up to 69.9% content could be monitored in one injection in Dan-Qi pair extract, showing a significant advantage over previous methods. The proposed method was expected to benefit the controllability of herbal medicines.
Experimental evidence of high pressure decoupling between charge transport and structural dynamics in a protic ionic glass-former
Authors: Wojnarowska Z. , Rams-Baron M. , Knapik-Kowalczuk J. , Połatyńska A. , Pochylski M. , Gapinski J. , Patkowski A. , Wlodarczyk P. , Paluch M. 
Published: July 2017

AbstractIn this paper the relaxation dynamics of ionic glass-former acebutolol hydrochloride (ACB-HCl) is studied as a function of temperature and pressure by using dynamic light scattering and broadband dielectric spectroscopy. These unique experimental data provide the first direct evidence that the decoupling between the charge transport and structural relaxation exists in proton conductors over a wide T-P thermodynamic space, with the time scale of structural relaxation being constant at the liquid-glass transition (τα = 1000 s). We demonstrate that the enhanced proton transport, being a combination of intermolecular H+ hopping between cation and anion as well as tautomerization process within amide moiety of ACB molecule, results in a breakdown of the Stokes-Einstein relation at ambient and elevated pressure with the fractional exponent k being pressure dependent. The dT
g
/dP coefficient, stretching exponent βKWW and dynamic modulus E
a
/ΔV
#
were found to be the same regardless of the relaxation processes studied. This is in contrast to the apparent activation volume parameter that is different when charge transport and structural dynamics are considered. These experimental results together with theoretical considerations create new ideas to design efficient proton conductors for potential electrochemical applications.
Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma
Authors: Batmanov Kirill , Wang Wei , Bjørås Magnar , Delabie Jan , Wang Junbai 
Published: July 2017

AbstractThe contribution of mutations in regulatory regions to tumorigenesis has been the subject of many recent studies. We propose a new framework for integrative analysis of genome-wide sequencing data by considering diverse genetic information. This approach is applied to study follicular lymphoma (FL), a disease for which little is known about the contribution of regulatory gene mutations. Results from a test FL cohort revealed three novel highly recurrent regulatory mutation blocks near important genes implicated in FL, BCL6 and BCL2. Similar findings were detected in a validation FL cohort. We also found transcription factors (TF) whose binding may be disturbed by these mutations in FL: disruption of FOX TF family near the BCL6 promoter may result in reduced BCL6 expression, which then increases BCL2 expression over that caused by BCL2 gene translocation. Knockdown experiments of two TF hits (FOXD2 or FOXD3) were performed in human B lymphocytes verifying that they modulate BCL6/BCL2 according to the computationally predicted effects of the SNVs on TF binding. Overall, our proposed integrative analysis facilitates non-coding driver identification and the new findings may enhance the understanding of FL.
Blood-testis barrier integrity depends on Pin1 expression in Sertoli cells
Authors: Islam Rabia , Yoon Heein , Kim Bong-soo , Bae Han-sol , Shin Hye-rim , Kim Woo-Jin , Yoon Won-joon , Lee Yun-Sil , Woo Kyung Mi , Baek Jeong-Hwa , Ryoo Hyun-Mo 
Published: July 2017

AbstractThe conformation and function of a subset of serine and threonine-phosphorylated proteins are regulated by the prolyl isomerase Pin1 through isomerization of phosphorylated Ser/Thr-Pro bonds. Pin1 is intensely expressed in Sertoli cells, but its function in this post mitotic cell remains unclear. Our aim was to investigate the role of Pin1 in the Sertoli cells. Lack of Pin1 caused disruption of the blood-testis barrier. We next investigated if the activin pathways in the Sertoli cells were affected by lack of Pin1 through immunostaining for Smad3 protein in testis tissue. Indeed, lack of Pin1 caused reduced Smad3 expression in the testis tissue, as well as a reduction in the level of N-Cadherin, a known target of Smad3. Pin1−/− testes express Sertoli cell marker mRNAs in a pattern similar to that seen in Smad3+/− mice, except for an increase in Wt1 expression. The resulting dysregulation of N-Cadherin, connexin 43, and Wt1 targets caused by lack of Pin1 might affect the mesenchymal–epithelial balance in the Sertoli cells and perturb the blood-testis barrier. The effect of Pin1 dosage in Sertoli cells might be useful in the study of toxicant-mediated infertility, gonadal cancer, and for designing male contraceptives.
Enhanced robustness of evolving open systems by the bidirectionality of interactions between elements
Authors: Ogushi Fumiko , Kertész János , Kaski Kimmo , Shimada Takashi 
Published: July 2017

AbstractLiving organisms, ecosystems, and social systems are examples of complex systems in which robustness against inclusion of new elements is an essential feature. A recently proposed simple model has revealed a general mechanism by which such systems can become robust against inclusion of elements with totally random interactions when the elements have a moderate number of links. The interaction is, however, in many systems often intrinsically bidirectional like for mutual symbiosis and competition in ecology. This study reports the strong reinforcement effect of the bidirectionality of the interactions on the robustness of evolving systems. We show that the system with purely bidirectional interactions can grow with twofold average degree, in comparison with the purely unidirectional system. This drastic shift of the transition point comes from the reinforcement of each node, not from a change in structure of the emergent system. For systems with partially bidirectional interactions we find that the regime of the growing phase gets expanded. In the dense interaction regime, there exists an optimum proportion of bidirectional interactions for the growth rate at around 1/3. In the sparsely connected systems, small but finite fraction of bidirectional links can change the system’s behaviour from non-growing to growing.
Development of an integrated Monte Carlo model for glioblastoma multiforme treated with boron neutron capture therapy
Authors: Moghaddasi Leyla , Bezak Eva 
Published: July 2017

AbstractGlioblastomas (GBM) are notorious for their high fatality rate. Boron Neutron Capture Therapy (BNCT) being a biochemically targeted type of radiotherapy is a potent modality for GBM. In the current work, a BNCT treatment modelling framework for GBM was developed. Optimal Clinical Target Volume (CTV) margins for GBM-BNCT and the BNCT efficacy have been investigated. The model integrated a cell-based dosimetry model, an in-house-developed epithermal neutron beam model and previously-developed Microscopic Extension Probability (MEP) model. The system was defined as a cubic ICRP-brain phantom divided into 20 μm side voxels. The corresponding 10B concentrations in GBM and normal brain cells were applied. The in-silico model was irradiated with the epithermal neutron beam using 2 and 2.5 cm CTV margins. Results from the cell-based dosimetry and the MEP models were combined to calculate GBM cell survival fractions (SF) post BNCT and compared to x-ray radiotherapy (XRT) SFs. Compared to XRT, the SF within the beam decreased by five orders of magnitudes and the total SF was reduced three times following BNCT. CTV extension by 0.5 cm reduced the SF by additional (53.8 ± 0.3)%. In conclusion, BNCT results in a more efficient cell kill. The extension of the CTV margin, however, may not increase the treatment outcome significantly.
Antibodies Against Modified NS1 Wing Domain Peptide Protect Against Dengue Virus Infection
Authors: Lai Yen-Chung , Chuang Yung-Chun , Liu Ching-Chuan , Ho Tzong-Shiann , Lin Yee-Shin , Anderson Robert , Yeh Trai-Ming 
Published: July 2017

AbstractDengue is the most common mosquito-transmitted viral infection for which an improved vaccine is still needed. Although nonstructural protein-1 (NS1) immunization can protect mice against dengue infection, molecular mimicry between NS1 and host proteins makes NS1-based vaccines challenging to develop. Based on the epitope recognized by the anti-NS1 monoclonal Ab (mAb) 33D2 which recognizes a conserved NS1 wing domain (NS1-WD) region but not host proteins, we synthesized a modified NS1-WD peptide to immunize mice. We found that both mAb 33D2 and modified NS1-WD peptide immune sera could induce complement-dependent lysis of dengue-infected but not un-infected cellsin vitro. Furthermore, either active immunization with the modified NS1-WD peptide or passive transfer of mAb 33D2 efficiently protected mice against all serotypes of dengue virus infection. More importantly, dengue patients with more antibodies recognized the modified NS1-WD peptide had less severe disease. Thus, the modified NS1-WD peptide is a promising dengue vaccine candidate.
Anti-diabetic Effects of Clostridium butyricum CGMCC0313.1 through Promoting the Growth of Gut Butyrate-producing Bacteria in Type 2 Diabetic Mice
Authors: Jia Lingling , Li Dongyao , Feng Ninghan , Shamoon Muhammad , Sun Zhenghua , Ding Lei , Zhang Hao , Chen Wei , Sun Jia , Chen Yong Q 
Published: July 2017

AbstractPatients with type 2 diabetes (T2D) have decreased butyrate-producing bacteria. We hypothesized that supplementation with butyrate-producing bacteria may exert beneficial effects on T2D. The current study investigated the effects of well-characterized butyrate-producing bacteria Clostridium butyricum CGMCC0313.1 (CB0313.1) on hyperglycemia and associated metabolic dysfunction in two diabetic mouse models. CB0313.1 was administered daily by oral gavage to leptin
db/db
mice for 5 weeks starting from 3 weeks of age, and to HF diabetic mice induced by high fat diet (HFD) plus streptozotocin (STZ) in C57BL/6J mice for 13 weeks starting from 4 weeks of age. CB0313.1 improved diabetic markers (fasting glucose, glucose tolerance, insulin tolerance, GLP-1 and insulin secretion), and decreased blood lipids and inflammatory tone. Furthermore, CB0313.1 reversed hypohepatias and reduced glucose output. We also found that CB0313.1 modulated gut microbiota composition, characterized by a decreased ratio of Firmicutes to Bacteroidetes, reduced Allobaculum bacteria that were abundant in HF diabetic mice and increased butyrate-producing bacteria. Changes in gut microbiota following CB0313.1 treatment were associated with enhanced peroxisome proliferator–activated receptor-γ (PPARγ), insulin signaling molecules and mitochondrial function markers. Together, our study suggests that CB0313.1 may act as a beneficial probiotic for the prevention and treatment of hyperglycemia and associated metabolic dysfunction.
Nanosecond laser coloration on stainless steel surface
Authors: Lu Yan , Shi Xinying , Huang Zhongjia , Li Taohai , Zhang Meng , Czajkowski Jakub , Fabritius Tapio , Huttula Marko , Cao Wei 
Published: July 2017

AbstractIn this work, we present laser coloration on 304 stainless steel using nanosecond laser. Surface modifications are tuned by adjusting laser parameters of scanning speed, repetition rate, and pulse width. A comprehensive study of the physical mechanism leading to the appearance is presented. Microscopic patterns are measured and employed as input to simulate light-matter interferences, while chemical states and crystal structures of composites to figure out intrinsic colors. Quantitative analysis clarifies the final colors and RGB values are the combinations of structural colors and intrinsic colors from the oxidized pigments, with the latter dominating. Therefore, the engineering and scientific insights of nanosecond laser coloration highlight large-scale utilization of the present route for colorful and resistant steels.
Conditional knockdown of hyaluronidase 2 in articular cartilage stimulates osteoarthritic progression in a mice model
Authors: Higuchi Yoshitoshi , Nishida Yoshihiro , Kozawa Eiji , Zhuo Lisheng , Arai Eisuke , Hamada Shunsuke , Morita Daigo , Ikuta Kunihiro , Kimata Koji , Ushida Takahiro , Ishiguro Naoki 
Published: July 2017

AbstractThe catabolism of hyaluronan in articular cartilage remains unclear. The aims of this study were to investigate the effects of hyaluronidase 2 (Hyal2) knockdown in articular cartilage on the development of osteoarthritis (OA) using genetic manipulated mice. Destabilization of the medial meniscus (DMM) model of Col2a promoter specific conditional Hyal2 knockout (Hyal
−/−
) mice was established and examined. Age related and DMM induced alterations of articular cartilage of knee joint were evaluated with modified Mankin score and immunohistochemical staining of MMP-13, ADAMTS-5, KIAA11199, and biotinylated- hyaluronan binding protein staining in addition to histomorphometrical analyses. Effects of Hyal2 suppression were also analyzed using explant culture of an IL-1α induced articular cartilage degradation model. The amount and size of hyaluronan in articular cartilage were higher in Hyal2
−/−
mice. Hyal2
−/−
mice exhibited aggravated cartilage degradation in age-related and DMM induced mice. MMP-13 and ADAMTS-5 positive chondrocytes were significantly higher in Hyal2
−/−
mice. Articular cartilage was more degraded in explant cultures obtained from Hyal2
−/−
mice. Knockdown of Hyal2 in articular cartilage induced OA development and progression possibly mediated by an imbalance of HA metabolism. This suggests that Hyal2 knockdown exhibits mucopolysaccharidosis-like OA change in articular cartilage similar to Hyal1 knockdown.