bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Impact of the Signet Ring Cell Type in Node-Negative Gastric Cancer
Authors: Kong Pengfei , Wu Ruiyan , Yang Chenlu , Geng Qirong , Liu Jianjun , Chen Shangxiang , Liu Xuechao , Ye Minting , He Wenzhuo , Yang Qiong , Xia Liangping , Xu Dazhi 
Published: July 2016

AbstractLittle is known regarding the prognostic impact of the signet ring cell (SRC) histotype on negative lymph nodes (LNs) in gastric cancer (GC). In this study, we aimed to investigate the differences between SRC and non-SRC GC patients without LN metastasis. The medical records of patients with GC who underwent gastrectomy at Sun Yat-Sen University Cancer Centre from 1996 to 2012 were reviewed to analyse the clinicopathologic characteristics associated with survival. A total of 480 cases of GC patients without LN metastasis were identified, which included 90 SRC GC patients and 390 non-SRC GC patients. Between the two groups, there were a host of significant differences in the American Joint Committee on Cancer, 7th edition (AJCC) stage. We found that SRC histology was correlated with a poor prognosis in terms of recurrence in node-negative GC patients and that SRC histologic analysis combined with AJCC staging maybe an effectual method for prediction of the recurrence rate. Additionally, we found that SRC GC presents a more dismal overall prognosis in patients with perineural or vascular invasion.
Locomotor preferences in terrestrial vertebrates: An online crowdsourcing approach to data collection
Authors: Lees John , Gardiner James , Usherwood James , Nudds Robert 
Published: July 2016

AbstractUnderstanding how animals move within their environment is a burgeoning field of research. Despite this, relatively basic data, such as the locomotor speeds that animals choose to walk at in the wild, are sparse. If animals choose to walk with dynamic similarity, they will move at equal dimensionless speeds, represented by Froude number (Fr). Fr may be interpreted from simple limb kinematics obtained from video data. Here, using Internet videos, limb kinematics were measured in 112 bird and mammal species weighing between 0.61 and 5400 kg. This novel method of data collection enabled the determination of kinematics for animals walking at their self-selected speeds without the need for exhaustive fieldwork. At larger sizes, both birds and mammals prefer to walk at slower relative speeds and relative stride frequencies, as preferred Fr decreased in larger species, indicating that Fr may not be a good predictor of preferred locomotor speeds. This may result from the observation that the minimum cost of transport is approached at lower Fr in larger species. Birds walk with higher duty factors, lower stride frequencies and longer stance times compared to mammals at self-selected speeds. The trend towards lower preferred Fr is also apparent in extinct vertebrate species.
Neural activity in the medial parietal area V6A while grasping with or without visual feedback
Authors: Breveglieri Rossella , Bosco Annalisa , Galletti Claudio , Passarelli Lauretta , Fattori Patrizia 
Published: July 2016

AbstractRecent works have reported that grasping movements are controlled not only by the dorsolateral visual stream, as generally thought, but also by the dorsomedial visual stream, and in particular by the medial posterior parietal area V6A. To date, the grasping activity of V6A neurons has been studied only in darkness. Here we studied the effect of visual feedback on grasp-related discharges of V6A neurons while the monkey was preparing and executing the grasping of a handle. We found that V6A grasping activity could be excited or inhibited by visual information. The neural population was divided into Visual, Motor, and Visuomotor cells. The majority of Visual and Visuomotor neurons did not respond to passive observation of the handle, suggesting that vision of action, rather than object vision, is the most effective factor. The present findings highlight the role of the dorsomedial visual stream in integrating visual and motor signals to monitor and correct grasping.
Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific Flyway of the United States
Authors: Bevins S. N. , Dusek R. J. , White C. L. , Gidlewski T. , Bodenstein B. , Mansfield K. G. , DeBruyn P. , Kraege D. , Rowan E. , Gillin C. , Thomas B. , Chandler S. , Baroch J. , Schmit B. , Grady M. J. , Miller R. S. , Drew M. L. , Stopak S. , Zscheile B. , Bennett J. , Sengl J. , Brady Caroline , Ip H. S. , Spackman E. , Killian M. L. , Torchetti M. K. , Sleeman J. M. , Deliberto T. J. 
Published: July 2016

AbstractA novel highly pathogenic avian influenza virus belonging to the H5 clade 2.3.4.4 variant viruses was detected in North America in late 2014. Motivated by the identification of these viruses in domestic poultry in Canada, an intensive study was initiated to conduct highly pathogenic avian influenza surveillance in wild birds in the Pacific Flyway of the United States. A total of 4,729 hunter-harvested wild birds were sampled and highly pathogenic avian influenza virus was detected in 1.3% (n = 63). Three H5 clade 2.3.4.4 subtypes were isolated from wild birds, H5N2, H5N8, and H5N1, representing the wholly Eurasian lineage H5N8 and two novel reassortant viruses. Testing of 150 additional wild birds during avian morbidity and mortality investigations in Washington yielded 10 (6.7%) additional highly pathogenic avian influenza isolates (H5N8 = 3 and H5N2 = 7). The geographically widespread detection of these viruses in apparently healthy wild waterfowl suggest that the H5 clade 2.3.4.4 variant viruses may behave similarly in this taxonomic group whereby many waterfowl species are susceptible to infection but do not demonstrate obvious clinical disease. Despite these findings in wild waterfowl, mortality has been documented for some wild bird species and losses in US domestic poultry during the first half of 2015 were unprecedented.
Nonlinear wave interactions between short pulses of different spatio-temporal extents
Authors: Sivan Y. , Rozenberg S. , Halstuch A. , Ishaaya A. A. 
Published: July 2016

AbstractWe study the nonlinear wave interactions between short pulses of different spatio-temporal extents. Unlike the well-understood mixing of quasi-monochromatic waves, this configuration is highly non-intuitive due to the complex coupling between the spatial and temporal degrees of freedom of the interacting pulses. We illustrate the process intuitively with transitions between different branches of the dispersion curves and interpret it in terms of spectral exchange between the interacting pulses. We verify our interpretation with an example whereby a spectrally-narrow pulse “inherits” the wide spectrum of a pump pulse centered at a different wavelength, using exact numerical simulations, as well as a simplified coupled mode analysis and an asymptotic analytical solution. The latter also provides a simple and intuitive quantitative interpretation. The complex wave mixing process studied here may enable flexible spatio-temporal shaping of short pulses and is the starting point of the study of more complicated systems.
Polarization domain wall pulses in a microfiber-based topological insulator fiber laser
Authors: Liu Jingmin , Li Xingliang , Zhang Shumin , Zhang Han , Yan Peiguang , Han Mengmeng , Pang Zhaoguang , Yang Zhenjun 
Published: July 2016

AbstractTopological insulators (TIs), are novel two-dimension materials, which can act as effective saturable absorbers (SAs) in a fiber laser. Moreover, based on the evanescent wave interaction, deposition of the TI on microfiber would create an effective SA, which has combined advantages from the strong nonlinear optical response in TI material together with the sufficiently-long-range interaction length in fiber taper. By using this type of TI SA, various scalar solitons have been obtained in fiber lasers. However, a single mode fiber always exhibits birefringence and hence can support two orthogonal degenerate modes. Here we investigate experimentally the vector characters of a TI SA fiber laser. Using the saturated absorption and the high nonlinearity of the TI SA, a rich variety of dynamic states, including polarization-locked dark pulses and their harmonic mode locked counterparts, polarization-locked noise-like pulses and their harmonic mode locked counterparts, incoherently coupled polarization domain wall pulses, including bright square pulses, bright-dark pulse pairs, dark pulses and bright square pulse-dark pulse pairs are all observed with different pump powers and polarization states.
Multicenter study on caries risk assessment in adults using survival Classification and Regression Trees
Authors: Arino Masumi , Ito Ataru , Fujiki Shozo , Sugiyama Seiichi , Hayashi Mikako 
Published: July 2016

AbstractDental caries is an important public health problem worldwide. This study aims to prove how preventive therapies reduce the onset of caries in adult patients and to identify patients with high or low risk of caries by using Classification and Regression Trees based survival analysis (survival CART). A clinical data set of 732 patients aged 20 to 64 years in nine Japanese general practices was analyzed with the following parameters: age, DMFT, number of mutans streptococci (SM) and Lactobacilli (LB), secretion rate and buffer capacity of saliva and compliance with a preventive program. Results showed the incidence of primary carious lesion was affected by SM, LB and compliance with a preventive program; secondary carious lesion was affected by DMFT, SM and LB. Survival CART identified high-risk patients for primary carious lesion according to their poor compliance with a preventive program and SM (≥106 CFU/ml) with a hazard ratio of 3.66 (p = 0.0002). In the case of secondary caries, patients with LB (≥105 CFU/ml) and DMFT (>15) were identified as high risk with a hazard ratio of 3.50 (p < 0.0001). We conclude that preventive programs can be effective in limiting the incidence of primary carious lesion.
Cationic lipid-nanoceria hybrids, a novel nonviral vector-mediated gene delivery into mammalian cells: investigation of the cellular uptake mechanism
Authors: Das Joydeep , Han Jae Woong , Choi Yun-Jung , Song Hyuk , Cho Ssang-Goo , Park Chankyu , Seo Han Geuk , Kim Jin-Hoi 
Published: July 2016

AbstractGene therapy is a promising technique for the treatment of various diseases. The development of minimally toxic and highly efficient non-viral gene delivery vectors is the most challenging undertaking in the field of gene therapy. Here, we developed dimethyldioctadecylammonium bromide (DODAB)–nanoceria (CeO2) hybrids as a new class of non-viral gene delivery vectors. These DODAB-modified CeO2 nanoparticles (CeO2/DODAB) could effectively compact the pDNA, allowing for highly efficient gene transfection into the selected cell lines. The CeO2/DODAB nanovectors were also found to be non-toxic and did not induce ROS formation as well as any stress responsive and pro-survival signaling pathways. The overall vector performance of CeO2/DODAB nanohybrids was comparable with lipofectamine and DOTAP and higher than calcium phosphate and DEAE-dextran for transfecting small plasmids. The increased cellular uptake of the nanovector/DNA complexes through clathrin- and caveolae-mediated endocytosis and subsequent release from the endosomes further support the increased gene transfection efficiency of the CeO2/DODAB vectors. Besides, CeO2/DODAB nanovectors could transfect genes in vivo without any sign of toxicity. Taken together, this new nano-vector has the potential to be used for gene delivery in biomedical applications.
New insight into the dynamical system of αB-crystallin oligomers
Authors: Inoue Rintaro , Takata Takumi , Fujii Norihiko , Ishii Kentaro , Uchiyama Susumu , Sato Nobuhiro , Oba Yojiro , Wood Kathleen , Kato Koichi , Fujii Noriko , Sugiyama Masaaki 
Published: July 2016

Abstractα-Crystallin possesses a dynamic quaternary structure mediated by its subunit dynamics. Elucidation of a mechanism of subunit dynamics in homo-oligomers of αB-crystallin was tackled through deuteration-assisted small-angle neutron scattering (DA-SANS) and electrospray ionization (ESI) native mass spectrometry (nMS). The existence of subunit exchange was confirmed with DA-SANS and monomers liberated from the oligomers were observed with nMS. With increasing temperature, an increase in both the exchange rate and monomer population was observed despite the absence of oligomer collapse. It is proposed that transiently liberated subunits, namely, “traveling subunits,” play a role in subunit exchange. Moreover, we propose that protein function is regulated by these traveling subunits.
Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass
Authors: Morrison Jessica M. , Elshahed Mostafa S. , Youssef Noha H. 
Published: July 2016

AbstractThe anaerobic fungus Orpinomyces strain C1A is capable of growth on various types of lignocellulosic substrates, and harbors an impressive reservoir of carbohydrate active enzymes (CAZymes). Using a minimum enzyme cocktail strategy, we constituted a four-component lignocellulolytic cocktail derived from highly transcribed C1A, and evaluated its efficacy against pretreated corn stover and switchgrass. Hydrolysis yields ranged between 65–77.4%, depending on the lignocellulosic substrate and pretreatment applied. Addition of a highly expressed anaerobic fungal swollenin improved hydrolysis yields by up to 7%. Compared to the commercial cocktail CTec2, these anaerobic fungal cocktails provided comparable or slightly lower hydrolysis yields. Further, the differences in efficacy between commercial and anaerobic cocktails were often only realized after extended (168 hr) incubations. Under certain conditions, the hydrolysis yields of the anaerobic fungal cocktail was slightly superior to that realized by CTec2. We attribute the observed high hydrolysis yields to the high specific activity and affinity of the individual enzymes of the cocktail, as well as the high level of synergy and multi-functionality observed in multiple components. Collectively, this effort provides a novel platform for constructing highly effective enzymes for biofuel production and represents the first lignocellulolytic enzyme cocktail created from anaerobic fungal enzymes.
Limbic areas are functionally decoupled and visual cortex takes a more central role during fear conditioning in humans
Authors: Lithari Chrysa , Moratti Stephan , Weisz Nathan 
Published: July 2016

AbstractGoing beyond the focus on isolated brain regions (e.g. amygdala), recent neuroimaging studies on fear conditioning point to the relevance of a network of mutually interacting brain regions. In the present MEG study we used Graph Theory to uncover changes in the architecture of the brain functional network shaped by fear conditioning. Firstly, induced power analysis revealed differences in local cortical excitability (lower alpha and beta power) between CS+ and CS− localized to somatosensory cortex and insula. What is more striking however is that the graph theoretical measures unveiled a re-organization of brain functional connections, not evident using conventional power analysis. Subcortical fear-related structures exhibited reduced connectivity with temporal and frontal areas rendering the overall brain functional network more sparse during fear conditioning. At the same time, the calcarine took on a more central role in the network. Interestingly, the more the connectivity of limbic areas is reduced, the more central the role of the occipital cortex becomes. We speculated that both, the reduced coupling in some regions and the emerging centrality of others, contribute to the efficient processing of fear-relevant information during fear learning.
The stability of aluminium oxide monolayer and its interface with two-dimensional materials
Authors: Song Ting Ting , Yang Ming , Chai Jian Wei , Callsen Martin , Zhou Jun , Yang Tong , Zhang Zheng , Pan Ji Sheng , Chi Dong Zhi , Feng Yuan Ping , Wang Shi Jie 
Published: July 2016

AbstractThe miniaturization of future electronic devices requires the knowledge of interfacial properties between two-dimensional channel materials and high-κ dielectrics in the limit of one atomic layer thickness. In this report, by combining particle-swarm optimization method with first-principles calculations, we present a detailed study of structural, electronic, mechanical, and dielectric properties of Al2O3 monolayer. We predict that planar Al2O3 monolayer is globally stable with a direct band gap of 5.99 eV and thermal stability up to 1100 K. The stability of this high-κ oxide monolayer can be enhanced by substrates such as graphene, for which the interfacial interaction is found to be weak. The band offsets between the Al2O3 monolayer and graphene are large enough for electronic applications. Our results not only predict a stable high-κ oxide monolayer, but also improve the understanding of interfacial properties between a high-κ dielectric monolayer and two-dimensional material.
Effect of water presence on choline chloride-2urea ionic liquid and coating platings from the hydrated ionic liquid
Authors: Du Cuiling , Zhao Binyuan , Chen Xiao-Bo , Birbilis Nick , Yang Haiyan 
Published: July 2016

AbstractIn the present study, hygroscopicity of the choline chloride-urea (ChCl-2Urea) ionic liquid (IL) was confirmed through Karl-Fisher titration examination, indicating that the water content in the hydrated ChCl-2Urea IL was exposure-time dependent and could be tailored by simple heating treatment. The impact of the absorbed water on the properties of ChCl-2Urea IL, including viscosity, electrical conductivity, electrochemical window and chemical structure was investigated. The results show that water was able to dramatically reduce the viscosity and improve the conductivity, however, a broad electrochemical window could be persisted when the water content was below ~6 wt.%. These characteristics were beneficial for producing dense and compact coatings. Nickel (Ni) coatings plating from hydrated ChCl-2Urea IL, which was selected as an example to show the effect of water on the electroplating, displayed that a compact and corrosion-resistant Ni coating was plated from ChCl-2Urea IL containing 6 wt.% water doped with 400 mg/L NA at a moderate temperature. As verified by FTIR analysis, the intrinsic reason could be ascribed that water was likely linked with urea through strong hydrogen bond so that the water decomposition was suppressed during plating. Present study may provide a reference to prepare some similar water-stable ILs for plating.
Telomere Visualization in Tissue Sections using Pyrrole–Imidazole Polyamide Probes
Authors: Sasaki Asuka , Ide Satoru , Kawamoto Yusuke , Bando Toshikazu , Murata Yukinori , Shimura Mari , Yamada Kazuhiko , Hirata Akiyoshi , Nokihara Kiyoshi , Hirata Tatsumi , Sugiyama Hiroshi , Maeshima Kazuhiro 
Published: July 2016

AbstractPyrrole–Imidazole (PI) polyamides bind to specific DNA sequences in the minor groove with high affinity. Specific DNA labeling by PI polyamides does not require DNA denaturation with harsh treatments of heat and formamide and has the advantages of rapid and less disruptive processing. Previously, we developed tandem hairpin PI polyamide probes (TH59 series), which label telomeres in cultured cell lines more efficiently than conventional methods, such as fluorescence in situ hybridization (FISH). Here, we demonstrate that a TH59 derivative, HPTH59-b, along with immunostaining for specifying cell types in the tissues, visualizes telomeres in mouse and human tissue sections. Quantitative measurements of telomere length with single-cell resolution suggested shorter telomeres in the proliferating cell fractions of tumor than in non-tumor tissues. Thus, PI polyamides are a promising alternative for telomere labeling in clinical research, as well as in cell biology.
Impaired neurodevelopment by the low complexity domain of CPEB4 reveals a convergent pathway with neurodegeneration
Authors: Shin Jihae , Salameh Johnny S. , Richter Joel D. 
Published: July 2016

AbstractCPEB4 is an RNA binding protein expressed in neuronal tissues including brain and spinal cord. CPEB4 has two domains: one that is structured for RNA binding and one that is unstructured and low complexity that has no known function. Unstructured low complexity domains (LCDs) in proteins are often found in RNA-binding proteins and have been implicated in motor neuron degenerative diseases such as amyotrophic lateral sclerosis, indicating that these regions mediate normal RNA processing as well as pathological events. While CPEB4 null knockout mice are normal, animals expressing only the CPEB4 LCD are neonatal lethal with impaired mobility that display defects in neuronal development such as reduced motor axon branching and abnormal neuromuscular junction formation. Although full-length CPEB4 is nearly exclusively cytoplasmic, the CPEB4 LCD forms nucleolar aggregates and CPEB4 LCD-expressing animals have altered ribosomal RNA biogenesis, ribosomal protein gene expression, and elevated levels of stress response genes such as the actin-bundling protein DRR1, which impedes neurite outgrowth. Some of these features share similarities with other LCD-related neurodegenerative disease. Most strikingly, DRR1 appears to be a common focus of several neurodevelopmental and neurodegenerative disorders. Our study reveals a possible molecular convergence between a neurodevelopmental defect and neurodegeneration mediated by LCDs.
A novel strain of Bacteroides fragilis enhances phagocytosis and polarises M1 macrophages
Authors: Deng Huimin , Li Zhengchao , Tan Yafang , Guo Zhaobiao , Liu Yangyang , Wang Ye , Yuan Yuan , Yang Ruifu , Bi Yujing , Bai Yang , Zhi Fachao 
Published: July 2016

AbstractCommensal Bacteroides fragilis possesses immune-regulatory characteristics. Consequently, it has been proposed as a potential novel probiotic because of its therapeutic effects on immune imbalance, mental disorders and inflammatory diseases. Macrophages play a central role in the immune response, developing either a classical-M1 or an alternative-M2 phenotype after stimulation with various signals. The interactions between macrophages and B. fragilis, however, remain to be defined. Here, a new isolate of B. fragilis, ZY-312, was shown to possess admirable properties, including tolerance to simulated gastric fluid, intestinal fluid and ox bile and good safety (MOI = 100, 200) and adherent ability (MOI = 100) to LoVo cells. Isolate ZY-312 cell lysate promoted phagocytosis of fluorescent microspheres and pathogenic bacteria in bone marrow-derived macrophage (BMDM) cells. Gene expression of IL-12, iNOS and IL-1β in BMDM cells was increased after treatment with ZY-312, indicating the induction of M1 macrophages, consistent with enhanced secretion of NO. Cell surface expression of CD80 and CD86 was also increased. This study is the first to demonstrate that B. fragilis enhances the phagocytic functions of macrophages, polarising them to an M1 phenotype. Our findings provide insight into the close relationship between B. fragilis and the innate immune system.