bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prior context in audition informs binding and shapes simple features
Authors: Chambers Claire , Akram Sahar , Adam Vincent , Pelofi Claire , Sahani Maneesh , Shamma Shihab , Pressnitzer Daniel 
Published: April 2017

AbstractA perceptual phenomenon is reported, whereby prior acoustic context has a large, rapid and long-lasting effect on a basic auditory judgement. Pairs of tones were devised to include ambiguous transitions between frequency components, such that listeners were equally likely to report an upward or downward ‘pitch’ shift between tones. We show that presenting context tones before the ambiguous pair almost fully determines the perceived direction of shift. The context effect generalizes to a wide range of temporal and spectral scales, encompassing the characteristics of most realistic auditory scenes. Magnetoencephalographic recordings show that a relative reduction in neural responsivity is correlated to the behavioural effect. Finally, a computational model reproduces behavioural results, by implementing a simple constraint of continuity for binding successive sounds in a probabilistic manner. Contextual processing, mediated by ubiquitous neural mechanisms such as adaptation, may be crucial to track complex sound sources over time.
Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability
Authors: Wang Xiangxi , Li Shi-Hua , Zhu Ling , Nian Qing-Gong , Yuan Shuai , Gao Qiang , Hu Zhongyu , Ye Qing , Li Xiao-Feng , Xie Dong-Yang , Shaw Neil , Wang Junzhi , Walter Thomas S. , Huiskonen Juha T. , Fry Elizabeth E. , Qin Cheng-Feng , Stuart David I. , Rao Zihe 
Published: April 2017

AbstractAlthough several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and molecular basis of this encephalitis is not fully understood. Here, we report the cryo-electron microscopy structure of mature Japanese encephalitis virus at near-atomic resolution, which reveals an unusual “hole” on the surface, surrounded by five encephalitic-specific motifs implicated in receptor binding. Glu138 of E, which is highly conserved in encephalitic flaviviruses, maps onto one of these motifs and is essential for binding to neuroblastoma cells, with the E138K mutation abrogating the neurovirulence and neuroinvasiveness of Japanese encephalitis virus in mice. We also identify structural elements modulating viral stability, notably Gln264 of E, which, when replaced by His264 strengthens a hydrogen-bonding network, leading to a more stable virus. These studies unveil determinants of neurovirulence and stability in Japanese encephalitis virus, opening up new avenues for therapeutic interventions against neurotropic flaviviruses.
Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach
Authors: Iborra-Egea Oriol , Gálvez-Montón Carolina , Roura Santiago , Perea-Gil Isaac , Prat-Vidal Cristina , Soler-Botija Carolina , Bayes-Genis Antoni 
Published: April 2017

AbstractSacubitril/Valsartan, proved superiority over other conventional heart failure management treatments, but its mechanisms of action remains obscure. In this study, we sought to explore the mechanistic details for Sacubitril/Valsartan in heart failure and post-myocardial infarction remodeling, using an in silico, systems biology approach. Myocardial transcriptome obtained in response to myocardial infarction in swine was analyzed to address post-infarction ventricular remodeling. Swine transcriptome hits were mapped to their human equivalents using Reciprocal Best (blast) Hits, Gene Name Correspondence, and InParanoid database. Heart failure remodeling was studied using public data available in gene expression omnibus (accession GSE57345, subseries GSE57338), processed using the GEO2R tool. Using the Therapeutic Performance Mapping System technology, dedicated mathematical models trained to fit a set of molecular criteria, defining both pathologies and including all the information available on Sacubitril/Valsartan, were generated. All relationships incorporated into the biological network were drawn from public resources (including KEGG, REACTOME, INTACT, BIOGRID, and MINT). An artificial neural network analysis revealed that Sacubitril/Valsartan acts synergistically against cardiomyocyte cell death and left ventricular extracellular matrix remodeling via eight principal synergistic nodes. When studying each pathway independently, Valsartan was found to improve cardiac remodeling by inhibiting members of the guanine nucleotide-binding protein family, while Sacubitril attenuated cardiomyocyte cell death, hypertrophy, and impaired myocyte contractility by inhibiting PTEN. The complex molecular mechanisms of action of Sacubitril/Valsartan upon post-myocardial infarction and heart failure cardiac remodeling were delineated using a systems biology approach. Further, this dataset provides pathophysiological rationale for the use of Sacubitril/Valsartan to prevent post-infarct remodeling.
Beclin-1-mediated Autophagy Protects Against Cadmium-activated Apoptosis via the Fas/FasL Pathway in Primary Rat Proximal Tubular Cell Culture
Authors: Liu Gang , Yuan Yan , Long Mengfei , Luo Tongwang , Bian Jianchun , Liu Xuezhong , Gu Jianhong , Zou Hui , Song Ruilong , Wang Yi , Wang Lin , Liu Zongping 
Published: April 2017

AbstractThe Fas/FasL signaling pathway is one of the primary apoptosis pathways, but the involvement and regulatory mechanism of this pathway by autophagy remain unclear. Here we demonstrated that cadmium (Cd) activated the Fas/FasL apoptosis pathway in rat proximal tubular (rPT) cells; this was accompanied by simultaneous activation of autophagy resulted in reduced apoptosis. In this model, we induced autophagy through RAPA and further demonstrated that autophagy protects against activation of Fas/FasL signaling and apoptosis. The antiapoptotic effect of autophagy was blocked by 3-MA, an autophagy inhibitor. The interactions between Beclin-1 and Fas, FasL, FADD, caspase-8 and BID/tBID were relatively weak, with the exception of cleaved caspase-8, indicated that minimal interactions between these proteins and Beclin-1 are involved in maintaining the balance of autophagy and apoptosis. Beclin-1 precipitated with cleaved caspase-8 in a dose-dependent mannter, and the expression was increased by siRNA against Beclin-1. These data suggested that Beclin-1-mediated autophagy impairs the expression and function of cleaved caspase-8 to protect against Cd-induced activation of apopotosis through Fas/FasL signaling pathway.
Transforming growth factor β plays an important role in enhancing wound healing by topical application of Povidone-iodine
Authors: Wang Li , Qin Wenhan , Zhou Yaying , Chen Bin , Zhao Xiaoqing , Zhao Hailin , Mi Emma , Mi Ella , Wang Qingmei , Ning Jiaolin 
Published: April 2017

AbstractPovidone-iodine (PVI) is principally used as an antimicrobial agent. It has been found that 0.5% PVI can attenuate congestion, edema and pain induced by pressure sores. Thus this study aimed to assess the effects of 0.5% PVI on acute skin wounds. Four full-thickness excisional wounds were generated on the dorsal skin of male Sprague-Dawley rats with a 10-mm sterile punch. Two wounds were left untreated and the other two were dressed with gauze with 0.5% PVI for 1 hour per day for the first 5 days after injury. 10-mm full-thickness excisional wounds were also generated on the dorsal skin of rats treated with 10 mg/kg SB431542 and all wounds were treated with 0.5% PVI for 5 days. PVI treatment enhanced wound healing via promotion of expression of α SMA and TGF β, neovascularization and re-epithelialization. Interleukin 6 was reduced following PVI treatment. Inhibition of TGF β abolished the effect of PVI treatment on wound closure. These data show that topical application of 0.5% PVI could promote acute skin wound healing though increased expression of TGF β leading to enhanced formation of granulation tissue, even in the absence of obvious infection.
A novel way to establish fertilization recommendations based on agronomic efficiency and a sustainable yield index for rice crops
Authors: Liu Chuang , Liu Yi , Li Zhiguo , Zhang Guoshi , Chen Fang 
Published: April 2017

AbstractA simpler approach for establishing fertilizer recommendations for major crops is urgently required to improve the application efficiency of commercial fertilizers in China. To address this need, we developed a method based on field data drawn from the China Program of the International Plant Nutrition Institute (IPNI) rice experiments and investigations carried out in southeastern China during 2001 to 2012. Our results show that, using agronomic efficiencies and a sustainable yield index (SYI), this new method for establishing fertilizer recommendations robustly estimated the mean rice yield (7.6 t/ha) and mean nutrient supply capacities (186, 60, and 96 kg/ha of N, P2O5, and K2O, respectively) of fertilizers in the study region. In addition, there were significant differences in rice yield response, economic cost/benefit ratio, and nutrient-use efficiencies associated with agronomic efficiencies ranked as high, medium and low. Thus, ranking agronomic efficiency could strengthen linear models relating rice yields and SYI. Our results also indicate that the new method provides better recommendations in terms of rice yield, SYI, and profitability than previous methods. Hence, we believe it is an effective approach for improving recommended applications of commercial fertilizers to rice (and potentially other crops).
Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae
Authors: Turmel Monique , Otis Christian , Lemieux Claude 
Published: April 2017

AbstractThe chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
Dynamic Behaviors of Condensing Clusters Based on Rayleigh Scattering Experiment
Authors: Lan Zhong , Wang Di , Cao Kejian , Xue Quan , Ma Xuehu 
Published: April 2017

AbstractCondensation is a common physical process which widely exists in natural phenomena and thermal energy systems. In a condensation process, cluster is considered as the important bridge between vapor body and condensates. However, limited by the minimum imaging dimension of traditional measurements, early experimental studies about initial stages of condensation process are not sufficient. This paper provides a powerful optical platform for the study of dynamic clusters process. Based on the Rayleigh law, optical experiments were firstly introduced to investigate the clusters spatial distribution close to and far from condensation surface. The results show that clusters are mainly generated in the vicinity of the condensation surface within the thickness of 200 μm. When they move away from the condensation surface, clusters progressively vanish and they have a life cycle of a fraction of a millisecond. Though scattering intensity is proportional to the 6th power of cluster radius r and cluster number density Nc theoretically, the scattering intensity does not increase sharply with the increase of subcooling degree from the experimental results, so we can infer that the cluster number density plays a dominate role in this process and the effect of cluster radius almost can be ignored.Zhong Lan and Di Wang contributed equally to this work.
Two-photon autofluorescence lifetime imaging of human skin papillary dermis in vivo: assessment of blood capillaries and structural proteins localization
Authors: Shirshin Evgeny A. , Gurfinkel Yury I. , Priezzhev Alexander V. , Fadeev Victor V. , Lademann Juergen , Darvin Maxim E. 
Published: April 2017

AbstractThe papillary dermis of human skin is responsible for its biomechanical properties and for supply of epidermis with chemicals. Dermis is mainly composed of structural protein molecules, including collagen and elastin, and contains blood capillaries. Connective tissue diseases, as well as cardiovascular complications have manifestations on the molecular level in the papillary dermis (e.g. alteration of collagen I and III content) and in the capillary structure. In this paper we assessed the molecular structure of internal and external regions of skin capillaries using two-photon fluorescence lifetime imaging (FLIM) of endogenous compounds. It was shown that the capillaries are characterized by a fast fluorescence decay, which is originated from red blood cells and blood plasma. Using the second harmonic generation signal, FLIM segmentation was performed, which provided for spatial localization and fluorescence decay parameters distribution of collagen I and elastin in the dermal papillae. It was demonstrated that the lifetime distribution was different for the inner area of dermal papillae around the capillary loop that was suggested to be due to collagen III. Hence, we propose a generalized approach to two-photon imaging of the papillary dermis components, which extends the capabilities of this technique in skin diagnosis.
CRL4BDCAF11 E3 ligase targets p21 for degradation to control cell cycle progression in human osteosarcoma cells
Authors: Chen Zhi , Wang Kun , Hou Canglong , Jiang Kaibiao , Chen Bin , Chen Jianwei , Lao Lifeng , Qian Lie , Zhong Guibin , Liu Zude , Zhang Caiguo , Shen Hongxing 
Published: April 2017

AbstractCell cycle progression in mammals is strictly controlled by a number of cyclin-dependent kinases (CDKs) and CDK inhibitors (CKIs), the expression of which is often dysregulated in cancer cells. Our previous work revealed that Cullin 4B (CUL4B), a critical component of the Cullin4B-RING E3 ligase complex (CRL4B), is overexpressed in human osteosarcoma cells through an unknown mechanism. Here, we demonstrated that CUL4B forms an E3 ligase with RBX1 (RING-box 1), DDB1 (DNA damage binding protein 1), and DCAF11 (DDB1 and CUL4 associated factor 11) in human osteosarcoma cells. In vitro and in vivo ubiquitination analyses indicated that CRL4BDCAF11 E3 ligase was able to specifically ubiquitinate a CDK inhibitor—p21Cip1 at K16, K154, K161 and K163 but not at K75 and K141. Knocking down any component of the CRL4BDCAF11 complex, including CUL4B, DDB1 or DCAF11, using short hairpin RNAs (shRNAs) attenuated the ubiquitination level of p21Cip1, inhibited osteosarcoma cell proliferation, led to cell cycle arrest at S phase, and decreased colony formation rate. Taken together, our data suggest that the CRL4BDCAF11 complex represents a unique E3 ligase that promotes the ubiquitination of p21Cip1 and regulates cell cycle progression in human osteosarcoma cells.
Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
Authors: Jeddi Iman , Saiz Leonor 
Published: April 2017

AbstractAptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
Hyperpolarized 13C Spectroscopic Evaluation of Oxidative Stress in a Rodent Model of Steatohepatitis
Authors: Wilson David M. , Di Gialleonardo Valentina , Wang Zhen J. , Carroll Valerie , Von Morze Cornelius , Taylor Andrew , Sai Victor , VanCriekinge Mark , Bok Robert , Ohliger Michael A. , Keshari Kayvan R. 
Published: April 2017

AbstractNonalcoholic fatty liver disease (NAFLD) has become highly prevalent, now considered the most common liver disease in the western world. Approximately one-third of patients with NASH develop non-alchoholic steatohepatitis (NASH), histologically defined by lobular and portal inflammation, and accompanied by marked oxidative stress. Patients with NASH are at increased risk for cirrhosis and hepatocellular carcinoma, and diagnosis currently requires invasive biopsy. In animal models of NASH, particularly the methionine-choline deficient (MCD) model, profound changes are seen in redox enzymes and key intracellular antioxidants. To study antioxidant status in NASH non-invasively, we applied the redox probe hyperpolarized [1-13C] dehydroascorbic acid (HP DHA), which is reduced to Vitamin C (VitC) rapidly in the normal liver. In MCD mice, we observed a significant decrease in HP DHA to VitC conversion that accompanied hepatic fat deposition. When these animals were subsequently placed on a normal diet, resonance ratios reverted to those seen in control mice. These findings suggest that HP DHA, a potentially clinically translatable imaging agent, holds special promise in imaging NASH and other metabolic syndromes, to monitor disease progression and response to targeted therapies.
Notch and Hippo signaling converge on Strawberry Notch 1 (Sbno1) to synergistically activate Cdx2 during specification of the trophectoderm
Authors: Watanabe Yusuke , Miyasaka Kota Y. , Kubo Atsushi , Kida Yasuyuki S. , Nakagawa Osamu , Hirate Yoshikazu , Sasaki Hiroshi , Ogura Toshihiko 
Published: April 2017

AbstractThe first binary cell fate decision occurs at the morula stage and gives rise to two distinct types of cells that constitute the trophectoderm (TE) and inner cell mass (ICM). The cell fate determinant, Cdx2, is induced in TE cells and plays an essential role in their differentiation and maintenance. Notch and Hippo signaling cascades are assumed to converge onto regulatory elements of Cdx2, however, the underlying molecular mechanisms are largely unknown. Here, we show involvement of Strawberry Notch1 (Sbno1), a novel chromatin factor of the helicase superfamily 2, during preimplantation development. Sbno1 knockout embryos die at the preimplantation stage without forming a blastocoel, and Cdx2 is not turned on even though both Yap and Tead4 reside normally in nuclei. Accordingly, Sbno1 acts on the trophectoderm-enhancer (TEE) of Cdx2, ensuring its robust and synergistic activation by the Yap/Tead4 and NICD/Rbpj complexes. Interestingly, this synergism is enhanced when cells are mechanically stretched, which might reflect that TE cells are continuously stretched by the expanding ICM and blastocoel cavity. In addition, the histone chaperone, FACT (FAcilitates Chromatin Transcription) physically interacts with Sbno1. Our data provide new evidence on TE specification, highlighting unexpected but essential functions of the highly conserved chromatin factor, Sbno1.
Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Authors: Lan Xi , Wang Yan , Tian Kai , Ye Fei , Yin Huadong , Zhao Xiaoling , Xu Hengyong , Huang Yong , Liu Haibo , Hsieh John C. F. , Lamont Susan J. , Zhu Qing 
Published: April 2017

AbstractAvian leukosis virus (ALV) is detrimental to poultry health and causes substantial economic losses from mortality and decreased performance. Because tumorigenesis is a complex mechanism, the regulatory architecture of the immune system is likely to include the added dimensions of modulation by miRNAs and long-noncoding RNA (lncRNA). To characterize the response to ALV challenge, we developed a novel methodology that combines four datasets: mRNA expression and the associated regulatory factors of miRNA and lncRNA, and ALV gene expression. Specific Pathogen-Free (SPF) layer chickens were infected with ALV-J or maintained as non-injected controls. Spleen samples were collected at 40 days post injection (dpi), and sequenced. There were 864 genes, 7 miRNAs and 17 lncRNAs differentially expressed between infected and non-infected birds. The combined analysis of the 4 RNA expression datasets revealed that ALV infection is detected by pattern-recognition receptors (TLR9 and TLR3) leading to a type-I IFN mediated innate immune response that is modulated by IRF7 and IRF1. Co-expression network analysis of mRNA with miRNA, lncRNA and virus genes identified key elements within the complex networks utilized during ALV response. The integration of information from the host transcriptomic, epigenetic and virus response also has the potential to provide deeper insights into other host-pathogen interactions.
Label-free volumetric optical imaging of intact murine brains
Authors: Ren Jian , Choi Heejin , Chung Kwanghun , Bouma Brett E. 
Published: April 2017

AbstractA central effort of today’s neuroscience is to study the brain’s ’wiring diagram’. The nervous system is believed to be a network of neurons interacting with each other through synaptic connection between axons and dendrites, therefore the neuronal connectivity map not only depicts the underlying anatomy, but also has important behavioral implications. Different approaches have been utilized to decipher neuronal circuits, including electron microscopy (EM) and light microscopy (LM). However, these approaches typically demand extensive sectioning and reconstruction for a brain sample. Recently, tissue clearing methods have enabled the investigation of a fully assembled biological system with greatly improved light penetration. Yet, most of these implementations, still require either genetic or exogenous contrast labeling for light microscopy. Here we demonstrate a high-speed approach, termed as Clearing Assisted Scattering Tomography (CAST), where intact brains can be imaged at optical resolution without labeling by leveraging tissue clearing and the scattering contrast of optical frequency domain imaging (OFDI).