bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum
Authors: Zhang Zhang , He Ziwen , Xu Shaohua , Li Xinnian , Guo Wuxia , Yang Yuchen , Zhong Cairong , Zhou Renchao , Shi Suhua 
Published: October 2016

AbstractThe mangrove fern genusAcrostichumgrows in the extremely unstable marine intertidal zone under harsh conditions, such as high salt concentrations, tidal rhythms and long-term climate changes. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species ofAcrostichum,A. aureumandA. speciosum, as well as a species in the sister genus,Ceratopteris thalictroides. We obtained 47,517, 36,420 and 60,823 unigenes for the three ferns, of which 24.39–45.63% were annotated using public databases. The estimated divergence time revealed thatAcrostichumadapted to the coastal region during the late Cretaceous, whereas the two mangrove ferns from the Indo West-Pacific (IWP) area diverged more recently. Two methods (the modified branch-site model and the Khmethod) were used to identify several positively selected genes, which may contribute to differential adaptation of the twoAcrostichumspecies to different light and salt conditions. Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone.
Identification and validation of candidate epigenetic biomarkers in lung adenocarcinoma
Authors: Daugaard Iben , Dominguez Diana , Kjeldsen Tina E. , Kristensen Lasse S. , Hager Henrik , Wojdacz Tomasz K. , Hansen Lise Lotte 
Published: October 2016

AbstractLung cancer is the number one cause of cancer-related deaths worldwide. DNA methylation is an epigenetic mechanism that regulates gene expression, and disease-specific methylation changes can be targeted as biomarkers. We have compared the genome-wide methylation pattern in tumor and tumor-adjacent normal lung tissue from four lung adenocarcinoma (LAC) patients using DNA methylation microarrays and identified 74 differentially methylated regions (DMRs). Eighteen DMRs were selected for validation in a cohort comprising primary tumors from 52 LAC patients and tumor-adjacent normal lung tissue from 32 patients by methylation-sensitive high resolution melting (MS-HRM) analysis. Significant increases in methylation were confirmed for 15 DMRs associated with the genes and genomic regions: OSR1, SIM1, GHSR, OTX2, LOC648987, HIST1H3E, HIST1H3G/HIST1H2BI, HIST1H2AJ/HIST1H2BM, HOXD10, HOXD3, HOXB3/HOXB4, HOXA3, HOXA5, Chr1(q21.1).A, and Chr6(p22.1). In particular the OSR1, SIM1 and HOXB3/HOXB4 regions demonstrated high potential as biomarkers in LAC. For OSR1, hypermethylation was detected in 47/48 LAC cases compared to 1/31 tumor-adjacent normal lung samples. Similarly, 45/49 and 36/48 LAC cases compared to 3/31 and 0/31 tumor-adjacent normal lung samples showed hypermethylation of the SIM1 and HOXB3/HOXB4 regions, respectively. In conclusion, this study has identified and validated 15 DMRs that can be targeted as biomarkers in LAC.
β-Arrestin 1’s Interaction with TC45 Attenuates Stat signaling by dephosphorylating Stat to inhibit antimicrobial peptide expression
Authors: Sun Jie-Jie , Yang Hui-Ting , Niu Guo-Juan , Feng Xiao-Wu , Lan Jiang-Feng , Zhao Xiao-Fan , Wang Jin-Xing 
Published: October 2016

AbstractImpaired phosphatase activity leads to the persistent activation of signal transducers and activators of transcription (Stat). In mammals, Stat family members are often phosphorylated or dephosphorylated by the same enzymes. To date, only one Stat similar to mammalian Stat5a/b has been found in crustaceans and there have been few studies in Stat signal regulation in crustaceans. Here, we report that β-arrestin1 interacts with TC45 (45-kDa form of T cell protein tyrosine phosphatase) in the nucleus to attenuate Stat signaling by promoting dephosphorylation of Stat. Initially, we showed that Stat translocates into the nucleus to induce antimicrobial peptide (AMP) expression after bacterial infection. βArr1 enters the nucleus of hemocytes and recruits TC45 to form the βarr1-TC45-Stat complex, which dephosphorylates Stat efficiently. The interaction of TC45 with Stat decreased and Stat phosphorylation increased in βarr1-silenced shrimp (Marsupenaeus japonicus) after challenge with Vibrio anguillarum. βArr1 directly interacts with Stat in nucleus and accelerates Stat dephosphorylation by recruiting TC45 after V. anguillarum challenge. Further study showed that βarr1 and TC45 also affect AMP expression, which is regulated by Stat. Therefore, βarr1 and TC45 are involved in the anti-V. anguillarum immune response by regulating Stat activity negatively to decrease AMP expression in shrimp.
Albumin Homodimers in Patients with Cirrhosis: Clinical and Prognostic Relevance of a Novel Identified Structural Alteration of the Molecule
Authors: Baldassarre Maurizio , Domenicali Marco , Naldi Marina , Laggetta Maristella , Giannone Ferdinando A. , Biselli Maurizio , Patrono Daniela , Bertucci Carlo , Bernardi Mauro , Caraceni Paolo 
Published: October 2016

AbstractDecompensated cirrhosis is associated to extensive post-transcriptional changes of human albumin (HA). This study aims to characterize the occurrence of HA homodimerization in a large cohort of patients with decompensated cirrhosis and to evaluate its association with clinical features and prognosis. HA monomeric and dimeric isoforms were identified in peripheral blood by using a HPLC-ESI-MS technique in 123 cirrhotic patients hospitalized for acute decompensation and 50 age- and sex-comparable healthy controls. Clinical and biochemical parameters were recorded and patients followed up to one year. Among the monomeric isoforms identified, the N- and C-terminal truncated and the native HA underwent homodimerization. All three homodimers were significantly more abundant in patients with cirrhosis, acute-on-chronic liver failure and correlate with the prognostic scores. The homodimeric N-terminal truncated isoform was independently associated to disease complications and was able to stratify 1-year survival. As a result of all these changes, the monomeric native HA was significantly decreased in patients with cirrhosis, being also associated with a poorer prognosis. In conclusion homodimerization is a novel described structural alteration of the HA molecule in decompensated cirrhosis and contributes to the progressive reduction of the monomeric native HA, the only isoform provided of structural and functional integrity.
Procedural performance following sleep deprivation remains impaired despite extended practice and an afternoon nap
Authors: Kurniawan Irma Triasih , Cousins James Nicholas , Chong Pearlynne L. H. , Chee Michael W. L. 
Published: October 2016

AbstractThe negative impact of sleep loss on procedural memory is well established, yet it remains unclear how extended practice opportunities or daytime naps can modulate the effect of a night of sleep deprivation. Here, participants underwent three training and test conditions on a sequential finger tapping task (SFTT) separated by at least one week. In the first condition they were trained in the evening followed by a night of sleep. Two further conditions took place where evening training was followed by a night of total sleep deprivation (TSD). One of the TSD conditions included a one-hour nap opportunity (15:00). Compared to the condition in which sleep was permitted, a night of TSD resulted in poorer performance across 4 practices the following day (10:00–19:00). The deleterious effect of a single night of TSD on procedural performance, was neither clearly alleviated by an afternoon nap nor by multiple practice opportunities. Interestingly, significant gains in performance were observed in all conditions after a one-week delay. Recovery sleep on subsequent nights thus appeared to nullify the effect of a single night of sleep deprivation, underscoring the importance of offline consolidation on the acquisition of procedural skill.
Valproate inhibits MAP kinase signalling and cell cycle progression in S. cerevisiae
Authors: Desfossés-Baron Kristelle , Hammond-Martel Ian , Simoneau Antoine , Sellam Adnane , Roberts Stephen , Wurtele Hugo 
Published: October 2016

AbstractThe mechanism of action of valproate (VPA), a widely prescribed short chain fatty acid with anticonvulsant and anticancer properties, remains poorly understood. Here, the yeast Saccharomyces cerevisiae was used as model to investigate the biological consequences of VPA exposure. We found that low pH strongly potentiates VPA-induced growth inhibition. Transcriptional profiling revealed that under these conditions, VPA modulates the expression of genes involved in diverse cellular processes including protein folding, cell wall organisation, sexual reproduction, and cell cycle progression. We further investigated the impact of VPA on selected processes and found that this drug: i) activates markers of the unfolded protein stress response such as Hac1 mRNA splicing; ii) modulates the cell wall integrity pathway by inhibiting the activation of the Slt2 MAP kinase, and synergizes with cell wall stressors such as micafungin and calcofluor white in preventing yeast growth; iii) prevents activation of the Kss1 and Fus3 MAP kinases of the mating pheromone pathway, which in turn abolishes cellular responses to alpha factor; and iv) blocks cell cycle progression and DNA replication. Overall, our data identify heretofore unknown biological responses to VPA in budding yeast, and highlight the broad spectrum of cellular pathways influenced by this chemical in eukaryotes.
Global-scale river flood vulnerability in the last 50 years
Authors: Tanoue Masahiro , Hirabayashi Yukiko , Ikeuchi Hiroaki 
Published: October 2016

AbstractThe impacts of flooding are expected to rise due to population increases, economic growth and climate change. Hence, understanding the physical and spatiotemporal characteristics of risk drivers (hazard, exposure and vulnerability) is required to develop effective flood mitigation measures. Here, the long-term trend in flood vulnerability was analysed globally, calculated from the ratio of the reported flood loss or damage to the modelled flood exposure using a global river and inundation model. A previous study showed decreasing global flood vulnerability over a shorter period using different disaster data. The long-term analysis demonstrated for the first time that flood vulnerability to economic losses in upper-middle, lower-middle and low-income countries shows an inverted U-shape, as a result of the balance between economic growth and various historical socioeconomic efforts to reduce damage, leading to non-significant upward or downward trends. We also show that the flood-exposed population is affected by historical changes in population distribution, with changes in flood vulnerability of up to 48.9%. Both increasing and decreasing trends in flood vulnerability were observed in different countries, implying that population growth scenarios considering spatial distribution changes could affect flood risk projections.
Terahertz reflectometry imaging for low and high grade gliomas
Authors: Ji Young Bin , Oh Seung Jae , Kang Seok-Gu , Heo Jung , Kim Sang-Hoon , Choi Yuna , Song Seungri , Son Hye Young , Kim Se Hoon , Lee Ji Hyun , Haam Seung Joo , Huh Yong Min , Chang Jong Hee , Joo Chulmin , Suh Jin-Suck 
Published: October 2016

AbstractGross total resection (GTR) of glioma is critical for improving the survival rate of glioma patients. One of the greatest challenges for achieving GTR is the difficulty in discriminating low grade tumor or peritumor regions that have an intact blood brain barrier (BBB) from normal brain tissues and delineating glioma margins during surgery. Here we present a highly sensitive, label-free terahertz reflectometry imaging (TRI) that overcomes current key limitations for intraoperative detection of World Health Organization (WHO) grade II (low grade), and grade III and IV (high grade) gliomas. We demonstrate that TRI provides tumor discrimination and delineation of tumor margins in brain tissues with high sensitivity on the basis of Hematoxylin and eosin (H&E) stained image. TRI may help neurosurgeons to remove gliomas completely by providing visualization of tumor margins in WHO grade II, III, and IV gliomas without contrast agents, and hence, improve patient outcomes.
A Carbonaceous Membrane based on a Polymer of Intrinsic Microporosity (PIM-1) for Water Treatment
Authors: Kim Hee Joong , Kim Dong-Gyun , Lee Kyuchul , Baek Youngbin , Yoo Youngjae , Kim Yong Seok , Kim Byoung Gak , Lee Jong-Chan 
Published: October 2016

AbstractAs insufficient access to clean water is expected to become worse in the near future, water purification is becoming increasingly important. Membrane filtration is the most promising technologies to produce clean water from contaminated water. Although there have been many studies to prepare highly water-permeable carbon-based membranes by utilizing frictionless water flow inside the carbonaceous pores, the carbon-based membranes still suffer from several issues, such as high cost and complicated fabrication as well as relatively low salt rejection. Here, we report for the first time the use of microporous carbonaceous membranes via controlled carbonization of polymer membranes with uniform microporosity for high-flux nanofiltration. Further enhancement of membrane performance is observed by O2 plasma treatment. The optimized membrane exhibits high water flux (13.30 LMH Bar−1) and good MgSO4 rejection (77.38%) as well as antifouling properties. This study provides insight into the design of microporous carbonaceous membranes for water purification.
Learning robust pulses for generating universal quantum gates
Authors: Dong Daoyi , Wu Chengzhi , Chen Chunlin , Qi Bo , Petersen Ian R. , Nori Franco 
Published: October 2016

AbstractConstructing a set of universal quantum gates is a fundamental task for quantum computation. The existence of noises, disturbances and fluctuations is unavoidable during the process of implementing quantum gates for most practical quantum systems. This paper employs a sampling-based learning method to find robust control pulses for generating a set of universal quantum gates. Numerical results show that the learned robust control fields are insensitive to disturbances, uncertainties and fluctuations during the process of realizing universal quantum gates.
Hydrogen-doped Brookite TiO2 Nanobullets Array as a Novel Photoanode for Efficient Solar Water Splitting
Authors: Choi Mingi , Lee June Ho , Jang Youn Jeong , Kim Donghyung , Lee Jae Sung , Jang Hyun Myung , Yong Kijung 
Published: October 2016

AbstractAs a representative photocatalyst for photoelectrochemical solar water splitting, TiO2 has been intensively studied but most researches have focused on the rutile and anatsase phases because brookite, another important crystalline polymorph of TiO2, rarely exists in nature and is difficult to synthesize. In this work, hydrogen doped brookite (H:brookite) nanobullet arrays were synthesized via a well-designed solution reaction for the first time. H:brookite shows highly improved PEC properties with excellent stability, enhanced photocurrent, and significantly high Faradaic efficiency for overall solar water splitting. To support the experimental data, ab initio density functional theory calculations were also conducted. At the interstitial doping site that has minimum formation energy, the hydrogen atoms act as shallow donors and exist as H+. which has the minimum formation energy among three states of hydrogen (H+. H0, and H−). The calculated density of states of H:brookite shows a narrowed bandgap and an increased electron density compared to the pristine brookite. The combined experimental and theoretical results provide frameworks for the exploration of the PEC properties of doped brookite and extend our knowledge regarding the undiscovered properties of brookite of TiO2.
Interspecific variation of warning calls in piranhas: a comparative analysis
Authors: Mélotte Geoffrey , Vigouroux Régis , Michel Christian , Parmentier Eric 
Published: October 2016

AbstractFish sounds are known to be species-specific, possessing unique temporal and spectral features. We have recorded and compared sounds in eight piranha species to evaluate the potential role of acoustic communication as a driving force in clade diversification. All piranha species showed the same kind of sound-producing mechanism: sonic muscles originate on vertebrae and attach to a tendon surrounding the bladder ventrally. Contractions of the sound-producing muscles force swimbladder vibration and dictate the fundamental frequency. It results the calling features of the eight piranha species logically share many common characteristics. In all the species, the calls are harmonic sounds composed of multiple continuous cycles. However, the sounds of Serrasalmus elongatus (higher number of cycles and high fundamental frequency) and S. manueli (long cycle periods and low fundamental frequency) are clearly distinguishable from the other species. The sonic mechanism being largely conserved throughout piranha evolution, acoustic communication can hardly be considered as the main driving force in the diversification process. However, sounds of some species are clearly distinguishable despite the short space for variations supporting the need for specific communication. Behavioural studies are needed to clearly understand the eventual role of the calls during spawning events.
High efficiency holographic Bragg grating with optically prolonged memory
Authors: Khoo Iam Choon , Chen Chun-Wei , Ho Tsung-Jui 
Published: October 2016

AbstractIn this paper, we show that photosensitive azo-dye doped Blue-phase liquid crystals (BPLC) formed by natural molecular self-assembly are capable of high diffraction efficiency holographic recording with memory that can be prolonged from few seconds to several minutes by uniform illumination with the reference beam. Operating in the Bragg regime, we have observed 50 times improvement in the grating diffraction efficiency and shorter recording time compared to previous investigations. The enabling mechanism is BPLC’s lattice distortion and index modulation caused by the action of light on the azo-dopant; upon photo-excitation, the azo-molecules undergo transformation from the oblong-shaped Trans-state to the bent-shaped Cis-state, imparting disorder and also cause the surrounding BPLC molecules to undergo coupled flow & reorientation leading to lattice distortion and index modulation. We also showed that the same mechanism at work here that facilitates lattice distortion can be used to frustrate free relaxation of the lattice distortion, thereby prolonging the lifetime of the written grating, provided the reference beam is kept on after recording. Due to the ease in BPLC fabrication and the availability of azo-dopants with photosensitivity throughout the entire visible spectrum, one can optimize the controlling material and optical parameters to obtain even better performance.
Molecular phylogeny of Polyneoptera (Insecta) inferred from expanded mitogenomic data
Authors: Song Nan , Li Hu , Song Fan , Cai Wanzhi 
Published: October 2016

AbstractThe Polyneoptera represents one of the earliest insect radiations, comprising the majority of hemimetabolous orders, in which many species have great economic importance. Here, we sequenced eleven mitochondrial genomes of the polyneopteran insects by using high throughput pooled sequencing technology, and presented a phylogenetic reconstruction for this group based on expanded mitochondrial genome data. Our analyses included 189 taxa, of which 139 species represent all the major polyneopteran lineages. Multiple results support the monophyly of Polyneoptera, the monophyly of Dictyoptera, and the monophyly of Orthoptera. Sister taxon relationships Plecoptera + Dermaptera, and Zoraptera + Embioptera are also supported by most analyses. Within Dictyoptera, the Blattodea is consistently retrieved as paraphyly due to the sister group relationship ofCryptocercuswith Isoptera. In addition, the results demonstrate that model selection, data treatment, and outgroup choice can have significant effects on the reconstructed phylogenetic relationships of Polyneoptera.
Effects of Pore-Scale Disorder on Fluid Displacement in Partially-Wettable Porous Media
Authors: Holtzman Ran 
Published: October 2016

AbstractWe present a systematic, quantitative assessment of the impact of pore size disorder and its interplay with flow rates and wettability on immiscible displacement of a viscous fluid. Pore-scale simulations and micromodel experiments show that reducing disorder increases the displacement efficiency and compactness, minimizing the fluid-fluid interfacial area, through (i) trapping at low rates and (ii) viscous fingering at high rates. Increasing the wetting angle suppresses both trapping and fingering, hence reducing the sensitivity of the displacement to the underlying disorder. A modified capillary number Ca*that includes the impact of disorderλon viscous forces (through pore connectivity) is direct related toλ, in par with previous works. Our findings bear important consequences on sweep efficiency and fluid mixing and reactions, which are key in applications such as microfluidics to carbon geosequestration, energy recovery, and soil aeration and remediation.
SIN1 promotes the proliferation and migration of breast cancer cells by Akt activation
Authors: Wang Deqiang , Wu Ping , Wang Hui , Zhu Lei , Zhao Wei , Lu Yuqin 
Published: October 2016

Stress-activated protein kinase (SAPK) interacting protein 1 (SIN1) is an essential TORC2 component and a key regulator of Akt pathway that plays an important role in various pathological conditions including cancer. Whereas its functional role in breast cancer has not been well characterized. In the present study, SIN1 is associated with the progression and survival of breast cancer patients, as well as human breast cancer cell proliferation and migration. SIN1 mRNA level was significantly up-regulated in human breast cancer samples compared with their corresponding paracancerous histological normal tissues. Furthermore, the expression levels of SIN1 were also increased in three human breast cancer cell lines compared with human breast epithelial cell MCF10A. Overexpression of SIN1 promoted cell proliferation, colony formation and migration of breast cancer cells. Knockdown of SIN1 in MDA-MB-468 cells inhibited cell proliferation, colony formation and migration. In addition, SIN1 overexpression increased phosphorylation of Akt and knockdown of SIN1 inhibited phosphorylation of Akt in MDA-MB-468 cells. In a tumour xenograft model, overexpression of SIN1 promoted tumour growth of MDA-MB-468 cells in vivo, whereas SIN1 knockdown inhibits the tumour growth. Taken together, our results reveal that SIN1 plays an important role in breast cancer and SIN1 is a potential biomarker and a promising target in the treatment of breast cancer.