bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies
Authors: Wu Nan , Song Yu-Long , Wang Bei , Zhang Xiang-Yang , Zhang Xu-Jie , Wang Ya-Li , Cheng Ying-Yin , Chen Dan-Dan , Xia Xiao-Qin , Lu Yi-Shan , Zhang Yong-An 
Published: November 2016

AbstractThe gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.
Hexacoordinated nitrogen(V) stabilized by high pressure
Authors: Kurzydłowski Dominik , Zaleski-Ejgierd Patryk 
Published: November 2016

AbstractIn all of its known connections nitrogen retains a valence shell electron count of eight therefore satisfying the golden rule of chemistry - the octet rule. Despite the diversity of nitrogen chemistry (with oxidation states ranging from + 5 to −3), and despite numerous efforts, compounds containing nitrogen with a higher electron count (hypervalent nitrogen) remain elusive and are yet to be synthesized. One possible route leading to nitrogen’s hypervalency is the formation of a chemical moiety containing pentavalent nitrogen atoms coordinated by more than four substituents. Here, we present theoretical evidence that a salt containing hexacoordinated nitrogen(V), in the form of an NF6− anion, could be synthesized at a modest pressure of 40 GPa (=400 kbar) via spontaneous oxidation of NF3 by F2. Our results indicate that the synthesis of a new class of compounds containing hypervalent nitrogen is within reach of current high-pressure experimental techniques.
Resonance states and beating pattern induced by quantum impurity scattering in Weyl/Dirac semimetals
Authors: Zheng Shi-Han , Wang Rui-Qiang , Zhong Min , Duan Hou-Jian 
Published: November 2016

AbstractCurrently, Weyl semimetals (WSMs) are drawing great interest as a new topological nontrivial phase. When most of the studies concentrated on the clean host WSMs, it is expected that the dirty WSM system would present rich physics due to the interplay between the WSM states and the impurities embedded inside these materials. We investigate theoretically the change of local density of states in three-dimensional Dirac and Weyl bulk states scattered off a quantum impurity. It is found that the quantum impurity scattering can create nodal resonance and Kondo peak/dip in the host bulk states, remarkably modifying the pristine spectrum structure. Moreover, the joint effect of the separation of Weyl nodes and the Friedel interference oscillation causes the unique battering feature. We in detail an- alyze the different contribution from the intra- and inter-node scattering processes and present various scenarios as a consequence of competition between them. Importantly, these behaviors are sensitive significantly to the displacement of Weyl nodes in energy or momentum, from which the distinctive fingerprints can be extracted to identify various semimetal materials experimentally by employing the scanning tunneling microscope.
High-efficient Synthesis of Graphene Oxide Based on Improved Hummers Method
Authors: Yu Huitao , Zhang Bangwen , Bulin Chaoke , Li Ruihong , Xing Ruiguang 
Published: November 2016

AbstractAs an important precursor and derivate of graphene, graphene oxide (GO) has received wide attention in recent years. However, the synthesis of GO in an economical and efficient way remains a great challenge. Here we reported an improved NaNO3-free Hummers method by partly replacing KMnO4 with K2FeO4 and controlling the amount of concentrated sulfuric acid. As compared to the existing NaNO3-free Hummers methods, this improved routine greatly reduces the reactant consumption while keeps a high yield. The obtained GO was characterized by various techniques, and its derived graphene aerogel was demonstrated as high-performance supercapacitor electrodes. This improved synthesis shows good prospects for scalable production and applications of GO and its derivatives.
Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count
Authors: Wada Yoshiko , Wada Kennosuke , Iwasaki Yuki , Kanaya Shigehiko , Ikemura Toshimichi 
Published: November 2016

AbstractEbolavirus, MERS coronavirus and influenza virus are zoonotic RNA viruses, which mutate very rapidly. Viral growth depends on many host factors, but human cells may not provide the ideal growth conditions for viruses invading from nonhuman hosts. The present time-series analyses of short and long oligonucleotide compositions in these genomes showed directional changes in their composition after invasion from a nonhuman host, which are thought to recur after future invasions. In the recent West Africa Ebola outbreak, directional time-series changes in a wide range of oligonucleotides were observed in common for three geographic areas, and the directional changes were observed also for the recent MERS coronavirus epidemics starting in the Middle East. In addition, common directional changes in human influenza A viruses were observed for three subtypes, whose epidemics started independently. Long oligonucleotides that showed an evident directional change observed in common for the three subtypes corresponded to some of influenza A siRNAs, whose activities have been experimentally proven. Predicting directional and reoccurring changes in oligonucleotide composition should become important for designing diagnostic RT-PCR primers and therapeutic oligonucleotides with long effectiveness.
SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis
Authors: Pulido-Tamayo Sergio , Weytjens Bram , De Maeyer Dries , Marchal Kathleen 
Published: November 2016

AbstractBecause of its clonal evolution a tumor rarely contains multiple genomic alterations in the same pathway as disrupting the pathway by one gene often is sufficient to confer the complete fitness advantage. As a result, many cancer driver genes display mutual exclusivity across tumors. However, searching for mutually exclusive gene sets requires analyzing all possible combinations of genes, leading to a problem which is typically too computationally complex to be solved without a stringent a priori filtering, restricting the mutations included in the analysis. To overcome this problem, we present SSA-ME, a network-based method to detect cancer driver genes based on independently scoring small subnetworks for mutual exclusivity using a reinforced learning approach. Because of the algorithmic efficiency, no stringent upfront filtering is required. Analysis of TCGA cancer datasets illustrates the added value of SSA-ME: well-known recurrently mutated but also rarely mutated drivers are prioritized. We show that using mutual exclusivity to detect cancer driver genes is complementary to state-of-the-art approaches. This framework, in which a large number of small subnetworks are being analyzed in order to solve a computationally complex problem (SSA), can be generically applied to any problem in which local neighborhoods in a network hold useful information.
Anticipation of guilt for everyday moral transgressions: The role of the anterior insula and the influence of interpersonal psychopathic traits
Authors: Seara-Cardoso Ana , Sebastian Catherine L. , McCrory Eamon , Foulkes Lucy , Buon Marine , Roiser Jonathan P. , Viding Essi 
Published: November 2016

AbstractPsychopathy is a personality disorder characterised by atypical moral behaviour likely rooted in atypical affective/motivational processing, as opposed to an inability to judge the wrongness of an action. Guilt is a moral emotion believed to play a crucial role in adherence to moral and social norms, but the mechanisms by which guilt (or lack thereof) may influence behaviour in individuals with high levels of psychopathic traits are unclear. We measured neural responses during the anticipation of guilt about committing potential everyday moral transgressions, and tested the extent to which these varied with psychopathic traits. We found a significant interaction between the degree to which anticipated guilt was modulated in the anterior insula and interpersonal psychopathic traits: anterior insula modulation of anticipated guilt was weaker in individuals with higher levels of these traits. Data from a second sample confirmed that this pattern of findings was specific to the modulation of anticipated guilt and not related to the perceived wrongness of the transgression. These results suggest a central role for the anterior insula in coding the anticipation of guilt regarding potential moral transgressions and advance our understanding of the neurocognitive mechanisms that may underlie propensity to antisocial behaviour.
Ethanol extract of Lophatheri Herba exhibits anti-cancer activity in human cancer cells by suppression of metastatic and angiogenic potential
Authors: Kim Aeyung , Im Minju , Gu Min Jung , Ma Jin Yeul 
Published: November 2016

AbstractLophatheri Herba (LH), dried leaf of Lophatherum gracile Brongn, has long been used to reduce thirst and treat fever and inflammation in Chinese medicine. Recent studies have shown that LH has anti-viral, anti-bacterial, anti-cancer, anti-oxidant, diuretic, and hyperglycemic properties. However, the effects of an ethanol extract of L. herba (ELH), at non-cytotoxic doses, on the metastatic and angiogenic abilities of malignant tumor cells have not been reported. We found that ELH significantly suppressed p38, JNK, and NF-κB activation and proteolytic activities under phorbol 12-myristate 13-acetate (PMA) stimulation, thus leading to a decrease in metastatic potential, including migration and invasion. In addition, ELH suppressed tumor-induced angiogenesis, including migration and tube formation in human umbilical vein endothelial cells (HUVECs) and microvessel sprouting from aortic rings via decreasing the pro-angiogenic factors in tumors. Interestingly, in ovo xenografts ELH-treated HT1080 cells did not increase in volume and eventually disappeared, owing to a lack of angiogenesis. Daily oral administration of ELH at 50 and 100 mg/kg markedly inhibited metastatic colonization of B16F10 cells in the lungs of C57BL/6J mice and caused no apparent side effects. These data collectively indicate that ELH is safe and may be useful for managing metastasis and growth of malignant cancers.
Evaluation of uttroside B, a saponin from Solanum nigrum Linn, as a promising chemotherapeutic agent against hepatocellular carcinoma
Authors: Nath Lekshmi R. , Gorantla Jaggaiah N. , Thulasidasan Arun Kumar T. , Vijayakurup Vinod , Shah Shabna , Anwer Shabna , Joseph Sophia M. , Antony Jayesh , Veena Kollery Suresh , Sundaram Sankar , Marelli Udaya K. , Lankalapalli Ravi S. , Anto Ruby John 
Published: November 2016

AbstractWe report, for the first time, the remarkable efficacy of uttroside B, a potent saponin fromSolanum nigrumLinn, against liver cancer. The compound has been isolated and characterized from the leaves ofSolanum nigrumLinn, a plant widely used in traditional medicine and is a rich resource of several anticancer molecules. Uttroside B, that comprises of β-D-glucopyranosyl unit at C-26 of the furostanol and β-lycotetraosyl unit at C-3, is ten times more cytotoxic to the liver cancer cell line, HepG2 (IC50: 0.5 μM) than sorafenib (IC50: 5.8 μM), the only FDA-approved drug for liver cancer. Moreover, it induces cytotoxicity in all liver cancer cell lines, irrespective of their HBV status, while being non-toxic to normal immortalized hepatocytes. It induces apoptosis in HepG2 cells by down-regulating mainly the activation of MAPK and mTOR pathways. The drastic reduction in HepG2-xenograft tumor size achieved by uttroside B in NOD-SCID mice and substantiation of its biological safety through both acute and chronic toxicity studies in Swiss albino mice warrants clinical validation of the molecule against hepatic cancer, for which, the chemotherapeutic armamentarium currently has limited weapons.
N-acetyl ornithine deacetylase is a moonlighting protein and is involved in the adaptation of Entamoeba histolytica to nitrosative stress
Authors: Shahi Preeti , Trebicz-Geffen Meirav , Nagaraja Shruti , Hertz Rivka , Alterzon-Baumel Sharon , Methling Karen , Lalk Michael , Mazumder Mohit , Samudrala Gourinath , Ankri Serge 
Published: November 2016

AbstractAdaptation of the Entamoeba histolytica parasite to toxic levels of nitric oxide (NO) that are produced by phagocytes may be essential for the establishment of chronic amebiasis and the parasite’s survival in its host. In order to obtain insight into the mechanism of E. histolytica’s adaptation to NO, E. histolytica trophozoites were progressively adapted to increasing concentrations of the NO donor drug, S-nitrosoglutathione (GSNO) up to a concentration of 110 μM. The transcriptome of NO adapted trophozoites (NAT) was investigated by RNA sequencing (RNA-seq). N-acetyl ornithine deacetylase (NAOD) was among the 208 genes that were upregulated in NAT. NAOD catalyzes the deacetylation of N-acetyl-L-ornithine to yield ornithine and acetate. Here, we report that NAOD contributes to the better adaptation of the parasite to nitrosative stress (NS) and that this function does not depend on NAOD catalytic activity. We also demonstrated that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is detrimental to E. histolytica exposed to NS and that this detrimental effect is neutralized by NAOD or by a catalytically inactive NAOD (mNAOD). These results establish NAOD as a moonlighting protein, and highlight the unexpected role of this metabolic enzyme in the adaptation of the parasite to NS.
Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration
Authors: Tsvetkova Milena , García-Gavilanes Ruth , Yasseri Taha 
Published: November 2016

AbstractDisagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.
Genomic analysis reveals selection in Chinese native black pig
Authors: Fu Yuhua , Li Cencen , Tang Qianzi , Tian Shilin , Jin Long , Chen Jianhai , Li Mingzhou , Li Changchun 
Published: November 2016

AbstractIdentification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.
Timing and causes of North African wet phases during the last glacial period and implications for modern human migration
Authors: Hoffmann Dirk L. , Rogerson Mike , Spötl Christoph , Luetscher Marc , Vance Derek , Osborne Anne H. , Fello Nuri M. , Moseley Gina E. 
Published: November 2016

AbstractWe present the first speleothem-derived central North Africa rainfall record for the last glacial period. The record reveals three main wet periods at 65-61 ka, 52.5-50.5 ka and 37.5-33 ka that lead obliquity maxima and precession minima. We find additional minor wet episodes that are synchronous with Greenland interstadials. Our results demonstrate that sub-tropical hydrology is forced by both orbital cyclicity and North Atlantic moisture sources. The record shows that after the end of a Saharan wet phase around 70 ka ago, North Africa continued to intermittently receive substantially more rainfall than today, resulting in favourable environmental conditions for modern human expansion. The encounter and subsequent mixture of Neanderthals and modern humans – which, on genetic evidence, is considered to have occurred between 60 and 50 ka – occurred synchronously with the wet phase between 52.5 and 50.5 ka. Based on genetic evidence the dispersal of modern humans into Eurasia started less than 55 ka ago. This may have been initiated by dry conditions that prevailed in North Africa after 50.5 ka. The timing of a migration reversal of modern humans from Eurasia into North Africa is suggested to be coincident with the wet period between 37.5 and 33 ka.
Cascading and Parallelising Curvilinear Inertial Focusing Systems for High Volume, Wide Size Distribution, Separation and Concentration of Particles
Authors: Miller B. , Jimenez M. , Bridle H. 
Published: November 2016

AbstractInertial focusing is a microfluidic based separation and concentration technology that has expanded rapidly in the last few years. Throughput is high compared to other microfluidic approaches although sample volumes have typically remained in the millilitre range. Here we present a strategy for achieving rapid high volume processing with stacked and cascaded inertial focusing systems, allowing for separation and concentration of particles with a large size range, demonstrated here from 30 μm–300 μm. The system is based on curved channels, in a novel toroidal configuration and a stack of 20 devices has been shown to operate at 1 L/min. Recirculation allows for efficient removal of large particles whereas a cascading strategy enables sequential removal of particles down to a final stage where the target particle size can be concentrated. The demonstration of curved stacked channels operating in a cascaded manner allows for high throughput applications, potentially replacing filtration in applications such as environmental monitoring, industrial cleaning processes, biomedical and bioprocessing and many more.
ApoA-I mimetic administration, but not increased apoA-I-containing HDL, inhibits tumour growth in a mouse model of inherited breast cancer
Authors: Cedó Lídia , García-León Annabel , Baila-Rueda Lucía , Santos David , Grijalva Victor , Martínez-Cignoni Melanie Raquel , Carbó José M. , Metso Jari , López-Vilaró Laura , Zorzano Antonio , Valledor Annabel F. , Cenarro Ana , Jauhiainen Matti , Lerma Enrique , Fogelman Alan M. , Reddy Srinivasa T. , Escolà-Gil Joan Carles , Blanco-Vaca Francisco 
Published: November 2016

AbstractLow levels of high-density lipoprotein cholesterol (HDLc) have been associated with breast cancer risk, but several epidemiologic studies have reported contradictory results with regard to the relationship between apolipoprotein (apo) A-I and breast cancer. We aimed to determine the effects of human apoA-I overexpression and administration of specific apoA-I mimetic peptide (D-4F) on tumour progression by using mammary tumour virus-polyoma middle T-antigen transgenic (PyMT) mice as a model of inherited breast cancer. Expression of human apoA-I in the mice did not affect tumour onset and growth in PyMT transgenic mice, despite an increase in the HDLc level. In contrast, D-4F treatment significantly increased tumour latency and inhibited the development of tumours. The effects of D-4F on tumour development were independent of 27-hydroxycholesterol. However, D-4F treatment reduced the plasma oxidized low-density lipoprotein (oxLDL) levels in mice and prevented oxLDL-mediated proliferative response in human breast adenocarcinoma MCF-7 cells. In conclusion, our study shows that D-4F, but not apoA-I-containing HDL, hinders tumour growth in mice with inherited breast cancer in association with a higher protection against LDL oxidative modification.