bluuebunny/crossref_metadata_2025_split huggingface dataset:
A voltage-dependent chloride channel fine-tunes photosynthesis in plants
Authors: Herdean Andrei , Teardo Enrico , Nilsson Anders K. , Pfeil Bernard E. , Johansson Oskar N. , Ünnep Renáta , Nagy Gergely , Zsiros Ottó , Dana Somnath , Solymosi Katalin , Garab Győző , Szabó Ildikó , Spetea Cornelia , Lundin Björn 
Published: May 2016

AbstractIn natural habitats, plants frequently experience rapid changes in the intensity of sunlight. To cope with these changes and maximize growth, plants adjust photosynthetic light utilization in electron transport and photoprotective mechanisms. This involves a proton motive force (PMF) across the thylakoid membrane, postulated to be affected by unknown anion (Cl−) channels. Here we report that a bestrophin-like protein from Arabidopsis thaliana functions as a voltage-dependent Cl− channel in electrophysiological experiments. AtVCCN1 localizes to the thylakoid membrane, and fine-tunes PMF by anion influx into the lumen during illumination, adjusting electron transport and the photoprotective mechanisms. The activity of AtVCCN1 accelerates the activation of photoprotective mechanisms on sudden shifts to high light. Our results reveal that AtVCCN1, a member of a conserved anion channel family, acts as an early component in the rapid adjustment of photosynthesis in variable light environments.
The child brain computes and utilizes internalized maternal choices
Authors: Lim Seung-Lark , Cherry J. Bradley C. , Davis Ann M. , Balakrishnan S. N. , Ha Oh-Ryeong , Bruce Jared M. , Bruce Amanda S. 
Published: May 2016

AbstractAs children grow, they gradually learn how to make decisions independently. However, decisions like choosing healthy but less-tasty foods can be challenging for children whose self-regulation and executive cognitive functions are still maturing. We propose a computational decision-making process in which children estimate their mother’s choices for them as well as their individual food preferences. By employing functional magnetic resonance imaging during real food choices, we find that the ventromedial prefrontal cortex (vmPFC) encodes children’s own preferences and the left dorsolateral prefrontal cortex (dlPFC) encodes the projected mom’s choices for them at the time of children’s choice. Also, the left dlPFC region shows an inhibitory functional connectivity with the vmPFC at the time of children’s own choice. Our study suggests that in part, children utilize their perceived caregiver’s choices when making choices for themselves, which may serve as an external regulator of decision-making, leading to optimal healthy decisions.
Fast generation of three-qubit Greenberger-Horne-Zeilinger state based on the Lewis-Riesenfeld invariants in coupled cavities
Authors: Huang Xiao-Bin , Chen Ye-Hong , Wang Zhe 
Published: May 2016

AbstractIn this paper, we propose an efficient scheme to fast generate three-qubit Greenberger-Horne-Zeilinger (GHZ) state by constructing shortcuts to adiabatic passage (STAP) based on the “Lewis-Riesenfeld (LR) invariants” in spatially separated cavities connected by optical fibers. Numerical simulations illustrate that the scheme is not only fast, but robust against the decoherence caused by atomic spontaneous emission, cavity losses and the fiber photon leakages. This might be useful to realize fast and noise-resistant quantum information processing for multi-qubit systems.
The defect-induced localization in many positions of the quantum random walk
Authors: Chen Tian , Zhang Xiangdong 
Published: May 2016

AbstractWe study the localization of probability distribution in a discrete quantum random walk on an infinite chain. With a phase defect introduced in any position of the quantum random walk (QRW), we have found that the localization of the probability distribution in the QRW emerges. Different localized behaviors of the probability distribution in the QRW are presented when the defect occupies different positions. Given that the coefficients of the localized stationary eigenstates relies on the coin operator, we reveal that when the defect occupies different positions, the amplitude of localized probability distribution in the QRW exhibits a non-trivial dependence on the coin operator.
Unpeeling the layers of language: Bonobos and chimpanzees engage in cooperative turn-taking sequences
Authors: Fröhlich Marlen , Kuchenbuch Paul , Müller Gudrun , Fruth Barbara , Furuichi Takeshi , Wittig Roman M. , Pika Simone 
Published: May 2016

AbstractHuman language is a fundamentally cooperative enterprise, embodying fast-paced and extended social interactions. It has been suggested that it evolved as part of a larger adaptation of humans’ species-unique forms of cooperation. Although our closest living relatives, bonobos and chimpanzees, show general cooperative abilities, their communicative interactions seem to lack the cooperative nature of human conversation. Here, we revisited this claim by conducting the first systematic comparison of communicative interactions in mother-infant dyads living in two different communities of bonobos (LuiKotale, DRC;Wamba, DRC) and chimpanzees (Taï South, Côte d’Ivoire;Kanyawara, Uganda) in the wild. Focusing on the communicative function of joint-travel-initiation, we applied parameters of conversation analysis to gestural exchanges between mothers and infants. Results showed that communicative exchanges in both species resemble cooperative turn-taking sequences in human conversation. While bonobos consistently addressed the recipient via gaze before signal initiation and used so-called overlapping responses, chimpanzees engaged in more extended negotiations, involving frequent response waiting and gestural sequences. Our results thus strengthen the hypothesis that interactional intelligence paved the way to the cooperative endeavour of human language and suggest that social matrices highly impact upon communication styles.
Soil Fertility Map for Food Legumes Production Areas in China
Authors: Li Ling , Yang Tao , Redden Robert , He Weifeng , Zong Xuxiao 
Published: May 2016

AbstractGiven the limited resources of fossil energy and the environmental risks of excess fertilizer on crops, it is time to reappraise the potential role of food legume biological nitrogen fixation (BNF) as sources of nitrogen for cropping systems in China. 150 soil samples across 17 provinces and 2 municipalities of China were collected and analyzed. A distribution map of the soil fertilities and their patterns of distribution was constructed. The pH results indicated that soils were neutral to slightly alkaline overall. The soil organic matter (SOM) and the available nitrogen (AN) content were relatively low, while the available phosphorus (AP) and available potassium (AK) contents were from moderate to high. Production areas of food legumes (faba bean, pea, adzuki bean, mung bean and common bean) were clearly separated into 4 soil fertility type clusters. In addition, regions with SOM, AN, AP and AK deficiency, high acidity and high alkalinity were listed as target areas for further soil improvement. The potential was considered for biological nitrogen fixation to substitute for the application of mineral nitrogen fertiliser.
Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot
Authors: He Tianhua , D’Agui Haylee , Lim Sim Lin , Enright Neal J. , Luo Yiqi 
Published: May 2016

AbstractSubstantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime.
Efficient selective breeding of live oil-rich Euglena gracilis with fluorescence-activated cell sorting
Authors: Yamada Koji , Suzuki Hideyuki , Takeuchi Takuto , Kazama Yusuke , Mitra Sharbanee , Abe Tomoko , Goda Keisuke , Suzuki Kengo , Iwata Osamu 
Published: May 2016

AbstractEuglena gracilis, a microalgal species of unicellular flagellate protists, has attracted much attention in both the industrial and academic sectors due to recent advances in the mass cultivation of E. gracilis that have enabled the cost-effective production of nutritional food and cosmetic commodities. In addition, it is known to produce paramylon (β-1,3-glucan in a crystalline form) as reserve polysaccharide and convert it to wax ester in hypoxic and anaerobic conditions–a promising feedstock for biodiesel and aviation biofuel. However, there remain a number of technical challenges to be solved before it can be deployed in the competitive fuel market. Here we present a method for efficient selective breeding of live oil-rich E. gracilis with fluorescence-activated cell sorting (FACS). Specifically, the selective breeding method is a repetitive procedure for one-week heterotrophic cultivation, staining intracellular lipids with BODIPY505/515 and FACS-based isolation of top 0.5% lipid-rich E. gracilis cells with high viability, after inducing mutation with Fe-ion irradiation to the wild type (WT). Consequently, we acquire a live, stable, lipid-rich E. gracilis mutant strain, named B1ZFeL, with 40% more lipid content on average than the WT. Our method paves the way for rapid, cost-effective, energy-efficient production of biofuel.
Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods
Authors: Morinière Jérôme , Van Dam Matthew H. , Hawlitschek Oliver , Bergsten Johannes , Michat Mariano C. , Hendrich Lars , Ribera Ignacio , Toussaint Emmanuel F.A. , Balke Michael 
Published: May 2016

AbstractThe underlying mechanisms responsible for the general increase in species richness from temperate regions to the tropics remain equivocal. Many hypotheses have been proposed to explain this astonishing pattern but additional empirical studies are needed to shed light on the drivers at work. Here we reconstruct the evolutionary history of the cosmopolitan diving beetle subfamily Colymbetinae, the majority of which are found in the Northern hemisphere, hence exhibiting an inversed latitudinal diversity gradient. We reconstructed a dated phylogeny using 12 genes, to investigate the biogeographical history and diversification dynamics in the Colymbetinae. We aimed to identify the role that phylogenetic niche conservatism plays in the inversed diversification pattern seen in this group. Our results suggest that Colymbetinae originated in temperate climates, which supports the hypothesis that their distribution is the result of an ancestral adaptation to temperate environmental conditions rather than tropical origins, and that temperate niche conservatism can generate and/or maintain inverse latitudinal diversity gradients.
Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis
Authors: Kumar Mukesh , Belcaid Mahdi , Nerurkar Vivek R. 
Published: May 2016

AbstractDifferential host responses may be critical determinants of distinct pathologies of West Nile virus (WNV) NY99 (pathogenic) and WNV Eg101 (non-pathogenic) strains. We employed RNA-seq technology to analyze global differential gene expression in WNV-infected mice brain and to identify the host cellular factors leading to lethal encephalitis. We identified 1,400 and 278 transcripts, which were differentially expressed after WNV NY99 and WNV Eg101 infections, respectively and 147 genes were common to infection with both the viruses. Genes that were up-regulated in infection with both the viruses were mainly associated with interferon signaling. Genes associated with inflammation and cell death/apoptosis were only expressed after WNV NY99 infection. We demonstrate that differences in the activation of key pattern recognition receptors resulted in the induction of unique innate immune profiles, which corresponded with the induction of interferon and inflammatory responses. Pathway analysis of differentially expressed genes indicated that after WNV NY99 infection, TREM-1 mediated activation of toll-like receptors leads to the high inflammatory response. In conclusion, we have identified both common and specific responses to WNV NY99 and WNV Eg101 infections as well as genes linked to potential resistance to infection that may be targets for therapeutics.
Seafloor heterogeneity influences the biodiversity–ecosystem functioning relationships in the deep sea
Authors: Zeppilli Daniela , Pusceddu Antonio , Trincardi Fabio , Danovaro Roberto 
Published: May 2016

AbstractTheoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystems.
Indoor radiocaesium contamination in residential houses within evacuation areas after the Fukushima nuclear accident
Authors: Yoshida-Ohuchi Hiroko , Kanagami Takashi , Satoh Yasushi , Hosoda Masahiro , Naitoh Yutaka , Kameyama Mizuki 
Published: May 2016

AbstractIndoor contaminants were investigated from July 2013 to January 2015 within ninety-five residential houses in five evacuation zones, Iitate village, Odaka district, and the towns of Futaba, Okuma, and Tomioka. A dry smear test was applied to the surface of materials and structures in rooms and in the roof-space of houses. We found that 134Cs and 137Cs were the dominant radionuclides in indoor surface contamination, and there was a distance dependence from the Fukushima Daiichi nuclear power plant (FDNPP). For surface contamination in Iitate village (29–49 km from the FDNPP), 24.8% of samples exceeded the detection limit, which is quite a low value, while in Okuma (<3.0 km from the FDNPP), 99.7% of samples exceeded the detection limit and surface contamination levels exceeded 20 Bq/cm2 (the value was corrected to March 2011). In residential houses in Okuma, Futaba, and Tomioka, closer to the FDNPP than those in Odaka district and Iitate village, surface contamination was inversely proportional to the square of the distance between a house and the FDNPP. In the houses closest to the FDNPP, the contribution of surface contamination to the ambient dose equivalent rate was evaluated to be approximately 0.3 μSv/h.
MetaTrans: an open-source pipeline for metatranscriptomics
Authors: Martinez Xavier , Pozuelo Marta , Pascal Victoria , Campos David , Gut Ivo , Gut Marta , Azpiroz Fernando , Guarner Francisco , Manichanh Chaysavanh 
Published: May 2016

AbstractTo date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).
Evidence supporting the conceptual framework of cancer chemoprevention in canines
Authors: Kondratyuk Tamara P. , Adrian Julie Ann Luiz , Wright Brian , Park Eun-Jung , van Breemen Richard B. , Morris Kenneth R. , Pezzuto John M. 
Published: May 2016

AbstractAs with human beings, dogs suffer from the consequences of cancer. We investigated the potential of a formulation comprised of resveratrol, ellagic acid, genistein, curcumin and quercetin to modulate biomarkers indicative of disease prevention. Dog biscuits were evaluated for palatability and ability to deliver the chemopreventive agents. The extent of endogenous DNA damage in peripheral blood lymphocytes from dogs given the dietary supplement or placebo showed no change. However, H2O2-inducible DNA damage was significantly decreased after consumption of the supplement. The expression of 11 of 84 genes related to oxidative stress was altered. Hematological parameters remained in the reference range. The concept of chemoprevention for the explicit benefit of the canine is compelling since dogs are an important part of our culture. Our results establish a proof-of-principle and provide a framework for improving the health and well-being of “man’s best friend”.
SUMO5, a Novel Poly-SUMO Isoform, Regulates PML Nuclear Bodies
Authors: Liang Ya-Chen , Lee Chia-Chin , Yao Ya-Li , Lai Chien-Chen , Schmitz M. Lienhard , Yang Wen-Ming 
Published: May 2016

AbstractPromyelocytic leukemia nuclear bodies (PML-NBs) are PML-based nuclear structures that regulate various cellular processes. SUMOylation, the process of covalently conjugating small ubiquitin-like modifiers (SUMOs), is required for both the formation and the disruption of PML-NBs. However, detailed mechanisms of how SUMOylation regulates these processes remain unknown. Here we report that SUMO5, a novel SUMO variant, mediates the growth and disruption of PML-NBs. PolySUMO5 conjugation of PML at lysine 160 facilitates recruitment of PML-NB components, which enlarges PML-NBs. SUMO5 also increases polySUMO2/3 conjugation of PML, resulting in RNF4-mediated disruption of PML-NBs. The acute promyelocytic leukemia oncoprotein PML-RARα blocks SUMO5 conjugation of PML, causing cytoplasmic displacement of PML and disruption of PML-NBs. Our work not only identifies a new member of the SUMO family but also reveals the mechanistic basis of the PML-NB life cycle in human cells.
Nonclassicality Invariant of General Two-Mode Gaussian States
Authors: Arkhipov Ievgen I. , Peřina Jan , Svozilík Jiří , Miranowicz Adam 
Published: May 2016

AbstractWe introduce a new quantity for describing nonclassicality of an arbitrary optical two-mode Gaussian state which remains invariant under any global photon-number preserving unitary transformation of the covariance matrix of the state. The invariant naturally splits into an entanglement monotone and local-nonclassicality quantifiers applied to the reduced states. This shows how entanglement can be converted into local squeezing and vice versa. Twin beams and their transformations at a beam splitter are analyzed as an example providing squeezed light. An extension of this approach to pure three-mode Gaussian states is given.
Contribution of the pod wall to seed grain filling in alfalfa
Authors: Wang Hui , Hou Longyu , Wang Mingya , Mao Peisheng 
Published: May 2016

AbstractThree genotypes of alfalfa viz. Medicago sativa (Zhongmu No. 1, Zhongmu No. 2) and M. varia (Caoyuan No. 3) grown in the filed were investigated for the contribution of pod wall and leaves by shading all pods and leaves on July 15, 20 and 25, respectively. Date was recorded for total pod weight (TPW), pod wall weight (PWW), seed weight per pod (SWP), seed number per pod (SNP) and single seed weight (SSW) of one-coil and two-coil spiral pods. TPW, SNP, PWW and SWP were reduced by shading all leaves or pods, whereas SSW was not significantly affected. The relative photosynthetic contribution of pod wall to SWP was 25.6–48.1% in three genotypes on July 15. The pod wall in one-coil spiral pods generated a greater relative contribution to the TPW and SWP than in two-coil spiral pods. In the last stage (July 25), the relative photosynthetic contribution of leaves to SWP sharply decreased, whereas the relative photosynthetic contribution of pod wall to SWP was stable in the late stage (July 20 and 25). In conclusion, the pod wall of alfalfa could carry out photosynthesis and the pod wall played an important role in pod filling at the late growth stage.