bluuebunny/crossref_metadata_2025 huggingface dataset:
Die Bundesländer in der nationalen Energie- und Klimapolitik: Räumliche Verteilungswirkungen und föderale Politikgestaltung der Energiewende
Authors: Monstadt Jochen , Scheiner Stefan
Published: May 2016

Until today, the academic and political debates on the German energy transition have primarily focused on policy activities and processes at either the national or local level. However, they have largely ignored how the Länder shape the federal decision-making on the allocation of greenhouse gas emissions according to their place-based economic interests. The starting point of this paper is the empirical evidence that effective national climate mitigation policies can go along with considerable and spatially unevenly distributed redistributive effects for regional energy industries, energy consumption sectors and thus public budgets of the Länder. Since the costs and benefits of climate mitigation policies are distributed unevenly, the Länder pursue place-based economic and political interests that shape their climate mitigation programs and their positions in federal decision-making. Based on an analysis of the regional economic interests and of the climate mitigation programs of the Länder, the paper uses the cases of the renewable energy policies and the European emission trading system to demonstrate how (re-)distributional conflicts in climate mitigation policies have been reconciled. The case studies show that redistributive policies could be implemented through concessions to single Länder. They also show that through distributive mechanisms, the externalization of costs to the users played a major role, and that the EU could partially dissolve blockades in decision-making. Contrary to findings in the academic debate on German federalism, federal climate mitigation policies have partially stimulated mechanisms for economic and innovation competition between the Länder. However, the findings also demonstrate that the concessions to regional economic interests have reduced the cost-efficiency and effectiveness of the German energy and climate mitigation policies.
Polycyclic aromatic hydrocarbons and pesticides in milk powder
Authors: Dobrinas Simona , Soceanu Alina , Popescu Viorica , Coatu Valentina
Published: May 2016

This Research Communication reports analysis of 37 compounds comprising polycyclic aromatic hydrocarbons (PAHs), organochlorine and organophosphate pesticides (OCPS and OPPS) in milk powder (one brand each of commercial infant formulae, follow-on formulae and baby formulae purchased from a local supermarket in Romania). The selected analytes were investigated using gas chromatography–mass spectrometry (GC-MS), gas chromatography with electron capture detector (GC-ECD) and gas chromatography with thermionic sensitive detection (GC-TSD). The estimated limits of detection for most target analytes were in the μg/kg level (range 0·001–0·320 µg/kg). The purpose of the study was to determine the selected analytes, to assess the exposure of babies and infants and to produce data for comparison with tolerable limits according to the European Union Regulations. In most of the samples the organochlorine pesticides values were under the limit of detection. Exceptions were heptachlor epoxide and endosulfan sulphate, the last of which was found in all analysed samples at low concentrations. We also found detectable levels of ethoprophos, parathion-methyl, chlorpyrifos, prothiofos, guthion, disulfoton and fenchlorphos in most of the analysed samples. Benzo[a]pyrene, which is used as an indicator for the presence of PAHs, was not detected in selected samples. The low level of exposure to contaminants indicates that there are no health risks for the infants and babies that consume this brand of milk powder formulae.
Engineering to support wellbeing of dairy animals
Authors: Caja Gerardo , Castro-Costa Andreia , Knight Christopher H.
Published: May 2016

Current trends in the global milk market and the recent abolition of milk quotas have accelerated the trend of the European dairy industry towards larger farm sizes and higher-yielding animals. Dairy cows remain in focus, but there is a growing interest in other dairy species, whose milk is often directed to traditional and protected designation of origin and gourmet dairy products. The challenge for dairy farms in general is to achieve the best possible standards of animal health and welfare, together with high lactational performance and minimal environmental impact. For larger farms, this may need to be done with a much lower ratio of husbandry staff to animals. Recent engineering advances and the decreasing cost of electronic technologies has allowed the development of ‘sensing solutions’ that automatically collect data, such as physiological parameters, production measures and behavioural traits. Such data can potentially help the decision making process, enabling early detection of health or wellbeing problems in individual animals and hence the application of appropriate corrective husbandry practices. This review focuses on new knowledge and emerging developments in welfare biomarkers (e.g. stress and metabolic diseases), activity-based welfare assessment (e.g. oestrus and lameness detection) and sensors of temperature and pH (e.g. calving alert and rumen function) and their combination and integration into ‘smart’ husbandry support systems that will ensure optimum wellbeing for dairy animals and thereby maximise farm profitability. Use of novel sensors combined with new technologies for information handling and communication are expected to produce dramatic changes in traditional dairy farming systems.
Neural effects of social environmental stress – an activation likelihood estimation meta-analysis
Authors: Mothersill O. , Donohoe G.
Published: May 2016

Background

Social environmental stress, including childhood abuse and deprivation, is associated with increased rates of psychiatric disorders such as schizophrenia and depression. However, the neural mechanisms mediating risk are not completely understood. Functional magnetic resonance imaging (MRI) studies have reported effects of social environmental stress on a variety of brain regions, but interpretation of results is complicated by the variety of environmental risk factors examined and different methods employed.

Method

We examined brain regions consistently showing differences in blood oxygen level-dependent (BOLD) response in individuals exposed to higher levels of environmental stress by performing a coordinate-based meta-analysis on 54 functional MRI studies using activation likelihood estimation (ALE), including an overall sample of 3044 participants. We performed separate ALE analyses on studies examining adults (mean age ⩾18 years) and children/adolescents (mean age <18 years) and a contrast analysis comparing the two types of study.

Results

Across both adult and children/adolescent studies, ALE meta-analysis revealed several clusters in which differences in BOLD response were associated with social environmental stress across multiple studies. These clusters incorporated several brain regions, among which the right amygdala was most frequently implicated.

Conclusions

These findings suggest that a variety of social environmental stressors is associated with differences in the BOLD response of specific brain regions such as the right amygdala in both children/adolescents and adults. What remains unknown is whether these environmental stressors have differential effects on treatment response in these brain regions.
Support networks of childless older people: informal and formal support in Europe
Authors: DEINDL CHRISTIAN , BRANDT MARTINA
Published: May 2016

Western societies are ageing rapidly. Today people do not only live longer, they also have fewer children. These developments exert considerable pressure on welfare states. Children have usually been the mainstay of old age support, especially when there is no partner. We thus face new challenges: On which support networks can a growing number of childless older people rely? (How) can the lack of children be compensated in the informal social network? What role does the state play and how is informal and formal support linked? Our comparative analyses of the support networks of childless elders are based on the first two waves of the Survey of Health, Ageing and Retirement in Europe, including 14,394 people with (instrumental) activities of daily living limitations aged 50 and over from 12 European countries. On average, 10 per cent of older Europeans today have no children. Sporadic informal support for these elders is often taken over by the extended family, friends and neighbours, and thus the lack of children is compensated within the social network. Intense care tasks, however, are more likely provided by professional providers, especially in the case of childless older people. In countries with low social service provision, childless elders are therefore likely to experience a lack of (formal) support, especially when depending on vital care.
The openness of the London Goldsmiths’ Company in the second half of the seventeenth century: an empirical study
Authors: Schwarzberg Raphaelle
Published: May 2016

In this article, we analyse geographical, occupational and kinship ties amongst apprentices and their masters of the London Goldsmiths’ Company in the second half of the seventeenth century, at a time when the profession was undergoing radical change, thus forming the cradle of British banking. Systematic comparisons of social capital of the guild's two subgroups (the ‘Bankers’ and the ‘Craftsmen and Retailers’) show few such ties at entry and only slightly more amongst office-holders. Overall, ‘Bankers’ display slightly greater social ties in the company overall. Hypotheses for such patterns are discussed, including activity specificity, wealth and position in the guild and households’ economic strategies. The article calls for a household-based approach to economic choices as opposed to one focusing on the guild.
A flexible three-dimensional electrode mesh: An enabling technology for wireless brain–computer interface prostheses
Authors: Xiang Zhuolin , Liu Jingquan , Lee Chengkuo
Published: May 2016

The neural interface is a key component in wireless brain–computer prostheses. In this study, we demonstrate that a unique three-dimensional (3D) microneedle electrode on a flexible mesh substrate, which can be fabricated without complicated micromachining techniques, is conformal to the tissues with minimal invasiveness. Furthermore, we demonstrate that it can be applied to different functional layers in the nervous system without length limitation. The microneedle electrode is fabricated using drawing lithography technology from biocompatible materials. In this approach, the profile of a 3D microneedle electrode array is determined by the design of a two-dimensional (2D) pattern on the mask, which can be used to access different functional layers in different locations of the brain. Due to the sufficient stiffness of the electrode and the excellent flexibility of the mesh substrate, the electrode can penetrate into the tissue with its bottom layer fully conformal to the curved brain surface. Then, the exposed contact at the end of the microneedle electrode can successfully acquire neural signals from the brain.
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

In 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

As 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.
Correction: Corrigendum: CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells
Authors: Mantsoki Anna , Devailly Guillaume , Joshi Anagha
Published: May 2016

Scientific Reports 5: Article number: 16791; published online: 19 November 2015; updated: 23 May 2016. This Article contained errors. In Figure 5c, the labels of the last two panels were inverted, where ‘H3K27me3’ and H3K4me3’ were incorrectly given as ‘H3K4me3’ and ‘H3K27me3’ respectively. The correct Figure 5 appears below as Fig.
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

In 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

We 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

Human 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

Given 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

Substantial 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

Euglena 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

The 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

Differential 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

Theoretical 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.
Correction: Corrigendum: Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
Authors: Ni Xumin , Yang Xiong , Guo Wei , Yuan Kai , Zhou Ying , Ma Zhiming , Xu Shuhua
Published: May 2016

Scientific Reports 6: Article number: 20048; published online: 28 January 2016; updated: 23 May 2016. In the original version of this Article, Affiliation 1 was omitted for Zhiming Ma. This error has now been corrected in the PDF and HTML versions of the Article.
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

Indoor 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.
Correction: Corrigendum: Genetic affinities of the Jewish populations of India
Authors: Chaubey Gyaneshwer , Singh Manvendra , Rai Niraj , Kariappa Mini , Singh Kamayani , Singh Ashish , Singh Deepankar Pratap , Tamang Rakesh , Rani Deepa Selvi , Reddy Alla G. , Singh Vijay Kumar , Singh Lalji , Thangaraj Kumarasamy
Published: May 2016

Scientific Reports 6: Article number: 19166; published online: 13 January 2016; updated: 23 May 2016. After publication of our paper, it was kindly brought to our attention that the genomewide dataset (11 samples) for the Indian Jewish2 group in its entirety is unpublished. It was accidentally shared with us as a part of the data we obtained from authors of Atzmon et al.
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

To 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

As 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

Promyelocytic 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

We 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

Three 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.
Enhanced photophysics from self-assembled cyclometalated Ir(iii) complexes in water
Authors: McGoorty Michelle M. , Khnayzer Rony S. , Castellano Felix N.
Published: May 2016

Two water-soluble anionic cyclometalated Ir(iii) complexes, Ir(ppy)2BPS [1] and Ir(F-mppy)2BPS [2] have been synthesized and display clear evidence of self-assembly in water.
Constructing chiral MOFs by functionalizing 4,2′:6′,4′′-terpyridine with long-chain alkoxy domains: rare examples of neb nets
Authors: Klein Y. Maximilian , Prescimone Alessandro , Pitak Mateusz B. , J.Coles Simon , Constable Edwin C. , Housecroft Catherine E.
Published: May 2016

Three chiral 3D MOFs with uncommon neb topologies assemble from Co(NCS)2 and 4′-(4-nalkyloxyphenyl)-4,2′:6′,4′′-terpyridines (alkyl = hexyl or nonyl).
X-Ray absorption spectra of microsolvated metal cations
Authors: Miteva T. , Wenzel J. , Klaiman S. , Dreuw A. , Gokhberg K.
Published: May 2016

Core excited states of microsolvated ions undergo substantial delocalisation whose degree strongly depends on the ion's charge.
Formation of supramolecular assemblies and liquid crystals by purine nucleobases and cyanuric acid in water: implications for the possible origins of RNA
Authors: Li C. , Cafferty B. J. , Karunakaran S. C. , Schuster G. B. , Hud N. V.
Published: May 2016

The free nucleobases and mononucleotides of RNA do not form Watson–Crick base pairs in water, a fact that presents several challenges for the prebiotic synthesis of RNA.
Decarboxylative/decarbonylative C3-acylation of indoles via photocatalysis: a simple and efficient route to 3-acylindoles
Authors: Shi Qing , Li Pinhua , Zhu Xianjin , Wang Lei
Published: May 2016

An efficient synthesis of 3-acylindoles via visible-light promoted C3-acylation of free (NH)- and N-substituted indoles with α-oxocarboxylic acids was developed.
Computation of the pressure field generated by surface acoustic waves in microchannels
Authors: Darinskii A. N. , Weihnacht M. , Schmidt H.
Published: May 2016

SAW induced acoustic pressures in a microchannel computed by solving two different boundary-value problems are compared.
Label-free and dual-amplified electrochemical detection of Hg2+ based on self-assembled DNA nanostructures and target-triggered exonuclease cleavage activity
Authors: Bao Ting , Wen Wei , Shu Lei , Zhang Xiuhua , Wang Shengfu
Published: May 2016

An electrochemical biosensor for Hg2+ detection via HCR and Hg2+-triggered Exo III-assisted target recycling for signal amplification.
Sex hormone therapy and progression of cardiovascular disease in menopausal women
Authors: Alhurani Rabe E. , Chahal C. Anwar A. , Ahmed Ahmed T. , Mohamed Essa A. , Miller Virginia M.
Published: May 2016

One of the most controversial health decisions facing women is deciding upon the use of hormonal treatments for symptoms of menopause. This brief review focuses on the historical context of use of menopausal hormone treatments (MHT), summarizes results of major observational, primary and secondary prevention studies of MHT and cardiovascular (CV) outcomes, provides evidence for how sex steroids modulate CV function and identifies challenges for future research. As medicine enters an era of personalization of treatment options, additional research into sex differences in the aetiology of CV diseases will lead to better risk identification for CV disease in women and identify whether a woman might receive CV benefit from specific formulations and doses of MHT.
A Randomized Controlled Clinical Trial Investigating the Effect of
Synbiotic Administration on Markers of Insulin Metabolism and Lipid Profiles in
Overweight Type 2 Diabetic Patients with Coronary Heart Disease
Authors: Tajabadi-Ebrahimi M. , Sharifi N. , Farrokhian A. , Raygan F. , Karamali F. , Razzaghi R. , Taheri S. , Asemi Z.
Published: May 2016

Objective: The current study was performed to evaluate the effects of
synbiotic administration on metabolic profiles in overweight diabetic patients
with coronary heart disease (CHD).

Methods: This randomized, double-blind, placebo-controlled trial was done
among 60 diabetic patients with CHD. Participants were randomly divided into 2
groups: group A (n=30) received synbiotic supplements containing 3 probiotic
bacteria spices Lactobacillus acidophilus 2×109,
Lactobacillus casei 2×109, Bifidobacterium bifidum
2×109 CFU/g plus 800 mg inulin and group B (n=30) received
placebo for 12 weeks. Fasting blood samples were taken at baseline and after
12-week intervention to determine metabolic profiles.

Results: After 12 weeks of intervention, patients who consumed synbiotic
capsule had significantly decreased fasting plasma glucose (− 19.6±74.6
vs.+19.2±66.9 mg/dL, P=0.03), serum insulin concentrations (− 0.7±5.1
vs.+3.3±6.3 µIU/mL, P=0.01), the homeostasis model of assessment-estimated b
cell function (− 3.4±19.5 vs.+11.5±21.0, P=0.006) and increased the quantitative
insulin sensitivity check index (+ 0.002±0.01 vs.−0.01±0.02, P=0.03) compared
with the placebo. In addition, changes in HLDL-cholesterol levels (+ 1.8±5.7
vs.−2.2±6.0 mg/dL, P=0.01) in supplemented patients were significantly different
from those of patients in the placebo group.

Conclusion: Synbiotic supplementation for 12 weeks among diabetic
patients with CHD had beneficial effects on markers of insulin metabolism and
HDL-cholesterol levels.
Der Stellenwert der bronchoalveolären Lavage bei der Diagnostik der idiopathischen Lungenfibrose – eine Analyse unter Berücksichtigung des Proteingehaltes
Authors: Schildge J. , Frank J. , Klar B.
Published: May 2016

Obwohl die bronchoalveoläre Lavage (BAL) bei der Diagnostik interstitieller Lungenkrankheiten (ILK) häufig zum Einsatz kommt, ist ihr Stellenwert insbesondere bei der idiopathischen Lungenfibrose (IPF) wissenschaftlich umstritten. Berücksichtigt werden in der klinischen Routine die Zellverteilungen in der BAL, nichtzelluläre Merkmale der BAL spielen keine Rolle.

Die vorliegende Arbeit untersucht mit Hilfe mathematischer Datenmodellierung, in welchem Umfang BAL-Merkmale einen Rückschluss auf die zugrundeliegende ILK zulassen und/oder eine IPF ausschließen können. In die Berechnung einbezogen werden zelluläre Befunde der BAL, daneben der Protein- und Albumin-Gehalt der BAL, die Nikotinanamnese (pack years) und die Spirometrie (IVC, FEV1).

Mittels linearer Diskriminanzanalyse und Erstellung von Klassifikationsbäumen wurde die Relevanz der Merkmale von 806 Patienten mit ILK untersucht (183 IPF, 191 kryptogen organisierende Pneumonie, 147 Lungenbeteiligung bei Autoimmunerkrankung, 97 respiratorische Bronchiolitis mit interstitieller Lungenkrankheit, 118 exogen allergische Alveolitis, 41 lymphozytische interstitielle Pneumonie (LIP), 23 nichtspezifische interstitielle Pneumonie (NSIP), 88 Kontrolle).

Protein zeigte in der Gesamtgruppe eine enge positive Beziehung zu den Lymphozyten. Bei IPF und NSIP ist diese Korrelation nicht vorhanden. Albumin ist in allen Gruppen eng mit dem Protein korreliert.

Die Lymphozyten sind am besten geeignet, die verschiedenen ILK voneinander abzugrenzen. Eine zuverlässige Kalkulation der ILK ist auf dem Boden der untersuchten Faktoren aber nicht möglich, der Klassifikationsfehler betrug zwischen 23,5 % (IPF) und 100 % (LIP, NSIP).

Konstellationen, die mit hoher Wahrscheinlichkeit gegen eine IPF sprechen, sind eine Lymphozytose > 34 % oder ein Proteingehalt > 347 mg/l. Gleiches gilt für die Konstellation Lymphozyten > 25 % und Protein > 250 mg/l.

Bei ILK können BAL-Befunde die Diagnose eingrenzen, sind aber selten diagnosesichernd. Zum Ausschluss einer IPF kann die BAL aber einen wichtigen Beitrag leisten.
Simulations of peeling-ballooning modes with electron cyclotron resonance heating
Authors: Huang J. , Chen S. Y. , Tang C. J.
Published: May 2016

The effects of the deposited power and deposited position of Electron Cyclotron Resonance Heating (ECRH) on Peeling-Ballooning (P-B) modes are simulated using BOUT++ code in this paper. The simulation results show that as the deposited position moves from the top to the bottom of the pedestal, the edge localized mode (ELM) size decreases first and then increases, finally decreases again. For ECRH with different deposited power, the effects on P-B modes are similar if they have the same peak value of the power deposition profile. These results show that the effects of ECRH on P-B modes are primarily determined by the change in pressure profile caused by ECRH. As long as ECRH can lead to large enough change in pressure profile, ECRH can efficiently affect the dynamics of P-B modes.
Flow transients in un-started and started modes of vacuum ejector operation
Authors: Arun Kumar R. , Rajesh G.
Published: May 2016

An experimental study has been carried out to investigate the nature of transients in vacuum ejector flows during start-up and the dynamics in flow characteristics. The results show that the secondary stream induction progresses with non-uniform rates with the ramping primary jet pressure during start-up. The initial evacuation period is subjected to gradual and highly perturbed secondary fluid entrainment. In this phase, the secondary stream induction by the shear layer is asymmetric leading to an un-even vacuum generation in the secondary chamber. In the second phase, the secondary pressure fluctuations are found to be ceased for a critical primary jet pressure followed by a rapid induction of the secondary fluid till the primary jet expands to the diffuser wall. The transition from the first phase to the second phase is caused by the secondary stream flow choking in the diffuser. Following the second phase, a stable stage exists in the third phase in which the vacuum pressure decreases only marginally. Any further attempt to increase the secondary chamber vacuum level beyond the third phase, by increasing the primary jet total pressure, results in flow reversal into the secondary chamber, spoiling the already achieved vacuum level. In the fourth phase of start-up, a complicated shock interaction transformation from a Mach reflection (MR) to regular reflection (RR) occurs within the diffuser. It is also observed that the primary jet pressures for the minimum secondary chamber pressure, the minimum secondary pressure, and the primary pressure for MR-RR transformation decrease initially with increase in diffuser length and then increase. It is found that the decreasing and increasing trends are caused by the pressure recovery and Fanno effects, respectively.
Tutorial: Electroporation of cells in complex materials and tissue
Authors: Rems L. , Miklavčič D.
Published: May 2016

Electroporation is being successfully used in biology, medicine, food processing, and biotechnology, and in some environmental applications. Recent applications also include in addition to classical electroporation, where cells are exposed to micro- or milliseconds long pulses, exposures to extremely short nanosecond pulses, i.e., high-frequency electroporation. Electric pulses are applied to cells in different structural configurations ranging from suspended cells to cells in tissues. Understanding electroporation of cells in tissues and other complex environments is a key to its successful use and optimization in various applications. Thus, explanation will be provided theoretically/numerically with relation to experimental observations by scaling our understanding of electroporation from the molecular level of the cell membrane up to the tissue level.
High pressure driven superconducting critical temperature tuning in Sb2Se3 topological insulator
Authors: Anversa Jonas , Chakraborty Sudip , Piquini Paulo , Ahuja Rajeev
Published: May 2016

In this letter, we are reporting the change of superconducting critical temperature in Sb2Se3 topological insulator under the influence of an external hydrostatic pressure based on first principles electronic structure calculations coupled with Migdal–Eliashberg model. Experimentally, it was shown previously that Sb2Se3 was undergoing through a transition to a superconducting phase when subjected to a compressive pressure. Our results show that the critical temperature increases up to 6.15 K under the pressure unto 40 GPa and, subsequently, drops down until 70 GPa. Throughout this pressure range, the system is preserving the initial Pnma symmetry without any structural transformation. Our results suggest that the possible relevant mechanism behind the superconductivity in Sb2Se3 is primarily the electron–phonon coupling.