bluuebunny/crossref_metadata_2025 huggingface dataset:
A Revised Radiocarbon Chronology of the Aceramic Shell Midden of Ra’s Al-Hamra 6 (Muscat, Sultanate of Oman): Implication For Occupational Sequence, Marine Reservoir Age, and Human Mobility
Authors: Zazzo Antoine , Munoz Olivia , Badel Emilie , Béguier Irène , Genchi Francesco , Marcucci Lapo Gianni
Published: February 2016

Ra’s al-Hamra 6 (RH-6) is one of the earliest stratified archaeological sites along the eastern littoral of the Arabian Peninsula. This shell midden was radiocarbon dated to the 6th–5th millennium cal BC, but the majority of the dates were obtained before the advent of accelerator mass spectrometry (AMS) 14C dating and suffer from large uncertainties. In addition, most of these dates were obtained on marine and mangrove shells and required correction for local variations from the global average marine 14C reservoir age (MRA). This proved difficult because no consensus value exists for this period in the area. Recent excavations at RH-6 offered the opportunity to redate this important site in order to precisely determine its occupation history and later use as a graveyard, and establish the marine reservoir effect for this time period. Thirty-eight samples of charcoal, shells, and human bone apatite were selected for 14C dating. Bayesian modeling of the 14C dates suggests that the formation of the shell midden spanned ~1 millennium, between the mid-6th and the mid-5th millennium cal BC. Positive and consistent ΔR values were calculated throughout the entire sequence, ranging from 99±27 to 207±43 14C yr. At the beginning of the 4th millennium cal BC, RH-6 was used as a graveyard, as suggested by the 14C dating of a shell in strict association with an individual buried at the surface of the site. 14C dating of human bone apatite allowed us to calculate that 89% of this individual’s diet derived from marine resources. This finding confirms previous observations showing the overwhelming presence of marine and mangrove-dwelling species in the faunal and charcoal assemblage, and implies a low mobility, or mobility restricted to the coast for this population during the 4th millennium cal BC.
Potato root infection byRhizoctonia solanianastomosis group-3 andColletotrichum coccodesunder current and future spring weather in northern Italy
Authors: MANICI L. M. , CAPUTO F. , NICOLETTI F.
Published: February 2016

A study was performed in controlled conditions to reproduce cold and warm spring regimes in the east Po valley, northern Italy with a temperate subcontinental climate, to evaluate whether and to what extent spring weather regimes favour the attack ofRhizoctonia solaniorColletotrichum coccodeson potato, in view of predicted climate change. The main experiment, preceded by a controlled chamber set of tests to quantify response to temperatures ofR. solanianastomosis group (AG)-3 andC. coccodesstrains, showed that limit temperatures (minimum, maximum and optimum of colony radial growth) ofR. solaniAG-3 are 6 °C lower than those ofC. coccodes. Then, a trial to reproduce early growth stages of potato was performed in phytotrons with sprouts of cvar Hermes to simulate cold and warm spring regimes with two different relative soil moisture contents. That simulation was carried out on native non-sterilized soil samples which were co-inoculated artificially withR. solaniAG-3 andC. coccodes. Species-abundance findings of fungal root colonization in potato roots and molecular quantification (quantitative polymerase chain reaction) ofC. coccodesandR. solaniAG-3 inoculum growth in soil showed that: (i)C. coccodesis more competitive thanR. solaniAG-3 in colonizing potato root both in warm and cold spring regimes; (ii)R. solaniAG-3 infected potato roots only in the coldest spring regimes regardless of soil moisture content; (iii) soil temperature is the greatest factor that influences root colonization ofC. coccodesandR. solanias well as that of soil inhabiting fungi including some potential antagonists; (iv)R. solaniAG-3 andC. coccodesseem to greatly increase in soil under the relative driest and warmest spring weather regimes expected according to the mean scenarios of climate changing in northern Italy; (v) binucleateRhizoctoniaAG-A, a common non-pathogenic fungus indigenous to agricultural soil of that area, appears to be antagonistic towards root fungal pathogens of potato.
Early stage squamous cell carcinoma of the lower lip: predictive factors for recurrence
Authors: Ozkul Y , Songu M , Imre A , Tunc E , Ozkul Z , Arslanoglu S , Pinar E , Onal K
Published: February 2016

Objective:

This study aimed to evaluate the effect of tumour thickness on other clinicopathological parameters in early stage lower lip squamous cell carcinoma.

Methods:

Forty-six consecutive patients with lower lip squamous cell carcinoma were included in the study. Demographic, clinical and pathological data were retrospectively collected.

Results:

The mean follow-up period for all patients was 32.0 ± 18.9 months. Forty-four tumours were staged as T1 and two were T2. Twelve patients underwent neck dissection. Two patients presented with neck metastasis in the follow-up period. Four patients (8.7 per cent) had local recurrence. Correlation analysis revealed a significant relationship between microscopic tumour thickness and local tumour recurrence (r = 0.328, p = 0.045).

Conclusion:

Surgical margin control is important to prevent local recurrence, especially in thicker tumours. In addition, neck metastasis is rare in early stage lower lip squamous cell carcinoma. A ‘wait and see’ policy might be preferred in early stage T1 lower lip squamous cell carcinoma cases.
¿Educación o desintegración? Parental Migration, Remittances and Left-behind Children's Education in Western Guatemala
Authors: DAVIS JASON
Published: February 2016

Many Guatemalan parents migrate to the United States with the intention of returning earned income to improve the human capital prospects of their left-behind children. This laudable goal is achieved by many – arguably benefiting girls more than boys. However, negative international migration externalities including migration failure, familial abandonment, psychosocial harms and a culture of migration that disproportionally limits the educational prospects of boys need to be considered. Based on qualitative field interviews in western Guatemala with parents and educators, this article presents a nuanced view of economic migration and left-behind children's education, capturing both its remittance-related benefits and parental absence harms.
A Vital Challenge to Materialism
Authors: Mulder Jesse M.
Published: February 2016

Life poses a threat to materialism. To understand the phenomena of animate nature, we make use of a teleological form of explanation that is peculiar to biology, of explanations in terms of what I call the ‘vital categories’ – and this holds even for accounts of underlying physico-chemical ‘mechanisms’. The materialist claims that this teleological form of explanation does not capture what is metaphysically fundamental, whereas her preferred physical form of explanation does. In this essay, I do three things. (1) I argue that the ‘vital categories’, such aslife formandlife-process, do not reduce to the ‘physical categories’ and show that there are no grounds for the materialist's metaphysically limiting claim; (2) I sketch a positive view on how vital and physical explanations can both apply to a given phenomenon, and on how they interrelate; and (3) I show that this view meshes nicely with evolutionary theory, despite being committed to a form of ‘biological essentialism’.
Too soon to fly the coop? Online journaling to support students’ learning during their Erasmus study visit
Authors: Gabaudan Odette
Published: February 2016

Undergraduate students whose programme includes a full academic year on an Erasmus study visit require a range of support before, during and after their year abroad. This study focuses on the support provided by the home academic coordinator during the students’ period of study abroad. The research is based on a case-study which explores how the maintenance of an online journal can enhance students’ new learning experiences. The outcomes of this investigation are of interest at a pragmatic level to Erasmus coordinators and educational institutions whose programmes include a study visit or an internship. At a theoretical level, this study brings together a number of areas that have each been the subject of prior research but that so far have not been pulled together, particularly in the context of a study visit to a foreign country. The areas referred to include the benefits and challenges of rolling out educational online journals; the use of blogging in language learning; the design of rubrics as a form of feedback and the activity of reflective writing in an online environment. The findings and the discussion show how the online journal has added a positive dimension to the year abroad, particularly in the areas of communication and feedback, peer support, language learning and technology.
Cross-cultural adaptation of the German version of the Quality of Life in Alzheimer's Disease scale - Nursing Home version (QoL-AD NH)
Authors: Dichter Martin Nikolaus , Wolschon Eva-Maria , Meyer Gabriele , Köpke Sascha
Published: February 2016

Dementia is a chronic and currently incurable syndrome. Therefore, quality of life (QoL) is a major goal when caring for people with dementia (Gibson et al., 2010) and a major outcome in dementia research (Moniz-Cook et al., 2008). The measurement of QoL, especially proxy-rating, is challenging because of the proxy-perspective (Pickard and Knight, 2005), reliability (Dichter et al., 2016), validity (O'Rourke et al., 2015), and responsiveness (Perales et al., 2013). Probably due to these challenges, it has not been possible to show positive effects for QoL in almost all non-pharmacological interventions for people with dementia (Cooper et al., 2012). One recommended (Moniz-Cook et al., 2008) and frequently used instrument is the Quality of Life in Alzheimer's Disease scale (QoL-AD), which was originally developed in the US for community-dwelling people with dementia. The QoL-AD consists of 13 items based on a 4-point Likert scale ranging from “1”=poor to “4”=excellent (Logsdon et al., 1999). The original instrument has been adapted for people living in nursing homes (NH) by Edelmann et al. (2005).
Deep brain stimulation for bipolar disorder—review and outlook
Authors: Gippert Sabrina M. , Switala Christina , Bewernick Bettina H. , Kayser Sarah , Bräuer Alena , Coenen Volker A. , Schlaepfer Thomas E.
Published: February 2016

Research on deep brain stimulation (DBS) for treatment-resistant psychiatric disorders has established preliminary efficacy signals for treatment-resistant depression. There are only few studies on DBS that included patients suffering from bipolar disorder. This article gives an overview of these studies concerning DBS targets, antidepressant efficacy, and the occurrence of manic/hypomanic symptoms under stimulation. First, promising results show that all patients experienced significant improvement in depressive symptomatology. In a single case, hypomanic symptoms occurred, but they could be resolved by adjusting stimulation parameters. Furthermore, this article highlights important clinical differences between unipolar and bipolar depression that have to be considered throughout the course of treatment.
Pseudo-elliptic dual-band filters based on TM dual-mode cavities
Authors: Nocella Valeria , Pelliccia Luca , El Ghannudi Hamza , Tomassoni Cristiano , Sorrentino Roberto
Published: February 2016

This paper presents possible configurations of dual band filters based on transverse magnetic (TM) Dual mode cavities. The concept is to use TM dual-mode cavities in order to design compact dual band filters. High flexibility is obtained in terms of transmission zero (TZ) positioning. By using this approach a number of TZs up to the number of poles is attainable. Zeros can be placed in both the lower and upper stop-bands as well as between the two pass-bands to increase their insulation. The use of TM cavities allows a dramatic reduction of the filter length without significantly reducing the RF performances. Two three-cavity TM dual-band filters with six symmetric and asymmetric TZs have been designed and manufactured to validate the proposed geometry.
Deep-Sea Microbes Can Leave Records of the Past
Authors: Sullivan Cody
Published: February 2016

Researchers use carbon signatures within sea sediments to identify microbial activity and also to date earthquakes.
NLRC5 shields T lymphocytes from NK-cell-mediated elimination under inflammatory conditions
Authors: Ludigs Kristina , Jandus Camilla , Utzschneider Daniel T. , Staehli Francesco , Bessoles Stéphanie , Dang Anh Thu , Rota Giorgia , Castro Wilson , Zehn Dietmar , Vivier Eric , Held Werner , Romero Pedro , Guarda Greta
Published: February 2016

NLRC5 is a transcriptional regulator of MHC class I (MHCI), which maintains high MHCI expression particularly in T cells. Recent evidence highlights an important NK–T-cell crosstalk, raising the question on whether NLRC5 specifically modulates this interaction. Here we show that NK cells from Nlrc5-deficient mice exhibit moderate alterations in inhibitory receptor expression and responsiveness. Interestingly, NLRC5 expression in T cells is required to protect them from NK-cell-mediated elimination upon inflammation. Using T-cell-specific Nlrc5-deficient mice, we show that NK cells surprisingly break tolerance even towards ‘self’ Nlrc5-deficient T cells under inflammatory conditions. Furthermore, during chronic LCMV infection, the total CD8+ T-cell population is severely decreased in these mice, a phenotype reverted by NK-cell depletion. These findings strongly suggest that endogenous T cells with low MHCI expression become NK-cell targets, having thus important implications for T-cell responses in naturally or therapeutically induced inflammatory conditions.
Maternal plasma folate impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns
Authors: Joubert Bonnie R. , den Dekker Herman T. , Felix Janine F. , Bohlin Jon , Ligthart Symen , Beckett Emma , Tiemeier Henning , van Meurs Joyce B. , Uitterlinden Andre G. , Hofman Albert , Håberg Siri E. , Reese Sarah E. , Peters Marjolein J. , Kulle Andreassen Bettina , Steegers Eric A. P. , Nilsen Roy M. , Vollset Stein E. , Midttun Øivind , Ueland Per M. , Franco Oscar H. , Dehghan Abbas , de Jongste Johan C. , Wu Michael C. , Wang Tianyuan , Peddada Shyamal D. , Jaddoe Vincent W. V. , Nystad Wenche , Duijts Liesbeth , London Stephanie J.
Published: February 2016

Folate is vital for fetal development. Periconceptional folic acid supplementation and food fortification are recommended to prevent neural tube defects. Mechanisms whereby periconceptional folate influences normal development and disease are poorly understood: epigenetics may be involved. We examine the association between maternal plasma folate during pregnancy and epigenome-wide DNA methylation using Illumina’s HumanMethyl450 Beadchip in 1,988 newborns from two European cohorts. Here we report the combined covariate-adjusted results using meta-analysis and employ pathway and gene expression analyses. Four-hundred forty-three CpGs (320 genes) are significantly associated with maternal plasma folate levels during pregnancy (false discovery rate 5%); 48 are significant after Bonferroni correction. Most genes are not known for folate biology, includingAPC2,GRM8,SLC16A12,OPCML,PRPH,LHX1,KLK4andPRSS21.Some relate to birth defects other than neural tube defects, neurological functions or varied aspects of embryonic development. These findings may inform how maternal folate impacts the developing epigenome and health outcomes in offspring.
Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion
Authors: Zhao Zhao , Fu Jinglin , Dhakal Soma , Johnson-Buck Alexander , Liu Minghui , Zhang Ting , Woodbury Neal W. , Liu Yan , Walter Nils G. , Yan Hao
Published: February 2016

Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology.
Novel nanowire-structured polypyrrole-cobalt composite as efficient catalyst for oxygen reduction reaction
Authors: Yuan Xianxia , Li Lin , Ma Zhong , Yu Xuebin , Wen Xiufang , Ma Zi-Feng , Zhang Lei , Wilkinson David P. , Zhang Jiujun
Published: February 2016

A novel nanowire-structured polypyrrole-cobalt composite, PPy-CTAB-Co, is successfully synthesized with a surfactant of cetyltrimethylammounium bromide (CTAB). As an electro-catalyst towards oxygen reduction reaction (ORR) in alkaline media, this PPy-CTAB-Co demonstrates a superior ORR performance when compared to that of granular PPy-Co catalyst and also a much better durability than the commercial 20 wt% Pt/C catalyst. Physiochemical characterization indicates that the enhanced ORR performance of the nanowire PPy-CTAB-Co can be attributed to the high quantity of Co-pyridinic-N groups as ORR active sites and its large specific surface area which allows to expose more active sites for facilitating oxygen reduction reaction. It is expected this PPy-CTAB-Co would be a good candidate for alkaline fuel cell cathode catalyst.
Purcell effect and Lamb shift as interference phenomena
Authors: Rybin Mikhail V. , Mingaleev Sergei F. , Limonov Mikhail F. , Kivshar Yuri S.
Published: February 2016

The Purcell effect and Lamb shift are two well-known physical phenomena which are usually discussed in the context of quantum electrodynamics, with the zero-point vibrations as a driving force of those effects in the quantum approach. Here we discuss the classical counterparts of these quantum effects in photonics and explain their physics trough interference wave phenomena. As an example, we consider a waveguide in a planar photonic crystal with a side-coupled defect and demonstrate a perfect agreement between the results obtained on the basis of quantum and classic approaches and reveal their link to the Fano resonance. We find that in such a waveguide-cavity geometry the Purcell effect can modify the lifetime by at least 25 times and the Lamb shift can exceed 3 half-widths of the cavity spectral line.
Inflammasome components ASC and AIM2 modulate the acute phase of biomaterial implant-induced foreign body responses
Authors: Christo Susan N. , Diener Kerrilyn R. , Manavis Jim , Grimbaldeston Michele A. , Bachhuka Akash , Vasilev Krasimir , Hayball John D.
Published: February 2016

Detailing the inflammatory mechanisms of biomaterial-implant induced foreign body responses (FBR) has implications for revealing targetable pathways that may reduce leukocyte activation and fibrotic encapsulation of the implant. We have adapted a model of poly(methylmethacrylate) (PMMA) bead injection to perform an assessment of the mechanistic role of the ASC-dependent inflammasome in this process. We first demonstrate that ASC−/−mice subjected to PMMA bead injections had reduced cell infiltration and altered collagen deposition, suggesting a role for the inflammasome in the FBR. We next investigated the NLRP3 and AIM2 sensors because of their known contributions in recognising damaged and apoptotic cells. We found that NLRP3 was dispensable for the fibrotic encapsulation; however AIM2 expression influenced leukocyte infiltration and controlled collagen deposition, suggesting a previously unexplored link between AIM2 and biomaterial-induced FBR.
Positron annihilation spectroscopy of vacancy-related defects in CdTe:Cl and CdZnTe:Ge at different stoichiometry deviations
Authors: Šedivý L. , Čížek J. , Belas E. , Grill R. , Melikhova O.
Published: February 2016

Positron annihilation spectroscopy (PAS) was used to examine the effect of defined Cd-rich and Te-rich annealing on point defects in Cl-doped CdTe and Ge-doped CdZnTe semi-insulating single crystals. The as-grown crystals contain open-volume defects connected with Cd vacancies "Equation missing". It was found that the Cd vacancies agglomerate into clusters coupled with Cl in CdTe:Cl, and in CdZnTe:Ge they are coupled with Ge donors. While annealing in Cd pressure reduces of the "Equation missing" density, subsequent annealing in Te pressure restores "Equation missing". The CdTe:Cl contains negatively-charged shallow traps interpreted as Rydberg states of "Equation missing" A-centres and representing the major positron trapping sites at low temperature. Positrons confined in the shallow traps exhibit lifetime, which is shorter than the CdTe bulk lifetime. Interpretation of the PAS data was successfully combined with electrical resistivity, Hall effect measurements and chemical analysis, and allowed us to determine the principal point defect densities.
Excess Entropy Scaling Law for Diffusivity in Liquid Metals
Authors: Jakse N. , Pasturel A.
Published: February 2016

Understanding how dynamic properties depend on the structure and thermodynamics in liquids is a long-standing open problem in condensed matter physics. A very simple approach is based on the Dzugutov contribution developed on model fluids in which a universal (i.e. species-independent) connection relates the pair excess entropy of a liquid to its reduced diffusion coefficient. However its application to “real” liquids still remains uncertain due to the ability of a hard sphere (HS) reference fluid used in reducing parameters to describe complex interactions that occur in these liquids. Here we use ab initio molecular dynamics simulations to calculate both structural and dynamic properties at different temperatures for a wide series of liquid metals including Al, Au, Cu, Li, Ni, Ta, Ti, Zn as well as liquid Si and B. From this analysis, we demonstrate that the Dzugutov scheme can be applied successfully if a self-consistent method to determine the packing fraction of the hard sphere reference fluid is used as well as the Carnahan-Starling approach to express the excess entropy.
On the reliability of powder diffraction Line Profile Analysis of plastically deformed nanocrystalline systems
Authors: Rebuffi Luca , Troian Andrea , Ciancio Regina , Carlino Elvio , Amimi Amine , Leonardi Alberto , Scardi Paolo
Published: February 2016

An iron-molybdenum alloy powder was extensively deformed by high energy milling, so to refine the bcc iron domain size to nanometer scale (~10 nm) and introduce a strong inhomogeneous strain. Both features contribute to comparable degree to the diffraction peak profile broadening, so that size and strain contributions can be easily separated by exploiting their different dependence on the diffraction angle. To assess the reliability of Line Profile Analysis, results were compared with evidence from other techniques, including scanning and transmission electron microscopy and X-ray small angle scattering. Results confirm the extent of the size broadening effect, whereas molecular dynamics simulations provide insight into the origin of the local atomic, inhomogeneous strain, pointing out the role of dislocations, domain boundaries and interactions among crystalline domains.
Few layer epitaxial germanene: a novel two-dimensional Dirac material
Authors: Dávila María Eugenia , Le Lay Guy
Published: February 2016

Monolayer germanene, a novel graphene-like germanium allotrope akin to silicene has been recently grown on metallic substrates. Lying directly on the metal surfaces the reconstructed atom-thin sheets are prone to lose the massless Dirac fermion character and unique associated physical properties of free standing germanene. Here, we show that few layer germanene, which we create by dry epitaxy on a gold template, possesses Dirac cones thanks to a reduced interaction. This finding established on synchrotron-radiation-based photoemission, scanning tunneling microscopy imaging and surface electron diffraction places few layer germanene among the rare two-dimensional Dirac materials. Since germanium is currently used in the mainstream Si-based electronics, perspectives of using germanene for scaling down beyond the 5 nm node appear very promising. Other fascinating properties seem at hand, typically the robust quantum spin Hall effect for applications in spintronics and the engineering of Floquet Majorana fermions by light for quantum computing.
Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
Authors: Xu Xi-Wen , Zhou Xiong-Hui , Wang Rui-Ru , Peng Wen-Lei , An Yue , Chen Ling-Ling
Published: February 2016

Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation.
Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Authors: Zhou Qian , Ding Wenchao , Jiang Longyan , Xin Jiaojiao , Wu Tianzhou , Shi Dongyan , Jiang Jing , Cao Hongcui , Li Lanjuan , Li Jun
Published: February 2016

Analysis of the transcriptome of peripheral blood mononuclear cells (PBMCs) from patients with hepatitis B-related acute-on-chronic liver failure (HBV-ACLF) is essential to elucidate the pathogenesis of HBV-ACLF and identify HBV-ACLF-specific biomarkers. In this study, high-throughput sequencing was performed to characterize the transcriptome of PMBCs from patients with HBV-ACLF. Specifically, 2381 differentially expressed genes (DEGs) and 776 differentially expressed transcripts were identified through comparisons with patients with chronic hepatitis B (CHB) and healthy controls. Gene Ontology (GO) analysis identified 114 GO terms that were clustered into 12 groups. We merged 10 dysregulated genes selected from these grouped GO terms and non-clustered terms with four significant genes with a specificity of >0.8 in the HBV-ACLF patients to obtain a set of 13 unique genes. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the top six genes (CYP19A1, SEMA6B, INHBA, DEFT1P, AZU1 and DEFA4) was consistent with the results of messenger ribonucleic acid (mRNA) sequencing. A further receiver operating characteristic (ROC) analysis revealed that the areas under the ROC curves of the six genes were all >0.8, which indicated their significant diagnostic potentials for HBV-ACLF. Conclusion: The transcriptome characteristics of PBMCs are altered in patients with HBV-ACLF, and six genes may serve as biomarkers of HBV-ACLF.
A comprehensive framework for functional diversity patterns of marine chromophytic phytoplankton using rbcL phylogeny
Authors: Samanta Brajogopal , Bhadury Punyasloke
Published: February 2016

Marine chromophytes are taxonomically diverse group of algae and contribute approximately half of the total oceanic primary production. To understand the global patterns of functional diversity of chromophytic phytoplankton, robust bioinformatics and statistical analyses including deep phylogeny based on 2476 form ID rbcL gene sequences representing seven ecologically significant oceanographic ecoregions were undertaken. In addition, 12 form ID rbcL clone libraries were generated and analyzed (148 sequences) from Sundarbans Biosphere Reserve representing the world’s largest mangrove ecosystem as part of this study. Global phylogenetic analyses recovered 11 major clades of chromophytic phytoplankton in varying proportions with several novel rbcL sequences in each of the seven targeted ecoregions. Majority of OTUs was found to be exclusive to each ecoregion, whereas some were shared by two or more ecoregions based on beta-diversity analysis. Present phylogenetic and bioinformatics analyses provide a strong statistical support for the hypothesis that different oceanographic regimes harbor distinct and coherent groups of chromophytic phytoplankton. It has been also shown as part of this study that varying natural selection pressure on form ID rbcL gene under different environmental conditions could lead to functional differences and overall fitness of chromophytic phytoplankton populations.
Experimental realization of the Yang-Baxter Equation via NMR interferometry
Authors: Vind F. Anvari , Foerster A. , Oliveira I. S. , Sarthour R. S. , Soares-Pinto D. O. , Souza A. M. , Roditi I.
Published: February 2016

The Yang-Baxter equation is an important tool in theoretical physics, with many applications in different domains that span from condensed matter to string theory. Recently, the interest on the equation has increased due to its connection to quantum information processing. It has been shown that the Yang-Baxter equation is closely related to quantum entanglement and quantum computation. Therefore, owing to the broad relevance of this equation, besides theoretical studies, it also became significant to pursue its experimental implementation. Here, we show an experimental realization of the Yang-Baxter equation and verify its validity through a Nuclear Magnetic Resonance (NMR) interferometric setup. Our experiment was performed on a liquid state Iodotrifluoroethylene sample which contains molecules with three qubits. We use Controlled-transfer gates that allow us to build a pseudo-pure state from which we are able to apply a quantum information protocol that implements the Yang-Baxter equation.
Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster
Authors: Yu Hong , Zhao Xuelin , Li Qi
Published: February 2016

An increasing amount of evidence suggests that long intergenic noncoding RNAs (lincRNAs) may play diverse roles in many cellular processes. However, little is known about lincRNAs in marine invertebrates. Here, we presented the first identification and characterization of lincRNAs in the Pacific oyster (Crassostrea gigas). We developed a pipeline and identified 11,668 lincRNAs in C. gigas based on RNA-Seq resources available. These lincRNAs exhibited many common characteristics with vertebrate lincRNAs: relatively short length, low exon numbers, low expression and low sequence conservation. 1,175 lincRNAs were expressed in a tissue-specific manner, with 35.2% preferentially expressed in male gonad. 776 lincRNAs were specifically expressed in juvenile during different developmental stages. In addition, 47 lincRNAs were found to be potentially related to oyster settlement and metamorphosis. Such diverse temporal and spatial patterns of expression suggest that these lincRNAs might function in cell differentiation during early development, as well as sex differentiation and reproduction. Based on a co-expression network analysis, five lincRNAs were detected that have an expression correlation with key hub genes in four modules significantly correlated with larval development. Our study provides the first large-scale identification of lincRNAs in molluscs and offers new insights into potential functions of lincRNAs in marine invertebrates.
Taxonomic status and molecular phylogeography of two sibling species of Polytremis (Lepidoptera: Hesperiidae)
Authors: Jiang Weibin , He Haiyan , Li Yingdong , Ren Mengyi , Ma Yazhong , Zheng Lingli , Zhu Jianqing , Yu Weidong
Published: February 2016

The skipperPolytremis thecaspecies complex is widely distributed in the south of the Qinling Mountains in China. A recent study of thePolytremisgenus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this agricultural pest based on nationwide sampling and the evaluation of mitochondrial and nuclear DNA markers. We show that this species is actually an amalgamation of two sibling taxa (P. t. thecaandP. t. fukia), which displayed levels of genetic divergence as great as those generally found between sister species in thePolytremisgenus, suggesting that they actually correspond to two distinct species. The Divergence time estimates suggest that an active period of speciation withinPolytremisoccurred within the Pleistocene eras. Based on its distinct phylogenetic placement and geographical isolation, we suggest that the subspecies should be elevated to full species status under the phylogenetic species concept, which has significant management implications.
Direct Band Gap Gallium Antimony Phosphide (GaSbxP1−x) Alloys
Authors: Russell H. B. , Andriotis A. N. , Menon M. , Jasinski J. B. , Martinez-Garcia A. , Sunkara M. K.
Published: February 2016

Here, we report direct band gap transition for Gallium Phosphide (GaP) when alloyed with just 1–2 at% antimony (Sb) utilizing both density functional theory based computations and experiments. First principles density functional theory calculations of GaSbxP1−x alloys in a 216 atom supercell configuration indicate that an indirect to direct band gap transition occurs at x = 0.0092 or higher Sb incorporation into GaSbxP1−x. Furthermore, these calculations indicate band edge straddling of the hydrogen evolution and oxygen evolution reactions for compositions ranging from x = 0.0092 Sb up to at least x = 0.065 Sb making it a candidate for use in a Schottky type photoelectrochemical water splitting device. GaSbxP1−x nanowires were synthesized by reactive transport utilizing a microwave plasma discharge with average compositions ranging from x = 0.06 to x = 0.12 Sb and direct band gaps between 2.21 eV and 1.33 eV. Photoelectrochemical experiments show that the material is photoactive with p-type conductivity. This study brings attention to a relatively uninvestigated, tunable band gap semiconductor system with tremendous potential in many fields.
Uniform Nickel Vanadate (Ni3V2O8) Nanowire Arrays Organized by Ultrathin Nanosheets with Enhanced Lithium Storage Properties
Authors: Wang Chang , Fang Dong , Wang Hong’en , Cao Yunhe , Xu Weilin , Liu Xiaoqing , Luo Zhiping , Li Guangzhong , Jiang Ming , Xiong Chuanxi
Published: February 2016

Development of three-dimensional nano-architectures on current collectors has emerged as an effective strategy for enhancing rate capability and cycling stability of the electrodes. Herein, a novel type of Ni3V2O8 nanowires, organized by ultrathin hierarchical nanosheets (less than 5 nm) on Ti foil, has been obtained by a two-step hydrothermal synthesis method. Studies on structural and thermal properties of the as-prepared Ni3V2O8 nanowire arrays are carried out and their morphology has changed obviously in the following heat treatment at 300 and 500 °C. As an electrode material for lithium ion batteries, the unique configuration of Ni3V2O8 nanowires presents enhanced capacitance, satisfying rate capability and good cycling stability. The reversible capacity of the as-prepared Ni3V2O8 nanowire arrays reaches 969.72 mAh·g−1 with a coulombic efficiency over 99% at 500 mA·g−1 after 500 cycles.
Yttrium Iron Garnet Thin Films with Very Low Damping Obtained by Recrystallization of Amorphous Material
Authors: Hauser Christoph , Richter Tim , Homonnay Nico , Eisenschmidt Christian , Qaid Mohammad , Deniz Hakan , Hesse Dietrich , Sawicki Maciej , Ebbinghaus Stefan G. , Schmidt Georg
Published: February 2016

We have investigated recrystallization of amorphous Yttrium Iron Garnet (YIG) by annealing in oxygen atmosphere. Our findings show that well below the melting temperature the material transforms into a fully epitaxial layer with exceptional quality, both structural and magnetic. In ferromagnetic resonance (FMR) ultra low damping and extremely narrow linewidth can be observed. For a 56 nm thick layer a damping constant of α = (6.15 ± 1.50) · 10−5 is found and the linewidth at 9.6 GHz is as small as 1.30 ± 0.05 Oe which are the lowest values for PLD grown thin films reported so far. Even for a 20 nm thick layer a damping constant of α = (7.35 ± 1.40) · 10−5 is found which is the lowest value for ultrathin films published so far. The FMR linewidth in this case is 3.49 ± 0.10 Oe at 9.6 GHz. Our results not only present a method of depositing thin film YIG of unprecedented quality but also open up new options for the fabrication of thin film complex oxides or even other crystalline materials.
Effects of Heterogeneous Diffuse Fibrosis on Arrhythmia Dynamics and Mechanism
Authors: Kazbanov Ivan V. , ten Tusscher Kirsten H. W. J. , Panfilov Alexander V.
Published: February 2016

Myocardial fibrosis is an important risk factor for cardiac arrhythmias. Previous experimental and numerical studies have shown that the texture and spatial distribution of fibrosis may play an important role in arrhythmia onset. Here, we investigate how spatial heterogeneity of fibrosis affects arrhythmia onset using numerical methods. We generate various tissue textures that differ by the mean amount of fibrosis, the degree of heterogeneity and the characteristic size of heterogeneity. We study the onset of arrhythmias using a burst pacing protocol. We confirm that spatial heterogeneity of fibrosis increases the probability of arrhythmia induction. This effect is more pronounced with the increase of both the spatial size and the degree of heterogeneity. The induced arrhythmias have a regular structure with the period being mostly determined by the maximal local fibrosis level. We perform ablations of the induced fibrillatory patterns to classify their type. We show that in fibrotic tissue fibrillation is usually of the mother rotor type but becomes of the multiple wavelet type with increase in tissue size. Overall, we conclude that the most important factor determining the formation and dynamics of arrhythmia in heterogeneous fibrotic tissue is the value of maximal local fibrosis.
Identification of a nucleotide in 5′ untranslated region contributing to virus replication and virulence of Coxsackievirus A16
Authors: Li Zhaolong , Liu Xin , Wang Shaohua , Li Jingliang , Hou Min , Liu Guanchen , Zhang Wenyan , Yu Xiao-Fang
Published: February 2016

Coxsackievirus A16 (CA16) and enterovirus 71 (EV71) are two main causative pathogens of hand, foot and mouth disease (HFMD). Unlike EV71, virulence determinants of CA16, particularly within 5′ untranslated region (5′UTR), have not been investigated until now. Here, a series of nucleotides present in 5′UTR of lethal but not in non-lethal CA16 strains were screened by aligning nucleotide sequences of lethal circulating Changchun CA16 and the prototype G10 as well as non-lethal SHZH05 strains. A representative infectious clone based on a lethal Changchun024 sequence and infectious mutants with various nucleotide alterations in 5′UTR were constructed and further investigated by assessing virus replication in vitro and virulence in neonatal mice. Compared to the lethal infectious clone, the M2 mutant with a change from cytosine to uracil at nucleotide 104 showed weaker virulence and lower replication capacity. The predicted secondary structure of the 5′UTR of CA16 RNA showed that M2 mutant located between the cloverleaf and stem-loop II, affected interactions between the 5′UTR and the heterogeneous nuclear ribonucleoprotein K (hnRNP K) and A1 (hnRNP A1) that are important for translational activity. Thus, our research determined a virulence-associated site in the 5′UTR of CA16, providing a crucial molecular target for antiviral drug development.
Maternal-foetal transfer of Plasmodium falciparum and Plasmodium vivax antibodies in a low transmission setting
Authors: Charnaud Sarah C. , McGready Rose , Herten-Crabb Asha , Powell Rosanna , Guy Andrew , Langer Christine , Richards Jack S. , Gilson Paul R. , Chotivanich Kesinee , Tsuboi Takafumi , Narum David L. , Pimanpanarak Mupawjay , Simpson Julie A. , Beeson James G. , Nosten François , Fowkes Freya J. I.
Published: February 2016

During pregnancy immunolglobulin G (IgG) antibodies are transferred from mother to neonate across the placenta. Studies in high transmission areas have shown transfer of P. falciparum-specific IgG, but the extent and factors influencing maternal-foetal transfer in low transmission areas co-endemic for both P. falciparum and P. vivax are unknown. Pregnant women were screened weekly for Plasmodium infection. Mother-neonate paired serum samples at delivery were tested for IgG to antigens from P. falciparum, P. vivax and other infectious diseases. Antibodies to malarial and non-malarial antigens were highly correlated between maternal and neonatal samples (median [range] spearman ρ = 0.78 [0.57–0.93]), although Plasmodium spp. antibodies tended to be lower in neonates than mothers. Estimated gestational age at last P. falciparum infection, but not P. vivax infection, was positively associated with antibody levels in the neonate (P. falciparum merozoite, spearman ρ median [range] 0.42 [0.33–0.66], PfVAR2CSA 0.69; P. vivax ρ = 0.19 [0.09–0.3]). Maternal-foetal transfer of anti-malarial IgG to Plasmodium spp. antigens occurs in low transmission settings. P. vivax IgG acquisition is not associated with recent exposure unlike P. falciparum IgG, suggesting a difference in acquisition of antibodies. IgG transfer is greatest in the final weeks of pregnancy which has implications for the timing of future malaria vaccination strategies in pregnant women.
Circadian variations in the liver metabolites of medaka (Oryzias latipes)
Authors: Fujisawa Koichi , Takami Taro , Kimoto Yoshitaka , Matsumoto Toshihiko , Yamamoto Naoki , Terai Shuji , Sakaida Isao
Published: February 2016

Circadian rhythms are biological rhythms with a period of around 24 hours. In this study, we compared the metabolome of the liver of medaka during the day and night. To comprehensively analyze the circadian variations in the levels of metabolites in the liver, livers were isolated from Zeitgeber time (ZT)4 and ZT16 and the variations in metabolite levels were evaluated. Inosinemonophosphate (IMP) and uridinemonophosphate (UMP) were found to be increased at night, indicating that nucleotide synthesis is most active during the night. Furthermore, the levels of metabolites of the tricarboxylic acid cycle were also reduced at night. In addition, the levels of many amino acids were reduced during the night, suggesting that the amino acids had been degraded. Moreover, the citrulline/ornithine ratio, which is related to arginine consumption, was lower during the day than at night. This pattern suggests that the urea cycle is activated during the day, whereas large amounts of nitric oxide and citrulline may be produced from arginine via nitric oxide synthase during the night. The results of this metabolomic analysis may be useful in future fundamental research to provide insight into chronobiology as well as applied research on drug evaluations using medaka as a model species.
Human Campylobacteriosis in Luxembourg, 2010–2013: A Case-Control Study Combined with Multilocus Sequence Typing for Source Attribution and Risk Factor Analysis
Authors: Mossong Joël , Mughini-Gras Lapo , Penny Christian , Devaux Anthony , Olinger Christophe , Losch Serge , Cauchie Henry-Michel , van Pelt Wilfrid , Ragimbeau Catherine
Published: February 2016

Campylobacteriosis has increased markedly in Luxembourg during recent years. We sought to determine which Campylobacter genotypes infect humans, where they may originate from and how they may infect humans. Multilocus sequence typing was performed on 1153 Campylobacter jejuni and 136 C. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. A nationwide case-control study (2010–2013) for domestic campylobacteriosis was also conducted, including 367 C. jejuni and 48 C. coli cases and 624 controls. Risk factors were investigated by Campylobacter species and for strains attributed to different sources using a combined case-control and source attribution analysis. 282 sequence types (STs) were identified: ST-21, ST-48, ST-572, ST-50 and ST-257 were prevailing. Most cases were attributed to poultry (61.2%) and ruminants (33.3%). Consuming chicken outside the home was the dominant risk factor for both Campylobacter species. Newly identified risk factors included contact with garden soil for either species and consuming beef specifically for C. coli. Poultry-associated campylobacteriosis was linked to poultry consumption in wintertime and ruminant-associated campylobacteriosis to tap-water provider type. Besides confirming chicken as campylobacteriosis primary source, additional evidence was found for other reservoirs and transmission routes.
Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing
Authors: Couto Rafael C. , Guarise Marco , Nicolaou Alessandro , Jaouen Nicolas , Chiuzbăian Gheorghe S. , Lüning Jan , Ekholm Victor , Rubensson Jan-Erik , Såthe Conny , Hennies Franz , Kimberg Victor , Guimarães Freddy F. , Agren Hans , Gel’mukhanov Faris , Journel Loïc , Simon Marc
Published: February 2016

The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12–14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of “dark” with “bright” final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.