bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interspecific hybridization, polyploidization and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables
Authors: Zhang Xiaohui , Liu Tongjin , Li Xixiang , Duan Mengmeng , Wang Jinglei , Qiu Yang , Wang Haiping , Song Jiangping , Shen Di 
Published: January 2016

AbstractBrassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops.
Physical activity and genetic predisposition to obesity in a multiethnic longitudinal study
Authors: Reddon Hudson , Gerstein Hertzel C. , Engert James C. , Mohan Viswanathan , Bosch Jackie , Desai Dipika , Bailey Swneke D. , Diaz Rafael , Yusuf Salim , Anand Sonia S. , Meyre David 
Published: January 2016

AbstractPhysical activity (PA) has been shown to reduce the impact of FTO variation and obesity genetic risk scores (GRS) on BMI. We examined this interaction using a quantitative measure of PA and two adiposity indexes in a longitudinal multi-ethnic study. We analyzed the impact of PA on the association between 14 obesity predisposing variants (analyzed independently and as a GRS) and baseline/follow-up obesity measures in the multi-ethnic prospective cohort EpiDREAM (17423 participants from six ethnic groups). PA was analyzed using basic (low-moderate-high) and quantitative measures (metabolic equivalents (METS)), while BMI and the body adiposity index (BAI) were used to measure obesity. Increased PA was associated with decreased BMI/BAI at baseline/follow-up. FTO rs1421085, CDKAL1 rs2206734, TNNl3K rs1514176, GIPR rs11671664 and the GRS were associated with obesity measures at baseline and/or follow-up. Risk alleles of three SNPs displayed nominal associations with increased (NTRK2 rs1211166, BDNF rs1401635) or decreased (NPC1 rs1805081) basic PA score independently of BMI/BAI. Both basic and quantitative PA measures attenuated the association between FTO rs1421085 risk allele and BMI/BAI at baseline and follow-up. Our results show that physical activity can blunt the genetic effect of FTO rs1421085 on adiposity by 36–75% in a longitudinal multi-ethnic cohort.
Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae
Authors: Khosa Sakshi , Frieg Benedikt , Mulnaes Daniel , Kleinschrodt Diana , Hoeppner Astrid , Gohlke Holger , Smits Sander H. J. 
Published: January 2016

AbstractLantibiotics are potent antimicrobial peptides. Nisin is the most prominent member and contains five crucial lanthionine rings. Some clinically relevant bacteria express membrane-associated resistance proteins that proteolytically inactivate nisin. However, substrate recognition and specificity of these proteins is unknown. Here, we report the first three-dimensional structure of a nisin resistance protein from Streptococcus agalactiae (SaNSR) at 2.2 Å resolution. It contains an N-terminal helical bundle and protease cap and core domains. The latter harbors the highly conserved TASSAEM region, which lies in a hydrophobic tunnel formed by all domains. By integrative modeling, mutagenesis studies and genetic engineering of nisin variants, a model of the SaNSR/nisin complex is generated, revealing that SaNSR recognizes the last C-terminally located lanthionine ring of nisin. This determines the substrate specificity of SaNSR and ensures the exact coordination of the nisin cleavage site at the TASSAEM region.
Metal-to-insulator crossover in alkali doped zeolite
Authors: Igarashi Mutsuo , Jeglič Peter , Krajnc Andraž , Žitko Rok , Nakano Takehito , Nozue Yasuo , Arčon Denis 
Published: January 2016

AbstractWe report a systematic nuclear magnetic resonance investigation of the 23Na spin-lattice relaxation rate, 1/T1, in sodium loaded low-silica X (LSX) zeolite, Nan/Na12-LSX, for various loading levels of sodium atoms n across the metal-to-insulator crossover. For high loading levels of n ≥ 14.2, 1/T1T shows nearly temperature-independent behaviour between 10 K and 25 K consistent with the Korringa relaxation mechanism and the metallic ground state. As the loading levels decrease below n ≤ 11.6, the extracted density of states (DOS) at the Fermi level sharply decreases, although a residual DOS at Fermi level is still observed even in the samples that lack the metallic Drude-peak in the optical reflectance. The observed crossover is a result of a complex loading-level dependence of electric potential felt by the electrons confined to zeolite cages, where the electronic correlations and disorder both play an important role.
A new hexapeptide from the leader peptide of rMnSOD enters cells through the oestrogen receptor to deliver therapeutic molecules
Authors: Borrelli Antonella , Schiattarella Antonietta , Mancini Roberto , Pica Alessandra , Pollio Maria Laura , Ruggiero Maria Grazia , Bonelli Patrizia , De Luca Viviana , Tuccillo Franca Maria , Capasso Clemente , Gori Enrico , Sanseverino Marina , Carpentieri Andrea , Birolo Leila , Pucci Piero , Rommelaere Jean , Mancini Aldo 
Published: January 2016

AbstractA 24-amino acid leader peptide of a new human recombinant manganese superoxide dismutase can enter cells and carry molecules. Here, we demonstrated that six of the 24 amino acids penetrate cells through a particular gate represented by a specific amino acid sequence of the oestrogen receptor (ER). We analysed the internalization of the synthetic hexapeptide and the cytotoxic activity of the hexapeptide conjugated to cisplatin on a cell line panel. In most cell lines, the hexapeptide delivered an amount of cisplatin that was 2 to 8 times greater than that released by cisplatin when the drug was used alone. This increased delivery increases the therapeutic index of cisplatin and reduces side effects caused by a high dosage or long-term treatment times. We may consider this hexapeptide a new molecular carrier to deliver molecules with therapeutic activity into ER+ cells for diagnostic purposes and clinical or immune therapy.
Fortilin potentiates the peroxidase activity of Peroxiredoxin-1 and protects against alcohol-induced liver damage in mice
Authors: Chattopadhyay Abhijnan , Pinkaew Decha , Doan Hung Q. , Jacob Reed B. , Verma Sunil K. , Friedman Hana , Peterson Alan C. , Kuyumcu-Martinez Muge N. , McDougal Owen M. , Fujise Ken 
Published: January 2016

AbstractFortilin, a pro-survival molecule, inhibits p53-induced apoptosis by binding to the sequence-specific DNA-binding domain of the tumor suppressor protein and preventing it from transcriptionally activating Bax. Intriguingly, fortilin protects cells against ROS-induced cell death, independent of p53. The signaling pathway through which fortilin protects cells against ROS-induced cell death, however, is unknown. Here we report that fortilin physically interacts with the antioxidant enzyme peroxiredoxin-1 (PRX1), protects it from proteasome-mediated degradation and keeps it enzymatically active by blocking its deactivating phosphorylation by Mst1, a serine/threonine kinase. At the whole animal level, the liver-specific overexpression of fortilin reduced PRX1 phosphorylation in the liver, enhanced PRX1 activity and protected the transgenic animals against alcohol-induced, ROS-mediated, liver damage. These data suggest the presence of a novel oxidative-stress-handling pathway where the anti-p53 molecule fortilin augments the peroxidase PRX1 by protecting it against degradation and inactivation of the enzyme. Fortilin-PRX1 interaction in the liver could be clinically exploited further to prevent acute alcohol-induced liver damage in humans.
Elevated serum complement factors 3 and 4 are strong inflammatory markers of the metabolic syndrome development: a longitudinal cohort study
Authors: Liu Zhenfang , Tang Qin , Wen Jing , Tang Yan , Huang DaMin , Huang Yuzhen , Xie Jinling , Luo Yawen , Liang Min , Wu Chunlei , Lu Zheng , Tan Aihua , Gao Yong , Wang Qiuyan , Jiang Yonghua , Yao Ziting , Lin Xinggu , Zhang Haiying , Mo Zengnan , Yang Xiaobo 
Published: January 2016

AbstractAn epidemiological design, consisting of cross-sectional (n = 2376) and cohort (n = 976) studies, was adopted to investigate the association between complement factors 3 (C3) and 4 and the metabolic syndrome (MetS) development. In the cross-sectional study, the C3 and C4 concentrations in the MetS group were higher than those in the non-MetS group (all P < 0.001) and the levels of immune globulin M (IgM), IgA, IgE and IgG exhibited no significant differences between MetS and non-MetS (all P > 0.050). After multi-factor adjustment, the odds ratios (ORs) in the highest quartile of C3 and C4 concentrations were 7.047 (4.664, 10.648) and 1.961 (1.349, 2.849), respectively, both Ptrend < 0.050. After a 4 years follow-up, total 166 subjects were diagnosed with MetS and the complement baseline levels from 2009 were used to predict the MetS risk in 2013. In the adjusted model, the relative risks (RRs) in the highest quartile of C3 and C4 levels were 4.779 (2.854, 8.003) and 2.590 (1.567, 4.280), respectively, both Ptrend < 0.001. Activation of complement factors may be an important part of inflammatory processes and our results indicated that the elevated C3 and C4 levels were independent risk factors for MetS development.
Amy63, a novel type of marine bacterial multifunctional enzyme possessing amylase, agarase and carrageenase activities
Authors: Liu Ge , Wu Shimei , Jin Weihua , Sun Chaomin 
Published: January 2016

AbstractA multifunctional enzyme is one that performs multiple physiological functions, thus benefiting the organism. Characterization of multifunctional enzymes is important for researchers to understand how organisms adapt to different environmental challenges. In the present study, we report the discovery of a novel multifunctional enzyme Amy63 produced by marine bacterium Vibrio alginolyticus 63. Remarkably, Amy63 possesses amylase, agarase and carrageenase activities. Amy63 is a substrate promiscuous α-amylase, with the substrate priority order of starch, carrageenan and agar. Amy63 maintains considerable amylase, carrageenase and agarase activities and stabilities at wide temperature and pH ranges and optimum activities are detected at temperature of 60 °C and pH of 6.0, respectively. Moreover, the heteroexpression of Amy63 dramatically enhances the ability of E. coli to degrade starch, carrageenan and agar. Motif searching shows three continuous glycosyl hydrolase 70 (GH70) family homologs existed in Amy63 encoding sequence. Combining serial deletions and phylogenetic analysis of Amy63, the GH70 homologs are proposed as the determinants of enzyme promiscuity. Notably, such enzymes exist in all kingdoms of life, thus providing an expanded perspective on studies of multifunctional enzymes. To our knowledge, this is the first report of an amylase having additional agarase and carrageenase activities.
Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes
Authors: Stepanenko Olesya V. , Baloban Mikhail , Bublikov Grigory S. , Shcherbakova Daria M. , Stepanenko Olga V. , Turoverov Konstantin K. , Kuznetsova Irina M. , Verkhusha Vladislav V. 
Published: January 2016

AbstractFluorescent proteins (FPs) engineered from bacterial phytochromes attract attention as probes for in vivo imaging due to their near-infrared (NIR) spectra and use of available in mammalian cells biliverdin (BV) as chromophore. We studied spectral properties of the iRFP670, iRFP682 and iRFP713 proteins and their mutants having Cys residues able to bind BV either in both PAS (Cys15) and GAF (Cys256) domains, in one of these domains, or without these Cys residues. We show that the absorption and fluorescence spectra and the chromophore binding depend on the location of the Cys residues. Compared with NIR FPs in which BV covalently binds to Cys15 or those that incorporate BV noncovalently, the proteins with BV covalently bound to Cys256 have blue-shifted spectra and higher quantum yield. In dimeric NIR FPs without Cys15, the covalent binding of BV to Сys256 in one monomer allosterically inhibits the covalent binding of BV to the other monomer, whereas the presence of Cys15 allosterically promotes BV binding to Cys256 in both monomers. The NIR FPs with both Cys residues have the narrowest blue-shifted spectra and the highest quantum yield. Our analysis resulted in the iRFP713/Val256Cys protein with the highest brightness in mammalian cells among available NIR FPs.
The DSF type quorum sensing signalling system RpfF/R regulates diverse phenotypes in the opportunistic pathogen Cronobacter
Authors: Suppiger Angela , Eshwar Athmanya Konegadde , Stephan Roger , Kaever Volkhard , Eberl Leo , Lehner Angelika 
Published: January 2016

AbstractSeveral bacterial pathogens produce diffusible signal factor (DSF)-type quorum sensing (QS) signals to control biofilm formation and virulence. Previous work showed that in Burkholderia cenocepacia the RpfFBc/RpfR system is involved in sensing and responding to DSF signals and that this signal/sensor gene pair is highly conserved in several bacterial species including Cronobacter spp. Here we show that C. turicensis LMG 23827T possesses a functional RpfF/R system that is involved in the regulation of various phenotypes, including colony morphology, biofilm formation and swarming motility. In vivo experiments using the zebrafish embryo model revealed a role of this regulatory system in virulence of this opportunistic pathogen. We provide evidence that the RpfF/R system modulates the intracellular c-di-GMP level of the organism, an effect that may underpin the alteration in phenotype and thus the regulated phenotypes may be a consequence thereof. This first report on an RpfF/R-type QS system of an organism outside the genus Burkholderia revealed that both the underlying molecular mechanisms as well as the regulated functions show a high degree of conservation.
Spatial Distribution of Oxygen Chemical Potential under Potential Gradients and Theoretical Maximum Power Density with 8YSZ Electrolyte
Authors: Lim Dae-Kwang , Im Ha-Ni , Song Sun-Ju 
Published: January 2016

AbstractThe maximum power density of SOFC with 8YSZ electrolyte as the function of thickness was calculated by integrating partial conductivities of charge carriers under various DC bias conditions at a fixed oxygen chemical potential gradient at both sides of the electrolyte. The partial conductivities were successfully taken using the Hebb-Wagner polarization method as a function of temperature and oxygen partial pressure and the spatial distribution of oxygen partial pressure across the electrolyte was calculated based on Choudhury and Patterson’s model by considering zero electrode polarization. At positive voltage conditions corresponding to SOFC and SOEC, the high conductivity region was expanded, but at negative cell voltage condition, the low conductivity region near n-type to p-type transition was expanded. In addition, the maximum power density calculated from the current-voltage characteristic showed approximately 5.76 W/cm2 at 700 oC with 10 μm thick-8YSZ, while the oxygen partial pressure of the cathode and anode sides maintained ≈0.21 and 10−22 atm.
The Relevance of Context in Understanding the Lived Experience of Aphasia: Lessons from South Africa
Authors: Legg Carol , Penn Claire 
Published: January 2016

Purpose: In this paper we describe a study of aphasia in a unique sociocultural context, to show the value of the anthropological perspective for the clinician faced with a diverse caseload.Methods: We present findings of an anthropological study of the experience of aphasia for adults living in Khayelitsha, a township on the outskirts of Cape Town, where the isiXhosa speaking residents live in conditions of poverty and where health and social resources are either lacking or in disarray (Legg, 2010). The study involved three years of intermittent fieldwork that included in-depth case studies of five adults living with aphasia in Khayelitsha and sustained contact with a number of healthcare and community institutions.Results: Interpretations and experiences of aphasia assumed a wider significance than communication disorder and were, essentially, a window onto the sociocultural and economic struggles that beset the lives of our participants. These struggles had profound influences on experiences of aphasia and responses to treatment.Conclusions: Understanding the unique contextual influences on experiences of aphasia will place the aphasia clinician in a more potent position to develop relevant interventions.
Quantum stochastic thermodynamic on harmonic networks
Authors: Deffner Sebastian 
Published: January 2016

Abstract
Fluctuation theorems are symmetry relations for the probability to observe an amount of entropy production in a finite-time process. In a recent paper Pigeon et al (2016 New. J. Phys.

18 013009) derived fluctuation theorems for harmonic networks by means of the large deviation theory. Their novel approach is illustrated with various examples of experimentally relevant systems. As a main result, however, Pigeon et al provide new insight how to consistently formulate quantum stochastic thermodynamics, and provide new and robust tools for the study of the thermodynamics of quantum harmonic networks.
Efficiency ranking method using DEA and TOPSIS (ERM-DT): case of an Indian bank
Authors: Chitnis Asmita , Vaidya Omkarprasad S 
Published: January 2016

Purpose
– The purpose of this paper is to present a tie-breaking procedure for computing performance efficiencies to improve benchmarking and performance evaluation process in a business situation.

Design/methodology/approach
– The authors propose a unified approach based on data envelopment analysis (DEA) and technique for order of preference by similarity to ideal solution (TOPSIS), to overcome the difficulty of unique ranking in the prevalent benchmarking and performance evaluation processes such as DEA, Super efficiency DEA model, etc., under constant return to scale (CRS) assumption. This model is called as efficiency ranking method using DEA and TOPSIS (ERM-DT). In order to check the consistency of the approach, various input-output combinations (to calculate the efficiencies) have been illustrated. Further, the authors present a case of an Indian Bank to illustrate an application of the proposed approach.

Findings
– The proposed approach, ERM-DT enables assign a unique rank to decision making units and provides a tie breaking procedure. Results obtained using the proposed approach are statistically compared with those obtained from the CRS DEA approach and super efficiency DEA approach using Friedman’s test.

Practical implications
– The proposed model provides an efficiency ranking method based on a score obtained by considering the minimum distance from the best value and maximum distance from the worst value. The proposed methodology is capable of handling negative data and undesirable output variables. This approach is unit invariant and makes the calculations simple. The authors present an application to compute the efficiency of various branches of an Indian bank. The authors hope the proposed method can enhance the decision-making ability of the management in complex situations.

Originality/value
– The authors propose an integrated DEA and TOPSIS framework for better benchmarking and performance evaluation. This approach provides a tie-breaking procedure for the efficiencies computed using CRS DEA approach. Ranks are assigned based on score obtained by considering the distance from the worst and the best solution. The proposed approach can be used with non-positive data points and undesirable output variables.
Towards a new measure of a country’s competitiveness: applying canonical correlation
Authors: Wenzel Lars , Wolf André 
Published: January 2016

Purpose– This paper aims to develop and implement a new approach of ranking countries according to their level of economic competitiveness.Design/methodology/approach– Competitiveness is conceptualized as the degree of participation in global integration, measured by the levels of exports, capital inflows and immigration. Based on a wide range of development indicators, composite indicators are constructed by means of a principal component analysis. In turn, these composites enter a canonical correlation analysis and estimated canonical weights are used as weights in the calculation of index scores.Findings– Measures of institutional and political quality are shown to be most closely connected to a country’s ability to export and to attract foreign factors of production. Inflows of foreign capital turn out to correlate much less with our weighting composites than export volumes.Research limitations/implications– Regarding prospects for future research, a broad range of further applications of this approach in the macro area is conceivable, including measures of a country’s quality of schooling, the quality of its health care system or of its governmental institutions.Originality/value– In comparison to prevailing macroeconomic indices, this method of index construction is superior in at least two respects. First, direct measures of a country’s performance are methodologically separated from mere performance drivers, contributing to higher clarity concerning the concept to be measured. Second, weights of performance drivers are not determined arbitrarily or based on subjective judgment, but emerge from a transparent and well-established statistical procedure.