bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire
Authors: Lomnitz Jason G , Savageau Michael A 
Published: September 2015

Abstract
Background:
The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process.

Methods:
The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters.

Results:
Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed.

Conclusions:
Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.
Genomic and transcriptomic insights into the efficient entomopathogenicity of Bacillus thuringiensis
Authors: Zhu Lei , Peng Donghai , Wang Yueying , Ye Weixing , Zheng Jinshui , Zhao Changming , Han Dongmei , Geng Ce , Ruan Lifang , He Jin , Yu Ziniu , Sun Ming 
Published: September 2015

AbstractBacillus thuringiensis has been globally used as a microbial pesticide for over 70 years. However, information regarding its various adaptions and virulence factors and their roles in the entomopathogenic process remains limited. In this work, we present the complete genomes of two industrially patented Bacillus thuringiensis strains (HD-1 and YBT-1520). A comparative genomic analysis showed a larger and more complicated genome constitution that included novel insecticidal toxicity-related genes (ITRGs). All of the putative ITRGs were summarized according to the steps of infection. A comparative genomic analysis showed that highly toxic strains contained significantly more ITRGs, thereby providing additional strategies for infection, immune evasion and cadaver utilization. Furthermore, a comparative transcriptomic analysis suggested that a high expression of these ITRGs was a key factor in efficient entomopathogenicity. We identified an active extra urease synthesis system in the highly toxic strains that may aid B. thuringiensis survival in insects (similar to previous results with well-known pathogens). Taken together, these results explain the efficient entomopathogenicity of B. thuringiensis. It provides novel insights into the strategies used by B. thuringiensis to resist and overcome host immune defenses and helps identify novel toxicity factors.
Jagged-2 enhances immunomodulatory activity in adipose derived mesenchymal stem cells
Authors: Xishan Zhu , Bin Zhang , Haiyue Zhao , Xiaowei Dou , Jingwen Bai , Guojun Zhang 
Published: September 2015

AbstractAdipose derived Mesenchymal stem cells (AMSCs) are able to expand in vitro and undergo differentiation into multiple cell lineages, yet have low immunogenicity while exhibiting several immunoregulatory characteristics. We sought to investigate the immunomodulatory mechanisms of AMSCs to better understand their immunogenic properties. Following 10 days of chondrogenic differentiation or 48 hours of IFN-γ pretreatment, AMSCs retained low level immunogenicity but prominent immunoregulatory activity and AMSC immunogenicity was enhanced by chondrogenic differentiation or IFN-γ treatment. We found Jagged-2 expression was significantly elevated following chondrogenic differentiation or IFN-γ pretreatment. Jagged-2-RNA interference experiments suggested that Jagged-2-siRNA2 suppresses Jagged-2 expression during chondrogenic differentiation and in IFN-γ pretreated AMSCs. Besides, Jagged-2 interference attenuated immunosuppressive activity by mixed lymphocyte culture and mitogen stimulation experiments. So, the immunoregulatory activity of AMSCs, to some extent dependent upon Jagged-2, might be stronger after multilineage differentiation or influence from inflammatory factors. This may also be why rejection does not occur after allogeneic AMSCs differentiate into committed cells.
Accommodative Behavior of Non-porous Molecular crystal at Solid-Gas and Solid-Liquid Interface
Authors: Mande Hemant M. , Ghalsasi Prasanna S. 
Published: September 2015

AbstractMolecular crystals demonstrate drastically different behavior in solid and liquid state, mainly due to their difference in structural frameworks. Therefore, designing of unique structured molecular compound which can work at both these interfaces has been a challenge. Here, we present remarkable ‘molecular’ property by non-porous molecular solid crystal, dinuclear copper complex (C6H5CH(X)NH2)2CuCl2, to reversibly ‘adsorb’ HCl gas at solid-gas interface as well as ‘accommodate’ azide anion at solid-liquid interface with crystal to crystal transformation. The latter process is driven by molecular recognition, self-assembly and anchimeric assistance. The observed transformations are feasible due to breathing of inner and outer coordination sphere around metal center resulting in change in metal polyhedra for ‘accommodating’ guest molecule. These transformations cause changes in optical, magnetic, and/or ferroelectric property offering diversity in ‘sensing’ application. With the proposed underlying principles in these exceptional reversible and cyclic transformations, we prepared a series of compounds, can facilitate designing of novel multifunctional molecular materials.
HMGA1 overexpression in adipose tissue impairs adipogenesis and prevents diet-induced obesity and insulin resistance
Authors: Arce-Cerezo Altamira , García Miquel , Rodríguez-Nuevo Aida , Crosa-Bonell Mireia , Enguix Natalia , Peró Albert , Muñoz Sergio , Roca Carles , Ramos David , Franckhauser Sylvie , Elias Ivet , Ferre Tura , Pujol Anna , Ruberte Jesús , Villena Josep A. , Bosch Fàtima , Riu Efrén 
Published: September 2015

AbstractHigh-Mobility-Group-A1 (HMGA1) proteins are non-histone proteins that regulate chromatin structure and gene expression during embryogenesis, tumourigenesis and immune responses. In vitro studies suggest that HMGA1 proteins may be required to regulate adipogenesis. To examine the role of HMGA1 in vivo, we generated transgenic mice overexpressing HMGA1 in adipose tissues. HMGA1 transgenic mice showed a marked reduction in white and brown adipose tissue mass that was associated with downregulation of genes involved in adipogenesis and concomitant upregulation of preadipocyte markers. Reduced adipogenesis and decreased fat mass were not associated with altered glucose homeostasis since HMGA1 transgenic mice fed a regular-chow diet exhibited normal glucose tolerance and insulin sensitivity. However, when fed a high-fat diet, overexpression of HMGA1 resulted in decreased body-weight gain, reduced fat mass, but improved insulin sensitivity and glucose tolerance. Although HMGA1 transgenic mice exhibited impaired glucose uptake in adipose tissue due to impaired adipogenesis, the increased glucose uptake observed in skeletal muscle may account for the improved glucose homeostasis. Our results indicate that HMGA1 plays an important function in the regulation of white and brown adipogenesis in vivo and suggests that impaired adipocyte differentiation and decreased fat mass is not always associated with impaired whole-body glucose homeostasis.
Titanium dioxide nanoparticles stimulate sea urchin immune cell phagocytic activity involving TLR/p38 MAPK-mediated signalling pathway
Authors: Pinsino Annalisa , Russo Roberta , Bonaventura Rosa , Brunelli Andrea , Marcomini Antonio , Matranga Valeria 
Published: September 2015

AbstractTitanium dioxide nanoparticles (TiO2NPs) are one of the most widespread-engineered particles in use for drug delivery, cosmetics and electronics. However, TiO2NP safety is still an open issue, even for ethical reasons. In this work, we investigated the sea urchin Paracentrotus lividus immune cell model as a proxy to humans, to elucidate a potential pathway that can be involved in the persistent TiO2NP-immune cell interaction in vivo. Morphology, phagocytic ability, changes in activation/inactivation of a few mitogen-activated protein kinases (p38 MAPK, ERK), variations of other key proteins triggering immune response (Toll-like receptor 4-like, Heat shock protein 70, Interleukin-6) and modifications in the expression of related immune response genes were investigated. Our findings indicate that TiO2NPs influence the signal transduction downstream targets of p38 MAPK without eliciting an inflammatory response or other harmful effects on biological functions. We strongly recommend sea urchin immune cells as a new powerful model for nano-safety/nano-toxicity investigations without the ethical normative issue.
Small hole polaron in CdTe: Cd-vacancy revisited
Authors: Shepidchenko A. , Sanyal B. , Klintenberg M. , Mirbt S. 
Published: September 2015

AbstractThe characteristics of electronic states of Cd-vacancies in CdTe, an important semiconductor for various technological applications, are under debate both from theoretical and experimental points of view. Experimentally, the Cd-vacancy in its negative charge state is found to have C3v symmetry and a (−1/−2) transition level at 0.4 eV. Our first principles density functional calculations with hybrid functionals confirm for the first time these experimental findings. Additionally, we find that the C3v symmetry and the position of the (−1/−2) transition level are caused by the formation of a hole polaron localised at an anionic site around the vacancy.
Evidence of a deep viral host switch event with beak and feather disease virus infection in rainbow bee-eaters (Merops ornatus)
Authors: Sarker Subir , Moylan Kathy G. , Ghorashi Seyed A. , Forwood Jade K. , Peters Andrew , Raidal Shane R. 
Published: September 2015

AbstractSince the characterization of psittacine beak and feather disease (PBFD) in 1984, a wide range of avian circoviruses have been discovered with varying pathogenic effects amongst a diverse range of avian hosts. Until recently these circovirus species were thought to be restricted to within avian Orders such as the Psittaciformes forbeak and feather disease virus(BFDV) and Columbiformes forpigeon circoviruswith little evidence of cross-family transmission or replication. We report evidence of a naturally occurring novel host switch event with self-limiting BFDV infection in a group of rainbow bee-eaters (Merops ornatus) a species of Coraciiformes unrelated to parrots and not previously known to be susceptible to any avian circovirus. The outbreak highlights important and unexpected aspects of disease emergence and host-switching pertinent to other situations when viruses might cross species boundaries as well as the potential of avian circoviruses to infect disparate host species.
Ethyl acetate fraction of Amomum xanthioides improves bile duct ligation-induced liver fibrosis of rat model via modulation of pro-fibrogenic cytokines
Authors: Kim Hyeong-Geug , Han Jong-Min , Lee Jin-Seok , Suk Lee Jong , Son Chang-Gue 
Published: September 2015

AbstractWe investigated anti-hepatofibrotic effects of ethyl acetate fraction of Ammomum xanthoides (EFAX) using bile duct ligation (BDL)-induced hepatic fibrosis in a rat model. Male SD rats (6 weeks old) underwent BDL followed by 15 days of orall administration of EFAX (12.5, 25 or 50 mg/kg) or ursodeoxycholic acid (25 mg/kg). BDL caused animal death, ascites formation, alterations in serum biochemistries and severe hepatic injury with excessive collagen deposition, whereas EFAX treatment significantly attenuated these effects. BDL markedly increased the pro-fibrogenic cytokines (TGF-β, PDGF-β and CTGF) and the extracellular matrix indicators α-SMA, TIMP-1 and collagen type 1 in hepatic proteins and gene expression levels, which were notably normalized by EFAX treatment. EFAX also markedly normalized pro-fibrogenic signaling molecules including Smad2/3, Smad7, Akt, p44/42 and p38. We further explored EFAX mechanisms of actions using LX-2 cells (human derived hepatic stellate cell line). Pre-treatment with EFAX drastically attenuated the activation of α-SMA and Smad2/3, which are downstream molecules of TGF-β. These findings suggest that EFAX may be a potent anti-hepatofibrotic agent and its corresponding mechanisms primarily involve the modulation of pro-fibrogenic cytokines.
Human Induced Pluripotent Stem Cell Derived Neuronal Cells Cultured on Chemically-Defined Hydrogels for Sensitive In Vitro Detection of Botulinum Neurotoxin
Authors: Pellett Sabine , Schwartz Michael P. , Tepp William H. , Josephson Richard , Scherf Jacob M. , Pier Christina L. , Thomson James A. , Murphy William L. , Johnson Eric A. 
Published: September 2015

AbstractBotulinum neurotoxin (BoNT) detection provides a useful model for validating cell-based neurotoxicity screening approaches, as sensitivity is dependent on functionally competent neurons and clear quantitative endpoints are available for correlating results to approved animal testing protocols. Here, human induced pluripotent stem cell (iPSC)-derived neuronal cells were cultured on chemically-defined poly(ethylene glycol) (PEG) hydrogels formed by “thiol-ene” photopolymerization and tested as a cell-based neurotoxicity assay by determining sensitivity to active BoNT/A1. BoNT/A1 sensitivity was comparable to the approvedin vivomouse bioassay for human iPSC-derived neurons and neural stem cells (iPSC-NSCs) cultured on PEG hydrogels or treated tissue culture polystyrene (TCP) surfaces. However, maximum sensitivity for BoNT detection was achieved two weeks earlier for iPSC-NSCs that were differentiated and matured on PEG hydrogels compared to TCP. Therefore, chemically-defined synthetic hydrogels offer benefits over standard platforms when optimizing culture conditions for cell-based screening and achieve sensitivities comparable to an approved animal testing protocol.
An increase in the biogenic aerosol concentration as a contributing factor to the recent wetting trend in Tibetan Plateau
Authors: Fang Keyan , Makkonen Risto , Guo Zhengtang , Zhao Yan , Seppä Heikki 
Published: September 2015

AbstractA significant wetting trend since the early 1980s in Tibetan Plateau (TP) is most conspicuous in central and eastern Asia as shown in the instrumental data and the long-term moisture sensitive tree rings. We found that anomalies in the large-scale oceanic and atmospheric circulations do not play a significant role on the wetting trend in TP. Meanwhile, the weak correlation between local temperature and precipitation suggests that the temperature-induced enhancement of the local water cycle cannot fully explain the wetting trend either. This may indicate the presence of nonlinear processes between local temperature and precipitation. We hypothesize that the current warming may enhance the emissions of the biogenic volatile organic compounds (BVOC) that can increase the secondary organic aerosols (SOA), contributing to the precipitation increase. The wetting trend can increase the vegetation cover and cause a positive feedback on the BVOC emissions. Our simulations indicate a significant contribution of increased BVOC emissions to the regional organic aerosol mass and the simulated increase in BVOC emissions is significantly correlated with the wetting trend in TP.
Design Space Exploration of the Violacein Pathway inEscherichia coliBased Cell-Free System
Authors: Nguyen Phuc H.B. , Wu Yong Y. , Guo Shaobin , Murray Richard M. 
Published: September 2015

AbstractIn this study, anEscherichia coli(E. coli) based transcription translation cell-free system (TX-TL) was employed to sample various enzyme expression levels of the violacein pathway. The pathway was successfully reconstructed in TX-TL. Its variation produced different metabolites as evident from the extracts’ assorted colors. Analysis of the violacein product via UV-Vis absorption and liquid chromatography-mass spectrometry (LC-MS) detected 68 ng of violacein per μl reaction volume. Significant buildup of prodeoxyviolacein intermediate was also detected in the equimolar TX-TL reaction. Finally, design space exploration experiments suggested an improvement in violacein production at high VioC and VioD DNA concentrations.
Behavioral flexibility and problem solving in an invasive bird
Authors: Logan Corina J. 
Published: September 2015

ABSTRACTBehavioral flexibility is considered an important trait for adapting to environmental change, but it is unclear what it is, how it works, and whether it is a problem solving ability. I investigated behavioral flexibility and problem solving abilities experimentally in great-tailed grackles, an invasive species and thus a likely candidate for possessing behavioral flexibility. I found that grackles are behaviorally flexible and good problem solvers, they vary in behavioral flexibility across contexts, flexibility did not correlate with problem solving ability, and those that are more flexible did not necessarily use more learning strategies. It appears that behavioral flexibility can be an independent trait that varies across contexts. Maintaining such a high level of variation could be a mechanism underlying successful species invasions. These results highlight the need to investigate how individuals use behavior to react to changing environments.
Why interest-rate cannot benchmark for Islamic financial product pricing?
Authors: Ghauri Shahid Mohammad Khan 
Published: September 2015

Purpose
– The purpose of this paper is to emphasize that interest-rate benchmark cannot be used for pricing of Islamic financial products. This paper will help in pricing basis for Islamic financial products, which are currently based on interest-rate benchmarks. Shariyah perspective and ground realities are considered as evident to the viewpoint.

Design/methodology/approach
– Viewpoint has been evident through comparison of conventional and Islamic financial product pricing, and through comparison of interest rate with macroeconomic indicators to analyze whether interest really represent economy, since Islamic finance based on real economic activities.

Findings
– It has been analyzed that interest based benchmarks do not represent real economic activities.

Originality/value
– This paper brings new light to the product development in Islamic financial instruments and institutions. Islamic finance should have its own footings in terms of product development.
Does Saudi Arabia’s economy benefit from foreign investments?
Authors: Albassam Bassam A. 
Published: September 2015

Purpose
– The current study contributes to filling the gap in studies that discuss the impact of foreign direct investment (FDI) on economic growth and employment in Saudi Arabia. Although the study found that FDI inflows contribute to the government effort to reduce or at least control the high unemployment rate, the study found no relationship between FDI inflows and economic growth in Saudi Arabia. However, we must be careful in interpreting the result of the positive influence of FDIs on employment since almost half of the Saudi workforce is employed by the public sector. The paper aims to discuss these issues.

Design/methodology/approach
– Data regarding FDI inflow to Saudi Arabia were collected from the World Bank database and the Saudi Arabian General Investment Authority (SAGIA), while GDP per capita (economic growth) used data from the World Bank database only. Unemployment rate data were collected from the SAMA annual book. This study covered the period from 1999 through 2012. The study used the time series analysis methodology to study the impact of FDI inflow on economic growth and employment in Saudi Arabia.

Findings
– Although the current study found that FDI inflows contribute to the government’s effort by reducing or at least controlling the country’s high unemployment rate, it also found no relationship between FDI inflows and economic growth in Saudi Arabia. However, we must be careful in interpreting the result of the positive influence of FDI on employment since almost half of the Saudi workforce is employed by the public sector.

Originality/value
– In recent years, the government of Saudi Arabia has issued a number of initiatives to achieve diversification of income sources, create jobs for Saudi workers, and transfer advanced administrative techniques and technology to the Saudi economy; one of these initiatives involves attracting foreign investors to the Saudi market. This study contributes to fill the gap in studies that discuss the impact of FDI inflows on economic growth and employment in Saudi Arabia.
Conceptualisation of the service experience by means of a literature review
Authors: Vasconcelos Alexandre Meira de , Barichello Rodrigo , Lezana Álvaro , Forcellini Fernando A. , Ferreira Marcelo Gitirana Gomes , Cauchick Miguel Paulo Augusto 
Published: September 2015

Purpose
– Service operations are currently growing in importance, with a consequent increase in academic interest in the matter. In this context, the purpose of this paper is to systematise the concept associated with the service experience by drawing from the definitions which have been established in the relevant scientific literature.

Design/methodology/approach
– A systematic search in the literature was conducted, aiming to identify the main articles, journals, references, and keywords on the subject of customer experience. Using bibliometric content and analysis a number of articles are analysed towards a concept of service experience.

Findings
– The study verifies that service experience and service quality are distinct concepts that have to be analysed separately. The construction of this proposed concept has been oriented by content analysis of the reviewed articles. Dimensions and components that categorise this concept in a singular manner have been identified. The service experience, which can be thought of as a process, is composed of the interdependent and complementary dimensions of “predispositions”, “interactions”, and “reactions”, which condition the perception of quality and affect current as well as future purchasing decisions. As a result of their strategic importance for service organisations, customer experiences therefore warrant careful analysis.

Research limitations/implications
– This work is theoretical so empirical studies are necessary in order to validate or reject the proposed concept.

Originality/value
– Very few systematic literature reviews of the characterisation and conceptualisation on service experience concept are available.