bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic anthropogenic disturbance as a secondary driver of ant community structure: interactions with soil type in Brazilian Caatinga
Authors: OLIVEIRA FERNANDA M. P. , RIBEIRO-NETO JOSÉ DOMINGOS , ANDERSEN ALAN N. , LEAL INARA R. 
Published: August 2016

SUMMARYHabitat loss is widely recognized as the major cause of global biodiversity decline, but remaining habitat is increasingly threatened by chronic human disturbances. Using a multi-model averaging approach we examined the association between five chronic disturbance surrogates and the richness and taxonomic and functional composition of ants in Brazilian Caatinga. Using pitfall traps in 47 plots near Parnamirim city (Pernambuco) across two soil types (sand and clay), we recorded 53 species from 27 genera. Ant species richness on sand was slightly higher than on clay, and was negatively related to most surrogates of anthropogenic disturbance. Soil type and human population size were the main predictors of ant species richness. Soil type was the most important predictor of functional group abundance. Taxonomic and functional composition were influenced by soil type and disturbance, but this relationship varied between clay and sandy soils. Ant functional composition showed a weak relationship with disturbance on sandy soils, but on clay soils it showed predictable winner–loser replacement. We attribute the greater effect of disturbance on clay soils to higher intensity of land use, and our study highlights the importance of considering context dependence when evaluating biodiversity responses to disturbance.
Digital design and manufacturing on the cloud: A review of software and services—RETRACTED
Authors: Wu Dazhong , Terpenny Janis , Schaefer Dirk 
Published: August 2016

AbstractThis paper (Wu 2016), which was published in AI EDAM online on August 22, 2016, has been retracted by Cambridge University Press as it is very similar in content to a published ASME Conference Proceedings paper. The article in question and the ASME Conference Proceedings paper were submitted for review with AI EDAM and the ASME at similar times, but copyright was assigned to ASME before the paper was accepted in AI EDAM and therefore the article in AI EDAM is being retracted. (In recent years, industrial nations around the globe have invested heavily in new technologies, software, and services to advance digital design and manufacturing using cyber-physical systems, data analytics, and high-performance computing. Many of these initiatives, such as cloud-based design and manufacturing, fall under the umbrella of what has become known as Industry 4.0 or Industrial Internet and are often hailed as pillars of a new industrial revolution. While an increasing number of companies are developing or already offer commercial cloud-based software packages and services for digital design and manufacturing, little work has been reported on providing a review of the state of the art of these commercial software and services as well as identifying research gaps in this field. The objective of this paper is to present a state-of-the-art review of digital design and manufacturing software and services that are currently available on the cloud. The focus of this paper is on assessing to what extent engineering design, engineering analysis, manufacturing, and production across all phases of the product development lifecycles can already be performed based on the software and services accessed through the cloud. In addition, the key capabilities and benefits of these software packages and services are discussed. Based on the assessment of the core features of commercial software and services, it can be concluded that almost all phases of product realization can be conducted through digital design and manufacturing software and services on the cloud. Finally, existing research gaps and related challenges to overcome are identified. The state-of-the-art review serves to provide a technology guide for decision makers in their efforts to select suitable cloud-based software and services as alternatives to existing in-house resources as well as to recommend new research areas.)
Antiretroviral treatment attrition in Swaziland: a population-based study
Authors: KHUMALO P. G. , CHOU Y. J. , PU C. 
Published: August 2016

SUMMARYSwaziland has the highest prevalence of human immunodeficiency virus (HIV) in the world. Attrition (loss to follow-up and mortality) in people living with HIV/AIDS (PLWHA) already on treatment is a major challenge, undermining achievements of the antiretroviral treatment (ART) programme in Swaziland. The contributing factors to attrition in the Swazi context are unclear. This study aims to (1) estimate attrition from the ART programme 12 months after ART initiation in Swaziland, and (2) determine the predictors of attrition in PLWHA treated with ART in Swaziland. A retrospective cohort study using national baseline data was conducted. A competing-risk Cox proportional hazard regression was used to determine the predictors of attrition. We estimated 10·3% (95% confidence interval 10·1–10·6) attrition in 16 423 participants that initiated ART in 2012. Attrition was significantly associated with sex, age, district, treatment supporter at initiation, co-infection of HIV and TB, functional status, WHO clinical stage, and ownership of facility. Our study can form a base of policies, plans, and service delivery strategies for preventing and controlling attrition in Swaziland.
The quantification of type-2 prudence in asset allocation by the trustees of a retirement fund
Authors: Thomson Robert J. , Reddy Taryn L. 
Published: August 2016

AbstractIn this paper, consideration is given to the normative use of expected-utility theory for the purposes of asset allocation by the trustees of retirement funds. A distinction is drawn between “type-1 prudence”, which relates to deliberate conservatism on the part of actuaries in the setting of assumptions and the determination of model parameters, and “type-2 prudence”, which relates to the risk aversion of the trustees. The intention of the research was to quantify type-2 prudence for the purposes of asset allocation, both for defined-contribution (DC) and defined-benefit (DB) funds. The authors propose new definitions of the objective variables used as the argument of the utility function: one for DC funds and another for DB funds. A new class of utility functions, referred to as the “weighted average relative risk aversion” class is proposed. Practicalities of implementation are discussed. Illustrative results of the application of the method are presented, and it is shown that the proposed approach resolves the paradox of counter-intuitive results found in the literature regarding the sensitivity of the optimal asset allocation to the funding level of a DB fund.
On the joint analysis of the total discounted payments to policyholders and shareholders: threshold dividend strategy
Authors: Cheung Eric C.K. , Liu Haibo 
Published: August 2016

AbstractIn insurance risk theory, dividend and aggregate claim amount are of great research interest as they represent the insurance company’s payments to its shareholders and policyholders, respectively. Since the analyses of these two quantities are performed separately in the literature, the companion paper by Cheung et al. generalised the Gerber–Shiu expected discounted penalty function by further incorporating the moments of the aggregate discounted claims until ruin and the discounted dividends until ruin. While Cheung et al. considered the compound Poisson model with a dividend barrier in which ruin occurs almost surely, the present paper looks at this generalised Gerber–Shiu function under a threshold dividend strategy where the insurer has a positive survival probability. Because the Gerber–Shiu function is only defined for sample paths leading to ruin, we will additionally study the joint moments of the aggregate discounted claims and the discounted dividends without ruin occurring. Some explicit formulas are derived when the individual claim distribution follows a combination of exponentials. Numerical illustrations involving the correlation between aggregate discounted claims and discounted dividends are given. For the case where ruin occurs, we additionally compute the correlations between the time of ruin and the above two quantities.
The fuzzy Bornhuetter–Ferguson method: an approach with fuzzy numbers
Authors: Heberle Jochen , Thomas Anne 
Published: August 2016

AbstractThis paper shows how the well-known Bornhuetter–Ferguson claims-reserving method can be extended by applying fuzzy methods. The a priori information for the ultimate claims derives from market statistics, organisational data, etc. and might contain vagueness. Likewise, the parameters of the claims development pattern can be vague or are adapted, retrospectively, due to subjective judgement. With the help of fuzzy numbers we develop new predictors for the ultimate claims. Furthermore, we quantify the uncertainty of the ultimate claims for single and aggregated accident years.
Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography
Authors: Sauguet Ludovic , Raia Pierre , Henneke Ghislaine , Delarue Marc 
Published: August 2016

AbstractArchaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same ‘double-psi β-barrel’ architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.
Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography
Authors: Nogly Przemyslaw , Panneels Valerie , Nelson Garrett , Gati Cornelius , Kimura Tetsunari , Milne Christopher , Milathianaki Despina , Kubo Minoru , Wu Wenting , Conrad Chelsie , Coe Jesse , Bean Richard , Zhao Yun , Båth Petra , Dods Robert , Harimoorthy Rajiv , Beyerlein Kenneth R. , Rheinberger Jan , James Daniel , DePonte Daniel , Li Chufeng , Sala Leonardo , Williams Garth J. , Hunter Mark S. , Koglin Jason E. , Berntsen Peter , Nango Eriko , Iwata So , Chapman Henry N. , Fromme Petra , Frank Matthias , Abela Rafael , Boutet Sébastien , Barty Anton , White Thomas A. , Weierstall Uwe , Spence John , Neutze Richard , Schertler Gebhard , Standfuss Jörg 
Published: August 2016

AbstractSerial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae
Authors: Tohge Takayuki , Wendenburg Regina , Ishihara Hirofumi , Nakabayashi Ryo , Watanabe Mutsumi , Sulpice Ronan , Hoefgen Rainer , Takayama Hiromitsu , Saito Kazuki , Stitt Mark , Fernie Alisdair R. 
Published: August 2016

AbstractIncidence of natural light stress renders it important to enhance our understanding of the mechanisms by which plants protect themselves from harmful effects of UV-B irradiation, as this is critical for fitness of land plant species. Here we describe natural variation of a class of phenylacylated-flavonols (saiginols), which accumulate to high levels in floral tissues of Arabidopsis. They were identified in a subset of accessions, especially those deriving from latitudes between 16° and 43° North. Investigation of introgression line populations using metabolic and transcript profiling, combined with genomic sequence analysis, allowed the identification of flavonol-phenylacyltransferase 2 (FPT2) that is responsible for the production of saiginols and conferring greater UV light tolerance in planta. Furthermore, analysis of polymorphism within the FPT duplicated region provides an evolutionary framework of the natural history of this locus in the Brassicaceae.
Crosstalk between MSH2–MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair
Authors: Lai Yanhao , Budworth Helen , Beaver Jill M. , Chan Nelson L. S. , Zhang Zunzhen , McMurray Cynthia T. , Liu Yuan 
Published: August 2016

AbstractStudies in knockout mice provide evidence that MSH2–MSH3 and the BER machinery promote trinucleotide repeat (TNR) expansion, yet how these two different repair pathways cause the mutation is unknown. Here we report the first molecular crosstalk mechanism, in which MSH2–MSH3 is used as a component of the BER machinery to cause expansion. On its own, pol β fails to copy TNRs during DNA synthesis, and bypasses them on the template strand to cause deletion. Remarkably, MSH2–MSH3 not only stimulates pol β to copy through the repeats but also enhances formation of the flap precursor for expansion. Our results provide direct evidence that MMR and BER, operating together, form a novel hybrid pathway that changes the outcome of TNR instability from deletion to expansion during the removal of oxidized bases. We propose that cells implement crosstalk strategies and share machinery when a canonical pathway is ineffective in removing a difficult lesion.
Nonlinear metamaterials for holography
Authors: Almeida Euclides , Bitton Ora , Prior Yehiam 
Published: August 2016

AbstractA hologram is an optical element storing phase and possibly amplitude information enabling the reconstruction of a three-dimensional image of an object by illumination and scattering of a coherent beam of light, and the image is generated at the same wavelength as the input laser beam. In recent years, it was shown that information can be stored in nanometric antennas giving rise to ultrathin components. Here we demonstrate nonlinear multilayer metamaterial holograms. A background free image is formed at a new frequency—the third harmonic of the illuminating beam. Using e-beam lithography of multilayer plasmonic nanoantennas, we fabricate polarization-sensitive nonlinear elements such as blazed gratings, lenses and other computer-generated holograms. These holograms are analysed and prospects for future device applications are discussed.
Retinoblastoma-binding protein 2 (RBP2) is frequently expressed in neuroendocrine tumors and promotes the neoplastic phenotype
Authors: Maggi E C , Trillo-Tinoco J , Struckhoff A P , Vijayaraghavan J , Del Valle L , Crabtree J S 
Published: August 2016

AbstractNeuroendocrine tumors (NETs), which can have survival rates as low as 4%, currently have limited therapeutic interventions available highlighting the dire need for the identification of novel biological targets for use as new potential drug targets. One such potential target is retinoblastoma-binding protein 2 (RBP2), an H3K4 demethylase whose overexpression has been linked to cancer formation and metastasis in non-endocrine tumor types. We measured RBP2 mRNA and protein levels in enteropancreatic NETs by measuring RBP2 in matched human normal and NET tissue samples. Further, proliferation, migration, invasion and colony formation assays were performed in the physiologically relevant NET cell lines βlox5, H727 and QGP-1 to understand the role of RBP2 and its demethylase activity on end points of tumorigenesis. Our data indicate a strong correlation between RBP2 mRNA and protein expression in NET specimens. RBP2 was overexpressed relative to tissue-matched normal controls in 80% of the human tumors measured. In vitro studies showed RBP2 overexpression significantly increased proliferation, migration, invasion and colony formation, whereas knockdown significantly decreases the same parameters in a demethylase-independent manner. The cell cycle inhibitors p21 and p57 decreased with RBP2 overexpression and increased upon its depletion, suggesting a regulatory role for RBP2 in cellular proliferation. Taken together, our results support the hypothesis that the aberrant overexpression of RBP2 is a frequent contributing factor to tumor formation and metastasis in enteropancreatic NETs.
Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers
Authors: Himbert Sebastian , Chapman Mindy , Deamer David W. , Rheinstädter Maikel C. 
Published: August 2016

AbstractRNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5′-adenosine monophosphate (AMP) and 5′-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.
Utilization of 134Cs/137Cs in the environment to identify the reactor units that caused atmospheric releases during the Fukushima Daiichi accident
Authors: Chino Masamichi , Terada Hiroaki , Nagai Haruyasu , Katata Genki , Mikami Satoshi , Torii Tatsuo , Saito Kimiaki , Nishizawa Yukiyasu 
Published: August 2016

AbstractThe Fukushima Daiichi nuclear power reactor units that generated large amounts of airborne discharges during the period of March 12–21, 2011 were identified individually by analyzing the combination of measured 134Cs/137Cs depositions on ground surfaces and atmospheric transport and deposition simulations. Because the values of 134Cs/137Cs are different in reactor units owing to fuel burnup differences, the 134Cs/137Cs ratio measured in the environment was used to determine which reactor unit ultimately contaminated a specific area. Atmospheric dispersion model simulations were used for predicting specific areas contaminated by each dominant release. Finally, by comparing the results from both sources, the specific reactor units that yielded the most dominant atmospheric release quantities could be determined. The major source reactor units were Unit 1 in the afternoon of March 12, 2011, Unit 2 during the period from the late night of March 14 to the morning of March 15, 2011. These results corresponded to those assumed in our previous source term estimation studies. Furthermore, new findings suggested that the major source reactors from the evening of March 15, 2011 were Units 2 and 3 and that the dominant source reactor on March 20, 2011 temporally changed from Unit 3 to Unit 2.
Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli
Authors: Berger Michael , Gerganova Veneta , Berger Petya , Rapiteanu Radu , Lisicovas Viktoras , Dobrindt Ulrich 
Published: August 2016

AbstractThe extent to which chromosomal gene position in prokaryotes affects local gene expression remains an open question. Several studies have shown that chromosomal re-positioning of bacterial transcription units does not alter their expression pattern, except for a general decrease in gene expression levels from chromosomal origin to terminus proximal positions, which is believed to result from gene dosage effects. Surprisingly, the question as to whether this chromosomal context independence is a cis encoded property of a bacterial transcription unit, or if position independence is a property conferred by factors acting in trans, has not been addressed so far. For this purpose, we established a genetic test system assessing the chromosomal positioning effects by means of identical promoter-fluorescent reporter gene fusions inserted equidistantly from OriC into both chromosomal replichores of Escherichia coli K-12. Our investigations of the reporter activities in mutant cells lacking the conserved nucleoid associated protein HU uncovered various drastic chromosomal positional effects on gene transcription. In addition we present evidence that these positional effects are caused by transcriptional activity nearby the insertion site of our reporter modules. We therefore suggest that the nucleoid-associated protein HU is functionally insulating transcription units, most likely by constraining transcription induced DNA supercoiling.
Reduction of obesity-associated white adipose tissue inflammation by rosiglitazone is associated with reduced non-alcoholic fatty liver disease in LDLr-deficient mice
Authors: Mulder Petra , Morrison Martine C. , Verschuren Lars , Liang Wen , van Bockel J. Hajo , Kooistra Teake , Wielinga Peter Y. , Kleemann Robert 
Published: August 2016

AbstractObesity is associated with chronic low-grade inflammation that drives the development of metabolic diseases, including non-alcoholic fatty liver disease (NAFLD). We recently showed that white adipose tissue (WAT) constitutes an important source of inflammatory factors. Hence, interventions that attenuate WAT inflammation may reduce NAFLD development. Male LDLr−/− mice were fed a high-fat diet (HFD) for 9 weeks followed by 7 weeks of HFD with or without rosiglitazone. Effects on WAT inflammation and NAFLD development were analyzed using biochemical and (immuno)histochemical techniques, combined with gene expression analyses. Nine weeks of HFD feeding induced obesity and WAT inflammation, which progressed gradually until the end of the study. Rosiglitazone fully blocked progression of WAT inflammation and activated PPARγ significantly in WAT. Rosiglitazone intervention did not activate PPARγ in liver, but improved liver histology and counteracted the expression of genes associated with severe NAFLD in humans. Rosiglitazone reduced expression of pro-inflammatory factors in WAT (TNF-α, leptin) and increased expression of adiponectin, which was reflected in plasma. Furthermore, rosiglitazone lowered circulating levels of pro-inflammatory saturated fatty acids. Together, these observations provide a rationale for the observed indirect hepatoprotective effects and suggest that WAT represents a promising therapeutic target for the treatment of obesity-associated NAFLD.