bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tea consumption and oxidative stress: a cross-sectional analysis of 889 premenopausal women from the Sister Study
Authors: Zhang Dongyu , Ferguson Kelly , Troester Melissa A. , Bensen Jeannette T. , Cai Jianwen , Milne Ginger L. , Sandler Dale P. , Nichols Hazel B. 
Published: December 2018

AbstractIn experimental and clinical studies, green or black tea consumption has been shown to reduce oxidative stress. However, these studies involved high levels of tea consumption and may not reflect patterns in the general population. Here, we examined the association between black or green tea consumption and oxidative stress in a cross-sectional study of 889 premenopausal US women aged 35–54 years. Tea consumption was measured using the Block-98 FFQ. Urinary 8-iso-PGF2α (F2-IsoP) and 2,3-dinor-5,6-dihydro-15-F2t-isoprostane (15-F2t-IsoP-M) were used as biomarkers of oxidative stress. These compounds were measured by MS and normalised to creatinine. Linear regression was used to calculate the geometric mean differences (GMD) and 95% CI for log-transformed urinary F2-IsoP or 15-F2t-IsoP-M in relation to black or green tea consumption. We further examined whether adjusting for caffeine impacted associations between tea and oxidative stress. Geometric means of urinary F2-IsoP and 15-F2t-IsoP-M were 1·44 (95% CI 1·39, 1·49) and 0·71 (95% CI 0·69, 0·73) ng/mg creatinine, respectively. Overall, green tea consumption was not associated with urinary F2-IsoP or 15-F2t-IsoP-M. High-level black tea consumption (≥5 cups/week compared with 0) was associated with higher 15-F2t-IsoP-M concentrations (adjusted GMD=0·10, 95 % CI 0·02–0.19) but not F2-IsoP. Adjusting for caffeine nullified the association between black tea and 15-F2t-IsoP-M. Our findings do not support the hypothesis that dietary tea consumption is inversely associated with oxidative stress.
Prevalence of a nematode castrator of the carrot weevil and impact on fecundity and survival
Authors: Gagnon Annie-Ève , Boivin Guy , Bélair Guy , Mimee Benjamin 
Published: December 2018

AbstractBradynema listronoti is a parasitic nematode described from infected specimens of the carrot weevil Listronotus oregonensis. Prevalence of infection by B. listronoti under field conditions was followed over a period of 16 years in an untreated carrot field. Susceptibility of different carrot weevil life stages was evaluated as well as the impact of infection on fecundity and mortality. Gene expression in infected and uninfected carrot weevils was also compared to evaluate the impact of the parasite on the host transcriptome. Prevalence of B. listronoti in carrot weevil populations was sustained over the years ranging from 20 to 63%. All the weevil stages exposed to B. listronoti inoculum were susceptible to infection, larvae being more vulnerable (59 ± 8% infected) compared with pupae (4 ± 3% infected) and adults (7 ± 3% infected). The fecundity of infected female weevils was greatly reduced (60-fold) due to an inhibition of the maturation of the reproductive system. Transcriptomic analyses revealed that this parasitic castration may have been triggered by the inhibition of reproductive hormone production. The B. listronoti–L. oregonensis interaction represents a case of parasitic castration with a unique potential for biological control of an important pest of carrots.
Indigenous Peoples, World Heritage, and Human Rights
Authors: Vrdoljak Ana Filipa 
Published: December 2018

Abstract:Indigenous peoples’ emphasis on protecting their cultural heritage (including land) through a human rights-based approach reveals the synergies and conflicts between the World Heritage Convention and the UN Declaration on the Rights of Indigenous Peoples (UNDRIP). This article focuses on how their insistence on the right to participate effectively in decision-making and centrality of free, prior, and informed consent as defined in the UNDRIP exposes the limitations of existing United Nations Educational, Scientific and Cultural Organization and World Heritage Convention processes effecting Indigenous peoples, cultures, and territories and how these shortcomings can be addressed. By tracking the evolution of the UNDRIP and the World Heritage Convention from their drafting and adoption to their implementation, it examines how the realization of Indigenous peoples’ right to self-determination concerning cultural heritage is challenging international law to become more internally consistent in its interpretation and application and international organizations to operate in accordance with their constitutive instruments.
Gene Drives and Genome Modification in Nonhuman Animals: A Concern for Informed Consent?
Authors: SMOLENSKI JOANNA 
Published: December 2018

Abstract:In recent years, CRISPR-Cas9 has become one of the simplest and most cost-effective genetic engineering techniques among scientists and researchers aiming to alter genes in organisms. As Zika came to the fore as a global health crisis, many suggested the use of CRISPR-Cas9 gene drives in mosquitoes as a possible means to prevent the transmission of the virus without the need to subject humans to risky experimental treatments. This paper suggests that using gene drives or other forms of genome editing in nonhumans (like mosquitos) for the purposes of disease prevention raises important issues about informed consent. Additionally, it examines the consequences this line of inquiry could have for the use of gene drives as a tool in public health and suggests that the guidance offered by informed consent protocols could help the scientific community deploy gene drives in a way that ensures that ongoing research is consistent with our ethical priorities.
Let Us Assume That Gene Editing is Safe—The Role of Safety Arguments in the Gene Editing Debate
Authors: HOLM SØREN 
Published: December 2018

Abstract:This paper provides an analysis of the statement, made in many papers and reports on the use of gene editing in humans, that we should only use the technology when it is safe. It provides an analysis of what the statement means in the context of nonreproductive and reproductive gene editing and argues that the statement is inconsistent with the philosophical commitments of some of the authors, who put it forward in relation to reproductive uses of gene editing, specifically their commitment to Parfitian nonidentity considerations and to a legal principle of reproductive liberty.But, if that is true it raises a question about why the statement is made. What is its discursive and rhetorical function? Five functions are suggested, some of which are more contentious and problematic than others. It is argued that it is possible, perhaps even likely, that the “only when it is safe” rider is part of a deliberate obfuscation aimed at hiding the full implications of the arguments made about the ethics of gene editing and their underlying philosophical justifications.
Measurement of OH* Generation by Pulverized Minerals Using Electron Spin Resonance Spectroscopy and Implications for the Reactivity of Planetary Regolith
Authors: Hendrix Donald A. , Port Sara T. , Hurowitz Joel A. , Schoonen Martin A. 
Published: December 2018

AbstractMineral analogs to silicate phases common to planetary regolith, including olivine; the pyroxenes augite and diopside; the plagioclase feldspars labradorite, bytownite, and albite; the Johnson Space Center‐1A lunar regolith simulant; as well as quartz (used as a reference), were subjected to mechanical pulverization by laboratory milling for times ranging from 5 to 45 min. Pulverized minerals were then incubated in an aqueous solution containing the free radical spin trapping compound 5,5‐Dimethyl‐1‐Pyrroline‐N‐Oxide for times ranging from 5 to 30 min. These slurries were then analyzed by Electron Paramagnetic Resonance spectroscopy to quantify the amount of hydroxyl radical (the neutral charge form of the hydroxide ion, denoted as OH*) formed in solution. We find that all tested materials generate an Electron Paramagnetic Resonance spectrum indicating the formation of OH* with concentrations ranging between 0.1 and 1.5 μM. We also find that, in general, mineral pulverization time is inversely correlated to OH* generation, while OH* generation is positively correlated to mineral fluid incubation time for phases that have iron in their nominal chemical formulae, suggesting the possible action of Fenton reaction as a cofactor in increasing the reactivity of these phases. Our results add to a body of literature that indicates that the finely comminuted minerals and rocks present in planetary regolith are capable of generating highly reactive and highly oxidizing radical species in solution. The results provide the foundation for further in vitro and in vivo toxicological studies to evaluate the possible health risks that future explorers visiting the surfaces of planetary bodies may face from these reactive regolith materials.
Volcanic, Coseismic, and Seasonal Changes Detected at White Island (Whakaari) Volcano, New Zealand, Using Seismic Ambient Noise
Authors: Yates A. S. , Savage M. K. , Jolly A. D. , Caudron C. , Hamling I. J. 
Published: December 2018

AbstractAmbient noise interferometry is becoming increasingly popular for studying seismic velocity changes. Such changes contain information on the structural and mechanical properties of Earth systems. Application to monitoring, however, is complicated by the large number of processes capable of inducing crustal velocity changes. We demonstrate this at White Island volcano over a 10‐year period containing multiple well‐documented eruptions. Using individual seismic stations, we detect velocity perturbations that we ascribe to volcanic activity, large earthquakes, and seasonality. Distant seismic stations capture widespread nonvolcanic changes that are also present at the volcano. Comparison between velocity changes recorded by distant and local stations then allows us to distinguish volcanic phenomena from seasonality. Through this, we resolve distinct features in ambient noise‐derived velocity changes that relate to volcanic unrest and a phreatic eruption, illustrating the strength of the approach.
Electromagnetic Fields of Magnetospheric ULF Disturbances in the Ionosphere: Current/Voltage Dichotomy
Authors: Pilipenko Vyacheslav A. , Fedorov Evgeniy N. , Hartinger Michael D. , Engebretson Mark J. 
Published: December 2018

AbstractA circuit analogy for magnetosphere‐ionosphere current systems has two extremes for drivers of ionospheric currents: the “voltage generator” (ionospheric electric fields/voltages are constant, while current varies) and the “current generator” (current is constant, while the electric field varies). Here we indicate another aspect of the magnetosphere‐ionosphere interaction, which should be taken into account when considering the current/voltage dichotomy. We show that nonsteady field‐aligned currents interact with the ionosphere in a different way depending on a forced driving or resonant excitation. A quasi‐DC driving of field‐aligned current corresponds to a voltage generator, when the ground magnetic response is proportional to the ionospheric Hall conductance. The excitation of resonant field line oscillations corresponds to the current generator, when the ground magnetic response only weakly depends on the ionospheric conductance. According to the suggested conception, quasi‐DC nonresonant disturbances correspond to a voltage generator. Such ultralow frequency (ULF) phenomena as traveling convection vortices and Pc5 waves should be considered as the resonant response of magnetospheric field lines, and they correspond to a current generator. However, there are quite a few factors that may obscure the determination of the current/voltage dichotomy.
Evaluating antimalarial efficacy by tracking glycolysis in Plasmodium falciparum using NMR spectroscopy
Authors: Shivapurkar Rupali , Hingamire Tejashri , Kulkarni Akshay S. , Rajamohanan P. R. , Reddy D. Srinivasa , Shanmugam Dhanasekaran 
Published: December 2018

AbstractGlucose is an essential nutrient for Plasmodium falciparum and robust glycolytic activity is indicative of viable parasites. Using NMR spectroscopy, we show that P. falciparum infected erythrocytes consume ~20 times more glucose, and trophozoites metabolize ~6 times more glucose than ring stage parasites. The glycolytic activity, and hence parasite viability, can be measured within a period of 2 h to 5 h, using this method. This facilitates antimalarial bioactivity screening on ring and trophozoite stage parasites, exclusively. We demonstrate this using potent and mechanistically distinct antimalarial compounds such as chloroquine, atovaquone, cladosporin, DDD107498 and artemisinin. Our findings indicate that ring stage parasites are inherently more tolerant to antimalarial inhibitors, a feature which may facilitate emergence of drug resistance. Thus, there is a need to discover novel antimalarial compounds, which are potent and fast acting against ring stage parasites. The NMR method reported here can facilitate the identification of such molecules.
Aminoglycoside antibiotic resistance conferred by Hpa2 of MDR Acinetobacter baumannii: an unusual adaptation of a common histone acetyltransferase
Authors: Tomar Jyoti Singh , Peddinti Rama Krishna , Hosur Ramakrishna V. 
Published: December 2018

Abstract
Antibiotic-resistant bacteria pose the greatest threat to human health. Among the list of such bacteria released by WHO, carbapenem-resistant Acinetobacter baumannii, for which almost no treatment exists, tops the list. A. baumannii is one of the most troublesome ESKAPE pathogens and mechanisms that have facilitated its rise as a successful pathogen are not well studied. Efforts in this direction have resulted in the identification of Hpa2-Ab, an uncharacterized histone acetyltransferase enzyme of GNAT superfamily. Here, we show that Hpa2-Ab confers resistance against aminoglycoside antibiotics using Escherichia coli DH5α strains in which Hpa2 gene is expressed. Resistivity for aminoglycoside antibiotics is demonstrated with the help of CLSI-2010 and KB tests. Isothermal titration calorimetry, MALDI and acetylation assays indicate that conferred resistance is an outcome of evolved antibiotic acetylation capacity in this. Hpa2 is known to acetylate nuclear molecules; however, here it is found to cross its boundary and participate in other functions. An array of biochemical and biophysical techniques were also used to study this protein, which demonstrates that Hpa2-Ab is intrinsically oligomeric in nature, exists primarily as a dimer and its interface is mainly stabilized by hydrophobic interactions. Our work demonstrates an evolved survival strategy by A. baumannii and provides insights into the mechanism that facilitates it to rise as a successful pathogen.
The role of LRRK2 in cell signalling
Authors: Harvey Kirsten , Outeiro Tiago F. 
Published: December 2018

Abstract
Parkinson's disease (PD) is a common late-onset neurodegenerative disorder known primarily for its motor features. Mutations and risk variants in LRRK2 cause familial and idiopathic forms of PD. Mutations segregating with disease are found in the LRRK2 GTPase and kinase domains, affecting catalytic activity and protein–protein interactions. This likely results in an overall gain of LRRK2 cell signalling function contributing to PD pathogenesis. This concept supports the development of LRRK2 kinase inhibitors as disease-modifying treatments, at least for a subset of patients. However, the function of LRRK2 as a cell signalling protein with two catalytic and several protein–protein interaction domains is highly complex. For example, LRRK2 plays important roles in several inflammatory diseases, raising the possibility that it may mediate immune responses in PD. Consistently, LRRK2-mediated cell signalling was not only shown to be important for neuronal function, including neuronal development and homeostasis, but also for peripheral and central immune responses. The catalytic activity of LRRK2 is regulated by autophosphorylation, protein monomer/dimer cycling, and upstream kinases and GTPases, affecting its subcellular localisation and downstream signalling. Part of LRRK2-mediated signalling is likely facilitated by Rab protein phosphorylation, affecting primarily membrane trafficking, including vesicle release at the trans-Golgi network. However, LRRK2 also displays intrinsic GTPase activity and functions as a signalling scaffold. As an example, LRRK2 was suggested to be part of the NRON complex and β-catenin destruction complex, inhibiting NFAT and canonical Wnt signalling, respectively. In summary, continuous research into LRRK2 signalling function contributes to novel diagnostic and therapeutic concepts in PD.
„Sein durch den Anderen – auch Versuch eines fruchtbaren Ost-West-Dialoges“
Authors: Trenkel Arthur 
Published: December 2018

ZusammenfassungAus Anlass eines Internationalen Kongresses für Psychotherapie wird das Verhältnis von professioneller Rolle und dem lebendigen Erleben und die damit verbundene Doppel-orientierung in der Praxis erläutert. Wenn ich Erlebender bin, dann helfe ich auch dem Anderen. Das gilt auch für den Interkulturellen Dialog.
Adjective-noun order in Papiamento-Dutch code-switching
Authors: Pablos Leticia , Parafita Couto M. Carmen , Boutonnet Bastien , de Jong Amy , Perquin Marlou , de Haan Annelies , Schiller Niels O. 
Published: December 2018

AbstractIn Papiamento-Dutch bilingual speech, the nominal construction is a potential ‘conflict site’ if there is an adjective from one language and a noun from the other. Adjective position is pre-nominal in Dutch (cf.rode wijn‘red wine’) but post-nominal in Papiamento (cf.biña kòrá‘wine red’). We test predictions concerning the mechanisms underpinning word order in noun-adjective switches derived from three accounts: (i) the adjective determines word order (Cantone & MacSwan, 2009), (ii) the matrix language determines word order (Myers-Scotton, 1993,2002), and (iii) either order is possible (Di Sciullo, 2014). An analysis of spontaneous Papiamento-Dutch code-switching production (Parafita Couto & Gullberg, 2017) could not distinguish between these predictions. We used event-related brain potentials (ERPs) to measure online comprehension of code-switched utterances. We discuss how our results inform the three theoretical accounts and we relate them to syntactic coactivation and the production-comprehension link.
Analyzing Components of Productivity Growth Using the Bennet‐Lowe Indicator: An Application to Welsh Sheep Farms
Authors: Ang Frederic 
Published: December 2018

AbstractThis article introduces the Bennet‐Lowe Total Factor Productivity (TFP) indicator. The proposed measure is difference‐based, additively complete, and transitive. We also develop a general nonparametric framework to exhaustively decompose all Bennet‐type TFP indicators, including the one introduced here, into technical change, technical efficiency change, scale efficiency change, and mix efficiency change. This decomposition provides a powerful tool for policy makers to guide financial decisions on research and development, extension, subsidies, and price support. The empirical application focuses on the Welsh sheep sector for the years 2001–2014. The results show that in this 14‐year period, Welsh sheep farms increased their TFP by 30.28% on average (2.33% p.a.). However, the exhaustive decomposition shows that TFP growth is not distributed equally across all farms, with an increasing divergence between front‐runners and laggards. The negative values of scale efficiency change and mix efficiency change cast doubt on the current subsidy policies.
Against Kripke’s solution to the problem of negative existentials
Authors: Hausmann Marco 
Published: December 2018

Abstract
In this paper, I try to show that Kripke’s proposed solution to the problem of negative existentials fails. I try to show that Kripke’s proposal fails because it entails that anybody who has (or had) good reasons to believe that there are no propositions has (or had) also good reasons to believe that he or she does not exist. However, there were philosophers (most notably Quine) who had good reasons to believe that there are no propositions even though they didn’t have good reasons to believe that they do not exist. I conclude that Kripke’s proposed solution to the problem of negative existentials fails.
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data
Authors: Poell Jos B , Mendeville Matias , Sie Daoud , Brink Arjen , Brakenhoff Ruud H , Ylstra Bauke 
Published: December 2018

Abstract

Summary
Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing, but analysis is hampered by the lack of knowledge on absolute DNA copy numbers and tumor purity. Here, we describe an analytical tool for Absolute Copy number Estimation, ACE, which scales relative copy number signals from chromosomal segments to optimally fit absolute copy numbers, without the need for additional genetic information, such as SNP data. In doing so, ACE derives an estimate of tumor purity as well. ACE facilitates analysis of large numbers of samples, while maintaining the flexibility to customize models and generate output of single samples.

Availability and implementation
ACE is freely available via www.bioconductor.org and at www.github.com/tgac-vumc/ACE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning
Authors: Li Xiangtao , Zhang Shixiong , Wong Ka-Chun 
Published: December 2018

Abstract

Motivation
In recent years, single-cell RNA sequencing enables us to discover cell types or even subtypes. Its increasing availability provides opportunities to identify cell populations from single-cell RNA-seq data. Computational methods have been employed to reveal the gene expression variations among multiple cell populations. Unfortunately, the existing ones can suffer from realistic restrictions such as experimental noises, numerical instability, high dimensionality and computational scalability.

Results
We propose an evolutionary multiobjective ensemble pruning algorithm (EMEP) that addresses those realistic restrictions. Our EMEP algorithm first applies the unsupervised dimensionality reduction to project data from the original high dimensions to low-dimensional subspaces; basic clustering algorithms are applied in those new subspaces to generate different clustering results to form cluster ensembles. However, most of those cluster ensembles are unnecessarily bulky with the expense of extra time costs and memory consumption. To overcome that problem, EMEP is designed to dynamically select the suitable clustering results from the ensembles. Moreover, to guide the multiobjective ensemble evolution, three cluster validity indices including the overall cluster deviation, the within-cluster compactness and the number of basic partition clusters are formulated as the objective functions to unleash its cell type discovery performance using evolutionary multiobjective optimization. We applied EMEP to 55 simulated datasets and seven real single-cell RNA-seq datasets, including six single-cell RNA-seq dataset and one large-scale dataset with 3005 cells and 4412 genes. Two case studies are also conducted to reveal mechanistic insights into the biological relevance of EMEP. We found that EMEP can achieve superior performance over the other clustering algorithms, demonstrating that EMEP can identify cell populations clearly.

Availability and implementation
EMEP is written in Matlab and available at https://github.com/lixt314/EMEP

Supplementary information
Supplementary data are available at Bioinformatics online.