bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferential Justification and the Transparency of Belief
Authors: James Barnett David 
Published: March 2015

AbstractThis paper critically examines currently influential transparency accounts of our knowledge of our own beliefs that say that self‐ascriptions of belief typically are arrived at by “looking outward” onto the world. For example, one version of the transparency account says that one self‐ascribes beliefs via an inference from a premise to the conclusion that one believes that premise. This rule of inference reliably yields accurate self‐ascriptions because you cannot infer a conclusion from a premise without believing the premise, and so you cannot infer from a premise that you believe the premise unless you do believe it. I argue that this procedure cannot be a source of justification, however, because one can be justified in inferring from p that q only if p amounts to strong evidence that q is true. This is incompatible with the transparency account because p often is not very strong evidence that you believe that p. For example, unless you are a weather expert, the fact that itwillrain is not very strong evidence that youbelieveit will rain. After showing how this intuitive problem can be made precise, I conclude with a broader lesson about the nature of inferential justification: that beliefs, when justified, must be underwritten by beliefs, when justified, must be underwritten by evidential relationships between the facts or propositions which those beliefs represent.
The tomato I‐3 gene: a novel gene for resistance to Fusarium wilt disease
Authors: Catanzariti Ann‐Maree , Lim Ginny T. T. , Jones David A. 
Published: March 2015

Summary

Plant resistance proteins provide race‐specific immunity through the recognition of pathogen effectors. The resistance genes I, I‐2 and I‐3 have been incorporated into cultivated tomato (Solanum lycopersicum) from wild tomato species to confer resistance against Fusarium oxysporum f. sp. lycopersici (Fol) races 1, 2 and 3, respectively. Although the Fol effectors corresponding to these resistance genes have all been identified, only the I‐2 resistance gene has been isolated from tomato.

To isolate the I‐3 resistance gene, we employed a map‐based cloning approach and used transgenic complementation to test candidate genes for resistance to Fol race 3.

Here, we describe the fine mapping and sequencing of genes at the I‐3 locus, which revealed a family of S‐receptor‐like kinase (SRLK) genes. Transgenic tomato lines were generated with three of these SRLK genes and one was found to confer Avr3‐dependent resistance to Fol race 3, confirming it to be I‐3.

The finding that I‐3 encodes an SRLK reveals a new pathway for Fol resistance and a new class of resistance genes, of which Pi‐d2 from rice is also a member. The identification of I‐3 also allows the investigation of the complex effector–resistance protein interaction involving Avr1‐mediated suppression of I‐2‐ and I‐3‐dependent resistance in tomato.
Impacts of urbanisation on biodiversity: the role of species mobility, degree of specialisation and spatial scale
Authors: Concepción Elena D. , Moretti Marco , Altermatt Florian , Nobis Michael P. , Obrist Martin K. 
Published: March 2015

Urbanisation has an important impact on biodiversity, mostly driving changes in species assemblages, through the replacement of specialist with generalist species, thus leading to biotic homogenisation. Mobility is also assumed to greatly affect species’ ability to cope in urban environments. Moreover, specialisation, mobility and their interaction are expected to greatly influence ecological processes such as metacommunity dynamics and assembly processes, and consequently the way and the spatial scale at which organisms respond to urbanisation. Here we investigate urbanisation impacts on distinct characteristics of species assemblages – namely specialisation degree in resource use, mobility and number of species, classified according to both characteristics and their combination – for vascular plants, butterflies and birds, across a range of spatial scales (from 1 × 1 km plots to 5 km‐radius buffers around them).We found that the degree of specialisation, mobility and their interaction, greatly influenced species’ responses to urbanisation, with highly mobile specialist species of all taxonomic groups being affected most. Two different patterns were found: for plants, urbanisation induced trait divergence by favouring highly mobile species with narrow habitat ranges. For birds and butterflies, however, it reduced the number of highly mobile specialist species, thus driving trait convergence. Mobile organisms, across and within taxonomic groups, tended to respond at larger spatial scales than those that are poorly mobile. These findings emphasize the need to take into consideration species’ ecological aspects, as well as a wide range of spatial scales when evaluating the impact of urbanisation on biodiversity. Our results also highlight the harmful impact of widespread urban expansion on organisms such as butterflies, especially highly mobile specialists, which were negatively affected by urban areas even at great distances.
Primary osteolysis syndromes: beware of difficult airway
Authors: Herd R. Scott , Sprung Juraj , Weingarten Toby N. 
Published: March 2015

SummaryBackgroundPrimary osteolysis syndromes represent a number of rare conditions characterized by destruction and resorption of bone that is unrelated to neoplasia, infection, or trauma.AimTo characterize the periprocedural course of patients with primary osteolysis syndrome undergoing procedures that require anesthesia care.MethodsThe medical records database from our institution was searched from 1976 to 2013 to identify patients with primary osteolysis syndromes who received anesthesia care. We reviewed demographic characteristics, comorbidities, and perioperative course of patients with different forms of primary osteolysis. A systematic review of the literature was performed to identify reports describing the anesthetic management of patients with these conditions.ResultsWe identified 11 patients with a primary osteolysis syndrome who received 111 anesthetics. The patients' ages at the time of surgery ranged from 3 to 62 years. Difficult airway management was a common finding. On preoperative examination, difficulty with endotracheal intubation was predicted in 8 of 11 patients. Three patients had preexisting tracheostomies. One patient required multiple awake fiberoptic intubations. Another two patients where successfully intubated early in life via direct laryngoscopy, but eventually required awake fiberoptic intubations as the disease process caused progressive distortion of airway structures. Intraoperative complications were absent. In the postoperative period, three patients required prolonged mechanical ventilation due to airway swelling, respiratory failure, and infection.ConclusionsAirway management may be challenging in patients with primary osteolysis syndromes. Because the osteolytic process advances with aging and craniofacial dysmorphism may progressively worsen, the airway should always be reassessed before surgery with an appropriate strategy for potentially difficult intubation. In all patients with primary osteolysis, a potential for pathologic fracture must be considered and careful intraoperative positioning is warranted.
Regulation of the alkaloid biosynthesis by miRNA in opium poppy
Authors: Boke Hatice , Ozhuner Esma , Turktas Mine , Parmaksiz Iskender , Ozcan Sebahattin , Unver Turgay 
Published: March 2015

SummaryOpium poppy (Papaver somniferum) is an important medicinal plant producing benzylisoquinoline alkaloids (BIA). MicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) of approximately 21 nucleotides. They are noncoding, but regulate gene expression in eukaryotes. Although many studies have been conducted on the identification and functions of plant miRNA, scarce researches on miRNA regulation of alkaloid biosynthesis have been reported. In this study, a total of 316 conserved and 11 novel miRNAs were identified in opium poppy using second‐generation sequencing and direct cloning. Tissue‐specific regulation of miRNA expression was comparatively analysed by miRNA microarray assays. A total of 232 miRNAs were found to be differentially expressed among four tissues. Likewise, 1469 target transcripts were detected using in silico and experimental approaches. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates carbohydrate metabolism and genetic‐information processing. Additionally, miRNA target transcripts were mostly involved in response to stress against various factors and secondary‐metabolite biosynthesis processes. Target transcript identification analyses revealed that some of the miRNAs might be involved in BIA biosynthesis, such as pso‐miR13, pso‐miR2161 and pso‐miR408. Additionally, three putatively mature miRNA sequences were predicted to be targeting BIA‐biosynthesis genes.
The space‐time continuum: the effects of elevated CO2 and temperature on trees and the importance of scaling
Authors: WAY DANIELLE A. , OREN RAM , KRONER YULIA 
Published: March 2015

AbstractTo predict how forests will respond to rising temperatures and atmospheric CO2 concentrations, we need to understand how trees respond to both of these environmental factors. In this review, we discuss the importance of scaling, moving from leaf‐level responses to those of the canopy, and from short‐term to long‐term responses of vegetation to climate change. While our knowledge of leaf‐level, instantaneous responses of photosynthesis, respiration, stomatal conductance, transpiration and water‐use efficiency to elevated CO2 and temperature is quite good, our ability to scale these responses up to larger spatial and temporal scales is less developed. We highlight which physiological processes are least understood at various levels of study, and discuss how ignoring differences in the spatial or temporal scale of a physiological process impedes our ability to predict how forest carbon and water fluxes forests will be altered in the future. We also synthesize data from the literature to show that light respiration follows a generalized temperature response across studies, and that the light compensation point of photosynthesis is reduced by elevated growth CO2. Lastly, we emphasize the need to move beyond single factorial experiments whenever possible, and to combine both CO2 and temperature treatments in studies of tree performance.
Steady‐State Spectroscopy of the 2‐(N‐methylacetimidoyl)‐1‐naphthol Molecule
Authors: del Valle Juan Carlos , Díaz‐Oliva Cristina 
Published: March 2015

AbstractThe steady‐state spectroscopy of 2‐(N‐methylacetimidoyl)‐1‐naphthol (MAN) reveals composite absorption and emission spectra from 298 to 193 K in hexane. The ground electronic state (So) absorption can be assigned to the sum of three molecular structures: the OH normal tautomer, and two NH proton transfer tautomers. The NH‐structures are the most stable ones in equilibrium with the OH tautomer for the S0 state. On photoexcitation of the OH tautomer the excited state intramolecular proton transfer is undergone, and the corresponding NH emission is monitored at 470 nm. On photoexcitation of the NH tautomers the previous emission is monitored in addition to another emission at 600 nm, which is ascribed to intramolecular hydrogen‐bonded (IHB) nonplanar NH structures generated from the IHB planar NH tautomers. A Jabłoński diagram is introduced which gathers all the experimental evidence as well as the theoretical calculations executed at the DFT‐B3LYP and TD‐DFT levels. The MAN molecule is compared with other analogs such as 1‐hydroxy‐2‐acetonaphthone (HAN), 2‐(1΄‐hydroxy‐2΄‐naphthyl)benzimidazole and methyl 1‐hydroxy‐2‐naphthoate to validate the theoretical calculations. Photoexcitation of MAN generates two emission bands at longer wavelengths than that of the emission band of HAN. The MAN molecule exhibits a great photostability in hydrocarbon solution which depends on the photophysics of the NH tautomers (keto forms).
Protecting Nature for the Sake of Human Beings
Authors: James Simon P. 
Published: March 2015

AbstractIt is often assumed that to say that nature should be protected for the sake of human beings just is to say that it should be protected because it is a means to one or more anthropocentric ends. I argue that this assumption is false. In some contexts, claims that a particular natural X should be protected for our sakes mean that X should be protected, not because it is a means to anthropocentric ends, but because it is part of something about human life that is of value: because, that is, its value is anthropocentric and constitutive rather than anthropocentric and instrumental. It follows, I suggest, that one does not need to endorse the non‐anthropocentric claim that nature should be protected for its own sake in order to challenge the instrumentalist notion that it should be protected simply because it is a means to anthropocentric ends (as, say, a provider of ecosystem services). To make my case, I consider the UK Government's failed attempt to sell off England's publicly‐owned forests.
Inflammatory markers and mortality amongUSadults with obstructive lung function
Authors: Ford Earl S. , Cunningham Timothy J. , Mannino David M. 
Published: March 2015

AbstractBackground and objectiveChronic obstructive pulmonary disease is characterized by an inflammatory state of uncertain significance. The objective of this study was to examine the association between elevated inflammatory marker count (white blood cell count,C‐reactive protein and fibrinogen) on all‐cause mortality in a national sample ofUSadults with obstructive lung function (OLF).MethodsData for 1144 adults aged 40–79 years in theNationalHealth andNutritionExaminationSurveyIII LinkedMortalityStudy were analysed. Participants entered the study from 1988 to 1994, and mortality surveillance was conducted through 2006. White blood cell count and fibrinogen were dichotomized at their medians, andC‐reactive protein was divided into >3 and ≤3 g/L. The number of elevated inflammatory markers was summed to create a score of 0–3.ResultsThe age‐adjusted distribution of the number of elevated inflammatory markers differed significantly among participants with normal lung function, mildOLF, and moderate or worseOLF. Of the three dichotomized markers, only fibrinogen was significantly associated with mortality among adults with anyOLF(maximally adjusted hazard ratio 1.49; 95% confidence interval (CI): 1.17–1.91). The maximally adjusted hazard ratios for having 1, 2 or 3 elevated markers were 1.17 (95%CI: 0.71–1.94), 1.44 (95%CI: 0.89–2.32) and 2.08 (95%CI: 1.29–3.37), respectively (P = 0.003).ConclusionsAn index of elevated inflammatory markers predicted all‐cause mortality among adults withOLF.
Systematic position of the enigmatic African cycad moths: an integrative approach to a nearly century old problem (Lepidoptera: Geometridae, Diptychini)
Authors: SIHVONEN PASI , STAUDE HERMANN S. , MUTANEN MARKO 
Published: March 2015

AbstractThe systematic position and hierarchical level of the moth taxon Diptychini Janse (Lepidoptera: Geometridae), the cycad moths, has remained controversial. This is partly due to their unique morphological and biological characteristics. To study the systematics, comprehensive molecular analyses of eight genes, in total 6157 bp, were carried out. We used Bayesian inference to construct phylogenetic trees. The first analysis (46 Geometridae and 7 non‐Geometridae taxa, representing all recently recognised Geometridae subfamilies) demonstrated that the Diptychini belong to the Geometridae subfamily Ennominae. The second analysis, focused on the Ennominae (70 taxa, representing 28 of 30 recently recognised Ennominae tribes worldwide), found that the Diptychini are nested well within the Ennominae; it is monophyletic and associated with the complex of southern Hemisphere Nacophorini, refuting many of the earlier hypotheses about Diptychini relationships. The Diptychini are considered tentatively valid at the tribe level, but relationships with the Nacophorini and the Lithinini need further research. The molecular findings were evaluated from a morphological point of view, which are mostly in agreement with the molecular results. The Diptychini genera are illustrated and characterised using morphological and life‐history traits. Within the Diptychini, three genera are considered valid. Durbana Warren (described in 1904) is proposed as a junior synonym of Veniliodes Warren (described in 1894) (n.syn.). Monotypic Larentioides Prout is combined with the tribe Lithinini (n.comb.). Homonymy of Diptychini Mirza (described in 1991) (Pisces: Cyprinidae, Schizothoracinae) with Diptychini Janse (described in 1933) (Lepidoptera: Geometridae, Ennominae) is noted, the former requiring a replacement name.
Equivalences in Euler-based diagram systems through normal forms
Authors: Fish Andrew , Taylor John 
Published: March 2015

AbstractThe form of information presented can influence its utility for the conveying of knowledge by affecting an interpreter’s ability to reason with the information. There are distinct types of representational systems (for example, symbolic versus diagrammatic logics), various sub-systems (for example, propositional versus predicate logics), and even within a single representational system there may be different means of expressing the same piece of information content. Thus, to display information, choices must be made between its different representations, depending upon many factors such as: the context, the reasoning tasks to be considered, user preferences or desires (for example, for short symbolic sentences or minimal clutter within diagrammatic systems). The identification of all equivalent representations with the same information content is a sensible precursor to attempts to minimise a metric over this class. We posit that defining notions of semantic redundancy and identifying the syntactic properties that encapsulate redundancy can help in achieving the goal of completely identifying equivalences within a single notational system or across multiple systems, but that care must be taken when extending systems, since refinements of redundancy conditions may be necessary even for conservative system extensions. We demonstrate this theory within two diagrammatic systems, which are Euler-diagram-based notations. Such notations can be used to represent logical information and have applications including visualisation of database queries, social network visualisation, statistical data visualisation, and as the basis of more expressive diagrammatic logics such as constraint languages used in software specification and reasoning. The development of the new associated machinery and concepts required is important in its own right since it increases the growing body of knowledge on diagrammatic logics. In particular, we consider Euler diagrams with shading, and then we conservatively extend the system to include projections, which allow for a much greater degree of flexibility of representation. We give syntactic properties that encapsulate semantic equivalence in both systems, whilst observing that the same semantic concept of redundancy is significantly more difficult to realise as syntactic properties in the extended system with projections.
Convergent Adaptation in the Dominant Global Hospital Clone ST239 of Methicillin-Resistant Staphylococcus aureus
Authors: Baines Sarah L. , Holt Kathryn E. , Schultz Mark B. , Seemann Torsten , Howden Brian O. , Jensen Slade O. , van Hal Sebastiaan J. , Coombs Geoffrey W. , Firth Neville , Powell David R. , Stinear Timothy P. , Howden Benjamin P. 
Published: March 2015

ABSTRACT

Infections caused by highly successful clones of hospital-associated methicillin-resistant
Staphylococcus aureus
(HA-MRSA) are a major public health burden. The globally dominant sequence type 239 (ST239) HA-MRSA clone has persisted in the health care setting for decades, but the basis of its success has not been identified. Taking a collection of 123 ST239 isolates spanning 32 years, we have used population-based functional genomics to investigate the evolution of this highly persistent and successful clone. Phylogenetic reconstruction and population modeling uncovered a previously unrecognized distinct clade of ST239 that was introduced into Australia from Asia and has perpetuated the epidemic in this region. Functional analysis demonstrated attenuated virulence and enhanced resistance to last-line antimicrobials, the result of two different phenomena, adaptive evolution within the original Australian ST239 clade and the introduction of a new clade displaying shifts in both phenotypes. The genetic diversity between the clades allowed us to employ genome-wide association testing and identify mutations in other essential regulatory systems, including
walKR
, that significantly associate with and may explain these key phenotypes. The phenotypic convergence of two independently evolving ST239 clades highlights the very strong selective pressures acting on HA-MRSA, showing that hospital environments have favored the accumulation of mutations in essential MRSA genes that increase resistance to antimicrobials, attenuate virulence, and promote persistence in the health care environment. Combinations of comparative genomics and careful phenotypic measurements of longitudinal collections of clinical isolates are giving us the knowledge to intelligently address the impact of current and future antibiotic usage policies and practices on hospital pathogens globally.

IMPORTANCE
Methicillin-resistant
Staphylococcus aureus
(MRSA) is responsible for innumerable drug-resistant health care-associated infections globally. This study, the first to investigate the evolutionary response of hospital-associated MRSA (HA-MRSA) over many decades, demonstrates how MRSA can persist in a region through the reintroduction of a previously unrecognized distinct clade. This study also demonstrates the crucial adaptive responses of HA-MRSA to the highly selective environment of the health care system, the evolution of MRSA isolates to even higher levels of antibiotic resistance at the cost of attenuated virulence. However,
in vivo
persistence is maintained, resulting in a clone of HA-MRSA able to resist almost all antimicrobial agents and still cause invasive disease in the heavily compromised hosts found in modern health care settings.