bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fire and grazing controlling a tropical tree line: Effects of long‐term grazing exclusion in Bale Mountains, Ethiopia
Authors: Johansson Maria Ulrika , Granström Anders 
Published: May 2020

AbstractAimsTropical tree lines are often associated with abrupt shifts in vegetation, soils and disturbance regimes, but the underlying mechanisms are poorly understood. We analysed the role of grazing, fuels and fire in maintaining a sharp tree line with flammable heathland above non‐flammable forest.LocationBale Mountains, Ethiopia.MethodsThe study used grazing exclosures, repeated vegetation sampling, soil analyses and burning and sowing experiments along an altitudinal gradient with Hagenia abyssinica forest, Erica trimera forest and Erica heathland; all were heavily grazed, the Erica heathland also burnt on short rotation.ResultsContrary to expectation, livestock exclusion did not increase flammability in the forest, but instead resulted in a dense carpet of non‐flammable herbs. In the heathland, livestock exclusion led to somewhat faster post‐fire fuel recovery, but no major change in vegetation. Seeding of tree species resulted in some seedling establishment, but notably Hagenia grew poorly in the heathland, even when protected from livestock. A bioassay, as well as observations of outpost trees on atypical soil above the tree line, suggests that this poor growth is caused by the acidic soils, rather than harsh climate. Despite frequent fires, heathland soils had lower pH and higher organic matter content than forest soils. Below the tree line, tree seedling establishment was successful only in forest gaps, and if livestock was excluded. In both forest and heathland rapid vegetative regeneration in the ground flora after disturbance restricted major species shifts.ConclusionsThese results suggest that the contrasting fire potential between heathland and forest, and thus the sharp tree line would be maintained, or possibly even accentuated, in the absence of livestock grazing, and that Hagenia colonization upwards into the heathland is restricted not only by fire and grazing, but also the acidic soils, which is a legacy of centuries of dominance by Erica.
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap
Authors: Cordier Tristan , Alonso‐Sáez Laura , Apothéloz‐Perret‐Gentil Laure , Aylagas Eva , Bohan David A. , Bouchez Agnès , Chariton Anthony , Creer Simon , Frühe Larissa , Keck François , Keeley Nigel , Laroche Olivier , Leese Florian , Pochon Xavier , Stoeck Thorsten , Pawlowski Jan , Lanzén Anders 
Published: May 2020

AbstractA decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end‐users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics‐based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy‐based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Low level of antifungal resistance of Candida glabrata blood isolates in Turkey: Fluconazole minimum inhibitory concentration and FKS mutations can predict therapeutic failure
Authors: Arastehfar Amir , Daneshnia Farnaz , Salehi Mohammadreza , Yaşar Melike , Hoşbul Tuğrul , Ilkit Macit , Pan Weihua , Hagen Ferry , Arslan Nazlı , Türk‐Dağı Hatice , Hilmioğlu‐Polat Süleyha , Perlin David S. , Lass‐Flörl Cornelia 
Published: May 2020

AbstractBackgroundCandida glabrata is the third leading cause of candidaemia in Turkey; however, the data regarding antifungal resistance mechanisms and genotypic diversity in association with their clinical implication are limited.ObjectivesTo assess genotypic diversity, antifungal susceptibility and mechanisms of drug resistance of C glabrata blood isolates and their association with patients' outcome in a retrospective multicentre study.Patients/MethodsIsolates from 107 patients were identified by ITS sequencing and analysed by multilocus microsatellite typing, antifungal susceptibility testing, and sequencing of PDR1 and FKS1/2 hotspots (HSs).ResultsCandida glabrata prevalence in Ege University Hospital was twofold higher in 2014‐2019 than in 2005‐2014. Six of the analysed isolates had fluconazole MICs ≥ 32 µg/mL; of them, five harboured unique PDR1 mutations. Although echinocandin resistance was not detected, three isolates had mutations in HS1‐Fks1 (S629T, n = 1) and HS1‐Fks2 (S663P, n = 2); one of the latter was also fluconazole‐resistant. All patients infected with isolates carrying HS‐FKS mutations and/or demonstrating fluconazole MIC ≥ 32 µg/mL (except one without clinical data) showed therapeutic failure (TF) with echinocandin and fluconazole; seven such isolates were collected in Ege (n = 4) and Gulhane (n = 3) hospitals and six detected recently. Among 34 identified genotypes, none were associated with mortality or enriched for fluconazole‐resistant isolates.ConclusionAntifungal susceptibility testing should be supplemented with HS‐FKS sequencing to predict TF for echinocandins, whereas fluconazole MIC ≥ 32 µg/mL may predict TF. Recent emergence of C glabrata isolates associated with antifungal TF warrants future comprehensive prospective studies in Turkey.
Effect of CYP2C19 polymorphism on the plasma voriconazole concentration and voriconazole‐to‐voriconazole‐N‐oxide concentration ratio in elderly patients
Authors: Shang Shenglan , Cheng Lin , Li Xiaoyu , Xiang Rongfeng , Yu Mingjie , Xiong Lirong , Chen Yongchuan 
Published: May 2020

AbstractBackgroundEffects of CYP2C19 polymorphism on voriconazole concentration (C0), dose‐adjusted trough concentrations (C0/dose) and voriconazole‐to‐voriconazole‐N‐oxide concentration ratio (C0/CN) have not been fully investigated.ObjectivesTo investigate correlations of CYP2C19 polymorphisms with plasma concentrations of voriconazole and the major metabolite voriconazole‐N‐oxide in elderly patients.MethodsA prospective, multi‐centre, non‐intervention, open clinical study was conducted within Southwestern Chinese patients clinically diagnosed with invasive fungal infections, to investigate the associations of CYP2C19∗2 (681G > A), CYP2C19∗3 (636G > A) and CYP2C19∗17 (−806C > T) genetic polymorphisms with voriconazole C0, C0/dose and C0/CN.ResultsThe study included 131 adult patients, of which 72 were elderly (≥60 years) and 59 were adults (<60 years). The allele frequencies of CYP2C19∗2, ∗3 and ∗17 in the elderly cohort were 61.1%, 29.9% and 7.6%, respectively, which were similar to those in the adult cohort (66.9%, 29.7% and 2.5%, respectively; P > .05). The median voriconazole C0 (C0), C0/dose and C0/CN ratio in patients with the CYP2C19∗1/∗2 and CYP2C19∗2/∗2 genotypes were significantly higher than those in patients with the CYP2C19∗1/∗1 genotype in the adult cohort (P < .05). The C0 and C0/dose in patients with the CYP2C19∗1/∗3 and CYP2C19∗2/∗2 genotypes, and the C0/CN ratio for patients with the CYP2C19∗1/∗2 genotype were numerically higher than those in patients with the CYP2C19∗1/∗1 genotype in the elderly cohort, but this difference was not statistically significant (P > 0.05). The C0, C0/dose and C0/CN in patients with poor metaboliser phenotypes were higher than in those with normal metaboliser phenotypes and C0 in patients with intermediate metaboliser phenotypes were significantly higher than in those with normal metaboliser phenotypes in the adult cohort (P < .05). However, there were no significant differences in the C0, C0/dose and C0/CN among different CYP2C19‐predicted metabolic phenotypes in the elderly cohort.ConclusionsVoriconazole C0, C0/dose and C0/CN ratio are not significantly affected by the CYP2C19∗2/∗3 polymorphisms in the elderly patients.
Aquinas’ Fifth Way
Authors: Owens John 
Published: May 2020

AbstractAquinas’ fifth way for demonstrating the existence of God shows a confidence in its argument that is not generally shared by the contemporary reader. Natural entities that lack awareness (or perhaps self-awareness) act in an end-directed manner; this implies a fundamental relation to goals they do not consciously choose; this in turn points to the existence of a governing mind. The article tries to make sense of this argument against the background of philosophical naturalism that is assumed by much contemporary thought. It addresses the question of what kinds of end-directed activity fall under the scope of the argument, and why Aquinas thinks that these imply a governing mind. The article notes the unusual structure of the argument, suggesting that it should be understood (as should all of the five ways) as an attempt to wake the reader up to something so fundamental that it is usually overlooked. The main difficulty for the contemporary reader is to recover an Aristotelian sense of what it means for something to exist. If readers can achieve this, they may come to appreciate why an argument that seems enormously controversial in the present day seemed reasonably obvious to Aquinas.
Re-thinking Truth: Assessing Heidegger's critique of Aquinas in light of Vallicella's critique of Heidegger
Authors: Lyonhart Jonathan 
Published: May 2020

AbstractIn this paper I argue that Heidegger's critique of Aquinas on truth must be seen in light of Vallicella's critique of Heidegger. Heidegger criticized Aquinas for allegedly placing truth in the ‘subjectivity’ of the human mind via correspondence (adequatio). While the accuracy of this reading of Aquinas is highly contested, the criticism itself has sometimes been turned back upon Heidegger. In three forgotten articles in the 1980s, William Vallicella contended that Heidegger reduces Being to truth, and truth to the alleged ‘subjectivity’ of Dasein. Though Vallicella garnered some minimal attention at the time, his argument was soon forgotten, along with its potential implications for Heidegger's criticism of Aquinas. This paper will first establish the nature of Heidegger's critique of Aquinas, followed by Vallicella's critique of Heidegger, evaluating the former in light of the latter. It will be shown that Heidegger critiques Thomas for a mistake he does not make, then makes that same mistake himself, only to retreat to a position similar to what Thomas actually holds, but in a way that solves nothing, for he lacks Thomas’ anchor in a divine mind. These points will coalesce in the ultimate conclusion that Vallicella can be used to both undermine Heidegger's critique and undergird the value of Aquinas’ position on truth.
“Liturgy as a Practical Cosmology: Jenkins and Lonergan in Conversation”
Authors: Briola Lucas 
Published: May 2020

AbstractThis article introduces Bernard Lonergan to environmental ethics through a conversation with Willis Jenkins. Jenkins represents a ripe dialogue partner for Lonergan because of his attentiveness to methodological questions within environmental ethics, as in his incisive critique of Lynn White's influence. To pursue this conversation, this article examines Jenkins's critique of White and then turns to Lonergan's thought to supplement and refine this critique. From this engagement, the article identifies the need for a “practical cosmology”: an ongoing Christian practice that can affectively motivate care for creation. It proposes that the Christian liturgy, through its rich symbolism and distinct cosmology, offers one such practice and thus can weave that care seamlessly within Christian identity. To test this conclusion, the article briefly considers the import of this conversation for contemporary ecclesial responses to the ecological crisis, such as in Laudato si’.
The atoms of self‐control
Authors: Sripada Chandra 
Published: May 2020

AbstractPhilosophers routinely invoke self‐control in their theorizing, but major questions remain about what exactly self‐control is. I propose a componential account in which an exercise of self‐control is built out of something more fundamental: basic intrapsychic actions called cognitive control actions. Cognitive control regulates simple, brief states called response pulses that operate across diverse psychological systems (think of one's attention being grabbed by a salient object or one's mind being pulled to think about a certain topic). Self‐control ostensibly seems quite different because it regulates complex, temporally extended states such as emotions and cravings. But critically, these complex states also exhibit important componential structure: They rely on response pulses as a key means by which they bring about action. The overall picture is that self‐control consists of skilled sequences of cognitive control directed against extended streams of response pulses that arise from states such as emotions and cravings, thus preventing these states from being effective in action. The account clarifies the “atoms” of self‐control—the elemental units that get combined in complex ways to produce different kinds of self‐control actions. Surprisingly, the account, which is derived from research in cognitive science, aligns nicely with the commonsense conception of self‐control.
The m6A reader ECT2 post‐transcriptionally regulates proteasome activity in Arabidopsis
Authors: Wu Jian , Peled‐Zehavi Hadas , Galili Gad 
Published: May 2020

Summary

Methylation of internal adenosine at nitrogen‐6 position (m6A) is the most abundant post‐transcriptional modification in eukaryotic RNAs. These modifications are recognized by m6A‐binding proteins (‘readers’) that affect downstream functions. In plants, the scope of gene expression regulation by reader proteins is not clear.

Here, overexpression and loss‐of‐function mutants were used to characterize the role of the Arabidopsis m6A reader ECT2 in proteasome regulation.

ECT2 regulates the mRNA levels of the proteasome regulator PTRE1 and of several 20S proteasome subunits, resulting in enhanced 26S proteasome activity. This regulation is dependent on ECT2 m6A binding function. Interestingly, though ECT2 positively regulates proteasome activity in both young and mature plants, PTRE1 has different regulatory effects in different developmental stages. In mature plants, PTRE1 inhibits 26S proteasome activity, while in seedlings PTRE1 knockout mutants have reduced 26S proteasome activity.

Taken together, our results suggest a novel epitranscriptomic mechanism of proteasome regulation by ECT2 that is used to fine tune proteasome activity by affecting the expression of PTRE1 and 20S proteasome subunits.
Diel‐ and temperature‐driven variation of leaf dark respiration rates and metabolite levels in rice
Authors: Rashid Fatimah Azzahra Ahmad , Scafaro Andrew P. , Asao Shinichi , Fenske Ricarda , Dewar Roderick C. , Masle Josette , Taylor Nicolas L. , Atkin Owen K. 
Published: May 2020

SummaryLeaf respiration in the dark (Rdark) is often measured at a single time during the day, with hot‐acclimation loweringRdarkat a common measuring temperature. However, it is unclear whether the diel cycle influences the extent of thermal acclimation ofRdark, or how temperature and time of day interact to influence respiratory metabolites.To examine these issues, we grew rice under 25°C : 20°C, 30°C : 25°C and 40°C : 35°C day : night cycles, measuringRdarkand changes in metabolites at five time points spanning a single 24‐h period.Rdarkdiffered among the treatments and with time of day. However, there was no significant interaction between time and growth temperature, indicating that the diel cycle does not alter thermal acclimation ofRdark. Amino acids were highly responsive to the diel cycle and growth temperature, and many were negatively correlated with carbohydrates and with organic acids of the tricarboxylic acid (TCA) cycle. Organic TCA intermediates were significantly altered by the diel cycle irrespective of growth temperature, which we attributed to light‐dependent regulatory control of TCA enzyme activities.Collectively, our study shows that environmental disruption of the balance between respiratory substrate supply and demand is corrected for by shifts in TCA‐dependent metabolites.
E‐Cigarette and palatal ulcer: a possible relationship?
Authors: Tsiouma O. , Andreou A. , Sklavounou‐Andrikopoulou A. 
Published: May 2020

AbstractTobacco smoking is a major public health issue with far‐reaching implications on the global economy. Electronic cigarettes are advertised as a new promising cessation treatment that can gratify the behavioural aspects of smoking. However, there are still many unanswered questions regarding e‐cigarette’s safety and effects on general and oral health. We report a case of a 68‐year‐old Caucasian male patient with a large ulcerative lesion on the hard palate that was possibly associated with the use of an electronic cigarette.
Insulin‐like Growth Factor‐1 Impacts p53 Target Gene Induction in UVB‐irradiated Keratinocytes and Human Skin
Authors: Alkawar Abdulrahman M.M. , Castellanos Amber J. , Carpenter Mae Alexandra , Hutcherson Rebekah J. , Madkhali Mariyyah A.O. , Johnson Ron Michael , Bottomley Michael , Kemp Michael G. 
Published: May 2020

AbstractThe tumor suppressor protein p53 limits mutagenesis in response to ultraviolet‐B (UVB) light exposure by activating the transcription of genes that mitigate the damaging effects of UVB radiation on DNA. Because most nonmelanoma skin cancers (NMSCs) occur in older individuals, it is important to understand the process of mutagenesis in the geriatric skin microenvironment. Based on previous studies demonstrating that geriatric skin expresses lower levels of the growth factor insulin‐like growth factor‐1 (IGF‐1) than young adult skin, a role for IGF‐1 in the regulation of p53 target genes was investigated in both human keratinocytes in vitro and human skin explants ex vivo. The products of the p53 target genes p21 and DNA polymerase eta (pol η) were found to be increased by UVB exposure in both experimental systems, and this induction was observed to be partially abrogated by depriving keratinocytes of IGF‐1 in vitro or by the treatment of keratinocytes in vitro and human skin explants with an IGF‐1 receptor antagonist. Because p21 and pol η function to limit mutagenic DNA replication following UVB exposure, these results suggest that NMSC risk in geriatric populations may be due to age‐dependent decreases in IGF‐1 signaling that disrupt p53 function in the skin.
Luminescence Activity Decreases When v‐coelenterazine Replaces Coelenterazine in Calcium‐Regulated Photoprotein—A Theoretical and Experimental Study
Authors: Ding Bo‐Wen , Eremeeva Elena V. , Vysotski Eugene S. , Liu Ya‐Jun 
Published: May 2020

AbstractCalcium‐regulated photoproteins are found in at least five phyla of organisms. The light emitted by those photoproteins can be tuned by mutating the photoprotein and/or by modifying the substrate coelenterazine (CTZ). Thirty years ago, Shimomura observed that the luminescence activity of aequorin was dramatically reduced when the substrate CTZ was replaced by its analog v‐CTZ. The latter is formed by adding a phenyl ring to the π‐conjugated moiety of CTZ. The decrease in luminescence activity has not been understood until now. In this paper, through combined quantum mechanics and molecular mechanics calculations as well as molecular dynamics simulations, we discovered the reason for this observation. Modification of the substrate changes the conformation of nearby aromatic residues and enhances the π‐π stacking interactions between the conjugated moiety of v‐CTZ and the residues, which weakens the charge transfer to form light emitter and leads to a lower luminescence activity. The microenvironments of CTZ in obelin and in aequorin are very similar, so we predicted that the luminescence activity of obelin will also dramatically decrease when CTZ is replaced by v‐CTZ. This prediction has received strong evidence from currently theoretical calculations and has been verified by experiments.
Purified Splenic amastigotes of Leishmania donovani‐Immunoproteomic approach for exploring Th1 stimulatory polyproteins
Authors: Misra Pragya , Tandon Rati , Basak Trayambak , Sengupta Shantanu , Dube Anuradha 
Published: May 2020

AbstractVisceral leishmaniasis (VL) represents one of the most challenging infectious diseases worldwide. The reason that once infected, patient develops immunity against Leishmania parasite has paved way to develop prophylactic vaccines against disease, but only some of these have moved ahead for clinical trials. Herein, the study to explore novel and potential vaccine candidates was extended to pathogenic form of parasite, that is, amastigote form which is less explored due to complexity of its purification process. Methods and results. Classical protocol of purification of splenic amastigotes was modified to obtain highly pure amastigotes which was confirmed by Western blotting in support with proteomics studies. Fractionation and sub‐fractionation of purified splenic amastigotes revealed four sub‐fractions, belonging to 97 to 68 kDa and 68 to 43 kDa ranges, which showed long‐lasting protection with remarkable Th1‐type cellular responses in hamsters vaccinated with these sub‐fractions (LTT, NO, QRT‐PCR). Further proteomics analysis, to identify and understand the precise nature and function of these protective protein sub‐fractions, identified a total of 47 proteins including twenty‐five hypothetical proteins/unknowns. Amastigote stage has potential Th1‐stimulatory vaccine candidates, notably, among identified proteins, major were uncharacterized proteins/hypothetical proteins, which once characterized may serve as novel and potential vaccine candidates/drug targets.