bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of asexual and sexual reproduction in the aspergilli
Authors: Ojeda-López M. , Chen W. , Eagle C.E. , Gutiérrez G. , Jia W.L. , Swilaiman S.S. , Huang Z. , Park H.-S. , Yu J.-H. , Cánovas D. , Dyer P.S. 
Published: October 2018

Aspergillus nidulanshas long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genusAspergillus, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings fromAspergillus, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction inA. nidulanswas investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in thePezizomycotina(e.g.AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (e.g.BrlA) had a more restricted distribution solely in theEurotiomycetes, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of thePezizomycotina. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of theA. nidulans abaAgene inMonascus ruberfailed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of theSaccharomycotinasupports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in thePezizomycotina. Investigations were also made into the evolution of sex and sexuality in the aspergilli.MATloci were identified from the heterothallicAspergillus(Emericella)heterothallicusandAspergillus(Neosartorya)fennelliaeand the homothallicAspergillus pseudoglaucus(=Eurotium repens). A consistent architecture of theMATlocus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement ofMATloci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made usingA. clavatusas a representative ‘asexual’ species. It was possible to induce a sexual cycle inA. clavatusgiven the correctMAT1-1andMAT1-2partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexual reproduction might be possible in many supposedly asexual aspergilli and beyond, providing general insights into the nature of asexuality in fungi.
Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance
Authors: Emri T. , Antal K. , Riley R. , Karányi Z. , Miskei M. , Orosz E. , Baker S.E. , Wiebenga A. , de Vries R.P. , Pócsi I. 
Published: October 2018

The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based onSaccharomyces cerevisiae,Schizosaccharomyces pombeandAspergillus nidulans. Although both yeast-based andA. nidulans-based models were suitable to trace evolutionary changes, theA. nidulans-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in theA. nidulans-based orS. cerevisiae-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O<inf>2</inf>-oxidoreductase, elements of the reductive iron assimilation pathway, in theS. cerevisiae-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in theA. nidulans-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H<inf>2</inf>O<inf>2</inf>-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H<inf>2</inf>O<inf>2</inf> induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.
The root-symbiotic Rhizoscyphus ericae aggregate and Hyaloscypha (Leotiomycetes) are congeneric: Phylogenetic and experimental evidence
Authors: Fehrer J. , Réblová M. , Bambasová V. , Vohník M. 
Published: October 2018

Data mining for a phylogenetic study including the prominent ericoid mycorrhizal fungus Rhizoscyphus ericae revealed nearly identical ITS sequences of the bryophilous Hyaloscypha hepaticicola suggesting they are conspecific. Additional genetic markers and a broader taxonomic
sampling furthermore suggested that the sexual Hyaloscypha and the asexual Meliniomyces may be congeneric. In order to further elucidate these issues, type strains of all species traditionally treated as members of the Rhizoscyphus ericae aggregate (REA) and related taxa
were subjected to phylogenetic analyses based on ITS, nrLSU, mtSSU, and rpb2 markers to produce comparable datasets while an in vitro re-synthesis experiment was conducted to examine the root-symbiotic potential of H. hepaticicola in the Ericaceae. Phylogenetic
evidence demonstrates that sterile root-associated Meliniomyces, sexual Hyaloscypha and Rhizoscyphus, based on R. ericae, are indeed congeneric. To this monophylum also belongs the phialidic dematiaceous hyphomycetes Cadophora finlandica and Chloridium
paucisporum. We provide a taxonomic revision of the REA; Meliniomyces and Rhizoscyphus are reduced to synonymy under Hyaloscypha. Pseudaegerita, typified by P. corticalis, an asexual morph of H. spiralis which is a core member of Hyaloscypha,
is also transferred to the synonymy of the latter genus. Hyaloscypha melinii is introduced as a new root-symbiotic species from Central Europe. Cadophora finlandica and C. paucisporum are confirmed conspecific, and four new combinations in Hyaloscypha are proposed.
Based on phylogenetic analyses, some sexually reproducing species can be attributed to their asexual counterparts for the first time whereas the majority is so far known only in the sexual or asexual state. Hyaloscypha bicolor sporulating in vitro is reported for the first
time. Surprisingly, the mycological and mycorrhizal sides of the same coin have never been formally associated, mainly because the sexual and asexual morphs of these fungi have been studied in isolation by different research communities. Evaluating all these aspects allowed us to stabilize
the taxonomy of a widespread and ecologically well-studied group of root-associated fungi and to link their various life-styles including saprobes, bryophilous fungi, root endophytes as well as fungi forming ericoid mycorrhizae and ectomycorrhizae.
Late Pleistocene records of speleothem stable isotopic compositions from Pinnacle Point on the South African south coast
Authors: Braun Kerstin , Bar-Matthews Miryam , Matthews Alan , Ayalon Avner , Cowling Richard M. , Karkanas Panagiotis , Fisher Erich C. , Dyez Kelsey , Zilberman Tami , Marean Curtis W. 
Published: October 2018

AbstractHighly resolved, well-dated paleoclimate records from the southern South African coast are needed to contextualize the evolution of the highly diverse extratropical plant communities of the Greater Cape Floristic Region (GCFR) and to assess the environmental impacts on early human hunter-gatherers. We present new speleothem stable oxygen and carbon isotope ratios (δ18Oc and δ13C) from two caves at Pinnacle Point, South Africa, covering the time between 330 and 43 ka. Composite δ18Oc and δ13C records were constructed for Staircase Cave and PP29 by combining all stable isotope analyses into a single time series and smoothing by a 3-point running mean. δ18Oc and δ13C values record changes in rainfall seasonality and the proportions of C3 and C4 plants in the vegetation, respectively. We show that in general increased summer rainfall brought about a wider spread of C4 grasses and retreat of the C3 plant–dominated GCFR communities. The occurrence of summer rainfall on the southern coast of South Africa was linked to total rainfall amounts in the interior region through tropical temperate troughs. These rainfall systems shifted the southern coastal climate toward more summer (winter) rainfall when precession was high (low) and/or the westerlies were in a northern (southern) position.
Hypocalcaemia following laryngectomy: prevalence and risk factors
Authors: Harris A S , Prades E , Passant C D , Ingrams D R 
Published: October 2018

AbstractObjectivesTo establish the prevalence of hypocalcaemia following laryngectomy and demonstrate that total thyroidectomy is a risk factor.MethodsA retrospective cohort study was conducted that included all patients who underwent total laryngectomy from 1st January 2006 to 1st August 2017. Exclusion criteria were: pre-operative calcium derangement, previous thyroid or parathyroid surgery, concurrent glossectomy, pharyngectomy, or oesophagectomy.ResultsNinety patients were included. Sixteen patients had early hypocalcaemia (18 per cent), seven had protracted hypocalcaemia (8 per cent) and six had permanent hypocalcaemia (10 per cent). Exact logistic regression values for hypocalcaemia following total thyroidectomy compared to other patients were: early hypocalcaemia, odds ratio = 15.5 (95 per cent confidence interval = 2.2–181.9; model p = 0.002); protracted hypocalcaemia, odds ratio = 13.3 (95 per cent confidence interval = 1.5–117.1; model p = 0.01); and permanent hypocalcaemia, odds ratio = 22.7 (95 per cent confidence interval = 1.9–376.5; model p = 0.005).ConclusionThis is the largest study to investigate the prevalence of hypocalcaemia following laryngectomy and the first to include follow up of longer than three months. Total thyroidectomy significantly increased the risk of hypocalcaemia at all time frames and independent of other variables.
Carotid Stenting without Angioplasty
Authors: Men S. , Lownie S.P. , Pelz D.M. 
Published: October 2018

Abstract:Background:Carotid angioplasty and stenting is gaining popularity as an alternative to carotid endarterectomy for the treatment of carotid bifurcation stenosis. The major concern with the procedure is the risk of embolic stroke which may be initiated by balloon angioplasty of friable atherosclerotic plaque. Elimination of angioplasty may result in a lower incidence of embolic complications.Method:We describe a case in which a self-expanding stent alone, without balloon angioplasty, was used to successfully dilate an atherosclerotic stenosis of the carotid bifurcation.Results:A moderate increase in vessel diameter, from 75% to 50%, was immediately observed after stent placement alone. No embolic complications were observed and follow-up plain film and ultrasound examinations showed progressive stent enlargement with excellent anatomic and hemodynamic results.Conclusions:In this case of severe carotid stenosis, the use of a self-expanding stent alone, without balloon angioplasty, resulted in excellent anatomic and hemodynamic improvement.
Cavernous Malformation of the Hypoglossal Nerve: Case Report and Review of the Literature
Authors: Chow Michael , Addas Bassam , Sangalang Virgilio , Holness Renn 
Published: October 2018

Abstract:Objective:To describe a patient who presented with a hypoglossal nerve palsy caused by a cavernous malformation, review the literature on cavernous malformations associated with cranial nerves and the differential diagnosis of hypoglossal palsy.Results:Partial resection of the lesion was achieved and the diagnosis of cavernous malformation proven histologically.Conclusions:Involvement of a cranial nerve by a cavernous malformation is very uncommon and the facial nerve is the example most frequently reported. This case report adds another possible site for this rare occurrence.
Successful switching of patients with acute schizophrenia from another antipsychotic to brexpiprazole: comparison of clinicians’ choice of cross-titration schedules in a post hoc analysis of a randomized, double-blind, maintenance treatment study
Authors: Correll Christoph U. , Shi Lily , Weiss Catherine , Hobart Mary , Eramo Anna , Duffy Ruth A. , Weiller Emmanuelle , Baker Ross A. 
Published: October 2018

ObjectiveTo compare the tolerability and efficacy of different antipsychotic cross-titration schedules, using data from a brexpiprazole study (Equator; NCT01668797).MethodsPatients with schizophrenia were cross-titrated from other antipsychotics to brexpiprazole monotherapy in a 1–4 week open-label conversion phase, then entered a single-blind brexpiprazole treatment phase. Patients were stratified into four “conversion groups,” according to the amount of time spent in the conversion phase. Discontinuation rates, treatment-emergent adverse events (TEAEs), and efficacy (Positive and Negative Syndrome Scale [PANSS]) were compared between conversion groups.ResultsOf the 404 patients treated with brexpiprazole, the majority (72.0%) spent 22–33 days in the conversion phase. Discontinuation rates due to lack of efficacy or adverse events were low in all conversion groups. Of the 292 patients who successfully switched and completed 8 weeks of brexpiprazole treatment, most were converted to brexpiprazole over 22–33 days (80.1%), and fewer were converted over 1–7 days (2.4%), 8–14 days (6.5%), or 15–21 days (11.0%). The incidence of TEAEs over 8 weeks was lower among those converted over 22–33 days (44.4%) than in other conversion groups (62.5–84.2%), although low patient numbers with shorter conversion times limit the generalizability of this finding. Each conversion group showed comparable improvement in PANSS total score from baseline.ConclusionThe majority of patients were cross-titrated to brexpiprazole over a period of 22–33 days, by investigators’ choice. Additional data on shorter conversions may help clinicians to choose a switching paradigm that best meets their patients’ needs.
Supplemental Nutrition Assistance Program participation and racial/ethnic disparities in food and beverage purchases
Authors: Grummon Anna H , Taillie Lindsey Smith 
Published: October 2018

AbstractObjectiveThe current study aimed to (i) describe racial/ethnic disparities in household food and beverage purchases among participants and non-participants in the Supplemental Nutrition Assistance Program (SNAP) and (ii) examine longitudinal associations between SNAP participation and purchases by race/ethnicity.DesignTo describe disparities, we estimated sociodemographic-adjusted mean purchases of seven unhealthy food and beverage groups (e.g. junk food, sugar-sweetened beverages) and four nutrients (e.g. sugar, Na) among white, black and Hispanic SNAP-participating and non-participating households. To examine longitudinal associations, we used multivariable linear regression with household fixed effects.SettingUSA, 2010–2014.SubjectsFood and beverage purchases among low-income (≤250 % federal poverty line) US households (n30 403) participating in the Nielsen Homescan Panel.ResultsAmong non-participants, there were significant black–white disparities (i.e. differences favouring white households) in households’ adjusted mean purchases of processed meat, sweeteners, sugar-sweetened beverages, energy and Na. These disparities persisted among SNAP participants. In contrast, the only significant Hispanic–white disparity among non-participants was for Na purchases; this disparity was reduced in magnitude and no longer significant among SNAP-participating households. Additionally, Hispanic households purchased less energy from junk foods than white households, regardless of SNAP status. In longitudinal models accounting for household fixed effects, SNAP participation was associated with increased energy purchased among black households. No other significant longitudinal associations between SNAP and purchase outcomes were observed.ConclusionsSNAP may not be meeting its potential to improve food and beverage purchases or reduce disparities. Research is needed to identify strategies for ensuring nutritious purchases across all racial/ethnic groups.
A Poroelastic Model of Serpentinization: Exploring the Interplay Between Rheology, Surface Energy, Reaction, and Fluid Flow
Authors: Evans Owen , Spiegelman Marc , Kelemen Peter B. 
Published: October 2018

AbstractThe interactions between reactive fluids and solids are critical in Earth dynamics. Implications of such processes are wide ranging: from earthquake physics to geologic carbon sequestration and the cycling of fluids and volatiles through subduction zones. Peridotite alteration is a common feature in many of these processes, which—despite its obvious importance—is relatively poorly understood from a geodynamical perspective. In particular, although frequently observed in nature, it is still unknown how rocks can undergo 100% hydration/carbonation. One potential explanation of this observation is the mechanism of reaction‐driven cracking: that volume changes associated with these reactions are large enough to fracture the surrounding rock, leading to a positive feedback where new reactive surfaces are exposed and fluid pathways are created. The purpose of this study is to investigate the relative roles of reaction, elastic stresses, and surface tension in alteration reactions. In this regard, we derive a system of equations describing reactive fluid flow in elastically deformable porous media, which we apply to a model of serpentinization in a subseafloor environment. The stoichiometry of the serpentinization reaction predicts net volume reduction of the multiphase system, which, according to our numerical simulations, can lead to failure in tension. We also explore a parameterization of surface energy in the model, which allows fluid to infiltrate regions of dry peridotite, significantly changing the stresses and potentially leading to growing crack fronts.
Echo of the Younger Dryas in Holocene Lake Sediments on the Tibetan Plateau
Authors: Ramisch Arne , Tjallingii Rik , Hartmann Kai , Diekmann Bernhard , Brauer Achim 
Published: October 2018

AbstractReading the sediment record in terms of past climates is challenging since linking climate change to the associated responses of sedimentary systems is not always straightforward. Here we analyze the erosional response of landscapes on the Tibetan Plateau to interglacial climate forcing. Using the theory of dynamical systems on Holocene time series of geochemical proxies, we derive a sedimentary response model that accurately simulates observed proxy variation in three lake records. The model suggests that millennial variations in sediment composition reflect a self‐organization of landscapes in response to abrupt climate change between 11.6 and 11.9 ka BP. The self‐organization is characterized by oscillations in sediment supply emerging from a feedback between physical and chemical erosion processes, with estimated response times between 3,000 to 18,000 years depending on catchment topography. The implications of our findings emphasize the need for landscape response models to decipher the paleoclimatic code in continental sediment records.
Identifying 3‐D Vortex Structures At/Around the Magnetopause Using a Tetrahedral Satellite Configuration
Authors: Cai D. , Lembège B. , Hasegawa H. , Nishikawa K.‐I. 
Published: October 2018

AbstractIdentifying vortices is the key to understanding the turbulence in plasma shear layers. This paper aims to provide general guidelines for identifying 3‐D vortex structures. Currently, no single precise definition of a vortex is universally accepted, despite the significance of vortices in fluid and plasma dynamics. Recently, various vortex identification methods using Galilean invariance have been proposed by numerous researchers. These methods are general for different fluid and plasma visualization applications. In the present paper, we describe how we have identified 105 vortex structures by applying these methods to Cluster data near the duskside of the magnetopause. Four sets of Cluster satellite magnetic field data are used to linearly approximate the magnetic field. We identify the 3‐D magnetic vortex structures by using various vortex identification criteria as follows: (i) the first criterion is Q‐criterion that defines vortices as regions in which the vorticity energy prevails over other energies; (ii) the second criterion is the λ2‐criterion that is related to the minus eigenvalue of the Hessian matrix of the pressure terms; and (iii) the third criterion called the geometrical line‐type method requires the existence of Galilean‐invariant vortex core inside the four Cluster tetrahedral regions. In reality, both Q‐ and λ2‐criteria are also related to Galilean invariance. The present analysis evidences that the geometrical line‐type method is more precise than the other two using Cluster satellite magnetic field data.