bluuebunny/crossref_metadata_2025_split huggingface dataset:
A test of community assembly rules using foliar endophytes from a tropical forest canopy
Authors: Donald Julian , Roy Mélanie , Suescun Uxue , Iribar Amaia , Manzi Sophie , Péllissier Léonie , Gaucher Philippe , Chave Jérôme 
Published: January 2020

Abstract

Community assembly theory assumes that ecological communities are spatially delimited into patches. Within these patches, coexistence results from environmental filtering, competition and immigration. Truly delineated communities exist in laboratory studies of microbial cultures in Petri dishes, yet empirical tests conducted in continuous environments often use patches defined by convention as opposed to realized boundaries.

Here we perform a test of ecological community assembly rules using foliar endophyte communities from a tropical rainforest, where leaves are considered as patches for both fungal and bacterial communities. We determined the diversity of fungal and bacterial endophytes using environmental DNA sequencing of 365 top‐canopy leaves, collected from 38 host trees belonging to 22 different species across a 4‐ha research plot. Three leaves were collected from three or more branches within each tree crown. We tested the effect of host tree species and their level of phylogenetic relatedness on community composition as well as the contribution of geographic distance between leaves to endophyte community diversity.

Endophyte diversity significantly differed across host tree species, as did community composition. Within certain endophytic orders (Xylariales, Rhizobiales) species assemblages significantly differed across host tree species, but this trend was weaker or non‐existent in other orders known to contain pathogens and saprotrophs (Polyporales, Solirubrobacterales). Phylogenetically related host tree species displayed more similar endophyte communities than expected by chance, but geographically close trees did not. Consistent with the finding of host‐specificity, nearby leaves tended to host more similar communities than distantly positioned ones.

These findings demonstrate that foliar endophytes are structured by dispersal across small spatial scales, but at the scale of the canopy they display patterns of neutral filtering, with only a small part of variation described by host tree differences. Endophyte communities thus act as a model system in evoking the rules predicted by theoretical community ecology.
Higher rates of liana regeneration after canopy fall drives species abundance patterns in central Amazonia
Authors: Rocha Elisangela X. , Schietti Juliana , Gerolamo Caian S. , Burnham Robyn J. , Nogueira Anselmo 
Published: January 2020

Abstract

In tropical rainforest, most vascular plants have some capacity to resprout, and lianas are often effective resprouters after canopy fall. However, the diversity of resprouting responses of liana species and the consequence for plant persistence are poorly understood. We hypothesized that variation in regeneration among liana species causes differences in liana species abundance in tropical rainforest through differential resprouting capacity, such that liana species with higher densities produce more resprouts after canopy falls.

We applied a manipulative field experiment investigating the effect of different levels of disturbance on the production of resprouts and adventitious roots in 10 liana species of the tribe Bignonieae (Bignoniaceae) with contrasting abundances in central Amazonia. We selected 15 individuals of each species and assigned the lianas to three distinct conditions: (a) total canopy fall with lianas severely damaged and detached from trees; (b) partial fall of lianas, without visible damage; and (c) intact lianas (control). We tested whether liana species regeneration patterns were related to species density. Liana species density was calculated using previous research on liana species distribution in 30 1‐ha plots systematically distributed in a 6 × 6 km2 grid at the Ducke Reserve.

The number of aerial resprouts produced by lianas under the total canopy fall treatment was twice that of plants under lower levels of disturbance, while the production of adventitious roots did not differ among treatments. Liana species showed different intensities of resprouting, and species with higher average densities on the forest landscape had more resprouts after the total canopy fall treatment.

Synthesis. Our results shed new light on the factors that influence liana species abundance, highlighting the role of resprouting after canopy fall and its variation among liana species. Resprouting mitigates the negative effects of canopy damage, suggesting that the impact of increased tree fall disturbances over time, which has been attributed to Amazonian forests in the literature, may increase already abundant liana species with effective resprouting capacity. We identify liana species that are more resilient to disturbance and may alter forest dynamics during climatic change.
The potential actions of angiotensin‐converting enzyme II (ACE2) activator diminazene aceturate (DIZE) in various diseases
Authors: Qaradakhi Tawar , Gadanec Laura Kate , McSweeney Kristen Renee , Tacey Alexander , Apostolopoulos Vasso , Levinger Itamar , Rimarova Kvetoslava , Egom Emmanuel E. , Rodrigo Luis , Kruzliak Peter , Kubatka Peter , Zulli Anthony 
Published: January 2020

AbstractThe renin angiotensin system (RAS) regulates fluid balance, blood pressure and maintains vascular tone. The potent vasoconstrictor angiotensin II (Ang II) produced by angiotensin‐converting enzyme (ACE) comprises the classical RAS. The non‐classical RAS involves the conversion of Ang II via ACE2 into the vasodilator Ang (1‐7) to counterbalance the effects of Ang II. Furthermore, ACE2 converts AngA into another vasodilator named alamandine. The over activation of the classical RAS (increased vasoconstriction) and depletion of the non‐classical RAS (decreased vasodilation) results in vascular dysfunction. Vascular dysfunction is the leading cause of atherosclerosis and cardiovascular disease (CVD). Additionally, local RAS is expressed in various tissues and regulates cellular functions. RAS dysregulation is involved in other several diseases such as inflammation, renal dysfunction and even cancer growth. An approach in restoring vascular dysfunction and other pathological diseases is to either increase the activity of ACE2 or reduce the effect of the classical RAS by counterbalancing Ang II effects. The antitrypanosomal agent, diminazene aceturate (DIZE), is one approach in activating ACE2. DIZE has been shown to exert beneficial effects in CVD experimental models of hypertension, myocardial infarction, type 1 diabetes and atherosclerosis. Thus, this review focuses on DIZE and its effect in several tissues such as blood vessels, cardiac, renal, immune and cancer cells.
Clinical significance of topoisomerase‐II expression in patients with advanced non‐small cell lung cancer treated with amrubicin
Authors: Sakurai Reiko , Kaira Kyoichi , Miura Yosuke , Sunaga Noriaki , Saito Ryusei , Oyama Tetsunari , Hisada Takeshi , Yamada Masanobu 
Published: January 2020

AbstractBackgroundAmrubicin chemotherapy is a treatment option for patients with non‐small cell lung cancer (NSCLC) after third‐line treatment in Japan. Although topoisomerase‐II (Topo‐II), a target of amrubicin, has been reported to be a prognostic or predictive marker for chemosensitivity and clinical outcomes in various types of malignancies, its effects in the Japanese population remain unknown.MethodsData regarding 44 patients with advanced NSCLC treated with amrubicin between April 2004 and May 2014 were retrospectively analyzed. We evaluated the expression levels of Topo‐II by immunohistochemical staining of tumor specimens obtained via biopsy or surgical resection.ResultsThe majority of enrolled patients were men (68%) with a median age of 67 (range, 43–78) years. The most common histological type was adenocarcinoma (70%). High Topo‐II expression was observed in 13 (30%) of the 44 patients. The median progression‐free survival and overall survival (OS) durations were 1.8 and 8.8 months, respectively. While there was no significant association between Topo‐II expression and progression‐free survival, patients with low Topo‐II expression had significantly longer OS than did those with high Topo‐II expression. Good performance status and low expression of Topo‐II were all significantly associated with a favorable OS.ConclusionLow expression of Topo‐II was identified as an independent prognostic factor for longer survival in patients with NSCLC receiving amrubicin, a Topo‐II inhibitor.Key pointsSignificant findings of the study
The median progression‐free survival and overall survival (OS) durations were 1.8 and 8.8 months, respectively.
While there was no significant association between Topo‐II expression and progression‐free survival, patients with low Topo‐II expression had significantly longer OS than did those with high Topo‐II expression.
Good performance status and low expression of Topo‐II were all significantly associated with a favorable OS.
What this study adds
This study is the first to assess the effects of topoisomerase‐II (Topo‐II), a target of amrubicin, as a prognostic or predictive marker for chemosensitivity and clinical outcomes in the Japanese population.
Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveys
Authors: Dillon Erin M. , Lafferty Kevin D. , McCauley Douglas J. , Bradley Darcy , Norris Richard D. , Caselle Jennifer E. , DiRenzo Graziella V. , Gardner Jonathan P. A. , O'Dea Aaron 
Published: January 2020

Abstract

It is challenging to assess long‐term trends in mobile, long‐lived and relatively rare species such as sharks. Despite ongoing declines in many coastal shark populations, conventional surveys might be too fleeting and too recent to describe population trends over decades to millennia. Placing recent shark declines into historical context should improve management efforts as well as our understanding of past ecosystem dynamics.

A new palaeoecological approach for surveying shark abundance on coral reefs is to quantify dermal denticle assemblages preserved in sediments. This approach assumes that denticle accumulation rates correlate with shark abundances. Here, we test this assumption by comparing the denticle record in surface sediments to three conventional shark survey methods at Palmyra Atoll, Line Islands, central Pacific Ocean, where shark density is high and spatially heterogeneous.

We generally found a significant positive correlation between denticle accumulation rates and shark abundances derived from underwater visual census, baited remote underwater video and hook and line surveys.

Denticle accumulation rates reflected shark abundances, suggesting that denticle assemblages can preserve a signal of time‐averaged shark abundance in low‐energy coral reef environments. We offer suggestions for applying this tool to measure shark abundance over long time‐scales in other contexts.
Does potassium iodide application following silver diamine fluoride reduce staining of tooth? A systematic review
Authors: Roberts A , Bradley J , Merkley S , Pachal T , Gopal JV , Sharma D 
Published: January 2020

AbstractObjectivesTo assess if using potassium iodide (KI) immediately after application of silver diamine fluoride (SDF) significantly reduces the staining of tooth structure.Data source and selectionFour online databases (OVID, Scopus, PubMed and Google Scholar) were searched (June 2019). Additional studies were sought through grey literature search and hand searching the reference list of included articles. All studies that analysed the effect of KI on SDF staining of tooth structure with access to full text in English language were included.Data synthesisOf the six articles included in the review, five reported stain reduction in the teeth treated with application of KI to carious tooth structure following the application of SDF while one article reported no significant beneficial effect on reducing staining, when compared to SDF alone. Of the materials selected to restore SDF + KI treated teeth, resin‐modified glass ionomer was found to produce the lightest results, followed by glass ionomer cement and composite resin. An in vivo case report also revealed some staining after six months, even with SDF + KI treatment.ConclusionsAlthough some studies reported a positive effect, insufficient evidence exists supporting a tangible clinical benefit of SDF + KI treatment on the tooth staining, mainly due to methodical variations within the current literature.
Effect of the double application of universal adhesives on the dentine bond strength after radiotherapy
Authors: Ugurlu M 
Published: January 2020

AbstractBackgroundThis study aimed to evaluate the effect of double application of universal adhesives on bond strength to dentine after ionizing radiation.MethodsOne hundred and forty caries‐free human third molars were used. Half of the teeth were irradiated (IR) (70.2 Gy). The IR and non‐IR teeth were assigned into seven groups (n = 10). Universal adhesives Single Bond Universal (3M Oral Care), Gluma Bond Universal (Heraeus Kulzer) and Prime&Bond Elect (Dentsply) were employed (following manufacturer’s instructions and double application). Two‐step self‐etch adhesive Clearfil SE Bond (Kuraray Noritake) was used as control. After composite build‐ups were bonded to mid‐coronal occlusal dentine surfaces, the specimens were stored in water (37°C/24 h) and sectioned into microspecimens. The specimens were subjected to μTBS testing (1.0 mm/min). Failure analysis was performed using stereomicroscope and scanning electron microscopy. Data were analysed with two‐way ANOVA and Tukey’s test (P = 0.05).ResultsThe radiotherapy caused reduction in the bond strength of universal adhesives when the adhesives were used with single application after radiotherapy (P < 0.05). The double application resulted in increased bond strength of the universal adhesives to IR dentine (P < 0.05).ConclusionsThe double application was beneficial in improving the dentine bond strength of universal adhesives affected by radiotherapy after ionizing radiation.
Identification of a major locus determining a pigmentation defect in cultivated gilthead seabream (Sparus aurata)
Authors: Bertolini F. , Ribani A. , Capoccioni F. , Buttazzoni L. , Utzeri V. J. , Bovo S. , Schiavo G. , Caggiano M. , Fontanesi L. , Rothschild M. F. 
Published: January 2020

SummaryThe gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole‐genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S. aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non‐pigmented fish collected among the offspring of the same broodstock nucleus. Whole‐genome resequencing reads from the two DNA pools were aligned to the S. aurata draft genome and variant calling was performed. A whole‐genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5 Mbp on chromosome 6 in the non‐pigmented pool that was not present in the normally coloured pool. The comparison of the non‐pigmented with the normally coloured fish using a whole‐genome FST analysis detected three main regions within the coordinates previously detected with the heterozygosity analysis. The results support the presence of a major locus affecting this discoloration defect in this fish population. The results of this study have practical applications, including the possibility of eliminating this defect from the breeding stock, with direct economic advantages derived from the reduction of discarded fry. Other studies are needed to identify the candidate gene and the causative mutation, which could add information to understand the complex biology of fish pigmentation.
Identification of potential functional variants underlying ovine resistance to gastrointestinal nematode infection by using RNA‐Seq
Authors: Chitneedi P. K. , Arranz J. J. , Suárez‐Vega A. , Martínez‐Valladares M. , Gutiérrez‐Gil B. 
Published: January 2020

SummaryIn dairy sheep flocks from Mediterranean countries, replacement and adult ewes are the animals most affected by gastrointestinal nematode (GIN) infections. In this study, we have exploited the information derived from an RNA‐Seq experiment with the aim of identifying potential causal mutations related to GIN resistance in sheep. Considering the RNA‐Seq samples from 12 ewes previously classified as six resistant and six susceptible animals to experimental infection by Teladorsagia circumcincta, we performed a variant calling analysis pipeline using two different types of software, gatk version 3.7 and Samtools version 1.4. The variants commonly identified by the two packages (high‐quality variants) within two types of target regions – (i) QTL regions previously reported in sheep for parasite resistance based on SNP‐chip or sequencing technology studies and (ii) functional candidate genes selected from gene expression studies related to GIN resistance in sheep – were further characterised to identify mutations with a potential functional impact. Among the genes harbouring these potential functional variants (930 and 553 respectively for the two types of regions), we identified 111 immune‐related genes in the QTL regions and 132 immune‐related genes from the initially selected candidate genes. For these immune‐related genes harbouring potential functional variants, the enrichment analyses performed highlighted significant GO terms related to apoptosis, adhesion and inflammatory response, in relation to the QTL related variants, and significant disease‐related terms such as inflammation, adhesion and necrosis, in relation to the initial candidate gene list. Overall, the study provides a valuable list of potential causal mutations that could be considered as candidate causal mutations in relation to GIN resistance in sheep. Future studies should assess the role of these suggested mutations with the aim of identifying genetic markers that could be directly implemented in sheep breeding programmes considering not only production traits, but also functional traits such as resistance to GIN infections.
Genome‐wide association study to identify genetic loci associated with gastrointestinal nematode resistance in Katahdin sheep
Authors: Becker G. M. , Davenport K. M. , Burke J. M. , Lewis R. M. , Miller J. E. , Morgan J. L. M. , Notter D. R. , Murdoch B. M. 
Published: January 2020

SummaryResistance to gastrointestinal nematodes has previously been shown to be a moderately heritable trait in some breeds of sheep, but the mechanisms of resistance are not well understood. Selection for resistance currently relies upon faecal egg counts (FEC), blood packed cell volumes and FAMACHA visual indicator scores of anaemia. Identifying genomic markers associated with disease resistance would potentially improve the selection process and provide a more reliable means of classifying and understanding the biology behind resistant and susceptible sheep. A GWAS was conducted to identify possible genetic loci associated with resistance to Haemonchus contortus in Katahdin sheep. Forty animals were selected from the top and bottom 10% of estimated breeding values for FEC from a total pool of 641 sires and ram lambs. Samples were genotyped using Applied Biosystems™ Axiom™ Ovine Genotyping Array (50K) consisting of 51 572 SNPs. Following quality control, 46 268 SNPs were included in subsequent analyses. Analyses were conducted using a linear regression model in plink v1.90 and a single‐locus mixed model in snp and variation suite. Genome‐wide significance was determined by a Bonferroni correction for multiple testing. Using linear regression, loci on chromosomes 2, 3, 16, 23 and 24 were significantly associated at the genome level with FEC estimated breeding values, and we identified a region on chromosome 2 that was significant using both statistical analyses. We suggest a potential role for the gene DIS3L2 for gastrointestinal nematode resistance in Katahdin sheep, although further research is needed to validate these findings.
Computed tomographic and radiographic morphometric study of cardiac and coelomic dimensions in captive blue‐fronted Amazon parrots (Amazona aestiva, Linnaeus, 1758) with varying body condition scores
Authors: dos Santos Gisele J. , da Silva Jeana P. , Hippólito Alícia G. , Ferro Bárbara S. , Oliveira Elton Luís R. , Okamoto Priscylla Tatiana C. G. , Lourenço Maria Lucia G. , de Vasconcelos Machado Vania Maria , Rahal Sheila C. , Teixeira Carlos R. , Melchert Alessandra 
Published: January 2020

AbstractThis study aimed to assess radiographic and tomographic cardiac parameters, including width and length of the heart, and the ratio of heart width to coelom width of blue‐fronted Amazon parrots (Amazona aestiva) with varying body condition scores. Thirty‐five captive birds were included in the study and were allocated into one of three groups according to their respective body condition score: lean, ideal and obese. No differences were observed among the groups with regard to radiographic and tomographic measurements. Computed tomography enabled better identification of the structures of the cardiovascular system without interference from the overlying structures of the celomatic cavity observed in radiographic images. However, radiographic examinations should still be considered the standard screening method to identify cardiac alterations, such as increased or reduced organ dimensions. Standardizing the techniques and measurements performed in this study may serve as a basis for further research in the field.
The preconception environment and sperm epigenetics
Authors: Marcho Chelsea , Oluwayiose Oladele A. , Pilsner J. Richard 
Published: January 2020

AbstractBackgroundInfertility is a common reproductive disorder, with male factor infertility accounting for approximately half of all cases. Taking a paternal perceptive, recent research has shown that sperm epigenetics, such as changes in DNA methylation, histone modification, chromatin structure, and noncoding RNA expression, can impact reproductive and offspring health. Importantly, environmental conditions during the preconception period has been demonstrated to shape sperm epigenetics.ObjectivesTo provide an overview on epigenetic modifications that regulate normal gene expression and epigenetic remodeling that occurs during spermatogenesis, and to discuss the epigenetic alterations that may occur to the paternal germline as a consequence of preconception environmental conditions and exposures.Materials and methodsWe examined published literature available on databases (PubMed, Google Scholar, ScienceDirect) focusing on adult male preconception environmental exposures and sperm epigenetics in epidemiologic studies and animal models.ResultsThe preconception period is a sensitive developmental window in which a variety of exposures such as toxicants, nutrition, drugs, stress, and exercise, affects sperm epigenetics.Discussion and ConclusionUnderstanding the environmental legacy of the sperm epigenome during spermatogenesis will enhance our understanding of reproductive health and improve reproductive success and offspring well‐being.