bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the bacterial and fungal microbiome on the skin ofAnaxyrus boreas,Rhinella marina, andXenopus laevisand implications related toBatrachochytrium dendrobatidissusceptibility
Authors: Elmassry Moamen M. , Dowd Scot , Carey Cynthia , San Francisco Michael J. 
Published: July 2020

ABSTRACTThe skin and its microbiome are the first lines of defense against environmental stressors and pathogens. The symbiotic relationships between the host and the microbiome and within the microbiome are critical to host health. In frogs, this research area is lacking especially in the context of their skin infection withBatrachochytrium dendrobatidis.B. dendrobatidisis a major fungal skin pathogen to amphibians that has caused the extinction of hundreds of amphibian species populations. While some frog species are known susceptible toB. dendrobatidisinfections, and others are resistant, we hypothesized that the skin microbiome of frogs plays a role in the prevention ofB. dendrobatidisinfections that is yet unknown. Therefore, in this work we have examined the bacterial and fungal skin microbiome of one species that is sensitive toB. dendrobatidisinfections,Anaxyrus boreas(formerly:Bufo boreas), and the resistant species,Xenopus laevisandRhinella marina(formerly:Bufo marinus). This was accomplished using tag-encoded FLX amplicon pyrosequencing (bTEFAP) of the 16S rRNA and ITS DNA regions. Our results showed that the bacterial and fungal skin microbiome ofA. boreasandR. marinawere more similar than to that ofX. laevis.We found distinct patterns between the skin microbiome ofB. dendrobatidissensitive and resistant frog species. For the bacterial microbiome, the most abundant bacterial genus observed in all frog samples wasMicrobacterium. The resistant species had higher abundance in the generaPseudomonas,Sphingobium,Pedobacter,Variovorax,Morganella,Sphingomonas,Giesbergeria, andAgromyces. In contrast, they had lower abundance ofElizabethkingia(formerly:Flavobacterium), Enterobacter,Ochrobactrum,Arthobacter,Stenotrophomonas,Shinella,Klebsiella,Aeromonas,Comomonas,Chitinophaga, andRhodococcus. Regarding the fungal microbiome, the resistant species showed higher abundance in the generaAspergillus,Cladosporium, Elaphomyces,Monascus,Tritirachium,Ceratostomella, andClaviceps, whileAsterotremella,Trichosporon, andMalasezziagenera were less represented in resistant species. We have also observed that in the resistant species, the skin microbiome had higher diversity in the fungal microbiota, but not in the bacterial microbiota. We speculate that those observed differences have implications inB. dendrobatidissusceptibility that are yet to be determined, possibly through competition for nutrients or the production of specific anti-fungal molecules.GRAPHICAL ABSTRACT
Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles
Authors: Hershewe Jasmine M. , Warfel Katherine F. , Iyer Shaelyn M. , Peruzzi Justin A. , Sullivan Claretta J. , Roth Eric W. , DeLisa Matthew P. , Kamat Neha P. , Jewett Michael C. 
Published: July 2020

AbstractCell-free gene expression (CFE) systems from crude cellular extracts have attracted much attention for accelerating the design of cellular function, on-demand biomanufacturing, portable diagnostics, and educational kits. Many essential biological processes that could endow CFE systems with desired functions, such as protein glycosylation, rely on the activity of membrane-bound components. However, without the use of synthetic membrane mimics, activating membrane-dependent functionality in bacterial CFE systems remains largely unstudied. Here, we address this gap by characterizing native, cell-derived membrane vesicles inEscherichia coli-based CFE extracts and describing methods to enrich vesicles with heterologous, membranebound machinery. We first use nanocharacterization techniques to show that lipid vesicles in CFE extracts are tens to hundreds of nanometers across, and on the order of ~3×1012particles/mL. We then determine how extract processing methods, such as post-lysis centrifugation, can be used to modulate concentrations of membrane vesicles in CFE systems. By tuning these methods, we show that increasing the number of vesicle particles to ~7×1012particles/mL can be used to increase concentrations of heterologous membrane protein cargo expressed prior to lysis. Finally, we apply our methods to enrich membrane-bound oligosaccharyltransferases and lipid-linked oligosaccharides for improvingN-linked andO-linked glycoprotein synthesis. We anticipate that our findings will facilitatein vitrogene expression systems that require membrane-dependent activities and open new opportunities in glycoengineering.
Prey availability and ambient temperature influence carrion persistence in the boreal forest
Authors: Peers Michael J. L. , Konkolics Sean M. , Lamb Clayton T. , Majchrzak Yasmine N. , Menzies Allyson K. , Studd Emily K. , Boonstra Rudy , Kenney Alice J. , Krebs Charles J. , Martinig April Robin , McCulloch Baily , Silva Joseph , Garland Laura , Boutin Stan 
Published: July 2020

AbstractScavenging by vertebrates can have important impacts on food web stability and persistence, and can alter the distribution of nutrients throughout the landscape. However, scavenging communities have been understudied in most regions around the globe, and we lack understanding of the biotic drivers of vertebrate scavenging dynamics.In this paper, we examined how changes in prey density and carrion biomass caused by population cycles of a primary prey species, the snowshoe hareLepus americanus, influence scavenging communities in the northern boreal forest. We further examined the impact of habitat and temperature on scavenging dynamics.We monitored the persistence time, time until first scavenger, and number of species scavenging experimentally‐placed hare carcasses over four consecutive years in the southwestern Yukon. We simultaneously monitored hare density and carrion biomass to examine their influence relative to temperature, habitat, and seasonal effects. For the primary scavengers, we developed species‐specific scavenging models to determine variation on the effects of these factors across species, and determine which species may be driving temporal patterns in the entire community.We found that the efficiency of the scavenging community was affected by hare density, with carcass persistence decreasing when snowshoe hare densities declined, mainly due to increased scavenging rates by Canada lynxLynx canadensis. However, prey density did not influence the number of species scavenging a given carcass, suggesting prey abundance affects carrion recycling but not necessarily the number of connections in the food web. In addition, scavenging rates increased in warmer temperatures, and there were strong seasonal effects on the richness of the vertebrate scavenging community.Our results demonstrate that vertebrate scavenging communities are sensitive to changes in species’ demography and environmental change, and that future assessments of food web dynamics should consider links established through scavenging.
More than meets the eye: Predator‐induced pupil size plasticity in a teleost fish
Authors: Vinterstare Jerker , Hulthén Kaj , Nilsson Dan E. , Nilsson Per Anders , Brönmark Christer 
Published: July 2020

Abstract

Most animals are visually oriented, and their eyes provide their ‘window to the world’. Eye size correlates positively with visual performance, because larger eyes can house larger pupils that increase photon catch and contrast discrimination, particularly under dim light, which have positive effects on behaviours that enhance fitness, including predator avoidance and foraging.

Recent studies have linked predation risk to selection for larger eyes and pupils, and such changes should be of importance for the majority of teleost fishes as they have a pupil that is fixed in size (eyes lack a pupillary sphincter muscle) and, hence, do not respond to changes in light conditions.

Here, we quantify eye and pupil size of individual crucian carp, a common freshwater fish, following controlled manipulations of perceived predation risk (presence/absence). We also tested if crucian carp responded to increased predation risk by shifts in diel activity patterns.

We found that crucian carp show phenotypic plasticity with regards to pupil size, but not eye size, as pupil size increased when exposed to predators (pike). Predator‐exposed crucian carp also shifted from diurnal to nocturnal activity. Using a modelling exercise, we moreover show that the plastically enlarged pupils significantly increase visual range, especially for small objects under dim light conditions.

Overall, our results provide compelling evidence for predator‐induced pupil enlargement resulting in enhanced visual capabilities in a teleost fish. Pupil size plasticity in combination with the observed shift towards nocturnal activity may allow for efficient foraging also under dark conditions when predation risk from diurnal and visually oriented predators is reduced. The data highlight the powerful role of predation risk for eye development and evolution.
Initial butyrate producers during infant gut microbiota development are endospore formers
Authors: Appert Olivia , Garcia Alejandro Ramirez , Frei Remo , Roduit Caroline , Constancias Florentin , Neuzil‐Bunesova Vera , Ferstl Ruth , Zhang Jianbo , Akdis Cezmi , Lauener Roger , Lacroix Christophe , Schwab Clarissa 
Published: July 2020

SummaryThe acquisition of the infant gut microbiota is key to establishing a host‐microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation‐derived short‐chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate‐forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate‐producing taxa during infant gut microbiota development have been little investigated. We determined the abundance of major butyrate‐forming groups and fermentation metabolites in faeces, isolated, cultivated and characterized the heat‐resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. The endospore community contributed about 0.001% to total cells, and was mainly composed of the pioneer butyrate‐producing Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate‐producing Lachnospiraceae and faecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared with Clostridium sensu stricto. Our data suggest that a successional arrangement and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity.
Re‐Evaluating ‘Best Interests’ in the Wake of Raqeeb v Barts NHS Foundation Trust & Anors
Authors: Auckland Cressida , Goold Imogen 
Published: July 2020

AbstractIn Raqeeb v Barts NHS Foundation Trust, the latest of a number of cases concerning whether a child can travel abroad for treatment that doctors in the UK do not consider to be in their best interests, the High Court held that the hospital had acted unlawfully by failing to consider the child's rights under EU law when refusing to allow her to travel. Although this derogation could be justified on public policy grounds, as such treatment was, on the facts, in her best interests, no further interference with her rights was justified. In making this finding, the court recognised the ‘stress’ that such a case placed on the best interests test, lending weight to the argument for moving instead to a risk of significant harm threshold for judicial intervention in parental decisions, which better accounts for legitimate differences of value and strikes a better balance under Article 8 ECHR.
Communication missteps during COVID‐19 hurt those already most at risk
Authors: Clark‐Ginsberg Aaron , Petrun Sayers Elizabeth L. 
Published: July 2020

AbstractEmergency risk communication is a crucial part responding to crises. Right now, vulnerable groups are experiencing disproportionately negative outcomes from communication missteps surrounding COVID‐19. In this commentary, we describe the missteps and outline strategies that response organizations can take to improve communication for vulnerable groups.
Differentiation of Morphologically Similar Human Head Hairs from Two Demographically Similar Individuals Using Amino Acid Ratios,
Authors: Macri Allison M. , Lam Sirena , Powers Robert H. , Marsico Alyssa L.M. 
Published: July 2020

AbstractHuman hair is frequently encountered as forensic evidence and can contribute valuable information to investigators. Conventional forensic hair analyses include microscopic hair comparison (MHC) and DNA analysis. However, MHC is not supported by statistics and DNA analysis cannot always be performed. Recent studies have demonstrated that evaluation of differences in the hair proteins may offer an alternate method to these analyses. In this study, an evaluation of the amino acids present in hair was investigated as an approach to differentiate morphologically indistinguishable hair samples from two demographically similar individuals. Proteins in the hair were digested using hydrochloric acid, and the resulting amino acids were derivatized with N,O‐Bis(trimethylsilyl)trifluoroacetamide (BSTFA) for analysis using gas chromatography‐mass spectrometry (GC‐MS). Eight derivatized amino acids were detected and quantified relative to an internal standard, L‐norvaline, and used to construct twenty‐eight amino acid ratios. Hair samples were collected from four areas of the head on various days over the course of one month, and no significant differences in amino acid ratios (p‐value > 0.05) were observed among the areas of the head, and the ratios were consistent over the time period of this study. Additionally, fifteen of these amino acid ratios were found to be significantly different between the two individuals when compared using a two‐sample t‐test (p‐value ≤ 0.05). These data indicate that amino acid analysis was able to differentiate two morphologically similar hair samples from different individuals and demonstrates the applicability of this method to distinguish similar hair samples when DNA analysis cannot be performed.
Comparison of the M‐Vac® Wet‐Vacuum‐Based Collection Method to a Wet‐Swabbing Method for DNA Recovery on Diluted Bloodstained Substrates*†‡
Authors: McLamb Jessica M. , Adams Lara D. , Kavlick Mark F. 
Published: July 2020

AbstractA wet‐vacuum‐based collection method with the M‐Vac® was compared to a wet‐swabbing collection method by examining the recovery of diluted blood on 22 substrates of varying porosity. The wet‐vacuum method yielded more total nuclear DNA than wet‐swabbing on 18 porous substrates, recovering on average 12 times more DNA. However, both methods yielded comparable amounts of total DNA on two porous and two nonporous substrates. In no instance did wet‐swabbing significantly recover more DNA. The wet‐vacuum method also successfully collected additional DNA on previously swabbed substrates. Mitochondrial DNA yields were assessed, and outcomes were generally similar to the nuclear DNA outcomes described above. Results demonstrate that wet‐vacuuming may serve as an alternative collection method to swabbing on difficult porous substrates and could potentially recover additional DNA on previously swabbed substrates. However, swabbing remains the preferred collection method on substrates with visible stains and/or nonporous surfaces for reasons of convenience, simplicity, and lower cost relative to the wet‐vacuum method.
Sustainable Flood Risk and Stormwater Management in Blue‐Green Cities; an Interdisciplinary Case Study in Portland, Oregon
Authors: O’Donnell Emily C. , Thorne Colin R. , Yeakley J. Alan , Chan Faith Ka Shun 
Published: July 2020

AbstractBlue‐Green Infrastructure (BGI) is recognized as a viable strategy to manage stormwater and flood risk, and its multifunctionality may further enrich society through the provision of multiple cobenefits that extend far beyond the hydrosphere. Portland, Oregon, is an internationally renowned leader in the implementation of BGI and showcases many best practice examples. Nonetheless, a range of interdisciplinary barriers and uncertainties continue to cloud decision making and impede wider implementation of BGI. In this paper, we synthesize research conducted by the “Clean Water for All” (CWfA) research project and demonstrate that interdisciplinary evaluation of the benefits of Portland’s BGI, focusing on green street bioswales and the East Lents Floodplain Restoration Project, is essential to address biophysical and sociopolitical barriers. Effective interdisciplinary approaches require sustained interaction and collaboration to integrate disciplinary expertise toward a common problem‐solving purpose, and strong leadership from researchers adapt at spanning disciplinary boundaries. While the disciplinary differences in methodologies were embraced in the CWfA project, and pivotal to providing evidence of the disparate benefits of multifunctional BGI, cross‐disciplinary engagement, knowledge coproduction, and data exchanges during the research process were of paramount importance to reduce the potential for fragmentation and ensure research remained integrated.
A 63‐bp insertion in exon 2 of the porcine KIF21A gene is associated with arthrogryposis multiplex congenita
Authors: Fang Z.‐H. , Nosková A. , Crysnanto D. , Neuenschwander S. , Vögeli P. , Pausch H. 
Published: July 2020

SummaryA recessive form of arthrogryposis multiplex congenita (AMC) was detected 20 years ago in the Swiss Large White (SLW) pig population. A diagnostic marker test enabled the identification of carrier animals, but the underlying causal mutation remains unknown. To identify the mutation underlying AMC, we collected SNP chip genotyping data for 11 affected piglets and 23 healthy pigs. Association testing using 47 829 SNPs confirmed that AMC maps to SSC5 (P = 9.4 × 10−13). Subsequent autozygosity mapping revealed a common 6.06 Mb region (from 66 757 970 to 72 815 151 bp) of extended homozygosity in 11 piglets affected by AMC. Using WGS data, we detected a 63‐bp insertion compatible with the recessive inheritance of AMC in the second exon of KIF21A gene encoding Kinesin Family Member 21A. The 63‐bp insertion is predicted to introduce a premature stop codon in KIF21A gene (p.Val41_Phe42insTer) that truncates 1614 amino acids (~97%) from the protein. We found that this deleterious allele still segregates at a frequency of 0.1% in the SLW pig population. Carrier animals can now be detected unambiguously and excluded from breeding.
Myths of Meritocracy, Friendship, and Fun Work: Class and Gender in North American Academic Communities
Authors: Leighton Mary 
Published: July 2020

ABSTRACTUsing the example of Andean archaeology, this article focuses on subtle forms of inequality that arise when academic communities are conceptualized as friendship‐based and egalitarian, rejecting explicit hierarchy. I describe this asperformative informalityand argue that it stems from a meritocratic ideology that inadvertently reproduces Euro‐American white‐male privilege. In a discipline that prides itself on its friendliness, openness, and alcohol‐fueled drinking culture, those who find themselves unable to enact or perform informality appropriately are at a distinct disadvantage. Drawing from a multisited ethnography of Andeanist archaeologists, I make the case that it is the ephemerality and plausible deniability of performative informality that makes it hard to recognize and thus mitigate against it. In doing so, I draw on and contribute to the theorization of gender/class intersectionality in anthropology and science studies, US conceptualizations of meritocracy in academia and higher education, and feminist Jo Freeman's concept of “the tyranny of structurelessness.” [anthropology of science, ethnography of archaeology, class, gender, anthropology of work and education]
Primary gastric melanoma in adult population: a systematic review of the literature
Authors: Schizas Dimitrios , Tomara Nefeli , Katsaros Ioannis , Sakellariou Stratigoula , Machairas Nikolaos , Paspala Anna , Tsilimigras Diamantis I. , Papanikolaou Ioannis S. , Mantas Dimitrios 
Published: July 2020

ABSTRACTBackgroundPrimary gastric melanoma (PGM) is a rare malignant tumour of the stomach with poor prognosis. The aim of this systematic review was to assess the available literature on this entity and to highlight its biological behaviour and preferred treatment approach.MethodsPubMed and Cochrane bibliographical databases were independently searched (last search: 2 February 2020) by two investigators for articles reporting on PGM in the adult population.ResultsTwenty‐five studies met the inclusion criteria and concerned collectively 25 patients (18 males and seven females) with an age of 63.4 ± 8.97 years (mean ± standard deviation). Main symptoms included abdominal pain (64%), weight loss (48%) and hematemesis or melena (32%). The most frequent tumour location was the body of the stomach (54.2%). All tumours were surgically resected and the majority of the patients had a partial gastrectomy (52%). Median recurrence time was 5 months and 12% of patients reached 5‐year survival landmark.ConclusionPGM is a rare disease characterized by an aggressive malignant behaviour. Its differential diagnosis from a metastatic lesion is crucial. A prompt diagnosis and therapeutic approach are needed. Further studies are required to elucidate the optimal management of this clinical entity.
Settlers, Workers, and the Logic of Accumulation by Dispossession
Authors: Englert Sai 
Published: July 2020

AbstractThis article offers a critique of the Wolfe‐an model, which has become so dominant within contemporary Settler Colonial Studies (SCS). It focuses particularly on the central claim made by Patrick Wolfe, and others after him, that settler colonialism is categorically differentiated from other forms of colonialism by its drive to “eliminate the native”, instead of exploiting them. This paper builds on the literature that shows how settler colonies have used elimination as well as exploitation in their relations with indigenous peoples—even transitioning from one to the other. Instead, the paper argues that focusing on accumulation by dispossession allows for an analysis of the specificity of settler social relations to emerge. It highlights the specific ways in which settlers collectively expropriate indigenous peoples and struggle amongst different settler classes over the distribution of the colonial loot.