bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanded Scope of Practice Fellowships for Radiologists: a Survey of Interest Amongst Current Canadian Radiology Residents
Authors: Barfett Joseph J , Colak Errol , Smith Christopher U , Vlachou Paraskevi , Mnatzakanian Aren , Lin Hui Ming , Bartlett Eric , Moody Alan 
Published: May 2019

AbstractRationale and ObjectivesRadiology residents acquire a diverse educational experience and skill set, including a general internship year, which may enable the direct management of patients. In order for radiology residents to define new scopes of practice, however, additional fellowship training may in certain instances be warranted.Materials and MethodsUsing the Canadian family medicine Enhanced Skills Program as a model, we conducted a Canada-wide survey of radiology residents to assess interest in additional fellowship training to expand their scope of practice.ResultsOur results indicate that a majority of residents (69.2%) would like to routinely see patients in clinic and more than half (52%) are willing to undergo an additional year of fellowship to enhance their skill set. The most popular choices for such fellowships were sports medicine (22.8%), emergency medicine (19.6%) and vascular medicine (18.5%). In addition, a majority (52.9%) of residents felt capable of offering incidentaloma clinics without additional training beyond their core radiology residency.ConclusionTraditional diagnostic and interventional radiology fellowships must be reconsidered to reflect the interests and capabilities of modern radiology trainees. Expansion of training options into the domain of direct patient management will likely prove popular among current residents.
Insect pollination is an ecological process involved in the assembly of the seed microbiota
Authors: Prado Alberto , Marolleau Brice , Vaissière Bernard E. , Barret Matthieu , Torres-Cortes Gloria 
Published: May 2019

ABSTRACTThe assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the vascular tissues of the plant, but also from the flower. Flowers are known to be a hub for microbial transmission between plants and insects. This floral-insect exchange opens the possibility for insect-transmitted bacteria to colonize the ovule and subsequently the seed, and to pass then into the next plant generation. In this study, we evaluated the contribution of insect pollination to the seed microbiota through high-throughput sequencing. Oilseed rape (OSR)Brassica napusflowers were exposed to visits and pollination by honey bees (Apis mellifera) or red mason bees (Osmia bicornis), hand pollination, or autonomous self-pollination (ASP). Sequence analyses revealed that honey bee visitation reduced the bacterial richness and diversity, increased the variability in the seed microbial structure, and introduced bee-associated taxa. In contrast, mason bee pollination had minor effects on the seed microbiota. We highlight the need to consider insect pollination as an ecological process involved in the transmission of bacteria from flower to seeds.IMPORTANCEInsect pollinators and flowering plants have a very old mutualistic relationship in which animal mobility is used for the dispersal of pollen. The pollination services provided by insects are extremely important to many natural plant populations as well as agricultural crops. Here we show that while visiting flowers, insect pollinators can disperse bacteria that are able to colonize the developing seed via the flower. Hence, insect pollination participates in the assembly of the seed microbiota, the inoculum for the next plant generation. This novel insight has important implications in terms of re-assessing pollinator services by including microbe transfer.
A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System
Authors: Kingan Sarah B. , Urban Julie , Lambert Christine C. , Baybayan Primo , Childers Anna K. , Coates Brad S. , Scheffler Brian , Hackett Kevin , Korlach Jonas , Geib Scott M. 
Published: May 2019

AbstractA high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gbde novogenome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 36-fold coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated withL. delicatula, each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
Isolation and Characterization of ΦGF1, a Morphotype C3 Bacteriophage that InfectsEscherichia coli
Authors: Punil Renzo , Talledo Miguel , Arcondo Mayra , Suárez Katherine , Zumaeta Kattya 
Published: May 2019

ABSTRACTIt has been isolated a lytic bacteriophage specific toEscherichia coli, which can infect at least one different bacterial group. Phage ФGF1 was isolated from a wastewater treatment plant. It is resistant to the effect of chloroform and is stable at 40 and 50 °C. In addition, it is stable in the range of pH 5-8. Its host range is wide, infecting even strains from another genus such asShigella. The one-step growth curve yielded a short latent period of 15 minutes and a burst size of 85 PFU per infected cell. Under the electron microscope, this phage presents the C3 morphotype, extremely rare among members of the Podoviridae family. Phage ФGF1 shows some characteristics that could be considered useful in biocontrol applications againstE. coli. Keywords: Bacteriophage,Escherichia coli, morphotype C3,Podoviridae.IMPORTANCEWastewater throughout the world is a heavy carrier of potential pathogens that live in their environment along with other biological agents, such as bacteriophages, which play a controlling role of the bacterial populations there, as in soil. The description of the diversity of such bacteriophages is of paramount importance since they could be used to intentionally reduce or remove those pathogens from that environment. Our work describes a bacteriophage that lives primarily in this type of water.
Spatial genome re-organization between fetal and adult hematopoietic stem cells
Authors: Chen C , Yu W , Tober J , Gao P , He B , Lee K , Trieu T , Blobel GA , Speck NA , Tan K 
Published: May 2019

AbstractFetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs. The functional properties of the HSCs change dramatically during this switch, including their cycling behavior, hematopoietic lineage outputs and proliferation rate. The relationship between three-dimensional (3D) genome organization, epigenomic state, and transcriptome is poorly understood during this critical developmental transition. Here we conducted a comprehensive survey of the 3D genome, epigenome and transcriptome of fetal and adult HSCs in mouse. We found that chromosomal compartments and topologically associating domains (TAD) are largely conserved between fetal and adult HSCs. However, there is a global trend of increased compartmentalization and TAD boundary strength in adult HSCs. In contrast, dynamics of intra-TAD chromatin interactions is much higher and more widespread, involving over a thousand gene promoters and distal enhancers. Such dynamic interactions target genes involved in cell cycle, metabolism, and hematopoiesis. These developmental-stage-specific enhancer-promoter interactions appear to be mediated by different sets of transcription factors in fetal and adult HSCs, such as TCF3 and MAFB in fetal HSCs, versus NR4A1 and GATA3 in adult HSCs. Loss-of-function studies of TCF3 confirms the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. In summary, our data suggest that the fetal-to-adult transition is accompanied by extensive changes in intra-TAD chromatin interactions that target genes underlying the phenotypic differences between fetal and adult HSCs.
Epigenetic Effects of Exposure to Insecticide on Early Differentiation of Mouse Embryonic Stem Cells
Authors: Wang Wenlong , Otsuka Satoshi , Nansai Hiroko , Ito Tomohiro , Abe Kuniya , Nakao Yoichi , Ohgane Jun , Yoneda Minoru , Sone Hideko 
Published: May 2019

AbstractIncreasing evidence indicates that insecticides induce various diseases via DNA methylation. DNA methylation plays an important role during cell differentiation and exhibits its greatest vulnerability to environmental factors during embryogenesis. Therefore, it is important to evaluate the effects on DNA methylation at the early stage of cell differentiation to understand developmental toxicity. However, DNA methylation induced by insecticides and the associated effects on cell differentiation are unclear. In this research, we introduced a high-content approach utilizing mouse embryonic stem cells harboring enhanced green fluorescent protein fused with methyl CpG-binding protein to evaluate global DNA methylation induced by various insecticides. DNA methylation was assessed in 22 genes after pesticide exposure to investigate the relationships with biological processes such as cell cycle, cell apoptosis, and cell differentiation. Exposure to acetamiprid, imidacloprid, carbaryl, ando,p′-DDT increased the granular intensity, indicating their global DNA-methylating effects. Exposure to imidacloprid decreased DNA methylation in genes such as Cdkn2a, Dapk1, Cdh1, Mlh1, Timp3, and Rarb, indicating the potential influence of the DNA methylation pattern on cell differentiation. We developed a promising approach for evaluating global DNA methylation, and our findings suggested that imidacloprid might exhibit developmental effects through DNA methylation pattern.
Rapid evolution of invasive traits facilitates the invasion of common ragweed, Ambrosia artemisiifolia
Authors: Sun Yan , Roderick George K. 
Published: May 2019

Abstract

Invasive alien plants, together with organisms introduced for biological control, are ideal study systems with which to address questions of whether, and how fast, organisms adapt to changing environments. We compared populations of common ragweed, Ambrosia artemisiifolia, from native (USA) and introduced (China) ranges at similar latitudes, together with herbivores introduced for biological control, to understand the rate of evolutionary adaptive response of an invasive plant to novel environments.

Evolution of phenotypic traits associated with invasiveness was assessed by comparing differentiation in quantitative traits (QST) to that of neutral microsatellite genetic loci (FST) and through climate data. A common‐garden experiment estimated quantitative genetic variation associated with competition with grasses and biological control history by beetles.

Three growth traits (height, total and stem biomass) and plasticity associated with additional nutrients were significantly greater in invasive compared to native populations and differed from expectations from genetic drift alone. Native, but not invasive, populations exhibited traits showing evidence of past selection and correlations with climate, consistent with the recent timing of introductions. Competition experiments between invasive populations and a US bunch grass showed reduced competitive ability in populations with a history of biological control that might indicate a trade‐off between competitive ability and herbivore resistance in invasive populations.

Synthesis. Our results demonstrate the rapid rate at which traits favouring invasion can evolve in invasive weeds, such as A. artemisiifolia, but also that adaptation may reflect joint effects of release from specialist herbivores and novel climatic conditions.
Mediterranean Eucalyptus plantations affect small mammal ectoparasites abundance but not individual body condition
Authors: Teixeira Daniela , Carrilho Maílis , Silva Marcelo , Nunes Mónica , Vieira Maria L. , Novo Maria T. , Santos‐Reis Margarida , Rosalino Luís M. 
Published: May 2019

AbstractBiodiversity is recognizably affected by land conversion for agriculture. However, the assessment of impacts on wildlife often lacks information on populations structure and individuals' condition, allowing only a limited view of the problem. Individual body condition/health can influence animal's reproductive success or survival. Eucalyptus globulus plantations are important forestry systems in Iberia, being the widest forested‐land use in Portugal, which hosts the broadest European E. globulus coverage. We tested Eucalyptus plantations' effects on small mammals' body condition (using the Scaled Mass Index‐SMI as surrogate) and ectoparasite abundance (number of mites, ticks and fleas per host). We applied a Generalized Linear Mixed Model (GLMM) approach for testing the influence of gender, habitat, species, season and understory cover on SMI and ectoparasites abundance. We captured 681 individuals, hosting overall 521 fleas (n = 305), mites (n = 159) and ticks (n = 57). Animal's body condition was not affected by plantations, but was lower for males and higher in spring. However, animals captured in Eucalyptus plantations and spring had higher parasite abundance (namely ticks and fleas), as well as males. Mites results were inconclusive. Body condition patterns seem to be determined by males demanding spatial/reproductive behavior (i.e., wider home‐ranges and search for females), while plantations promote ectoparasites abundance (e.g., induced by habitat disturbance and dilution effect). Results highlight that plantations may have negative effects on wildlife, but the evaluation of anthropic landscapes impact upon wildlife should encompass several bio‐ecological indicators, since the use of a restricted set (e.g., body condition) may induce a biased view.
Comparison of Blood Compatibility in Various Membrane Materials for Continuous Renal Replacement Therapy
Authors: Togo Konomi , Yamamoto Masahito , Imai Motoyuki , Akiyama Keiichi , Yamashita Akihiro C. 
Published: May 2019

AbstractBecause hemofilters used for continuous renal replacement therapy contact with blood over a prolonged period during treatments, platelet activation may occur stronger. The purpose of this study is to clarify the blood compatibility in three hemofilters mostly used in Japan. We compared the blood compatibility of the two polysulfone (AEF: Asahi Kasei Medical Co., Tokyo, Japan and SHG: Toray Medical Co., Ltd., Tokyo, Japan) and one polymethylmethacrylate membranes (CH: Toray Medical Co., Ltd.). First, test blood was collected from healthy volunteers. Subsequently, the blood was circulated by a roller pump at the rate of 100 mL/min. We measured the platelet counts and platelet factor 4 (PF4). The platelet counts at 48 h in polymethylmethacrylate membrane were significantly less than that in polysulfone membranes. Levels of the PF4 after the circulation were 978.5 ± 200.0 ng/dL with AEF, 863.0 ± 233.9 ng/dL with SHG and 1780.0 ± 465.1 ng/dL with CH, respectively. Hemofilters with polysulfone membranes showed less platelet activation. It was inferred that the amount of PVP, the smoothness of the membrane surface, and the inner diameter of the hollow fiber affect the blood compatibility in the hemofilter.
One‐vector CRISPR/Cas9 genome engineering of the industrial fungus Ashbya gossypii
Authors: Jiménez Alberto , Muñoz‐Fernández Gloria , Ledesma‐Amaro Rodrigo , Buey Rubén M. , Revuelta José L. 
Published: May 2019

SummaryThe filamentous fungus Ashbya gossypii is currently used for the industrial production of vitamin B2. Furthermore, the ability of A. gossypii to grow using low‐cost substrates together with the inexpensive downstream processing makes this fungus an attractive biotechnological chassis. Indeed, the production in A. gossypii of other high‐added value compounds such as folic acid, nucleosides and biolipids has been described. Hence, the development of new methods to expand the molecular toolkit for A. gossypii genomic manipulation constitutes an important issue for the biotechnology of this fungus. In this work, we present a one‐vector CRISPR/Cas9 system for genomic engineering of A. gossypii. We demonstrate the efficiency of the system as a marker‐less approach for nucleotide deletions and substitutions both with visible and invisible phenotypes. Particularly, the system has been validated for three types of genomic editions: gene inactivation, the genomic erasure of loxP scars and the introduction of point mutations. We anticipate that the use of the CRISPR/Cas9 system for A. gossypii will largely contribute to facilitate the genomic manipulations of this industrial fungus in a marker‐less manner.
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Authors: Weilguny Lukas , Kofler Robert 
Published: May 2019

AbstractTransposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
Declining use of radical prostatectomy and pelvic lymphadenectomy despite more robotics: National population data over 15 years
Authors: Roberts Matthew J. , Papa Nathan , Perera Marlon , Joshi Andre , Scott Susan , Bolton Damien , Lawrentschuk Nathan , Yaxley John 
Published: May 2019

AbstractAimTo describe national surgical patterns of prostate cancer (PCa) care considering radical prostatectomy with or without pelvic lymphadenectomy and consideration of robotic‐assisted techniques.MethodsRetrospective analysis of publicly accessible Medicare claims data was performed for the period 2001–2016 and included patients undergoing radical prostatectomy with or without pelvic lymphadenectomy relative to total and PCa‐specific populations among men aged 45–84 years. Proportion of cases performed robotically was considered.ResultsTotal procedures performed increased from 2001, peaked in 2009 and subsequently decreased until 2016. Since 2009, the age‐specific rate of surgery in men aged 75–84 increased by 2.3‐fold, whereas the rates for men aged 55–64 and 45–54 reduced by 44% and 55%, respectively. Rates of concurrent pelvic lymphadenectomy fell until 2009 with subsequent stabilization (ratio 1.05–1.14) through to 2016. Significant regional practice patterns were observed, as was an increasing trend toward a robotic‐assisted laparoscopic approach, comprising more than 80% of radical prostatectomies in 2016.ConclusionSince the peak in 2009, radical prostatectomy is performed less in men <65 years and more in men ≥65 years. An increasing proportion of cases omit concurrent pelvic lymphadenectomy and are performed robotically.
Collateral Consequences for Juveniles in the Justice System: Change in Perceptions after an Educational Intervention
Authors: Janssen Jennica , Wagage Suraji , Cole Lindsey M. , Gale‐Bentz Elizabeth , Goldstein Naomi E. S. 
Published: May 2019

AbstractThere is a dearth of empirical research investigating public awareness or perceptions of the impact of collateral consequences of juvenile justice system involvement on youths’ lives. The current study recruited 555 Pennsylvania residents through Amazon Mechanical Turk to participate in a brief, educational intervention on collateral consequences of system involvement. Participants read a short vignette about a hypothetical youth who was adjudicated delinquent in Pennsylvania, answered 20 knowledge‐based questions, and provided pre‐ and postintervention ratings of the impact the delinquency finding would have on the youth's life in the short term and in the long term. Results of linear mixed model analysis revealed significant fixed effects of both phase (pre‐post educational intervention), b = .62, p < .001, 95% CI [.47, .78] and timing (before the youth turns age 18 and after the youth turns age 18), b = –.98, p < .001, 95% CI [–1.18, –.78], on impact ratings (i.e., how big an impact a juvenile adjudication will have on the youth's life). Participants provided incorrect responses to approximately half of collateral consequences, indicating a gap in knowledge. Findings from the current study can inform targeted intervention efforts to increase public awareness of the consequences of juvenile justice system involvement.