bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link
Authors: Freitas Ana R , Tedim Ana P , Duarte Bárbara , Elghaieb Houyem , Abbassi Mohamed S , Hassen Abdennaceur , Read Antónia , Alves Valquíria , Novais Carla , Peixe Luísa 
Published: May 2020

Abstract

Objectives
poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts.

Methods
poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996–2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives.

Results
poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30–100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment.

Conclusions
poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.
Understanding enterprise data warehouses to support clinical and translational research
Authors: Campion Thomas R , Craven Catherine K , Dorr David A , Knosp Boyd M 
Published: May 2020

Abstract

Objective
Among National Institutes of Health Clinical and Translational Science Award (CTSA) hubs, adoption of electronic data warehouses for research (EDW4R) containing data from electronic health record systems is nearly ubiquitous. Although benefits of EDW4R include more effective, efficient support of scientists, little is known about how CTSA hubs have implemented EDW4R services. The goal of this qualitative study was to understand the ways in which CTSA hubs have operationalized EDW4R to support clinical and translational researchers.

Materials and Methods
After conducting semistructured interviews with informatics leaders from 20 CTSA hubs, we performed a directed content analysis of interview notes informed by naturalistic inquiry.

Results
We identified 12 themes: organization and data; oversight and governance; data access request process; data access modalities; data access for users with different skill sets; engagement, communication, and literacy; service management coordinated with enterprise information technology; service management coordinated within a CTSA hub; service management coordinated between informatics and biostatistics; funding approaches; performance metrics; and future trends and current technology challenges.

Discussion
This study is a step in developing an improved understanding and creating a common vocabulary about EDW4R operations across institutions. Findings indicate an opportunity for establishing best practices for EDW4R operations in academic medicine. Such guidance could reduce the costs associated with developing an EDW4R by establishing a clear roadmap and maturity path for institutions to follow.

Conclusions
CTSA hubs described varying approaches to EDW4R operations that may assist other institutions in better serving investigators with electronic patient data.
Integrated displays to improve chronic disease management in ambulatory care: A SMART on FHIR application informed by mixed-methods user testing
Authors: Curran Rebecca L , Kukhareva Polina V , Taft Teresa , Weir Charlene R , Reese Thomas J , Nanjo Claude , Rodriguez-Loya Salvador , Martin Douglas K , Warner Phillip B , Shields David E , Flynn Michael C , Boltax Jonathan P , Kawamoto Kensaku 
Published: May 2020

Abstract

Objective
The study sought to evaluate a novel electronic health record (EHR) add-on application for chronic disease management that uses an integrated display to decrease user cognitive load, improve efficiency, and support clinical decision making.

Materials and Methods
We designed a chronic disease management application using the technology framework known as SMART on FHIR (Substitutable Medical Applications and Reusable Technologies on Fast Healthcare Interoperability Resources). We used mixed methods to obtain user feedback on a prototype to support ambulatory providers managing chronic obstructive pulmonary disease. Each participant managed 2 patient scenarios using the regular EHR with and without access to our prototype in block-randomized order. The primary outcome was the percentage of expert-recommended ideal care tasks completed. Timing, keyboard and mouse use, and participant surveys were also collected. User experiences were captured using a retrospective think-aloud interview analyzed by concept coding.

Results
With our prototype, the 13 participants completed more recommended care (81% vs 48%; P &lt; .001) and recommended tasks per minute (0.8 vs 0.6; P = .03) over longer sessions (7.0 minutes vs 5.4 minutes; P = .006). Keystrokes per task were lower with the prototype (6 vs 18; P &lt; .001). Qualitative themes elicited included the desire for reliable presentation of information which matches participants’ mental models of disease and for intuitive navigation in order to decrease cognitive load.

Discussion
Participants completed more recommended care by taking more time when using our prototype. Interviews identified a tension between using the inefficient but familiar EHR vs learning to use our novel prototype. Concept coding of user feedback generated actionable insights.

Conclusions
Mixed methods can support the design and evaluation of SMART on FHIR EHR add-on applications by enhancing understanding of the user experience.
Abbreviated Breast MRI: Road to Clinical Implementation
Authors: Heacock Laura , Reig Beatriu , Lewin Alana A , Toth Hildegard K , Moy Linda , Lee Cindy S 
Published: May 2020

Abstract
Breast MRI offers high sensitivity for breast cancer detection, with preferential detection of high-grade invasive cancers when compared to mammography and ultrasound. Despite the clear benefits of breast MRI in cancer screening, its cost, patient tolerance, and low utilization remain key issues. Abbreviated breast MRI, in which only a select number of sequences and postcontrast imaging are acquired, exploits the high sensitivity of breast MRI while reducing table time and reading time to maximize availability, patient tolerance, and accessibility. Worldwide studies of varying patient populations have demonstrated that the comparable diagnostic accuracy of abbreviated breast MRI is comparable to a full diagnostic protocol, highlighting the emerging role of abbreviated MRI screening in patients with an intermediate and high lifetime risk of breast cancer. The purpose of this review is to summarize the background and current literature relating to abbreviated MRI, highlight various protocols utilized in current multicenter clinical trials, describe workflow and clinical implementation issues, and discuss the future of abbreviated protocols, including advanced MRI techniques.
A novel method of quantifying sperm to determine the potential for sperm depletion in male American lobstersHomarus americanus(H. Milne Edwards, 1837) (Decapoda: Astacidea: Nephropidae)
Authors: Gutzler Benjamin C , Pugh Tracy L , Watson Winsor H 
Published: May 2020

AbstractSperm limitation is a concern for a number of heavily fished decapods; however, work to assess this concern is sometimes hampered by a lack of simple techniques to quantify sperm transferred during reproduction. Our primary goal was to determine if DNA measurements could be used to quantify the sperm content of spermatophores and thus facilitate investigations of sperm limitation in American lobsters (Homarus americanus H. Milne Edwards, 1837). This was achieved by measuring the amount of DNA in a sample and then calibrating those values by using flow cytometry to count the number of individual sperm present in the sample. Our results show that the DNA quantification technique provides a fast and accurate way to quantify sperm. We then demonstrated the utility of the method by using it to examine the rate at which males can produce sperm under simulated conditions of repeated mating events, a situation that might lead to a reduction in the number of sperm per spermatophore. While spermatophores obtained from male lobsters at three-day intervals varied substantially in the number of sperm they contained (range 427,090–5,028,996; mean 2,306,473), there was no clear decline in sperm count over time. These results suggest that male lobsters replenish their sperm supplies rapidly, and that sperm recharge rate is unlikely to be a factor that could lead to sperm limitation in American lobster populations.
Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767) (Decapoda: Anomura: Coenobitidae), from Okinawa, Japan
Authors: Veldsman Werner P , Wang Yaqin , Niu Jiaojiao , Baeza J Antonio , Chu Ka Hou 
Published: May 2020

AbstractWe present a full description and analysis of the complete mitochondrial genome of a Pacific Ocean specimen of the coconut crab Birgus latro (Linnaeus, 1767), the largest extant terrestrial arthropod in the world. Our de novo-assembled mitogenome has a massive 16,161 times organelle read coverage, a length of 16,411 bp, contains 22 tDNAs (20 unique), 13 protein-coding genes, two rDNAs, and a putative control region of length 1,381 bp. The control region contains three microsatellites and two pairs of inverted repeats. Contrary to the mitochondrial sentinel gene concept, two-dimensional nucleotide analysis reveals higher GC-content in cox gene families than in nadh gene families. Moreover, cox gene families are more conserved than nadh gene families among the species of Coenobitidae selected for comparison. Secondary structure prediction of the 22 tDNAs shows major deviations from the cloverleaf pattern, which points to a relatively high rate of mutation in these genes. We also present a repertoire of mitochondrial variation between our male Okinawan coconut crab and an Indian Ocean specimen that consists of one insertion, one deletion, 135 SNPs, three MNPs and nine complex polymorphisms. We provide confirmatory evidence that the superfamily Paguroidea, to which the coconut crab belongs, is polyphyletic, that all the protein-coding genes of B. latro are under purifying selection, and that a Pacific versus Indian Ocean coconut crab population divergence occurred during the Pleistocene.
X-Ray-Based Irradiation of Larvae and Pupae of the Navel Orangeworm (Lepidoptera: Pyralidae)
Authors: Haff Ronald , Ovchinnikova Inna , Liang Peishih , Mahoney Noreen , Gee Wai , Gomez Joseph , Toyofuku Natsuko , Jackson Eric , Hnasko Robert , Light Douglas 
Published: May 2020

AbstractThe suitability of adult male the navel orangeworm, Amyelois transitella (Walker) for Sterile Insect Technique (SIT) has been reported for both high energy gamma (&gt;1 MeV) and low energy x-ray (90 keV) sterilization. However, research regarding sterilization of NOW larvae and pupae by gamma irradiation indicated nonsuitability due to high mortality. Here, NOW larvae and pupae were irradiated to doses up to 50 Gy with 90 keV x-rays, then paired with nonirradiated colony mates. Sterility of surviving insects was determined by the presence or absence of hatched neonates. While presence of offspring does not guarantee viability, the absence does guarantee sterility (as is appropriate for SIT) and was thus the measure used here. Early stage larvae experienced 77% mortality at a dose of 30 Gy, versus 20% for nonirradiated control. At 40 Gy, mortality reached 98%. Of surviving early stage larvae at 30 Gy, 29% of moth pairs produced offspring. For late stage larvae, no offspring were produced at 40 Gy, but mortality was 73%. For pupae, mortality reached 53% at 30 Gy with 13% still producing neonates, while mortality reached 98% at 40 Gy. These results are consistent with reported results for gamma irradiation of NOW larvae where sterility was observed somewhere between the 30 Gy and 60 Gy data points, but mortality was high. This further confirms the lack of suitability of NOW irradiated in the larval stage, whether by gamma or x-ray, and supports the hypothesis that x-ray and gamma treatments are biologically equivalent at equal doses.
A Simple, Inexpensive Method for Mark-Recapture of Ixodid Ticks
Authors: White Alexis , Minch Robin , Bidder Lindsey , Gaff Holly 
Published: May 2020

Abstract
Mark-recapture techniques have been widely used and specialized to study organisms throughout the field of biology. To mark-recapture ticks (Ixodida), we have created a simple method to mark ticks using nail polish applied with an insect pin secured in a pencil that allows for a variety of questions to be answered. For measuring tick control efficacy, estimating population estimates, or measuring movement of ticks, this inexpensive mark-recapture method has been easily applied in the field and in the lab to provide useful data to answer a variety of questions about ticks.
Training fails to elicit behavioral change in a marsupial suffering evolutionary loss of antipredator behaviors
Authors: Jolly Chris J , Webb Jonathan K , Gillespie Graeme R , Phillips Ben L 
Published: May 2020

Abstract
Attempts to reintroduce threatened species from ex situ populations (zoos or predator-free sanctuaries) regularly fail because of predation. When removed from their natural predators, animals may lose their ability to recognize predators and thus fail to adopt appropriate antipredator behaviors. Recently, northern quolls (Dasyurus hallucatus; Dasyuromorpha: Dasyuridae) conserved on a predator-free “island ark” for 13 generations were found to have no recognition of dingoes, a natural predator with which they had coevolved on mainland Australia for about 8,000 years. A subsequent reintroduction attempt using quolls acquired from this island ark failed due to predation by dingoes. In this study, we tested whether instrumental conditioning could be used to improve predator recognition in captive quolls sourced from a predator-free “island ark.” We used a previously successful scent-recognition assay (a giving-up density experiment) to compare predator-scent recognition of captive-born island animals before and after antipredator training. Our training was delivered by pairing live predators (dingo and domestic dog) with an electrified cage floor in repeat trials such that, when the predators were present, foraging animals would receive a shock. Our training methodology did not result in any discernible change in the ability of quolls to recognize and avoid dingo scent after training. We conclude either that our particular training method was ineffective (though ethically permissible); or that because these quolls appear unable to recognize natural predators, predator recognition may be extremely difficult to impart in a captive setting given ethical constraints. Our results point to the difficulty of reinstating lost behaviors, and to the value of maintaining antipredator behaviors in conservation populations before they are lost.
Acute appendicitis with four appendicoliths: a first case report in the English literature
Authors: Lafleche Patrick , Pillay Yagan 
Published: May 2020

Abstract
This is an extremely rare presentation of multiple appendicoliths in one appendix. Multiple appendicoliths as well as appendicoliths larger than 5 mm have been implicated in severe appendicitis as well as perforation and gangrene of the appendix. There is no known correlation with appendicular malignancy. The controversy arises in the surgical management of asymptomatic patients. There is emerging evidence that justifies an elective appendicectomy in asymptomatic patients.
Cystic lymphangioma in adult: a case report and a review of the literature
Authors: Colangeli Walter , Facchini Valerio , Kapitonov Aleksandr , Zappalà Marta , Bozza Fabrizio , Becelli Roberto 
Published: May 2020

Abstract
Cystic lymphangioma (CL) in adult is a very rare pathology. Its etiology remains unclear, but it is supposed to be congenital or to be a result of obstruction and lymph fluid retention of developing lymphatic vessels. It generally occurs in the head and neck region, probably because of the rich lymphatics in this area. It can be easily misdiagnosed with other cervicofacial masses. We present the case of a 56-year-old-female presented with a right-sided painless cervical swelling. Ultrasonography and magnetic resonance imaging were performed and a surgical complete removal was carried out. Histological examination revealed that the mass was composed by a variety of dilated lymph vessels involved in a fibrovascular stroma. Diagnose of CL was done. With this article, we want to highlight the features of CL and its role in the differential diagnoses of adults’ cervicofacial masses.
Weak CS emission in an extremely metal-poor galaxy DDO 70
Authors: Du Kaiyi , Shi Yong , Zhang Zhi-Yu , Wang Junzhi , Gao Yu 
Published: May 2020

ABSTRACT
In most galaxies like the Milky Way, stars form in clouds of molecular gas. Unlike the CO emission that traces the bulk of molecular gas, the rotational transitions of HCN and CS molecules mainly probe the dense phase of molecular gas, which has a tight and almost linear relation with the far-infrared luminosity and star formation rate (SFR). However, it is unclear whether dense molecular gas exists at very low metallicity, and if exists, how it is related to star formation. In this work, we report ALMA observations of the CS J = 5 → 4 emission line of DDO 70, a nearby gas-rich dwarf galaxy with $\sim \!7{{\ \rm per\ cent}}$ solar metallicity. We did not detect CS emission from all regions with strong CO emission. After stacking all CS spectra from CO-bright clumps, we find no more than a marginal detection of CS J = 5 → 4 transition, at a signal-to-noise ratio of ∼3.3. This 3σ upper limit deviates from the $L^\prime _{\rm CS}$–LIR and $L^\prime _{\rm CS}$–SFR relationships found in local star-forming galaxies and dense clumps in the Milky Way, implying weaker CS emission at given infrared luminosity and SFR. We discuss the possible mechanisms that suppress CS emission at low metallicity.
MDM2’s dual mRNA binding domains co-ordinate its oncogenic and tumour suppressor activities
Authors: Gnanasundram Sivakumar Vadivel , Malbert-Colas Laurence , Chen Sa , Fusée Leila , Daskalogianni Chrysoula , Muller Petr , Salomao Norman , Fåhraeus Robin 
Published: May 2020

Abstract
Cell growth requires a high level of protein synthesis and oncogenic pathways stimulate cell proliferation and ribosome biogenesis. Less is known about how cells respond to dysfunctional mRNA translation and how this feeds back into growth regulatory pathways. The Epstein-Barr virus (EBV)-encoded EBNA1 causes mRNA translation stress in cis that activates PI3Kδ. This leads to the stabilization of MDM2, induces MDM2’s binding to the E2F1 mRNA and promotes E2F1 translation. The MDM2 serine 166 regulates the interaction with the E2F1 mRNA and deletion of MDM2 C-terminal RING domain results in a constitutive E2F1 mRNA binding. Phosphorylation on serine 395 following DNA damage instead regulates p53 mRNA binding to its RING domain and prevents the E2F1 mRNA interaction. The p14Arf tumour suppressor binds MDM2 and in addition to preventing degradation of the p53 protein it also prevents the E2F1 mRNA interaction. The data illustrate how two MDM2 domains selectively bind specific mRNAs in response to cellular conditions to promote, or suppress, cell growth and how p14Arf coordinates MDM2’s activity towards p53 and E2F1. The data also show how EBV via EBNA1-induced mRNA translation stress targets the E2F1 and the MDM2 - p53 pathway.
Tox21BodyMap: a webtool to map chemical effects on the human body
Authors: Borrel Alexandre , Auerbach Scott S , Houck Keith A , Kleinstreuer Nicole C 
Published: May 2020

Abstract
To support rapid chemical toxicity assessment and mechanistic hypothesis generation, here we present an intuitive webtool allowing a user to identify target organs in the human body where a substance is estimated to be more likely to produce effects. This tool, called Tox21BodyMap, incorporates results of 9,270 chemicals tested in the United States federal Tox21 research consortium in 971 high-throughput screening (HTS) assays whose targets were mapped onto human organs using organ-specific gene expression data. Via Tox21BodyMap's interactive tools, users can visualize chemical target specificity by organ system, and implement different filtering criteria by changing gene expression thresholds and activity concentration parameters. Dynamic network representations, data tables, and plots with comprehensive activity summaries across all Tox21 HTS assay targets provide an overall picture of chemical bioactivity. Tox21BodyMap webserver is available at https://sandbox.ntp.niehs.nih.gov/bodymap/.
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Authors: Jalili Vahid , Afgan Enis , Gu Qiang , Clements Dave , Blankenberg Daniel , Goecks Jeremy , Taylor James , Nekrutenko Anton 
Published: May 2020

AbstractGalaxy (https://galaxyproject.org) is a web-based computational workbench used by tens of thousands of scientists across the world to analyze large biomedical datasets. Since 2005, the Galaxy project has fostered a global community focused on achieving accessible, reproducible, and collaborative research. Together, this community develops the Galaxy software framework, integrates analysis tools and visualizations into the framework, runs public servers that make Galaxy available via a web browser, performs and publishes analyses using Galaxy, leads bioinformatics workshops that introduce and use Galaxy, and develops interactive training materials for Galaxy. Over the last two years, all aspects of the Galaxy project have grown: code contributions, tools integrated, users, and training materials. Key advances in Galaxy's user interface include enhancements for analyzing large dataset collections as well as interactive tools for exploratory data analysis. Extensions to Galaxy's framework include support for federated identity and access management and increased ability to distribute analysis jobs to remote resources. New community resources include large public servers in Europe and Australia, an increasing number of regional and local Galaxy communities, and substantial growth in the Galaxy Training Network.