bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domains, tasks, and knowledge for health informatics practice: results of a practice analysis
Authors: Gadd Cynthia S , Steen Elaine B , Caro Carla M , Greenberg Sandra , Williamson Jeffrey J , Fridsma Douglas B 
Published: February 2020

Abstract

Objective
To develop a comprehensive and current description of what health informatics (HI) professionals do and what they need to know.

Materials and Methods
Six independent subject-matter expert panels drawn from and representative of HI professionals contributed to the development of a draft HI delineation of practice (DoP). An online survey was distributed to HI professionals to validate the draft DoP. A total of 1011 HI practitioners completed the survey. Survey respondents provided domain, task, knowledge and skill (KS) ratings, qualitative feedback on the completeness of the DoP, and detailed professional background and demographic information.

Results
This practice analysis resulted in a validated, comprehensive, and contemporary DoP comprising 5 domains, 74 tasks, and 144 KS statements.

Discussion
The HI practice analysis defined “health informatics professionals” to include practitioners with clinical (eg, dentistry, nursing, pharmacy), public health, and HI or computer science training. The affirmation of the DoP by reviewers and survey respondents reflects the emergence of a core set of tasks performed and KSs used by informaticians representing a broad spectrum of those currently practicing in the field.

Conclusion
The HI practice analysis represents the first time that HI professionals have been surveyed to validate a description of their practice. The resulting HI DoP is an important milestone in the maturation of HI as a profession and will inform HI certification, accreditation, and education activities.
N 1-methyladenosine (m1A) RNA modification: the key to ribosome control
Authors: Shima Hiroki , Igarashi Kazuhiko 
Published: February 2020

AbstractRNA displays diverse functions in living cells. The presence of various chemical modifications of RNA mediated by enzymes is one of the factors that impart such functional diversity to RNA. Among more than 100 types of RNA modification, N1-methyladenosine (m1A) is found mainly in tRNA and rRNA of many living organisms and is known to be deeply implicated in the topology or function of the two classes of RNA. In this commentary article, we would like to deal with the functional significance of m1A in RNA, and also to describe one methyltransferase installing m1A in a large subunit rRNA, whose orthologue in Caenorhabditis elegans was discovered recently and was reported in this journal.
Systematics and paleoecology of Miocene brachyuran crabs (Decapoda: Brachyura: Cancroidea, Portunidae) from the St. Marys Formation, Maryland, USA
Authors: Bahman Heedar , Feldmann Rodney M , Schweitzer Carrie E 
Published: February 2020

AbstractA collection of decapod fossils from the Miocene St. Marys Formation, Little Cove Point Member (Maryland, USA), yielded six species belonging to three genera of brachyuran crabs, NecronectesA. Milne-Edwards, 1881, CallinectesStimpson, 1860, and CancerLinnaeus, 1758. Cancer included four species, Cancer irroratusSay, 1817; C. borealisStimpson, 1859; and two new species, C. nancei and C. zahrae. Necronectes is represented by N. drydeniRathbun, 1935. Callinectes was also represented by a single species, C. sapidusRathbun, 1896. Most of the fossils were small relative to normal adult size, suggesting that the environment served as a nursery to developing individuals. The paleoecology of Chesapeake Bay was similar to the present-day ecology based on study of recent faunas, lithology, and paleoecology. The paleoenvironment was a shallow embayment within the temperate climate zone.
Embedded spectral descriptors: learning the point-wise correspondence metric via Siamese neural networks
Authors: Sun Zhiyu , He Yusen , Gritsenko Andrey , Lendasse Amaury , Baek Stephen 
Published: February 2020

Abstract
A robust and informative local shape descriptor plays an important role in mesh registration. In this regard, spectral descriptors that are based on the spectrum of the Laplace–Beltrami operator have been a popular subject of research for the last decade due to their advantageous properties, such as isometry invariance. Despite such, however, spectral descriptors often fail to give a correct similarity measure for nonisometric cases where the metric distortion between the models is large. Hence, they are not reliable for correspondence matching problems when the models are not isometric. In this paper, it is proposed a method to improve the similarity metric of spectral descriptors for correspondence matching problems. We embed a spectral shape descriptor into a different metric space where the Euclidean distance between the elements directly indicates the geometric dissimilarity. We design and train a Siamese neural network to find such an embedding, where the embedded descriptors are promoted to rearrange based on the geometric similarity. We demonstrate our approach can significantly enhance the performance of the conventional spectral descriptors by the simple augmentation achieved via the Siamese neural network in comparison to other state-of-the-art methods.
Ethnic Disparities in ImagingUtilization at Diagnosis of Non-Small Cell Lung Cancer
Authors: Morgan Rustain L , Karam Sana D , Bradley Cathy J 
Published: February 2020

AbstractBackgroundPrior research demonstrated statistically significant racial disparities related to lung cancer treatment and outcomes. We examined differences in initial imaging and survival between blacks, Hispanics, and non-Hispanic whites.MethodsThe linked Surveillance, Epidemiology, and End Results-Medicare database between 2007 and 2015 was used to compare initial imaging modality for patients with lung cancer. Participants included 28 881 non-Hispanic whites, 3123 black, and 1907 Hispanics, patients age 66 years and older who were enrolled in Medicare fee-for-service and diagnosed with lung cancer. The primary outcome was comparison of positron emission tomography (PET) imaging with computerized tomography (CT) imaging use between groups. A secondary outcome was 12-month cancer-specific survival. Information on stage, treatment, and treatment facility was included in the analysis. Chi-square test and logistic regression were used to evaluate factors associated with imaging use. Kaplan-Meier method and Cox proportional hazards regression were used to calculate adjusted hazard ratios and survival. All statistical tests were two-sided.ResultsAfter adjusting for demographic, community, and facility characteristics, blacks were less likely to undergo PET or CT imaging at diagnosis compared with non-Hispanic whites odds ratio (OR) = 0.54 (95% confidence interval [CI] = 0.50 to 0.59; P &lt; .001). Hispanics were also less likely to receive PET with CT imaging (OR = 0.72, 95% CI = 0.65 to 0.81; P &lt; .001). PET with CT was associated with improved survival (HR = 0.61, 95% CI = 0.57 to 0.65; P &lt; .001).ConclusionsBlacks and Hispanics are less likely to undergo guideline-recommended PET with CT imaging at diagnosis of lung cancer, which may partially explain differences in survival. Awareness of this issue will allow for future interventions aimed at reducing this disparity.
At the Junction Between Subsistence and Reference: A Pragmatist Take on Interaction Analysis
Authors: Martine Thomas , Brummans Boris H J M , Cooren François 
Published: February 2020

AbstractThis paper presents a view of interaction analysis that departs from the intersubjectivist assumptions that underlie its ethnomethodological tradition. Adopting a pragmatist perspective, we propose to treat phenomena as being composed of relations; that is, as being constituted by passing through various things and beings. Extending Latour’s work on modernity, we argue that interaction analysts aim to capture social phenomena at the junction between two modes of existence or two manners of passing through others. In the mode of subsistence, social phenomena are (re)produced by continuously passing through new elements. In the mode of reference, social phenomena sustain themselves by going back and forth between various inscriptions. Based on a case study, we show how the movement of subsistence always eludes that of reference, and how analysts can only move along with this movement by limiting their corroboration techniques, both in number and in range. Thus, this paper makes an important contribution to research on language and social interaction, as well as science and technology studies.
Gender Differences in Political Media Coverage: A Meta-Analysis
Authors: Van der Pas Daphne Joanna , Aaldering Loes 
Published: February 2020

AbstractDo the media cover men and women politicians and candidates differently? This article performs a systematic analysis of 90 studies covering over 25,000 politicians in over 750,000 media stories, and presents the accumulated knowledge in a comprehensive theoretical framework. The paper shows that there is a gender bias in the amount of coverage of politicians in proportional electoral systems, where women politicians lag behind men in media attention, but that, surprisingly, this gender bias is absent in majoritarian electoral systems. In addition, we systematically review gender differences in the content of media reports on political candidates, such as differences in attention to private life and family, viability and horse-race coverage, issue coverage, and gender stereotypes. Overall, women politicians receive more attention to their appearance and personal life, more negative viability coverage, and, to some extent, stereotypical issue and trait coverage. We conclude by pointing out promising avenues for future research.
Dynamics in the emergence of dormant and non-dormant herbaceous species from the soil seed bank from a Brazilian dry forest
Authors: de Souza José Djalma , de Souza Aguiar Bruno Ayron , dos Santos Danielle Melo , de Araujo Vanessa Kelly Rodrigues , Simões Júlia Arruda , de Andrade Juliana Ramos , de Lima Araújo Elcida 
Published: February 2020

AbstractAimsIn dry tropical forests, herbaceous species may have dormancy mechanisms and form persistent and transient seed banks in the soil. Evolutionarily acquired, these mechanisms are efficient for the establishment and survival of these herbs, especially in forests with unpredictable climates, such as the Caatinga. Thus, our objective was to verify whether the studied herbaceous species adopt the physical dormancy mechanism and how these natural barriers are overcome, to understand the temporal dynamics existing in the soil seed bank from a Brazilian dry tropical forest.MethodsSeeds of five native herbaceous species from the Caatinga forests were selected and submitted to pre-germinative treatments for verifying the presence of physical dormancy. We collected soil samples in the rainy and dry seasons for four consecutive years and monitored the emergence of the selected herbaceous in the greenhouse. We verified the differences in germination and seed bank emergence in the soil by generalized linear models.Important FindingsThe presence and absence of physical dormancy were observed in seeds from Caatinga herbaceous species. We found intraspecific and interspecific differences in the herbaceous emergence from soil seed banks between years and climatic seasons. In perennial herbs, consecutive lack of emergence between seasons and years was frequent, which suggests a direct relationship with the mechanism of physical dormancy and the environmental conditions necessary to overcome integument barriers. In these species, seed dimorphism and dormancy may confer additional advantages to their survival. Moreover, presenting intermediate levels of physical dormancy in an annual species may be an evolutionary adjustment to rainfall unpredictability. In contrast, we found that the annual herb without dormancy is more sensitive to seasonal and interannual climate changes, as evidenced by the increase and significant reduction of its emergence in the soil seed bank. These differences acquired evolutionarily are advantageous for the establishment of herbaceous populations, mainly in semiarid regions with an unpredictable climate.
Whole Genome Sequencing Detects Minimal Clustering Among Escherichia coli Sequence Type 131-H30 Isolates Collected From United States Children’s Hospitals
Authors: Miles-Jay Arianna , Weissman Scott J , Adler Amanda L , Baseman Janet G , Zerr Danielle M 
Published: February 2020

Abstract
We applied whole genome sequencing to identify putative transmission clusters among clinical multidrug-resistant Escherichia coli sequence type 131-H30 isolates from 4 United States children’s hospitals. Of 126 isolates, 17 were involved in 8 putative transmission clusters; 4 clusters showed evidence of healthcare-associated epidemiologic linkages. Geographic clustering analyses showed weak geographic clustering.
OASTL-A1 functions as a cytosolic cysteine synthase and affects arsenic tolerance in rice
Authors: Wang Chengcheng , Zheng Lihua , Tang Zhong , Sun Shengkai , Ma Jian Feng , Huang Xin-Yuan , Zhao Fang-Jie 
Published: February 2020

Abstract
Arsenic (As) contamination in paddy soil can cause phytotoxicity and elevated As accumulation in rice grains. Arsenic detoxification is closely linked to sulfur assimilation, but the genes involved have not been described in rice. In this study, we characterize the function of OASTL-A1, an O-acetylserine(thiol) lyase, in cysteine biosynthesis and detoxification of As in rice. Tissue expression analysis revealed that OsOASTL-A1 is mainly expressed in roots at the vegetative growth stage and in nodes at the reproductive stage. Furthermore, the expression of OsOASTL-A1 in roots was strongly induced by As exposure. Transgenic rice plants expressing pOsOASTL-A1::GUS (β-glucuronidase) indicated that OsOASTL-A1 was strongly expressed in the outer cortex and the vascular cylinder in the root mature zone. Subcellular localization using OsOASTL-A1:eGFP (enhanced green fluorescent protein) fusion protein showed that OsOASTL-A1 was localized to the cytosol. In vivo and in vitro enzyme activity assays showed that OsOASTL-A1 possessed the O-acetylserine(thiol) lyase activity. Knockout of OsOASTL-A1 led to significantly lower levels of cysteine, glutathione, and phytochelatins in roots and increased sensitivity to arsenate stress. Furthermore, the osoastl-a1 knockout mutants reduced As accumulation in the roots, but increased As accumulation in shoots. We conclude that OsOASTL-A1 is the cytosolic O-acetylserine(thiol) lyase that plays an important role in non-protein thiol biosynthesis in roots for As detoxification.
Overexpression of bHLH95, a basic helix–loop–helix transcription factor family member, impacts trichome formation via regulating gibberellin biosynthesis in tomato
Authors: Chen Yao , Su Dan , Li Jie , Ying Shiyu , Deng Heng , He Xiaoqing , Zhu Yunqi , Li Ying , Chen Ya , Pirrello Julien , Bouzayen Mondher , Liu Yongsheng , Liu Mingchun 
Published: February 2020

AbstractTrichomes are epidermal protuberances on aerial parts of plants known to play an important role in biotic and abiotic stresses. To date, our knowledge of the regulation of trichome formation in crop species is very limited. Through phenotyping of the Solanum pennellii×S. lycopersicum (cv. M82) introgression population, we identified the SlbHLH95 transcription factor as a negative regulator of trichome formation in tomato. In line with this negative role, SlbHLH95 displayed a very low expression in stems where trichomes are present at high density. Overexpression of SlbHLH95 resulted in a dramatically reduced trichome density in stems and a significant down-regulation of a set of trichome-related genes. In addition to the lower trichome density, overexpressing lines also showed pleiotropic alterations affecting both vegetative and reproductive development. While most of these phenotypes were reminiscent of gibberellin (GA)-deficient phenotypes, expression studies showed that two GA biosynthesis genes, SlGA20ox2 and SlKS5, are significantly down-regulated in SlbHLH95-OE plants. Moreover, in line with a decrease in active GA content, the glabrous and dwarf phenotypes were rescued by exogenous GA treatment. In addition, yeast one-hybrid and transactivation assays revealed that SlbHLH95 represses the expression of SlGA20ox2 and SlKS5 via direct binding to their promoters. Taken together, our study established a link between SlbHLH95, GA, and trichome formation, and uncovered the role of this gene in modulating GA biosynthesis in tomato.
Three rationalities for making sense of internal displacement in Ukraine
Authors: Uehling Greta Lynn 
Published: February 2020

Abstract
The territorial disputes between Russian Federation and Ukraine over Crimea and Donbas have led to the forcible internal displacement of at least 1.6 million people. While Although the literature on forced migration and internal displacement have been framed predominantly in terms of trauma and disenfranchisement (IOM 2018; Dunn 2018), this article argues that a fuller range of Internally Displaced Person (IDP) subjectivities can be made intelligible by considering the rationalities organizing IDP survival. Based on a comparative analysis of 155 interviews with IDPs from Crimea and Donbas, the article demonstrates that forced displacement is more heterogenous than has previously been allowed. I theorize this diversity by using analytics of governmentality to examine the logics or ‘rationalities’ used to make sense of forced migration. The conceptual tools offered by studies of governmentality are ideal for this case because they overlap with themes that predominated in data collected during ethnographic fieldwork in Ukraine between 2015 and 2017: agency, responsibility, and freedom. The article contributes a framework for comparing IDP subjectivities that encompasses diversity and provides a new vocabulary for describing the strategic efforts forced migrants exert to mend their lives.
Methanol and water maser observations separate disc and outflow sources in IRAS 19410+2336
Authors: Darwish M S , Edris K A , Richards A M S , Etoka S , Saad M S , Beheary M M , Fuller G A 
Published: February 2020

ABSTRACT
We investigate the kinematics of high-mass protostellar objects within the high-mass star-forming region IRAS 19410+2336. We performed high angular resolution observations of 6.7-GHz methanol and 22 GHz water masers using the Multi-Element Radio Linked Interferometer Network (MERLIN) and e-MERLIN interferometers. The 6.7-GHz methanol maser emission line was detected within the ∼16–27 km s−1 velocity range with a peak flux density ∼50 Jy. The maser spots are spread over ∼1.3 arcsec on the sky, corresponding to ∼2800 au at a distance of 2.16 kpc. These are the first astrometric measurements at 6.7 GHz in IRAS 19410+2336. The 22-GHz water maser line was imaged in 2005 and 2019 (the latter with good astrometry). Its velocities range from 13 to ∼29 km s−1. The peak flux density was found to be 18.7 and 13.487 Jy in 2005 and 2019, respectively. The distribution of the water maser components is up to 165 mas, ∼350 au at 2.16 kpc. We find that the Eastern methanol masers most probably trace outflows from the region of millimetre source mm1. The water masers to the West lie in a disc (flared or interacting with outflow/infall) around another more evolved millimetre source (13-s). The maser distribution suggests that the disc lies at an angle of 60° or more to the plane of the sky and the observed line-of-sight velocities then suggest an enclosed mass between 44 M⊙ and as little as 11 M⊙ if the disc is edge-on. The Western methanol masers may be infalling.
Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking
Authors: Waldern Justin , Schiraldi Nicholas J , Belfort Marlene , Novikova Olga 
Published: February 2020

Abstract
Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.
Ancient Coretention of Paralogs of Cid Centromeric Histones and Cal1 Chaperones in Mosquito Species
Authors: Kursel Lisa E , Welsh Frances C , Malik Harmit S 
Published: February 2020

AbstractDespite their essential role in chromosome segregation in most eukaryotes, centromeric histones (CenH3s) evolve rapidly and are subject to gene turnover. We previously identified four instances of gene duplication and specialization of Cid, which encodes for the CenH3 in Drosophila. We hypothesized that retention of specialized Cid paralogs could be selectively advantageous to resolve the intralocus conflict that occurs on essential genes like Cid, which are subject to divergent selective pressures to perform multiple functions. We proposed that intralocus conflict could be a widespread phenomenon that drives evolutionary innovation in centromeric proteins. If this were the case, we might expect to find other instances of coretention and specialization of centromeric proteins during animal evolution. Consistent with this hypothesis, we find that most mosquito species encode two CenH3 (mosqCid) genes, mosqCid1 and mosqCid2, which have been coretained for over 150 My. In addition, Aedes species encode a third mosqCid3 gene, which arose from an independent gene duplication of mosqCid1. Like Drosophila Cid paralogs, mosqCid paralogs evolve under different selective constraints and show tissue-specific expression patterns. Analysis of mosqCid N-terminal protein motifs further supports the model that mosqCid paralogs have functionally diverged. Extending our survey to other centromeric proteins, we find that all Anopheles mosquitoes encode two CAL1 paralogs, which are the chaperones that deposit CenH3 proteins at centromeres in Diptera, but a single CENP-C paralog. The ancient coretention of paralogs of centromeric proteins adds further support to the hypothesis that intralocus conflict can drive their coretention and functional specialization.