bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burden of Candidemia in the United States, 2017
Authors: Tsay Sharon V , Mu Yi , Williams Sabrina , Epson Erin , Nadle Joelle , Bamberg Wendy M , Barter Devra M , Johnston Helen L , Farley Monica M , Harb Sasha , Thomas Stepy , Bonner Lindsay A , Harrison Lee H , Hollick Rosemary , Marceaux Kaytlynn , Mody Rajal K , Pattee Brittany , Shrum Davis Sarah , Phipps Erin C , Tesini Brenda L , Gellert Anita B , Zhang Alexia Y , Schaffner William , Hillis Sherry , Ndi Danielle , Graber Caroline R , Jackson Brendan R , Chiller Tom , Magill Shelley , Vallabhaneni Snigdha 
Published: February 2020

Abstract

Background
Candidemia is a common healthcare-associated bloodstream infection with high morbidity and mortality. There are no current estimates of candidemia burden in the United States (US).

Methods
In 2017, the Centers for Disease Control and Prevention conducted active population-based surveillance for candidemia through the Emerging Infections Program in 45 counties in 9 states encompassing approximately 17 million persons (5% of the national population). Laboratories serving the catchment area population reported all blood cultures with Candida, and a standard case definition was applied to identify cases that occurred in surveillance area residents. Burden of cases and mortality were estimated by extrapolating surveillance area cases to national numbers using 2017 national census data.

Results
We identified 1226 candidemia cases across 9 surveillance sites in 2017. Based on this, we estimated that 22 660 (95% confidence interval [CI], 20 210–25 110) cases of candidemia occurred in the US in 2017. Overall estimated incidence was 7.0 cases per 100 000 persons, with highest rates in adults aged ≥ 65 years (20.1/100 000), males (7.9/100 000), and those of black race (12.3/100 000). An estimated 3380 (95% CI, 1318–5442) deaths occurred within 7 days of a positive Candida blood culture, and 5628 (95% CI, 2465–8791) deaths occurred during the hospitalization with candidemia.

Conclusions
Our analysis highlights the substantial burden of candidemia in the US. Because candidemia is only one form of invasive candidiasis, the true burden of invasive infections due to Candida is higher. Ongoing surveillance can support future burden estimates and help assess the impact of prevention interventions.
A Prospective, Population-based Study to Determine the Incidence and Bacteriology of Bacterial Conjunctivitis in Children &lt;2 Years of Age Following 7-Valent and 13-Valent Pneumococcal Conjugate Vaccine Sequential Implementation
Authors: Dagan Ron , Ben-Shimol Shalom , Greenberg David , Givon-Lavi Noga 
Published: February 2020

AbstractBackgroundBacterial conjunctivitis is most commonly caused by nontypeable Haemophilus influenzae (NTHi), followed by Streptococcus pneumoniae. No population-based data on the impact of pneumococcal conjugate vaccines (PCVs) on the incidence of bacterial conjunctivitis have been published. We assessed rate dynamics of overall, pneumococcal, and NTHi conjunctivitis in children aged 2–23 months in southern Israel before and after PCV implementation.MethodsThis is a 12-year prospective, population-based surveillance, from July 2004 through June 2017. Our medical center serves a captive population of approximately 30 000 children &lt; 2 years of age, and its clinical microbiology laboratory processes &gt; 80% of all community-derived cultures, enabling incidence calculation. The 7-valent and 13-valent PCVs (PCV7 and PCV13, respectively) were implemented in the national immunization program in July 2009 and November 2010, respectively. Pneumococci, NTHi, Moraxella catarrhalis, and Streptococcus pyogenes were considered pathogens. Continuous annual incidences and incidence rate ratios comparing the PCV13 period (2015–2017) to the pre-PCV period (2004–2008) were calculated.ResultsDisease caused by PCV13 serotypes declined by 93%, without significant replacement with non-PCV13 serotypes. Rates of pneumococcal, NTHi, and overall culture-positive episodes declined by 59%, 41%, and 42%, respectively, while rates of culture-negative and other pathogens episodes did not change significantly. An overall reduction in all submitted culture rates of 35% was observed. This pattern was seen across all ages, including infants aged 2–5 months.ConclusionsPCV7/PCV13 implementation resulted in a marked and significant decline in pneumococcal, NTHi, and overall conjunctivitis rates in children &lt; 2 years of age. The impact on NTHi episodes alludes to the role of pneumococcus–NTHi interaction in conjunctivitis. The impact in infants aged &lt; 6 months suggests herd protection.
A Case Series of Children With 2019 Novel Coronavirus Infection: Clinical and Epidemiological Features
Authors: Jiehao Cai , Jin Xu , Daojiong Lin , Zhi Yang , Lei Xu , Zhenghai Qu , Yuehua Zhang , Hua Zhang , Ran Jia , Pengcheng Liu , Xiangshi Wang , Yanling Ge , Aimei Xia , He Tian , Hailing Chang , Chuning Wang , Jingjing Li , Jianshe Wang , Mei Zeng 
Published: February 2020

Abstract
We first described the 2019 novel coronavirus infection in 10 children occurring in areas other than Wuhan. The coronavirus diseases in children are usually mild and epidemiological exposure is a key clue to recognize pediatric case. Prolonged virus shedding is observed in respiratory tract and feces at the convalescent stage.
A Well Infant With Coronavirus Disease 2019 With High Viral Load
Authors: Kam Kai-qian , Yung Chee Fu , Cui Lin , Tzer Pin Lin Raymond , Mak Tze Minn , Maiwald Matthias , Li Jiahui , Chong Chia Yin , Nadua Karen , Tan Natalie Woon Hui , Thoon Koh Cheng 
Published: February 2020

Abstract
A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. This case highlights the difficulties in establishing the true incidence of COVID-19, as asymptomatic individuals can excrete the virus. These patients may play important roles in human-to-human transmission in the community.
Epigenomics and gene regulation in mammalian social systems
Authors: Guerrero Tania P , Fickel Jörns , Benhaiem Sarah , Weyrich Alexandra 
Published: February 2020

AbstractSocial epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene–environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.
The Limits of “Communication Mode” as a Construct
Authors: Hall Matthew L , Dills Sheila 
Published: February 2020

AbstractQuestions about communication mode (a.k.a. “communication options” or “communication opportunities”) remain among the most controversial issues in the many fields that are concerned with the development and well-being of children (and adults) who are d/Deaf or hard of hearing. In this manuscript, we argue that a large part of the reason that this debate persists is due to limitations of the construct itself. We focus on what we term “the crucial question”: namely, what kind of experience with linguistic input during infancy and toddlerhood is most likely to result in mastery of at least one language (spoken or signed) by school entry. We argue that the construct of communication mode—as currently construed—actively prevents the discovery of compelling answers to that question. To substantiate our argument, we present a review of a relevant subset of the recent empirical literature and document the prevalence of our concerns. We conclude by articulating the desiderata of an alternative construct that, if appropriately measured, would have the potential to yield answers to what we identify as “the crucial question.”
Ulcerative Colitis and Cytomegalovirus Infection: From A to Z
Authors: Mourad Fadi H , Hashash Jana G , Kariyawasam Viraj C , Leong Rupert W 
Published: February 2020

Abstract
Despite multiple studies, the role of cytomegalovirus [CMV] infection in exacerbating the severity of inflammation in ulcerative colitis [UC], and its response to treatment, remain debatable. Additionally, the optimal diagnostic tests for CMV infection in the setting of UC relapse, and timing of antiviral treatment initiation, remain unclear. The challenge faced by gastroenterologists is to differentiate between an acute UC flare and true CMV colitis. It seems that the presence of CMV colitis, as defined by the presence of intranuclear or intracellular inclusion bodies on haematoxylin and eosin [H&E] staining and/or positive immunohistochemistry [IHC] assay on histology, is associated with more severe colitis. Patients with CMV infection and acute severe colitis are more resistant to treatment with corticosteroids than non-infected patients. This refractoriness to steroids is related to colonic tissue CMV viral load and number of inclusion bodies [high-grade CMV infection] which may have a pronounced effect on clinical outcomes and colectomy rates. Whereas many studies showed no effect for antiviral treatment on colectomy rates in CMV-infected UC patients, there was a significant difference in colectomy rates of patients with high-grade infection who received anti-viral therapy compared with those who did not receive treatment. It was therefore proposed that high-grade CMV disease indicates that the virus is acting as a pathogen, whereas in those with low-grade CMV disease, the severity of IBD itself is more likely to influence outcome. The different algorithms that have been put forward for the management of patients with UC and concomitant CMV infection are discussed.
Outcome of extracorporeal membrane oxygenation support in patients with liver cirrhosis: a nationwide population-based cohort study
Authors: Chou An-Hsun , Wu Victor Chien-Chia , Chen Dong-Yi , Hung Kuo-Chun , Chang Shang-Hung , Chu Pao-Hsien , Chen Shao-Wei 
Published: February 2020

AbstractOBJECTIVESExtracorporeal membrane oxygenation (ECMO) is used for life support in patients with liver cirrhosis (LC). However, there have been no studies evaluating the outcome of ECMO support in patients with LC.METHODSUsing Taiwan’s National Health Insurance (NHI) database, we retrospectively evaluated patients with LC who received veno-venous or veno-arterial ECMO between 1 January 2000 and 31 December 2013. The outcomes included ECMO-related complications, in-hospital mortality, all-cause mortality and long-term outcomes in patients with and without LC.RESULTSA total of 7003 patients who received ECMO, of whom 233 (3.3%) had LC, were eligible for analysis. The LC patients who received ECMO support had a significantly higher risk of in-hospital mortality than the non-LC group (76.4% vs 60.7%; odds ratio 1.97; 95% confidence interval 1.44–2.70). The LC group also had a higher risk of complications, including de novo dialysis and massive blood transfusion with &gt;10 units of red blood cells. Patients ≥65 years of age, patients with respiratory disease, patients with hypoalbuminaemia and liver transplant patients had higher in-hospital and 1-year mortality. The mortality rates for patients with 2 or more risk factors were 90.3% and 95.8%, respectively. LC was associated with a higher incidence of all-cause mortality and liver-related outcomes during follow-up.CONCLUSIONSOur findings raise questions regarding the utility of ECMO for LC patients, especially when &gt;2 risk factors have been identified. ECMO support for LC patients should be used with caution and with careful patient selection.
An EFL Teacher’s Investment in Digital Multimodal Composing
Authors: Jiang Lianjiang , Yu Shulin , Zhao Yi 
Published: February 2020

Abstract
Although there is a growing call for L2 teachers to invest in using digital multimodal composing (DMC) as an instructional activity, there is a paucity of research on whether and how L2 teachers invest in DMC, and the impact of DMC on their teaching and changing identities remains underexplored. This study reports on a longitudinal case study of an EFL teacher’s investment in DMC in a university-based EFL classroom in China. A qualitative analysis of the data gathered from observation, interview, and informal conversation reveals that through investing in DMC this teacher started to renegotiate herself as a composing guide, a peer mentor, and a change agent. These shifts of identity were mainly driven by her enhanced cultural and social capital after investing in DMC, despite constraints from ideology and the policing of technology, language-dominant assessment, and other institutional demands. Implications on using DMC are also discussed.
Radiomics based on artificial intelligence in liver diseases: where are we?
Authors: Hu Wenmo , Yang Huayu , Xu Haifeng , Mao Yilei 
Published: February 2020

AbstractRadiomics uses computers to extract a large amount of information from different types of images, form various quantifiable features, and select relevant features using artificial-intelligence algorithms to build models, in order to predict the outcomes of clinical problems (such as diagnosis, treatment, prognosis, etc.). The study of liver diseases by radiomics will contribute to early diagnosis and treatment of liver diseases and improve survival and cure rates of liver diseases. This field is currently in the ascendant and may have great development in the future. Therefore, we summarize the progress of current research in this article and then point out the related deficiencies and the direction of future research.
Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels
Authors: Shenton Matt , Kobayashi Masaaki , Terashima Shin , Ohyanagi Hajime , Copetti Dario , Hernández-Hernández Tania , Zhang Jianwei , Ohmido Nobuko , Fujita Masahiro , Toyoda Atsushi , Ikawa Hiroshi , Fujiyama Asao , Furuumi Hiroyasu , Miyabayashi Toshie , Kubo Takahiko , Kudrna David , Wing Rod , Yano Kentaro , Nonomura Ken-ichi , Sato Yutaka , Kurata Nori 
Published: February 2020

Abstract
The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes, and a genomic resource for the exploitation of the Oryza tertiary gene pool.
Mutational Load and the Functional Fraction of the Human Genome
Authors: Galeota-Sprung Benjamin , Sniegowski Paul , Ewens Warren 
Published: February 2020

Abstract
The fraction of the human genome that is functional is a question of both evolutionary and practical importance. Studies of sequence divergence have suggested that the functional fraction of the human genome is likely to be no more than ∼15%. In contrast, the ENCODE project, a systematic effort to map regions of transcription, transcription factor association, chromatin structure, and histone modification, assigned function to 80% of the human genome. In this article, we examine whether and how an analysis based on mutational load might set a limit on the functional fraction. In order to do so, we characterize the distribution of fitness of a large, finite, diploid population at mutation-selection equilibrium. In particular, if mean fitness is ∼1, the fitness of the fittest individual likely to occur cannot be unreasonably high. We find that at equilibrium, the distribution of log fitness has variance nus, where u is the per-base deleterious mutation rate, n is the number of functional sites (and hence incorporates the functional fraction f), and s is the selection coefficient of deleterious mutations. In a large (N=109) reproducing population, the fitness of the fittest individual likely to exist is ∼e5nus. These results apply to both additive and recessive fitness schemes. Our approach is different from previous work that compared mean fitness at mutation-selection equilibrium with the fitness of an individual who has no deleterious mutations; we show that such an individual is exceedingly unlikely to exist. We find that the functional fraction is not very likely to be limited substantially by mutational load, and that any such limit, if it exists, depends strongly on the selection coefficients of new deleterious mutations.
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study
Authors: Han Xia , Guo Jindan , Pang Erli , Song Hongtao , Lin Kui 
Published: February 2020

AbstractHow have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.
Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa
Authors: Smith Theresa J , Xie Gary , Williamson Charles H D , Hill Karen K , Fernández Rafael A , Sahl Jason W , Keim Paul , Johnson Shannon L 
Published: February 2020

Abstract
Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.
Power, control, communities and health inequalities. Part II: measuring shifts in power
Authors: Ponsford Ruth , Collins Michelle , Egan Matt , Halliday Emma , Lewis Sue , Orton Lois , Powell Kate , Barnes Amy , Salway Sarah , Townsend Anne , Whitehead Margaret , Popay Jennie 
Published: February 2020

Abstract
In the health field, there is great interest in the role empowerment might play in reducing social inequalities in health. Empowerment is understood here as the processes of developing capabilities that individuals and/or communities need to exercise control over decisions and actions impacting on their lives and health. There is a fundamental problem, however, in identifying and measuring capabilities for collective control that emerge at the level of the collective, with much of the existing literature focusing on individual measures even where community-level processes are concerned. Collective measures need to capture the dynamics of interactions within and between groups, not simply aggregate individual-level measures. This article, Part 2 in a three-part series, takes up the challenge of identifying qualitative markers of capabilities for collective control. We applied the emancipatory power framework (EPF) reported in Part 1 of the series, to qualitative data generated during a longitudinal evaluation of a major English area-based empowerment initiative, the Big Local (BL). We identified empirical ‘markers’ of shifts towards greater collective control pertaining to each of the ‘power’ dimensions in the EPF—‘power within’, ‘power with’ and ‘power to’—and markers of communities exercising ‘power over’ other institutions/community members. These markers can usefully be applied in the evaluation planning and evaluation of empowerment initiatives. Part 3 in the series uses these markers and a second analytical framework developed during our evaluation of BL to explore how power dynamics unfold in participatory spaces in BL neighbourhoods.