bluuebunny/crossref_metadata_2025_split huggingface dataset:
SureTypeSC—a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data
Authors: Vogel Ivan , Blanshard Robert C , Hoffmann Eva R 
Published: May 2019

AbstractMotivationAccurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single-cell environment is challenging due to the errors caused by whole-genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single-cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole-genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single-cell applications.ResultsIn this study, we have created a resource of 28.7 million SNPs, typed at high confidence from whole-genome amplified DNA from single cells using the Illumina SNP bead array technology. The resource is generated from 104 single cells from two cell lines that are available from the Coriell repository. We used mother–father–proband (trio) information from multiple technical replicates of bulk DNA to establish a high quality reference genotype for the two cell lines on the SNP array. This enabled us to develop SureTypeSC—a two-stage machine learning algorithm that filters a substantial part of the noise, thereby retaining the majority of the high quality SNPs. SureTypeSC also provides a simple statistical output to show the confidence of a particular single-cell genotype using Bayesian statistics.Availability and implementationThe implementation of SureTypeSC in Python and sample data are available in the GitHub repository: https://github.com/puko818/SureTypeSCSupplementary informationSupplementary data are available at Bioinformatics online.
Country Is Yarning to Me: Worldview, Health and Well-Being Amongst Australian First Nations People
Authors: Terare Mareese , Rawsthorne Margot 
Published: May 2019

Abstract
Health inequalities experienced by Australian First Nations People are amongst the most marked in the world, with First Nations People dying some ten years earlier than non-Indigenous Australians. The failure of existing responses to health inequalities suggests new knowledges and questions that need to be explored. It is likely that these new knowledges sit outside of western research or practice paradigms. Through the Indigenous practice of yarning, the importance of worldview and Country emerged as an under-acknowledged social determinant of Australian First Nations People well-being. Yarning is a process of storytelling that involves both sound and silence. It requires embodied deep listening through which stories emerge that create new knowledge and understanding. We anchor our learning by re-telling John’s creation story, a story of healing through discovering his Aboriginal Worldview through reconnecting to Country. Country for First Nations People is more than a physical place; it is a place of belonging and a way of believing. We argue for the recognition of trauma, recognition of diversity and the use of yarning in social work practice. We conclude that reconnecting to Aboriginal Worldview provides hopeful insights into the well-being of Australia’s First Nations People and the social determinants of health.
Stability-Indicating Chromatographic Methods for the Investigation of Ritodrine Hydrochloride Stability and Characterization of the Oxidative Degradation Product
Authors: Rashed Noha Salem , Abdallah Ola Mostafa , El-Olemy Ahmed , Eldin Asmaa Ibrahim Hosam 
Published: May 2019

Abstract
Two simple and sensitive chromatographic methods were developed and validated for quantitative determination of ritodrine hydrochloride in presence of its oxidative degradation product. The first method depends on densitomeric determination of thin-layer chromatograms of the intact drug in presence of its oxidative degradate. Excellent separation was achieved at 220 nm using a mobile phase of dichloromethane–methanol–glacial acetic acid (15 : 5 : 0.25, v/v/v). The second was an HPLC method, in which efficient separation was carried out on C18 column (150 × 4.6 × 5 μm) using a mobile phase consisting of water: acetonitrile (70,30, v/v) at a flow rate of 1 mL min−1 and UV detection at 220 nm. Beer’s law was obeyed in the range of 0.025–0.3 μg/spot and 5–40 μg mL−1 of the intact drug using the two methods, respectively. The proposed methods were validated according to International Conference on Harmonization guidelines and successfully applied for the determination of ritodrine hydrochloride in bulk powder, laboratory prepared mixtures and pharmaceutical dosage form with good accuracy and precision. The results obtained were compared with those of the reported method and were found to be in good agreement.
Risk of dementia in stroke-free patients diagnosed with atrial fibrillation: data from a population-based cohort
Authors: Kim Dongmin , Yang Pil-Sung , Yu Hee Tae , Kim Tae-Hoon , Jang Eunsun , Sung Jung-Hoon , Pak Hui-Nam , Lee Myung-Yong , Lee Moon-Hyoung , Lip Gregory Y H , Joung Boyoung 
Published: May 2019

Abstract

Aims
Atrial fibrillation (AF) is generally regarded as a risk factor for dementia, though longitudinal studies assessing the association between AF and dementia have shown inconsistent results. This study aimed to determine the effect of AF on the risk of developing dementia using a longitudinal, community-based, and stroke-free elderly cohort.

Methods and results
The association of incident AF with the development of incident dementia was assessed from 2005 to 2012 in 262 611 dementia- and stroke-free participants aged ≥60 years in the Korea National Health Insurance Service-Senior cohort. Incident AF was observed in 10 435 participants over an observational period of 1 629 903 person-years (0.64%/year). During the observational period, the incidence of dementia was 4.1 and 2.7 per 100 person-years in the incident AF and propensity score-matched AF-free groups, respectively. After adjustment, the risk of dementia was significantly increased by incident AF with a hazard ratio (HR) of 1.52 [95% confidence interval (CI) 1.43–1.63], even after censoring for stroke (1.27, 95% CI 1.18–1.37). Incident AF increased the risk of both Alzheimer (HR 1.31, 95% CI 1.20–1.43) and vascular dementia (HR 2.11, 95% CI 1.85–2.41). Among patients with incident AF, oral anticoagulant use was associated with a preventive effect on dementia development (HR 0.61, 95% CI 0.54–0.68), and an increasing CHA2DS2-VASc score was associated with a higher risk of dementia.

Conclusion
Incident AF was associated with an increased risk of dementia, independent of clinical stroke in an elderly population. Oral anticoagulant use was linked with a decreased incidence of dementia.
Knowledge, Skills, Craft? The Skilled Worker in West German Industry and the Resilience of Vocational Training, 1970–2000
Authors: Raphael Lutz 
Published: May 2019

Abstract
The spread of computer technology in West German industry during the 1980s and 1990s dramatically changed the demand for skilled and unskilled work in manufacturing. As a result the knowledge used in production was redefined and reformers pushed for radical reform in vocational and general education. In these decades a corporate agreement across trade unions, associations of employers and state bureaucracy brought about a series of adaptive reforms of existing apprenticeships and the creation of new apprenticeships in new branches. This survival of the dual system is analysed as part of the strategies of modernizing West German manufacturing industries. Both employers and trade unions defended the central role of skilled workers in the new system of flexible quality production that developed during this period of rapid technological change. Data from the Socio-Economic Panel and from other sources enable analysis of the social effects of this economically successful strategy. They show the large-scale use of skilled workers in industrial production and their opportunities for upward mobility and additional qualifications. At the same time unskilled workers, and unskilled migrant workers in particular, experienced greater risks of unemployment and increased job uncertainty.
The Second Act: Seeking Best Practices for Encore Worker Management
Authors: Boyle Pam A 
Published: May 2019

AbstractBackground and ObjectivesThe Baby Boomers are the largest generation in history, and as they reach the traditional retirement age of 65, many leave the workforce and seek encore jobs. This exodus of Boomers creates a knowledge gap that the Gen X and Millennial generations lack the numbers and often the experience to fill. As the knowledge gap increases, managers can recruit and hire encore workers to fill the gap and retain human capital. This article answers the question: What processes can managers implement to close knowledge gaps by hiring or retaining Boomers seeking encore jobs?Research Design and MethodsThis article examined the factors for filling knowledge gaps with encore workers and the necessary processes for hiring or retaining encore workers to attain organizational goals. A systematic review of 32 published articles and four dissertations was conducted using Super’s amended career development theory. A thematic analysis approach was used to examine the evidence.ResultsThe findings led to the development of best practices to guide managers who want to hire encore workers to close the knowledge gap, and increase organizational knowledge capital.Discussion and ImplicationsBaby Boomers are responsible for finding and sustaining encore worker positions, but managers can support Boomers through best practices including skills assessments, revised HR policies, reverse-mentoring programs, and training opportunities for managers and encore workers.
Impaired mitochondrial maturation of sulfite oxidase in a patient with severe sulfite oxidase deficiency
Authors: Bender Daniel , Kaczmarek Alexander Tobias , Santamaria-Araujo Jose Angel , Stueve Burkard , Waltz Stephan , Bartsch Deniz , Kurian Leo , Cirak Sebahattin , Schwarz Guenter 
Published: May 2019

AbstractSulfite oxidase (SO) is encoded by the nuclear SUOX gene and catalyzes the final step in cysteine catabolism thereby oxidizing sulfite to sulfate. Oxidation of sulfite is dependent on two cofactors within SO, a heme and the molybdenum cofactor (Moco), the latter forming the catalytic site of sulfite oxidation. SO localizes to the intermembrane space of mitochondria where both—pre-SO processing and cofactor insertion—are essential steps during SO maturation. Isolated SO deficiency (iSOD) is a rare inborn error of metabolism caused by mutations in the SUOX gene that lead to non-functional SO. ISOD is characterized by rapidly progressive neurodegeneration and death in early infancy. We diagnosed an iSOD patient with homozygous mutation of SUOX at c.1084G>A replacing Gly362 to serine. To understand the mechanism of disease, we expressed patient-derived G362S SO in Escherichia coli and surprisingly found full catalytic activity, while in patient fibroblasts no SO activity was detected, suggesting differences between bacterial and human expression. Moco reconstitution of apo-G362S SO was found to be approximately 90-fold reduced in comparison to apo-WT SO in vitro. In line, levels of SO-bound Moco in cells overexpressing G362S SO were significantly reduced compared to cells expressing WT SO providing evidence for compromised maturation of G362S SO in cellulo. Addition of molybdate to culture medium partially rescued impaired Moco binding of G362S SO and restored SO activity in patient fibroblasts. Thus, this study demonstrates the importance of the orchestrated maturation of SO and provides a first case of Moco-responsive iSOD.
PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy
Authors: Abbas Ata , Padmanabhan Roshan , Romigh Todd , Eng Charis 
Published: May 2019

Abstract
Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation and premature termination. Pol II pausing is a phenomenon where Pol II complex pauses within 30–60 nucleotides after initiating the transcription. Negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF) contribute in the establishment of Pol II pausing, and positive transcription elongation factor b releases (P-TEFb) paused complex after phosphorylating DSIF that leads to dissociation of NELF. Pol II pausing is observed in most expressed genes across the metazoan. The precise role of Pol II pausing is not well understood; however, it’s required for integration of signals for gene regulation. In the present study, we investigated the role of phosphatase and tensin homolog (PTEN) in genome-wide transcriptional regulation using PTEN overexpression and PTEN knock-down models. Here we identify that PTEN alters the expression of hundreds of genes, and its restoration establishes genome-wide Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes Pol II occupancy across the genome and possibly impacts Pol II pause duration, release and elongation rate in order to enable precise gene regulation at the genome-wide scale. Our observations demonstrate an imperative role of PTEN in global transcriptional regulation that will provide a new direction to understand PTEN-associated pathologies and its management.
Conversations on the Frontier: Finding the Dialogic in Nineteenth-century Anthropological Archives
Authors: Gibson Jason , Gardner Helen 
Published: May 2019

Abstract
While anthropological archives tend to be named after the collector of the material, they are often the product of conversations and long-term engagements with informants. Focusing on the concept of the dialogic, this article contends that these materials ought to be equally conceived as co-productions, often made via complex, asymmetrical researcher/researched engagements. We specifically home in on the dialogic traces left in the archive of the nineteenth century Australian ethnographer A. W. Howitt and his various conversations with an Aboriginal man named Ienbin. We argue that by being attentive to the dialogic aspects of ethnographic sources we can recognize that the Indigenous or anthropological knowledge contained within them is to a significant degree co-constructed in as much as it emerges from social encounter and interaction. More than merely acknowledging the agency of Indigenous informants we propose a more dynamic reading of these texts as products of discursive interactions and shifting relationships.
The Cost of Inflammatory Bowel Disease: An Initiative From the Crohn’s & Colitis Foundation
Authors: Park K T , Ehrlich Orna G , Allen John I , Meadows Perry , Szigethy Eva M , Henrichsen Kim , Kim Sandra C , Lawton Rachel C , Murphy Sean M , Regueiro Miguel , Rubin David T , Engel-Nitz Nicole M , Heller Caren A 
Published: May 2019

Abstract

Background
The Crohn’s & Colitis Foundation’s Cost of Inflammatory Bowel Disease (IBD) Care Initiative seeks to quantify the wide-ranging health care costs affecting patients living with IBD. We aimed to (1) describe the annualized direct and indirect costs of care for patients with Crohn’s disease (CD) or ulcerative colitis (UC), (2) determine the longitudinal drivers of these costs, and (3) characterize the cost of care for newly diagnosed patients.

Methods
We analyzed the Optum Research Database from the years 2007 to 2016, representing commercially insured and Medicare Advantage–insured patients in the United States. Inclusion for the study was limited to those who had continuous enrollment with medical and pharmacy benefit coverage for at least 24 months (12 months before through 12 months after the index date of diagnosis). The value of patient time spent on health care was calculated as number of workplace hours lost due to health care encounters multiplied by the patients’ estimated average wage derived from the Bureau of Labor Statistics. Comparisons between IBD patients and non-IBD patients were analyzed based on demographics, health plan type, and length of follow-up. We used generalized linear models to estimate the association between total annual costs and various patient variables.

Results
There were 52,782 IBD patients (29,062 UC; 23,720 CD) included in the analysis (54.1% females). On a per-annual basis, patients with IBD incurred a greater than 3-fold higher direct cost of care compared with non-IBD controls ($22,987 vs $6956 per-member per-year paid claims) and more than twice the out-of-pocket costs ($2213 vs $979 per-year reported costs), with all-cause IBD costs rising after 2013. Patients with IBD also experienced significantly higher costs associated with time spent on health care as compared with controls. The burden of costs was most notable in the first year after initial IBD diagnosis (mean = $26,555). The study identified several key drivers of cost for IBD patients: treatment with specific therapeutics (biologics, opioids, or steroids); ED use; and health care services associated with relapsing disease, anemia, or mental health comorbidity.

Conclusion
The costs of care for IBD have increased in the last 5 years and are driven by specific therapeutics and disease features. In addition, compared with non-IBD controls, IBD patients are increasingly incurring higher costs associated with health care utilization, out-of-pocket expenditures, and workplace productivity losses. There is a pressing need for cost-effective strategies to address these burdens on patients and families affected by IBD.
Modeling the Effects of Resource-Driven Immune Defense on Parasite Transmission in Heterogeneous Host Populations
Authors: Hall Richard J 
Published: May 2019

Abstract
Individuals experience heterogeneous environmental conditions that can affect within-host processes such as immune defense against parasite infection. Variation among individuals in parasite shedding can cause some hosts to contribute disproportionately to population-level transmission, but we currently lack mechanistic theory that predicts when environmental conditions can result in large disease outbreaks through the formation of immunocompromised superspreading individuals. Here, I present a within-host model of a microparasite’s interaction with the immune system that links an individual host’s resource intake to its infectious period. For environmental scenarios driving population-level heterogeneity in resource intake (resource scarcity and resource subsidy relative to baseline availability), I generate a distribution of infectious periods and simulate epidemics on these heterogeneous populations. I find that resource scarcity can result in large epidemics through creation of superspreading individuals, while resource subsidies can reduce or prevent transmission of parasites close to their invasion threshold by homogenizing resource allocation to immune defense. Importantly, failure to account for heterogeneity in competence can result in under-prediction of outbreak size, especially when parasites are close to their invasion threshold. More generally, this framework suggests that differences in conditions experienced by individual hosts can lead to superspreading via differences in resource allocation to immune defense alone, even in the absence of other heterogeneites such as host contacts.
New developments in innovation and entrepreneurial ecosystems
Authors: Feldman Maryann , Siegel Donald S , Wright Mike 
Published: May 2019

AbstractIn this article, we provide a rationale for this Special Section on innovation and entrepreneurial ecosystems. We also present a summary of the papers presented in the Special Section, highlighting research questions, theories, data and methods, and principal findings and conclusions. A research agenda is also identified, involving multi-level research on agents, institutions, and regions on the context, process, and impact of innovation and entrepreneurial ecosystems.
Eliminating mcr-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system
Authors: Wang Pengxia , He Dongmei , Li Baiyuan , Guo Yunxue , Wang Weiquan , Luo Xiongjian , Zhao Xuanyu , Wang Xiaoxue 
Published: May 2019

AbstractObjectivesTo eliminate mcr-1-harbouring plasmids and MDR plasmids in clinical Escherichia coli isolates.MethodsPlasmid pMBLcas9 expressing Cas9 was constructed and used to clone target single-guide RNAs (sgRNAs) for plasmid curing. The recombinant plasmid pMBLcas9-sgRNA was transferred by conjugation into two clinical E. coli isolates. The curing efficiency of different sgRNAs targeting conserved genes was tested. The elimination of targeted plasmids and the generation of transposase-mediated recombination of p14EC033a variants were characterized by PCR and DNA sequencing.ResultsIn this study, four native plasmids in isolate 14EC033 and two native plasmids in isolate 14EC007 were successfully eliminated in a step-by-step manner using pMBLcas9. Moreover, two native plasmids in 14EC007 were simultaneously eliminated by tandemly cloning multiple sgRNAs in pMBLcas9, sensitizing 14EC007 to polymyxin and carbenicillin. In 14EC033 with two mcr-1-harbouring plasmids, IncI2 plasmid p14EC033a and IncX4 plasmid p14EC033b, a single mcr-1 sgRNA mediated the loss of p14EC033b and generated a mutant p14EC033a in which the mcr-1 gene was deleted. An insertion element, IS5, located upstream of mcr-1 in p14EC033a was responsible for transposase-mediated recombination, resulting in mcr-1 gene deletion instead of plasmid curing.ConclusionsCRISPR/Cas9 can be used to efficiently sensitize clinical isolates to antibiotics in vitro. For isolates with multiple plasmids, the CRISPR/Cas9 approach can either remove each plasmid in a stepwise manner or simultaneously remove multiple plasmids in one step. Moreover, this approach can be used to delete multiple gene copies by using only one sgRNA. However, caution must be exercised to avoid unwanted recombination events during genetic manipulation.
A new species of alvinocaridid shrimp Rimicaris Williams & Rona, 1986 (Decapoda: Caridea) from hydrothermal vents on the Mariana Back Arc Spreading Center, northwestern Pacific
Authors: Komai Tomoyuki , Giguère Thomas 
Published: May 2019

AbstractA new species of the alvinocaridid shrimp genus RimicarisWilliams & Rona, 1986, R. falkoraen. sp., is described and illustrated based on material from deep-sea hydrothermal vents (3,630–3,912 m deep) on the Mariana Back Arc Spreading Centre, northwestern Pacific, representing the tenth described species of the genus. The new species is morphologically most similar to R. paulexa (Martin & Shank, 2005), but the presence of numerous short setae scattered on the carapace surface, the relatively long antennular stylocerite usually reaching the distal margin of article 2 of the antennular peduncle and the spiniform posteromesial projection of the uropodal protopod distinguish the new species from all congeners. Genetic analysis using the barcoding region of the mitochondrial COI gene supports the recognition of the species as new.