bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid cost-effective viral genome sequencing by V-seq
Authors: Guo Longhua , Boocock James , Tome Jacob M. , Chandrasekaran Sukantha , Hilt Evann E. , Zhang Yi , Sathe Laila , Li Xinmin , Luo Chongyuan , Kosuri Sriram , Shendure Jay A. , Arboleda Valerie A. , Flint Jonathan , Eskin Eleazar , Garner Omai B. , Yang Shangxin , Bloom Joshua S. , Kruglyak Leonid , Yin Yi 
Published: August 2020

ABSTRACTConventional methods for viral genome sequencing largely use metatranscriptomic approaches or, alternatively, enrich for viral genomes by amplicon sequencing with virus-specific PCR or hybridization-based capture. These existing methods are costly, require extensive sample handling time, and have limited throughput. Here, we describe V-seq, an inexpensive, fast, and scalable method that performs targeted viral genome sequencing by multiplexing virus-specific primers at the cDNA synthesis step. We designed densely tiled reverse transcription (RT) primers across the SARS-CoV-2 genome, with a subset of hexamers at the 3’ end to minimize mis-priming from the abundant human rRNA repeats and human RNA PolII transcriptome. We found that overlapping RT primers do not interfere, but rather act in concert to improve viral genome coverage in samples with low viral load. We provide a path to optimize V-seq with SARS-CoV-2 as an example. We anticipate that V-seq can be applied to investigate genome evolution and track outbreaks of RNA viruses in a cost-effective manner. More broadly, the multiplexed RT approach by V-seq can be generalized to other applications of targeted RNA sequencing.
BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion ofArthrobacterphage cluster FE
Authors: Demo Stephanie , Kapinos Andrew , Bernardino Aaron , Guardino Kristina , Hobbs Blake , Hoh Kimberly , Lee Edward , Vuong Iphen , Reddi Krisanavane , Freise Amanda C. , Parker Jordan Moberg 
Published: August 2020

AbstractBacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of relatedMycobacteriaandArthrobacterphage genomes relied on nucleotide identity thresholds but, more recently, clustering ofGordoniaandMicrobacteriumphages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novelArthrobacterphage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity withArthrobacterphages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clusteringGordoniaandMicrobacteriumphages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.
Exploring how independent directors view CSR inequality using a quasi-natural experiment
Authors: Ongsakul Viput , Jiraporn Napatsorn , Jiraporn Pornsit 
Published: August 2020

Purpose
The purpose of this paper is to explore corporate social responsibility (CSR) inequality, which is the inequality across different CSR categories. Higher inequality suggests a less balanced CSR policy. To determine if CSR inequality is beneficial or harmful, this paper investigates how independent directors view CSR inequality, using an exogenous regulatory shock introduced by the passage of the Sarbanes–Oxley Act.

Design/methodology/approach
To draw causality, this study relies on a quasi-natural experiment based on an exogenous regulatory shock that forced certain firms to raise board independence. This approach is significantly less vulnerable to endogeneity and is much more likely to show a causal effect. The results using propensity score matching, principal component analysis and instrumental-variable analysis are confirmed.

Findings
The difference-in-difference estimates show that independent directors view CSR inequality unfavorably. Specifically, board independence diminishes CSR inequality by approximately 34%-43%. Because the empirical strategy is based on a quasi-natural experiment, the results are more likely to show causality. The results also imply that CSR inequality is a crucially important aspect of CSR.

Originality/value
Although a substantial volume of research has examined CSR, one vital aspect of CSR has been largely unexplored. Filling this void in the literature, the CSR inequality is investigated. The study is the first to explore how independent directors view CSR inequality using a quasi-natural experiment.
A systematic review of circular economy research in the construction industry
Authors: Osobajo Oluyomi A. , Oke Adekunle , Omotayo Temitope , Obi Lovelin Ifeoma 
Published: August 2020

PurposeWhile circular economy (CE) is fast becoming a political and economic agenda for global urban development, there are still substantial knowledge gaps in possible strategies to speed up such transition, especially in the construction industry. This study analyses literature surrounding CE to unpack current trends possible future research directions to foster CE implementation in the construction industry.Design/methodology/approachThe study undertakes a systematic review of CE literature published between 1990 and 2019. It adopts a five-stage procedure as a methodological approach for the review: formulation of the research question(s), locating and identifying relevant studies, selection and evaluation of studies, analysis or synthesis and results reporting.FindingsThe findings on CE research in the construction industry show extensive focus on resource use and waste management. There are limited investigations in other areas of construction such as supply chain integration, building designs, policy, energy efficiency, land use, offsite manufacturing, whole life costing, and risk, cost reduction, cost management, health and safety management. The study findings provide evidence that current CE practice fails to incorporate other areas that would facilitate the network of true circular construction industry.Originality/valueThis research provides a comprehensive overview of research efforts on CE in the construction context, identifying areas of extensive and limited coverage over three decades. Besides, it identifies possible pathways for future research directions on CE implementation, towards the accelerated transition to a true circular construction industry for the benefit of funding bodies and researchers.
Development of a sustainability rating tool for heritage buildings: future implications
Authors: Al-Sakkaf Abobakr , Zayed Tarek , Bagchi Ashutosh , Mahmoud Sherif , Pickup David 
Published: August 2020

PurposeHeritage buildings are significant for their historical and architectural value. Due to the lack of rating systems designed specifically for heritage buildings, it is essential to develop and validate a heritage building assessment tool that considers its specific characteristics. The purpose of this study is to provide an extensive review of research on Sustainability of Heritage Buildings (SHBs).Design/methodology/approachThis review highlights methodologies applied in SHBs research and analyzes major global rating systems in order to identify their deficiencies for SHBs assessment. A systematic review was employed and articles from the top 10 high impact factor journals were studied. Twelve major global rating systems and their assessment criteria were identified.FindingsSignificant variability was observed among the assessment tools since each tool assesses several criteria, factors and indicators that fit its local context. Part of this variability can also be seen in the rating scales, threshold values and accreditation titles. As a result, the final sustainability ranking for a given building cannot be compared among the 12 rating systems. Most importantly, these systems fail to analyze some factors such as energy that are considered important with respect to heritage building assessment.Originality/valueSince no specific rating system could be identified in this review as the most appropriate for heritage buildings, a new sustainability assessment tool that is specific to heritage buildings should be developed. Such a tool will enable facility managers to evaluate and improve the sustainability of their heritage buildings while preserving them.
Tenacissoside H promotes neurological recovery of cerebral ischaemia/reperfusion injury in mice by modulating inflammation and oxidative stress via TrkB pathway
Authors: Zhang Rui , Liu Cui , Li Yang , Chen Liang , Xiang Jianfeng 
Published: August 2020

AbstractCerebral ischaemia/reperfusion (I/R)‐induced acute brain injury remains a troublesome condition in clinical practice. The present study aimed to investigate the protective effect of tenacissoside H (TH) on I/R‐induced cerebral injury in mice. Here, a mouse model of middle cerebral artery occlusion (MCAO) was established by an improved Longa‐Zea method. TH was given by intraperitoneal injection once a day within 1 week before establishing the mouse MCAO model. The neurological functions of mice were evaluated and the apoptosis of neurons was also detected by the TUNEL method and Nissl's staining. ELISA and western blot were used to detect the expression of inflammatory factors, oxidation factors and proteins in the cerebral ischaemic cortex. The results revealed that TH dose‐dependently reduced neurological impairment, neuron apoptosis and brain oedema induced by MCAO. Furthermore, TH attenuated the expression of pro‐inflammatory cytokines (including interleukin (IL)‐1β, IL‐6 and tumour necrosis factor (TNF)‐α), iNOS and nuclear factor (NF)‐κB while increased production of anti‐inflammatory cytokines (IL‐4, IL‐10 and BDNF) and proteins of tropomyosin‐related kinase receptor B (TrkB) and PPARγ. Nevertheless, after the addition of TrkB inhibitor, the effects of TH above were mostly restrained. In conclusion, TH can protect mice against I/R‐induced neurological impairments via modulating inflammation and oxidative stress through TrkB signalling.
The applying functions of tax regulation for state development
Authors: Zeynalova Zivar Z. 
Published: August 2020

AbstractTaxes are a complicated and influential category affecting all the economic phenomena and financial processes. To ensure a stable flow of funds to the state and local budgets, all the participants of the tax legal relations should properly perform their obligations before the state and observe the applicable legislation. The aim of the paper is to make an analysis of the positive experience of European countries in the field of taxation and their possible application in developing countries. The considered practice in the part of the luxury tax showed that almost all the developed foreign countries introduced this kind of tax, however, in some of them, it has not been established for some reasons. The experience of the majority of countries shows that social contributions are paid in the majority of cases both by the employer and the employee in a compound and in some cases – by the employee and the employer separately. In the sphere of taxation of transport, the authors suppose that the experience of the foreign states is rather progressive and has a number of positive peculiarities.
Clinical characteristics and risk factors for mortality in obstetric patients with severe COVID‐19 in Brazil: a surveillance database analysis
Authors: Takemoto MLS , Menezes MO , Andreucci CB , Knobel R , Sousa L , Katz L , Fonseca EB , Nakamura‐Pereira M , Magalhães CG , Diniz CSG , Melo ASO , Amorim MMR ,   Brazilian Group for Studies of COVID‐19 and Pregnancy
Published: August 2020

ObjectiveTo describe clinical characteristics of pregnant and postpartum women with severe COVID‐19 in Brazil and to examine risk factors for mortality.DesignCross‐sectional study based on secondary surveillance database analysis.SettingNationwide Brazil.Population or sample978 Brazilian pregnant and postpartum women notified as COVID‐19 Acute Respiratory Distress Syndrome (ARDS) cases with complete outcome (death or cure) up to 18 June 2020.MethodsData was abstracted from the Brazilian ARDS Surveillance System (ARDS‐SS) database. All eligible cases were included. Data on demographics, clinical characteristics, intensive care resources use and outcomes were collected. Risk factors for mortality were examined by multivariate logistic regression.Main outcome measuresCase fatality rate.ResultsWe identified 124 maternal deaths, corresponding to a case fatality rate among COVID‐19 ARDS cases in the obstetric population of 12.7%. At least one comorbidity was present in 48.4% of fatal cases compared with 24.9% in survival cases. Among women who died, 58.9% were admitted to ICU, 53.2% had invasive ventilation and 29.0% had no respiratory support. The multivariate logistic regression showed that the main risk factors for maternal death by COVID‐19 were being postpartum at onset of ARDS, obesity, diabetes and cardiovascular disease, whereas white ethnicity had a protective effect.ConclusionsNegative outcomes of COVID‐19 in this population are affected by clinical characteristics but social determinants of health also seem to play a role. It is urgent to reinforce containment measures targeting the obstetric population and ensure high quality care throughout pregnancy and the postpartum period.Tweetable abstractA total of 124 COVID‐19 maternal deaths were identified in Brazil. Symptoms onset at postpartum and comorbidities are risk factors.
Effects of restorative justice pre‐file diversion legislation on juvenile filing rates: An interrupted time‐series analysis
Authors: Sliva Shannon M. , Plassmeyer Mark 
Published: August 2020

Research SummaryThis study uses an interrupted time‐series design to analyze the impacts of legislatively supported restorative justice pilot projects in Colorado on overall juvenile filing rates in implementing districts, and it compares those outcomes with nonimplementing districts. On average, pilot districts demonstrate statistically significant reductions in juvenile filing rates during the first year of funding, and significant rates of decline are sustained in the years after initiation. The effects of restorative justice pre‐file diversion systems, however, vary by judicial district, and they can be partially explained by differences in implementation.Policy ImplicationsRestorative justice pre‐file diversion programs accompanied by funding supports and accountability measures—introduced by the Colorado legislature in 2014—are associated with varying declines in juvenile court filings. Implementation matters, however. States considering the use of similar reforms should account for how to best support pilot sites’ localized characteristics. Funding restorative justice pre‐file diversion presents one mechanism for reducing court involvement, but it should not be offered as a panacea.
An analysis of cellulose‐ and dextrose‐based radicals in sweet potatoes as irradiation markers
Authors: Tonyali Bade , Sommers Christopher , Ceric Olgica , Smith J. Scott , Yucel Umut 
Published: August 2020

AbstractDried sweet potatoes (SPs) are often irradiated for improved safety and shelf life. Formation of irradiation‐derived radicals was analyzed using electron paramagnetic resonance (EPR) spectroscopy. These irradiation‐specific radicals can be used to characterize the irradiation history of dry plant‐based foods containing cellulose and sugars. The signal characteristics (intensity and peak shape) were evaluated at different sample locations (skin and flesh), as a function of sample preparation method (grinding, sieving, and pelletizing). The signal intensity was quantified using a double integration method of the peaks based on the area under the curve. The sieving caused ca. 50% decrease in total signal intensity as compared to nonsieved samples due to loss of cellulose‐based radicals. The flesh of irradiated SP showed complex EPR spectra with multiple satellite peaks of cellulose radicals (333.5 and 338.8 mT) and split peak of dextrose radicals (337.4 mT); while skin spectra were distinctive of cellulose radicals. In this study, we demonstrated the effects of sample composition and preparation method on formation and analysis of irradiation‐specific radicals based on EPR.Practical ApplicationIn the last decade or so, there have been health concerns related to the consumption of irradiated pet food products. Electron paramagnetic resonance spectroscopy can be used to analyze the irradiation history of dry products containing cellulose and sugar, such as the popular dog treat dried sweet potatoes, to ensure the products were irradiated within safe limits. This work demonstrates that the formation of irradiation‐specific radicals is affected by the sample location (skin and flesh) and moisture content.
Development and verification of a quantitative real‐time PCR method to identify and quantify gelatin derived from animal hide
Authors: Yang Yange , Li Li , Wang Hongyue , Liu Minchang , Wu Yajun 
Published: August 2020

AbstractThe species origin of hide gelatin is a crucial issue with respect to health concerns and religious restrictions. Analysis of the animal‐derived ingredients of gelatin by reliable methods is necessary to ensure its authenticity. However, due to the highly processed nature of gelatin, it remains a challenge to identify gelatin end products accurately and robustly. Our study established and verified a quantitative real‐time PCR (qPCR) method based on careful selection of target genes and a DNA extraction method. The middle products of the gelatin production streamline were investigated to explore the influence of each critical processing step on the method. Gelatin reference samples were used to quantify the levels of target species. Commercial gelatin commodities were surveyed to highlight the mislabeling situation. In summary, the qPCR method was demonstrated to be highly specific and sensitive, with limits of detection (LOD) of 0.1 to 1 pg/µL and gelatin LODs of 0.1% to 5% (w/w). The transition from decoction to concentrated gel was found to have the most severe effect on the qPCR. Intensification of pressure or temperature or employment of enzyme hydrolysis aggravated the DNA damage, resulting in elevated Cq values. Quantitation of gelatin products was feasible; gelatin products produced from 5% target hide and 95% matrix hide mixtures showed 2.9% to 5.2% target species. The 26% relative error for low gelatin content is acceptable for semiquantitation purposes. A market survey showed that 52.6% of the gelatin products were mislabeled as being of animal origin.
High‐dose proton pump inhibitor and amoxicillin dual therapy with or without bismuth for 14 days as rescue therapies after Helicobacter pylori treatment failure
Authors: Goh Khean‐Lee , Chang Joven , Leow Alex H.‐R. 
Published: August 2020

ObjectiveHelicobacter pylori (H. pylori) treatment failures are difficult to treat. In this study we aimed to test the efficacy of two high‐dose dual therapy regimens with or without bismuth for 2 weeks as a rescue therapy for patients with previous H. pylori treatment failure.MethodsH. pylori‐positive patients were randomly assigned to either dexlansoprazole 60 mg twice a day and amoxicillin 1 g 4 times a day without (high‐dose dual therapy [HDDT]) or with colloidal bismuth subcitrate 240 mg twice a day (HDDT‐Bi) for 14 days. Eradication of H. pylori was tested using the 13C‐urea breath test at least 4 weeks (HDDT) or 8 weeks (HDDT‐Bi) after the completion of therapy.ResultsH. pylori was eradicated in 84.6% (33/39) of patients (95% confidence interval [CI]: 70.3‐92.8%) in the HDDT group, compared with 80.5% (33/41) (95% CI: 66.0‐89.8%) in the HDDT‐Bi group on an intention‐to‐treat (ITT) analysis, and in 89.2% (33/37) (95% CI: 75.3‐95.7%) in the HDDT group compared with 82.5% (33/40) (95% CI: 68.1‐91.3%) in the HDDT‐Bi group on a per‐protocol (PP) analysis. There was no significant difference in the eradication rates in both groups on ITT and PP analysis. Both treatment regimens were well tolerated.ConclusionsAdding bismuth to HDDT did not increase H. pylori eradication rates after treatment failure. HDDT and HDDT‐Bi achieved a satisfactory eradication rate of more than 80% as rescue therapies. Both treatment regimens were well tolerated by patients and compliance with treatment was good.
Nursing Diagnoses for Coronavirus Disease, COVID‐19: Identification by Taxonomic Triangulation
Authors: González‐Aguña Alexandra , Jiménez‐Rodríguez María Lourdes , Fernández‐Batalla Marta , Herrero‐Jaén Sara , Monsalvo‐San Macario Enrique , Real‐Martínez Verónica , Santamaría‐García José María 
Published: August 2020

PURPOSETo identify the nursing care problems related to the clinical process of disease by COVID‐19.METHODThe study applied the taxonomic triangulation technique on a clinical management guide to coronavirus disease, COVID‐19, from the World Health Organization. The technique is divided into the phases: extraction of knowledge in natural language about assessment, planning and intervention, translation into standard language NOC and NIC, linking to NANDA‐I diagnoses, triangulation looking for diagnostic matches in the three sets, and, finally, validation by a panel of experts from a hospital and a university.FINDINGSThe extraction identified 159 terms in natural language that were translated into 173 variables: 34 NOC for assessment, 19 NOC for planning, and 120 NIC for intervention. The relationships to NANDA‐I diagnoses recorded 2,182 links and the triangulation returned 109 diagnoses, 54 of them for a critical situation. The panel of experts unanimously validated the 29 diagnoses with the highest number of links.CONCLUSIONCoronavirus disease, COVID‐19, involves a complex situation with multiple associated care problems that can be identified using the taxonomic triangulation technique.IMPLICATIONS FOR NURSING PRACTICEThe links between taxonomies and the taxonomic triangulation technique are an important tool for generating knowledge. The results of this study may guide the diagnosis and treatment of coronavirus disease, COVID‐19, as well as similar processes that occur with acute respiratory distress syndrome.