bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Throughput, Lysis-free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets
Authors: van Loo Bert , Heberlein Magdalena , Mair Philip , Zinchenko Anastasia , Schüürmann Jan , Eenink Bernard D. G. , Holstein Josephin M. , Dilkaute Carina , Jose Joachim , Hollfelder Florian , Bornberg-Bauer Erich 
Published: November 2018

AbstractDirected evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of a high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Display of the sulfatase variants on living E. coli cells ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1-variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a non-trivial, previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.Table of contents graphic
Using the modified male osteoporosis self-assessment tool for Taiwan to predict osteoporosis onset – a sub-study of the Taiwan osteoporosis survey
Authors: Liu Dung-Huan , Cheng Tien-Tsai , Chen Jia-Feng , Yu Shan-Fu , Chiu Wen-Chan , Hsu Chung-Yuan , Chen Ying-Chou 
Published: November 2018

AbstractPurposeTo develop a risk index by item reduction from multiple variable regression, which can identify male Taiwanese patients at risk of developing osteoporosis.MethodsTo develop the model, a risk index was identified by item reduction from multivariate regression analysis. Using receiver operating characteristic (ROC) curve analysis and their sensitivity/specificity, MOSTAi was validated in a separate cohort of Taiwanese men and its performance with compared with the National Osteoporosis Foundation recommendations (NOF 2013).ResultsBetween 2008 and 2011 a total of 4,323 males were enrolled for bone mineral density (BMD) measurements. Univariate analysis identified four major risk factors for osteoporosis, including age, body weight (BW), previous fracture and body height. The ROC analysis showed the area under the curve (AUC) for the model based on the three-variable, two-variable (age and BW), and one-variable models (BW), was 0.701 (p<0.001, 95% confidence interval [CI] 0.658-0.744), 0.700 (p<0.001, 95% CI, 0.656-0.742), and 0.690 (p<0.001, 95% CI, 0.646-0.734), respectively. Using the optimal cutoff value (−2) for the OSTA, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) in the validation cohort were 64.0%, 65.7%, 26.9% and 90.2%, respectively. The ROC curves for predicting osteoporosis by MOSTAi, OSTA and NOF 2013 and the AUC for MOSTAi, OSTA and NOF 2013 was 0.706 (p<0.001, 95% CI: 0.664-0.748) and 0.697(p<0.001, 95% CI: 0.657-0.738), respectively.ConclusionThe results showed that MOSTAi could be a more precise model than OSTA and NOF 2013, for identifying men in Taiwan with osteoporosis who require referrals for DXA scans. It was demonstrated that MOSTAi is a simple tool with fair sensitivity/specificity and PPV, and high NPV. MOSTAi could also be a more accurate model than OSTA for identifying men in Taiwan at risk of osteoporosis. In comparison with NOF 2013, MOSTAi is a more accurate and simpler tool for the referral of Taiwanese men for DXA scans.
Acute and chronic stage adaptations of vascular architecture and cerebral blood flow in a mouse model of TBI
Authors: Steinman Joe , Cahill Lindsay S. , Koletar Margaret M. , Stefanovic Bojana , Sled John G. 
Published: November 2018

AbstractThe 3D organization of cerebral blood vessels determines the overall capacity of the cerebral circulation to meet the metabolic requirements of the brain. This study used Arterial Spin Labeling (ASL) MRI with a hypercapnic challenge and ex vivo Serial Two-Photon Tomography (STPT) to examine the relationship between blood flow and 3D microvascular structure following traumatic brain injury (TBI) in a mouse. Mice were exposed to a controlled cortical impact TBI and allowed to recover for either 1 day or 4 weeks. At each time point, ASL MRI was performed to quantify cerebral perfusion and the brain vasculature was imaged in 3D with STPT. Registration of ASL to STPT enabled flow changes to be related to the underlying microvascular structure in each ASL voxel. Hypoperfusion under rest and hypercapnia was observed both 1 day and 4 weeks post-TBI. Vessel density and vascular volume were reduced 1 day post-TBI, recovering by 4 weeks; however, the reorganized vasculature at the latter time point possessed an abnormal radial pattern. Our findings demonstrate functionally significant long-term changes in the vascular architecture following injury and illustrate why metrics beyond traditional measures of vessel density are required to understand the impact of vascular structure on function.
Sufficiency analysis of estrogen responsive enhancers using synthetic activators
Authors: Ginley-Hidinger Matthew , Carleton Julia B. , Rodriguez Adriana C. , Berrett Kristofer C. , Gertz Jason 
Published: November 2018

AbstractMultiple regulatory regions bound by the same transcription factor have been shown to simultaneously control a single gene’s expression. However, it remains unclear how these regulatory regions combine to regulate transcription. Here we test the sufficiency of promoter-distal estrogen receptor α (ER)-binding sites (ERBS) for activating gene expression by recruiting synthetic activators in the absence of estrogens. Targeting either dCas9-VP16(10x) or dCas9-p300(core) to ERBS induces H3K27ac and activates nearby expression in a manner similar to an estrogen induction, with dCas9-VP16(10x) acting as a stronger activator. The sufficiency of individual ERBS is highly correlated with their necessity, indicating an inherent activation potential that is associated with the binding of RNA polymerase II and several transcription factors. By targeting ERBS combinations, we found that ERBS work independently to control gene expression when bound by synthetic activators. The sufficiency results contrast necessity assays that show synergy between these ERBS, suggesting that synergy occurs between ERBS in terms of activator recruitment, whereas directly recruiting activators leads to independent effects on gene expression.
miRNA activity contributes to accurate RNA splicing inC. elegansintestine and body muscle tissues
Authors: Kotagama Kasuen , Schorr Anna L , Steber Hannah S , Mangone Marco 
Published: November 2018

ABSTRACTMicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. In order to study their contribution to tissue-specific gene expression, we developed novel tools to profile miRNA targets in theC. elegansintestine and body muscle.We validated many previously described interactions, and identified ~3,500 novel targets. Many of the miRNA targets curated are known to modulate the functions of their respective tissues. Within our datasets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors.We developedin vivogenetic tools to validate and further study three RNA splicing factors identified as miRNA targets in our study (asd-2,hrp-2andsmu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3’UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60,unc-52,lin-10andret-1) is dysregulated when the miRNA pathway is disrupted.A re-annotation of the transcriptome data inC. elegansstrains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.
Base editing generates substantial off-target single nucleotide variants
Authors: Zuo Erwei , Sun Yidi , Wei Wu , Yuan Tanglong , Ying Wenqin , Steinmetz Lars M. , Li Yixue , Yang Hui 
Published: November 2018

AbstractGenome editing tools including CRISPR/Cas9 and base editors hold great promise for correcting pathogenic mutations. Unbiased genome-wide off-target effects of the editing in mammalian cells is required before clinical applications, but determination of the extent of off-target effects has been difficult due to the existence of single nucleotide polymorphisms (SNPs) in individuals. Here, we developed a method named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) to detect off-target mutations without interference of SNPs. We applied GOTI to both the CRISPR-Cas9 and base editing (BE3) systems by editing one blastomere of the two-cell mouse embryo and then compared whole genome sequences of progeny-cell populations at E14.5 stage. Sequence analysis of edited and non-edited cell progenies showed that undesired off-target single nucleotide variants (SNVs) are rare (average 10.5) in CRISPR-edited mouse embryos, with a frequency close to the spontaneous mutation rate. By contrast, BE3 editing induced over 20-fold higher SNVs (average 283), raising the concern of using base-editing approaches for biomedical application.
Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins
Authors: Hoffmann Mareike D. , Aschenbrenner Sabine , Grosse Stefanie , Rapti Kleopatra , Domenger Claire , Fakhiri Julia , Mastel Manuel , Eils Roland , Grimm Dirk , Niopek Dominik 
Published: November 2018

ABSTRACTThe rapid development of CRISPR/Cas technologies brought a personalized and targeted treatment of genetic disorders into closer reach. To render CRISPR-based therapies precise and safe, strategies to confine the activity of Cas(9) to selected cells and tissues are highly desired. Here, we developed a cell type-specific Cas-ON switch based on miRNA-regulated expression of anti-CRISPR (Acr) proteins. We inserted target sites for miR-122 or miR-1, which are abundant specifically in liver and muscle cells, respectively, into the 3’UTR of Acr transgenes. Co-expressing these with Cas9 and sgRNAs resulted in Acr knockdown and correspondingly in Cas9 activation solely in hepatocytes or myocytes, while Cas9 was efficiently inhibited in off-target cells. We demonstrate control of genome editing and gene activation using a miR-dependent AcrIIA4 in combination with different Streptococcus pyogenes (Spy)Cas9 variants (full-length Cas9, split-Cas9, dCas9-VP64). Finally, to showcase its modularity, we adapted our Cas-ON system to the smaller and more target-specific Neisseria meningitidis (Nme)Cas9 orthologue and its cognate inhibitors AcrIIC1 and AcrIIC3. Our Cas-ON switch should facilitate cell-specific activation of any CRISPR/Cas orthologue, for which a potent anti-CRISPR protein is known.
Wellbore anti-corrosion technique research in B block on the right bank of Amu Darya river sour gas field
Authors: Qiu Zhichao , Xiong Chunming , Ye Zhengrong , Yi Ran , Zhang Na 
Published: November 2018

PurposeThe purpose of this paper is to solve the tubing corrosion problem of B Block on the Right Bank of Amu Darya river sour gas field.Design/methodology/approachBy using four-point-bending method, the tubing’s ability to resist sulfide-stress cracking was tested. Simulating the wellbore corrosive environment, the corrosion inhibitor which was suitable for gas filed had been screened. According to the characteristic of Amu Darya river gas field, the corrosion monitor system had been designed.FindingsFrom the feedback of wellbore corrosion monitor result, the corrosion rate was lower than 0.076 mm/a.Originality/valueThis anti-corrosion technique provides security for the development of gas field.
A spatiotemporal analysis of fire incidents in Manila from 2011-2016
Authors: Bringula Rex , Balahadia Francis 
Published: November 2018

Purpose
The purpose of this paper is to report the results of spatiotemporal analysis of the 3,506 fire incidents in the city of Manila from 2011 to 2016.

Design/methodology/approach
A spatiotemporal and statistical analysis was carried out to determine the pattern of fire incidents in the city of Manila.

Findings
Fire incidence in Manila did not exhibit any pattern in terms of time, day of the week or month of the year. However, fire incidence did exhibit a pattern in terms of location. Faulty electrical connections are the major cause of fires throughout the year and throughout the 14 municipalities of Manila. Thus, the null hypothesis stating that spatiotemporal characteristics of cases of fire in the city of Manila do not exhibit a pattern is partially rejected.

Research limitations/implications
Future studies may investigate the influence of building maintenance, government control, and cooking and cigarette-disposal behaviors on fire occurrence. It is recommended that the study be replicated in other cities of Metro Manila.

Practical implications
Based on the causes and the spatiotemporal characteristics of fires, stakeholders (e.g. government, Bureau of Fire Protection, local government units (LGUs), communities and residents) can be informed about how to prevent fires. LGUs and government agencies can utilize the findings of this study in developing fire prevention programs for the municipalities with the highest incidence of fires.

Originality/value
These findings can serve as a basis for policy formulation and as a reference for the allocation of fire prevention resources and for the literature on strategic planning for fire prevention in Manila.
Building conditions in Norwegian local governments: trends and determinants
Authors: Hopland Arnt O. , Kvamsdal Sturla 
Published: November 2018

PurposeIn light of evidence of low levels of maintenance of public buildings, this paper aims to investigate trends and determinants of public building conditions in Norwegian local governments.Design/methodology/approachThe authors consider data from surveys and public records in regression analyses.FindingsOn average, the condition of Norwegian local public facilities has improved slightly in the period 2004-2016. The survey data suggest substantial fluctuations in building conditions and a negative relationship between building conditions in 2004 and 2016. Local governments with poor building conditions in 2004 had higher investment in the following years. The authors find no systematic relationship between the conditions in 2004 and maintenance expenditures in subsequent years. They conclude that if maintenance levels are too low, the results suggest that investment levels are too high. Further, they find that both political and fiscal factors are important in explaining building conditions.Originality/valueThe authors provide insight into determinants and trends of building conditions in Norwegian local governments. The results hint at an unhealthy balance between maintenance spending and public investments.
Rogue waves, homoclinic breather waves and soliton waves for a (3 + 1)-dimensional non-integrable KdV-type equation
Authors: Mao Jin-Jin , Tian Shou-Fu , Zhang Tian-Tian 
Published: November 2018

PurposeThe purpose of this paper is to find the exact solutions of a (3 + 1)-dimensional non-integrable Korteweg-de Vries type (KdV-type) equation, which can be used to describe the stability of soliton in a nonlinear media with weak dispersion.Design/methodology/approachThe authors apply the extended Bell polynomial approach, Hirota’s bilinear method and the homoclinic test technique to find the rogue waves, homoclinic breather waves and soliton waves of the (3 + 1)-dimensional non-integrable KdV-type equation. The used approach formally derives the essential conditions for these solutions to exist.FindingsThe results show that the equation exists rogue waves, homoclinic breather waves and soliton waves. To better understand the dynamic behavior of these solutions, the authors analyze the propagation and interaction properties of the these solutions.Originality/valueThese results may help to investigate the local structure and the interaction of waves in KdV-type equations. It is hoped that the results can help enrich the dynamic behavior of such equations.
Considering the effectiveness of philanthropic collective action: a community ecology perspective
Authors: Hwang Hyunseok , Young Tiffany Amorette 
Published: November 2018

PurposeThe purpose of this paper is to explore the relationship between social capital and collective action at the county level in the US while incorporating the moderating effects of community racial diversity and urbanity and to find the changing effects of social capital on philanthropic collective action for community education.Design/methodology/approachThis paper employs a quantitative research design. The dependent variable measures philanthropic collective action for community education while the independent variable for social capital is measured as a community level index. Moderating variables include a community racial diversity index and urbanity. This analysis tests and interprets interaction effects using moderated multiple regression (MMR), with the baselines of MMR being grounded to multivariate ordinary least squares (OLS) regression. Analyses are carried out in the context of the USA during 2006 and 2010, with US counties employed as the unit of analysis.FindingsThe effects of social capital on philanthropic contributions decline in counties with low- and mid-levels of racial diversity. On the contrary, the effects of social capital increase in highly racially diverse counties. The three-way interaction model result suggests that racial diversity positively moderates social capital on philanthropic collective action for community education where the effect of social capital is strong and positive in highly racially diverse urban communities.Originality/valueThis research complicates the notion that social capital and racial diversity are negatively associated when exploring collective action and community education, and suggests effects of social capital varies with moderating effects on philanthropic collective action for community education.
Analysis of tweets to find the basis of popularity based on events semantic similarity
Authors: Mudgal Rajat Kumar , Niyogi Rajdeep , Milani Alfredo , Franzoni Valentina 
Published: November 2018

PurposeThe purpose of this paper is to propose and experiment a framework for analysing the tweets to find the basis of popularity of a person and extract the reasons supporting the popularity. Although the problem of analysing tweets to detect popular events and trends has recently attracted extensive research efforts, not much emphasis has been given to find out the reasons behind the popularity of a person based on tweets.Design/methodology/approachIn this paper, the authors introduce a framework to find out the reasons behind the popularity of a person based on the analysis of events and the evaluation of a Web-based semantic set similarity measure applied to tweets. The methodology uses the semantic similarity measure to group similar tweets in events. Although the tweets cannot contain identical hashtags, they can refer to a unique topic with equivalent or related terminology. A special data structure maintains event information, related keywords and statistics to extract the reasons supporting popularity.FindingsAn implementation of the algorithms has been experimented on a data set of 218,490 tweets from five different countries for popularity detection and reasons extraction. The experimental results are quite encouraging and consistent in determining the reasons behind popularity. The use of Web-based semantic similarity measure is based on statistics extracted from search engines, it allows to dynamically adapt the similarity values to the variation on the correlation of words depending on current social trends.Originality/valueTo the best of the authors’ knowledge, the proposed method for finding the reason of popularity in short messages is original. The semantic set similarity presented in the paper is an original asymmetric variant of a similarity scheme developed in the context of semantic image recognition.
Climate change risk perceptions among green conscious young consumers: implications for green commodity marketing
Authors: Perera Chamila , Hewege Chandana 
Published: November 2018

Purpose
This study aims to explore how young adults understand the climate change problem. It also explores whether environmental paradigms explain how young adults perceive climate change risks in their everyday green conscious behavior.

Design/methodology/approach
This interpretive research draws on in-depth interviews with 20 young Australians (aged between 19-25 years) who engage in green conscious behavior.

Findings
Three thematic categories (“non-local” climate change risk, oscillation between environmental paradigms and anthropocentric environmentalism) emerged from the data. The study finds that “non-local” climate change risk perceptions and environmental paradigms inform green conscious behavior. However, no association between environmental paradigms and climate change risk perceptions is found. The study postulates a skeletal theoretical framework for understanding the green conscious behavior of young adults.

Practical implications
Recommendations are provided on how to sustain young adults’ interest in environmental wellbeing and in promoting green commodities in young consumer markets. Suggestions include creating a clear awareness of climate change with a constructive or positive appeal resolving ‘non-local’ climate change risk perceptions and position green commodities as “pro-actions” or “solutions”, as opposed to “reactions”, when reaching young consumer markets.

Originality/value
A high level of green consciousness among young adults is recorded in recent global surveys. This green conscious young consumer segment, however, appears to be largely ignored by green commodity marketers. This study provides green commodity marketers with necessary insights to explore the opportunities that might arise in this unique market segment.