bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism study&nbsp;on the enhanced DHA synthesis in the mutant&nbsp;Thraustochytriidae sp.&nbsp;through comparative transcriptomic analysis
Authors: liu liangxu , Hu Zhangli , Li Shuangfei , Yang Hao , Li Siting , Lv Chuhan , Zaynab Madiha , Cheng Christopher H.K. , Chen Huapu , Yang Xuewei 
Published: February 2020

Abstract
Background: Docosahexaenoic acid (DHA) is an essential omega-3 fatty acid for the human retina, skin, and cerebral cortex. Marine eukaryote Thraustochytriidae sp. was considered as a promising source for the n -3 LC-PUFAs production. However, the mechanism how the LC-PUFAs was synthesized in Thraustochytriidae sp. still remained unclarified. To explore the vital genes responsible for the DHA enrichment, the functional transcriptomic annotation was compared between the wild type and preeminent mutant of Thraustochytriidae sp. X2. Results: After the UV irradiation (50 W, 30 s), the mutant X2 showed enhanced lipid (78.88 % more) and DHA (23.77 % more) production compared with the wild type. Instead of EPA, 9.07 % of DPA was observed in the mutant X2. The comparative transcriptomic analysis showed that in both wild type and mutant strain, FAS was incomplete and lacked key desaturases, but genes related to the PKS pathway were observed. It was oberved that mRNA expression levels of CoA-transferase (CoAT) , acyltransferase (AT), enoyl reductase (ER) , dehydratase (DH) and methyltransferase (MT) down-regulated in wild type but up-regulated in mutant X2, corresponding to the increased intercellular DHA accumulation. Conclusion: These findings indicated the potential genes that can be exploited for high DHA yields in Thraustochytriidae sp..
Effect of pH on metabolite excretion and cell morphology of Euglena gracilis under dark, anaerobic conditions
Authors: Yoshioka Kazumasa , Suzuki Kengo , Osanai Takashi 
Published: February 2020

Abstract
Background Euglena gracilis is a unicellular eukaryotic microalgae found in aquatic environments. It can adapt its morphology in response to various environmental stress factors such as changes in temperature, light, and ion concentrations. E. gracilis cells excrete succinate and amino acids under dark and anaerobic conditions; however, only a few studies on the effect of these conditions on the cell morphology of E. gracilis have been conducted thus far. In the present study, we aimed to evaluate the effects of pH on succinate, glutamine and glutamate production in E. gracilis and the correlation between the levels of these metabolites and cell morphology under dark, anaerobic conditions. Results The production of succinate, glutamine and glutamate by E. gracilis was pH dependent. Glutamate and glutamine excretion increased under acidic conditions (pH 3–5), irrespective of the buffer salts. On the contrary, succinate production depended on the buffer salts; succinate levels were higher when GTA or citrate buffer were used and were lower when acetate buffer was used (pH 4 or 5). The number of spindle cells tended to increase under acidic conditions and the aspect ratio of the cells was positively correlated with glutamine and glutamate levels. Increase in cell density particularly enhanced glutamine and succinate production; in particular, the succinate titre reached 1.5 g/L, which is the highest reported level of succinate produced from photosynthetic eukaryotes till date. Conclusions Our findings indicate that pH of the media alters metabolite production and cell morphology of E. gracilis cells under dark, anaerobic conditions. A deeper understanding of eukaryotic fermentation will benefit the biorefinery industry, mainly for the production of value-added products using anaerobic microorganisms.
The Efficacy of Surgery in Advanced Hepatocellular Carcinoma: A Propensity Score Analysis
Authors: Chen Lei , Sun Tao , Chen Shi , Ren Yanqiao , Yang Fan , Zheng Chuansheng 
Published: February 2020

Abstract
Background There is still controversial that whether hepatocellular carcinoma (HCC) patients with lymph node invasion should receive surgery treatment. This study is to evaluate the efficacy of surgery in HCC patients with regional lymph node invasion. Methods The study utilized data from the Surveillance, Epidemiology, and End Results-18 (SEER-18) cancer registry. 1434 patients were included in the analysis. Among them, 168 patients were treated surgically and 1266 received non-surgery treatment. Propensity Score Matching (PSM) model was used to reduce selection bias. Results Before PSM, the median overall survival (mOS) and median cancer-specific survival (mCSS) of patients treated surgically were longer than in patients receiving non-surgery treatment (mOS: 20 months vs. 7 months, P<0.001; mCSS: 21 months vs. 6 months, P<0.001). Subgroup analysis did not detect a significant difference in mOS and mCSS between liver resection and non-liver resection surgery cohorts (P>0.05). Similar results were obtained in the PSM analysis. The mOS and mCSS in the surgery group were longer than in the non-surgery group (mOS: 20 months vs. 7 months, P<0.001; mCSS: 20 months vs. 6 months, P<0.001). The multivariate analysis documented that surgery was an independent predictor for OS and CSS before and after PSM. Conclusions HCC patients with invasion of regional lymph nodules may get more survival benefit from surgery than other types of treatment.
Anti-rhinovirus and anti-influenza virus activities of mucoactive secretolytic agents and plant extracts – a comparative in vitro study
Authors: Walther Christin , Schmidtke Michaela 
Published: February 2020

Abstract
Background: Rhinoviruses and influenza viruses cause the majority of acute respiratory infections (ARIs). Symptoms of ARIs are commonly treated with over-the-counter products like ambroxol, bromhexine, and N-acetylcysteine, as well as thyme and pelargonium extracts. Because the antiviral activity of these over-the-counter products has not been studied in a systematic way, the current study aimed to compare their antiviral effect against two rhinovirus and two influenza virus strains in an in vitro setting. Methods: The cytotoxicity of ambroxol, bromhexine, and N-acetylcysteine, as well as of thyme and pelargonium extracts was analyzed in Madin-Darby canine kidney (MDCK) and HeLa cells. The antiviral effect of these over-the-counter products was compared by analyzing the dose-dependent inhibition (i) of rhinovirus A2- and B14-induced cytopathic effect in HeLa cells and (ii) of influenza virus A/Hong Kong/68 (subtype H3N2)- and A/Jena/8178/09 (subtype H1N1, pandemic)-induced cytopathic effect in MDCK cells at non-cytotoxic concentrations. Results: The results revealed a good compatibility (no or only marginal cytotoxicity in MDCK and HeLa cells) of the agents that were tested. No anti-rhinoviral activity was detected at non-cytotoxic concentrations in this in vitro study setting. Ambroxol, bromhexine, and N-acetylcysteine inhibited the influenza virus-induced cytopathic effect in MDCK cells no or less than 50%. In contrast, a dose-dependent anti-influenza virus activity of thyme and pelargonium extracts was demonstrated. Conclusions: The results of our comparative in vitro study indicate differences in the antiviral efficacy of ambroxol, bromhexine, and N-acetylcysteine, as well as of thyme and pelargonium extracts and suggest that the inhibition of influenza virus replication by thyme and pelargonium extracts may contribute to the beneficial effects of these plant extracts on ARI symptoms.
Is a Differentiated Care Model needed for Patients with TB? A cohort analysis of outcomes among TB patients in two states in south India.
Authors: Washington Reynold , Potty RAJARAM Subramanian , Rajesham A , Seenappa T , Singarajipura Anil , Swamickan Reuben , Shah Amar , Prakash KH , Kar Arin , Kumaraswamy Karthikeyan , BS Prarthana , Maryala Bala Krishna , Sushma J , Dasari Ramesh , Shetty Bharath , Panibatla Vikas , Mohan HL , Becker Marissa 
Published: February 2020

Abstract
Background India’s National Strategy to ‘End TB by 2025’ aims to reduce unfavourable TB treatment outcomes. There is need for innovative approaches to improve TB treatment outcomes. Methods Under a USAID-THALI, Community Health Workers using a pre-designed tool assessed TB patients in three states in south India for risks of non-adherence and risk of unfavourable outcomes. We examined whether those with identified risk had higher levels of two unfavourable treatment outcomes; death and unfavourable outcome including death, lost to follow up and failure, as compared to no risk. Bivariate and multivariate logistic regression was used to assess each of the individual risks and the combined risk, for experiencing death or unfavourable outcome as described earlier, after initiation of TB. Results A significantly higher likelihood of death and experiencing unfavourable outcomes was observed for individuals having one risk (AOR: 3.28; 95% CI: 2.11-5.10 for death; AOR 1.71; 95% CI: 1.29-2.26 for unfavourable outcome) and more than one risk (AOR: 4.19; 95% CI: 2.47-7.11 for death; AOR 2.21; 95% CI: 1.56-3.12) as compared to TB patients with no identified risk. In addition to the risk characterisation, TB patients with initial weight below the national median weight were 2.1 times and 2.0 times more likely to die and experience unfavourable outcomes, as compared to patients with initial weight equal to the median or higher. Conclusion The results of our analysis point to the need for a ‘differentiated care model’, beginning with a risk and needs assessment and continuing with tailored care and support for TB patients, based on their identified risk. While all TB patients require a minimum package of care and support there are a substantial proportion who require more specific interventions and services in order to successfully complete their treatment. We identified a number of important risk factors that could be predictive of an unfavourable outcome and which could be used by TB programs in order to optimize patient treatment outcomes.
An Audit Tool for Longitudinal Assessment of Health-Related Characteristics of Urban Neighborhoods: Implementation Methods and Reliability Results
Authors: Dastidar Bonnie Ghosh , Hunter Gerald , Sloan Jennifer C , Collins Rebecca L , Richardson Andrea S , Troxel Wendy , Colabianchi Natalie , Dubowitz Tamara 
Published: February 2020

Abstract
Background: Improving the neighborhood environment may help address chronic disease and mortality. To identify neighborhood features that are predictors of health, objective assessments of the environment are used. Multiple studies have reported on cross-sectional assessments of health-related neighborhood features using direct observation. As study designs expand to better understand causation and predictors of change, there is a need to test whether direct observation methods are adequate for longitudinal assessment. To our knowledge, this is the first study to report on repeated direct observations of the neighborhood environment. Methods : The Pittsburgh Hill/Homewood Research on Neighborhood Change and Health (PHRESH) study conducted longitudinal assessments in two low-income, African American neighborhoods at three waves (years 2012, 2015, 2017). The PHRESH audit tool is a modification of earlier validated tools, with an emphasis on environment features relevant for physical activity, sleep, and obesogenic behaviors. Trained data-collector pairs conducted direct observations of a 25% sample of street segments in each neighborhood. At each wave, we audited a sub-sample of street segments twice and assessed reliability using percentage inter-observer agreement and krippendorf’s alpha statistics. Stability of these items was assessed as exhibiting moderate or high agreement at every time point. Results : Across waves, a majority (81%) of the items consistently demonstrated moderate to high agreement except for items such as public/communal space, amount of shade, sidewalk features, number of traffic lanes, garden/flower bed/planter, art/statue/monument, amount of trash, and physical disorder. The list of items with poor agreement includes features that are easy to miss (e.g. flower bed/planter), hard to assess from outside (e.g. public/communal space), or may change quickly (e.g. amount of trash). Conclusion: In this paper, we have described implementation methods, reliability results and lessons learned to inform future studies of change. We found the use of consistent methods allowed us to conduct reliable, replicable longitudinal assessments of the environment. Items that did not exhibit stability are less useful for detecting real change over time. Overall, the SSA direct observation tool is an effective and practical instrument to detect change in the neighborhood environment.
Levels of support for the licensing of tobacco retailers in Australia: Findings from the National Drug Strategy Household Survey 2004-2016
Authors: Baker John , Begg Stephen , Masood Mohd , Rahman Muhammad Aziz 
Published: February 2020

Abstract
Background: Assessing public opinion towards tobacco policies is important, particularly when determining the possible direction of future public health policies. The aim of this study was to describe the implementation of tobacco retailer licensing systems by state and territory governments in Australia, and use the National Drug Strategy Household Survey (NDSHS) to assess levels of public support for a retailer licensing system in each jurisdiction over time and by a range of socio-demographic and behavioural attributes. Methods: National and state/territory estimates of public support for a tobacco retailer licensing system were derived as proportions using NDSHS data from 2004 to 2016. The effect of the type of licensing system of one’s jurisdiction of residence on the likelihood of supporting such an initiative in 2016 was assessed using logistic regression while controlling for various socio-demographic characteristics. Results: Public support for a tobacco retailer licensing system ranged from a high of 67.2% (95% CI 66.5% – 67.9%) nationally in 2007 and declined to 59.5% (95% CI 58.9% – 60.2%) in 2016. In 2016, support was greatest amongst those aged 50 years and older, females, those from the least disadvantaged areas, those living in major cities, never-smokers and never-drinkers. Those living in jurisdictions with a ‘negative’ licensing system were more likely to support a licensing system than those living in jurisdictions without any system in place (OR = 1.09, 95% CI 1.01 – 1.17); however this difference disappears after adjusting for the socio-demographic and behavioural attributes of respondents (OR = 1.04, 95% CI 0.96 – 1.12). Conclusions: A clear majority of the public support a tobacco retailer licensing system, regardless of whether or not such a system is already in place in their jurisdiction of residence. While there is variation between jurisdictions in levels of support, this variation largely disappears when the different socio-demographic and behavioural attributes of the respective populations are taken into account.
Image-and-text health warning labels on alcohol and food: potential effectiveness and acceptability
Authors: Pechey Emily , Clarke Natasha , Mantzari Eleni , Blackwell Anna , De-loyde Katie , Morris Richard , Marteau Theresa , Hollands Gareth 
Published: February 2020

Abstract
Background Health warning labels (HWLs) using images and text to depict the negative health consequences of tobacco consumption are effective and acceptable for changing smoking-related outcomes. There is currently limited evidence concerning their effectiveness and acceptability for reducing consumption of alcoholic drinks and energy-dense foods. Aim To describe potential effectiveness and acceptability of image-and-text (also known as pictorial or graphic) HWLs applied to : i. alcoholic drinks and ii. energy-dense snack foods. Methods Two online studies were conducted using between-subjects designs with general population samples. Participants rated one of 21 image-and-text HWLs on alcoholic drinks (n=5528), or one of 18 image-and-text HWLs on energy-dense snacks (n=4618). HWLs comprised a graphic image with explanatory text, depicting, respectively, seven diseases linked to excess alcohol consumption, and six diseases linked to excess energy intake. Diseases included heart disease and various cancers. Outcomes were negative emotional arousal, desire to consume the labelled product, and acceptability of the label. Free-text comments relating to HWLs were content analysed. Results For both alcoholic drinks and energy-dense snacks, HWLs depicting bowel cancer generated the highest levels of negative emotional arousal and lowest desire to consume the product, but were the least acceptable. Acceptability was generally low for HWLs applied to alcohol, with 3 of 21 rated as acceptable, and was generally high for snacks, with 13 of 18 rated as acceptable. The majority of free-text comments expressed negative reactions to HWLs on alcohol or energy-dense snacks. Conclusions Image-and-text health warning labels depicting bowel cancer showed greatest potential for reducing selection and consumption of alcoholic drinks and energy-dense snacks, although they were the least acceptable. Laboratory and field studies are needed to assess their impact on selection and consumption.
Validation of a generic Bayesian method for prevalence estimation under misclassification
Authors: Flor Matthias , Weiβ Michael , Selhorst Thomas , Müller-Graf Christine , Greiner Matthias 
Published: February 2020

Abstract
Background: Various methods exist for statistical inference about a prevalence that consider misclassifications due to an imperfect diagnostic test. However, traditional methods are known to suffer from censoring of the prevalence estimate and the confidence intervals constructed around the point estimate, as well as from under-performance of the confidence intervals' coverage. Methods: In this study, we used simulated data sets to validate a Bayesian prevalence estimation method and compare its performance to frequentist methods, i.e. the Rogan-Gladen estimate for prevalence, RGE, in combination with several methods of confidence interval construction. Our performance measures are (i) bias of the point estimate against the simulated true prevalence and (ii) coverage and length of the confidence interval, or credible interval in the case of the Bayesian method. Results: Across all data sets, the Bayesian point estimate and the RGE produced similar bias distributions with slight advanteges of the former over the latter. In addition, the Bayesian estimate did not suffer from the RGE's censoring problem at zero or unity. With respect to coverage performance of the confidence and credible intervals, all of the traditional frequentist methods exhibited strong under-coverage, whereas the Bayesian credible interval as well as a newly developed frequentist method by Lang and Reiczigel performed as desired, with the Bayesian method having a very slight advantage in terms of interval length. Conclusion: The Bayesian prevalence estimation method should be prefered over traditional frequentist methods. An acceptable alternative is to combine the Rogan-Gladen point estimate with the Lang-Reiczigel confidence interval.
Methanol expression regulator 1 (Mxr1p) promotes xylulose 5-phosphate recycle via increaseing transketolase activity in Pichia pastoris
Authors: Zhan Chunjun , Pan Yingyue , Liu Xiuxia , Liu Chunli , Zhan Jinling , Xu Dinghua , Bai Zhonghu , Yang Yankun 
Published: February 2020

Abstract
Background Methanol expression regulator 1 (Mxr1p) is a key transcription factor that plays a vital role in the methanol utilization pathway in Pichia pastoris ( P. pastoris ). Most genes referred to the methanol utilization pathway were regulated by Mxr1p. However, some genes did not show a significant difference between methanol and glycerol even though they play an important role in the methanol utilization pathway. So far, the regulation mechanism about these genes and the relationship with Mxr1p are still unknown. Results Methanol metabolic pathway analysis revealed that most of the methanol-induced genes were upregulated in transcriptional level when cultured in methanol. Whereas some genes like tkl1 (transketolase 1) did not show significant up-regulation in methanol even though it plays a very important role in Xu5P recycle, the reason is still not clear. To clarify this point, firstly, pull-down and MS experiments were performed. The result shows that Tkl1p protein combined with Mxr1p in vitro . Subsequently, this result was further confirmed by yeast two-hybrid in vivo , and the binding region mainly located from 150AA to 400AA. Moreover, Ser215 phosphorylation did not affect this interaction. In addition, Mxr1p-400AA integration into Δmxr1 could rescue cell growth in methanol. All the above results proved that Mxr1p played a post-translational role in the methanol utilization pathway and Mxr1p-400AA may achieved most of Mxr1p functions. Secondly, the function of Mxr1p-Tkl1p complex was expounded by detecting formaldehyde consumption and xylulose production in cell-free systems. Results showed that Mxr1p-Tkl1p mixture could promote formaldehyde consumption and xylulose production in vitro . Conclusion Mxr1p promotes methanol utilization via combining with Tkl1p to accelerate Xu5P recycle and this interaction was not affected by Ser215 phosphorylation.
Analysis of fungal diversity of the rotten wooden pillars of a historic building
Authors: Ma Xingxia , Zhang Bin , Liu Bo 
Published: February 2020

Abstract
High-throughput sequencing technology was used to analyze the fungal community structure and its association with the cause of decay on the wooden pillars of an ancient archway in Beijing. The dominant fungi on the rotten pillars belonged to Ascomycetes regardless of the sampling position. Compared with the fungal community composition of discolored wood previously studied, the proportion of Basidiomycetes in rotten wood pillars increased at the highest value of 37.9%. High-throughput sequencing showed that the main fungi in the first pillar were Ascomycetes ( Phoma , Lecythophora , and Scedosporium ) and Basidiomycetes (Sporidiobolales). Ascomycetes Lecythophora and Basidiomycetes Cryptcoccus and Postia were the main fungi in pillar 2. Phoma , Trichoderma, and Entoloma were isolated from pillar 1, whereas Alternaria and Phaeosphaeriaceae were obtained from pillar 2 using culture isolation. Traditional isolation failed to obtain all dominant fungi. The importance of high-throughput sequencing technology in ancient wooden structure building biodeterioration analysis was further explained. At the three sampling sites, the contact-ground fungal community composition was similar to that of in-ground wood, whereas above-ground fungal community composition was significantly different from the other two sites. The high moisture content of the wood caused decay. The bottom of the pillar was immersed in groundwater, whereas that cement coating prevents the evaporation of water,cause the wood moisture content to be high. By comparing the fungal diversities of decaying wood and discolored and dry, decayed wood, the relative content of Basidiomycetes may be used as an indicator of wood decay state.