bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary case inference in viral outbreaks through analysis of intra-host variant population
Authors: Gussler J. Walker , Campo David S , Dimitrova Zoya , Skums Pavel , Khudyakov Yury 
Published: September 2020

AbstractInvestigation of outbreaks to identify the primary case is crucial for the interruption and prevention of transmission of infectious diseases. These individuals may have a higher risk of participating in near future transmission events when compared to the other patients in the outbreak, so directing more transmission prevention resources towards these individuals is a priority. Genetic characterization of intra-host viral populations, although highly efficient in the identification of transmission clusters, is not as efficient in routing transmissions during outbreaks, owing to complexity of viral evolution. Here, we present a new computational framework, PYCIVO:primarycaseinference inviraloutbreaks. This framework expands upon our earlier work in development of QUENTIN, which builds a probabilistic disease transmission tree based on simulation of evolution of intra-host hepatitis C virus (HCV) variants between cases involved in direct transmission during an outbreak. PYCIVO improves upon QUENTIN by also implementing a custom heterogeneity index which empowers PYCIVO to make the important ‘No primary case’ prediction. One or more samples, possibly including the primary case, may have not been sampled, and this designation is meant to account for these scenarios. These approaches were validated using a set of 105 sequence samples from 11 distinct HCV transmission clusters identified during outbreak investigations, in which the primary case was epidemiologically verified. Both models can detect the correct primary case in 9 out of 11 transmission clusters (81.8%). However, while QUENTIN issues erroneous predictions on the remaining 2 transmission clusters, PYCIVO issues a null output for these clusters, giving it an effective prediction accuracy of 100%. To further evaluate accuracy of the inference, we created 10 modified transmission clusters in which the primary case had been removed. In this scenario, PYCIVO was able to correctly identify that there was no primary case in 8/10 (80%) of these modified clusters. This model was validated with HCV; however, this approach may be applicable to other microbial pathogens.A version of this software is publicly available at the following url:https://www.github.com/walkergussler/PYCIVO
Evolution of the Analytical Scattering Model of LiveEscherichia Coli
Authors: Semeraro Enrico F. , Marx Lisa , Mandl Johannes , Frewein Moritz P. K. , Scott Haden L. , Prévost Sylvain , Bergler Helmut , Lohner Karl , Pabst Georg 
Published: September 2020

AbstractWe have revised a previously reported multi-scale model for (ultra) small angle X-ray (USAXS/SAXS) and (very) small angle neutron scattering (VSANS/SANS) of liveEscherichia colibased on compositional/metabolomic and ultrastructural constraints. The cellular body is modelled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was substituted by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data ofE. coliATCC 25922 over four orders of magnitude in length scale, providing specifically detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. Consecutively, the model was also successfully applied toE. coliK12, used for our original modelling, as well as for two otherE. colistrains, detecting significant differences between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of our approach to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labelling agents.
Dissociation of tonotopy and pitch in human auditory cortex
Authors: Allen Emily J. , Mesik Juraj , Kay Kendrick N. , Oxenham Andrew J. 
Published: September 2020

SUMMARYFrequency-to-place mapping, or tonotopy, is a fundamental organizing principle from the earliest stages of auditory processing in the cochlea to subcortical and cortical regions. Although cortical maps are referred to as tonotopic, previous studies employed sounds that covary in spectral content and higher-level perceptual features such as pitch, making it unclear whether these maps are inherited from cochlear organization and are indeed tonotopic, or instead reflect transformations based on higher-level features. We used high-resolution fMRI to measure BOLD responses in 10 participants as they listened to pure tones that varied in frequency or complex tones that independently varied in either spectral content or fundamental frequency (pitch). We show that auditory cortical gradients are in fact a mixture of maps organized both by spectral content and pitch. Consistent with hierarchical organization, primary regions were tuned predominantly to spectral content, whereas higher-level pitch tuning was observed bilaterally in surrounding non-primary regions.
High-dose pyruvate treatment alters skeletal muscle differentiation and expression of inflammation-related genes
Authors: Hasegawa Kazuya , Yamaguchi Yuya , Pengjam Yutthana 
Published: September 2020

ABSTRACTPyruvic acid therapy is used for various diseases, but the therapeutic effect decreases at high doses. The molecular mechanism of high-dose pyruvate is not well understood. The purpose of this study was to identify the effects of high dose pyruvate addition on skeletal muscle using C2C12. The gene expression profile for the GSE5497 dataset was taken from the Gene Expression Omnibus database. GEO2R was used to identify specifically expressed genes (DEGs). Functional analysis and pathway enrichment analysis of DEG were performed using the DAVID database. The protein-protein interaction (PPI) network was built in the STRING database and visualized using Cytoscape. GO analysis showed that up-regulated DEG was primarily involved in angiogenesis, cell adhesion, and inflammatory response. We also showed that down-regulated DEG is involved in the regulation of muscle contraction, skeletal muscle fiber development. In addition, the upregulated KEGG pathway of DEG included Rheumatoid arthritis, Chemokine signaling pathway, and Cytokine-cytokine receptor interaction. Downregulated DEG included Calcium signaling pathway, hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy, Neuroactive ligand-receptor interaction, and Cardiac muscle contraction. Further, analysis of two modules selected from the PPI network showed that high-dose pyruvate exposure to C2C12 was primarily associated with muscle contraction, muscle organ morphogenesis, leukocyte chemotaxis, and chemokine activity. In conclusion, High-dose pyruvate treatment of C2C12 was found to be associated with an increased inflammatory response and decreased skeletal muscle formation. However, further studies are still needed to verify the function of these molecules at high doses of pyruvate.
Antithrombotic Therapy After Transcatheter Aortic Valve Implantation in Patients with Long-Term Indication for Anticoagulation: Systematic Review and Meta-Analysis
Authors: Costa Gonçalo , Sousa José Pedro , Gonçalves Lino , Teixeira Rogério 
Published: September 2020

AbstractObjectiveThe aim of this study was to compare antithrombotic regimens following transcatheter aortic valve implantation (TAVI) in patients requiring long-term oral anticoagulation (OAC).MethodsWe systematically searched PubMed, Embase, and Cochrane databases for interventional and observational studies comparing OAC to OAC plus single antiplatelet therapy (SAPT).ResultsFive studies were included (four registry-based and one randomized controlled trial), comprising a total of 1318 patients. Our meta-analysis revealed lower rates of severe bleeding (pooled odds ratio [OR] 0.46 [0.31, 0.69], P<0.01, I2=0%) and major bleeding (pooled OR 0.46 [0.27,0.79], P<0.01, I2=0%) for the OAC group than for the OAC-plus-SAPT group. There was a nonsignificant trend towards reduced life-threatening bleeding events in the OAC group (pooled OR 0.54 [0.27,1.08], P=0.08, I2=11%). There was no difference between groups in the risks of stroke (pooled OR 1.02 [0.58,1.80], P=0.58, I2= 0%) or all-cause mortality (pooled OR 1.04 [0.75,1.42], P=0.83, I2= 0%) after TAVI.ConclusionsOur pooled analysis suggests that for patients with an indication for long-term OAC after TAVI, double anti-thrombotic therapy, compared to OAC alone, increased the risk of bleeding without reducing cerebrovascular events and all-cause mortality.Key questionsWhat is already known about this subject?Transcatheter Aortic Valve Implantation (TAVI) is a landmark techinique in interventional cardiology with growing clinical experience and continuous refinement of procedural techniques and devices. Nevertheless, the post-TAVI antithrombotic regimen guidelines are largely based on expert opinions and followed variably across the globe.What does this study add?Our pooled analysis suggests that for patients with an indication for long-term anticoagulation after TAVI, double anti-thrombotic therapy, compared to OAC alone, increased the risk of bleeding without reducing cerebrovascular events and all-cause mortality.How might this impact on clinical practice?Our finding may prove insightful for future recommendations regarding the conundrum of the best antithrombotic strategy, particularly for patients with AF.
Smoking is associated with worse outcomes of COVID-19 particularly among younger adults: A systematic review and meta-analysis
Authors: Patanavanich Roengrudee , Glantz Stanton A. 
Published: September 2020

AbstractBackgroundSmoking impairs lung immune functions and damages upper airways, increasing risks of contracting and severity of infectious diseases.MethodsWe searched PubMed and Embase for studies published from January 1-May 25, 2020. We included studies reporting smoking behavior of COVID-19 patients and progression of disease, including death. We used a random effects meta-analysis and used meta-regression and lowess regressions to examine relationships in the data.ResultsWe identified 47 peer-reviewed papers with a total of 31,871 COVID-19 patients, 5,759 (18.1%) experienced disease progression and 5,734 (18.0%) with a history of smoking. Among smokers, 29.2% experienced disease progression, compared with 21.1% of non-smokers. The meta-analysis confirmed an association between smoking and COVID-19 progression (OR 1.56, 95% CI 1.32-1.83, p=0.001). Smoking was associated with increased risk of death from COVID-19 (OR 1.19, 95% CI 1.05-1.34, p=0.007). We found no significant difference (p=0.432) between the effects of smoking on COVID-19 disease progression between adjusted and unadjusted analyses, suggesting that smoking is an independent risk factor for COVID-19 disease progression. We also found the risk of having COVID-19 progression among younger adults (p=0.023), with the effect most pronounced among people under about 45 years old.ConclusionsSmoking is an independent risk for having severe progression of COVID-19, including mortality. The effects seem to be higher among young people. Smoking prevention and cessation should remain a priority for the public, physicians, and public health professionals during the COVID-19 pandemic.
A temporally resolved transcriptome for developing “Keller” explants of theXenopus laevisdorsal marginal zone
Authors: Kakebeen Anneke D. , Huebner Robert , Shindo Asako , Kwon Kujin , Kwon Taejoon , Wills Andrea E. , Wallingford John B. 
Published: September 2020

AbstractExplanted tissues from vertebrate embryos reliably develop in culture and have provided essential paradigms for understanding embryogenesis, from early embryological investigations of induction, to the extensive study ofXenopusanimal caps, to the current studies of mammalian gastruloids. Cultured explants of theXenopusdorsal marginal zone (“Keller” explants) serve as a central paradigm for studies of convergent extension cell movements, yet we know little about the global patterns of gene expression in these explants. In an effort to more thoroughly develop this important model system, we provide here a time-resolved bulk transcriptome for developing Keller explants.
Experimental investigation of diaphragm material combinations in a small-scale shock tube
Authors: Singh Anugya , Satheesh Kumar Aravind , B.T. Kannan 
Published: September 2020

Purpose
The purpose of this study is to experimentally investigate the trends in shock wave Mach number that were observed when different diaphragm material combinations were used in the small-scale shock tube.

Design/methodology/approach
A small-scale shock tube was designed and fabricated having a maximum Mach number production capacity to be 1.5 (theoretically). Two microphones attached in the driven section were used to calculate the shock wave Mach number. Preliminary tests were conducted on several materials to obtain the respective bursting pressures to decide the final set of materials along with the layered combinations.

Findings
According to the results obtained, 95 GSM tracing paper was seen to be the strongest reinforcing material, followed by 75 GSM royal executive bond paper and regular 70 GSM paper for aluminium foil diaphragms. The quadrupled layered diaphragms revealed a variation in shock Mach number based on the position of the reinforcing material. In quintuple layered combinations, the accuracy of obtaining a specific Mach number was seen to be increasing. Optimization of the combinations based on the production of the shock wave Mach number was carried out.

Research limitations/implications
The shock tube was designed taking maximum incident shock Mach number as 1.5, the experiments conducted were found to achieve a maximum Mach number of 1.437. Thus, an extension to further experiments was avoided considering the factor of safety.

Originality/value
The paper presents a detailed study on the effect of change in the material and its position in the layered diaphragm combinations, which could lead to variation in Mach numbers that are produced. This could be used to obtain a specific Mach number for a required study accurately, with a low-cost setup.
Effect of hydrocolloid addition on batter properties and quality of deep-fried banana (Musa spp.) fritters
Authors: Vengu Sharmila , Ravandran Haswini Paniker , Gannasin Sri Puvanesvari , Muhammad Kharidah 
Published: September 2020

PurposeDeep-fried banana (Musa spp.) fritters is one of the frequently consumed fruit based snacks in Southeast Asian countries despite its substantial amount of oil content. Consistent with the demand for low fat food with maintained palatability, this study aimed to determine the quality of banana fritters as affected by batter system containing selected hydrocolloids such as pectin (PCN), whey protein isolate (WPI) and soy protein isolate (SPI).Design/methodology/approachBanana fritter batters were prepared with individual addition of 2% PCN (w/w), 10% WPI (w/w), 10% SPI (w/w), combination of 2% PCN and 10% WPI, combination of 2% PCN and 10% SPI and control (without hydrocolloid addition). Batter viscosity (Pa.s) and batter pick-up (%) were determined. Banana fritters were analysed for moisture and fat contents, moisture loss, colour, hardness and sensory characteristics.FindingsHydrocolloid addition in the batter system resulted in a higher batter pick-up and viscosity in comparison to control batter system. Moisture loss from banana fritters with batter formulation of 2% PCN and 10% SPI was the lowest while the reduction in oil content (55%) was the highest. Banana fritters with inclusion of hydrocolloids in the batter formulation were equally accepted as the control sample by the sensory panelists with a score range between 6 and 7 for most of the sensory attributes evaluated except for oiliness.Originality/valueApplication of PCN and SPI in batter system to develop banana fritters with low oil content, moist fruit core and crunchy crust is reported for the first time. Batter premix containing PCN and SPI can be produced for fresh and frozen fritters preparation.
Birds of a feather flock together: ownership in cross-border acquisitions by emerging multinationals
Authors: Domínguez Beatriz , Fuentelsaz Lucio , Garrido Elisabet , González Minerva 
Published: September 2020

PurposeDespite prior studies on cross-border acquisitions (CBAs) have analyzed the determinants of ownership strategies; there is still a quest for evidence on how the differences between home and host market characteristics affect the ownership percentage. Prior studies have acknowledged that entering host countries with greater uncertainty makes multinationals reluctant to acquire high levels of ownership. Nevertheless, emerging multinationals (EMNEs) are usually used to operating under greater levels of uncertainty than multinationals from advanced countries (AMNEs), which can imply different ownership strategies. The purpose of this study is to analyze the ownership percentage acquired by MNEs when designing a CBA in emerging or in advanced countries, and to analyze the extent to which the ownership strategy in emerging countries differs between EMNEs and AMNEs.Design/methodology/approachMobile telecommunications industry is used as research setting to provide empirical evidence of the interaction effect of the advanced versus emerging nature of the host and home countries on the ownership acquired in CBAs.FindingsResults confirm that both home and host countries' characteristics are relevant in explaining the ownership strategies of MNEs.Originality/valueThe authors contribute to the strategy and IB literatures by providing empirical evidence on the recent debate on whether the internationalization strategies followed by EMNEs are similar to the traditional patterns of AMNEs, and analyze how EMNEs differ from AMNEs in their ownership strategies in emerging countries. Focusing in the mobile telecommunications industry, the authors also contribute by extending the analysis to an international and cross-cultural setting that includes 48 mobile groups that come from 35 home and 81 host countries.
Research on the regional leading industry selection of “Kashgar urban agglomerations” based on multi-attribute weighted intelligent grey target decision-making evaluation model
Authors: Bai Xiao , Xu Yan , Liu Sifeng 
Published: September 2020

PurposeThe purpose of this paper is to establish the index system of leading industries in Kashgar urban agglomeration, and use the multi-attribute weighted intelligent grey target decision-making evaluation model to measure the comprehensive effect, so as to select the leading industries of Kashgar urban agglomeration.Design/methodology/approachFirst, 18 industries in Kashgar urban agglomerations are taken as objectives, and four indexes, namely, demand income elasticity index, growth rate index, labor productivity growth rate index and contribution rate of output value, are selected to construct an evaluation system for leading industry selection in Kashgar urban agglomerations. Then, grey incidence degree method is used to determine the decision-making power of each decision-making objective. Finally, multi-attribute weighted intelligent grey target decision-making evaluation model is used to measure the comprehensive effect of the objective system of leading industries in Kashgar urban agglomerations.FindingsIt can be seen that the multi-attribute weighted intelligent grey target decision-making evaluation model is more convenient to be used in selecting regional leading industries, and the results are accurate and feasible. Based on the calculation results and the actual economic development requirements of Kashgar urban agglomeration, the leading industries of Kashgar urban agglomeration can be determined as: wood processing, furniture, paper making and printing; wholesale and retail; construction; equipment manufacturing; transportation, storage and postal services.Originality/valueFirst, it is a new method in selecting regional leading industry by using the multi-attribute weighted intelligent grey target decision-making evaluation model. Second, since there is relatively little research on Kashgar urban agglomeration, especially on leading industries in Kashgar urban agglomeration. The research in this paper can not only enrich the research on selecting leading industries in urban agglomeration but also provide scientific reference for relevant government agencies to formulate economic development plans.
Investigating the relationship between working capital management and business performance: evidence from the 2008 financial crisis of EU-28
Authors: Akgün Ali İhsan , Memiş Karataş Ayyüce 
Published: September 2020

PurposeThis study examines the relationship between working capital management and business performance.Design/methodology/approachThe relationship between the working capital management and business performance is examined using panel data analysis for a sample of EU-28 listed firms for the period from 2003 to 2012. To examine this relationship, an ordinary least squares (OLS) regression model is used to analyze the data obtained from the sample. The dependent variable consists of three measurements, namely return on asset (ROA), return on equity (ROE) and earnings before interest and taxes margin (EBITM), which are used as proxies for accounting-based measures of performance.FindingsThe authors examined the aforementioned relationship during the 2008 financial crisis. The OLS regression analysis suggests that there is a negative relationship between gross working capital and business performance for code law countries. The results also show that liquidity measures estimated by current ratio have a statistically significant impact on business performance indicated by ROA for all EU countries. The 2008 financial crisis had a significantly negative impact on ROA. Additionally, the findings regarding financial inclusion show a negative relationship between gross working capital and business performance among EU and other performer countries.Practical implicationsOverall, the empirical findings are consistent with Afrifa's (2016), who suggests that cash flow should increase investment in working capital to improve performance indicated by EBITM for old EU members.Originality/valueWhile many empirical studies investigate the relationship between working capital and firm profitability, most do not consider the impact of the 2008 financial crisis apart from Tsurate (2019). The authors examine whether legal origins are important determinants of working capital management policies and business performance. Thus, empirically, the code law countries have a negative relationship between gross working capital, business performance and EBITM.