bluuebunny/crossref_metadata_2025_split huggingface dataset:
The secreted protein signature of hydatid fluid from pulmonary cystic echinococcosis
Authors: dos Santos Guilherme Brzoskowski , da Silva Edileuza Danieli , Kitano Eduardo Shigueo , Battistella Maria Eduarda , Monteiro Karina Mariante , de Lima Jeferson Camargo , Ferreira Henrique Bunselmeyer , de Toledo Serrano Solange Maria , Zaha Arnaldo 
Published: July 2020

AbstractThe vast majority of cystic echinococcosis cases in Southern Brazil are caused byEchinococcus granulosusandEchinococcus ortleppi. Comparative proteomic studies of helminths have increased the knowledge about the molecular survival strategies adopted by parasites. Here, we surveyed the protein contents of the hydatid fluid compartment ofE. granulosusandE. ortleppipulmonary bovine cysts, in an attempt to compare their molecular arsenal in this host-parasite interface. Hydatid fluid samples from three isolates of each species were analyzed by trypsin digestion and mass spectrometry. We identified 280 proteins inE. granulosusand 251 proteins inE. ortleppi, highlighting a core of 52 proteins common to all samples of hydatid fluid. Thein silicofunctional analysis revealed important molecular functions and processes active in pulmonary cystic echinococcosis. Some were more evident in one species, such as apoptosis inE. ortleppi, and cysteine protease activity inE. granulosus, while many molecular activities have been found in fluids of both species, such as proteolysis, development signaling and extracellular structures organization. The similar molecular tools employed byE. granulosusandE. ortleppifor their survival within the host are potential targets for new therapeutic approaches to deal with cystic echinococcosis and other larval cestodiases.
Activity throughout the lichen phylogeny indicates a focus on regulation of specialized metabolites
Authors: Roze Ludmila V. , Laivenieks Maris , Gdanetz Kristi , Linz John E. , Fryday Alan M. , Trail Frances 
Published: July 2020

AbstractLichens are complex multi-microorganismal communities that have evolved the ability to share their thalli with a variety of microorganisms. As such, the lichenized fungus becomes a scaffold for a variety of microbes and occasionally insects. Lichens are known to produce a plethora of unique specialized (secondary) compounds that demonstrate biological activities, including antibacterial, antifungal, antiviral, and antioxidant, that may provide protection from harmful microbes. The longevity of lichens and their robustness, despite a close association with diverse microbes, provides an interesting study system to view the role of specialized metabolites in managing a microbial community. The objective of this study was to identify the effects lichens may have on basic functions of fungi in and on the lichens. We tested chemical extracts from lichen species across the phylogenetic tree for their effects on sporulation, hyphal growth and specialized metabolite production, using two well-studied mycotoxigenic fungi (Aspergillus parasiticus(aflatoxin) andFusarium graminearum(trichothecenes) whose functions are easily observed in culture. By far the most prevalent activity among the 67 lichens we tested were effects on accumulation of fungal specialized metabolites, which appeared in 92% of the lichen species analyzed across the phylogeny, although the lichen extracts were also active against fungal sporulation (31%) and growth (12%). The consistent presence of this regulatory activity for specialized metabolism indicates this is an important aspect of lichen integrity. Interestingly, inhibition of accumulation of products of the aflatoxin biosynthetic pathway was the predominant activity, whereas increased accumulation versus decreased accumulation of the production of trichothecenes were about equal. This suggests multiple mechanisms for addressing fungal processes. We performed microbiome analysis of four lichen species and identified oomycetes as members of the microbiomes. Although a small sample size was used for comparing microbiomes, the lichen species exhibiting lower effects on the test fungi had a higher number of OTUs. Members of the lichen community may manipulate specialized metabolism of the essential and transient fungal members and thus attenuate negative interactions with the incumbent fungi or, alternatively, may support the production of compounds by beneficial fungal partners. The ability to control the microbiome by specialized metabolites as opposed to controlling by reducing sporulation of growth, can be effective, discerning, and energetically thrifty, allowing the microbiome members to be controlled without being invasive. Elucidating the role of specialized metabolites in the mechanisms underlying lichen assembly and function has important implications for understanding not only lichen community assembly but for revealing the fundamental processes in microbiota in general.
Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments
Authors: Teufel Ashley I. , Liu Wu , Draghi Jeremy A. , Cameron Craig E. , Wilke Claus O. 
Published: July 2020

AbstractViruses experience selective pressure on the timing and order of events during infection to maximize the number of viable offspring they produce. Additionally, they may experience variability in cellular environments encountered, as individual eukaryotic cells can display variation in gene expression among cells. This leads to a dynamic phenotypic landscape that viruses must face to produce offspring. To examine replication dynamics displayed by viruses faced with this variable landscape, we have developed a method for fitting a stochastic mechanistic model of viral infection to growth data from high-throughput single-cell poliovirus infection experiments. The model’s mechanistic parameters provide estimates of several aspects associated with the virus’s intracellular dynamics. We examine distributions of parameter estimates and assess their variability to gain insight into the root causes of variability in viral growth dynamics. We also fit our model to experiments performed under various drug treatments and examine which parameters differ under these conditions. We find that parameters associated with translation and early stage viral replication processes are essential for the model to capture experimentally observed dynamics. In aggregate, our results suggest that differences in viral growth data generated under different treatments can largely be captured by steps that occur early in the replication process.Author SummaryUnderstanding the intercellular processes associated with virus replication is essential for controlling viral diseases. Single-cell infection experiments with poliovirus have shown that viral growth differs among individual cells in terms of both the total amount of virus produced and the rate of viral production. To better understand the source of this variation we here develop a modeling protocol that simulates viral growth and we then fit our model to data from high-throughput single-cell experiments. Our modeling approach is based on generating time course simulations of populations of single-cell infections. We aggregate metrics from our simulated populations such that we can describe our simulated viral growth in terms of several distributions. Using the corresponding distributions calculated from experimental data we minimize the difference between our simulated and experimental data to estimate parameters of our simulation model. Each parameter corresponds to a specific aspect of the intercellular viral replication process. By examining our estimates of these parameters, we find that steps that occur early in the viral replication process are essential for our model to capture the variability observed in experimental data.
Unravelling the molecular players at the cholinergic efferent synapse of the zebrafish lateral line
Authors: Carpaneto Freixas Agustín E. , Moglie Marcelo J. , Castagnola Tais , Salatino Lucia , Domene Sabina , Marcovich Irina , Gallino Sofia , Wedemeyer Carolina , Goutman Juan D. , Plazas Paola V. , Elgoyhen Ana Belén 
Published: July 2020

AbstractThe lateral line (LL) is a sensory system that allows fish and amphibians to detect water currents. LL responsiveness to external stimuli is modulated by descending efferent neurons. LL efferent modulation aids the animal to distinguish between external and self-generated stimuli, maintaining sensitivity to relevant cues. One of the main components of the efferent system is cholinergic, the activation of which inhibits afferent activity. Since LL hair cells (HC) share structural, functional and molecular similarities with those of the cochlea, one could propose that the receptor at the LL efferent synapse is a α9α10 nicotinic cholinergic one (nAChR). However, the identity of the molecular players underlying acetylcholine (ACh)-mediated inhibition in the LL remain unknown. Surprisingly, through the analysis of single-cell expression data andin situhybridization, we describe that α9, but not α10 subunits, are enriched in zebrafish HC. Moreover, the heterologous expression of zebrafish α9 subunits indicates that α9 homomeric receptors are functional and exhibit robust ACh-gated currents which are blocked by α-Bungarotoxin (α-Btx). In addition,in vivoCa2+imaging on mechanically-stimulated zebrafish LL HC showed that ACh elicits a decrease in evoked Ca2+signals, irrespective of HC polarity. This effect was blocked by both α-Btx and apamin, indicating coupling of ACh mediated effects to SK potassium channels. Collectively, our results indicate that an α9-containing (α9*) nAChR operates at the zebrafish LL efferent synapse. Moreover, the activation of α9* nAChRs most likely leads to LL HC hyperpolarization served by the ACh-dependent activation of Ca2+-dependent SK potassium channels.Significance StatementFishes and amphibians have a mechanosensory system, the lateral line (LL), which serves to detect hydromechanical variations around the animal’s body. The LL receives descending efferent innervation from the brain that modulates its responsiveness to external stimuli. LL efferent inhibition is mediated by ACh, however the identity of the molecular players at the LL efferent synapse is unknown. Here we demonstrate that a nicotinic cholinergic receptor (nAChR) composed of α9 subunits operates at the LL efferent synapse. Activation of α9-containing (α9*) nAChRs leads to LL hair cell hyperpolarization. The inhibitory signature of this process is brought about by the subsequent activation of Ca2+-dependent potassium SK channels, functionally coupled to α9* nAChRs.
A transgenic line that reports CSF1R protein expression provides a definitive marker for the mouse mononuclear phagocyte system
Authors: Grabert Kathleen , Sehgal Anuj , Irvine Katharine M. , Wollscheid-Lengeling Evi , Ozdemir Derya D. , Stables Jennifer , Luke Garry A. , Ryan Martin D. , Adamson Antony , Humphreys Neil E. , Sandrock Cheyenne J. , Rojo Rocio , Verkasalo Veera A. , Mueller Werner , Hohenstein Peter , Pettit Allison R. , Pridans Clare , Hume David A. 
Published: July 2020

AbstractThe proliferation, differentiation and survival of cells of the mononuclear phagocyte system (MPS, progenitors, monocytes, macrophages and classical dendritic cells) is controlled by signals from the macrophage colony-stimulating factor receptor (CSF1R). Cells of the MPS lineage have been identified using numerous surface markers and transgenic reporters but none is both universal and lineage-restricted. Here we report the development and characterization of a novel CSF1R reporter mouse. A Fusion Red (FRed) cassette was inserted in-frame with the C-terminus of CSF1R, separated by a T2A-cleavable linker. The insertion had no effect of CSF1R expression or function. CSF1R-FRed was expressed in monocytes and macrophages and absent from granulocytes and lymphocytes. In bone marrow, CSF1R-FRed was absent in lineage-negative hematopoietic stem cells (HSC), arguing against a direct role for CSF1R in myeloid lineage commitment. It was highly-expressed in marrow monocytes and common myeloid progenitors (CMP) but significantly lower in granulocyte-macrophage progenitors (GMP). In sections of bone marrow, CSF1R-FRed was also detected in osteoclasts, CD169+resident macrophages and, consistent with previous mRNA analysis, in megakaryocytes. In lymphoid tissues, CSF1R-FRed highlighted diverse MPS populations including classical dendritic cells. Whole mount imaging of non-lymphoid tissues in mice with combined CSF1R-FRed/Csf1r-EGFP confirmed the restriction of CSF1R expression to MPS cells. The two markers highlight the remarkable abundance and regular distribution of tissue MPS cells including novel macrophage populations within tendon and skeletal muscle and underlying the mesothelial/serosal/capsular surfaces of every major organ. The CSF1R-FRed mouse provides a novel reporter with exquisite specificity for cells of the MPS.
Improving recombinant protein production using TISIGNER.com
Authors: Bhandari Bikash K. , Lim Chun Shen , Gardner Paul P. 
Published: July 2020

ABSTRACTPlanning experiments using accurate prediction algorithms could mitigate failures in recombinant protein production. We have developedTISIGNER.comwith the aim of addressing the technical challenges in recombinant protein production. We offer two web services, TIsigner (Translation Initiation coding region designer) and SoDoPE (SolubleDomain forProteinExpression), which are specialised in prediction/optimisation of recombinant protein expression and solubility, respectively. Importantly, TIsigner and SoDoPE are linked, which allows users to switch between the tools when optimising their genes of interest.
Operational TBE incidence forecasts for Austria, Germany, and Switzerland 2019–2021
Authors: Rubel Franz , Brugger Katharina 
Published: July 2020

AbstractIn spring 2019, forecasts of the incidence of tick-borne encephalitis (TBE) for the next two years, i.e. 2019 and 2020, were made for the first time. For this purpose, negative binomial regression models with 4–5 predictors were fitted to the time series of annual human TBE incidences from Austria, Germany and Switzerland. The most important predictor for TBE incidences is the fructification index of the European beech (Fagus sylvatica) 2 years prior as a proxi for the intensity of the TBE virus transmission cycle. These forecasts were repeated in spring 2020 after the updated predictors and the confirmed TBE cases for 2019 became available. Forecasting TBE incidences for 2020 and 2021 results in 156±19 and 131±23 TBE cases for Austria, 663±95 and 543±112 TBE cases for Germany as well as 472±56 and 350±62 TBE cases for Switzerland. The newly implemented operational TBE forecasts will be verified every year with confirmed TBE cases. An initial verification for 2019 demonstrates the high reliability of the forecasts.
ALeRT-COVID: Attentive Lockdown-awaRe Transfer Learning for Predicting COVID-19 Pandemics in Different Countries
Authors: Li Yingxue , Jia Wenxiao , Wang Junmei , Guo Jianying , Liu Qin , Li Xiang , Xie Guotong , Wang Fei 
Published: July 2020

AbstractCountries across the world are in different stages of COVID-19 trajectory, among which many have implemented the lockdown measures to prevent its spread. Although the lockdown is effective in such prevention, it may put the economy into a depression. Predicting the epidemic progression with government switching the lockdown on or off is critical. We propose a transfer learning approach called ALeRT-COVID using attention-based recurrent neural network (RNN) architecture to predict the epidemic trends for different countries. A source model was trained on the pre-defined source countries and then transferred to each target country. The lockdown measure was introduced to our model as a predictor and the attention mechanism was utilized to learn the different contributions of the confirmed cases in the past days to the future trend. Results demonstrated that the transfer learning strategy is helpful especially for early-stage countries. By introducing the lockdown predictor and the attention mechanism, ALeRT-COVID showed a significant improvement on the prediction performance. We predicted the confirmed cases in one week when extending and easing lockdown separately. Results showed the lockdown measures is still necessary for a number of countries. We expect our research can help different countries to make better decisions on the lockdown measures.
Solving two-dimensional linear partial differential equations based on Chebyshev neural network with extreme learning machine algorithm
Authors: Liu Min , Hou Muzhou , Wang Juan , Cheng Yangjin 
Published: July 2020

Purpose
This paper aims to develop a novel algorithm and apply it to solve two-dimensional linear partial differential equations (PDEs). The proposed method is based on Chebyshev neural network and extreme learning machine (ELM) called Chebyshev extreme learning machine (Ch-ELM) method.

Design/methodology/approach
The network used in the proposed method is a single hidden layer feedforward neural network. The Kronecker product of two Chebyshev polynomials is used as basis function. The weights from the input layer to the hidden layer are fixed value 1. The weights from the hidden layer to the output layer can be obtained by using ELM algorithm to solve the linear equations established by PDEs and its definite conditions.

Findings
To verify the effectiveness of the proposed method, two-dimensional linear PDEs are selected and its numerical solutions are obtained by using the proposed method. The effectiveness of the proposed method is illustrated by comparing with the analytical solutions, and its superiority is illustrated by comparing with other existing algorithms.

Originality/value
Ch-ELM algorithm for solving two-dimensional linear PDEs is proposed. The algorithm has fast execution speed and high numerical accuracy.
The relationship between logistics performance and carbon emissions: an empirical investigation on Balkan countries
Authors: Karaduman Hasan Ağan , Karaman-Akgül Arzu , Çağlar Mehmet , Akbaş Halil Emre 
Published: July 2020

PurposeThe purpose of this paper is to analyze the impact of logistics performance on the carbon (CO2) emissions of Balkan countries.Design/methodology/approachFixed-effects panel regression analysis is used to estimate the causal relationship between CO2 emissions and logistic performances of Balkan countries. Logistics performance is measured by logistics performance index (LPI) which was published by the World Bank in 2007, 2010, 2012, 2014 and 2016 and used for ranking countries by means of their logistics performance. LPI is based on six main indicators: customs procedures, logistics costs and the quality of the infrastructure for overland and maritime transport. As a measure of carbon emissions of sampled countries, the natural logarithm of carbon dioxide emission per capita is used in this study.FindingsThe results obtained reveal that there is a positive and significant relationship between logistics performance and CO2 performances of the sampled Balkan countries.Research limitations/implicationsThis study is based on only 11 Balkan countries. In this sense, the data used in the analysis is limited.Originality/valueConsidering the important geostrategic position of the Balkan region, logistics sector has an important role for the development of the countries in that region. In this sense, the findings of this study may provide useful insights for policymakers to achieve sustainable economic development. Furthermore, as far as the authors know, this is the first study that focuses on the relationship between logistics performance and carbon emissions of Balkan countries.
Gendered and diversified? Leadership in global hospitality and tourism academia
Authors: Gewinner Irina 
Published: July 2020

Purpose
This paper aims to represent a unique and original piece of research on full professors in global hospitality and tourism academia. Aimed at revisiting academic leadership, this study identifies its components and gains insight into the so far understudied dimensions of diversity in academic contexts worldwide.

Design/methodology/approach
This study examines the careers of senior researchers (R3 and R4, according to European Commission) in hospitality and tourism, with special attention given to diversity. Based on quantitative methodology and a standardised online search, it uses individual-level data to give insights into dimensions of academic leadership. Full professors from the UK, the USA, German-speaking countries (Germany, Austria and Switzerland) and the Asia-Pacific region (Australia, New Zealand, China, Malaysia, Singapore and South Korea) build the sample.

Findings
Academic leadership in hospitality and tourism academia is not yet fully tied to cooperation with industry, as predicted by the “Triple Helix” model. Currently, the majority of the intellectual component constitutes academic leadership, outweighing administrative and innovative angles. Gender, age and ethnic diversity are underrepresented. While some regions can be considered sealed to ethnic diversity, others are more open and attract international scholars.

Originality/value
Rooted in interdisciplinary explanations, this study is the first of its kind to consider various diversity dimensions of academic leadership from a global perspective. It not only enriches the notion of academic leadership but also provides several practical implications and suggestions for further research.
The evolution of predictive models and tourism
Authors: Gharibi Najmeh 
Published: July 2020

PurposeThis study aims to investigate the predictive technology acceptance models and their evolution in the tourism context. These predictive models make a knowledgeable decision about the possibility of future outcomes by analysing data. As futurists are interested in making a prediction about the likelihood of different behaviours over time, researchers of these predictive models have focussed on behaviour and predicting the intentions of users. This study proposes to demonstrate the revolution of these models and how are changed overtime. It also indicates the role of them in future studies.Design/methodology/approachBy reviewing the predictive models and literature, this study looks in-depth in the process of alteration of these models.FindingsThis study explores the reasons of the evolution of predictive models and how they are changed. It shed light on the role of predictive models in future research and will suggest new directions for forthcoming studies.Research limitations/implicationsOne of the main limitations of this study is that as the world is currently struggling with COVID-19 and predictability of these models will be changed. As the future is disruptive, it cannot be concluded that how these models will be altered in future.Practical implicationsRole of predictive behavioural models of tourists is fundamentally crucial in assessing the performance of planners and marketers of tourism services in the future. It will also vastly helps the successful development of tourism sectors, and it has practical value for all tourism stakeholders.Originality/valueFew studies have focussed on the evaluation of these models and their role in future research.