bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the microbial community structure and metabolic gene clusters during silage fermentation of paper mulberry, and developing the high-protein woody plant as ruminant feed
Authors: Du Zhumei , Sun Lin , Chen Chao , Lin Jing , Yang Fuyu , Cai Yimin 
Published: July 2020

ABSTRACTTo develop a new high-protein woody forage resource for livestock, we applied PacBio single-molecule, real-time (SMRT) sequencing technology to explore the community structure, species diversity, and metabolic gene clusters of nature microbes associated with paper mulberry (PM) silage fermentation. The microbial diversity and abundance were rich in PM raw material and decreases with the progress of silage fermentation. Woody ensiling is process that the dominant bacteria shifted from Gram-negative pathogenicProteobacteriato Gram-positive beneficialFirmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in the terminal silages. Global and overview maps, carbohydrate metabolism and amino acid metabolism were the important microbial metabolic pathways that impact final fermentation product of silage. PM is rich in nutrients and preserved well during ensiling, indicating PM can develop as new woody resources suitable for ruminants. PacBio SMRT sequencing revealed specific microbial-related information about silage.IMPORTANCEIn the tropics, there is often a shortage of forage during the dry season. Failure to obtain high-quality feed will reduce the milk and meat production of ruminants. Therefore, it is essential to maximize the use of land and biomass resources through strategic development of alternative feed. Paper mulberry (PM) is a perennial deciduous tree in tropics, with a variety of nutrients and biologically active ingredients, and it adapts to various soils and climates, with high production capacity, and low cultivation costs. In order to develop new potential woody forage, we firstly used PacBio single-molecule real-time (SMRT) sequencing technology to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms related to the fermentation of silage. PacBio SMRT revealed information about specific microorganisms related to silage, indicating PM can prepare as good-quality silage, and will become a new potential woody feed resources for livestock.
Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2
Authors: Rohaim Mohammed A , Clayton Emily , Sahin Irem , Vilela Julianne , Khalifa Manar , Al-Natour Mohammad , Bayoumi Mahmoud , Poirier Aurore , Branavan Manoharanehru , Tharmakulasingam Mukunthan , Chaudhry Nouman S , Sodi Ravinder , Brown Amy , Burkhart Peter , Hacking Wendy , Botham Judy , Boyce Joe , Wilkinson Hayley , Williams Craig , Bates Michelle , La Ragione Roberto , Balachandran Wamadeva , Fernando Anil , Munir Muhammad 
Published: July 2020

AbstractUntil vaccines and effective therapeutics become available, the practical way to transit safely out of the current lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms, and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ∼200 coronavirus disease (CoVID-19)-suspected patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. The system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.
Effect of acute low oxygen exposure on the proliferation rate, viability and gene expression of C2C12myoblastsin vitro
Authors: Sharkey Jack V 
Published: July 2020

ABSTRACTINTRODUCTIONChanges in the oxygen concentration of cellular microenvironments play a significant role in regulating cell function during muscle regeneration. Generally, mostin-vitrocell culture experiments have been carried out in atmospheric conditions with 21% O2, which compared to the actual micro-environment of mature skeletal muscle of between 1% and 10% pO2 is extremely hyperoxic (Li et al, 2007). Culturing skeletal muscle cellsin vitrowithin their typical physiologically hypoxic environmentin situ(2-10% pO2) has been shown to increase proliferation rate, reduce apoptosis and increase multiple MRF gene expressions, compared to culturing in a normoxic environment (21% O2). However, chronic exposure (>24 hr) to a semi-severe hypoxic environment (≤5% O2) can lead to a decrease in cell proliferation and differentiation (Chakravarthy et al, 2001). The effects of acute hypoxic exposure (24 h) has limited research and could be important in understanding the effects of hypoxia on skeletal muscle during brief exposures such as those observed within intermittent hypoxic training programmes. The purpose of this work was to examine the role of acute hypoxia (24 h) on C2C12proliferation and relevant gene expression in 2D culture.METHODSC2C12mouse myoblast cells were seeded into six well plates. The cells were maintained in DMEM with 20% FCS. C2C12myoblasts were either exposed to 21% or 5% O2. The effects of acute hypoxic exposure (24hours) at different time points during the proliferative phase of myogenesis, rather than chronic exposure, on cell proliferation, cellular viability and myogenic regulatory factor gene expression was examined. At 24, 48, 72 and 96 hours RNA was extracted using the Trizol®method and mRNA expression of myogenic regulatory factors, myoD, myf5 and myogenin were detected using the 2-ΔΔCT method. Cell counts and cell viability were also quantifiedRESULTSNo significant difference was found between cells cultured in normoxic conditions (21%) and those that were exposed to low oxygen conditions for 24hours at various time points over a 96 hour culture period, with regards to proliferation rate, cell viability, and myogenic regulatory gene expression (Myf5, MyoDandMyogenin).DISCUSSIONThe effect of acute low oxygen exposure lasting 24hours appears to not be insufficient in having an effect on the proliferation rate, viability or transcription factor expression of C2C12 cells during the proliferative phase of myogenesis.
Comprehensive variant and haplotype landscapes of 50,500 global SARS-CoV-2 isolates and accelerating accumulation of country-private variant profiles
Authors: Shen Lishuang , Bard Jennifer Dien , Biegel Jaclyn A. , Judkins Alexander R. , Gai Xiaowu 
Published: July 2020

AbstractUnderstanding the genetic etiology of COVID-19 requires a comprehensive understanding of the variant and haplotype landscape of all reported genomes of SARS-COV-2, the causative virus of the disease. Country-, state/region- and possibly even city-private variant profiles may contribute to varied disease exemplifications and fatality rates observed across the globe along with host factors such as age, ethnicity and comorbidity. The Children’s Hospital of Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) captures up-to-date fulllength SARS-CoV-2 sequences of ~50,500 isolates from GISAID, GenBank, CHLA Center for Personalized Medicine, and other sources (as of June 18, 2020). Among which, 49,637 isolates carry at least one variation from the reference genome NC_045512, a total of 6,070 variants and 2,513 haplotypes were detected in at least three isolates independently. Together, they constituted the most likely SARS-CoV-2 variant and haplotype landscapes world-wide currently.Evidence supporting positive (orf3a, orf8, S genes) and purifying (M gene) selections were detected, which warrants further investigation. Most interestingly, we identified 1,583 countryprivate variants from 10,238 isolates (20.6% overall) reported in 48 countries. 807 countryprivate haplotypes, defined as a haplotype shared by at least 5 isolates all of which came from the same country, were identified in in 8,656 isolates from 39 countries. United Kingdom, USA, and Australia had 464, 166 and 32 private haplotypes respectively, comprising 22.4%, 16.6% and 16.4% of the isolates from each country. Together with their descendent and private haplotypes with fewer members, 22,171 (45.8%) isolates carried country-private haplotypes globally. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions. The localization of the variant profiles appeared to be similarly accelerating from 14.2% in March and 28.4% in April to over 40% isolates carrying the country-private variants around May.In summary, a common pattern is seen world-wide in COVID-19 in which at the onset of disease there appeared to be a significant number of SARS-CoV-2 variants that accumulate quickly and then begin to rapidly coalesce into distinct haplotypes. This may be the result of localized outbreaks due to factors such as multiple points viral introduction, geographic separation and the introduction of policies such as travel restriction, social distancing and quarantine, resulting in the emergence of country-private haplotypes.
Metabolite patterns in human myeloid hematopoiesis result from lineage-dependent active metabolic pathways
Authors: Kaiser Lars , Weinschrott Helga , Quint Isabel , Wenzel Folker , Blaess Markus , Jung Manfred , Kohl Matthias , Deigner Hans-Peter 
Published: July 2020

AbstractAssessment of hematotoxicity from environmental or xenobiotic compounds is of notable interest and is frequently assessed via the colony forming unit (CFU) assay. Identification of the mode of action of single compounds is of further interest, as such often enables transfer of results across different tissues and compounds. Metabolomics displays one promising approach for identifying such, nevertheless, suitability with current protocols is restricted. Here, we combined an HSPC expansion approach with distinct lineage differentiations, resulting in formation of erythrocytes, dendritic cells and neutrophils. We examined the unique combination of fluxes in glycolysis, glutaminolysis, polyamine synthesis, fatty acid oxidation and synthesis, as well as glycerophospholipid and sphingolipid metabolism. We further assessed their interconnections and essentialness for each lineage formation. By this, we provide further insights into metabolic fluxes during differentiation of HSPC into different lineages, enabling profound understanding of possible metabolic changes in each lineage caused by exogenous compounds.
Combined Effect of Shear Stress and Laser-Patterned Topography on Schwann cell Outgrowth: Synergistic or Antagonistic?
Authors: Babaliari Eleftheria , Kavatzikidou Paraskevi , Mitraki Anna , Papaharilaou Yannis , Ranella Anthi , Stratakis Emmanuel 
Published: July 2020

AbstractAlthough the peripheral nervous system exhibits a higher rate of regeneration than that of the central nervous system through a spontaneous regeneration after injury, the functional recovery is fairly infrequent and misdirected. Thus, the development of successful methods to guide neuronal outgrowth,in vitro, is of great importance. In this study, a precise flow controlled microfluidic system with specific custom-designed chambers, incorporating laser-microstructured polyethylene terephthalate (PET) substrates comprising microgrooves, was fabricated to assess the combined effect of shear stress and topography on Schwann cells’ behavior. The microgrooves were positioned either parallel or perpendicular to the direction of the flow inside the chambers. Additionally, the cell culture results were combined with computational flow simulations to calculate accurately the shear stress values. Our results demonstrated that wall shear stress gradients may be acting either synergistic or antagonistic depending on the substrates groove orientation relative to the flow direction. The ability to control cell alignmentin vitrocould potentially be used in the fields of neural tissue engineering and regenerative medicine.
A Poorly Understood Disease? The Unequal Distribution of Excess Mortality Due to COVID-19 Across French Municipalities*
Authors: Brandily Paul , Brébion Clément , Briole Simon , Khoury Laura 
Published: July 2020

AbstractWhile COVID-19 was already responsible for more than 500,000 deaths worldwide as of July 3, 2020, very little is known on the socio-economic heterogeneity of its impact on mortality. In this paper, we combine several administrative data sources to estimate the relationship between mortality due to COVID-19 and poverty at a very local level (i.e. the municipality level) in France, one of the most severely hit country in the world. We find strong evidence of an income gradient in the impact of the pandemic on mortality: it is twice as large in the poorest municipalities compared to other municipalities. We then show that both poor housing conditions and higher occupational exposure are likely mechanisms. Overall, these mechanisms accounts for up to 60% of the difference observed between rich and poor municipalities.
Sustainability reporting after the Costa Concordia disaster: a multi-theory study on legitimacy, impression management and image restoration
Authors: Corazza Laura , Truant Elisa , Scagnelli Simone Domenico , Mio Chiara 
Published: July 2020

PurposeCan sustainability disclosures be a tool for executing image restoration strategies after corporate manslaughter? This is the question explored in this study of Costa Crociere's sustainability reports after the Concordia disaster.Design/methodology/approachMerging traditional textual content analysis with visual analysis and supported by machine learning tools, this is a predominantly qualitative study framed by legitimacy theory, image restoration theory and impression management.FindingsCosta Crociere's voluntary sustainability reporting is strongly influenced by a mix of text and visual signals that distract readers' attention from the disaster. A “nothing really happened” communication strategy pervades the disclosures, with the only rational motivation being to change perceptions and erase memories of this tragic and avoidable event.Research limitations/implicationsAlthough the analysis covered multiple sources of corporate information, media coverage was not one of them. A more in-depth exploration of sustainability reporting in the cruise industry, including evidence of similar cases, to test impression management theory would be a worthwhile avenue for future research.Social implicationsWhile Costa Crociere technically followed the customary guidelines of disclosing human resource impacts, there was almost no acknowledgement of the people involved in the accident. Costa Concierevastly understated their responsibility for the accident, did not apologize, and conveyed very little remorse. The majority of disclosures centred on disaster recovery management.Originality/valueThe authors discuss why and how a company can overcome a legitimacy threat by completely freezing its voluntary sustainability reporting, and the authors show how a company can restore its image by minimizing specific aspects of an accident and shifting attention from the human victims to corporate operations. Incorporating image recognition driven by AI models and combining the results with narrative disclosures contributes an innovative and original analysis technique to the field of impression management. In addition, this research also contributes to our knowledge on the cruise industry – a sector currently under scrutiny for its ethical, social and environmental practices.
Managing the communicative organization: a qualitative analysis of knowledge-intensive companies
Authors: Pekkala Kaisa 
Published: July 2020

PurposeThe purpose of this paper is to explore how employees' work-related communication is managed in knowledge-intensive organizations.Design/methodology/approachThe study was conducted by applying an exploratory, qualitative approach. The data were collected from six knowledge-intensive organizations operating in the professional service sector in Finland, and the data set used included altogether 23 interviews.FindingsThe interviews confirmed that employees' work-related communication on social media is regarded as an increasingly important area, and that it has required companies to establish new managerial processes that are aimed to affect employees’ communication behaviors (ECB) either as enablers or motivators. How companies apply these processes depends on contextual factors, and three different managerial approaches were identified, namely, individual-, corporate- and business-oriented approaches.Research limitations/implicationsBased on the findings, this article proposes a new field for the communication management literature, management of the communicative organization (MCO), which builds on behavior management knowledge and focuses on managing employee communicators in multivocal organizational communication systems (MOCSs) that are dependent on employee-generated content.Originality/valueThe study advances the field of communication management and ECB by empirically proving that organizations manage their employees' work-related communication and the management processes and practices identified derive from behavioral management tradition. The proposed MCO framework introduces a novel area for academic discussion on how communication management affects ECB and attitudes, such as motivation.
Assessing disaster capitalism in post-disaster processes in Chile: neoliberal reforms and the role of the corporate class
Authors: Sandoval Vicente , Gonzalez-Muzzio Claudia , Villalobos Carlos , Sarmiento Juan Pablo , Hoberman Gabriela 
Published: July 2020

PurposeThis paper examines disaster capitalism in Chile, that is, the relationships between disasters and neoliberalism. It looks at two post-disaster dimensions: disasters as windows of opportunity to introduce political reforms and disasters as occasions for the corporate class to capitalize on such disasters.Design/methodology/approachTwo indices, disaster capitalism (DC) and post-disaster private involvement (PDPI), are proposed for cross-case analysis. They are based on legal records, institutional reports and economic data. The DC assesses the introduction of reforms following disasters, while PDPI evaluates the share of public-private funding used for recovery. Both indices are applied here to two disasters in Chile: the 2010 Maule earthquake, and the 2008 Chaitén volcanic eruption.FindingsResults show that the highly neoliberal Chilean context leaves limited space for new neoliberal reforms. Although recovery is implemented predominantly through the private sector, the state still assumes greater responsibility for recovery costs. Results also detect poor levels of participation from the private sector in accounting their efforts and making them publicly available. Likewise, the research suggests that neoliberal reforms become more likely after disasters. However, the preexisting politico-economic context matters. Finally, there is clearly a need for data systematization in post-disaster recovery.Originality/valueIn the Chilean context, the indices proved beneficial as a strategy for data collection and a method for scrutinizing the implications of neoliberal policy implemented in the wake of disasters, as well as in evaluating the role of the corporate class during recovery.
Direct energy deposition metamodeling using a meshless method
Authors: Abbes Boussad , Anedaf Tahar , Abbes Fazilay , Li Yuming 
Published: July 2020

Purpose
Direct energy deposition (DED) is an additive manufacturing process that allows to produce metal parts with complex shapes. DED process depends on several parameters, including laser power, deposition rate and powder feeding rate. It is important to control the manufacturing process to study the influence of the operating parameters on the final characteristics of these parts and to optimize them. Computational modeling helps engineers to address these challenges. This paper aims to establish a framework for the development, verification and application of meshless methods and surrogate models to the DED process.

Design/methodology/approach
Finite pointset method (FPM) is used to solve conservation equations involved in the DED process. A surrogate model is then established for the DED process using design of experiments with powder feeding rate, laser power and scanning speed as input parameters. The surrogate model is constructed using neutral networks (NN) approximations for the prediction of maximum temperature, clad angle and dilution.

Findings
The simulations of thin wall built of Ti-6Al-4V titanium alloy clearly demonstrated that FPM simulation is successful in predicting temperature distribution for different process conditions and compare favorably with experimental results from the literature. A methodology has been developed for obtaining a surrogate model for DED process.

Originality/value
This methodology shows how to achieve realistic simulations of DED process and how to construct a surrogate model for further use in optimization loop.
Owner capabilities in social infrastructure projects: towards an expansion of the dynamic capabilities’ framework
Authors: Gulino Maria Luz , Sergeeva Natalya , Winch Graham 
Published: July 2020

PurposeThe project organising literature has increasingly paid attention to the dynamic capabilities required for the development of projects. The current research aims to expand the dynamic capabilities framework by including owner capabilities required throughout the whole project life cycle.Design/methodology/approachThe research uses an interpretive qualitative research approach. Nineteen semi-structured interviews were conducted with the key actors of a social infrastructure project.FindingsThe findings suggest that the expansion of the dynamic capabilities framework to include owner capabilities required throughout a project life cycle could positively impact the success of a project. “Transformational capabilities” are recommended to enable the owner to overcome challenges and lead the evolution towards project organisations that are capable of transforming its outputs into beneficial use.Originality/valueExisting research on dynamic capabilities does not address the particular challenges of social infrastructure projects such as housing. The current research fills this gap by exposing the challenges experienced by owners in the development of certain capabilities and their impact on the performance of a project.