bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regeneration in spongeSycon ciliatummimics postlarval development
Authors: Soubigou Anael , Ross Ethan G , Touhami Yousef , Chrismas Nathan , Modepalli Vengamanaidu 
Published: May 2020

AbstractSomatic cells dissociated from an adult sponge can re-organize and develop into a functional juvenile. However, the extent to which regeneration recapitulates embryonic developmental signaling pathways has remained enigmatic for more than a century. To this end, we have standardized and established a spongeSycon ciliatumregeneration protocol to achieve consistent regeneration in cell culture. From the morphological analysis, we demonstrated that dissociated sponge cells follow a series of morphological events resembling embryonic and postlarval development. Hence, we propose that sponge regeneration represents somatic development. To support our hypothesis, we performed high-throughput sequencing on regenerating samples and compared the data with regular embryonic and postlarval development ofSycon ciliatum. Our comparative transcriptomic analysis illuminates that sponge regeneration is equally as dynamic as embryogenesis. We find that sponge regeneration is orchestrated by complex regulatory mechanisms by recruiting signaling pathways like those utilized in embryonic development to organize into a functional juvenile. In the current study, we lay down the basic framework to studySycon ciliatumregeneration. Since sponges are likely to be the first branch of extant multicellular animal and the sister lineage to nearly all animals, we suggest that this system can be explored to study the genetic features underlying the evolution of multicellularity and regeneration.
Hallmarks of basidiomycete soft- and white-rot in wood-decay -omics data ofArmillaria
Authors: Sahu Neha , Merényi Zsolt , Bálint Balázs , Kiss Brigitta , Sipos György , Owens Rebecca , Nagy László G. 
Published: May 2020

AbstractThe genusArmillariaspp. (Fungi, Basidiomycota) includes devastating pathogens of temperate forests and saprotrophs that decay wood. Pathogenic and saprotrophicArmillariaspecies can efficiently colonize and decay woody substrates, however, mechanisms of wood penetration and colonization are poorly known. We assayed the colonization and decay of autoclaved spruce roots using the conifer-specialistsArmillaria ostoyaeandA. cepistipesusing transcriptomic and proteomic data. Transcript and protein levels were altered more extensively in the saprotrophicA. cepistipesthan in the pathogenicA. ostoyaeand in invasive mycelia of both species compared to their rhizomorphs. Diverse suites of carbohydrate-active enzyme genes (CAZymes), in particular pectinolytic ones and expansins, were upregulated in both species, whereas ligninolytic genes were mostly downregulated. Our gene expression data, together with previous comparative genomic and decay-chemistry analyses suggest that wood decay byArmillariadiffers from that of typical white-rot fungi and shows features resembling soft rot. We propose thatArmillariaspecies have modified the ancestral white-rot machinery so that it allows for selective ligninolysis based on environmental conditions and/or host types.
Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data
Authors: Pintacuda Greta , Lassen Frederik H. , Hsu Yu-Han H. , Kim April , Martín Jacqueline M. , Malolepsza Edyta , Lim Justin K. , Fornelos Nadine , Eggan Kevin C. , Lage Kasper 
Published: May 2020

AbstractCombining genetic and cell-type-specific proteomic datasets can lead to new biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present an open-source computational tool called Genoppi that enables robust, standardized, and intuitive integration of quantitative proteomic results with genetic data. We used Genoppi to analyze sixteen cell-type-specific protein interaction datasets of four proteins (TDP-43, MDM2, PTEN, and BCL2) involved in cancer and neurological disease. Through systematic quality control of the data and integration with published protein interactions, we show a general pattern of both cell-type-independent and cell-type-specific interactions across three cancer and one human iPSC-derived neuronal type. Furthermore, through the integration of proteomic and genetic datasets in Genoppi, our results suggest that the neuron-specific interactions of these proteins are mediating their genetic involvement in neurodevelopmental and neurodegenerative diseases. Importantly, our analyses indicate that human iPSC-derived neurons are a relevant model system for studying the involvement of TDP-43 and BCL2 in amyotrophic lateral sclerosis.
Bioengineered human skeletal muscle with a Pax7+ satellite cell niche capable of functional regeneration
Authors: Fleming J.W. , Capel A.J. , Rimington R.P. , Wheeler P. , Davies O.G. , Lewis M.P. 
Published: May 2020

AbstractSkeletal muscle (SkM) regenerates following injury, replacing damaged tissue with high fidelity. However, in serious injuries non-regenerative defects leave patients with loss of function, increased re-injury risk and often chronic pain. Progress in treating these non-regenerative defects has been slow, with advances only occurring where a comprehensive understanding of regeneration has been gained. Tissue engineering has allowed the development of bioengineered models of SkM which regenerate following injury to support research in regenerative physiology. To date however, no studies have utilised human myogenic precursor cells (hMPCs) to closely mimic human physiology due to difficulties generating sufficient cell numbers and the relatively low myogenic potential of hMPCs. Here we address problems associated with cell number and hMPC mitogenicity using magnetic association cell sorting (MACS), for the marker CD56, and media supplementation with fibroblast growth factor 2 (FGF-2) and B-27 supplement. Cell sorting allowed extended expansion of myogenic cells and supplementation was shown to improve myogenesis within engineered tissues and force generation at maturity. In addition, these engineered human SkM contained a Pax7+ niche and regenerated following Barium Chloride (BaCl2) injury. Following injury, reductions in function (87.5%) and myotube number (33.3%) were observed, followed by a proliferative phase with increased MyoD+ cells and a subsequent recovery of function and myotube number. An expansion of the Pax7+ cell population was observed across recovery suggesting an ability to generate Pax7+ cells within the tissue, similar to the self-renewal of satellite cells seenin vivo.This work outlines an engineered human SkM capable of functional regeneration following injury, built upon an open source system adding to the pre-clinical testing toolbox to improve the understanding of basic regenerative physiology.
Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma
Authors: Olsen Thale K. , Otte Jörg , Mei Shenglin , Kameneva Polina , Björklund Åsa , Kryukov Emil , Hou Ziyi , Johansson Anna , Sundström Erik , Martinsson Tommy , Fransson Susanne , Johnsen John Inge , Kogner Per , Adameyko Igor , Kharchenko Peter V. , Baryawno Ninib 
Published: May 2020

AbstractNeuroblastoma is a heterogeneous embryonal malignancy and the most deadly tumor of childhood, although a minor subset may show spontaneous differentiation. It arises from the multipotent neural crest lineage during development. Some of this multipotency is retained in neuroblastoma, which can give rise to both adrenergic and mesenchymal tumor cells. The mechanisms enabling such dual fates are unknown, but likely help neuroblastoma to evade existing therapies. To understand neuroblastoma plasticity, we analyzed patient tumors using single-cell transcriptomics. In addition to the heterogeneous adrenergic and mesenchymal populations, we identify a subpopulation of malignant cells resembling Schwann cell precursors (SCPs). This SCP-like population connects the adrenergic and mesenchymal compartments through transitions structurally reminiscent of the SCP cell-fate decision fork that occurs during normal development. While the directionality of such transitions in neuroblastoma remains to be established, this finding expands the potential reservoirs of malignant cells, and suggests intratumoral plasticity mechanisms relevant for therapeutic resistance and relapse.
PARP12-catalyzed mono-ADP-ribosylation of Golgin-97 controls the transport of E-cadherin
Authors: Grimaldi Giovanna , Schembri Laura , Monte Matteo Lo , Spano Daniela , Di Martino Rosaria , Beccari Andrea R , Valente Carmen , Corda Daniela 
Published: May 2020

AbstractADP-ribosylation is a post-translational modification involved in physiological and pathological events catalyzed by Poly-ADP-Ribosyl-Polymerase (PARP) enzymes. Substrates of this reaction have been identified by mass-spectrometry, but the definition of PARPs-regulated cellular functions remains scarce. Here, we have analyzed the control of intracellular membrane traffic by the mono-ADP-ribosyl-transferase PARP12, motivated by its localization at thetrans-Golgi network. By using bioinformatics, mutagenesis and cell biology approaches we identified Golgin-97, a protein regulating exocytosis, as a PARP12-specific substrate. Mono-ADP-ribosylation of Golgin-97 residues E558-E559-E565 is required for supporting traffic from thetrans-Golgi network to the plasma membrane. This step is halted when PARP12 is deleted or when the Golgin-97 ADP-ribosylation-defective mutant is expressed. Under these conditions E-cadherin, whose transport is controlled by Golgin-97, does not reach the plasma membrane but accumulates in atrans-Golgi proximal compartment. Thus, we demonstrate that the ADP-ribosylation of Golgin-97 is required for E-cadherin exocytosis and thus this event may regulate the sorting of exocytic carriers as well as epithelial-to-mesenchymal transition.
Automatic deep learning driven label-free image guided patch clamp system for human and rodent in vitro slice physiology
Authors: Koos Krisztian , Oláh Gáspár , Balassa Tamas , Mihut Norbert , Rózsa Márton , Ozsvár Attila , Tasnadi Ervin , Barzó Pál , Faragó Nóra , Puskás László , Molnár Gábor , Molnár József , Tamás Gábor , Horvath Peter 
Published: May 2020

ABSTRACTPatch clamp recording of neurons is a labor-intensive and time-consuming procedure. We have developed a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model was trained on a new image database of neurons in unlabeled brain tissue slices. The pipette tip detection and approaching phase use image analysis techniques for precise movements. High-quality measurements were performed on hundreds of human and rodent neurons. We also demonstrate that further molecular and anatomical analysis can be performed on the recorded cells. The software has a diary module that automatically logs patch clamp events. Our tool can multiply the number of daily measurements to help brain research.ONE SENTENCE SUMMARYNovel deep learning and image analysis algorithms for automated patch clamp systems to reliably measure neurons in human and rodent brain slices.
Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandisL.f)
Authors: Maheswari P. , Kunhikannan C. , Yasodha R. 
Published: May 2020

AbstractAvailability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status ofTectona grandisL.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction an expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested thatTectonacould qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as,rps16-trnQ,atpH-atpI,psc4-psbJ,ndhF,rpl32andycf1which have high potential in DNA barcoding applications.
Manufacturing and value-added dynamics in global value chains: the case of Italy
Authors: Burlina Chiara , Di Maria Eleonora 
Published: May 2020

Purpose
This paper aims to provide a snapshot of various countries’ contributions to value produced along global value chains (GVCs). It focusses on manufacturing activities and their evolution over time, in the context of GVC regionalisation.

Design/methodology/approach
The Trade in Value Added (TiVA) and World Integrated Trade Solution databases for the period of 2005-2015 were used to explore the case of Italy and its industries’ specialisations (Made in Italy): fashion, furniture, automotive and machinery traditionally organised into clusters. Various analyses were used to show the dynamics of gross import–export and imported–exported value-added. Moreover, the revealed comparative advantage index was computed to test whether the Made in Italy sector remains a source of competitive advantage for Italy within GVCs.

Findings
The results highlight how the geography of value-added is changing over time, with growing importance placed on the countries close to Italy and with a different pace according to each considered GVC.

Originality/value
The paper applied new methods to compare trade and analyse value-added dynamics through a recent database released by the Organization for Economic Co-operation and Development within the TiVA initiative that is useful for scholars and policymakers.
Linking project complexity to project success: a hybrid SEM–FCM method
Authors: Luo Lan , Zhang Limao , He Qinghua 
Published: May 2020

PurposeThe purpose of this study is to develop a novel hybrid approach that incorporates the structural equation model (SEM) and fuzzy cognitive map (FCM) to investigate the impacts of the variation in project complexity on project success.Design/methodology/approachThis study adopts SEM to identify and validate a correlation between project complexity variables and PS. Standardized causal coefficients estimated in SEM are used to construct an FCM model to illustrate the effect of complexity on PS with linkage direction and weights. Predictive and diagnostic analyses are performed to dynamically model the variation in project complexity on the evolution of PS.FindingsResults indicate that (1) the hybrid SEM–FCM approach is capable of modeling the dynamic interactions between project complexity and PS; (2) information, goal and environmental complexities are negatively correlated with PS, and technological, task and organizational complexities are positively correlated with PS and (3) the recommendations of complexity management for construction projects are put forward under the guideline of success monitoring.Originality/valueThis research contributes to (1) the state of knowledge by proposing a hybrid methodology that can model the dynamic interactions between project complexity and PS and (2) the state of practice by providing a new perspective of PS evaluation to enhance the probability of success in complex construction projects.
A dual simplex method for grey linear programming problems based on duality results
Authors: Darvishi Salookolaei Davood , Nasseri Seyed Hadi 
Published: May 2020

PurposeFor extending the common definitions and concepts of grey system theory to the optimization subject, a dual problem is proposed for the primal grey linear programming problem.Design/methodology/approachThe authors discuss the solution concepts of primal and dual of grey linear programming problems without converting them to classical linear programming problems. A numerical example is provided to illustrate the theory developed.FindingsBy using arithmetic operations between interval grey numbers, the authors prove the complementary slackness theorem for grey linear programming problem and the associated dual problem.Originality/valueComplementary slackness theorem for grey linear programming is first presented and proven. After that, a dual simplex method in grey environment is introduced and then some useful concepts are presented.
Life is better in flip flops. Digital nomads and their transformational travels to Thailand
Authors: Orel Marko 
Published: May 2020

Purpose
The metamorphosis within the Thai segment of the hospitality industry has influenced the global outlook for hospitality services, shifting the focus from leisure to a hybrid approach of providing all-inclusive work-leisure offerings. The purpose of this paper is, therefore, to outline the hybridisation of the hospitality industry in Thailand that is frequented by digital nomads, and to discuss the adaptation of local infrastructure to accommodate this trend.

Design/methodology/approach
Taking the form of a research note, this paper assesses the impact that digital nomads are having upon the hospitality industry in Thailand, and describes how different localities have begun to respond to the challenges and opportunities this trend presents. Additionally, the paper proposes an empirical study that would evaluate the success of various types of work–leisure hubs in adapting to the needs of digital nomads, and the alignment of their offerings with the expectations of these travellers.

Findings
A preliminary review of available resources reveals that there are a variety of work–leisure spaces catering to the needs of digital nomads. These spaces tend to combine lodging accommodations with a shared office environment, incorporating design elements and social activities that are likely to foster interpersonal relationships between guests. Be that as it may, the exact nature of the work–leisure space models behind these environments is unclear.

Originality/value
The paper envisions a study that will enhance scholarly understanding of the transformation which the Thai hospitality industry is currently undergoing in response to the influx of digital nomads. These insights will enable industry experts to assess both the feasibility and profitability of diverse work-leisure models, and assist policymakers in different jurisdictions.
Gender differences in retirement in Chile and Uruguay
Authors: Biehl Andres , Canales Andrea , Salinas Viviana , Wormald Guillermo 
Published: May 2020

PurposeThis study compares retirement in Chile and Uruguay, and focuses on current individuals legally entitled to retire, particularly women. The article analyses how labour market and family resources shape the access of women and men to social insurance by investigating the likelihood of retirement after reaching the legal age of retirement.Design/methodology/approachThis study uses the Longitudinal Social Protection Survey (LSPS), a biannual or triennial longitudinal survey carried out in six Latin American countries. To study gender differences in the chance of being retired, the study conducts a series of logit regression models to model retirement as a function of labour market and life course conditions as well as providing descriptive and contextual information.FindingsMain findings support labour market explanations of gender differences in retirement. Work experience, human capital and contribution densities largely explain the chances of retirement and economic autonomy among elderly women. Further analysis reveal that they are both less likely than men to retire but also to work in old age, limiting their economic autonomy.Research limitations/implicationsData for Uruguay are recent. To maximize comparison between countries, the paper selects the more recent waves with complete administrative information. As a result, the article uses cross-sectional data that might not capture the accumulation of family resources and could fail to provide a complete gendered life course explanation of current disadvantages faced by women.Originality/valueThe article uses novel data in order to place two Latin American countries within mainstream sociological theories of retirement, thus complementing literature that mainly focuses on European and North-American societies. The paper also documents gender gaps in retirement in two different Latin American societies, one with a traditionally generous public pension system (Uruguay) and one with a largely privately-run contributory system (Chile).
Returns and volatility spillover between food prices and exchange rate in Nigeria
Authors: Akanni Lateef Olawale 
Published: May 2020

PurposeEmpirical studies have documented the linkage between exchange rate movement and food prices. However, the purpose of this study is to investigate the degree and direction of returns and volatility spillover transmission between exchange rate and domestic food prices in Nigeria.Design/methodology/approachThe study uses weekly data from January 2010 to January 2019. Also, the study adopts the improved Diebold and Yilmaz (2012) approach to evaluate the return and volatility spillover between food price and naira to dollar exchange rate. The study also account for 2016 exchange rate crash in the interconnectedness between food prices and naira to dollar exchange rate.FindingsThe paper finds evidence of directional interdependence among the considered food prices and exchange rate based on the obtained spillover indexes. In addition, exchange rate returns and volatility transmission to food prices is more than it receives, particularly after the exchange rate crash.Research limitations/implicationsThe high consumption of staple foods requires policies on price stabilisation such as massive investment in local production and reduction in import dependence, in order to cushion the effects of exchange rate depreciation on domestic prices of food.Originality/valueThis study is the first empirical study to investigate the interconnectedness between exchange rate and domestic food prices for a food import–dependent developing country using the Diebold and Yilmaz approach.