bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-Projection Pumping of Fibroblast Contents into Osteosarcoma SAOS-2 Cells Correlates with Increased SAOS-2 Proliferation and Migration, and also with Altered Morphology
Authors: Mahadevan Swarna , Cornwell James A , Chami Belal , Kelly Elizabeth , Zoellner Hans 
Published: November 2021

AbstractWe earlier reported that cell-projection pumping transfers fibroblast contents to cancer cells, and this alters cancer cell phenotype. We now report on single-cell tracking of time lapse recordings from co-cultured fluorescent fibroblasts and SAOS-2 osteosarcoma cells, tracking 5,201 cells across 7 experiments. The fluorescent lipophilic marker DiD was used to label fibroblast organelles, and to trace transfer of fibroblast cytoplasm into SAOS-2. We related SAOS-2 phenotypic change to levels of fluorescence transfer from fibroblasts to SAOS-2, and also to what we term ‘compensated fluorescence’, that numerically projects mother cell fluorescence post-mitosis, into daughter cells. Comparison of absolute with compensated fluorescence, allowed deduction if phenotypic effects in mother SAOS-2, were inherited by their daughters. SAOS-2 receipt of fibroblast fluorescence correlated by Kendall’s tau: with cell-profile area, and without evidence for persistence in daughter cells (median tau = 0.51, p < 0. 016); negatively and weakly with cell circularity, and with evidence for persistence (median tau = −0.19, p < 0.05); and very weakly with cell migration velocity, and without evidence for persistence (median tau = 0.01, p < 0.016). Also, mitotic SAOS-2 had higher rates of prior fluorescence uptake (median = 64.9 units/day), compared with non dividing cells (median = 35.6 units/day, p < 0.016), and there was no evidence for persistence post-mitosis. We conclude there is appreciable impact of cell-projection pumping on cancer cell phenotype, relevant to cancer histopathological diagnosis, clinical spread, and growth, with most effects ‘reset’ by cancer cell mitosis.
CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis
Authors: Nuzhat Nafisa , Van Schil Kristof , Liakopoulos Sandra , Bauwens Miriam , Rey Alfredo Duenas , Käseberg Stephan , Jäger Melanie , Willer Jason R. , Winter Jennifer , Truong Hanh , Gruartmoner Nuria , Van Heetvelde Mattias , Wolf Joachim , Merget Robert , Grasshoff-Derr Sabine , Van Dorpe Jo , Hoorens Anne , Stöhr Heidi , Mansard Luke , Roux Anne-Françoise , Langmann Thomas , Dannhausen Katharina , Rosenkranz David , Wissing Karl Martin , Van Lint Michel , Rossmann Heidi , Häuser Friederike , Nürnberg Peter , Thiele Holger , Zechner Ulrich , Pearring Jillian N. , De Baere Elfride , Bolz Hanno J. 
Published: November 2021

AbstractDefects in primary or motile cilia result in a variety of human pathologies, and retinal degeneration is frequently associated with these so-called ciliopathies. We show that homozygosity for a truncating variant in CEP162, a centrosome and microtubule-associated protein required for transition zone (TZ) assembly during ciliogenesis and neuronal differentiation in the retina, causes late-onset retinitis pigmentosa in 2 unrelated families. The mutant CEP162-E646R*5 protein is expressed and properly localized to the mitotic spindle but missing from the basal body in primary and photoreceptor cilia. This impairs recruitment of TZ components to the basal body and corresponds to complete loss of CEP162 function at the ciliary compartment, reflected by delayed formation of dysmorphic cilia. In contrast, rescue of increased cell death in the developing mouse retina after shRNA knockdown of Cep162 by expression of CEP162-E646R*5 indicates that the mutant retains its role for retinal neurogenesis. Human retinal degeneration thus results from specific loss of ciliary CEP162 function.Graphical abstract
Inhibition of infection-induced vascular permeability modulates host leukocyte recruitment to Mycobacterium marinum granulomas in zebrafish
Authors: Kam Julia Y , Cheng Tina , Garland Danielle C , Britton Warwick J , Tobin David M , Oehlers Stefan H 
Published: November 2021

AbstractMycobacterial granuloma formation involves significant stromal remodeling and the growth of leaky, granuloma-associated vasculature. These permeable blood vessels aid mycobacterial growth, as anti-angiogenic or vascular normalizing therapies are beneficial host-directed therapies in pre-clinical models of tuberculosis. Here we demonstrate that vascular normalization through vascular endothelial-protein tyrosine phosphatase inhibition decreases granuloma hypoxia, the opposite effect of hypoxia-inducing anti-angiogenic therapy. Vascular normalization leads to increased T cell and decreased neutrophil recruitment to granulomas, correlates of a protective immune response against mycobacterial infection.
Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice
Authors: Liu Yuting , Wang Kehui , Huang Li , Zhao Jicheng , Chen Xinpeng , Wu Qiang , Yu Zhouliang , Li Guohong 
Published: November 2021

ABSTRACTCentromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.
Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean
Authors: Pinto Maria , Zhao Zihao , Klun Katja , Libowitzky Eugen , Herndl Gerhard J 
Published: November 2021

AbstractPolyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analysed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for two years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harboured genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This study identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential of utilizing LDPE-associated compounds as carbon and energy source.ImportanceLow-density polyethylene (LDPE) is one of the most used plastics worldwide and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After two years of incubation, two of the microbial communities exhibited a very similar taxonomic composition mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean, that might have the potential to degrade LDPE-associated compounds, and that alkane degradation pathways might be involved.
Interplay of adherens junctions and matrix proteolysis determines the invasive pattern and growth of squamous cell carcinoma
Authors: Kato Takuya , Jenkins Robert P. , Derzsi Stefanie , Tozluoglu Melda , Rullan Antonio , Hooper Steven , Chaleil Raphael A. G. , Fu Xiao , Joyce Holly , Thavaraj Selvam , Bates Paul A. , Sahai Erik 
Published: November 2021

AbstractCancers, such as squamous cell carcinoma, frequently invade as multicellular units. However, these invading units can be organized in a variety of ways, ranging from thin discontinuous strands to thick ‘pushing’ collectives. Here we employ an integrated experimental and computational approach to identify the factors that determine the mode of collective cancer cell invasion. We find that matrix proteolysis is linked to the formation of wide strands, but has little effect on the maximum extent of invasion. Cell-cell junctions also favour wide strands, but our analysis also reveals a requirement for cell-cell junctions for efficient invasion in response to uniform directional cues. Unexpectedly, the ability to generate wide invasive strands is coupled to the ability to grow effectively when surrounded by ECM in 3D assays. Combinatorial perturbation of both matrix proteolysis and cell-cell adhesion demonstrates that the most aggressive cancer behaviour, both in terms of invasion and growth, is achieved at high levels of cell-cell adhesion and high levels of proteolysis. Contrary to expectation, cells with canonical mesenchymal traits – no cell-cell junctions and high proteolysis – exhibit reduced growth and lymph node metastasis. Thus, we conclude that the ability of squamous cell carcinoma cells to invade effectively is also linked to their ability to generate space for proliferation in confined contexts. These data provide an explanation for the apparent advantage of retaining cell-cell junctions in SCC.
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells
Authors: Zhang Chen , Han Xueshuai , Liu Jingkun , Chen Lei , Lei Ying , Chen Kunying , Si Jia , Wang Tian-yi , Zhou Hui , Zhao Xiaoyun , Zhang Xiaohui , An Yihua , Li Yueying , Wang Qian-fei 
Published: November 2021

AbstractEx vivo-expanded mesenchymal stem cells (MSCs) have been demonstrated to be a heterogeneous mixture of cells exhibiting varying proliferative, multipotential, and immunomodulatory capacities. However, the exact characteristics of MSCs remain largely unknown. By single-cell RNA sequencing of 61,296 MSCs derived from bone marrow and Wharton’s jelly, we revealed five distinct subpopulations. The developmental trajectory of these five MSC subpopulations were mapped, revealing a differentiation path from stem-like active proliferative cells (APCs) to multipotent progenitor cells, followed by the branching into two paths – adipogenesis or osteochondrogenesis – and subsequent differentiation into unipotent prechondrocytes. The stem-like APCs, expressing the perivascular mesodermal progenitor markers CSPG4/MCAM/NES, uniquely exhibited strong proliferation and stemness signatures. Remarkably, the prechondrocyte subpopulation specifically expressed immunomodulatory genes and was able to suppress activated CD3+ T cell proliferation in vitro, supporting the role of this population in immunoregulation. In summary, our analysis mapped the heterogeneous subpopulations of MSCs and identified two subpopulations with potential functions in self-renewal and immunoregulation. Our findings advance the definition of MSCs by identifying the specific functions of its heterogeneous cellular composition, allowing for more specific and effective MSC application through the purification of its functional subpopulations.
A Community-Developed Extension to Darwin Core for Reporting the Chronometric Age of Specimens
Authors: Brenskelle Laura , Wieczorek John , Davis Edward , Wallis Neill J. , Emery Kitty , LeFebvre Michelle J. , Guralnick Rob 
Published: November 2021

AbstractDarwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data providers putting these data in fields where they cannot easily be found by users, which impedes the reuse and improvement of these data by other researchers. Here we describe the development of the Chronometric Age Extension to Darwin Core, a ratified, community-developed extension that enables the reporting of ages of specimens from deeper time and the evidence supporting these estimates. The extension standardizes reporting about the methods or assays used to determine an age and other critical information like uncertainty. It gives data providers flexibility about the level of detail reported, focusing on the minimum information needed for reuse while still allowing for significant detail if providers have it. Providing a standardized format for reporting these data will make them easier to find and search and enable researchers to pinpoint specimens of interest for data improvement or accumulate more data for broad temporal studies. The Chronometric Age Extension was also the first community-managed vocabulary to undergo the new Biodiversity Informatics Standards (TDWG) review and ratification process, thus providing a blueprint for future Darwin Core extension development.
Transcriptional expression changes during compensatory plasticity in the prothoracic ganglion of the adult cricket Gryllus bimaculatus
Authors: Wang Felicia , Fisher Harrison , Morse Maeve , Ledwidge Lisa L. , O’Brien Jack , Kingston Sarah E. , Beckman Justin , Johnson Jasmine J. , Miranda Portillo Lyn S. , Al Musawi Tabarak N. , Rubenstein Alexandra W. , Michaelson David A. , Horch Hadley Wilson 
Published: November 2021

AbstractMost adult organisms are limited in their capacity to recover from neurological damage. The auditory system of the Mediterranean field cricket, Gryllus bimaculatus, presents a compelling model for investigating neuroplasticity due to its unusual capabilities for structural reorganization into adulthood. Specifically, the dendrites of the central auditory neurons of the prothoracic ganglion sprout in response to the loss of auditory afferents. Deafferented auditory dendrites grow across the midline, a boundary they normally respect, and form functional synapses with the contralateral auditory afferents, restoring tuning-curve specificity. The molecular pathways underlying these changes are entirely unknown. Here, we used a multiple k-mer approach to re-assemble a previously reported prothoracic ganglion transcriptome that included ganglia collected one, three, and seven days after unilateral deafferentation in adult, male animals. We used EdgeR and DESeq2 to perform differential expression analysis and we examined Gene Ontologies to further understand the potential molecular basis of this compensatory anatomical plasticity. Enriched GO terms included those related to protein translation and degradation, enzymatic activity, and Toll signaling. Extracellular space GO terms were also enriched and included the upregulation of several protein yellow family members one day after deafferentation. Investigation of these regulated GO terms help to provide a broader understanding of the types of pathways that might be involved in this compensatory growth and can be used to design hypotheses around identified molecular mechanisms that may be involved in this unique example of adult structural plasticity.
Host Species is Linked to Pathogen Genotype for the Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis)
Authors: Byrne Allison Q. , Waddle Anthony W. , Saenz Veronica , Ohmer Michel , Jaeger Jef R. , Richards-Zawacki Corinne L. , Voyles Jamie , Rosenblum Erica Bree 
Published: November 2021

AbstractHost-pathogen specificity can arise from certain selective environments mediated by both the host and pathogen. Therefore, understanding the degree to which host species identity is correlated with pathogen genotype can help reveal historical host-pathogen dynamics. One animal disease of particular concern is chytridiomycosis, typically caused by the global panzootic lineage of the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd), termed the Bd-GPL. This pathogen lineage has caused devastating declines in amphibian communities around the world. However, the origin of Bd-GPL and the fine-scale transmission dynamics of this lineage have remained a mystery. This is especially the case in North America where Bd-GPL is widespread, but disease outbreaks occur sporadically. Herein, we use Bd genetic data collected throughout the United States from amphibian skin swab and cultured isolate samples to investigate Bd genetic patterns. We highlight two case studies in Pennsylvania and Nevada where Bd-GPL genotypes are strongly correlated with host species identity. Specifically, in some localities bullfrogs (Rana catesbeiana) are infected with Bd-GPL lineages that are distinct from those infecting other sympatric amphibian species. Overall, we reveal a previously unknown association of Bd genotype with host species and identify the eastern United States as a Bd diversity hotspot and potential ancestral population for Bd-GPL.
Lessons learned from quality management system ISO 9001:2015 certification: practices and barrier identification from Brazilian industrial companies
Authors: Barbosa Luís César Ferreira Motta , de Oliveira Otávio José , Machado Marcio Cardoso , Morais Ana Clara Tomaz , Bozola Patrícia Maria , Santos Manuel Gilberto Freitas 
Published: November 2021

PurposeThis study used a qualitative approach on five case studies in Brazilian industrial companies. The research used interviews, document analysis and on-site visits to collect and analyze data. The companies were selected based on the following criteria: operating in the industrial sector, updating their quality management system (QMS) process to ISO 9001: 2015 and agreeing to participate in this study.Design/methodology/approachThis article aims to investigate the strategies of industrial companies adopted for ISO-9001:2015 certification in light of the six major advances concerning the previous version. Thus, QMS of other organizations can incorporate identified lessons learned, whether certified or not.FindingsThe main finding of the research is the systematization of a set of lessons learned in the experiences of implementing the six significant advances of ISO 9001 concerning the previous version by industrial companies in the State of São Paulo in Brazil. These lessons can and should be used by other organizations to improve their QMSs.Practical implicationsThe practices identified in this empirical research can serve as benchmarking to assist quality managers from other companies in QMS certification based on ISO 9001: 2015 or even those not certified but interested in updating their QMSs. Therefore, lessons learned can significantly minimize efforts to improve your projects, processes, products and services. These findings can also help industrial companies improve their production efficiency and effectiveness through quality improvement.Originality/valueThe main novelty of the research is the consolidation of theoretical and practical analysis of the main changes in the latest version of the ISO 9001 standards. The efforts to fulfill those changes result in lessons learned. The “lessons learned” will form a new block of knowledge that will subsidize theoretical (new research) and practical (formulation of a new ISO 9001 standard and helps quality managers improve their systems).
Effects of uniform injection and suction through perforated pentagonal cylinders on the flow and heat transfer
Authors: Vakhshouri Mir Elyad , Çuhadaroğlu Burhan 
Published: November 2021

Purpose
The purpose of this paper is to study the effects of uniform injection and suction through a perforated pentagonal cylinder on the flow field and heat transfer.

Design/methodology/approach
The finite-volume method has been used to solve the ensemble-averaged Navier-Stokes equations for incompressible flow at moderate Reynolds number (Re = 22,000) with the k-ɛ turbulence model equations.

Findings
A computational fluid dynamics analysis of turbulent flow past a non-regular pentagonal cylinder with three different aspect ratios aspect ratios has been carried out to investigate the effects of uniform injection/suction through the front and all surfaces of the cylinder. It is found that flow field parameters such as drag coefficient, pressure coefficient and Nusselt number are affected considerably in some cases depend on injection/suction rate (Γ) and perforated wall position.

Research limitations/implications
To optimize the efficiency of the injection and suction through a perforated surface, both wide-ranging and intensive further studies are required. Using various perforation ratios and injection/suction intensities are some possibilities.

Practical implications
Control of the vortex shedding and wake region behind bluff bodies is of vital interest in fluid dynamics. Therefore, applying uniform injection and suction from a perforated bluff body into the main flow can be used as a drag reduction mechanism, thermal protection and heat transfer enhancement.

Originality/value
This study provides unique insights into the active flow control method around pentagonal cylinders that can be useful for researchers in the field of fluid dynamics and aeronautics.
Software reliability prediction and release time management with coverage
Authors: Panwar Saurabh , Kumar Vivek , Kapur P.K. , Singh Ompal 
Published: November 2021

PurposeSoftware testing is needed to produce extremely reliable software products. A crucial decision problem that the software developer encounters is to ascertain when to terminate the testing process and when to release the software system in the market. With the growing need to deliver quality software, the critical assessment of reliability, cost of testing and release time strategy is requisite for project managers. This study seeks to examine the reliability of the software system by proposing a generalized testing coverage-based software reliability growth model (SRGM) that incorporates the effect of testing efforts and change point. Moreover, the strategic software time-to-market policy based on costreliability criteria is suggested.Design/methodology/approachThe fault detection process is modeled as a composite function of testing coverage, testing efforts and the continuation time of the testing process. Also, to assimilate factual scenarios, the current research exhibits the influence of software users refer as reporters in the fault detection process. Thus, this study models the reliability growth phenomenon by integrating the number of reporters and the number of instructions executed in the field environment. Besides, it is presumed that the managers release the software early to capture maximum market share and continue the testing process for an added period in the user environment. The multiattribute utility theory (MAUT) is applied to solve the optimization model with release time and testing termination time as two decision variables.FindingsThe practical applicability and performance of the proposed methodology are demonstrated through real-life software failure data. The findings of the empirical analysis have shown the superiority of the present study as compared to conventional approaches.Originality/valueThis study is the first attempt to assimilate testing coverage phenomenon in joint optimization of software time to market and testing duration.