bluuebunny/crossref_metadata_2025_split huggingface dataset:
Newly developed silicone airway stent (GINA stent):Mechanical characteristics and performance evaluation in pigs
Authors: Jung Hwa Sik , Chae Ganghee , Kim Jin Hyoung , Bae Soohyun , Park Chui Yong , Lim Soyeoun , Park Soon Eun , Jung Moon Sik , Park Ju Ik , Lee Young Jae , Kang Sung Kwon , Kim Don Han , Lee Yongjik , Lee Taehoon 
Published: October 2020

ABSTRACTOBJECTIVESCentral airway obstruction (CAO) is caused by various malignant and benign processes. Surgery is a preferred option for CAO, but if not possible, bronchoscopic treatment could be performed. Recently, bronchoscopic treatments have been improved. Particularly in airway stents, new attempts are being made to overcome the existing shortcomings of stents (migration, mucostasis, and granulation tissue formation). We recently developed a new silicone airway stent (GINA stent). The GINA stent has anti-migration design, dynamic structure enabling reduction of stent cross-sectional area, and radiopaqueness. We sought to evaluate mechanical characteristics and performance of our novel GINA stent in a pig tracheal stenosis model.METHODSAll tests were performed by comparing GINA stent [outer diameter (OD, mm) 14, length (L, mm) 55] with Dumon stent (OD14L50). Mechanical tests were done using digital force gage to determine the anti-migration force, expansion force, and flexibility. Short-term (3 weeks) performance was evaluated after stent implantations [GINA (n = 4) vs. Dumon (n = 3)] in a pig model of tracheal stenosis.RESULTSMechanical properties outcomes for GINA vs. Dumon: anti-migration force [18.4 vs. 12.8 Newton (N)]; expansion force (11.9 vs. 14.5 N); flexibility (3.1 vs. 4.5 N). Short-term (3 weeks) GINA vs. Dumon performances: mucus retention (0/4 vs. 0/3); granulation tissue formation (0/4 vs. 0/3); migration (1/4 vs. 2/3).CONCLUSIONSGINA stent demonstrated better mechanical properties than Dumon stent with a stent performance not inferior to Dumon stent.
A comprehensive investigation of colorectal cancer progression, from the early to late-stage, a systems biology approach
Authors: Ghorbani Mohammad , Asgari Yazdan 
Published: October 2020

AbstractColorectal cancer is a widespread malignancy with a concerning mortality rate. It could be curable at the first stages, but the progress of the disease and reaching to the stage-4 could make shift the treatments from curative to palliative. In this stage, the survival rate is meager, and therapy options are limited. The question is, what are the hallmarks of this stage and what genes are involved? What mechanism and pathways could drive such a malign shift from stage-1 to stage-4? In this study, first we identified the core modules for both the stage-1 and stage-4 which four of them have a significant role in stage-1 and two of them have a role in stage-4. Then we investigated the gene ontology and hallmarks analysis for each stage. According to the results, the immune-related process, especially interferon-gamma, impacts stage-1 in colorectal cancer. Concerning stage-4, extracellular matrix ontologies, and metastatic hallmarks are in charge. At last, we performed a differentially expressed gene analysis of stage-4 vs. stage-1 and analyzed their pathways which reasonably undergone a hypo/hyperactivity or being abnormally regulated through the cancer progression. We found that lncRNA in canonical WNT signaling and colon cancer has the most significant pathways, followed by WNT signaling, which means that these pathways may be the driver for the development from early-stage to late-stage. Of these lncRNAs, we had two upregulated kind, H19, and HOTAIR, which both can be involved and mediate metastasis and invasion in colorectal cancer.
The effective population size and mutation rate of influenza A virus in acutely infected individuals
Authors: McCrone John T. , Woods Robert J. , Monto Arnold S. , Martin Emily T. , Lauring Adam S. 
Published: October 2020

AbstractThe global evolutionary dynamics of influenza viruses ultimately derive from processes that take place within and between infected individuals. Recent work suggests that within-host populations are dynamic, but anin vivoestimate of mutation rate and population size in naturally infected individuals remains elusive. Here we model the within-host dynamics of influenza A viruses using high depth of coverage sequence data from 200 acute infections in an outpatient, community setting. Using a Wright-Fisher model, we estimate a within-host effective population size of 32-72 and anin vivomutation rate of 3.4×10−6per nucleotide per generation.
High oil accumulation in tuber of yellow nutsedge compared to purple nutsedge is associated with more abundant expression of genes involved in fatty acid synthesis and triacylglycerol storage
Authors: Ji Hongying , Liu Dantong , Yang Zhenle 
Published: October 2020

AbstractYellow nutsedge is a specific plant species that contains significant amounts of both starch and oil as the main reserves in storage tuber. Its tuber can accumulate up to 35% oil of dry weight, perhaps the highest level observed in the tuber tissues of plant kingdom. To gain insight into the molecular mechanism that leads to high oil accumulation in yellow nutsedge, gene expression profiles of oil production pathways involved carbon metabolism, fatty acid synthesis, triacylglycerol synthesis, and triacylglycerol storage during tuber development were compared with purple nutsedge, a very close relative of yellow nutsedge that is poor in oil accumulation. Compared with purple nutsedge, the high oil content in yellow nutsedge was associated with much higher transcripts for seed-like oil-body proteins, almost all fatty acid synthesis enzymes, and specific key enzymes of plastid Rubisco bypass as well as malate and pyruvate metabolism. However, transcript levels for carbon metabolism toward pyruvate generation were comparable and for triacylglycerol synthesis were similar in both species. Two seed-like master transcription factors ABI3 and WRI1 were found to display similar temporal transcript patterns but be expressed at 6.5- and 14.3-fold higher levels in yellow nutsedge than in purple nutsedge, respectively. A weighted gene co-expression network analysis revealed thatABI3is in strong transcriptional coordination withWRI1and other key oil-related genes. Together, these results implied that plastidial pyruvate availability and fatty acid synthesis, along with triacylglycerol storage in oil body, rather than triacylglycerol synthesis in endoplasmic reticulum, are the major factors responsible for high oil production in tuber of yellow nutsedge, and ABI3 is most likely to play a critical role in regulating oil accumulation. This study will aid understanding in underlying molecular mechanism controlling carbon partitioning toward oil production in oil-rich tuber and provide valuable reference for enhancing oil accumulation in non-seed tissues of crops through genetic breeding or metabolic engineering.
Multi-Scale Modeling of Intensive Macroalgae Cultivation and Marine Nitrogen Sequestration
Authors: Zollmann Meiron , Rubinsky Boris , Liberzon Alexander , Golberg Alexander 
Published: October 2020

AbstractMulti-scale macroalgae growth models are required for the efficient design of sustainable, economically viable and environmentally safe farms. Here, we develop a multi-scale model for Ulva sp. macroalgae growth and nitrogen sequestration in an intensive cultivation farm, regulated by temperature, light and nutrients. The model incorporates a range of scales by incorporating spatial effects in two steps: light extinction at the reactor scale (1 m) and nutrient absorption at the farm scale (1 km). The model was validated on real data from an experimental reactor installed in the sea. Biomass production rates, chemical compositions and nitrogen removal were simulated under different seasons, levels of dilution in the environment and water-exchange rate in the reactor. This multi-scale model provides an important tool for environmental authorities and seaweed farmers who desire to upscale to large bioremediation and/or macroalgae biomass production farms, thus promoting the marine sustainable development and the macroalgae-based bioeconomy.
ShinyCell: Simple and sharable visualisation of single-cell gene expression data
Authors: Ouyang John F. , Kamaraj Uma S. , Cao Elaine Y. , Rackham Owen J. L. 
Published: October 2020

AbstractMotivationAs the generation of complex single-cell RNA sequencing datasets becomes more commonplace it is the responsibility of researchers to provide access to these data in a way that can be easily explored and shared. Whilst it is often the case that data is deposited for future bioinformatic analysis many studies do not release their data in a way that is easy to explore by non-computational researchers.ResultsIn order to help address this we have developed ShinyCell, an R package that converts single-cell RNA sequencing datasets into explorable and shareable interactive interfaces. These interfaces can be easily customised in order to maximise their usability and can be easily uploaded to online platforms to facilitate wider access to published data.AvailabilityShinyCell is available athttps://github.com/SGDDNB/ShinyCell.Contactowen.rackham@duke-nus.edu.sg
Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum
Authors: He Jing , Kleyman Michael , Chen Jianjiao , Alikaya Aydin , Rothenhoefer Kathryn M. , Ozturk Bilge Esin , Wirthlin Morgan , Fish Kenneth , Byrne Leah C. , Pfenning Andreas R. , Stauffer William R. 
Published: October 2020

SUMMARYThe striatum is the interface between dopamine reward signals and cortico-basal ganglia circuits that mediate diverse behavioral functions. Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and are traditionally classified as direct- or indirect-pathway neurons. However, that traditional model does not explain the anatomical and functional diversity of MSNs. Here, we defined molecularly distinct MSN types in the primate striatum, including (1) dorsal striatum MSN types associated with striosome and matrix compartments, (2) ventral striatum types associated with the nucleus accumbens shell and olfactory tubercle, and (3) an MSN-like type restricted to μ-opioid receptor rich islands in the ventral striatum. These results lay the foundation for achieving cell type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific processing.
CaMKII binds both substrates and activators at the active site
Authors: Özden Can , Sloutsky Roman , Mitsugi Tomohiro , Santos Nicholas , Agnello Emily , Gaubitz Christl , Foster Joshua , Lapinskas Emily , Esposito Edward A. , Saneyoshi Takeo , Kelch Brian A. , Garman Scott C. , Hayashi Yasunori , Stratton Margaret M. 
Published: October 2020

ABSTRACTCa2+/calmodulin dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. Once activated by Ca2+/CaM, it sustains activity even after the Ca2+dissipates. In addition to well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A longstanding model invokes two distinct S- and T-sites. If an interactor binds at the T-site, it will preclude autoinhibition and allow substrates to be phosphorylated at the S-site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model that persistent CaMKII activity is facilitated by high affinity binding partners, which kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.
TheHistoplasma capsulatum DDR48Gene Is Required For Survival Within Macrophages, Response To Oxidative Stress, And Resistance to Antifungal Drugs
Authors: Blancett Logan T. , Runge Kauri A. , Reyes Gabriella M. , Kennedy Lauren A. , Jackson Sydney C. , Scheuermann Sarah E. , Harmon Mallory B. , Williams Jamease C. , Shearer Glenmore 
Published: October 2020

AbstractHistoplasma capsulatum (Hc)is a systemic, dimorphic fungal pathogen that affects upwards of 500,000 individuals in the United States annually.Hcgrows as a multicellular mold at environmental temperatures; whereas, upon inhalation into a human or other mammalian host, it transforms into a unicellular, pathogenic yeast. This manuscript is focused on characterizing the DNA damage-responsive geneHcDDR48.HcDDR48was originally isolated via a subtractive DNA library enriched for transcripts enriched in the mold-phase ofHcgrowth. Upon further analysis we found thatHcDDR48is not just expressed in the mold morphotype, but both growth programs dependent upon the environment. We found thatHcDDR48is involved in oxidative stress response, antifungal drug resistance, and survival within resting and activated macrophages. Growth ofddr48Δyeasts was severely decreased when exposed to the reactive oxygen species generator paraquat, as compared to wildtype controls. We also found thatddr48Δyeasts were 2-times more sensitive to the antifungal drugs amphotericin b and ketoconazole. To testHcDDR48’s involvementin vivo, we infected resting and activated RAW 264.7 murine macrophages withHcyeasts and measured yeast survival 24-hours post-infection. We observed a significant decrease in yeast recovery in theddr48Δstrain compared to wildtypeHclevels. Herein, we demonstrate the importance of maintaining a functional copy ofHcDDR48in order forHcyeasts to sense and respond to numerous environmental and host-associated stressors.ImportanceHistoplasma capsulatumis an intracellular pathogen of phagocytes, where it subverts immune recognition and avoids killing by the innate immune system. Macrophages provide a permissive environment forHcreplication and killing only occurs upon the onset of the T-cell driven adaptive immune response.Hchas evolved numerous virulence factors that aid in its survival against host-derived ROS and RNSin vivo. While these virulence factors have been described in past years, only a few reports describing the regulation of these genes and how this intricate system leads to fungal survival. In this study, we characterized the stress response geneDDR48and determined it to be indispensable forHcsurvival within macrophages.HcDDR48regulates transcript levels of superoxide dismutases and catalases responsible for detoxification of ROS and contributes to antifungal drug resistance. Our studies highlightDDR48as a potential target to controlHcinfection and decrease the severity of the disease process.
Multi-dimensional digital bioassay platform based on an air-sealed femtoliter reactor array device
Authors: Honda Shingo , Minagawa Yoshihiro , Noji Hiroyuki , Tabata Kazuhito V. 
Published: October 2020

AbstractSingle-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multi-conditional or multi-parametric assays, hindering understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a new digital bioassay platform with easy solution exchanges, called multi-dimensional (MD) digital bioassay, and tested its quantitativity and utility. We immobilized single analytes in arrayed femtoliter (10−15L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. To show the utility of our system, we investigated neuraminidase inhibitor (NAI) sensitivity on single influenza A virus (IAV) particles in a multi-conditional assay. We proved that IAV particles show a heterogeneous response to the NAI. Further, to demonstrate multi-parametric assays, we examined the sensitivity of individual IAV particles or model enzyme molecules to two different inhibitors. Our results support that MD digital bioassay is a versatile platform to unveil heterogeneities of biological entities in unprecedented resolution.
Research environment and organisational learning mechanisms in the age of pandemics: the case of accounting research
Authors: Troshani Indrit 
Published: October 2020

PurposeThe university research environment, the broader context where academics produce research, is changing rapidly as a result of the COVID-19 pandemic. The study looks at the role of the research environment and organisational learning mechanisms with respect to the capacity of accounting academics to achieve research outcomes.Design/methodology/approachThe theoretical concepts of research environment and organisational learning mechanisms are used as a basis for analysing documentary and qualitative interview evidence. Interviews were conducted with accounting academics and higher degrees research accounting students based at Australian universities.FindingsA key finding is that COVID-19 restrictions are affecting the capacity of accounting academics to conduct research. The restrictions are affecting meaningful interactions and engagement amongst accounting academics which are essential in maintaining and developing networks, research dialogue and debate, and research culture. Significant and deliberate efforts and innovation are required in attempts to replicate traditional face-to-face engagement and interaction benefits in online settings.Originality/valueThe study explains how and why the research environment and organisational learning mechanisms are changing as a result of the COVID-19 restrictions. In doing so, it highlights the implications on the capacity of accounting academics to achieve research outcomes.
“Maybe we can work together”: researchers’ outcome expectations for sharing knowledge on social media
Authors: Alshahrani Hussain , Pennington Diane 
Published: October 2020

PurposeThis study aims to investigate the outcomes that researchers expect from using social media for knowledge sharing and to explore how these outcomes impact their use.Design/methodology/approachThe authors conducted 30 semi-structured interviews with researchers at a major Scottish university. They analysed the interview transcripts using directed content analysis.FindingsResearchers expect social and personal outcomes from the use of social media to share knowledge. Each type has positive and negative forms. The positive outcomes motivate researchers to use it, whereas negative outcomes prevent them from using it.Research limitations/implicationsThis study extends the integrative theoretical framework of outcome expectations within the social cognitive theory by exploring these outcomes and their relative amount of influence on sharing ideas, experiences, questions and research outputs on social media. While the participants included academic staff and postdoctoral researchers, the majority were PhD students.Practical implicationsThe findings will help individual researchers and universities to use social media effectively in sharing ideas and promoting research through identifying the positive outcomes. Identifying the negative outcomes will help in using solutions to overcome them.Originality/valueThis is the first known study to investigate the outcome expectations that impact researchers’ use of social media for knowledge sharing.
E-rickshaws on urban streets: sustainability issues and policies
Authors: Khan Eijaz Ahmed , Quaddus Mohammed 
Published: October 2020

PurposeIn urban streets of developing countries, informal e-rickshaw operation can contribute to the development of economically viable, citizen-oriented and environmentally friendly transport systems. Even though informal e-rickshaw operation is important, significant gaps are apparent in the literature in relation to e-rickshaw sustainability issues and policies, and the development of a methodology grounded in a robust theoretical base. The current paper aims to address these gaps by integrating stakeholder theory (ST) and resource dependency theory (RDT) as we consider the linkage between e-rickshaw operation and the sustainability concept.Design/methodology/approachWe apply fuzzy quality function deployment (QFD), integrated with the 0–1 non-linear optimisation technique, to identify optimal policies for the e-rickshaw informal sector on Khulna city's urban streets in Bangladesh.FindingsThe results suggest that optimal policies should be formalised to regularise e-rickshaw operation. Appropriate supervision and monitoring; infrastructural support for battery charging, parking, battery recycling and solar panel installation; and training and development should all be provided.Research limitations/implicationsThe theoretical and managerial implications of our results are discussed, with future research suggestions presented.Originality/valueTo the best of our knowledge, no previous study has used ST and RDT in e-rickshaw sector research. We recognised that the stakeholder settings for sustainability policies can well influence the behaviour of informal e-rickshaw operators while allotting the necessary resources to this sector. This move assists researchers and policymakers to understand the stakeholders and resource dependency sustainability requirements of this sector and the implementation of the required policies.
Pre-service teachers' concerns about diversity
Authors: Sunthonkanokpong Wisuit , Murphy Elizabeth 
Published: October 2020

PurposeThe purpose of this study was to investigate pre-service teachers' concerns about including diverse learners in their classrooms. The study identified which concerns they ranked highest and lowest and which types of diversity they were most concerned about. The study also compared results in relation to demographic variables of gender, year and major.Design/methodology/approachData collection relied on the Concerns about Inclusive Education Scale administered online with 343 pre-service teachers enrolled in higher education in Thailand. Analysis aimed to identify what were the highest categories of concerns as well as any significant relationships between concerns and demographic variables of gender, year and major. Analysis also identified the types of diversity about which pre-service teachers were most concerned along with any significant relationships between types of diversity and gender, year and major.FindingsResults revealed that pre-service teachers ranked lack of resources as their highest concern about teaching diverse learners. Analysis revealed a significant difference for gender with females (p = 0.014) having a significantly higher level of concern about lack of resources than males. Mental health disabilities along with physical and learning disabilities were ranked highest in terms of types of diversity about which they were most concerned. There were no statistically significant differences for demographics regarding type of diversity about which teachers were most concerned.Originality/valueThere is a lack of research related to higher education's role in preparing teachers to teach in contexts of diversity. This study goes beyond traditional definitions to include 12 types of diversity.