bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unified framework for localized patterns in reaction–diffusion systems; the Gray–Scott and Gierer–Meinhardt cases
Authors: Al Saadi Fahad , Champneys Alan 
Published: November 2021

A recent study of canonical activator-inhibitor Schnakenberg-like models posed on an infinite line is extended to include models, such as Gray–Scott, with bistability of homogeneous equilibria. A homotopy is studied that takes a Schnakenberg-like glycolysis model to the Gray–Scott model. Numerical continuation is used to understand the complete sequence of transitions to two-parameter bifurcation diagrams within the localized pattern parameter regime as the homotopy parameter varies. Several distinct codimension-two bifurcations are discovered including cusp and quadruple zero points for homogeneous steady states, a degenerate heteroclinic connection and a change in connectedness of the homoclinic snaking structure. The analysis is repeated for the Gierer–Meinhardt system, which lies outside the canonical framework. Similar transitions are found under homotopy between bifurcation diagrams for the case where there is a constant feed in the active field, to it being in the inactive field. Wider implications of the results are discussed for other pattern-formation systems arising as models of natural phenomena.
This article is part of the theme issue ‘Recent progress and open frontiers in Turing’s theory of morphogenesis’.
Pattern formation from spatially heterogeneous reaction–diffusion systems
Authors: Van Gorder Robert A. 
Published: November 2021

First proposed by Turing in 1952, the eponymous Turing instability and Turing pattern remain key tools for the modern study of diffusion-driven pattern formation. In spatially homogeneous Turing systems, one or a few linear Turing modes dominate, resulting in organized patterns (peaks in one dimension; spots, stripes, labyrinths in two dimensions) which repeats in space. For a variety of reasons, there has been increasing interest in understanding irregular patterns, with spatial heterogeneity in the underlying reaction–diffusion system identified as one route to obtaining irregular patterns. We study pattern formation from reaction–diffusion systems which involve spatial heterogeneity, by way of both analytical and numerical techniques. We first extend the classical Turing instability analysis to track the evolution of linear Turing modes and the nascent pattern, resulting in a more general instability criterion which can be applied to spatially heterogeneous systems. We also calculate nonlinear mode coefficients, employing these to understand how each spatial mode influences the long-time evolution of a pattern. Unlike for the standard spatially homogeneous Turing systems, spatially heterogeneous systems may involve many Turing modes of different wavelengths interacting simultaneously, with resulting patterns exhibiting a high degree of variation over space. We provide a number of examples of spatial heterogeneity in reaction–diffusion systems, both mathematical (space-varying diffusion parameters and reaction kinetics, mixed boundary conditions, space-varying base states) and physical (curved anisotropic domains, apical growth of space domains, chemicalsimmersed within a flow or a thermal gradient), providing a qualitative understanding of how spatial heterogeneity can be used to modify classical Turing patterns.
This article is part of the theme issue ‘Recent progress and open frontiers in Turing’s theory of morphogenesis’.
Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity
Authors: Keum Dong Ho , Yeon Jun Mo , Yun Chan-Seok , Lee Soon Youl , Im Wan-Taek 
Published: November 2021

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped and yellow-pigmented bacterium, designated strain Gsoil 183T, was isolated from ginseng-cultivation soil sampled in Pocheon Province, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 183T grew at 10–37 °C and at pH 5.0–9.0 on tryptic soy agar. Strain Gsoil 183T had β-glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 (one of the dominant active components of ginseng) to F2. Based on 16S rRNA gene sequencing, strain Gsoil 183T clustered with species of the genus

Chryseobacterium

and appeared to be closely related to

Chryseobacterium sediminis

LMG 28695T (99.1 % sequence similarity),

Chryseobacterium lactis

NCTC 11390T (98.6%),

Chryseobacterium rhizoplanae

LMG 28481T (98.6%),

Chryseobacterium oncorhynchi

CCUG 60105T (98.5%),

Chryseobacterium viscerum

CCUG 60103T (98.4%) and

Chryseobacterium joostei

DSM 16927T (98.3%). Menaquinone MK-6 was the predominant respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c). The polar lipids were phosphatidylethanolamine, six unidentified glycolipids, five unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 36.6 mol%. Digital DNA–DNA hybridization between strain Gsoil 183T and the type strains of

C. sediminis

,

C. lactis

,

C. rhizoplanae

,

C. oncorhynchi

,

C. viscerum

and

C. joostei

resulted in values below 70 %. Strain Gsoil 183T could be differentiated genotypically and phenotypically from the recognized species of the genus

Chryseobacterium

. The isolate therefore represents a novel species, for which the name Chryseobacterium panacisoli sp. nov. is proposed, with the type strain Gsoil 183T (=KACC 15033T=LMG 23397T)
Identifiability of pharmacological models for online individualization
Authors: Wahlquist Ylva , Gojak Amina , Soltesz Kristian 
Published: November 2021

AbstractThere is a large variability between individuals in the response to anesthetic drugs, that seriously limits the achievable performance of closed-loop controlled drug dosing. Full individualization of patient models based on early clinical response data has been suggested as a means to improve performance with maintained robustness (safety). We use estimation theoretic analysis and realization theory to characterize practical identifiability of the standard pharmacological model structure from anesthetic induction phase data and conclude that such approaches are not practically feasible.
A switch in the development: microRNA arm usage screening in zebrafish suggests an important role of arm switching events in ontogenesis
Authors: Oliveira Arthur C. , Bovolenta Luiz A. , Figueiredo Lucas , Patton James G. , Pinhal Danillo 
Published: November 2021

AbstractIn metazoan, regulatory molecules tightly control gene expression. Among them, microRNAs (miRNAs) are key regulators of several important features, like cell proliferation, differentiation, and homeostasis. During miRNA biogenesis, the canonical strand that loads onto RISC can be switched, in a process called “arm switching.” Due to the miRNA-to-target pairing peculiarities, switching events can lead to changes on the gene-targeted repertoire, promoting the modulation of a distinct set of biological routes. To understand how these events affect cell regulation, we conducted an extensive and detailed in silico analysis of RNA-seq datasets from several tissues and key developmental stages of zebrafish. We identified interesting patterns of miRNA arm switching occurrence, mainly associated with the control of protein coding genes during embryonic development. Additionally, our data show that miRNA isoforms (isomiRs) play an important role in differential arm usage. Our findings provide new insights on how such events emerge and coordinate gene expression regulation, opening perspectives for novel investigations in the area.
Analysis of Corticosteroids in Immune Checkpoint Inhibitors (ICE) Induced Myocarditis – A Systematic Review of 352 Screened Articles
Authors: Sheikh Mona , Patel Saumil , Nagpal Shavy , Yulkselen Zeynep , Zahid Samina , Jha Vivek , Sánchez-Velazco Diana F 
Published: November 2021

ABSTRACTIntroductionImmune Checkpoint Inhibitors (ICI) are used as a single agent or as a combination therapies for early or late-stage malignancies. The common malignancies that ICI targets include the following: melanoma, lung cancer, renal cell carcinoma, and hematological malignancies such as Hodgkin’s lymphoma. ICI use is associated with many immune-related adverse events, and ICI-induced myocarditis is one of the rare and most severe AE with a high mortality rate. There are no consensus evidence-based treatment guideline; the expert recommendation is to use high-dose steroids. We aim in this review to assess the effectiveness of steroids in treating ICI-induced myocarditis.MethodsWe searched the following database Pubmed, Scopus, Cinhale, and Google Scholar, using the following keywords: ICI-induced myocarditis, treatment, steroid. We included articles in the English language, case reports, case series, and published in the last five years.Results352 articles were screened using PRISMA guidelines. After excluding the articles that were duplicate, irrelevant, and did not meet inclusion criteria, 35 articles with a total number of 50 patients were included. All patients treated with ICI either as a single or combination regimen. The onset of symptoms post initiation varied from one day to a year. 46 out of the 50 cases received high doses of Intravenous steroids as a loading dose followed by an oral or intravenous maintenance dose. Out of 50 patients 14 patients (28 %) died but 34 (68 %) patients survived, and 2 (4 %) patients data were not available. The mean age of the patients was 66.31 ± 14.071 (range 23-88 years), 29 were male (58%), 21 were female (42%). Most of the cases were from the USA (42%), followed by Australia (20 %), Japan (14%), Germany, France, and China (4%), Switzerland, Canada, and Spain (2%), and for (6%) cases. A total of 23 patients had cardiovascular comorbidities (46%), which were HTN (14 patients, 60.87%), hyperlipidemia (5 patients, 21.73%), and less than 1 % of patients had myocardial ischemia, congestive heart failure, atrial fibrillation, and peripheral vascular disease. While 26 patients (52%) had normal basal cardiac status.ConclusionOur results showed that high doses of steroids were effective in controlling cardiac myocyte inflammation and mortality by 28%. Race was not included in the analysis as it was not reported. More in – depth studies are needed to provide a broader representation of steroids in myocarditis.
Integrated analyses of the single-cell ATAC-seq and RNA-seq reveal the epigenetic landscape of human ovarian aging
Authors: Xu Yunzhao , Chen Jinling , Gu Shuting , Liu Yuanlin , Ni Huihua , Huang Yan , Gao Sainan , Sheng Nan , Zhang Xiaojing , He Xin , Zhou Songlin , Ge Wenliang 
Published: November 2021

AbstractStudying the molecular mechanisms of ovarian aging is crucial for understanding the age-related fertility issues in females. Recently, a single-cell transcriptomic roadmap of ovarian aging based on non-human primates revealed the molecular signatures of the oocytes at different developmental stages. Herein, we present the first epigenetic landscape of human ovarian aging, through an integrated analysis of the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and single-cell RNA-seq. We depicted the transcriptional profiles and chromatin accessibility of the ovarian tissues isolated from old (n=4) and young (n=2) donors. The unsupervised clustering of data revealed seven distinct cell populations in the ovarian tissues and six subtypes of oocytes, which could be distinguished by age difference. Further analysis of the scATAC-seq data from the young and old oocytes revealed that the interaction between the Notch signaling pathway and AP-1 family transcription factors may crucially determine oocyte aging. Finally, a machine-learning algorithm was applied to calculate the optimal model based on the single-cell dataset for predicting oocyte aging, which exhibited excellent accuracy with a cross-validated area under the receiver operating characteristics score of 0.99. In summary, this study provides a comprehensive understanding of human ovarian aging at both the transcriptomic and epigenetic levels, based on an integrated analysis of large-scale single-cell datasets. We believe our results will shed light on the discovery of potential therapeutic targets or diagnostic markers for age-related ovarian disorders.
Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome
Authors: Kawakami Keisuke , Hamaguchi Tasuku , Hirose Yuu , Kosumi Daisuke , Miyata Makoto , Kamiya Nobuo , Yonekura Koji 
Published: November 2021

SummaryCyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.
The impact of China's trade, aid and FDI on African economies
Authors: Cudjoe Derrick Anquanah , Yumei He , Hu Hanhui 
Published: November 2021

PurposeThis study examines the impact of China’s trade, aid and foreign direct investment (FDI) on the economic growth of Africa.Design/methodology/approachOur study covered 41 countries in Africa, cutting across the western, eastern, central, southern and northern sub-regions. The study adopted the dynamic system generalized method of moments (SGMM), feasible generalized least squares (FGLS) and Dumitrescu–Hurlin Panel Granger causality techniques for estimations.FindingsOverall, FDI, trade and aid from China have a nonlinear relationship with Africa’s economic growth. The findings reveal a key novelty in that the marginal effect on real per capita GDP increases when China’s FDI interacts with the manufacturing sector in Africa. These findings are robust to long-run estimations.Research limitations/implicationsGiven that we have examined the short-and long-run symbiotic effects of China’s FDI and Africa’s manufacturing sector and China’s aid and Africa’s manufacturing sector, more studies are warranted in this area, particularly to produce further empirical evidence of these findings. Moreover, future work could focus on investigating the country-specific effects of China’s trade, China’s FDI and China’s aid on real GDP per capita in each African country as our results reflect within-country elasticities.Originality/valueThis study provides new evidence on the impact of China’s trade, aid and FDI on the growth of African economies. To the best of our knowledge, this is the first study to empirically explore the long-run effects of China’s trade, FDI and aid on economic growth in African countries. This study also tests the claim of the displacement of Africa’s manufacturing industry by its Chinese counterparts.
Sustainability reporting at EU level: leading by example?
Authors: Bryan Katharina 
Published: November 2021

PurposeThis paper aims to contribute to research on public sector sustainability reporting, by focussing on the sustainability reporting of EU institutions and agencies. It seeks to examine to what extent the EU is leading by example in this area and to highlight the challenges for developing sustainability reporting at EU level.Design/methodology/approachThe paper is based on the European Court of Auditors’ (ECA) review on reporting on sustainability and presents the results of qualitative research, including a survey conducted among EU institutions and agencies. Additional secondary literature analysis puts the review's findings into the current research context on sustainability reporting.FindingsThe paper provides an overview of how the EU and its institutions and agencies report on sustainable development. It finds that the EU, as well as its institutions and agencies, are not yet leading by example on sustainability reporting. Of the 53 EU institutions and agencies surveyed, only 2 published sustainability reports. Additionally, the paper identifies key challenges for sustainability reporting in the public sector and highlights future research areas.Originality/valueThis is the first academic article on sustainability reporting of EU institutions and agencies. It contributes to our understanding of the status and challenges of public sector, supranational sustainability reporting and the auditing of such activities.
All grown up? Market maturity and investment in London's purpose-built student accommodation sector
Authors: Livingstone Nicola , Sanderson Danielle 
Published: November 2021

PurposeThe UK's purpose-built student accommodation (PBSA) sector has seen significant institutional investment in recent decades. This paper unpacks contemporary trends and perspectives on the sector. It questions whether PBSA has moved from being an “alternative” to “mainstream” residential asset class, framing the analysis through the lens of market maturity.Design/methodology/approachThe methods triangulate perspectives drawn from literature on the evolution of PBSA as an asset class with illustrations of investment trends across the UK between 2005 and 2020 using data from Real Capital Analytics (RCA), combined with findings from 40 semi-structured interviews with investors and stakeholders in PBSA in the UK London is the focus of the work, whilst other regional cities are integrated for comparison.FindingsThe results demonstrate that London's PBSA market is ahead of trends currently being replicated in regional cities. However, the regions currently offer greater return potential and opportunities for risk taking compared to London, where yields are compressed, and the market is considered lower risk. The concept of maturity remains useful as a framework for evaluating markets, however a more granular analysis of sectors is necessary to further understand asset classes within sectors. PBSA continues to trade at a premium across the UK; it is considered the most mature residential asset class.Practical implicationsThe emergence of PBSA as an asset class continues to play a developing role within the residential sector and UK investment market. Risk, value and local context remain key when integrating PBSA into institutional portfolios, and as the first to consider the UK market from a qualitative research approach, this research provides a snapshot of these influences in 2021.Originality/valueOur approach offers original insight into investment trends across the UK and is the first to focus reflections on the London market specifically. The research highlights the role of PBSA as a vanguard asset class for investors into residential, situating its growth within the framework of market maturity and drawing out market nuances from interviews.
Ontologies application in the sharing economy domain: a systematic review
Authors: Mohamad Ummul Hanan , Ahmad Mohammad Nazir , Zakaria Ahmad Mujahid Ubaidillah 
Published: November 2021

PurposeThis systematic literature review (SLR) paper presents the overview and analysis of the existing ontologies application in the SE domain. It discusses the main challenges in terms of its ontologies development and highlights the key knowledge areas for subdomains in the SE domain that provides a direction to develop ontologies application for SE systematically. The SE is not as straightforward as the traditional economy. It transforms the existing economy ecosystem through peer-to-peer collaborations mediated by the technology. Hence, the complexity of the SE domain accentuates the need to make the SE domain knowledge more explicit.Design/methodology/approachFor the review, the authors only focus on the journal articles published from 2010 to 2020 and mentioned ontology as a solution to overcome the issues specific for the SE domain. The initial identification process produced 3,326 papers from 10 different databases.FindingsAfter applying the inclusion and exclusion criteria, a final set of 11 articles were then analyzed and classified. In SE, good ontology design and development is essential to manage digital platforms, deal with data heterogeneity and govern the interoperability of the SE systems. Yet the preference to build an application ontology, lack of perdurant design and minimal use of the existing standard for building SE common knowledge are deterring the ontology development in this domain. From this review, an anatomy of the SE key subdomain areas is visualized as a reference to further develop the domain ontology for the SE domain systematically.Originality/valueWith the arrival of the Fourth Industrial Revolution (4IR), the sharing economy (SE) has become one of the important domains whose impact has been explosive, and its domain knowledge is complex. Yet, a comprehensive overview and analysis of the ontology applications in the SE domain is not available or well presented to the research community.
Gross profit manipulation in emerging economies: evidence from India
Authors: Bansal Manish , Kumar Ashish , Kumar Vivek 
Published: November 2021

Purpose
This study aims to explore peer performance as the motivation behind gross profit manipulation through two different channels, namely, cost of goods sold (COGS) misclassification and revenue misclassification.

Design/methodology/approach
Gross profit expectation model (Poonawala and Nagar, 2019) and operating revenue expectation model (Malikov et al., 2018) are used to measure COGS and revenue misclassification, respectively. The panel data regression models are used to analyze the data for this study.

Findings
The study results show that firms engage in gross profit manipulation to meet the industry’s average gross margin, implying that peer performance is an important benchmark that firms strive to achieve through misclassification strategies. Further results exhibit that firms prefer COGS misclassification over revenue misclassification for manipulating gross profit, implying that firms choose the shifting strategy based on the relative advantage of each shifting tool.

Practical implications
The findings suggest that firms that just meet or slightly beat industry-average profitability levels are highly likely to engage in classification shifting (CS). Thus, investors and analysts should be careful when evaluating such firms by comparing them with other firms in the same industry.

Originality/value
First, this study is among earlier attempts to investigate CS motivated by peer performance. Second, this study investigates both tools of gross profit manipulation by taking a uniform sample of firms over the same period and provides compelling evidence that firms prefer one shifting tool over another depending on the relative advantage of each shifting tool.