bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability and dynamics of a spectral graph model of brain oscillations
Authors: Verma Parul , Nagarajan Srikantan , Raj Ashish 
Published: December 2021

AbstractWe explore the stability and dynamic properties of a hierarchical, linearized, and analytic spectral graph model for neural oscillations that integrates the structuring wiring of the brain. Previously we have shown that this model can accurately capture the frequency spectra and the spatial patterns of the alpha and beta frequency bands obtained from magnetoencephalography recordings without regionally varying parameters. Here, we show that this macroscopic model based on long-range excitatory connections exhibits dynamic oscillations with a frequency in the alpha band even without any oscillations implemented at the mesoscopic level. We show that depending on the parameters, the model can exhibit combinations of damped oscillations, limit cycles, or unstable oscillations. We determined bounds on model parameters that ensure stability of the oscillations simulated by the model. Finally, we estimated time-varying model parameters to capture the temporal fluctuations in magnetoencephalography activity. We show that a dynamic spectral graph modeling framework with a parsimonious set of biophysically interpretable model parameters can thereby be employed to capture oscillatory fluctuations observed in electrophysiological data in various brain states and diseases.
Transfreq: a Python package for computing the theta-to-alpha transition frequency from resting state EEG data
Authors: Vallarino Elisabetta , Sommariva Sara , Arnaldi Dario , Famà Francesco , Piana Michele , Nobili Flavio 
Published: December 2021

AbstractA classic approach to estimate the individual theta-to-alpha transition frequency requires two electroencephalographic (EEG) recordings, one acquired in restingstate condition and one showing an alpha de-synchronisation due e.g. to task execution. This translates into longer recording sessions that my be cumbersome in studies involving patients. Moreover, incomplete de-synchronisation of the alpha rhythm may compromise the final estimation of the transition frequency. Here we present transfreq, a Python library that allows the computation of the transition frequency from resting-state data by clustering the spectral profiles at different EEG channels based on their content in the alpha and theta bands. We first provide an overview of the transfreq core algorithm and of the software architecture. Then we demonstrate its feasibility and robustness across different experimental setups on a publicly available EEG data set and on in-house recordings. A detailed documentation of transfreq and the codes for reproducing the analysis of the paper with the open-source data set are available online at https://elisabettavallarino.github.io/transfreq/
Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors – Dependencies and Novel Pitfalls
Authors: Marquardt André , Kollmannsberger Philip , Krebs Markus , Argentiero Antonella , Knott Markus , Solimando Antonio Giovanni , Kerscher Alexander 
Published: December 2021

AbstractPersonalized Oncology is a rapidly evolving area and offers cancer patients therapy options more specific than ever. Yet, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Applying two unsupervised dimension reduction methods (t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation Projection (UMAP)) on three datasets of metastases (n=682 samples) with three different data transformations (unprocessed, log10 as well as log10+1 transformed values), we visualized potential underlying clusters. Additionally, we analyzed two datasets (n=616 samples) containing metastases and primary tumors of one entity, to point out potential familiarities. Using these methods, no tight link between site of resection and cluster formation outcome could be demonstrated, neither for datasets consisting of solely metastasis nor mixed datasets. Instead, dimension reduction methods and data transformation significantly impacted visual clustering results. Our findings strongly suggest data transformation to be considered as another key element in interpretation of visual clustering approaches along with initialization and different parameters. Furthermore, the results indicate only minor transcriptional differences for metastases and corresponding primary tumors.
Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold
Authors: DeKraker Jordan , Haast Roy AM , Yousif Mohamed D , Karat Bradley , Lau Jonathan C , Köhler Stefan , Khan Ali R 
Published: December 2021

AbstractLike neocortical structures, the archicortical hippocampus differs in its folding patterns across individuals. Here, we present an automated and robust BIDS-App, HippUnfold, for defining and indexing individual-specific hippocampal folding in MRI, analogous to popular tools used in neocortical reconstruction. Such tailoring is critical for inter-individual alignment, with topology serving as the basis for homology. This topological framework enables qualitatively new analyses of morphological and laminar structure in the hippocampus or its subfields. It is critical for refining current neuroimaging analyses at a meso- as well as micro-scale. HippUnfold uses state-of-the-art deep learning combined with previously developed topological constraints to generate uniquely folded surfaces to fit a given subject’s hippocampal conformation. It is designed to work with commonly employed sub-millimetric MRI acquisitions, with possible extension to microscopic resolution. In this paper we describe the power of HippUnfold in feature extraction, and highlight its unique value compared to several extant hippocampal subfield analysis methods.
Activating alternative transport modes in a multidrug resistance efflux pump to confer chemical susceptibility
Authors: Spreacker Peyton J. , Thomas Nathan E. , Beeninga Will F. , Brousseau Merissa , Porter Colin J. , Hibbs Kylie M. , Henzler-Wildman Katherine A. 
Published: December 2021

AbstractSmall multidrug resistance (SMR) transporters contribute to antibiotic resistance through proton-coupled efflux of toxic compounds from the bacterial cytoplasm. Previous biophysical studies of the E. coli SMR transporter EmrE suggested that it should also be capable of performing proton/toxin symport or uniport, leading to toxin susceptibility rather than resistance in vivo. Here we show EmrE does confer susceptibility to several newly characterized small-molecule substrates in E. coli, including harmane. In vitro experiments show that harmane binding to EmrE triggers uncoupled proton uniport and this protein-mediated dissipation of the transmembrane pH gradient underlies the in vivo phenotype. This leads to synergy with some existing antibiotics, such as kanamycin. Furthermore, this shows that it is possible to not just inhibit multidrug efflux but activate alternative transport modes that are detrimental to bacterial growth and metabolism.
Modeling implanted metals in electrical stimulation applications
Authors: Mercadal Borja , Salvador Ricardo , Biagi Maria Chiara , Bartolomei Fabrice , Wendling Fabrice , Ruffini Giulio 
Published: December 2021

AbstractBackgroundMetal implants impact the dosimetry assessment in electrical stimulation techniques. Therefore, they need to be included in numerical models. While currents in the body are ionic, metals only allow electron transport. In fact, charge transfer between tissues and metals requires electric fields to drive the electrochemical reactions at the interface. Thus, metal implants may act as insulators or as conductors depending on the scenario.Objective/HypothesisThe aim of this paper is to provide a theoretical argument that guides the choice of the correct representation of metal implants using purely electrical models but considering the electrochemical nature of the problem in the technology of interest.MethodsWe built a simple model of a metal implant exposed to a homogeneous electric field of various magnitudes to represent both weak (e.g., tDCS), medium (TMS) or strong field stimulation. The same geometry was solved using two different models: a purely electric one (with different conductivities for the implant), and an electrochemical one. As an example of application, we also modeled a transcranial electrical stimulation (tES) treatment in a realistic head model with a skull plate using a high and low conductivity value for the plate.ResultsMetal implants generally act as electric insulators when exposed to electric fields up to around 100 V/m (tES and TMS range) and they only resemble a perfect conductor for fields in the order of 1000 V/m and above. The results are independent of the implant’s metal, but they depend on its geometry.Conclusion(s)Metal implants can be accurately represented by a simple electrical model of constant conductivity, but an incorrect model choice can lead to large errors in the dosimetry assessment. In particular, tES modeling with implants incorrectly treated as conductors can lead to errors of 50% in induced fields or more. Our results can be used as a guide to select the correct model in each scenario.
Seasonality and interspecific temporal partitioning in a semiarid grassland bat assemblage
Authors: Mohan Ram , Chhaya Vaibhav , Krishnan Anand 
Published: December 2021

ABSTRACTArid and semiarid environments of the world are prone to dramatic seasonal changes that affect the availability of scarce, patchily distributed resources such as water. In response to these changes, animals migrate or partition resources to minimize competition, resulting in temporal patterns within assemblages across multiple scales. Here, we demonstrate that the winter dry season bat assemblage in a semiarid grassland of northwest India exhibits both seasonal changes in composition and temporal avoidance between coexisting species at water bodies. Using a passive acoustic monitoring framework to quantify activity patterns at different points in the season, we show that two species (Rhinolophus lepidus and Tadarida aegyptiaca) exhibit seasonal differences in activity, being more frequently detected in the early and late parts of the dry season respectively. Two other species (Pipistrellus tenuis and Scotophilus heathii) do not exhibit seasonal changes in activity, but structure their diel activity patterns to minimize temporal overlap (and thus competition) at water bodies. These data, some of the first on bats from this region, demonstrate the complex temporal patterns structuring bat assemblages in arid and semiarid biomes. Our results hold promise for monitoring efforts, as a baseline to ascertain how climate change may influence the behavior and ecology of desert and grassland organisms.
Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane
Authors: Kim Siyoung , Chung Jeeyun , Arlt Henning , Pak Alexander J. , Farese Robert V. , Walther Tobias C. , Voth Gregory A. 
Published: December 2021

ABSTRACTLipid droplets (LDs) are organelles formed in the endoplasmic reticulum (ER) to store triacylglycerol (TG) and sterol esters. The ER protein seipin is key for LD biogenesis. Seipin forms a cage-like structure, with each seipin monomer containing a conserved hydrophobic helix (HH) and two transmembrane (TM) segments. How the different parts of seipin function in TG nucleation and LD budding is poorly understood. Here, we utilized molecular dynamics simulations of human seipin, along with cell-based experiments, to study seipin’s functions in protein-lipid interactions, lipid diffusion, and LD maturation. All-atom (AA) simulations indicate that most seipin TM segment residues located in the phospholipid (PL) tail region of the bilayer attract TG. We also find seipin TM segments control lipid diffusion and permeation into the protein complex. Simulating larger, growing LDs with coarse-grained (CG) models, we find that the seipin TM segments form a constricted neck structure to facilitate conversion of a flat oil lens into a budding LD. Using cell experiments and simulations, we also show that conserved, positively charged residues at the end of seipin’s TM segments affect LD maturation. We propose a model in which seipin TM segments critically function in TG nucleation and LD growth.
“Fumifugium: Or the inconvenience of the Aer and Smoake of London Dissipated”: emancipatory social accounting in 17th century London
Authors: Atkins Jill , McBride Karen 
Published: December 2021

PurposeThis paper extends the nature and relevance of exploring the historical roots of social and environmental accounting by investigating an account that recorded and made visible pollution in 17th century London. John Evelyn's Fumifugium (1661) is characterised as an external social account that bears resemblance to contemporary external accounting particularly given its problematising intentionality.Design/methodology/approachAn interpretive content analysis of the text draws out the themes and features of social accounting. Emancipatory accounting theory is the theoretical lens through which Evelyn's social account is interpreted, applying a microhistory research approach. We interpret Fumifugium as a social account with reference to the context of the reporting accountant.FindingsIn this early example of a stakeholder “giving an account” rather than an “account rendered” by an entity, Evelyn problematises industrial pollution and its impacts with the stated intention of changing industrial practices. We find that Fumifugium was used in challenging, resisting and seeking to solve an environmental problem by highlighting the adverse consequences to those in power and rendering new solutions thinkable.Originality/valueThis is the first research paper to extend investigations of the historical roots of social and environmental accounting into the 17th century. It also extends research investigating alternative forms of account by focusing on a report produced by an interested party and includes a novel use of the emancipatory accounting theoretical lens to investigate this historic report. Fumifugium challenged the lack of accountability of businesses in ways similar to present-day campaigns to address the overwhelming challenge of climate change.
Beyond the authenticity–standardisation paradox in international gastronomy retailing: Twisting the hosting city brand with the place of origin
Authors: Pasquinelli Cecilia , Trunfio Mariapina , Rossi Simona 
Published: December 2021

PurposeThis study aims to frame the authenticity–standardisation relationship in international gastronomy retailing and explores how and to what extent the food place of origin and the urban context in which the gastronomy stores are located shape customers' in-store experience.Design/methodology/approachThis paper analyses the case of Eataly, which combines specialty grocery stores and restaurants disseminating the Italian eating style, quality food and regional traditions internationally. Facebook reviews (1,018) of four Eataly stores – New York City, Rome, Munich and Istanbul were analysed, adopting a web content mining approach.FindingsPlace of origin, quality and hosting city categories frame the gastronomic in-store experience. Standardisation elements (shared across the four analysed stores) and authenticity elements (specific to a single store) are identified towards defining three archetypical authenticity–standardisation relationships, namely originated authenticity, standardised authenticity and localised authenticity.Originality/valueThis study proposes original modelling that disentangles the authenticity–standardisation paradox in international gastronomy retailing. It provides evidence of the intertwining of the place of origin and the city brand in customers' in-store experience.
Exploring disaster ontologies from Chinese and Western perspectives: commonalities and nuances
Authors: Goodall Susie , Li Yajun , Chmutina Ksenia , Dijkstra Tom , Meng Xingmin , Jordan Colm 
Published: December 2021

PurposeThis paper explores ontological assumptions of disasters and introduces some concepts from Chinese disaster scholarship. The authors suggest an approach to explore and engage with different ontologies of disaster without direct comparison, that can further interdisciplinary and cross-cultural collaboration.Design/methodology/approachBy reviewing the academic literature and focussing on two recent key translational texts by Chinese scholars, the authors show what can be revealed about ontology and the potential influence on thinking about human-environment interactions and disaster risk reduction (DRR) policy.FindingsIn Chinese disaster studies, the goal of a “harmonious human-environment relationship” is a foundational concept. There is a clear hierarchical and ontological distinction between humans and the natural ecological system viewed as an integrated whole, with underlying rules that can be discovered by scientific research to enable management of a harmonious relationship.Practical implicationsThe authors suggest a practical way to begin with the following questions: What is the societal goal/aim? What is nature? What is society? How do these interact to create disasters? And what are the implications for DRR research and practice? The authors also demonstrate the importance of probing and understanding the underlying ontologies that are the foundation for theory, which in turn is the foundation for policy and action.Originality/valueIdentification of ontological differences in interdisciplinary and cross-cultural research collaborations and working across these boundaries is challenging and rarely questioned. Yet, as demonstrated here, considering ontological assumptions of the causes of disaster, within and across cultures and disciplines, is essential for collaboration and further research.
World wide fund for nature South Africa (WWF) and the case of the West Coast rock lobster
Authors: Miller Taryn 
Published: December 2021

Subject area
The following subjects are addressed through the case: Integrated thinking; professional skills; ethics and values; sustainability; and responsible leadership.

Study level/applicability
This teaching case is aimed at Postgraduate accounting honours or masters students or MBA students.

Case overview
The case begins on 16 May 2018, with Jason Roberts, Head of Environmental Programmes at World wide fund for nature (WWF), reflecting over bad news. The Department of Agriculture, Forestry and Fisheries (“DAFF”, also referred to as “government”), have just approved the 2017/2018 Total Allowable Catch (“TAC”) for the West Coast (WC) rock lobster at 1,924 tons, almost three times the amount recommended by the scientific community. The events describe a history of tension between the primary objectives of the WWF and the government; difficulties in stakeholder management, and the potential consequences for the survival of the WC rock lobster and those who depend on it for their livelihood. The different perspectives held by different stakeholders; the relevance of the scientific evidence; the legal provisions in place and the process applicable to making the TAC decision; all highlight the complex environment in which decisions were made; to which the WWF is wondering how to respond.

Expected learning outcomes
The case’s primary learning objective is to highlight the variety of considerations involved in complex decision-making, also known as “integrated thinking”. Students will be required to critically analyse and evaluate the information in the case, as well as the exhibits; to comment on the appropriateness of various decisions and recommendations; evaluate the ethical/moral responsibilities of WWF; understand different perspectives and the reasons for these perspectives; identify actions and statements that reflect responsible leadership, as well as those that reflect the contrary; and apply learnings from this case to personally reflect on one’s role as a responsible business leader.

Supplementary materials
Teaching Notes are available for educators only.

Subject code
CSS 1: Accounting and Finance.
Love books: sustained success amidst uncertainties
Authors: Hawarden Verity , Moore Amy Fisher 
Published: December 2021

Subject area:
The sub field of academia that the case is designed to teach is small business development, entrepreneurship or women in business.

Study level/applicability:
This case is appropriate for graduate and post-graduate, MBA and executive education students focusing on entrepreneurship, small business development or women in business.

Case overview
This real-life case is based on interviews that took place with Kate Rogan, the co-founder of Love Books, and other stakeholders associated with the small bookselling business that is based in the suburb of Melville in Johannesburg. It describes how Rogan’s past influenced how she saw and was open to the opportunity; and how, through passion, commitment, dedication and stakeholder management, she created a business that brought meaning to her and others’ lives. Rogan’s vast experience in editing, publishing and radio influenced how she evaluated the bookstore opportunity. For the past 11 years, she focused on building a loyal customer base through knowing her customers, staying on top of current industry and market trends and constantly thinking about how she could add value through minimal financial outlay. COVID-19 further complicated her thinking about how to traditionally market and sell books to her client base. As the case concludes, Rogan wonders how to build upon the foundations of her successful bookshop and grow profitability while remaining true to her and the business’s values.

Expected learning outcomes
The case allows students to consider the key enablers for assessing entrepreneurial opportunities and drivers of small business growth. Following discussion and analysis of the case, students should be able to: explore how cognitive dynamics affect an entrepreneur’s evaluation of opportunities; analyze the case against the 4Cs (continuity, community, connection and command) of competitive business advantage; evaluate building blocks for sustainable business profitability; and assess and recommend different learnings for entrepreneurs and small business owners.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 7: Management Science.