bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-molecule sizing through nano-cavity confinement
Authors: Jacquat Raphaël P. B. , Krainer Georg , Peter Quentin A. E. , Babar Ali Nawaz , Vanderpoorten Oliver , Xu Catherine K. , Welsh Timothy J. , Kaminski Clemens F. , Keyser Ulrich F. , Baumberg Jeremy J. , Knowles Tuomas P. J. 
Published: December 2021

AbstractAn approach relying on nano-cavity confinement is developed in this paper for the sizing of nanoscale particles and single biomolecules in solution. The approach, termed nano-cavity diffusional sizing (NDS), measures particle residence times within fluidic nano-cavities to determine their hydrodynamic radii. Using theoretical modeling and simulation, we show that the residence time of particles within nano-cavities above a critical timescale depends on the diffusion coefficient of the particle, which allows estimation of the particle’s size. We demonstrate this approach experimentally through measurement of particle residence times within nano-fluidic cavities using single-molecule confocal microscopy. Our data show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates and single DNA oligonucleotides. NDS thus constitutes a new single molecule optofluidic approach that allows rapid and quantitative sizing of nanoscale particles for potential application in nanobiotechnology, biophysics, and clinical diagnostics.Table of content graphic
Characterizing the Behavioral and Neuroendocrine Features of Susceptibility and Resilience to Social Stress
Authors: Murra Dalia , Hilde Kathryn L. , Fitzpatrick Anne , Maras Pamela M. , Watson Stanley J. , Akil Huda 
Published: December 2021

ABSTRACTEvaluating and coping with stressful social events as they unfold is a critical strategy in overcoming them without long-lasting detrimental effects. Individuals display a wide range of responses to stress, which can manifest in a variety of outcomes for the brain as well as subsequent behavior. Chronic Social Defeat Stress (CSDS) in mice has been widely used to model individual variation following a social stressor. Following a course of repeated intermittent psychological and physical stress, mice diverge into separate populations of social reactivity: resilient (socially interactive) and susceptible (socially avoidant) animals. A rich body of work reveals distinct neurobiological and behavioral consequences of this experience that map onto the resilient and susceptible groups. However, the range of factors that emerge over the course of defeat have not been fully described. Therefore, in the current study, we focused on characterizing behavioral, physiological, and neuroendocrine profiles of mice in three separate phases: before, during, and following CSDS. We found that following CSDS, traditional read-outs of anxiety-like and depression-like behaviors do not map on to the resilient and susceptible groups. By contrast, behavioral coping strategies used during the initial social stress encounter better predict which mice will eventually become resilient or susceptible. In particular, mice that will emerge as susceptible display greater escape behavior on Day 1 of social defeat than those that will emerge as resilient, indicating early differences in coping mechanisms used between the two groups. We further show that the social avoidance phenotype in susceptible mice is specific to the aggressor strain and does not generalize to conspecifics or other strains, indicating that there may be features of threat discrimination that are specific to the susceptible mice. Our findings suggest that there are costs and benefits to both the resilient and susceptible outcomes, reflected in their ability to cope and adapt to the social stressor.
Effects of active and passive enrichment regimes on fecal glucocorticoid metabolite levels in captive Indian leopards (Panthera pardus fusca)
Authors: Panchal Nirali , Desai Chena , Ghosal Ratna 
Published: December 2021

AbstractEnvironmental enrichment improves health and wellbeing of zoo animals. To test this hypothesis, we used Indian leopards, one of the popular zoo animals, as a model system to understand effects of active (interacting) and passive (noninteracting) enrichment elements on stress hormone levels of captive individuals. We included three enrichment categories, category ‘A’ (having both active: large size cage, and passive: controlled temperature, playback of forest sounds and sound proof glasses to filter visitors’ noise, enrichment elements), category ‘B’ (active enrichment type I, small size cage with air coolers), and category C (active enrichment type II, medium size cage without air coolers) for the leopards (n=14) housed in two Indian zoos. We standardized a non-invasive method to measure fecal glucocorticoid metabolite (fGCM) levels in captive leopards. The standardized fGCM assay was further validated by analysing samples from free-ranging leopards, as well. The fGCM levels (Mean±SE) were 10.45±2.01 and 0.95±0.003μg/g dry wt of feces in captive and free-ranging leopards, respectively. Our results demonstrated that fGCM levels of leopards in categories B and C were significantly (P<0.05) different from each other, thus, indicating cage size (an active enrichment element) as an important factor in influencing the physiology of the sampled animals. Overall, the findings of the study will contribute towards informing policies for management of the Indian leopards.
Pose-gait analysis for cetaceans with biologging tags
Authors: Zhang Ding , Goodbar Kari , West Nicole , Lesage Veronique , Parks Susan , Wiley Dave , Barton Kira , Shorter K. Alex 
Published: December 2021

AbstractBiologging tags are a key enabling tool for investigating cetacean behavior and locomotion in their natural habitat. Identifying and then parameterizing gait from movement sensor data is critical for these investigations. But how best to characterize gait from tag data remains an open question. Further, the location and orientation of the tag on an animal in the field are variable and can change multiple times during deployment. As a result, the relative orientation of the tag with respect to (wrt) the animal must be determined before a wide variety of further analyses. Currently, custom scripts that involve specific manual heuristics methods tend to be used in the literature. These methods require a level of knowledge and experience that can affect the reliability and repeatability of the analysis. The authors of this work argue that an animal’s gait is composed of a sequence of body poses observed by the tag, demonstrating a specific spatial pattern in the data that can be utilized for different purposes. This work presents an automated data processing pipeline (and software) that takes advantage of the common characteristics of pose and gait of the animal to 1) Identify time instances associated with occurrences of relative motion between the tag and animal; 2) Identify the relative orientation of tag wrt the animal’s body for a given data segment; and 3) Extract gait parameters that are invariant to pose and tag orientation. The authors included biologging tag data from bottlenose dolphins, humpback whales, and beluga whales in this work to validate and demonstrate the approach. Results show that the average relative orientation error of the tag wrt the dolphin’s body after processing was within 11 degrees in roll, pitch, and yaw directions. The average precision and recall for identifying relative tag motion were 0.87 and 0.89, respectively. Examples of the resulting pose and gait analysis demonstrate the potential of this approach to enhance studies that use tag data to investigate movement and behavior. MATLAB source code and data presented in the paper were made available to the public (https://github.com/ding-z/cetacean-pose-gait-analysis.git), with suggestions related to tag data processing practices provided in this paper. The proposed analysis approach will facilitate the use of biologging tags to study cetacean locomotion and behavior.
Characterization of metabolic compartmentalization in the liver using spatially resolved metabolomics
Authors: van der Reest Jiska , Stopka Sylwia A. , Abdelmoula Walid M. , Ruiz Daniela F. , Joshi Shakchhi , Ringel Alison E. , Haigis Marcia C. , Agar Nathalie Y. R. 
Published: December 2021

AbstractCells adapt their metabolism to physiological stimuli, and metabolic heterogeneity exists between cell types, within tissues, and subcellular compartments. The liver plays an essential role in maintaining whole-body metabolic homeostasis and is structurally defined by metabolic zones. These zones are well-understood on the transcriptomic level, but have not been comprehensively characterized on the metabolomic level. Mass spectrometry imaging (MSI) can be used to map hundreds of metabolites directly from a tissue section, offering an important advance to investigate metabolic heterogeneity in tissues compared to extraction-based metabolomics methods that analyze tissue metabolite profiles in bulk. We established a workflow for the preparation of tissue specimens for matrix-assisted laser desorption/ionization (MALDI) MSI and achieved broad coverage of central carbon, nucleotide, and lipid metabolism pathways. We used this approach to visualize the effect of nutrient stress and excess on liver metabolism. Our data revealed a highly organized metabolic compartmentalization in livers, which becomes disrupted under nutrient stress conditions. Fasting caused changes in glucose metabolism and increased the levels of fatty acids in the circulation. In contrast, a prolonged high-fat diet (HFD) caused lipid accumulation within liver tissues with clear zonal patterns. Fatty livers had higher levels of purine and pentose phosphate related metabolites, which generates reducing equivalents to counteract oxidative stress. This MALDI MSI approach allowed the visualization of liver metabolic compartmentalization at high resolution and can be applied more broadly to yield new insights into metabolic heterogeneityin vivo.
TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity
Authors: Caraballo-Ortiz Marcos A. , Miura Sayaka , Sanderford Maxwell , Dolker Tenzin , Tao Qiqing , Weaver Steven , Pond Sergei L. K. , Kumar Sudhir 
Published: December 2021

AbstractMotivationBuilding reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of SARS-CoV-2 strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites and millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate phylogenetic inference of resolvable phylogenetic features.ResultsWe present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. To assess topological robustness, we develop a bootstrap resampling strategy that resamples genomes spatiotemporally. The application of TopHap to build a phylogeny of 68,057 genomes (68KG) produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major variants of concern.AvailabilityTopHap is available on the web at https://github.com/SayakaMiura/TopHap.Contacts.kumar@temple.edu
Mitochondrial Dysfunction is a Driver for SP-2509 Drug Resistance in Ewing Sarcoma
Authors: Tokarsky E. John , Crow Jesse C. , Guenther Lillian M. , Sherman John , Taslim Cenny , Alexe Gabriela , Pishas Kathleen I. , Rask Galen , Justis Blake S. , Kasumova Ana , Stegmaier Kimberly , Lessnick Stephen L. , Theisen Emily R. 
Published: December 2021

AbstractExpression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine specific demethylase-1 (LSD1) inhibitors, which are currently in early phase clinical trials. Single agent targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP- 2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509. These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents which prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.
Arousal elevation drives the development of oscillatory vocal output
Authors: Zhang Yisi S. , Alvarez John L. , Ghazanfar Asif A. 
Published: December 2021

AbstractAdult behaviors, such as vocal production, often exhibit temporal regularity. In contrast, their immature forms are more irregular. We ask whether the coupling of motor behaviors with arousal changes give rise to temporal regularity. Do they drive the transition from variable to regular motor output over the course of development? We used marmoset monkey vocal production to explore this putative influence of arousal on the nonlinear changes in their developing vocal output patterns. Based on a detailed analysis of vocal and arousal dynamics in marmosets, we put forth a general model incorporating arousal and auditory-feedback loops for spontaneous vocal production. Using this model, we show that a stable oscillation can emerge as the baseline arousal increases, predicting the transition from stochastic to periodic oscillations observed during marmoset vocal development. We further provide a solution for how this model can explain vocal development as the joint consequence of energetic growth and social feedback. Together, we put forth a plausible mechanism for the development of arousal-mediated adaptive behavior.
How does perceived severity of COVID-19 influence purchase intention of organic food?
Authors: Wang Hong , Ma Baolong , Cudjoe Dan , Bai Rubing , Farrukh Muhammad 
Published: December 2021

PurposeThe COVID-19 outbreak has been rapidly spreading around the world for more than a year. However, few studies have explored the connection between the perceived severity of COVID-19 and purchase intention of the health-related products, for example, organic food. Based on the stimulus–organism–response (S-O-R) framework, this study examines the influencing mechanism of perceived severity of COVID-19 on purchase intention of organic food.Design/methodology/approachTo evaluate the proposed model, an online survey was utilized to collect 1,104 valid questionnaires from China.FindingsThe findings suggest that (1) the perceived severity of COVID-19 has a significant positive impact on purchasing intention; (2) health consciousness acts as a mediating role between perceived severity of COVID-19 and purchasing intention and (3) perceived inconvenience negatively moderates the connection between perceived severity and purchase intention.Originality/valueThe findings of this paper provide new insights into the positive effects of COVID-19 and pave the way for governments and enterprises to promote the purchase behaviour of organic food.
Development of a sustainable brand identity model: fostering the implementation of SDGs in the Brazilian power sector
Authors: Caldana Adriana Cristina Ferreira , Lourenção Marina , Krüger Caroline , Pennabel Adriana Fiorani , dos Santos Neusa Maria Bastos Fernandes 
Published: December 2021

PurposeThis study aims to develop a sustainable brand identity model to help organizations align their managerial practices to sustainable development goals (SDGs) and examine its applicability for a Brazilian electrical sector company.Design/methodology/approachA systematic qualitative review of the literature was carried out to provide a theoretical basis for the attributes chosen to compose the sustainable brand identity management (SBIM) model. To apply the model, the authors collected the data from internal and public domain documents, semi-structured in-depth interviews and non-participant observation of the company's work environment.FindingsThe first SBIM model was developed. The Brazilian power sector company implemented sustainable actions related to most of the models' attributes, contributing to the SDGs. A research agenda was presented.Research limitations/implicationsThe theoretical contribution is provided toward brand identity and sustainability literature with the sustainable brand identity model development and the conceptual explanation regarding its attributes.Practical implicationsThe practical implications are provided from the model application to an electrical company leading to some managerial suggestions that might be used to companies willing to align their practices to sustainability.Originality/valueThe studies on SDG and brand identity models were analyzed in order to create the first SBIM model. This article extends the concept of the brand identity of marketing theory by linking its core to sustainability actions, so far not addressed in academic studies.
The impact of user innovator mindset on feedback volume, feedback diversity and new product development performance
Authors: Wu Jiajun , O'Hern Matthew , Ye Jun 
Published: December 2021

PurposeThis study examines the influence of different user innovator mindsets on new product development (NPD) performance. The current research explores the relative impact of a product-focused user innovator mindset vs a customer-focused mindset on feedback volume and feedback diversity and investigates the effect of each type of feedback on product improvement and product diffusion.Design/methodology/approachThis study examines these relationships using two distinct types of data. Data on user innovator mindset, feedback characteristics and user innovator improvisation were obtained via an online survey. Archival data on NPD performance measures were acquired directly from an online research database, and results were obtained using confirmatory factor analysis.FindingsThe authors find that while neither type of user innovator mindset directly influences NPD performance, user innovators, who are highly customer-focused, have a significant advantage in sourcing knowledge from users in the form of a higher volume of feedback and more diverse feedback. In turn, feedback volume appears to positively influence product improvement, while feedback diversity positively influences product diffusion. Finally, the effect of both types of feedback on product improvement is enhanced for user innovators who are highly improvisational.Originality/valueThis research highlights the important role that customer focus plays in directly obtaining knowledge from customers (i.e. customer feedback) and the effects of that feedback on NPD performance. This study provides evidence that a user innovator's interest in accurately understanding the needs of their peers improves their access to external knowledge and enhances their innovation efforts.
The industrial relations chameleon: collective bargaining in the facility management business
Authors: Godino Alejandro , Molina Oscar 
Published: December 2021

PurposeThe paper aims to analyze collective bargaining in the facility management business of these six countries to explore similarities and differences between them. The analysis serves to test the differential impact of the national institutional setting on the protection provided by collective agreements to facility management workers.Design/methodology/approachThe paper adopts a case study methodology to approach a facility management multinational company providing services in six European countries (France, Italy, The Netherlands, Poland, Spain and the UK) that represent different industrial relations systems with variance in key dimensions of collective bargaining, including its structure, coverage and extension of agreements.FindingsThe extension of the facility management business model has not always adopted a high-road strategy aimed at enhancing the quality and efficiency through the integrated management and delivery of services, which is expected to positively impact employment conditions. Rather, it has, in many cases, been a deliberate, low-road attempt to undercut working standards, taking advantage of the multiple services provided by the company in a context of growing de-centralization in collective bargaining. The results point to an important role of industrial relations institutions in shaping facility management strategies and outcomes.Originality/valueSimilar to other forms of outsourcing, facility management leads to fragmented employment relations. However, the concentration of outsourced workers under the same supplier organization introduces opportunities to ensure the protection of workers, depending on the adoption of a high- or low-road competitive strategy. This paper provides for the first time comparative evidence about industrial relations in facility management businesses, a largely under-researched area.