bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methodological considerations when assessing mitochondrial respiration and biomarkers for mitochondrial content in human skeletal muscle
Authors: Kuang Jujiao , Saner Nicholas J , Botella Javier , Lee Matthew J-C , Granata Cesare , Wang Zhenhuan , Yan Xu , Li Jia , Genders Amanda J , Bishop David J 
Published: March 2021

AbstractBackgroundThe assessment of mitochondrial respiration and mitochondrial content are two common measurements in the fields of skeletal muscle research and exercise science. However, to verify the validity of the observed changes in both mitochondrial respiration and mitochondrial content following an intervention such as exercise training, it is important to determine the reliability and reproducibility of the experimental design and/or techniques employed. We examined the repeatability of widely used methodologies for assessing mitochondrial respiration and mitochondrial content, respectively; the measurement of maximal mitochondrial oxidative phosphorylation in permeabilized muscle fibres using high-resolution respirometry, and the measurement of citrate synthase activity as a biomarker for mitochondrial content in a microplate with spectrophotometer.ResultFor mitochondrial respiration, the coefficient of variation for repeated measurements using muscle sampled from same biopsy decreased from 12.7% to 11% when measured in triplicate with outliers excluded, rather than in duplicate. The coefficient of variation was 9.7% for repeated muscle biopsies sampled across two separated days. For measurements of citrate synthase activity, the coefficient of variation was 3.5% of three technical repeats on the same plate, 10.2% for duplicate analyses using the same muscle lysate when conducted in the same day, and 30.5% when conducted four weeks apart.ConclusionWe have provided evidence for important technical considerations when measuring mitochondrial respiration with human skeletal muscle: 1) the relatively large technical variability can be reduced by increasing technical repeats and excluding outliers; 2) the biological variability and absolute mitochondrial respiration value of the participants should be considered when estimating the required sample size; 3) a new threshold of 15% for the increase in respiration rate after the addition of cytochromectest for testing mitochondrial outer membrane integrity. When analysing citrate synthase activity, our evidence suggests it is important to consider the following: 1) all samples from the same study should be homogenized and measured at the same time using the same batch of freshly made chemical reagents; 2) biological variability should be considered when detecting small change in mitochondrial content; 3) the relative change should be used to compare the outcomes from different studies.
LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data
Authors: Morisse Pierre , Legeai Fabrice , Lemaitre Claire 
Published: March 2021

AbstractLinked-Reads technologies, popularized by 10x Genomics, combine the high-quality and low cost of short-reads sequencing with a long-range information by adding barcodes that tag reads originating from the same long DNA fragment. Thanks to their high-quality and long-range information, such reads are thus particularly useful for various applications such as genome scaffolding and structural variant calling. As a result, multiple structural variant calling methods were developed within the last few years. However, these methods were mainly tested on human data, and do not run well on non-human organisms, for which reference genomes are highly fragmented, or sequencing data display high levels of heterozygosity. Moreover, even on human data, most tools still require large amounts of computing resources. We present LEVIATHAN, a new structural variant calling tool that aims to address these issues, and especially better scale and apply to a wide variety of organisms. Our method relies on a barcode index, that allows to quickly compare the similarity of all possible pairs of regions in terms of amount of common barcodes. Region pairs sharing a sufficient number of barcodes are then considered as potential structural variants, and complementary, classical short reads methods are applied to further refine the breakpoint coordinates. Our experiments on simulated data underline that our method compares well to the state-of-the-art, both in terms of recall and precision, and also in terms of resource consumption. Moreover, LEVIATHAN was successfully applied to a real dataset from a non-model organism, while all other tools either failed to run or required unreasonable amounts of resources. LEVIATHAN is implemented in C++, supported on Linux platforms, and available under AGPL-3.0 License athttps://github.com/morispi/LEVIATHAN.
Neurogenesis-mediated forgetting of complex paired-associates memories
Authors: Epp Jonathan R , Botly Leigh C.P. , Josselyn Sheena A , Frankland Paul W 
Published: March 2021

AbstractThe hippocampus is a critical structure involved in many forms of learning and memory. It is also one of the only regions in the adult mammalian brain that continues to generate new neurons throughout adulthood. This process of adult neurogenesis may increase the plasticity of the hippocampus which could be beneficial for learning but has also been demonstrated to decrease the stability of previously acquired memories. Here we test whether increased production of new neurons following the formation of a gradually acquired paired-associates task will result in forgetting of this type of memory. We trained mice in a touchscreen-based object/location task and then increased neurogenesis using voluntary exercise. Our results indicate that mice with increased neurogenesis show poor recall of the previously established memory. When subsequently exposed to a reversal task we also show that mice with increased neurogenesis require fewer correction trials to acquire the new task contingencies. This suggests that prior forgetting reduces perseveration on the now outdated memory. Together our results add to a growing body of literature which indicates the important role of adult neurogenesis in destabilizing previously acquired memories to allow for flexible encoding of new memories.
A numerical framework for genetic hitchhiking in populations of variable size
Authors: Friedlander Eric , Steinrücken Matthias 
Published: March 2021

AbstractNatural selection on beneficial or deleterious alleles results in an increase or decrease, respectively, of their frequency within the population. Due to chromosomal linkage, the dynamics of the selected site affect the genetic variation at nearby neutral loci in a process commonly referred to as genetic hitchhiking. Changes in population size, however, can yield patterns in genomic data that mimic the effects of selection. Accurately modeling these dynamics is thus crucial to understanding how selection and past population size changes impact observed patterns of genetic variation.Here, we model the evolution of haplotype frequencies with the Wright-Fisher diffusion to study the impact of selection on linked neutral variation. Explicit solutions are not known for the dynamics of this diffusion when selection and recombination act simultaneously. Thus, we present a method for numerically evaluating the Wright-Fisher diffusion dynamics of two linked loci separated by a certain recombination distance when selection is acting. We can account for arbitrary population size histories explicitly using this approach. A key step in the method is to express the moments of the associated transition density, or sampling probabilities, as solutions to ordinary differential equations. Numerically solving these differential equations relies on a novel accurate and numerically efficient technique to estimate higher order moments from lower order moments.We demonstrate how this numerical framework can be used to quantify the reduction and recovery of genetic diversity around a selected locus over time and elucidate distortions in the site-frequency-spectra of neutral variation linked to loci under selection in various demographic settings. The method can be readily extended to more general modes of selection and applied in likelihood frameworks to detect loci under selection and infer the strength of the selective pressure.
Can collaborative buffering strategies reduce distribution costs while improving product returns?: A case of an Asian e-retailer
Authors: Shah Bhavin , Singh Gaganpreet 
Published: March 2021

PurposeIn order to achieve competitive advantage over the physical marketplace, the e-retailers are insisted on endowing with lenient return policies. The piece-wise returns-and-reordering process incurs excessive buffering and unwanted logistics costs which raises overall fulfillment charges. The objective of this study is to re-design e-retail distribution policy by providing temporal storage at logistics service provides' (LSP) location. The impact of recurrent returns on pricing and profit margins are also investigated over time continuum.Design/methodology/approachA framework is developed to reduce the non-value added (NVA) storage and distribution efforts by providing collaborative buffering between LSP and e-retailer. The knapsack based buffering approach is tested and compared with traditional e-retail distribution practices. The revenue sharing concept is mathematically modelled and implemented in GAMS, which finally validated through multiple return scenarios.FindingsThe proposed model outperforms the existing one under all scenarios with different configuration settings of re-ordering, profit margins, and buffer time windows. The distribution cost is found, linearly related to the necessary product buffering space. The findings help to re-design sustainable return policies for individual products so that maximum customer value can be yield with minimum costs.Research limitations/implicationsThis study helps to determine the NVA efforts incurred while storing and delivering multi-time returned products to ensure desired service levels. The revenue sharing model provides pricing strategies for e-retail practitioners deciding which product should store in what quantity for how much time at the shipping agency location so that it fulfils the re-ordering at least waiting and sufficient buffering.Originality/valueThe proposed model extends the role of LPSs as temporary buffer providers to reduce returns-and-reordering fulfilment efforts in the e-retail network. This Collaborative framework offers an opportunity to amend the distribution contracts and policies time by time that enhances e-retailer's performance and customer satisfaction.
Developing physical resilience strategies in passive defense according to identification of endangered areas of urban environments (case study: Ahvaz city)
Authors: Pouryarmohammadi Mozhdeh , Ahmadi Hasan , Salaripour AliAkbar 
Published: March 2021

Purpose
This paper aims to focus on reducing the vulnerability of Ahvaz city against urban disasters and lowering the number of casualties and amount of financial losses using modern approaches to develop resilience strategies that can increase urban safety to an acceptable level. The strategic situation of Ahvaz city, because of its abundant resources, the war experience and its location on the boundary regions of Iran, highlights its significance. Ahvaz has a high population and an extended texture, and the existence of extraordinary constructions increases the importance of physical resilience in this city.

Design/methodology/approach
The present study investigates built environment aspects such as the urban structure, the urban form, land-use proximity pattern, urban road network and crucial and vulnerable centres in Ahvaz, using a combination of qualitative and quantitative methods. Hence, the areas at risk in Ahvaz were identified and illustrated in a comprehensive risk assessment map, and then, by using the strengths, weaknesses, opportunities and threats technique and finally by using the Delphi method, some strategies and plans were presented to reduce the level of vulnerability in Ahvaz. Then, these strategies are prioritized by applying quality function deployment (QFD) technique.

Findings
The risk assessment result shows that most parts of Ahvaz’s urban areas are highly at risk. The central and northern parts of Ahvaz have the highest vulnerability at a time of crisis. These zones include district 1 (city centre) and districts 2, 3 and 7 at the city’s margins. The result of QFD process showed that the essential urban resilience strategy is to positively consider the passive defence studies with a physical resilience approach. Also, the proper distribution of strategic points in the city, moving the industrial and oil companies from the peripheral area, and facilitating access to vital, crucial centres to support urban regions are considered the most effective strategic plans.

Originality/value
This paper, with an integrated approach, examines and prioritizes the main physical problems of Ahvaz city based on the spatial analysis and opinions of experts. The physical strategies presented in this paper can significantly reduce the risks and increase the urban resilience of Ahvaz city in the face of crisis.
Unravelling collaboration mechanisms for green logistics: the perspectives of shippers and logistics service providers
Authors: Jazairy Amer , von Haartman Robin , Björklund Maria 
Published: March 2021

PurposeThe green logistics literature remains undecided on how collaboration between shippers (i.e. logistics buyers) and logistics service providers (LSPs) may facilitate green logistics practices (GLPs). This paper identifies two types of collaboration mechanisms, relation specific and knowledge sharing, to systematically examine their influence on facilitating the different types of GLPs – as seen by shippers versus LSPs.Design/methodology/approachSurvey responses of 169 shippers and 162 LSPs in Sweden were collected and analysed using exploratory- and confirmatory factor analysis, followed by multiple regression analysis.FindingsThe findings reveal that neither of the actors consistently favour a certain type of collaboration mechanisms for facilitating all types of GLPs. Although it was found that both actors share the same view on the role of collaboration mechanisms for some GLPs, their views took contrasting forms for others.Research limitations/implicationsThis study contributes to the green logistics literature by incorporating a trilateral distinction to present collaboration recommendations for GLPs, based on (1) the collaboration mechanism at play, (2) the actor's perspective and (3) the GLP in question.Practical implicationsInsights are offered to managers at shipper/LSP firms to apply the right (“fit for purpose”) collaboration mechanisms in their relationships with their logistics partners with respect to the desired GLPs.Originality/valueThis is one of the first large-scale studies to systematically reveal in what way collaboration can facilitate the different types of GLPs.
Towards a taxonomy of crowdsourced delivery business models
Authors: Ciobotaru Georgiana , Chankov Stanislav 
Published: March 2021

PurposeThe paper aims to develop (1) a comprehensive framework for classifying crowdshipping business models and (2) a taxonomy of currently implemented crowdshipping business models.Design/methodology/approachThe business models of 105 companies offering crowdsourced delivery services are analysed. Cluster analysis and principal component analysis are applied to develop a business model taxonomy.FindingsA detailed crowdsourced delivery business model framework with 74 features is developed. Based on it, six distinct clusters of crowdshipping business models are identified. One cluster stands out as the most appealing to customers based on social media metrics, indicating which type of crowdshipping business models is the most successful.Research limitations/implicationsDetailed investigations of each of the six clusters and of recent crowdshipping business model developments are needed in further research in order to enhance the derived taxonomy.Practical implicationsThis paper serves as a best-practices guide for both start-ups and global logistics operators for establishing or further developing their crowdsourced delivery business models.Originality/valueThis paper provides a holistic understanding of the business models applied in the crowdshipping industry and is a valuable contribution to the yet small amount of studies in the crowd logistics field.
Task scheduling on cloud computing based on sea lion optimization algorithm
Authors: Masadeh Raja , Alsharman Nesreen , Sharieh Ahmad , Mahafzah Basel A. , Abdulrahman Arafat 
Published: March 2021

Purpose
Sea Lion Optimization (SLnO) algorithm involves the ability of exploration and exploitation phases, and it is able to solve combinatorial optimization problems. For these reasons, it is considered a global optimizer. The scheduling operation is completed by imitating the hunting behavior of sea lions.

Design/methodology/approach
Cloud computing (CC) is a type of distributed computing, contributory in a massive number of available resources and demands, and its goal is sharing the resources as services over the internet. Because of the optimal using of these services is everlasting challenge, the issue of task scheduling in CC is significant. In this paper, a task scheduling technique for CC based on SLnO and multiple-objective model are proposed. It enables decreasing in overall completion time, cost and power consumption; and maximizes the resources utilization. The simulation results on the tested data illustrated that the SLnO scheduler performed better performance than other state-of-the-art schedulers in terms of makespan, cost, energy consumption, resources utilization and degree of imbalance.

Findings
The performance of the SLnO, Vocalization of Whale Optimization Algorithm (VWOA), Whale Optimization Algorithm (WOA), Grey Wolf Optimization (GWO) and Round Robin (RR) algorithms for 100, 200, 300, 400 and 500 independent cloud tasks on 8, 16 and 32 VMs was evaluated. The results show that SLnO algorithm has better performance than VWOA, WOA, GWO and RR in terms of makespan and imbalance degree. In addition, SLnO exhausts less power than VWOA, WOA, GWO and RR. More precisely, SLnO conserves 5.6, 21.96, 22.7 and 73.98% energy compared to VWOA, WOA, GWO and RR mechanisms, respectively. On the other hand, SLnO algorithm shows better performance than the VWOA and other algorithms. The SLnO algorithm's overall execution cost of scheduling the cloud tasks is minimized by 20.62, 39.9, 42.44 and 46.9% compared with VWOA, WOA, GWO and RR algorithms, respectively. Finally, the SLnO algorithm's average resource utilization is increased by 6, 10, 11.8 and 31.8% compared with those of VWOA, WOA, GWO and RR mechanisms, respectively.

Originality/value
To the best of the authors’ knowledge, this work is original and has not been published elsewhere, nor is it currently under consideration for publication elsewhere.
Improvement of the cultural heritage perception potential model by the usage of eye-tracking technology
Authors: Doğan Huriye Armağan 
Published: March 2021

PurposeThe aim of this paper is to develop and present the methodology of the model which can predict the perception and assessment of cultural heritage by the point of view of the non-experts through analysing the façades of buildings for adaptive re-use and sustainable development strategy.Design/methodology/approachThis paper focuses on the improvement and validation of the original cultural heritage perception potential model (CHPP) by adding new indicators which can be used as a part of the model. The method adopted includes the explanation of the older (original) model and its limitations. The assessment process follows the Integrated Cultural Heritage Management Approach to identify the new indicators which can be implemented on understanding the cultural heritage from the user/observer perspective, furthermore, for the sustainability of the environment.FindingsThe results demonstrate that the perception of the society regarding the perception of the built heritage can be affected by various indicators. When the indicators are well identified, it is possible to predict the potential of the buildings to be perceived as cultural heritage or not. The knowledge which is gained by the proposed model can assist the sustainability and continuity of both heritage objects and the environment by helping the adaptive re-use process and strategies.Originality/valueNo similar prior studies on the perception of cultural heritage as an approach to adaptive re-use strategies have been carried out. Furthermore, the usage of eye-tracking technology in the field of cultural heritage is rare. Therefore, it is hoped that the experiments performed in this study and the model which is created can lead and guide further research.
Coaching skills for recovery a decade of providing coaching skills for recovery training at a healthcare NHS foundation trust
Authors: Cyrus Helen Kathryn 
Published: March 2021

Purpose
Overview of coaching for recovery. The paper aims to show an overview of work that was carried out over 11 years with groups of mental health and physical staff. As the facilitator who had run this course for the duration in Nottingham, this was an excellent opportunity to be at the forefront of a brand new project.

Design/methodology/approach
The introduction of the skills are taught over two consecutive days followed by a further day a month later. The idea of coaching is to be enabled to find the answers in themselves by the use of powerful questions and using the technique of the grow model, combined with practice enables the brain to come up with its own answers. Using rapport and enabling effective communication to deliver the outcome.

Findings
Evidence from staff/clients and the purpose of the paper shows that when you step back it allows the individual patients/staff to allow the brain to process to create to come up with their solutions, which then helps them to buy into the process and creates ownership.

Research limitations/implications
The evidence suggests that the approach that was there prior to the course was very much a clinical approach to working with clients and treating the person, administering medication and not focussing on the inner person or personal recovery. The staff review has shown that in the clinical context change is happening from the inside out.

Practical implications
“Helps change culture”; “change of work practice”; “it changed staff focus – not so prescriptive”; “powerful questions let clients come to their own conclusions”; “coaching gives the ability to find half full. Helps to offer reassurance and to find one spark of hope”.

Social implications
This has shown that the approach is now person-centred/holistic. This has been the “difference that has made the difference”. When this paper looks at the issues from a different angle in this case a coaching approach, applying technique, knowledge and powerful questions the results have changed. The same clients, same staff and same problems but with the use of a different approach, there is the evidence of a different outcome, which speaks for itself. The coaching method is more facilitative, therefore it illicit’s a different response, and therefore, result.

Originality/value
The results/evidence starts with the individual attending and their commitment to the process over the two-day course. Then going away for the four weeks/six for managers and a commitment again to practice. Returning to share the impact if any with the group. This, in turn, helps to inspire and gain motivation from the feedback to go back to work invigorated to keep going.