bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terrestrial force production by the limbs of a semi-aquatic salamander provides insight into the evolution of terrestrial locomotor mechanics
Authors: Kawano Sandy M. , Blob Richard W. 
Published: May 2021

AbstractAmphibious fishes and salamanders are valuable functional analogs for vertebrates that spanned the water-to-land transition. However, investigations of walking mechanics have focused on terrestrial salamanders and, thus, may better reflect the capabilities of stem tetrapods that were already terrestrial. The earliest tetrapods were aquatic, so salamanders that are not primarily terrestrial may yield more appropriate data for modelling the incipient stages of terrestrial locomotion. In the present study, locomotor biomechanics were quantified from semi-aquaticPleurodeles waltl, a salamander that spends most of its adult life in water, and then compared to a primarily terrestrial salamander (Ambystoma tigrinum) and semi-aquatic fish (Periophthalmus barbarus) to evaluate whether walking mechanics show greater similarity between species with ecological versus phylogenetic similarities. Ground reaction forces (GRFs) from individual limbs or fins indicated that the pectoral appendages of each taxon had distinct patterns of force production, but hind limb forces were comparable between the salamanders. The rate of force development (‘yank’) was sometimes slower inP. waltlbut generally comparable between the three species. Finally, medial inclination of the GRF inP. waltlwas intermediate between semi-aquatic fish and terrestrial salamanders, potentially elevating bone stresses among more aquatic taxa as they move on land. These data provide a framework for modelling stem tetrapods using an earlier stage of quadrupedal locomotion that was powered primarily by the hind limbs (i.e., “rear-wheel drive”), and reveal mechanisms for appendages to generate propulsion in three locomotor strategies that are presumed to have occurred across the water-to-land transition in vertebrate evolution.Summary statementSemi-aquatic salamanders had limb mechanics that were intermediate in magnitude yet steadier than the appendages of terrestrial salamanders and semi-aquatic fish, providing a framework to model semi-aquatic early tetrapods.
Retention Time Standardization and Registration (RTStaR): An algorithm that matches corresponding and identifies unique species in nanoliquid chromatography-nanoelectrospray ionization-mass spectrometry lipidomic datasets
Authors: Blanchard Alexandre P. , Wang Yun , Taylor Graeme P. , Granger Matthew W. , Fai Stephen , Figeys Daniel , Paus Tomas ,   SYS Consortium, Pausova Zdenka , Xu Hongbin , Bennett Steffany A.L. 
Published: May 2021

AbstractBioinformatic tools capable of registering, rapidly and reproducibly, large numbers of nanoliquid chromatography-nanoelectrospray ionization-tandem mass spectrometry (nLC-nESI-MS/MS) lipidomic datasets are lacking. We provide here a freely available Retention Time Standardization and Registration (RTStaR) algorithm that aligns nLC-nESI-MS/MS spectra within a single dataset and compares these aligned retention times across multiple datasets. This two-step calibration matches corresponding and identifies unique lipid species in different lipidomes from different matrices and organisms. RTStaR was developed using a population-based study of 1001 human serum samples composed of 71 distinct glycerophosphocholine metabolites comprising a total of 68,572 analytes. Platform and matrix independence were validated using different MS instruments, nLC methodologies, and mammalian lipidomes. The complete algorithm is packaged in two modular ExcelTM workbook templates for easy implementation. RTStaR is freely available from the India Taylor Lipidomics Research Platformhttp://www.neurolipidomics.ca/rtstar/rtstar.html. Technical support is provided throughldomic@uottawa.ca
Evolutionary dynamics of circular RNAs in primates
Authors: Santos-Rodriguez Gabriela , Voineagu Irina , Weatheritt Robert J 
Published: May 2021

AbstractMany primate genes produce non-coding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.
Left Hemisphere Dominance for Bilateral Kinematic Encoding in the Human Brain
Authors: Merrick Christina M. , Dixon Tanner C. , Breska Assaf , Lin Jack J. , Chang Edward F. , King-Stephens David , Laxer Kenneth D. , Weber Peter B. , Carmena Jose M. , Knight Robert T. , Ivry Richard B. 
Published: May 2021

ABSTRACTNeurophysiological studies in humans and non-human primates have revealed movement representations in both the contralateral and ipsilateral hemisphere. Inspired by clinical observations, we ask if this bilateral representation differs for the left and right hemispheres. Electrocorticography (ECoG) was recorded in human participants during an instructed-delay reaching task, with movements produced with either the contralateral or ipsilateral arm. Using a cross-validated kinematic encoding model, we found stronger bilateral encoding in the left hemisphere, an effect that was present during preparation and was amplified during execution. Consistent with this asymmetry, we also observed better across-arm generalization in the left hemisphere, indicating similar neural representations for right and left arm movements. Notably, these left hemisphere electrodes were centered over premotor and parietal regions. The more extensive bilateral encoding in the left hemisphere adds a new perspective to the pervasive neuropsychological finding that the left hemisphere plays a dominant role in praxis.
Transmembrane helices are an overlooked and evolutionarily conserved source of major histocompatibility complex class I and II epitopes
Authors: Bilderbeek Richèl J.C. , Baranov Maxim , van den Bogaart Geert , Bianchi Frans 
Published: May 2021

AbstractCytolytic T cell responses are predicted to be biased towards membrane proteins. The peptide-binding grooves of most haplotypes of histocompatibility complex class I (MHC-I) are relatively hydrophobic, therefore peptide fragments derived from human transmembrane helices (TMHs) are predicted to be presented more often as would be expected based on their abundance in the proteome. However, the physiological reason of why membrane proteins might be over-presented is unclear. In this study, we show that the over-presentation of TMH-derived peptides is general, as it is predicted for bacteria and viruses and for both MHCI and MHC-II. Moreover, we show that TMHs are evolutionarily more conserved, because single nucleotide polymorphisms (SNPs) are present relatively less frequently in TMH-coding chromosomal regions compared to regions coding for extracellular and cytoplasmic protein regions. Thus, our findings suggest that both cytolytic and helper T cells respond more to membrane proteins, because these are evolutionary more conserved. We speculate that TMHs therefore are less prone to escape mutations that enable pathogens to evade T cell responses.
Vibrio choleraebiofilm dispersal regulator causes cell release from matrix through type IV pilus retraction
Authors: Singh Praveen K. , Rode Daniel K.H. , Buffard Pauline , Nosho Kazuki , Bayer Miriam , Jeckel Hannah , Jelli Eric , Neuhaus Konstantin , Jiménez-Siebert Eva , Peschek Nikolai , Glatter Timo , Papenfort Kai , Drescher Knut 
Published: May 2021

AbstractThe extracellular matrix is a defining feature of bacterial biofilms and provides structural stability to the community by binding cells to the surface and to each other. Transitions between bacterial biofilm initiation, growth, and dispersion require different regulatory programs, all of which result in modifications to the extracellular matrix composition, abundance, or functionality. However, the mechanisms by which individual cells in biofilms disengage from the matrix to enable their departure during biofilm dispersal are unclear. Here, we investigated active biofilm dispersal ofVibrio choleraeduring nutrient starvation, resulting in the discovery of the conservedVibriobiofilm dispersal regulator VbdR. We show that VbdR triggers biofilm dispersal by controlling cellular release from the biofilm matrix, which is achieved by inducing the retraction of the mannose-sensitive hemagglutinin (MSHA) type IV pili and the expression of a matrix protease IvaP. We further show that MSHA pili have numerous binding partners in the matrix and that the joint effect of MSHA pilus retraction and IvaP activity is necessary and sufficient for causing biofilm dispersal. These results highlight the crucial role of type IV pilus dynamics during biofilm dispersal and provide a new target for controllingV. choleraebiofilm abundance through the induction and manipulation of biofilm dispersal.
Multi-tissue methylation clocks for age estimation in the common bottlenose dolphin
Authors: Robeck Todd R. , Fei Zhe , Haghani Amin , Zoller Joseph A. , Li Caesar Z. , Steinman Karen J. , DiRocco Stacy , Staggs Lydia , Schmitt Todd , Osborn Steve , Montano Gisele , Rodriguez Magdalena , Horvath Steve 
Published: May 2021

ABSTRACTAccurate identification of individual ages within wild bottlenose dolphins (Tursiops truncatus) is critical for determining population health and the development of population management strategies. As such, we analyzed DNA methylation patterns by applying a custom methylation array (HorvathMammalMethyl40) to both blood (n = 140) and skin samples (n = 87) from known age or approximate age (0 to 57 years) bottlenose dolphins. We present three bottlenose dolphin specific age estimation clocks using combined blood and skin (48 CpGs, R = 0.93, median absolute error = 2.13 years), blood only (64 CpGs, R = 0.97, error= 1.46 years) and skin only (39 CpGs, R = 0.95, error= 2.53). Our sex estimator based on 71 CpGs predicts the sex of any odontocete species with 99.5% accuracy. We characterize individual cytosines that correlate with sex and age in dolphins.The presented epigenetic clocks are expected to be useful for conservation efforts and for studying anthropogenic events.
Robust ensemble of handcrafted and learned approaches for DNA-binding proteins
Authors: Nanni Loris , Brahnam Sheryl 
Published: May 2021

PurposeAutomatic DNA-binding protein (DNA-BP) classification is now an essential proteomic technology. Unfortunately, many systems reported in the literature are tested on only one or two datasets/tasks. The purpose of this study is to create the most optimal and universal system for DNA-BP classification, one that performs competitively across several DNA-BP classification tasks.Design/methodology/approachEfficient DNA-BP classifier systems require the discovery of powerful protein representations and feature extraction methods. Experiments were performed that combined and compared descriptors extracted from state-of-the-art matrix/image protein representations. These descriptors were trained on separate support vector machines (SVMs) and evaluated. Convolutional neural networks with different parameter settings were fine-tuned on two matrix representations of proteins. Decisions were fused with the SVMs using the weighted sum rule and evaluated to experimentally derive the most powerful general-purpose DNA-BP classifier system.FindingsThe best ensemble proposed here produced comparable, if not superior, classification results on a broad and fair comparison with the literature across four different datasets representing a variety of DNA-BP classification tasks, thereby demonstrating both the power and generalizability of the proposed system.Originality/valueMost DNA-BP methods proposed in the literature are only validated on one (rarely two) datasets/tasks. In this work, the authors report the performance of our general-purpose DNA-BP system on four datasets representing different DNA-BP classification tasks. The excellent results of the proposed best classifier system demonstrate the power of the proposed approach. These results can now be used for baseline comparisons by other researchers in the field.
Internal communication torn between employees' and management's expectations: an empirical study of employee magazines
Authors: Viererbl Benno , Koch Thomas , Denner Nora 
Published: May 2021

PurposeEditors of employee magazines may be torn between diverging expectations among their stakeholders. The management might be interested in strategically supportive communication, whereas employees might expect objective, independent, or critical coverage. Based on quantitative data, the paper aims to analyze how the editors perceive these expectations, how they see their professional role in this field of tension and how critically the magazines report.Design/methodology/approachThe authors conducted a quantitative survey of 197 editors of employee magazines and a quantitative content analysis of 200 articles of employee magazines.FindingsEditors perceive differences regarding the expectations of management and employees. These discrepancies, in turn, contribute to the experience of role conflicts. Our analysis reveals three types of editors: the voice of the management, the critical observer and the consensus-oriented mediator.Originality/valueThe study addresses the scarcely investigated area of conflict in which editors of employee magazines work. It is one of the first studies to analyze editors' perceived expectations of stakeholders, their professional self-perception and potential role conflicts with a quantitative survey. For the first time, quantitative methods are used to examine the causes of editors' role conflicts.
Archivists’ golden egg: environmental sustainability practices of archives
Authors: Faulkner James , Lu Liuxing , Chen Jiangping 
Published: May 2021

Purpose
Archivists are charged with the preservation of their collections by reducing deterioration because of temperature, relative humidity, atmospheric pollutants and other factors. The methods archivists use to preserve their collections may have a negative impact on the environment. This paper aims to identify factors for building environmentally sustainable archives to help guide archival environmental sustainability practices.

Design/methodology/approach
This paper identifies factors through a literature review, and conducts a content analysis of the websites of seven national/state archives. The analysis focuses on the policy statements of these archives.

Findings
The authors found that the literature lists 31 factors under 7 categories: electricity, facilities, water, exhibitions, pollution, collection practices and education and outreach. The content analysis of the policy documents or statements demonstrated that archives applied and addressed mostly “resource-related” efforts to protect the environment, such as factors related to electricity, facilities, water and pollution. However, factors related to “work-related” efforts, such as exhibitions, collection practices and education and outreach, were ignored.

Practical implications
This study can provide insights to archivists on current implementation and help to guide their further environmental sustainability practices.

Originality/value
Little is known regarding archivists’ implementation of environmentally sustainable practices. This study focuses on identifying factors for environmental sustainability of archives addressed by literature and existing archives, trying to find the gap between literature and practice.
An evaluation of public policy student placements: outcomes of a Malta-based study
Authors: Thake Anne Marie 
Published: May 2021

PurposeThe purpose of this paper is to evaluate short-term, unpaid placements offered to students reading for a degree in public policy. They provide added value to their tertiary education experience. Elective placements were offered in 2012 and became a mandatory requirement for students reading for a three-year bachelor of commerce degree in public policy in 2018. To date, no research has been carried out on these placements and this may serve as a model for a post-evaluation assessment.Design/methodology/approachData were collected from students who undertook placements, embedded in the public policy undergraduate programme. A document analysis of selected student and placement provider's reports was carried out to complement the students' responses to an online questionnaire.FindingsPlacements are of value to students as they served as an introduction to the working world. They enable students to establish connections with the course content and carry out research. They were exposed to real-life situations, developing their knowledge, acquiring soft skills and learning new tools, sought after by employers. These placements were valued as a route to graduate employment tailor-made to the degree's requirements. Students were able to embark on a soul-searching, introspective discovery and journey which made them mature and shed light in the direction of future work prospects.Research limitations/implicationsPlacements give students the opportunity to gain insights into real-work environments and are able to link theories learnt in the class-room with real-life situations. Placements have positive implications on students adjusting to their work life easily after graduation. The limitations are that the sample size was small and that the reflective reports which were randomly selected may not have necessarily been representative of the full complement.Practical implicationsThe practical implications are that the placements system and process can easily be implemented and replicated in other academic disciplines and universities as a compulsory component of their studies.Social implicationsPlacements gave students the opportunity to reflect on their learning, develop non-technical skills and enhance their confidence levels. They were also able to network and communicate with different employees.Originality/valuePlacements provided exposure to relevant organisations and personal enrichment in terms of acquiring skills, autonomy and independence. Students with placement experience are also more likely to secure future employment, relevant to their undergraduate degree.
Healthy food exposition attendees’ purchasing strategies: a mental budgeting perspective
Authors: Fu Xiaoxiao , Lin Bingna , Wang Yao-Chin 
Published: May 2021

PurposeGrounded in the theory of mental budgeting, this paper aims to investigate how the regret and perfectionism of exposition attendees influences their purchasing strategy.Design/methodology/approachThis research collected on-site data at a well-established specialty food exposition in China. Confirmatory factor analysis and structural equation modeling were applied to test the proposed model.FindingsThe findings confirm the effect of psychological mechanism (regret and perfectionism) on exposition attendees’ purchasing strategy as one that boosts/impairs their confidence in purchasing healthy food at the exposition. Specifically, regret and perfectionism show differential contributions to purchasing strategy dimensions. Variety seeking has a positive effect, whereas price consciousness has a negative effect, on purchase confidence.Practical implicationsEvent organizers and exhibitors should understand attendees’ consumption-related psychological mechanism and devise effective management and marketing strategies for optimal consumption experiences at expositions. They can create an informative and worry-free experience that facilitates a pleasant thought process to reduce uncertainty in attendees’ on-site decision-making.Originality/valueThe current research pioneered a unique model conceptualizing the important, yet underexplored, phenomenon of purchasing mechanism in the exposition setting. Addressing the emerging interest in food expositions, to the best of the authors’ knowledge, this study is the first for examining purchasing mechanism from the perspective of mental budgeting, providing insightful knowledge about how the psychological mechanism affects exposition attendees’ pre-purchase evaluation and confidence toward purchasing healthy food at expositions.
Online flight path planning with flight time constraints for fixed-wing UAVs in dynamic environments
Authors: Babel Luitpold 
Published: May 2021

PurposeA major challenge for mission planning of aircraft is to generate flight paths in highly dynamic environments. This paper presents a new approach for online flight path planning with flight time constraints for fixed-wing UAVs. The flight paths must take into account the kinematic restrictions of the vehicle and be collision-free with terrain, obstacles and no-fly areas. Moreover, the flight paths are subject to time constraints such as predetermined time of arrival at the target or arrival within a specified time interval.Design/methodology/approachThe proposed flight path planning algorithm is an evolution of the well-known RRT* algorithm. It uses three-dimensional Dubins paths to reflect the flight capabilities of the air vehicle. Requirements for the flight time are realized by skillfully concatenating two rapidly exploring random trees rooted in the start and target point, respectively.FindingsThe approach allows to consider static obstacles, obstacles which might pop up unexpectedly, as well as moving obstacles. Targets might be static or moving with constantly changing course. Even a change of the target during flight, a change of the target approach direction or a change of the requested time of arrival is included.Originality/valueThe capability of the flight path algorithm is demonstrated by simulation results. Response times of fractions of a second qualify the algorithm for real-time applications in highly dynamic scenarios.