bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Validation of a Deep Learning Algorithm and Open-Source Platform for the Automatic Labelling of Motion Capture Markers
Authors: Clouthier Allison L. , Ross Gwyneth B. , Mavor Matthew P. , Coll Isabel , Boyle Alistair , Graham Ryan B.
Published: February 2021

The purpose of this work was to develop an open-source deep learning-based algorithm for motion capture marker labelling that can be trained on measured or simulated marker trajectories. In the proposed algorithm, a deep neural network including recurrent layers is trained on measured or simulated marker trajectories. Labels are assigned to markers using the Hungarian algorithm and a predefined generic marker set is used to identify and correct mislabeled markers. The algorithm was first trained and tested on measured motion capture data. Then, the algorithm was trained on simulated trajectories and tested on data that included movements not contained in the simulated data set. The ability to improve accuracy using transfer learning to update the neural network weights based on labelled motion capture data was assessed. The effect of occluded and extraneous markers on labelling accuracy was also examined. Labelling accuracy was 99.6% when trained on measured data and 92.8% when trained on simulated trajectories, but could be improved to up to 98.8% through transfer learning. Missing or extraneous markers reduced labelling accuracy, but results were comparable to commercial software. The proposed labelling algorithm can be used to accurately label motion capture data in the presence of missing and extraneous markers and accuracy can be improved as data are collected, labelled, and added to the training set. The algorithm and user interface can reduce the time and manual effort required to label optical motion capture data, particularly for those with limited access to commercial software.
RNA fragment assembly with experimental restraints
Authors: Chojnowski Grzegorz , Zaborowski Rafał , Magnus Marcin , Bujnicki Janusz M.
Published: February 2021

We present RNA Masonry, a computer program and a web service for a fully automated assembly of RNA fragments into geometrically plausible models fulfilling user-provided secondary structure constraints and restraints on tertiary contacts and Small Angle X-ray Scattering (SAXS) data. We illustrate the method description with its recent application to structural studies of viral RNAs with SAXS restraints. The program web server is available athttp://iimcb.genesilico.pl/rnamasonry.

Contact

gchojnowski@embl-hamburg.de
How much does it take to be old? Modelling the time since the last harvesting to infer the distribution of overmature forests in France
Authors: Thompson Lucie , Cateau Eugénie , Debaive Nicolas , Bray Frédéric , Torre André , Vallet Patrick , Paillet Yoan
Published: February 2021

Aim

The distribution of overmature forests in metropolitan France is poorly known, with only a few well-studied prominent sites, and has never been evaluated countrywide. Here, we modelled French forest reserves’ time since the last harvesting operation - a proxy for forest maturity - then inferred the current statistical distribution of overmature forests (i.e. forests over 50 years without harvesting) in France.

Location

Metropolitan France

Methods

We used inventories from forest reserves and managed forests to calibrate a generalised linear mixed model explaining the time since the last harvesting with selected structural attributes and environmental variables. We then projected this model on the independent National Forest Inventory dataset. We thus obtained an updated estimation of the proportion and a rough distribution of overmature forest stands in metropolitan France.

Results

We found that high basal area of very large trees, high volumes of standing and downed deadwood, high diversity of tree-related microhabitats and more marginally diversity of decay stages best characterized the time since the last harvesting. Volumes of stumps and high density of coppices translating legacy of past forest management also distinguished more overmature plots. Our projection yielded an estimated 3% of French forests over 50 years without harvesting mostly located in more inaccessible areas (i.e. mountainous areas) and a promising proportion of future overmature forests if left unharvested.

Main conclusions

Our study showed that the time since the last harvesting is a good proxy for a combination of stand structure attributes key in characterising overmature temperate forests. It gives the first robust statistical estimate of the proportion of overmature forests and may serve to report on their status in metropolitan France. Our method could be implemented at a larger spatial scale, notably in countries with accessible National Forest Inventory and calibration data, to produce indicators at international level.
A novel and specific regulator of neuronal V-ATPase inDrosophila
Authors: Dulac Amina , Issa Abdul-Raouf , Sun Jun , Matassi Giorgio , Chérif-Zahar Baya , Cattaert Daniel , Birman Serge
Published: February 2021

The V-ATPase is a highly conserved enzymatic complex that ensures appropriate levels of organelle acidification in virtually all eukaryotic cells. While the general mechanisms of this proton pump have been well studied, little is known about the specific regulations of neuronal V-ATPase. Here, we studied CG31030, a previously uncharacterizedDrosophilaprotein predicted from its sequence homology to be part of the V-ATPase family. We found that this protein is essential and apparently specifically expressed in neurons, where it is addressed to synaptic terminals. We observed that CG31030 co-immunoprecipitated with V-ATPase subunits, in particular with ATP6AP2, and that synaptic vesicles of larval motoneurons were not properly acidified inCG31030knockdown context. This defect was associated with a decrease in quantal size at the neuromuscular junction, severe locomotor impairments and shortened lifespan. Overall, our data provide evidence that CG31030 is a specific regulator of neuronal V-ATPase that is required for synaptic vesicle acidification and neurotransmitter release.
Adoptive transfer of allogeneic gamma delta T cells promotes HIV replication in a humanized mouse model
Authors: Biradar Shivkumar , Agarwal Yash , Lotze Michael T. , Rinaldo Charles R. , Bility Moses T. , Mailliard Robbie B.
Published: February 2021

Gamma-delta (γδ) T cells recognize antigens in an MHC-independent manner, with demonstrable cytotoxicity against cancer and virally infected cells. Human immunodeficiency virus (HIV) infection severely depletes the Vγ9Vδ2 (Vδ2) subset of these T cells in most infected individuals, with the exception of elite controllers. The capacity of Vδ2 cells to kill HIV-infected targets has been demonstratedin vitro, but this has not been verifiedin vivo. Here, we examined the immunotherapeutic potential of Vδ2 cells in controlling HIV replicationin vivoand provide the first characterization of reconstituted γδ T cell subsets in the peripheral blood and lymphoid tissue in a humanized mouse model. We demonstrate the depletion of Vδ2 cells and increase in Vδ1 cells in the blood following HIV infection, similar to that observed in HIV-infected humans. The functionality of human Vδ2 cells isolated from humanized mice was confirmed viaex vivoexpansion in response to zoledronate and IL-2 treatment. The adoptive transfer of activated Vδ2 cells failed to control HIV infectionin vivobut instead exacerbated viremia by serving as early targets for HIV infection. Our findings suggest that Vδ2 cells play a critical and unappreciated role as early HIV targets of infection to promote viral dissemination.
A refinement to gene editing in Atlantic salmon using asymmetrical oligonucleotide donors
Authors: Straume Anne Hege , Kjærner-Semb Erik , Skaftnesmo Kai Ove , Güralp Hilal , Lillico Simon , Wargelius Anna , Edvardsen Rolf Brudvik
Published: February 2021

Selective breeding programs in aquaculture are limited by the heritability of the trait and long generation time in most fish species. New breeding technology (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) have the potential to expedite genetic improvement in aquaculture, but the method requires optimization. Here we show that asymmetrical oligonucleotide (ODN) donors induce highly efficient and precise edits in individual Atlantic salmon founder animals. We performed single nucleotide replacement (SNR) indndwith up to 59.2% efficiency, and inserted FLAG elements intoslc45a2anddnd, with up to 36.7 % and 32.7% efficiency, respectively. We found HDR efficiency to be dependent on template concentration, but a trade-off with respect to toxicity was observed. Using this NBT in salmon we demonstrate that precise modification of the genome can be achieved in a single generation, allowing efficient introgression of favorable alleles and bypassing challenges associated with traditional selective breeding.
Body size dependent dispersal influences stability in heterogeneous metacommunities
Authors: Anderson Kurt E. , Fahimipour Ashkaan K.
Published: February 2021

Body size affects key biological processes across the tree of life, with particular importance for food web dynamics and stability. Traits influencing movement capabilities depend strongly on body size, yet the effects of allometrically-structured dispersal on food web stability are less well understood than other demographic processes. Here we study the stability properties of spatially-arranged model food webs in which larger bodied species occupy higher trophic positions, while species’ body sizes also determine the rates at which they traverse spatial networks of heterogeneous habitat patches. Our analysis shows an apparent stabilizing effect of positive dispersal rate scaling with body size compared to negative scaling relationships or uniform dispersal. However, as the global coupling strength among patches increases, the benefits of positive body size-dispersal scaling disappear. A permutational analysis shows that breaking allometric dispersal hierarchies while preserving dispersal rate distributions rarely alters qualitative aspects of metacommunity stability. Taken together, these results suggest that the oft-predicted stabilizing effects of large mobile predators may, for some dimensions of ecological stability, be attributed to increased patch couplingper se, and not necessarily coupling by top trophic levels in particular.
Diet High in Soybean Oil Increases Susceptibility to Colitis in Mice
Authors: Deol Poonamjot , Ruegger Paul , Logan Geoffrey D. , Shawki Ali , Li Jiang , Mitchell Jonathan D. , Yu Jacqueline , Piamthai Varadh , Radi Sarah H. , Borkowski Kamil , Newman John W. , McCole Declan F. , Nair Meera G. , Hsiao Ansel , Borneman James , Sladek Frances M.
Published: February 2021

The current American diet is high in soybean oil (SO), which consists of unsaturated fatty acids, most notably linoleic acid (LA, C18:2 omega-6). While LA is an essential fatty acid that must be obtained from the diet, high LA consumption has been linked to the development of inflammatory bowel disease (IBD) in humans. Here, we show that a high fat diet (HFD) based on soybean oil increases susceptibility to colitis in wild-type and IL10 knockout mice. It causes immune dysfunction, decreases colon and crypt length and increases intestinal epithelial barrier permeability; these effects were not observed in low LA HFDs. The SO diet also disrupts the balance of isoforms encoded by the IBD susceptibility gene Hepatocyte Nuclear Factor 4α (HNF4α). Both the SO diet and an LA gavage cause gut dysbiosis: the SO diet increases the abundance of an adherent, invasiveEscherichia coli(AIEC), which can use LA as a carbon source, and the LA gavage decreases the beneficial bacteriaLactobacillus murinus. Metabolomic analysis of both host-associated and cultured bacteria shows that SO increases levels of LA and oxylipins while decreasing eicosapentaenoic acid (EPA, C20:5 omega-3) and endocannabinoids. Our results suggest that excess LA, obtained from a diet high in soybean oil, increases susceptibility to colitis by alterations in intestinal HNF4α, gut microbiota and bioactive metabolites.
Feedforward and feedback interactions between visual cortical areas use different population activity patterns
Authors: Semedo João D. , Jasper Anna I. , Zandvakili Amin , Aschner Amir , Machens Christian K. , Kohn Adam , Yu Byron M.
Published: February 2021

Brain function relies on the coordination of activity across multiple, recurrently connected, brain areas. For instance, sensory information encoded in early sensory areas is relayed to, and further processed by, higher cortical areas and then fed back. However, the way in which feedforward and feedback signaling interact with one another is incompletely understood. Here we investigate this question by leveraging simultaneous neuronal population recordings in early and midlevel visual areas (V1-V2 and V1-V4). Using a dimensionality reduction approach, we find that population interactions are feedforward-dominated shortly after stimulus onset and feedback-dominated during spontaneous activity. The population activity patterns most correlated across areas were distinct during feedforward- and feedback-dominated periods. These results suggest that feedforward and feedback signaling rely on separate “channels”, such that feedback signaling does not directly affect activity that is fed forward.
Mechanistic underpinning of nonuniform collective motions in swarming bacteria
Authors: Bera Palash , Wasim Abdul , Mondal Jagannath , Ghosh Pushpita
Published: February 2021

Self-propelled bacteria can exhibit a large variety of non-equilibrium self-organized phenomena. Swarming is one such fascinating dynamical scenario where a number of motile individuals grouped into clusters and move in synchronized flows and vortices. While precedent investigations in rod-like particles confirm that increased aspect-ratio promotes alignment and order, recent experimental studies in bacteriaBacillus subtilisshow a non-monotonic dependence of cell-aspect ratio on their swarming motion. Here, by computer simulations of an agent-based model of selfpropelled, mechanically interacting, rod-shaped bacteria in overdamped condition, we explore the collective dynamics of bacterial swarm subjected to a variation of cell-aspect ratio. When modeled with an identical self-propulsion speed across a diverse range of cell aspect ratio, simulations demonstrate that both shorter and longer bacteria exhibit slow dynamics whereas the fastest speed is obtained at an intermediate aspect ratio. Our investigation highlights that the origin of this observed non-monotonic trend of bacterial speed and vorticity with cell-aspect ratio is rooted in the cell-size dependence of motility force. The swarming features remain robust for a wide range of surface density of the cells, whereas asymmetry in friction attributes a distinct effect. Our analysis identifies that at an intermediate aspect ratio, an optimum cell size and motility force promote alignment, which reinforces the mechanical interactions among neighboring cells leading to the overall fastest motion. Mechanistic underpinning of the collective motions reveals that it is a joint venture of the short-range repulsive and the size-dependent motility forces, which determines the characteristics of swarming.
Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy
Authors: Miyazaki Naoyuki , Murakami Kosuke , Oka Tomoichiro , Miki Motohiro , Iwasaki Kenji , Katayama Kazuhiko , Murata Kazuyoshi
Published: February 2021

Sapovirus is a cause of acute gastroenteritis in humans and animals. Infants and younger children have the greatest disease burden. Although it shares many similarities with norovirus, the lack of detailed structural information has hampered the development of vaccines and therapeutics. Here, we investigated the human sapovirus VLP by single particle cryo-electron microscopy and are the first to report the atomic structure of the capsid at 2.9 Å resolution. The atomic model revealed the domain interactions of the capsid protein and functionally important amino acid residues. The extended loop from the P1 subdomain was involved in interactions in the P2 domain, forming unique arch-like dimeric protrusions of capsid proteins. All hypervariable regions that are important candidates for immune response or receptor binding, formed a large cluster at the top of the P domain. These results pave the way for developing vaccines, antiviral drugs, and diagnostic systems for this infectious disease.
Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species
Authors: Mikkelsen Else K. , Irwin Darren
Published: February 2021

Contact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren(Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer
Authors: Taavitsainen S , Engedal N , Cao S , Handle F , Erickson A , Prekovic S , Wetterskog D , Tolonen T , Vuorinen EM , Kiviaho A , Nätkin R , Häkkinen T , Devlies W , Henttinen S , Kaarijärvi R , Lahnalampi M , Kaljunen H , Nowakowska K , Syvälä H , Bläuer M , Cremaschi P , Claessens F , Visakorpi T , Tammela TLJ , Murtola T , Granberg KJ , Lamb AD , Ketola K , Mills IG , Attard G , Wang W , Nykter M , Urbanucci A
Published: February 2021

Prostate cancer is profoundly heterogeneous and patients would benefit from methods that stratify clinically indolent from more aggressive forms of the disease. We employed single-cell assay for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identified pre-existing and treatment-persistent cell subpopulations that possess transcriptional stem-like features and regenerative potential when subjected to treatment. We found distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent stem-like cells were able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal hitherto unrecognized molecular predictors of treatment response. This suggests that high analytical resolution of pre-clinical models may powerfully inform clinical decision-making.
Linking Labs: Interconnecting Experimental Environments
Authors: Schultz Tanja , Putze Felix , Fehr Thorsten , Meier Moritz , Mason Celeste , Ahrens Florian , Herrmann Manfred
Published: February 2021

We introduce the concept ofLabLinking: a technology-based interconnection of experimental laboratories across institutions, disciplines, cultures, languages, and time zones - in other wordsexperiments without borders. In particular, we introduce LabLinking levels (LLL), which define the degree of tightness of empirical interconnection between labs. We describe the technological infrastructure in terms of hard- and software required for the respective LLLs and present examples of linked laboratories along with insights about the challenges and benefits. In sum, we argue that linked labs provide a unique platform for a continuous exchange between scientists and experimenters, thereby enabling a time synchronous execution of experiments performed with and by decentralized user and researchers, improving outreach and ease of subject recruitment, allowing to establish new experimental designs and to incorporate a panoply of complementary biosensors, devices, hard- and software solutions.
Transcriptome signature of cell viability predicts drug response and drug interaction for Tuberculosis
Authors: Srinivas Vivek , Ruiz Rene A. , Pan Min , Christinal Immanuel Selva Rupa , Peterson Eliza J.R. , Baliga Nitin S.
Published: February 2021

The treatment of tuberculosis (TB), which kills 1.8 million each year, remains difficult, especially with the emergence of multidrug resistant strains ofMycobacterium tuberculosis(Mtb). While there is an urgent need for new drug regimens to treat TB, the process of drug evaluation is slow and inefficient owing to the slow growth rate of the pathogen, the complexity of performing bacteriologic assays in a high-containment facility, and the context-dependent variability in drug sensitivity of the pathogen. Here, we report the development of “DRonA” and “MLSynergy”, algorithms to perform rapid drug response assays and predict response of Mtb to novel drug combinations. Using a novel transcriptome signature for cell viability, DRonA accurately detects bacterial killing by diverse mechanisms in broth culture, macrophage infection and patient sputum, providing an efficient, and more sensitive alternative to time- and resource-intensive bacteriologic assays. Further, MLSynergy builds on DRonA to predict novel synergistic and antagonistic multi-drug combinations using transcriptomes of Mtb treated with single drugs. Together DRonA and MLSynergy represent a generalizable framework for rapid monitoring of drug effects in host-relevant contexts and accelerate the discovery of efficacious high-order drug combinations.
Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5
Authors: Harris Andrzej , Wagner Manuel , Du Dijun , Raschka Stefanie , Gohlke Holger , Smits Sander H. J. , Luisi Ben F. , Schmitt Lutz
Published: February 2021

Pdr5, a member of the extensive ABC transporter superfamily, is representative of a clinically relevant subgroup involved in pleiotropic drug resistance. Through the coupling of nucleotide hydrolysis with drug efflux, Pdr5 homologues enable pathogenic species to survive in the presence of chemically diverse antifungal agents. Our structural and functional results reveal details of an ATP-driven conformational cycle, which mechanically drives drug translocation through an amphipathic channel, and a clamping switch within a conserved linker loop that acts as a nucleotide sensor. One half of the transporter remains nearly invariant throughout the cycle, while its partner undergoes changes that are transmitted across interdomain interfaces to support a peristaltic motion of the pumped molecule. The efflux model proposed here rationalises the pleiotropic impact of Pdr5 and opens avenues for the development of effective antifungal compounds.
Interspecies activation correlations reveal functional correspondences between marmoset and human brain areas
Authors: Hori Yuki , Cléry Justine C. , Schaeffer David J. , Menon Ravi S. , Everling Stefan
Published: February 2021

The common marmoset has enormous promise as a nonhuman primate model of human brain functions. While resting-state functional magnetic resonance imaging (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. This limitation can be overcome by movie-driven fMRI (md-fMRI), which has become a popular tool for non-invasively mapping the neural patterns generated by rich and naturalistic stimulation. Here, we used md-fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between New World marmoset monkeys and humans. However, while face patches in humans and marmosets were activated by marmoset faces, only human face patches responded to the faces of other animals. Together, the results demonstrate that md-fMRI is a powerful tool for interspecies functional mapping and characterization of higher-order visual functions.
Theforaginggene affects alcohol sensitivity, metabolism and memory inDrosophila
Authors: Oepen Anne S. , Catalano Jamie , Azanchi Reza , Kaun Karla R.
Published: February 2021

The genetic basis of alcohol use disorder (AUD) is complex. Understanding how natural genetic variation contributes to alcohol phenotypes can help identify mechanisms underlying the genetic contribution of AUD. Recently, a single nucleotide polymorphism in the human foraging (for) gene ortholog, Protein Kinase cGMP-Dependent 1 (PRKG1), was found to be associated with stress-induced risk for alcohol abuse. However, the mechanistic role that PRKG1 plays in AUD is not well understood. We use natural variation in theDrosophila forgene to describe how variation of cGMP-dependent protein kinase (PKG) activity modifies ethanol-induced phenotypes. We found that variation inforaffects ethanol-induced increases in locomotion and memory of the appetitive properties of ethanol intoxication. Further, these differences may stem from the ability to metabolize ethanol. Together, this data suggests that natural variation in PKG modulates cue reactivity for alcohol, and thus could influence alcohol cravings by differentially modulating metabolic and behavioral sensitivities to alcohol.
Differential bioactivity of four BMP-family members as function of biomaterial stiffness
Authors: Sales Adrià , Khodr Valia , Machillot Paul , Fourel Laure , Guevara-Garcia Amaris , Migliorini Elisa , Albigès-Rizo Corinne , Picart Catherine
Published: February 2021

Whereas soft biomaterial is not able to induce cell spreading, BMP-2 presented by a soft film has been described to be sufficient to trigger cell spreading, migration and downstream BMP-2 signaling. Based on thin polyelectrolyte films of controlled stiffness, we investigated whether the presentation of four BMP members (2, 4, 7, 9) in a matrix-bound manner may differentially impact cell adhesion and bone differentiation of skeletal progenitors. We performed high content and automated screening of cellular responses, including cell number, cell spreading area, SMAD phosphorylation and alkaline phosphatase activity. The basolateral presentation of the different BMPs allowed us to discriminate the specificity of cellular response and the role of BMP receptors type I, type II, as well as three β integrins, in a BMP type and stiffness-dependent manner.
Prenatal environmental conditions underlie alternative reproductive tactics that drive the formation of a mixed-kin cooperative society
Authors: Shah Shailee S. , Rubenstein Dustin R.
Published: February 2021

Although animal societies often evolve due to limited natal dispersal that results in kin clustering and facilitates cooperation among relatives, many species form cooperative groups with low and variable kin structure. Groups in such mixed-kin societies often comprise residents and immigrants of the same sex that compete for breeding opportunities. To understand how such mixed-kin societies form despite their potential for social conflict, we investigated the environmental causes and subsequent fitness consequences of dispersal decisions in male cooperatively breeding superb starlings (Lamprotornis superbus) that live in a climatically unpredictable environment. We show that the two alternative reproductive tactics—natal dispersal or philopatry—exhibit reproductive tradeoffs resulting in equal lifetime inclusive fitness. The tactic an individual adopts is governed by the environment its parents experience prior to laying rather than the environment it experiences during its juvenile stage. When individuals adopt the tactic not predicted by early life environmental conditions, their fitness is reduced. Ultimately, climate-driven oscillating selection may help stabilize mixed-kin animal societies, despite their reduced kin structure and potential for social conflict.
Characterization and performance evaluation of the XSPA-500k detector using synchrotron radiation
Authors: Nakaye Yasukazu , Sakumura Takuto , Sakuma Yasutaka , Mikusu Satoshi , Dawiec Arkadiusz , Orsini Fabienne , Grybos Pawel , Szczygiel Robert , Maj Piotr , Ferrara Joseph D. , Taguchi Takeyoshi
Published: February 2021

Hybrid photon counting (HPC) detectors are widely used at both synchrotron facilities and in-house laboratories. The features of HPC detectors, such as no readout noise, high dynamic range, high frame rate, excellent point spread function, no blurring etc. along with fast data acquisition, provide a high-performance detector with a low detection limit and high sensitivity. Several HPC detector systems have been developed around the world. A number of them are commercially available and used in academia and industry. One of the important features of an HPC detector is a fast readout speed. Most HPC detectors can easily achieve over 1000 frames s−1, one or two orders of magnitude faster than conventional CCD detectors. Nevertheless, advanced scientific challenges require ever faster detectors in order to study dynamical phenomena in matter. The XSPA-500k detector can achieve 56 kframes s−1 continuously, without dead-time between frames. Using `burst mode', a special mode of the UFXC32k ASIC, the frame rate reaches 1 000 000 frames s−1. XSPA-500k was fully evaluated at the Metrology beamline at Synchrotron SOLEIL (France) and its readout speed was confirmed by tracking the synchrotron bunch time structure. The uniformity of response, modulation transfer function, linearity, energy resolution and other performance metrics were also verified either with fluorescence X-rays illuminating the full area of the detector or with the direct beam.
Improving assessment accountability in initial teacher education programs through benchmarking
Authors: Knaus Marianne June , Kirk Gill , Roberts Pauline , Barblett Lennie , Adkin Bev
Published: February 2021

Purpose

In Australia, political imperatives that drive the Tertiary Education Quality and Standards Agency (TEQSA) and Australian Institute for Teaching and School Leadership (AITSL) call for a new understanding of assessment at the tertiary level. Assessment strategies are under the microscope to provide accountability but are increasingly called to measure a wider set of attributes considered important in equipping graduates to meet 21st century opportunities and challenges. This paper reports on a shared benchmarking exercise between two universities to ensure the current assessment strategies in their undergraduate early childhood programs meet such requirements.

Design/methodology/approach

Data were collected using qualitative methodology and conceptualised using an interpretivist frame that enabled the collaborative groups to socially construct the meaning of assessment and identify what was specific, unique and different across the two programs. A cross-case analysis enabled a robust examination of the data.

Findings

Findings identified key structural and procedural differences between the two benchmarked university programs in terms of cohort size, university policies around assessment points, the use of exams and the choices surrounding professional experience placements.

Practical implications

Implications of the research note the complexity of contextual factors such as university policies on assessment and the impact these have on the quality of assessment.

Originality/value

This paper is unique in that it used the conceptual framework for self-evaluation from TEQSA and followed their six key phases of benchmarking.
Measuring operational efficiency of isolation hospitals during COVID-19 pandemic using data envelopment analysis: a case of Egypt
Authors: Kamel Mahmoud Abdelrahman , Mousa Mohamed El-Sayed
Published: February 2021

Purpose

This study used Data Envelopment Analysis (DEA) to measure and evaluate the operational efficiency of 26 isolation hospitals in Egypt during the COVID-19 pandemic, as well as identifying the most important inputs affecting their efficiency.

Design/methodology/approach

To measure the operational efficiency of isolation hospitals, this paper combined three interrelated methodologies including DEA, sensitivity analysis and Tobit regression, as well as three inputs (number of physicians, number of nurses and number of beds) and three outputs (number of infections, number of recoveries and number of deaths). Available data were analyzed through R v.4.0.1 software to achieve the study purpose.

Findings

Based on DEA analysis, out of 26 isolation hospitals, only 4 were found efficient according to CCR model and 12 out of 26 hospitals achieved efficiency under the BCC model, Tobit regression results confirmed that the number of nurses and the number of beds are common factors impacted the operational efficiency of isolation hospitals, while the number of physicians had no significant effect on efficiency.

Research limitations/implications

The limits of this study related to measuring the operational efficiency of isolation hospitals in Egypt considering the available data for the period from February to August 2020. DEA analysis can also be an important benchmarking tool for measuring the operational efficiency of isolation hospitals, for identifying their ability to utilize and allocate their resources in an optimal manner (Demand vs Capacity Dilemma), which in turn, encountering this pandemic and protect citizens' health.

Originality/value

Despite the intensity of studies that dealt with measuring hospital efficiency, this study to the best of our knowledge is one of the first attempts to measure the efficiency of hospitals in Egypt in times of health' crisis, especially, during the COVID-19 pandemic, to identify the best allocation of resources to achieve the highest level of efficiency during this pandemic.
Emergency management system design for accurate data: a cognitive analytics management approach
Authors: Tarhini Abbas , Balozain Puzant , Srour F.Jordan
Published: February 2021

Purpose

This paper uses a cognitive analytics management approach to analyze, understand and solve the problems facing the implementation of information systems and help management do the needed changes to enhance such a critical process; the emergency management system in the health industry is analyzed as a case study.

Design/methodology/approach

Cognitive analytics management (CAM) framework (Osman and Anouz, 2014) is used. Cognitive process: The right questions are asked to understand the behavior of every process and the flow of its corresponding data; critical data variables were identified, guidelines for identifying data sources were set. Analytics process: Techniques of data analytics were applied to the selected data sets, problems were identified in user–system interaction and in the system design. The analysis process helped the management in the management process to make right decisions for the right change.

Findings

Using the CAM framework, the analysis to the Lebanese Red Cross case study identified system user-behavior problems and also system design problems. It identified cases where distributed subsystems are vulnerable to time keeping errors and helped the management make knowledgeable decisions to overcome major obstacles by implementing several changes related to hardware design, software implementation, human resource training, operational and human-technology changes. CAM is a novel and feasible software engineering approach for handling system failures.

Originality/value

The paper uses CAM framework as an approach to overcome system failures and help management do the needed changes to enhance such a critical process. This work contributes to the software engineering literature by introducing CAM as a new agile methodology to be used when dealing with system failures. Furthermore, this study is an action research that validated the CAM theoretical framework in a health emergency context in Lebanon.
Racial characteristics of areas and police decisions to arrest in traffic stops: multilevel analysis of contextual racial effects
Authors: Zhang Yan , Zhang Lening
Published: February 2021

Purpose

The present study assesses the contextual racial effects on police decisions to arrest in traffic stops.

Design/methodology/approach

A hierarchical logistic regression model is conducted using data collected from the Houston Police Department and US census.

Findings

The authors’ multilevel analysis indicates that the racial effect on police decision to arrest is more likely to be contextual than individual. Black and Hispanic drivers have no significant difference from White drivers in police decisions to arrest when area variations are controlled. In contrast, the concentrations of Blacks and other racial minorities in areas are significantly associated with the chance of being arrested by police in traffic stops. However, as the level of racial diversity increases in an area, the chance of being arrested is likely to decrease.

Originality/value

This study demonstrates the importance of racial characteristics of areas in the study of racial profiling and related police practice.
Thwarted psychological needs: the negative impact of customer mistreatment on service employees and the moderating role of empowerment HRM practices
Authors: Chen Jiuming , Kang Haiying , Wang Ying , Zhou Mingjian
Published: February 2021

Purpose

Drawing on self-determination theory (SDT), this study aims to understand the adverse effects of customer mistreatment on employee performance and well-being by thwarting the satisfaction of employees' basic psychological needs. It also examines how these negative effects may be mitigated by empowerment human resource management (HRM) practices.

Design/methodology/approach

Two studies were conducted using survey data collected in China. In Study 1, cross-sectional data from 321 telemarketing employees were analyzed to examine how customer mistreatment reduces the satisfaction of employees' basic psychological needs, harming job performance and job satisfaction. In Study 2, multiwave, multisource data were collected from 149 property agents and their supervisors to replicate the findings of Study 1 and further test empowerment HRM as a moderator of the relationship between customer mistreatment and satisfaction of needs.

Findings

The results from both studies show that customer mistreatment leads to low job performance and job satisfaction via reduced satisfaction of employees' needs for autonomy and competence but not relatedness. Moreover, the negative effect on the satisfaction of employees' needs for autonomy and competence was buffered when organizations had high empowerment HRM practices in place.

Originality/value

This study provides new insights on customer mistreatment by understanding its effects from a motivational perspective, which has not been considered in prior research. It also explores how HRM practices can help satisfy employee needs in adverse work environments induced by customer mistreatment.
Exposing policy gaps: the experience of Kazakhstan in implementing distance learning during the COVID-19 pandemic
Authors: Bokayev Baurzhan , Torebekova Zulfiya , Abdykalikova Marta , Davletbayeva Zhuldyz
Published: February 2021

Purpose

The purpose of this study is analysing the experince of Kazakhstan in implementing distance/online learning during pandemic. The COVID-19 pandemic has affected all areas of social and economic life, including education. More than 1.3 billion students worldwide have switched to online/distance learning. In Kazakhstan, more than 6 million active participants in the educational process are navigating this online migration. There is significant criticism of the process among the general population, demanding scholarly investigations into the government’s actions.

Design/methodology/approach

This paper examines the re-organization of education in Kazakhstan during the COVID-19 pandemic. Methods to uncover this included an express survey of 31,300 households, in interviews with 65 parents, 15 children, 9 school/college/university administration and teachers and 15 representatives of the Government of Kazakhstan, and in analyses of statistical and regulatory documents.

Findings

This study finds that the government of Kazakhstan has faced significant issues in the transition to distance/online learning due to weak internet infrastructure and a lack of effective interaction with all stakeholders, as well as biased statistical and analytical information.

Originality/value

The pandemic has functioned as a test of government readiness for crisis and has exposed several fault lines where official development policy has been ineffective. While the “gap” between policy and outcome is often attributed to failures in local implementation, the unique factors at play here – an interested citizenry and committed teachers – show that considerably more work has to be put into bringing “best practices” from developed countries to developing ones.
Assessing unintended human‐mediated dispersal using visitation networks
Authors: Runghen Rogini , Bramon Mora Bernat , Godoy‐Lorite Antonia , Stouffer Daniel B.
Published: February 2021

Human visitors are associated with the unintended dispersal of weeds, seeds and pathogens across ecological communities. With the increasing popularity of nature‐based tourism, access to protected areas has increased, in turn increasing the risks of unintended dispersal of exotic species to these areas.

Here, we assess the potential contribution of both international and domestic visitors travelling within New Zealand to the spread of exotic species. To get an overview of the visitors’ travelling patterns across the country, we constructed visitation networks at two spatial scales—a regional scale (which is a coarse scale) and a local territorial scale (which is a finer scale).

We then used a Mixed Membership Stochastic Block Model to identify characteristic groups of visitors and places based on the similarities of the visitors’ travelling patterns across the country. Overall, we found that there are 10 characteristic groups of visitors travelling to 12 characteristic groups of places at the regional scale and 6 characteristic groups of visitors travelling to 6 characteristic groups of places at the territorial scale.

The resulting characteristic travelling patterns of the visitors across New Zealand further allowed us to estimate the different visitor groups’ likelihood to travel to protected areas. Overall, we found that some visitor groups are much more likely than others to travel to protected areas of high protection status, at both spatial scales.

Synthesis and applications. Our results highlight the importance of accounting for human behaviour—that is, understanding how visitors travel to places—when assessing human‐mediated dispersal. More specifically, we illustrate how to assess the relative contribution of a potential vector dispersing exotic species based on their travelling patterns—especially in cases where the target exotic species are not yet identified or when there is limited information regarding the dispersal routes of exotic species and their potential vectors. As a result, our work offers a holistic perspective on human‐mediated dispersal of exotic species. Moreover, it provides a potential baseline against which both field biologists and practitioners can identify areas that would benefit from further investigation to better understand invasion processes in their focal systems.
Phytic acid and its interactions: Contributions to protein functionality, food processing, and safety
Authors: Wang Ruican , Guo Shuntang
Published: February 2021

Is phytic acid (IP6) an undesirable constituent for vegetables and foods? This question is getting harder to answer. Phytic acid contributes to mineral/protein deficiency, but also brings about potential physiological benefits. Both the positive and negative effects boil down to the interactions among IP6, metal ions, and biopolymers. In the wake of the booming market of plant‐based foods, an unbiased understanding of these interactions and their impacts on the foods themselves is a necessity to the smart control and utilization of plant‐sourced phytates. This overview presents updated knowledge of IP6‐related interactions, with a strong focus on their contributions to food functionality, processability, and safety.
Preparation and antioxidant activity of selenium nanoparticles decorated by polysaccharides from Sargassum fusiforme
Authors: Wang Tian , Zhao Hongying , Bi Yongguang , Fan Xiaodan
Published: February 2021

In this study, the response surface method was employed to optimize the extraction conditions of the ultrasonic‐assisted extraction of Sargassum fusiforme polysaccharides (SFPS). The effects of four independent variables (hot water extraction time, ultrasonic time, ultrasonic power, and material‐to‐liquid ratio) on the extraction rate of SFPS were tested. In addition, the SFPS functionalized nanoselenium (SFPS‐SeNPs) was prepared by chemical reduction method, whose characterization and in vitro antioxidant activity were investigated. The results showed that the yield of the crude SFPS was 25.8% at the optimal conditions of material‐to‐liquid ratio 1:50 (w/v), ultrasonic power 200 W, ultrasonic time 15 min, and water bath time 130 min. A series of characterization experiments showed that the SFPS‐SeNPs performed higher dispersion and stability than naked SeNPs. Furthermore, the in vitro antioxidant activity assay indicated that SFPS functioned as a modifier improved the free radical scavenging activity of SeNPs significantly. In conclusion, this study provided a method to extract SFPS as a carrier for SeNPs, and SFPS‐SeNPs could not only improve the stability of SeNPs, but also exerted the biological activities of SFPS.

Practical Application

This research provided new ideas for the application of SFPS and the development of nanoselenium preparation carriers.