bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulatory signatures of drought response in stress resilientSorghum bicolor
Authors: Parvathaneni Rajiv K. , Kumar Indrajit , Braud Max , Ozersky Philip , Mockler Todd C. , Eveland Andrea L.
Published: August 2020

The effects of drought stress can be devastating to crop production worldwide. A grand challenge facing agriculture is development of crop varieties with improved drought resilience through breeding or biotechnology. To accelerate this, a mechanistic understanding is needed of the regulatory networks underlying drought response in crop genomes and the genetic elements that modulate them. Here, we explore the regulatory landscape of sorghum [Sorghum bicolor(L.) Moench] in response to controlled-environment drought stress. Sorghum is a C4cereal crop with innate drought resilience. To define molecular signatures of drought response, we mapped genome-wide chromatin accessibility using an Assay for Transposase Accessible Chromatin by sequencing and analyzed parallel transcriptional profiles in drought-stressed sorghum shoot and root tissues. Drought-responsive changes in accessibility were largely in proximal promoters of differentially expressed genes and also in distal regions. Data were integrated to infer gene network connections andcis-regulatory modules underlying drought response and the transcription factors that control them. Inspection of pan-genomic data and phenotyping across sorghum diversity revealed variation in genomic signatures that associated with water use efficiency. Our analyses provide drought-inducible regulatory modules in sorghum that can be leveraged for fine-tuning responses to stress, mining for advantageous alleles, and translating across species.
The Rcs stress response system modulatesSerratia marcescensinduced inflammation and bacterial proliferation in a rabbit keratitis model
Authors: Romanowski Eric G. , Stella Nicholas A. , Romanowski John , Yates Kathleen A. , Dhaliwal Deepinder K. , Shanks Robert M. Q.
Published: August 2020

In this study, we tested the hypothesis that the conserved bacterial Rcs stress response system mediates corneal pathogenesis associated withSerratia marcescensocular infections. This was accomplished by modifying Rcs activity using mutant strains. These include a mutant that has a hyper-active Rcs system due to deletion of the IgaA family gene,gumB, and agumB rcsCdouble mutant that is defective for Rcs signaling. The role of the Rcs system and bacterial stress response systems for microbial keratitis is not known. Here we observed that the Rcs-activatedgumBmutant had a >50-fold reduction in proliferation compared to the wild type within rabbit corneas at 48 h, and demonstrated a notable reduction in inflammation based on inflammatory signs and proinflammatory markers measured at the RNA and protein levels. ThegumBmutant phenotypes could be complemented by wild-typegumBon a plasmid and partially complemented by restoration ofshlAcytolysin expression and elimination of capsular polysaccharide production. We observed that inactivation of the Rcs stress response system completely restored corneal virulence to thegumBmutant. NanoString transcriptional analysis of bacterial genes expressed during microbial keratitis demonstrated expression ofgumB, rcsB, shlA, and three metalloprotease genes. Data suggest that the bacterial capsular polysaccharide is not necessary for infection, but capsule overexpression reduces inflammation. Together, these data indicate that GumB regulates virulence factor production through the Rcs system and this overall stress response system is a key mediator of a bacterium’s ability to induce vision-threatening keratitis.
RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis
Authors: Zhang Tongchuan , Singh Jaswinder , Litfin Thomas , Zhan Jian , Paliwal Kuldip , Zhou Yaoqi
Published: August 2020

Motivation

The accuracy of RNA secondary and tertiary structure prediction can be significantly improved by using structural restraints derived from evolutionary or direct coupling analysis. Currently, these coupling analyses relied on manually curated multiple sequence alignments collected in the Rfam database, which contains 3016 families. By comparison, millions of non-coding RNA sequences are known. Here, we established RNAcmap, a fully automatic method that enables evolutionary coupling analysis for any RNA sequences. The homology search was based on the covariance model built by Infernal according to two secondary structure predictors: a folding-based algorithm RNAfold and the latest deep-learning method SPOT-RNA.

Results

We show that the performance of RNAcmap is less dependent on the specific evolutionary coupling tool but is more dependent on the accuracy of secondary structure predictor with the best performance given by RNAcmap (SPOT-RNA). The performance of RNAcmap (SPOT-RNA) is comparable to that based on Rfam-supplied alignment and consistent for those sequences that are not in Rfam collections. Further improvement can be made with a simple meta predictor RNAcmap (SPOT-RNA/RNAfold) depending on which secondary structure predictor can find more homologous sequences. Reliable base-pairing information generated from RNAcmap, for RNAs with high effective homologous sequences, in particular, will be useful for aiding RNA structure prediction.

Availability and implementation

RNAcmap is available as a web server athttps://sparks-lab.org/server/rnacmap/) and as a standalone application along with the datasets athttps://github.com/sparks-lab-org/RNAcmap.
ATP-responsive biomolecular condensates tune bacterial kinase signaling
Authors: Saurabh Saumya , Chong Trisha N. , Bayas Camille , Dahlberg Peter D. , Cartwright Heather N. , Moerner W. E. , Shapiro Lucy
Published: August 2020

Biomolecular condensates formed via phase separation enable spatial and temporal organization of enzyme activity. The emergent properties of many condensates have been shown to be responsive to intracellular Adenosine triphosphate (ATP) levels, although the consequences of such mechanisms on enzyme activity are unknown. Here, we show that ATP depletion promotes phase separation in condensates composed of a disordered protein, thereby enhancing the activity of a client kinase enabling robust signaling and maintenance of viability under the stress posed by nutrient scarcity. We propose that a diverse repertoire of condensates can serve as control knobs to tune multivalency and reactivity in response to the metabolic state of bacterial cells.

One Sentence Summary

Bacterial condensates boost kinase activity under ATP depletion
Zbtb16regulates social cognitive behaviors and neocortical development
Authors: Usui Noriyoshi , Berto Stefano , Konishi Ami , Kondo Makoto , Konopka Genevieve , Matsuzaki Hideo , Shimada Shoichi
Published: August 2020

Recent genetic studies have underscored the pleiotropic effects of single genes to multiple cognitive disorders. Mutations ofZBTB16are associated with autism spectrum disorder (ASD) and schizophrenia (SCZ), but how the function of ZBTB16 is related to ASD or SCZ remains unknown. Here we show the deletion ofZbtb16in mice leads to both ASD- and SCZ-like behaviors such as social impairment, repetitive behaviors, risk-taking behaviors, and cognitive impairment. To elucidate the mechanism underlying the behavioral phenotypes, we carried out histological studies and observed impairments in thinning of neocortical layer 6 (L6) and a reduction of TBR1+ neurons in the prefrontal cortex (PFC) ofZbtb16KO mice. Furthermore, we found increased dendritic spines and microglia as well as developmental defects in oligodendrocytes and neocortical myelination in the PFC ofZbtb16KO mice. Using a genomics approach, we identified theZbtb16-transcriptome that includes genes involved in both ASD and SCZ pathophysiology and neocortical maturation such as neurogenesis and myelination. Co-expression networks further identifiedZbtb16-correlated modules that are unique to ASD or SCZ respectively. Our study provides insight into the differential role ofZBTB16in ASD and SCZ.
Emergent properties of a mitotic Kif18b-MCAK-EB network
Authors: McHugh Toni , Welburn Julie P.I.
Published: August 2020

The precise regulation of microtubule length during mitosis is essential to assemble and position the mitotic spindle and segregate chromosomes. Prior work has identified key molecular players in this process, including the kinesin-18 Kif18b and the kinesin-13 Kif2C/MCAK, which both promote microtubule depolymerization. MCAK acts as a potent microtubule depolymerase diffusing short distances on microtubules, while Kif18b is a mitotic processive motor with weak depolymerase activity. However the individual activities of these factors cannot explain the dramatic increase in microtubule dynamics in mitosis. Usingin vitroreconstitution and single molecule imaging, we demonstrate that Kif18b, MCAK and the plus-end tracking protein EB3 act in an integrated manner to potently promote microtubule depolymerization. We find Kif18b acts as a microtubule plus end delivery factor for its cargo MCAK, and that Kif18b also promotes EB accumulation to plus ends independently of lattice nucleotide state. Together, our work defines the mechanistic basis for a cooperative Kif18b-EB-MCAK network with emergent properties, that acts to efficiently shorten microtubules in mitosis.
Chloroform-injection (CI) and Spontaneous-phase-transition (SPT) are Novel Methods, Simplifying the Fabrication Liposomes
Authors: Khan Muhammad Ijaz , Ahmed Naveed , Umer Muhammad Farooq , Riaz Amina , Ahmad Nasir Mehmood , Khan Gul Majid
Published: August 2020

Intricate formulation methods and/or use of sophisticated equipment limit the prevalence of liposomal dosage-forms. Simple techniques are developed to assemble amphiphiles into globular lamellae while transiting from immiscible organic to the aqueous phase. Various parameters are optimized by injecting chloroform solution of amphiphiles into the aqueous phase and subsequent removal of the organic phase. Further simplification is achieved by reorienting amphiphiles through a spontaneous phase transition in a swirling biphasic system during evaporation of the organic phase under vacuum. Although the chloroform injection yields smaller size and PDI yet spontaneous phase transition method overrides simplicity and productivity. The size distribution of liposomes and solid/solvent ratio in both or any phases of formulation show direct relation. Surface charge dependant large unilamellar vesicles with a narrow distribution have PDI <0.4 in 10 μM saline. As small and monodisperse liposomes are prerequisites in targeted drug delivery strategies. Hence the desired size distribution <200 d.nm and PDI <0.15 is obtained through serial membrane-filtration method. Phosphatidylcholine/water 4 μmol/ml is achieved at a temperature of 10°C below the phase-transition temperature of phospholipids ensuing suitability for thermolabile entities and high entrapment efficiency. Both methods furnish the de-novo rearrangement of amphophiles into globular lamellae aiding in the larger entrapped volume. The immiscible organic phase facilitates faster and complete removable of the organic phase. High cholesterol content (55.6 mol%) imparts stability in primary hydration medium at 5+3°C for 6 months in light-protected type-1 glass vial. Collectively the reported methods are novel, scalable, time-efficient yielding high productivity in simple equipment.
Anti-diabetic Potential of Aqueous Extract ofMoringa oleifera, Ocimum gratissimumandVernonia amygdalinain Alloxan-Induced Diabetic Rats
Authors: Ayobami A. L. , Kade E. A. , Oladimeji K. A. , Kehinde S. , Gurpreet K.
Published: August 2020

The incidence of diabetes mellitus (DM) is increasing globally and it is a major source of concern. This study was undertaken to assess the antidiabetic effect of the aqueous extract of Moringa oleifera, Ocimum gratissimum and Vernonia amygdalina. Sixty adult Wistar rats with body weight of 120-150 g were randomly assigned to groups of five rats each (n=12). Groups 1 served as normal control; Groups 2-5 were diabetic groups; group 2 served as negative control; group 3-5 received 100, 200 and 400 mg/kg of triherbal formula respectively. The body weight (BW) and fasting blood glucose level (FBSL) of the rats were monitored weekly. At the end of the experiment, all the rats were anaesthetized intraperitoneally (I.P) and blood samples were collected by cardiac puncture for biochemical analysis. There was an increase in the BW of the control group and varying doses of tri-herbal formation. It caused 88.0% decrease in FBSL; 371.7%, 386.6% and 296.0% with respect to 100, 200 and 400 mg/kg. Sub-chronic study of the effect of the extract showed a significant increase (P<0.05) in packed cell volume (PCV), white blood counts in rat induced diabetes. The histological studies showed that the diabetic rats with the architecture of the pancreas distorted, was restored to normal by the extract. Its LD50 was found to be greater than 1000 mg/kg indicating its safety in rats. This study has shown that triherbal formula has hypoglycemic and haematogical effects.
Diversity and biogeography of Woesearchaeota: A comprehensive analysis of multi-environment data
Authors: Xiao Jing , Zhang Yu , Chen Wanning , Xu Yanbing , Zhao Rui , Tao Liwen , Wu Yuanqi , Zhang Yida , Xiao Xiang , Zhu Ruixin
Published: August 2020

Woesearchaeota is a newly proposed archaeal phylum frequently detected in various environments. Due to the limited systematical study, little is known about their distribution, taxonomy, and metabolism. Here, we conducted a comprehensive study for Woesearchaeota with 16S ribosomal RNA (rRNA) gene sequencing data of 27,709 samples and metagenomic whole genome sequencing (WGS) data of 1,266 samples. We find that apart from free-living environments, Woesearchaeota also widely distribute in host-associated environments. And host-associated environmental parameters greatly affect their distribution. 81 Woesearchaeota genomes, including 33 genomes firstly reconstructed in this project, were assigned to 59 Woesearchaeota species, suggesting their high taxonomic diversity. Comparative analysis indicated that Woesearchaeota have an open pan-genome with small core genome. Metabolic reconstruction showed that particular metabolic pathway absence in specific environments, demonstrated the metabolic diversity of Woesearchaeota varies in differences environments. These results have placed host-associated environments into the global biogeography of Woesearchaeota and have demonstrated their genomic diversity for future investigation of adaptive evolution.
Identification of QTLs for dynamic and steady state photosynthetic traits in a barley mapping population
Authors: Salter William T. , Li Si , Dracatos Peter M. , Barbour Margaret M.
Published: August 2020

Enhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programs, with the potential to substantially increase whole canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we phenotypically assessed the rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min−1in the slowest genotype and 0.74 min−1in the fastest genotype. A QTL for rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for rubisco activation ratein plantaand the discovery opens the door to marker assisted breeding to improve whole canopy photosynthesis of barley. Further strength is given to this finding as this QTL colocalised with QTLs identified for steady state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts.

Highlight

Significant variation exists in the photosynthetic induction response after a switch from moderate to saturating light across a barley doubled haploid population. A QTL for rubisco activation rate was identified on chromosome 7H, as well as overlapping QTLs for steady state photosynthesis and stomatal conductance.
Neonatal LPS exposure reduces ATP8A2 level in the prefrontal cortex in mice via increasing IFN-γ level
Authors: Deng Jiapeng , Song Linyang , Yang Zhiqin , Zheng Sixie , Du Zhuolin , Luo Li , Liu Jing , Jin Xiaobao , Yang Junhua
Published: August 2020

Neonatal lipopolysaccharide (LPS) exposure can cause depressive-like behaviors in rodents involving elevated interferon (IFN)-γ. Studies have linked down-regulation of prefrontal cortex (PFC) ATPase phospholipid transporting 8A2(ATP8A2) expression to depressive-like behaviors. In non-neuronal cells, IFN-γ could reduce ATP8A2 expression. We therefore hypothesized that neonatal LPS exposure might induce PFC ATP8A2 down-regulation by increasing IFN-γ level. Here, C57BL6/J mice of both sexes received 3-dose-injections of LPS (50μg/kg bodyweight, i.p.) on postnatal day (PND)5, PND7 and PND9. LPS-treated mice showed a transiently decreased PFC ATP8A2 expression. Moreover, a negative correlation of PFC ATP8A2 expression was found with IFN-γ level. Using neutralizing mAb, IFN-γ was identified as the key mediator of LPS-induced PFC ATP8A2 decrease. Besides, neutralizing IFN-γ during neonatal LPS exposure attenuated the depressive-like behaviors in adulthood. In sum, neonatal LPS exposure reduced ATP8A2 level in PFC in mice via increasing IFN-γ level, maybe associated with mechanism underlying LPS-induced brain and behavior impairments.
A simple Ca2+-imaging approach to neural network analysis in cultured neurons
Authors: Sun Zijun , Südhof Thomas C.
Published: August 2020

Background

Ca2+-imaging is a powerful tool to measure neuronal dynamics and network activity. To monitor network-level changes in cultured neurons, neuronal activity is often evoked by electrical or optogenetic stimulation and assessed using multi-electrode arrays or sophisticated imaging. Although such approaches allow detailed network analyses, multi-electrode arrays lack single-cell precision, whereas optical physiology generally requires advanced instrumentation.

New Method

Here we developed a simple, stimulation-free protocol with associated Matlab algorithms that enables scalable analyses of network activity in cultured human and mouse neurons. The approach allows analysis of overall networks and single-neuron dynamics, and is amenable to scale-up for screening purposes.

Results

We validated the protocol by assessing human neurons with a heterozygous conditional deletion of Munc18-1, and mouse neurons with a homozygous conditional deletion of neurexins. The approach described here enabled identification of differential changes in these mutant neurons at the network level and of the amplitude and frequency of calcium peaks at the single-neuron level. These results demonstrate the utility of the approach.

Comparison with existing method

Compared with current imaging platforms, our method is simple, scalable, and easy to implement. It enables quantification of more detailed parameters than multi-electrode arrays, but does not have the resolution and depth of more sophisticated yet labour-intensive analysis methods, such as electrophysiology.

Conclusion

This method is scalable for a rapid assessment of neuronal function in culture, and can be applied to both human and mouse neurons. Thus, the method can serve as a basis for phenotypical analysis of mutations and for drug discovery efforts.
Adult-born neurons promote cognitive flexibility by improving memory precision and indexing
Authors: Berdugo-Vega Gabriel , Lee Chi-Chieh , Garthe Alexander , Kempermann Gerd , Calegari Federico
Published: August 2020

The dentate gyrus (DG) of the hippocampus is fundamental for cognitive flexibility and has the extraordinary ability to generate new neurons throughout life. Recent evidence suggested that adult-born neurons differentially modulate input to the DG during the processing of spatial information and novelty. However, how this differential regulation by neurogenesis is translated into different aspects contributing cognitive flexibility is unclear. Here, we increased adult-born neurons by a genetic expansion of neural stem cells and studied their influence during navigational learning. We found that increased neurogenesis improved memory precision, indexing and retention and that each of these gains was associated with a differential activation of specific DG compartments and better separation of memory representations in the DG-CA3 network. Our results highlight the role of adult-born neurons in promoting memory precision in the infrapyramidal and indexing in the suprapyramidal blade of the DG and together contributing to cognitive flexibility.

One sentence summary

Neurogenesis improves memory precision and indexing.
Ecological theory predicts ecosystem stressor interactions in freshwater ecosystems, but highlights the strengths and weaknesses of the additive null model
Authors: Burgess Benjamin J. , Purves Drew , Mace Georgina , Murrell David J.
Published: August 2020

Understanding and predicting how multiple co-occurring environmental stressors combine to affect biodiversity and ecosystem services is an on-going grand challenge for ecology. So far progress has been made through accumulating large numbers of smaller-scale individual studies that are then investigated by meta-analyses to look for general patterns. In particular there has been an interest in checking for so-called ecological surprises where stressors interact in a synergistic manner. Recent reviews suggest that such synergisms do not dominate, but few other generalities have emerged. This lack of general prediction and understanding may be due in part to a dearth of ecological theory that can generate clear hypotheses and predictions to tested against empirical data. Here we close this gap by analysing food web models based upon classical ecological theory and comparing their predictions to a large (546 interactions) dataset for the effects of pairs of stressors on freshwater communities, using trophic- and population-level metrics of abundance, density, and biomass as responses. We find excellent overall agreement between the stochastic version of our models and the experimental data, and both conclude additive stressor interactions are the most frequent, but that meta-analyses report antagonistic summary interaction classes. Additionally, we show that the statistical tests used to classify the interactions are very sensitive to sampling variation. It is therefore likely that current weak sampling and low sample sizes are masking many non-additive stressor interactions, which our theory predicts to dominate when sampling variation is removed. This leads us to suspect ecological surprises may be more common than currently reported. Our results highlight the value of developing theory in tandem with empirical tests, and the need to examine the robustness of statistical machinery, especially the widely-used null models, before we can draw strong conclusions about how environmental drivers combine.
The MRC IEU OpenGWAS data infrastructure
Authors: Elsworth Ben , Lyon Matthew , Alexander Tessa , Liu Yi , Matthews Peter , Hallett Jon , Bates Phil , Palmer Tom , Haberland Valeriia , Smith George Davey , Zheng Jie , Haycock Philip , Gaunt Tom R , Hemani Gibran
Published: August 2020

Data generated by genome-wide association studies (GWAS) are growing fast with the linkage of biobank samples to health records, and expanding capture of high-dimensional molecular phenotypes. However the utility of these efforts can only be fully realised if their complete results are collected from their heterogeneous sources and formats, harmonised and made programmatically accessible.

Here we present the OpenGWAS database, an open source, open access, scalable and high-performance cloud-based data infrastructure that imports and publishes complete GWAS summary datasets and metadata for the scientific community. Our import pipeline harmonises these datasets against dbSNP and the human genome reference sequence, generates summary reports and standardises the format of results and metadata. Users can access the data via a website, an application programming interface, R and Python packages, and also as downloadable files that can be rapidly queried in high performance computing environments.

OpenGWAS currently contains 126 billion genetic associations from 14,582 complete GWAS datasets representing a range of different human phenotypes and disease outcomes across different populations. We developed R and Python packages to serve as conduits between these GWAS data sources and a range of available analytical tools, enabling Mendelian randomization, genetic colocalisation analysis, fine mapping, genetic correlation and locus visualisation.

OpenGWAS is freely accessible athttps://gwas.mrcieu.ac.uk, and has been designed to facilitate integration with third party analytical tools.
Oculomotor Target Selection is Cortically Mediated by Complex Objects
Authors: Kehoe Devin H. , Lewis Jennifer , Fallah Mazyar
Published: August 2020

Successful oculomotor target selection often requires discriminating visual features but it remains contentious whether oculomotor substrates encoding saccade vectors functionally contribute to this process. One possibility is that visual features are discriminated cortically and oculomotor modules select the object with the highest activation in the set of all preprocessed cortical object representations, while an alternative possibility is that oculomotor modules actively discriminate potential targets based on visual features. If the latter view is correct, these modules should not require input from specialized visual cortices encoding the task relevant features. We therefore examined whether the latency of visual onset responses elicited by abrupt distractor onsets is consistent with input from specialized visual cortices by non-invasively measuring human saccade metrics (saccade curvature, endpoint deviations, saccade frequency, error proportion) as a function of distractor processing time for novel, visually complex distractors that had to be discriminated from a target to guide saccades. Visual onset response latencies were ~110 ms, consistent with projections from anterior cortical sites specialized for object processing. Surprisingly, oculomotor visual onset responses encoded features, as we manipulated the visual similarity between targets and distractors and observed an increased visual onset response magnitude and duration when the distractor was highly similar to the target, which was not attributable to an inhibitory processing delay. Visual onset responses were dynamically modulated by executive function, as these responses were anticipatorily extinguished over the time course of the experiment. As expected, the latency of distractor-related inhibition was modulated by the behavioral relevance of the distractor.

Significance Statement

We provide novel insights into the role of the oculomotor system in saccadic target selection by challenging the convention that neural substrates that encode oculomotor vectors functionally contribute to target discrimination. Our data show that the oculomotor system selects a winner from amongst the preprocessed object representations output from specialized visual cortices as supposed to discriminating visual features locally. We also challenge the convention that oculomotor visual onset responses are feature-invariant, as they encoded task-relevance.
A comprehensive transcriptome signature of murine hematopoietic stem cell aging
Authors: Svendsen Arthur Flohr , Yang Daozheng , Kim KyungMok , Lazare Seka , Skinder Natalia , Zwart Erik , Mura-Meszaros Anna , Ausema Albertina , von Eyss Björn , de Haan Gerald , Bystrykh Leonid
Published: August 2020

We surveyed 16 published and unpublished data sets to determine whether a consistent pattern of transcriptional deregulation in aging murine hematopoietic stem cells (HSC) exists. Despite substantial heterogeneity between individual studies, we uncovered a core and robust HSC aging signature. We detected increased transcriptional activation in aged HSCs, further confirmed by chromatin accessibility analysis. Unexpectedly, using two independent computational approaches, we established that deregulated aging genes consist largely of membrane-associated transcripts, including many cell surface molecules previously not associated with HSC biology. We show thatSelp, the most consistent deregulated gene, is not merely a marker for aged HSCs but is associated with HSC functional decline. Additionally, single-cell transcriptomics analysis revealed increased heterogeneity of the aged HSC pool. We identify the presence of transcriptionally “young-like” HSCs in aged bone marrow. We share our results as an online resource and demonstrate its utility by confirming that exposure to sympathomimetics, and deletion of Dnmt3a/b, molecularly resembles HSC rejuvenation or aging, respectively.

Key Points

A comprehensive transcriptome analysis of aged murine hematopoietic stem cells identifies an aging signature;

The HSC aging signature is highly enriched for cell membrane-related transcripts and identifies age-associated heterogeneity.
Synthesis, structural characterization, and electronic structure of the novel Zintl phase Ba2ZnP2
Authors: Balvanz Adam , Baranets Sviatoslav , Bobev Svilen
Published: August 2020

The novel Zintl phase dibarium zinc diphosphide (Ba2ZnP2) was synthesized for the first time. This was accomplished using the Pb flux technique, which allowed for the growth of crystals of adequate size for structural determination via single-crystal X-ray diffraction methods. The Ba2ZnP2 compound was determined to crystallize in a body-centered orthorhombic space group, Ibam (No. 72). Formally, this crystallographic arrangement belongs to the K2SiP2 structure type. Therefore, the structure can be best described as infinite [ZnP2]4− polyanionic chains with divalent Ba2+ cations located between the chains. All valence electrons are partitioned, which conforms to the Zintl–Klemm concept and suggests that Ba2ZnP2 is a valence-precise composition. The electronic band structure of this new compound, computed with the aid of the TB–LMTO–ASA code, shows that Ba2ZnP2 is an intrinsic semiconductor with a band gap of ca 0.6 eV.
Chinese consumers' perceptions of food safety cues and maximising the effectiveness of food safety communications
Authors: Mirosa Miranda , Liu Yang , Bremer Phil
Published: August 2020

Purpose

Food safety is an issue of key concern for Chinese consumers. This study identifies intrinsic and extrinsic cues on product labels or websites that Chinese consumers use to assess a product's perceived safety.

Design/methodology/approach

Five structured focus groups (total participants n = 41) were run in Suzhou China, in Chinese, to gather consumers' perceptions towards food safety cues.

Findings

A total of 18 safety cues were identified during the focus group discussions. Certifications, country of origin, production date and shelf life, ingredients and materials and nutritional information were the five safety cues consumers perceived to be the most important. The risks perceived by consumers differed based on: product category (e.g. meat, dairy, cereal); product form (e.g. fresh, chilled, frozen) and degree of processing. Interestingly, consumers used different food safety cues to assess a packaged product compared to the product shown on a website.

Research limitations/implications

While providing deep qualitative insights into perceptions of food safety cues, further studies which seek to conduct quantitative work within a wider demographic context are encouraged.

Practical implications

This information will help to provide best practice advice for international marketers and government risk communicators on how and where to communicate the safety of food products so that they can maximise the effectiveness of their messaging within the appropriate information channels and thereby ensure that it resonates well with Chinese consumers.

Originality/value

This study contributes to the academic knowledge of consumer perceptions of cues related to food safety.
Role of reciprocity in firms' open source strategies
Authors: Yu Yiqing
Published: August 2020

Purpose

Interorganizational reciprocity plays a key role in relationships among software firms and open source communities. This study seeks to illuminate how a firm's open source strategy, characterized by its participation in the open source community, contributes to its financial performance.

Design/methodology/approach

Based on the norm of reciprocity and social capital theory, the study proposes a model comprising the behavioral antecedents and business results of a firm's symbiotic relationship with the open source community. Data were collected through a survey. Partial least squares-based structural equation modeling (PLS-SEM) was used to assess the results.

Findings

A firm's participative behaviors can have three dimensions: technology giving, technology taking and social participation. Technology taking directly impacts financial performance, whereas the effects of technology giving and social participation on financial performance are fully mediated by the firm's symbiotic relationship with the open source community.

Practical implications

Managers can understand how a specific behavior ultimately contributes to a symbiotic relationship or a firm's financial performance and how to flexibly align participation strategies with the business orientation.

Originality/value

The study adds to the open source literature by refining and enriching the conceptual domain of a firm's participative behaviors in open source communities. It also reveals how contrasting behavioral strategies impact a firm's financial performance.
Rivigo
Authors: Raghuram G. , Sanghani Pooja
Published: August 2020

Rivigo, a new entrant in the trucking business in India, believed that a new paradigm in the trucking/logistics industry could be brought about that would not only improve the quality of service dramatically, but also upgrade a truck driver's lifestyle. While the industry faced driver shortage largely due to long stays away from home, Rivigo hoped to attract drivers by offering them roles which would bring them back home in 24 hours. Drivers would be part of a relay, handing over the truck at pit stops. Further, they leveraged an IT-enabled IoT platform on a fleet of owned trucks. All this revolutionized most of the traditions then followed in the industry. The entrepreneur and his core team comprised professionals from premium institutes of the country, with experience in professional organizations in related domains. By offering services like assured delivery at half the time and full shipment visibility, Rivigo had to charge a premium to market segments that would value this. The case raises the question of sustainability in the future.
The Airport Authority of India Case: Public Corporations and the Fundamental Rights
Authors: Pathak Akhileshwar
Published: August 2020

The Fundamental Rights, guaranteed by the Constitution of India, are very substantive rights. The rights, however, are available only against the State as defined in Article 12 of the Constitution. The definition of State includes the Union and States' legislatures and executive. The meaning of these terms is clear and definite. The last entry in the definition is Other Authorities. This term has been subject to judicial interpretations. The Airport Authority of India Case was a landmark judgement expanding the scope of Other Authorities. It formulated that a public corporation, which was an instrumentality or agency of the government, should be considered as Other Authority.
Formation of Contracts: Gibson v. Manchester City Council
Authors: Pathak Akhileshwar
Published: August 2020

Business contracts are formed through negotiations, where the parties agree on some terms, disagree on others and keep yet others undecided. Over a period of time, they see themselves as having moved from being negotiating parties to contracting parties, settling on most of the terms. The law, however, states that a contract is formed when a person makes an offer and the other accepts it. The principle arose from the rudimentary trade practices in the past. The principles coming from the prior centuries and the modern business practices may not be in consonance. The Gibson v. Manchester City Council Case, a judgement of the House of Lords of the United Kingdom, reviewed attempts to modernize the law.
GMR KUAEL: The Longest Road PPP
Authors: Raghuram G. , Udayakumar Prashanth D.
Published: August 2020

GMR Infrastructure Limited (GMRIL) had to make a decision on its continued role in the 555.48 km Kishangarh Udaipur Ahmedabad (KUA) Expressway Project, India's then longest road public-private partnership (PPP) project. GMR had terminated the contract citing NHAI's failure in fulfilling Conditions Precedent (CP) of providing (i) environment clearance (EC), (ii) revised toll free notification and (iii) 80% of required land. The case intends to educate the reader on the concessionaire-authority dynamics in typical Indian infrastructure PPPs. Taking into account its internal strategy, the extant unfavourable investment climate, the Central Government's steps to revive private interest in the highways sector and NHAI's quick turnaround in fulfilling CP, GMR had to decide how to respond.
A user-friendly method for constructing realistic dental model based on two-dimensional/three-dimensional registration
Authors: Ke Yongzhen , Zhao Wenjie , Yang Shuai , Wang Kai , Liu Jiaying
Published: August 2020

Purpose

This paper aims to obtain a texture dental model with real images and improve the rendering effect of the dental model.

Design/methodology/approach

The paper proposes a semiautomatic method to construct a realistic dental model with real images based on two-dimensional/three-dimensional (2D/3D) registration. First, a 3D digital dental model and three intraoral images are obtained by a 3D scanner and digital single-lens reflex camera. Second, the camera projection poses for every intraoral images are calculated by using the single-objective optimization algorithm. Third, with camera poses, the preliminary projection texture mapping is performed; besides, the seam between two textures is marked. Finally, the marked regions are fused based on the image pyramid to eliminate obvious seams.

Findings

The paper provides a method to construct a realistic dental model. The method can map three intraoral images to the dental model. The experimental results show that the textured dental model without obvious distortion, dislocation and seams is constructed with simple interactions.

Originality/value

The proposed method can be applied to the digital smile design system to improve the communication efficiency between doctors, patients and technicians.
Revolutionising cost structure for integrated project delivery: a BIM-based solution
Authors: Elghaish Faris , Abrishami Sepehr , Hosseini M. Reza , Abu-Samra Soliman
Published: August 2020

Purpose

The amalgamation of integrated project delivery (IPD) and building information modelling (BIM) is highly recommended for successful project delivery. However, IPD lacks an accurate cost estimation methodology at the “front-end” of projects, when little project information is available. This study aims to tackle this issue, through presenting analytical aspects, theoretical grounds and practical steps/procedures for integrating target value design (TVD), activity-based costing (ABC) and Monte Carlo simulation into the IPD cost structure, within a BIM-enabled platform.

Design/methodology/approach

A critical review was conducted to study the status of cost estimation within IPD, as well as exploring methods and tools that can enhance the cost estimation process for IPD. Thereafter, a framework is developed to present the proposed methodology of cost estimation for IPD throughout its entire stages. A case project is used to validate the practicality of the developed solution through comparing the profit-at-risk percentage for each party, using both traditional cost estimation and the proposed solution.

Findings

After applying the proposed IPD's cost estimation framework, on a real-life case project, the findings demonstrated significant deviations in the profit-at-risk value for various work packages of the project (approximately 100% of the finishing package and 22% of openings package). By providing a precise allocation of overhead costs, the solution can be used in real-life projects to change the entire IPD cost structure and ensure a fair sharing of risk–rewards among the involved parties in IPD projects.

Practical implications

Using the proposed methodology of cost estimation for IPD can enhance the relationship among IPD's core team members; all revealed financial deficiencies will be considered (i.e. compensation structure, profit pooling), hence enhancing the IPD performance.

Originality/value

This paper presents a comprehensive solution for integrating BIM and IPD in terms of cost estimation, offering three main contributions: (1) an innovate approach to utilise five-dimensional (5D) BIM capabilities with Monte Carlo simulation, hence providing reliable cost estimating during the conceptual TVD stage; (2) mathematical models that are developed through integrating ABC into the detailed 5D BIM to determine the three IPD's cost structure limbs; and (3) a novel mechanism of managing cost saving (rewards) through distinguishing between saved resources from organisation level, to daily task level, to increase trust among parties.
Nestlé South Africa and Department of Transport: response to food security during COVID-19
Authors: Pillay Ravi , Scheepers Caren Brenda
Published: August 2020

Learning outcomes

Gaining skills in analyzing context during a crisis situation, using a political, economic, social, technological, legal and environmental framework understanding strategic leadership engagement with stakeholders to cultivate an environment for emergent change gaining skills in drawing up a strategic communications plan.

Case overview/synopsis

On 15 May 2020, Alec Moemi, Director-General of the South African Government’s Department of Transport (DoT), contemplates how his department can use the opportunity that COVID-19 presents to transform the transport system and to maintain relationships with business and the taxi industry beyond COVID-19? The nation was just reeling from a first: the President announced a “lockdown” which meant that all economic activity except “essential services” could operate. Life almost ground to halt and South Africans faced a new reality. No movement out of your property unless it was a medical emergency or if you needed to buy food. The minibus taxi, an economic enabler to millions of South Africans also had to stop operating. The South African DoT had a mammoth task of communicating to a range of stakeholders. However, the most sensitive being the minibus taxi owners, drivers and their related associations. How would they accept the news that they will not have a livelihood for the next few weeks or perhaps even months? Given the nature of industrial shift patterns and need for a more flexible transport system for workers, some organisation’s such as Nestlé contracted private transport services to ensure their staff travelled to work safely. Nestlé also had their own compulsory sanitizing protocols in place to support private transporters.

Complexity academic level

Postgraduate programmes, including MBA, MPhil Corporate Strategy and Masters’ Public Administration and Executive Education Programmes.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS: 7 Management Science.
‘Read it, now what? Engaging students with information literacy’
Authors: Foord Karen
Published: August 2020

Purpose

The purpose of this action research study was to explore whether enabling work-based students to identify their information literacy (IL) needs and participate in activity design would increase their IL and enhance their academic performance.

Design/methodology/approach

Initially students reflected on their own knowledge, skills and engagement with IL. Next, they identified aspects of IL that challenged them. Students worked in small groups to identify tasks and activities to enhance their skills. They completed practical IL tasks during a taught session. A scoring rubric assessed student engagement with IL. Concurrently a qualitative questionnaire was developed and used to explore the student experience of the intervention.

Findings

The study found that students did engage with information literacy and there was an improvement in the pass rate from previous cohorts. The qualitative analysis demonstrated that students felt that the interaction had benefitted their engagement with IL and their learning and understanding as a result.

Research limitations/implications

This study was a small study at one higher education institution and cannot therefore be considered generalizable. It does nevertheless provide valuable insights in terms of student engagement with IL.

Practical implications

This study influenced the delivery of the subsequent modules. It has the potential to influence the delivery of information literacy skills on health and social care apprenticeships.

Originality/value

This paper adds to the literature exploring the relationship between students and information literacy. Enhancing the discourse from the instructor perspective rather than that of the information professional.
The motives behind consumers’ intention to use peer-to-peer accommodation: an fsQCA application
Authors: De Canio Francesca , Nieto-García Marta , Martinelli Elisa , Pellegrini Davide
Published: August 2020

Purpose

Literature on the motives influencing consumers’ intention to use peer-to-peer (P2P) platforms has become vast and fragmented. The purpose of this paper is to shed light on this research stream by applying a novel methodological approach that reveals the existence of alternative combinations of motives that equally boost consumers’ intention to use P2P accommodation.

Design/methodology/approach

The methodological approach builds on the complexity theory and includes both linear and nonlinear techniques. The empirical analysis combines multiple regression analysis and fuzzy-set qualitative comparative analysis (fsQCA). The sample comprises 458 users of a leading P2P accommodation platform.

Findings

The fsQCA reveals four distinct combinations of motives. Social interaction and social esteem, either combined themselves or in partial combination with economic benefits, emerge as two important drivers of behavioral intention to use P2P accommodation. Sustainability appears in three of the combinations.

Originality/value

This paper contributes to the P2P accommodation literature by adopting a novel methodological approach that shows the complexity behind consumers’ intention to use P2P accommodation. Consumer motives cannot be considered as separate entities because their effect on consumer intention depends on the interplay among them. Therefore, the different combinations of motives should be managed simultaneously.