bluuebunny/crossref_metadata_2025 huggingface dataset:
Capturing large genomic contexts for accurately predicting enhancer-promoter interactions
Authors: Chen Ken , Zhao Huiying , Yang Yuedong
Published: September 2021

Accurately identifying enhancer-promoter interactions (EPIs) is challenging because enhancers usually act on the promoters of distant target genes. Although a variety of machine learning and deep learning models have been developed, many of them are not designed to or could not be well applied to predict EPIs in cell types different from the training data. In this study, we develop the TransEPI model for EPI prediction based on datasets derived from Hi-C and ChIA-PET data. TransEPI compiles genomic features from large intervals harboring the enhancer-promoter pair and adopts a Transformer-based architecture to capture the long-range dependencies. Thus, TransEPI could achieve more accurate prediction by addressing the impact of other genomic loci that may competitively interact with the enhancer-promoter pair. We evaluate TransEPI in a challenging scenario, where the independent test samples are predicted by models trained on the data from different cell types and chromosomes. TransEPI robustly predicts cross-cell-type EPI prediction by achieving comparable performance in cross-validation and independent test. More importantly, TransEPI significantly outperforms the state-of-the-art EPI models on the independent test datasets, with the Area Under Precision-Recall Curve (auPRC) score increasing by 48.84 % on average. Hence, TransEPI is applicable for accurate EPI prediction in cell types without chromatin structure data. Moreover, we find the TransEPI framework could also be extended to identify the target gene of non-coding mutations, which may facilitate studying pathogenic non-coding mutations.
Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome
Authors: de Oliveira André Luiz , Mitchell Jessica , Girguis Peter , Bright Monika
Published: September 2021

The mutualism between the giant tubewormRiftia pachyptilaand its endosymbiontCandidatusEndoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface inRiftia. Here we described the high-quality draft genome ofRiftia, its complete mitogenome, and tissue-specific transcriptomic data. TheRiftiagenome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research inRiftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
Sex-specific divergent maturational trajectories in the postnatal rat basolateral amygdala
Authors: Guily Pauline , Lassalle Olivier , Chavis Pascale , Manzoni Olivier JJ
Published: September 2021

The basolateral amygdala (BLA), the part of the amygdala complex involved in the transduction of perceptual stimuli into emotion, undergoes profound reorganization at adolescence in rodents and humans. How cellular and synaptic plasticity evolve throughout postnatal development in both sexes is only partially understood. We used a cross-sectional approach to compare the morphology, neuronal, and synaptic properties of BLA neurons in rats of both sexes at adolescence and adulthood. While BLA pyramidal neurons from rats of both sexes displayed similar current-voltage relationships, rheobases, and resting potentials during pubescence, differences in these parameters emerged between sexes at adulthood: BLA neurons were more excitable in males than females. During pubescence, BLA neuron excitability was highest in females and unchanged in males; male action potentials were smaller and shorter than females and fast afterhyperpolarizations were larger in males. During post-natal maturation, no difference in spine density was observed between groups or sexes but spine length increased and decreased in females and males, respectively. A reduction in spine head diameter and volume was observed exclusively in females. Basic synaptic properties also displayed sex-specific maturational differences. Stimulus-response relationships and maximal fEPSP amplitudes where higher in male adolescents compared with adults but were similar in females of both ages. Spontaneous excitatory postsynaptic currents mediated by AMPA receptors were smaller in BLA neurons from adolescent female compared with their adult counterparts but were unchanged in males. These differences did not directly convert into changes in overall synaptic strength estimated from the AMPA/NMDA ratio, which was smaller in adolescent females. Finally, the developmental courses of long-term potentiation and depression (LTP, LTD) were sexually dimorphic. LTP was similarly present during the adolescent period in males and females but was not apparent at adulthood in females. In contrast, LTD followed an opposite development: present in adolescent females and expressed in both sexes at adulthood. These data reveal divergent maturational trajectories in the BLA of male and female rats and suggest cellular substrates to the BLA linked sex-specific behaviors at adolescence and adulthood.
Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity
Authors: Kumazawa Minoru , Nishide Hiroyo , Nagao Ryo , Inoue-Kashino Natsuko , Shen Jian-Ren , Nakano Takeshi , Uchiyama Ikuo , Kashino Yasuhiro , Ifuku Kentaro
Published: September 2021

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e., fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identified 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggested that these FCPs could be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, had orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seemed to be diversified in each diatom species, and the number of Lhcqs differed among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs was common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provided insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

One sentence summary

Phylogenetic analysis of fucoxanthin-chlorophyll a/c proteins in C. gracilis revealed five major subfamilies and one minor subfamily, providing insights into the diversification of light-harvesting systems in red algae.
USP28 enables oncogenic transformation of respiratory cells and its inhibition potentiates molecular therapy targeting mutant EGFR, BRAF and PI3K
Authors: Prieto-Garcia Cristian , Hartmann Oliver , Reissland Michaela , Braun Fabian , Bozkurt Süleyman , Fuss Carmina , Schülein-Völk Christina , Buchberger Alexander , Calzado Canale Marco A. , Rosenfeldt Mathias , Dikic Ivan , Münch Christian , Diefenbacher Markus E.
Published: September 2021

Oncogenic transformation of lung epithelial cells is a multi-step process, frequently starting with the inactivation of tumor suppressors and subsequent activating mutations in proto-oncogenes, such as members of the PI3K or MAPK family. Cells undergoing transformation have to adjust to changes, such as metabolic requirements. This is achieved, in part, by modulating the protein abundance of transcription factors, which manifest these adjustments. Here, we report that the deubiquitylase USP28 enables oncogenic reprogramming by regulating the protein abundance of proto-oncogenes, such as c-JUN, c-MYC, NOTCH and ΔNP63, at early stages of malignant transformation. USP28 is increased in cancer compared to normal cells due to a feed-forward loop, driven by increased amounts of oncogenic transcription factors, such as c-MYC and c-JUN. Irrespective of oncogenic driver, interference with USP28 abundance or activity suppresses growth and survival of transformed lung cells. Furthermore, inhibition of USP28 via a small molecule inhibitor reset the proteome of transformed cells towards a ‘pre-malignant’ state, and its inhibition cooperated with clinically established compounds used to target EGFRL858R, BRAFV600Eor PI3KH1047Rdriven tumor cells. Targeting USP28 protein abundance already at an early stage via inhibition of its activity therefore is a feasible strategy for the treatment of early stage lung tumours and the observed synergism with current standard of care inhibitors holds the potential for improved targeting of established tumors.
Inhibition of the SHP-1 activity by PKC-θ regulates NK cell activation threshold and cytotoxicity
Authors: Ben-Shmuel Aviad , Sabag Batel , Biber Guy , Puthenveetil Abhishek , Levy Moria , Jubany Tammir , Joseph Noah , Matalon Omri , Kivelevitz Jessica , Barda-Saad Mira
Published: September 2021

Natural Killer (NK) cells play a crucial role in immunity, killing virally infected and cancerous cells. The balance of signals initiated upon engagement of activating and inhibitory NK receptors with cognate ligands determines killing or tolerance. Nevertheless, the molecular mechanisms regulating rapid NK cell discrimination between healthy and malignant cells in a heterogeneous tissue environment are incompletely understood. The SHP-1 tyrosine phosphatase is the central negative NK cell regulator, which dephosphorylates key activating signaling proteins. Though the mechanism by which SHP-1 mediates NK cell inhibition has been partially elucidated, the pathways by which SHP-1 is itself regulated remain unclear. Here, we show that phosphorylation of SHP-1 in NK cells on the S591 residue by PKC-θ promotes the inhibited SHP-1 “folded” state. Silencing PKC-θ maintains SHP-1 in the active conformation, reduces NK cell activation and cytotoxicity, and promotes tumor progression in-vivo. This study reveals a molecular pathway that sustains the NK cell activation threshold through suppression of SHP-1 activity.
Geometrical Study of Virus RNA Sequences
Authors: Belinsky Alex , Kouzaev Guennadi
Published: September 2021

In this contribution, some applications of the earlier developed fast algorithm of calculating coordinates of single nucleotides and RNA fragments are considered to create multi-scale geometrical models of RNAs and their mutations. The algorithm allows to plot single nucleotides and RNA’s fragments on one figure and to track the RNA mutations of any level visually and numerically using interpolation formulas and point-to-point estimates of coordinates of ATG starting triplets and single nucleotides. The performed study of many samples of SARS CoV-2 viruses shows perturbations of ATG starting triplet coordinates in the vicinity of orf1ab gene end only.
CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders
Authors: Murphy Kitty B. , Ye Yuqian , Tsalenchuk Maria , Nott Alexi , Marzi Sarah J.
Published: September 2021

Acetylation of histone H3 lysine 27 (H3K27ac) has emerged as an informative disease-associated epigenetic mark. However, cell type-specific contributions to epigenetic dysregulation in disease are unclear as studies have often used bulk brain tissue. Therefore, methods for the deconvolution of bulk H3K27ac profiles are critical. Here we developed the Cell type-specific Histone Acetylation Score (CHAS), a computational tool for inferring cell type-specific signatures in bulk brain H3K27ac profiles. We applied CHAS to > 300 H3K27ac ChIP-seq samples from studies of Alzheimer’s disease, Parkinson’s disease, autism spectrum disorder, schizophrenia, and bipolar disorder in bulk post-mortem brain tissue. In addition to recapitulating known disease-associated shifts in cellular proportions, we identified novel cell type-specific biological insights into brain disorder associated regulatory variation. In most cases, genetic risk and epigenetic dysregulation targeted different cell types, thus suggesting independent mechanisms. For instance, Alzheimer’s disease genetic risk was exclusively enriched within microglia, while epigenetic dysregulation predominantly fell within oligodendrocyte-specific H3K27ac regions. In addition, reanalysis of the original datasets using CHAS enabled identification of biological pathways associated with each neurological and psychiatric disorder at cellular resolution.
Novel effector recognition capacity engineered into a paired NLR complex
Authors: Wang Shanshan , Huang Weijie , Duxbury Zane , Hogenhout Saskia A. , Jones Jonathan D. G.
Published: September 2021

The Arabidopsis RRS1-R Resistance gene confers recognition of the bacterial acetyltransferase PopP2 and another bacterial effector, AvrRps4. The RRS1-S allele recognizes AvrRps4 but not PopP2. RRS1- R/RRS1-S heterozygotes cannot recognize PopP2. RRS1-R and RRS1-S also suppress the constitutive RPS4-dependent autoactivity of RRS1-Rslh1. Phytoplasmas cause important plant diseases, and their effectors can cause degradation of specific host proteins. We tested whether attaching a pathogen effector-dependent degron to RRS1-R, enabling its degradation by phytoplasma effector SAP05, could derepress RRS1-Rslh1 autoactivity, resulting in SAP05-dependent resistance. In transient assays in tobacco, RRS1-R-derived constructs can confer a hypersensitive response (HR) to SAP05. However, phytoplasma infection assays in transgenic Arabidopsis resulted in delayed disease symptoms but not full resistance. We provide a proof-of-concept strategy utilizing the recessiveness of a plant immune receptor gene to engineer recognition of a pathogen effector that promotes degradation of a specific host protein.
Speech categorization reveals the role of early-stage temporal-coherence processing in auditory scene analysis
Authors: Viswanathan Vibha , Shinn-Cunningham Barbara G. , Heinz Michael G.
Published: September 2021

Temporal coherence of sound fluctuations across spectral channels is thought to aid auditory grouping and scene segregation. Although prior studies on the neural bases of temporal-coherence processing focused mostly on cortical contributions, neurophysiological evidence suggests that temporal-coherence-based scene analysis may start as early as the cochlear nucleus (i.e., the first auditory region supporting cross-channel processing over a wide frequency range). Accordingly, we hypothesized that aspects of temporal-coherence processing that could be realized in early auditory areas may shape speech understanding in noise. We then explored whether physiologically plausible computational models could account for results from a behavioral experiment that measured consonant categorization in different masking conditions. We tested whether within-channel masking of target-speech modulations predicted consonant confusions across the different conditions, and whether predicted performance was improved by adding across-channel temporal-coherence processing mirroring the computations known to exist in the cochlear nucleus. Consonant confusions provide a rich characterization of error patterns in speech categorization, and are thus crucial for rigorously testing models of speech perception; however, to the best of our knowledge, they have not been utilized in prior studies of scene analysis. We find that within-channel modulation masking can reasonably account for category confusions, but that it fails when temporal fine structure (TFS) cues are unavailable. However, the addition of across-channel temporal-coherence processing significantly improves confusion predictions across all tested conditions. Our results suggest that temporal-coherence processing strongly shapes speech understanding in noise, and that physiological computations that exist early along the auditory pathway may contribute to this process.
Expectations boost the reconstruction of auditory features from electrophysiological responses to noisy speech
Authors: Corcoran Andrew W. , Perera Ricardo , Koroma Matthieu , Kouider Sid , Hohwy Jakob , Andrillon Thomas
Published: September 2021

Online speech processing imposes significant computational demands on the listening brain, the underlying mechanisms of which remain poorly understood. Here, we exploit the perceptual ‘pop-out’ phenomenon (i.e. the dramatic improvement of speech intelligibility after receiving information about speech content) to investigate the neurophysiological effects of prior expectations on degraded speech comprehension. We recorded electroencephalography and pupillometry from 21 adults while they rated the clarity of noise-vocoded and sine-wave synthesised sentences. Pop-out was reliably elicited following visual presentation of the corresponding written sentence, but not following incongruent or neutral text. Pop-out was associated with improved reconstruction of the acoustic stimulus envelope from low-frequency EEG activity, implying that improvements in perceptual clarity were mediated via top-down signals that enhance the quality of cortical speech representations. Spectral analysis further revealed that pop-out was accompanied by a reduction in theta-band power, consistent with predictive coding accounts of acoustic filling-in and incremental sentence processing. Moreover, delta-band power, alpha-band power, and pupil diameter were all increased following the provision of any written sentence information, irrespective of content. Together, these findings reveal distinctive profiles of neurophysiological activity that differentiate the content-specific processes associated with degraded speech comprehension from the context-specific processes invoked under adverse listening conditions.
Bee-associated fungi mediate effects of fungicides on bumble bees
Authors: Rutkowski Danielle , Litsey Eliza , Maalouf Isabelle , Vannette Rachel L.
Published: September 2021

Bumble bees are important pollinators that face threats from multiple sources, including agrochemical application. Declining bumble bee populations have been linked to fungicide application, which could directly affect the fungi often found in the stored food and GI tract of healthy bumble bees. Here, we test the hypothesis that fungicides impact bee health by disrupting bee-fungi interactions. We examine the interactive effects of the fungicide propiconazole and fungal supplementation on the survival, reproduction, and microbiome composition of microcolonies (queenless colonies) using two species,Bombus vosnesenskiiandB. impatiens. We found that both bee species benefitted from fungi, but were differentially affected by fungicides. InB. vosnesenskii, fungicide exposure decreased survival while fungal supplementation mitigated fungicide effects. ForB. impatiens, fungicide application had no effect, but fungal supplementation improved survival and offspring production. Fungicides reduced fungal abundance inB. vosnesenskiimicrocolonies, but not inB. impatiens, where instead fungal addition decreased fungal abundance. InB. vosnesenskii, the abundance of the pathogenAscosphaerawas negatively associated with survival, while the yeastZygosaccharomyceswas positively associated with survival. Our results highlight species-specific differences in response to fungicides and the nature of bee-fungi associations, and caution the use of results obtained using one species to predict responses of other species. These results demonstrate that fungicides can alter bee-fungi interactions with consequences for bee survival and reproduction, and suggest that exploring the mechanisms of such interactions, including interactions among fungi in the bee GI tract, may offer insights into bumble bee biology and conservation strategies.

Significance statement

Wild bumble bee populations are declining globally, and a major predictor of these declines is agricultural fungicide application. We test the hypothesis that bee-associated fungi mediate fungicide effects on bees, examining how fungicide exposure and subsequent fungal supplementation impact bumble bee survival and microbiome. Fungal supplementation enhanced survival in both bumble bee species tested here, with fungi mediating effects of fungicide exposure in one species. Differences in bee survival were associated with changes in the gut mycobiome: negatively with the pathogenAscosphaeraand positively withZygosaccharomycesyeasts. This study highlights the importance of the mycobiome in bumble bee health both as a mechanism by which fungicides impact bumble bees and as an avenue of further research on beneficial bee-associated fungi.
Subacute Inhalation of Ultrafine Particulate Matter Triggers Inflammation Without Altering Amyloid Beta Load in 5xFAD mice
Authors: Saveleva Liudmila , Vartiainen Petra , Gorova Veronika , Chew Sweelin , Belaya Irina , Konttinen Henna , Zucchelli Martina , Korhonen Paula , Kaartinen Emma , Kortelainen Miika , Lamberg Heikki , Sippula Olli , Malm Tarja , Jalava Pasi I , Kanninen Katja M
Published: September 2021

Epidemiological studies reveal that air pollution exposure may exacerbate neurodegeneration. Ultrafine particles (UFPs) are pollutants that remain unregulated in ambient air by environmental agencies. Due to their small size (<100nm), UFPs have the most potential to cross the bodily barriers and thus impact the brain. However, little information exists about how UFPs affect brain function. Alzheimer’s disease (AD) is the most common form of dementia, which has been linked to air pollutant exposure, yet limited information is available on the mechanistic connection between them. This study aims to decipher the effects of UFPs in the brain and periphery using the 5xFAD mouse model of AD. In our study design, AD mice and their wildtype littermates were subjected to 2-weeks inhalation exposure of UFPs in a whole-body chamber. That subacute exposure did not affect the blood-brain barrier integrity or amyloid-beta accumulation. However, when multiple cytokines were analyzed, we found increased levels of proinflammatory cytokines in the brain and periphery, with a predominant alteration of interferon-gamma in response to UFP exposure in both genotypes. Following exposure, mitochondrial superoxide dismutase was significantly upregulated only in the 5xFAD hippocampi, depicting oxidative stress induction in the exposed AD mouse group. These data demonstrate that short-term exposure to inhaled UFPs induces inflammation without affecting amyloid-beta load. This study provides a better understanding of adverse effects caused by short-term UFP exposure in the brain and periphery, also in the context of AD.

GRAPHICAL ABSTRACT
Talent management processes and outcomes in a virtual organization
Authors: Vecchi Alessandra , Della Piana Bice , Feola Rosangela , Crudele Chiara
Published: September 2021

Purpose

This paper investigates how global talent management processes are adopted and implemented in a virtual organization to successfully address the challenges of global work arrangements and the sustainable human and social outcomes that can be achieved.

Design/methodology/approach

Adopting a single, exploratory and critical case study methodology, this paper analyzes a global distributed company, Automattic Inc., to provide in-depth and rich insights on successful business process management in the human resources (HR) domain.

Findings

The findings offer some exemplary and valuable lessons in sustainable human resource management for firms in all sectors on how to embrace global talent management in a more creative and sustainable way – and the benefits in terms of efficiency and effectiveness that can be derived – by identifying talent through auditions, recruiting by inspiring others to apply, developing talent by sharing the value of learning and retaining talent by having fun.

Originality/value

The study contributes a more rounded understanding of successful business process management in the HR domain. Due to the COVID-19 pandemic, this is particularly relevant and timely for all organizations (traditional or virtual) venturing into successful global work arrangements.
The glass slipper effect: understanding the Nordic gender equality paradox from an identity fit perspective
Authors: Spangsdorf Sabrina , Forsythe Alex
Published: September 2021

Purpose

This paper aims to introduce an identity fit perspective adding to the understanding of the Nordic gender equality paradox of top managing positions using a Danish sample as case.

Design/methodology/approach

In total, five hypotheses concerning identity perception of top managing positions and the relationship with own identity and type of industry were tested through a correlational research design utilizing a cross-sectional survey methodology. A total of 1,054 women aged 18–60 participated in the survey.

Findings

The analysis revealed a strong masculine perception of a top managing position whereas women's own identity perception was much more diverse. The more masculine a woman perceives herself to be, the more motivated she is to climb the career ladder. Type of industry moderates the relationship between identity fit and motivation for top positions, but only for the masculine traits. The relationship between identity fit and motivation is stronger for women in high masculine industries.

Originality/value

Apart from being the first study of identity fit in a Nordic setting, this study contributes to the identity fit theory by employing a semi-objective fit approach exploring identity fit on an industry level, including female-dominated industries, as well as examining identity fit in relation to motivation to pursue a top managing position.
Entrepreneurship and economic growth: does gender matter?
Authors: Crane Sarah R.
Published: September 2021

Purpose

Entrepreneurial firms contribute to economic growth, but the potential gendered nature of this contribution must be investigated as outcomes of male-owned and female-owned firms differ. The study investigates the female underperformance hypothesis in a cross-country analysis of Schumpeterian entrepreneurs. Next, it investigates if there is a gendered dimension of Schumpeterian firm contribution to economic growth.

Design/methodology/approach

The study utilizes both nonparametric and parametric methodologies. Through nonparametric methods, the success of female-owned and male-owned firms is compared. Next, a parametric ordinary least squares regression model tests if there is a gendered nature of an entrepreneurial firm's economic contribution.

Findings

In nonparametric analyses, female-owned entrepreneurial firms in developed countries perform similarly to male-owned firms, while in developing countries male-owned firms significantly outperform female-owned firms. The author also finds strong evidence that the gender of the Schumpeterian entrepreneur does not matter in the contribution in economic growth.

Research limitations/implications

In all countries, the number of female-owned entrepreneurial firms was significantly lower than that of male-owned firms. The findings point to consistent cultural barriers for women in innovation-related fields and persistent gendered norms in entrepreneurship. Thus, removal of cultural barriers and continued support for Schumpeterian entrepreneurship will benefit women and contribute to a country's economic growth.

Originality/value

The data for this study is a unique utilization of the Enterprise World Survey to identify Schumpeterian entrepreneurial firms. Additionally, the study challenges the female underperformance hypothesis and contributes to the literature on the role of entrepreneurship in economic growth.
Modelling supply chain risks and their impacts on the performance of the sago starch agro-industry
Authors: Anwar Syamsul , Djatna Taufik , Sukardi  , Suryadarma Prayoga
Published: September 2021

Purpose

Supply chain risks (SCRs) have uncertainty and interdependency characteristics that must be incorporated into the risk assessment stage of the SCR management framework. This study aims to develop SCR networks and determine the major risk drivers that impact the performance of the sago starch agro-industry (SSA).

Design/methodology/approach

The risk and performance variables were collected from the relevant literature and expert consultations. The Bayesian network (BN) approach was used to model the uncertain and interdependent SCRs. A hybrid method was used to develop the BN structure through the expert’s knowledge acquisitions and the learning algorithm application. Sensitivity analyses were performed to examine the significant risk driver and their related paths.

Findings

The analyses of model indicated several significant risk drivers that could affect the performance of the SSA. These SCR including both operational and disruption risks across sourcing, processing and delivery stage.

Research limitations/implications

The implementation of the methodology was only applied to the Indonesian small-medium size sago starch agro-industry. The generalization of findings is limited to industry characteristics. The modelled system is restricted to inbound, processing and outbound logistics with the risk perspective from the industry point of view.

Practical implications

The results of this study assist the related actors of the sago starch agro-industry in recognizing the major risk drivers and their related paths in impacting the performance measures.

Originality/value

This study proposes the use of a hybrid method in developing SCR networks. This study found the significant risk drivers that impact the performance of the sago starch agro-industry.
Idea work online: shelters and crutches in remote collaborative autoethnography
Authors: Dziuba Anna , Tienari Janne , Välikangas Liisa
Published: September 2021

Purpose

The three authors of this paper are intrigued by ideas and how they are created. The purpose of this paper is to explore idea creation and work by means of remote collaborative autoethnography.

Design/methodology/approach

During the COVID-19 lockdown in 2020, the authors sent texts to each other, followed up on each other's thoughts and discussed them in online meetings. They shared, analyzed and eventually theorized their lived experiences in order to understand creating ideas as social and cultural experience.

Findings

The authors develop the notions of “shelter” and “crutch” to make sense of the complexity of creating ideas together; theorize how emotions and identities are entangled in idea work; and discuss how time, space and power relations condition it.

Originality/value

The authors contribute to understanding idea work in a remote collaborative autoethnography by highlighting its emotional, identity-related and power-laden nature.
Talent management: four “buying versus making” talent development approaches
Authors: Cooke Gordon B. , Chowhan James , Mac Donald Kelly , Mann Sara
Published: September 2021

Purpose

This paper presents a typology exploring employers’ perceptions of the quality of available applicants and employers decisions to buy qualified staff vs. to hire available workers and then make i.e. develop them via employer-supported training.

Design/methodology/approach

This study uses 2015 survey data from Southwestern Ontario, Canada, based on responses from 834 employers regarding their hiring, separations, training and other HRM policies.

Findings

Among surveyed employers, 10% are “Reliants” who found the quality of available applicants to be low, yet these employers do not provide employee training. Almost half of employers (at 45%) are “Developers” who find the quality of applicants to be low but they do provide employee training. Approximately, 7% of employers are “Poachers” who find that the quality of applicants is high and do not provide employee training, while 38% are Refiners, who find the quality of applicants is high and they provide employee training.

Originality/value

Employers need to make their training decisions in alignment with their assessment of the quality of job applicants to whom they have access. In this paper, decisions on training and applicant quality are considered concurrently. From an academic viewpoint, the findings raise the issue as to whether other stakeholders (such as educational institutions) are sufficiently helping individuals gain the skills, credentials and work experiences that employers are seeking. If job openings are remaining unfilled because employers are unwilling to hire those available, then applicants lose, employers lose and societies lose.
Limits of arbitrage and mispricing: evidence from mergers and acquisitions
Authors: Ma Qingzhong , Whidbee David A. , Zhang Wei
Published: September 2021

Purpose

This paper examines the extent to which noise demand and limits of arbitrage affect the pricing of acquirer stocks both at the announcement period and over the longer horizon.

Design/methodology/approach

An event study approach was adopted to measure announcement-period cumulative abnormal returns. Long-horizon returns are measured using buy-and-hold abnormal returns (BHARs), calendar time portfolios (CTPRs), and subsequent earnings announcement period abnormal returns. Main methodologies include ordinary least squared (OLS) regressions, Logit regressions, and portfolio analysis.

Findings

(1) Acquirer stocks with high idiosyncratic volatility (the proxy for the security level characteristic most directly associated with limits to arbitrage) earn higher announcement-period abnormal returns. (2) The return pattern reverses over the subsequent longer horizon, resembling news-driven transitory mispricing. (3) The mispricing is greater when deal and firm characteristics exacerbate the limits of arbitrage, and it weakens over time. (4) Transactions by higher idiosyncratic volatility acquirers are more likely to fail.

Originality/value

Limits of arbitrage theory have been tested mostly in information-free circumstances. The findings in this paper extend the supporting evidence for limits of arbitrage explaining mispricing beyond the boundaries of information-free circumstances.
Organizing worn-out neighborhoods with the new-urbanism approach using mixed methods in Rudsar, northern Iran
Authors: Askarizad Reza , Dadashpour Akram , Faghirnavaz Javad , He Jinliao , Safari Hossein
Published: September 2021

Purpose

The vulnerability of worn-out textures in the face of natural disasters is one of the most significant challenges that have forced planners and urban managers to intervene in these structures. In this context, the new-urbanism, or the new urbanization, movement is one of the most novel approaches. This paper aims to organizing one of the worn-out neighborhoods in Rudsar, northern Iran with an approach toward the new urbanism.

Design/methodology/approach

The procedure adopted in this research is a combination of both quantitative and qualitative practices with an applied approach. Therefore, through utilizing the analytical hierarchy process (AHP) and space syntax methods, the principles of the new urbanism are examined using the Expert Choice and Depthmap software. Subsequently, the appropriate priorities are mentioned for organizing the neighborhood with the new-urbanism approach using the building information system (BIM) and strengths, weaknesses, opportunities and threats (SWOT) techniques.

Findings

The findings of this study indicate that among the main characteristics of the new urbanism, walkability is recognized as the most important factor. Afterward, the components of maintaining the traditional structure of neighborhoods and connectivity were in the second and third ranks, respectively, of importance. Accordingly, by identifying the societal potential of roads according to their spatial configuration, it is possible to boost walkability, as well as economic prosperity in these areas.

Originality/value

The combination and correlation of the four utilized methods in this research can be adopted in the future studies as a new outlook of the mixed methods in the field of urban studies.
Multispecies modelling reveals potential for habitat restoration to re‐establish boreal vertebrate community dynamics
Authors: Beirne Christopher , Sun Catherine , Tattersall Erin R. , Burgar Joanna M. , Fisher Jason T. , Burton A. Cole
Published: September 2021

The restoration of habitats degraded by industrial disturbance is essential for achieving conservation objectives in disturbed landscapes. In boreal ecosystems, disturbances from seismic exploration lines and other linear features have adversely affected biodiversity, most notably leading to declines in threatened woodland caribou. Large‐scale restoration of disturbed habitats is needed, yet empirical assessments of restoration effectiveness on wildlife communities remain rare.

We used 73 camera trap deployments from 2015 to 2019 and joint species distribution models to investigate how habitat use by the larger vertebrate community (>0.2 kg) responded to variation in key seismic line characteristics (line‐of‐sight, width, density and mounding) following restoration treatments in a landscape disturbed by oil and gas development in northeastern Alberta.

The proportion of variation explained by line characteristics was low in comparison to habitat type and season, suggesting short‐term responses to restoration treatments were relatively weak. However, we found that lines with characteristics consistent with restored conditions were predicted to support an altered community composition, with reduced use by wolf and coyote, thereby indicating that line restoration will result in reduced contact rates between caribou and these key predators.

Synthesis and applications. Our analysis provides a framework to assess and predict wildlife community responses to emerging restoration efforts. With the growing importance of habitat restoration for caribou and other vertebrate species, we recommend longer‐term monitoring combined with landscape‐scale comparisons of different restoration approaches to more fully understand and direct these critical conservation investments. Only by combining rigorous multispecies monitoring with large‐scale restoration, will we effectively conserve biodiversity within rapidly changing environments.
Solid diet manipulates rumen epithelial microbiota and its interactions with host transcriptomic in young ruminants
Authors: Chai Jianmin , Lv Xiaokang , Diao Qiyu , Usdrowski Hunter , Zhuang Yimin , Huang Wenqin , Cui Kai , Zhang Naifeng
Published: September 2021

Solid diet supplementation in the early life stages of ruminants could improve rumen microbiota and tissue development. However, most studies focus on bacteria in the rumen content community. The microbiota attached on rumen epithelium are rarely investigated, and their correlations with rumen content bacteria and host transcripts are unknown. In this study, rumen digesta attached in the epithelium from goats in three diet regimes (milk replacer only, milk replacer supplemented concentrate and milk replacer supplemented concentrate plus alfalfa pellets) were collected for measurement of the epithelial microbiota using next generation sequencing. Correspondingly, the rumen tissues of the same animals were measured with the host transcriptome. The distinct microbial structures and compositions between rumen content and epithelial communities were associated with solid diet supplementation. Regarding rumen development in pre‐weaning ruminants, a solid diet, especially its accompanying neutral detergent fibre nutrients, was the most significant driver that influenced the rumen microbiota and epithelium gene expression. Compared with content bacteria, rumen epithelial microbiota had a stronger association with the host transcriptome. The host transcriptome correlated with host phenotypes were associated with rumen epithelial microbiota and solid diet. This study reveals that the epithelial microbiota is crucial for proper rumen development, and solid diet could improve rumen development through both the rumen content and epithelial microbiota.
Directed evolution predicts cytochrome b G37V target site modification as probable adaptive mechanism towards the QiI fungicide fenpicoxamid in Zymoseptoria tritici
Authors: Fouché Guillaume , Michel Thomas , Lalève Anaïs , Wang Nick X. , Young David H. , Meunier Brigitte , Debieu Danièle , Fillinger Sabine , Walker Anne‐Sophie
Published: September 2021

Acquired resistance is a threat to antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms and highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the resistance risk to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complex III of the respiratory chain at the ubiquinone reduction site (Qi site) of the mitochondrially encoded cytochrome b, a different site than the widely used strobilurins which inhibit the same complex at the ubiquinol oxidation site (Qo site). We identified the G37V change within the cytochrome b Qi site as the most likely resistance mechanism to be selected in Z. tritici. This change triggered high fenpicoxamid resistance and halved the enzymatic activity of cytochrome b, despite no significant penalty for in vitro growth. We identified negative cross‐resistance between isolates harbouring G37V or G143A, a Qo site change previously selected by strobilurins. Double mutants were less resistant to both QiIs and quinone outside inhibitors compared to single mutants. This work is a proof of concept that experimental evolution can be used to predict adaptation to fungicides and provides new perspectives for the management of QiIs.
Aridity modulates belowground bacterial community dynamics in olive tree
Authors: Marasco Ramona , Fusi Marco , Rolli Eleonora , Ettoumi Besma , Tambone Fulvia , Borin Sara , Ouzari Hadda‐Imene , Boudabous Abdellatif , Sorlini Claudia , Cherif Ameur , Adani Fabrizio , Daffonchio Daniele
Published: September 2021

Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant‐associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co‐occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity‐winner and aridity‐loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co‐occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity‐winners or aridity‐losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
Effects of affiliation network membership on hospital quality and financial performance
Authors: Jin Bonnie , Nembhard Ingrid M.
Published: September 2021

Objective

To examine the effects of hospital membership in affiliation networks—franchise‐like networks sponsored by high‐quality health systems in which affiliate hospitals pay an annual fee for access to sponsor's operational and clinical resources—on clinical quality, patient experience ratings, and financial performance of affiliates and their competitors.

Data sources

Network membership data from press releases and websites of four sponsors (Mayo Clinic, Cleveland Clinic, MD Anderson, Memorial Sloan Kettering), American Hospital Association's Annual Survey, Centers for Medicare & Medicaid Services' Hospital Compare, and Healthcare Cost Report Information System, all for 2005–2016.

Study design

We used a quasi‐experimental design and estimated hospital‐level regressions with hospital‐fixed effects. Dependent variables were measures of clinical quality, patient experience, and financial performance. Independent variables included an indicator for affiliate versus nonaffiliate and fixed effects for hospital characteristics and year. To analyze effects on competitors, we repeated analyses by comparing hospitals in the same county as an affiliate to nonaffiliated, noncompetitor hospitals.

Data collection

Membership was obtained through press releases and network websites then linked across datasets by name and Medicare's identification number.

Principal findings

Across networks, affiliates (N = 199) experienced insignificant clinical quality changes but increased net income by $38,500 and operating margin by 6.6% (p values = 0.01–0.08) compared to nonaffiliates. Multispecialty affiliates improved on no measures. Cancer‐specific affiliates improved their net income ($96,900) and operating margin (3.6%; p‐values < 0.05). Affiliates' competitors experienced mixed changes in clinical measures relative to hospitals without affiliates in market (p‐value < 0.05) but no financial effects. Affiliation was not associated with patient experience ratings for affiliates nor competitors.

Conclusions

Despite quality‐focused missions, affiliation networks are not guaranteed to improve public measures of quality in affiliated hospitals, although hospitals in these communities improve financially. Future research should assess the conditions and mechanisms by which affiliation improves quality consistently and which forms of quality.