bluuebunny/crossref_metadata_2025 huggingface dataset:
Explainable Deep Generative Models, Ancestral Fragments, and Murky Regions of the Protein Structure Universe
Authors: Draizen Eli J. , Mura Cameron , Bourne Philip E.
Published: November 2022

Modern proteins did not arise abruptly, as singular events, but rather over the course of at least 3.5 billion years of evolution. Can machine learning teach us how this occurred? The molecular evolutionary processes that yielded the intricate three-dimensional (3D) structures of proteins involve duplication, recombination and mutation of genetic elements, corresponding to short peptide fragments. Identifying and elucidating these ancestral fragments is crucial to deciphering the interrelationships amongst proteins, as well as how evolution acts upon protein sequences, structures & functions. Traditionally, structural fragments have been found using sequence-based and 3D structural alignment approaches, but that becomes challenging when proteins have undergone extensive permutations—allowing two proteins to share a common architecture, though their topologies may drastically differ (a phenomenon termed theUrfold). We have designed a new framework to identify compact, potentially-discontinuous peptide fragments by combining (i) deep generative models of protein superfamilies with (ii) layerwise relevance propagation (LRP) to identify atoms of great relevance in creating an embedding during an allsuperfamilies× alldomainsanalysis. Our approach recapitulates known relationships amongst the evolutionarily ancient smallβ-barrels (e.g. SH3 and OB folds) and amongst P-loop–containing proteins (e.g. Rossmann and P-loop NTPases), previously established via manual analysis. Because of the generality of our deep model’s approach, we anticipate that it can enable the discovery of new ancestral peptides. In a sense, our framework uses LRP as an ‘explainable AI’ approach, in conjunction with a recent deep generative model of protein structure (termedDeepUrfold), in order to leverage decades worth of structural biology knowledge to decipher the underlying molecular bases for protein structural relationships—including those which are exceedingly remote, yet discoverable via deep learning.
Label-free cleared tissue microscopy and machine learning for 3D histopathology of biomaterial implants
Authors: Ngo Tran B , DeStefano Sabrina , Liu Jiamin , Su Yijun , Shroff Hari , Vishwasrao Harshad D , Sadtler Kaitlyn
Published: November 2022

Tissue clearing of whole intact organs has enhanced imaging by enabling the exploration of tissue structure at a subcellular level in three-dimensional space. Although clearing and imaging of the whole organ have been used to study tissue biology, the microenvironment in which cells evolve to adapt to biomaterial implants or allografts in the body is poorly understood. Obtaining high-resolution information from complex cell-biomaterial interactions with volumetric landscapes represents a key challenge in the fields of biomaterials and regenerative medicine. To provide a new approach to examine how tissue responds to biomaterial implants, we apply cleared tissue light-sheet microscopy and three-dimensional reconstruction to utilize the wealth of autofluorescence information for visualizing and contrasting anatomical structures. This study demonstrates the adaptability of the clearing and imaging technique to provide sub-cellular resolution (0.6μm isotropic) 3D maps of various tissue types, using samples from fully intact peritoneal organs to volumetric muscle loss injury specimens, with and without biomaterials implants. We further apply computational-driven image classification to analyze the autofluorescence spectrum at multiple emission wavelengths to categorize tissue types in the tissue-biomaterial microenvironment.
Continuous monitoring of cost-to-go for flexible reaching control and online decisions
Authors: De Comite Antoine , Lefèvre Philippe , Crevecoeur Frédéric
Published: November 2022

Humans consider the parameters linked to movement goal during reaching to adjust their control strategy online. Indeed, rapid changes in target structure or disturbances interfering with their initial plan elicit rapid changes in behavior. Here, we hypothesize that these changes could result from the continuous use of a decision variable combining motor and cognitive components. We combine an optimal feedback controller with a real-time monitoring of the expected cost-to-go, which considers target- and movement-related costs, in a common theoretical framework. This model reproduces human behaviors in presence of changes in the target structure occurring during movement and of online decisions to flexibly change target following external perturbations. It also predicts that the time taken to decide to select a novel goal after a perturbation depends on the amplitude of the disturbance and on the rewards of the different options, which is a direct result of the continuous monitoring of the cost-to-go. We show that this result was present in our previously collected dataset. Together our developments point towards a continuous monitoring of the cost-to-go during reaching to update control online and make efficient decisions about movement goal.

Author summary

The way humans perform reaching movements is compatible with models considering that they result from the minimization of a task-related cost function. However, these models typically assume a cost function that does not change within movement, which is incompatible with experimental findings highlighting humans’ ability to adjust reaching control online and change target flexibly. We hypothesized that this later ability relied on the cost-to-go, which integrates task- and body-related information, being evaluated continuously during movement. We show that this model can optimally select and adjust control during movement in a way that reproduces human behavior in a set of tasks involving change in cost function and change in goal target. Our model predicted that decision-time to change target must be postponed when limb displacements and alternative rewards are smaller, which was borne out in our previous experimental dataset. To conclude, our model explains dynamic updates in reach control and suggests the cost-to-go as decision variable linking decision-making and motor control.
Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution
Authors: Pierre Platre Matthieu , Preyanka Mehta , Zachary Halvorson , Zhang Ling , Lukas Brent , Matias Gleason F. , Kian Faizi , Callum Goulding , Wolfgang Busch
Published: November 2022

Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth. Consequently, using root growth as a readout for signal perception can help decipher which external cues are perceived by roots, and how these signals are integrated. To date, studies measuring root growth responses using large numbers of roots have been limited by a lack of high-throughput image acquisition, poor scalability of analytical methods, or low spatiotemporal resolution. Here, we developed the Root Walker pipeline, which uses automated microscopes to acquire time-series images of many roots exposed to controlled treatments with high-spatiotemporal-resolution, in conjunction with fast and automated image analysis software. We demonstrate the power of Root Walker by quantifying root growth rate responses at different time and throughput scales upon treatments with natural auxin, and upon treatment with two mitogen-associated protein kinase cascade inhibitors. We find a concentration-dependent root growth response to auxin and reveal the specificity of one MAPK inhibitor. We further demonstrate the ability of Root Walker for conducting genetic screens by performing a genome wide association study on 260 accessions under 2 weeks. This revealed known and unknown root growth regulators. Root Walker promises to be a useful toolkit for the plant science community, allowing large-scale screening of root growth dynamics for a variety of purposes, including genetic screens for root sensing and root growth response mechanisms.
Integrative single cell multiomics analysis of human retina indicates a role for hierarchical transcription factors collaboration in genetic effects on gene regulation
Authors: Wang Jun , Cheng Xuesen , Liang Qingnan , Owen Leah A. , Wang Meng , DeAngelis Margaret M. , Li Yumei , Chen Rui
Published: November 2022

Background

Systematic characterization of how genetic variation modulates gene regulation in a cell type specific context is essential for understanding complex traits. To address this question, we profiled gene expression and chromatin state of cells from healthy retinae of 20 human donors with a single-cell multiomics approach, and performed genomic sequencing.

Results

We mapped single-cell eQTL (sc-eQTLs), single-cell caQTL (sc-caQTL), single-cell allelic specific chromatin accessibility (sc-ASCA) and single-cell allelic specific expression (sc-ASE) in major retinal cell types. By integrating these results, we identified and characterized regulatory elements and genetic variants effective on gene regulation in individual cell types. Most of the sc-eQTLs and sc-caQTLs identified show cell type specific effects, while the cis-elements containing the genetic variants with cell type specific effects tend to be accessible in multiple cell types. Furthermore, the transcription factors with binding sites perturbed by genetic variants tend to have higher expression in the cell types, where the variants have effect, than the cell types where the variants do not have effect. Finally, we identified the enriched cell types, candidate causal variants and genes, and cell type specific regulatory mechanism underlying GWAS loci.

Conclusions

Overall, genetic effects on gene regulation are highly context dependent. Our results suggest that among cell types sharing a similar lineage, cell type dependent genetic effect is primarily driven by trans-factors rather than cell type specific chromatin state of cis-elements. Our findings indicate a role for hierarchical transcription factors collaboration in cell type specific effects of genetic variants on gene regulation.
Integrative Teaching of Metabolic Modeling and Flux Analysis with Interactive Python Modules
Authors: Kaste Joshua A.M. , Green Antwan , Shachar-Hill Yair
Published: November 2022

The modeling of rates of biochemical reactions – fluxes – in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint-based (Metabolic Flux Analysis and Flux Balance Analysis) approaches. Although different resources exist for teaching these methods individually, to-date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, Metabolic Control Analysis, l3C-Metabolic Flux Analysis and Flux Balance Analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands-on computer laboratory component of a four-day metabolic modeling workshop and participant survey results showed improvements in learners’ self-assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.
Structured surveys of Australian native possum excreta predict Buruli ulcer occurrence in humans
Authors: Vandelannoote Koen , Buultjens Andrew H. , Porter Jessica L. , Velink Anita , Wallace John R. , Blasdell Kim R. , Dunn Michael , Boyd Victoria , Fyfe Janet A. M. , Tay Ee Laine , Johnson Paul D. R. , Windecker Saras , Golding Nick , Stinear Timothy P.
Published: November 2022

Buruli ulcer (BU) is a neglected tropical disease caused by infection of subcutaneous tissue withMycobacterium ulcerans. BU is commonly reported across rural regions of Central and West Africa but has been increasing dramatically in temperate southeast Australia around the major metropolitan city of Melbourne. Previous research has shown that Australian native possums are reservoirs ofM. ulceransand that they shed the bacteria in their fecal material (excreta). Field surveys show that locales where possums harborM. ulceransoverlap with human cases of BU, raising the possibility of using possum excreta surveys to predict the risk of disease occurrence in humans. We thus established a highly structured 12-month possum excreta surveillance program across an area of 350 km2in the Mornington Peninsula area 70 km south of Melbourne, Australia. The primary objective of our study was to assess ifM. ulceranssurveillance of possum excreta provided useful information for predicting future human BU case locations. Over two sampling campaigns in summer and winter, we collected 2282 possum excreta specimens of which 11% were PCR positive forM. ulcerans-specific DNA. Using the spatial scanning statistical toolSatScan, we observed non-random, co-correlated clustering of bothM. ulceranspositive possum excreta and human BU cases. We next trained a statistical model with the Mornington Peninsula excreta survey data to predict the future likelihood of human BU cases occurring in the region. By observing where human BU cases subsequently occurred, we show that the excreta model performance was superior to a null model trained using the previous year’s human BU case incidence data (AUC 0.66 vs 0.55). We then used data unseen by the excreta-informed model from a new survey of 661 possum excreta specimens in Geelong, a geographically separate BU endemic area to the southwest of Melbourne, to prospectively predict the location of human BU cases in that region. As for the Mornington Peninsula, the excreta-based BU prediction model outperformed the null model (AUC 0.75 vs 0.50) and pinpointed specific locations in Geelong where interventions could be deployed to interrupt disease spread. This study highlights theOne Healthnature of BU by confirming a quantitative relationship between possum excreta shedding ofM. ulceransand humans developing BU. The excreta survey-informed modeling we have described will be a powerful tool for efficient targeting of public health responses to stop BU.
Cell type-specific assessment of cholesterol distribution in models of neurodevelopmental disorders
Authors: Czernecki Charlotte , Dixit Shirley , Riezman Isabelle , Innocenti Sabrina , Bornmann Caroline , Pfrieger Frank W. , Riezman Howard , Scheiffele Peter
Published: November 2022

Most nervous system disorders manifest through alterations in neuronal signaling based on abnormalities in neuronal excitability, synaptic transmission, and cell survival. However, such neuronal phenotypes are frequently accompanied – or even caused – by metabolic dysfunctions in neuronal or non-neuronal cells. The tight packing and highly heterogenous properties of neural, glial and vascular cell types pose significant challenges to dissecting metabolic aspects of brain disorders. Perturbed cholesterol homeostasis has recently emerged as key parameter associated with sub-sets of neurodevelopmental disorders. However, approaches for tracking and visualizing endogenous cholesterol distribution in the brain have limited capability of resolving cell type-specific differences. We here develop tools for genetically-encoded sensors that report on cholesterol distribution in the mouse brain with cellular resolution. We apply these probes to examine sub-cellular cholesterol accumulation in two genetic mouse models of neurodevelopmental disorders,Npc1andPtchd1knock-out mice. While both genes encode proteins with sterol-sensing domains that have been implicated in cholesterol transport, we uncover highly selective and cell type-specific phenotypes in cholesterol homeostasis. The tools established in this work should facilitate probing sub-cellular cholesterol distribution in complex tissues like the mammalian brain and enable capturing cell type-specific alterations in cholesterol flow between cells in models of brain disorders.
Resolution of fibrosis in mdx dystrophic mouse after oral consumption of N-163 strain ofAureobasidium pullulansproduced biological response modifier β-glucan (BRMG)
Authors: Preethy Senthilkumar , Aoki Yoshitsugu , Minegishi Katsura , Iwasaki Masaru , Senthilkumar Rajappa , Abraham Samuel JK
Published: November 2022

Recent advances in the management of Duchenne Muscular Dystrophy (DMD), such as exon skipping therapy, have reached a clinical stage, and although gene therapy is in clinical trials, the outcome at its best is still considered suboptimal to yield clinically discernible progress. In this study, we evaluated a novel N-163 strain ofAureobasidium pullulansproduced biological response modifier β-glucan (BRMG) for its potential as an adjuvant to slow down the progression of the disease by anti-inflammatory and anti-fibrotic effects. This N-163 β-glucan is a safe and orally consumable food supplement with similar effects that have been previously proven in pre-clinical studies of organ fibrosis, and their beneficial effects have been proven in DMD clinical studies through blood parameters as well. In this study, 45 mice in the three groups, 15 each in a group; Gr. 1 normal mice, Gr.2 mdx mice as vehicle, and Gr.3 mdx mice administered the N-163 strain produced β-glucan for 45 days. Blood biochemical parameters, body weight, muscle weight, inflammation score, and fibrosis score were evaluated using H&E and Masson’s trichrome staining. The N-163 β-glucan group showed a significant decrease in the plasma ALT, AST, and LDH levels (126 ± 69, 634 ± 371, 3335 ± 1258 U/l) compared with the vehicle group (177 ± 27 U/l, 912 ± 126 U/l, 4186 ± 398 U/l). Plasma TGF-β levels increased, and plasma IL-13 levels decreased in the N-163 group. The inflammation score of HE-stained muscle sections in the N-163 group (1.5 ± 0.8) was lower than that in the vehicle group (2.0 ± 0.8). The percentage of centrally nucleated fibres (CNF) evaluated by Masson’s trichrome staining was 0 in the normal group, while it increased to 80% in the vehicle group and 76.8% in the N-163 group. The N-163 β-glucan group (24.22 ± 4.80) showed a significant decrease in the fibrosis area (Masson’s trichrome-positive area). The N-163 β-glucan thus, demonstrated its anti-fibrotic effect in this study. Considering their safety and easy oral consumption, this BRMG could be worth large multicentre clinical studies as adjuvant in slowing down the progress of DMD.
Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction
Authors: Rodríguez Bárbara Díez , Galanti Dario , Nunn Adam , Peña-Ponton Cristian , Pérez-Bello Paloma , Sammarco Iris , Jandrasits Katharina , Becker Claude , De Paoli Emanuele , Verhoeven Koen J.F , Opgenoorth Lars , Heer Katrin
Published: November 2022

- Environmental changes can trigger phenotypic variation in plants through epigenetic mechanisms, but strong genetic influences make it difficult to isolate and study epigenetic effects. Clonal trees with low genetic variation, such as the Lombardy poplar(Populus nigracv. ‘Italica’ Duroi), offer a unique system to study epigenetic variation associated with the environment.

- We collected cuttings (ramets) of Lombardy poplar along a wide geographical range in Europe. We performed whole-genome-bisulfite sequencing of 164 ramets grown in a common garden and of a subset of 35 of the original parental individuals. Using historical bioclimatic data, we tested the relationship between DNA methylation and climatic gradients.

- We found that average methylation levels in TEs and promoter regions correlate with biologically relevant climatic variables. Furthermore, we observed that DNA methylation was transmitted to the next clonal generation, but a fraction of the methylome changed relatively fast when comparing the parental individuals with the clonal offspring.

- Our results suggest that the poplar methylome is a dynamic layer of information that can be transmitted to the clonal offspring and potentially affect how poplars acclimate to new environmental conditions.
Reconceptualizing the retrieval state as an internal attention state
Authors: Long Nicole M.
Published: November 2022

Large-scale brain states or distributed patterns of brain activity modulate downstream processing and behavior. Sustained attention and memory retrieval states impact subsequent memory, yet how these states relate to one another is unclear. We hypothesize that the retrieval state reflects internal attention. The alternative is that the retrieval state reflects a controlled, episodic retrieval mode, specifically engaged when intentionally accessing events situated within a spatiotemporal context. To test our hypothesis, we developed a mnemonic state classifier independently trained to measure retrieval state evidence and applied this classifier to a spatial attention task. We find that retrieval state evidence increases during delay and response intervals when participants are maintaining spatial information. Critically, retrieval state evidence is positively related to the amount of maintained spatial location information and predicts target detection reaction times. Together, these findings strongly support the hypothesis that the retrieval state constitutes internal attention.
A meiotic midbody structure in mouse oocytes acts as a barrier for nascent translation to ensure developmental competence
Authors: Jung Gyu Ik , Londoño-Vásquez Daniela , Park Sungjin , Skop Ahna R. , Balboula Ahmed Z. , Schindler Karen
Published: November 2022

Successful embryo development is dependent upon maternally deposited components. During egg formation, developmental competence is acquired through regulated translation of maternal mRNA stores. In addition, egg precursors undergo two rounds of chromosome segregation, each coupled to an asymmetric cytokinesis that produces two non-functional polar bodies. In somatic cells, cytokinesis produces two daughter cells and one midbody remnant (MBR), a signaling organelle assembled from the midbody (MB), which first appears in Telophase. MBs contain transcription and translation factors, and epigenetic modifiers. Once MBs mature to MBRs by abscission, they can be subsequently phagocytosed by another cell and influence cellular function or fate. Although the significance of MBs is elucidated in several cell types like neurons, cancer cells and stem cells, the presence and function of MBs in gametes and their roles in reproductive fitness are unknown. Here, we examined the formation and regulation of meiotic midbodies (mMB) in mouse oocytes. We find that although mouse oocyte mMBs contain analogous structures to somatic MBs, they also have a unique cap-like structure composed of the centralspindlin complex, and that cap formation depends upon an asymmetric microtubule abundance in the egg compared to the polar body. Furthermore, our results show that mMBs are translationally active ribonucleoprotein granules, supported by detection of ribosomes, polyadenylated mRNAs and nascent translation. Finally, by pharmacological and laser ablation-based approaches, we demonstrate that the mMB cap is a barrier to prevent translated products from leaving the egg and escaping into the polar body. Crucially, this barrier is critical for successful early embryonic development. Here, we document an evolutionary adaptation to the highly conserved process of cytokinesis in mouse oocytes and describe a new structure and new mechanism by which egg quality and embryonic developmental competence are regulated.
Locations, city connectivity and innovation zones in China: a dynamic perspective of knowledge community
Authors: Du Juana , Krusekopf Charles
Published: November 2022

Purpose

This study aims to examine two innovation zones in China, including the Suzhou Industrial Park and Tianjin Eco-city, to gain a comprehensive understanding of city locations attributes and its relationship to inward foreign direct investment (FDI) from multinational enterprises (MNEs) in innovation zones embedded in nonhub cities in China.

Design/methodology/approach

This research incorporates two site visits and in-depth interviews with 39 personnel working with innovation zones. Thematic analysis is used to analyze interview data and documents.

Findings

The results highlight that cities can use innovation zones as a strategy to build high scale knowledge community precincts to connect MNEs and other global actors. As an important institutional feature of city locations, innovation zones increase within-city connectivity and connect cities in global networks resulting in cross-city connectivity to attract FDI from MNEs. From a dynamic knowledge community perspective, this research also compares active and passive approaches toward building knowledge communities and identifies several elements of knowledge communities within innovation zones in China.

Research limitations/implications

The research results could be further explored in other institutional and economic contexts, to understand the interplay of city locations, FDI and innovation zones, and the dynamics of building knowledge communities.

Practical implications

This research has several implications for policymakers and administrators who work with municipal economic development and the development and enhancement of innovation zones. It offers recommendations for MNEs to consider where to make foreign investments and the advantages innovation zones may offer to support FDI.

Originality/value

This research contributes to the literature related to economic development and how nonhub cities can attract FDI and join global networks. It offers empirical insights drawn from two successful innovation zones located in nonhub cities in China.
Governance and social responsibility: what factors impact corporate performance in a small banking-oriented country?
Authors: Neves Maria Elisabete , Proença Catarina , Cancela Beatriz
Published: November 2022

Purpose

This paper aims to analyze the corporate governance and corporate social responsibility (CSR) determinants of the Portuguese listed companies’ performance, considering a different point of view by managers, shareholders and other external stakeholders and investors.

Design/methodology/approach

To achieve this aim, the authors have used a sample of 34 nonfinancial listed companies in Euronext Lisbon between 2015 and 2020. The authors use the panel data methodology to test the hypotheses formulated according to the literature review, specifically the generalized method of moments (GMM) system estimation model proposed by Arellano and Bond (1991).

Findings

The main results point out that the determinants of the corporate performance vary depending on the dependent variable considered. From the managers’ perspective, the existence of an audit committee and expenses with the environment increase costs and reduce results, negatively influencing corporate performance, but the company’s maturity adds synergies in resource management and positively influences performance. Shareholders consider that gender diversity and board independence positively influence performance, whereas, for external stakeholders and long-term investors, gender diversity and the social responsibility committee harm the performance of Portuguese companies. However, environmental and social expenditures have a positive effect, showing that the market’s perception is that, in the long run, it is essential to eradicate poverty and protect the environment.

Originality/value

To the best of the authors’ knowledge, this study is the first one to analyze corporate governance and CSR determinants on the performance of listed Portuguese companies. This study shows that in a small banking-oriented country, there is still a long way to go in terms of increasing social responsibility and governance among different stakeholders. It is essential to promote actions that lead to effective governance and awareness of social responsibility.
Ritual-based redesign of routines: an experimental approach in the restaurant industry
Authors: Cozzio Claudia , Furlan Andrea
Published: November 2022

Purpose

This study aims to investigate the impact of the innovative ritual-based redesign of a routine in the challenging context of the dining-out sector, characterized by low employee commitment and high turnover.

Design/methodology/approach

This study adopts a mixed methods experimental design. This study focuses on a field experiment in a real restaurant centered on the restaurant’s welcome entrée routine. The routine is first observed as it happens, after which it is redesigned as a ritual.

Findings

The ritual-based redesign of the routine enhances employee sharing of the purpose of the routine and reduces the variability of the execution time of the routine, which increases group cohesion among the restaurant staff. Besides the positive impact on the routine’s participants, the ritual-based redesign has a beneficial effect on the performance of the routine by increasing the enjoyment of the end-consumers at the restaurant.

Research limitations/implications

The ritual-based redesign of routines is a powerful managerial tool that bonds workers into a solidary community characterized by strong and shared values. This allows guidance of the behavior of new and existing employees in a more efficient and less time-consuming way.

Originality/value

Rituals have been traditionally analyzed from the customer perspective as marketing tools. This research investigates the employees’ perspective, leveraging ritual-based redesign as a managerial tool for increasing cohesion among workers.
Determinants of SMEs’ performance: amalgamation of entrepreneurial, market and brand orientations
Authors: Ismail Ahmed Rageh , Mohamad Bahtiar
Published: November 2022

Purpose

Scholars and practitioners alike are paying attention to entrepreneurial orientation (EO) as an antecedent of the financial performance of SMEs. Other factors foster and improve SMEs' financial performance. This paper aims to shed the light on other two different strategic orientations that may help enhance SMEs' financial performance in addition to EO, namely; market orientation (MO) and brand orientation (BO).

Design/methodology/approach

The three different important strategic orientations are explored through two different studies. The first study was conducted to determine the different effects of the three orientations on SMEs' financial performance. Data were collected using a questionnaire among a convenient sample (131) of business owners/managers, and next PLS-SEM was used for data analysis. The financial performance of firms in the second study is hypothesized to be an outcome of a combination of different strategic orientations; therefore, the fsQCA method is applied to explore the causal recipes of those orientations.

Findings

The paper concluded that the three different strategic orientations are collectively, of paramount importance to strategic managers of SMEs.

Originality/value

The brand, market and EOs have been discussed discretely in previous studies and this study attempted to provide managers/owners of SMEs with a holistic view of the three different orientations and the amalgamation among them to be beneficial for better financial performance.
The role of data sharing in survey dropout: a study among scientists as respondents
Authors: Fichtner Urs Alexander , Horstmeier Lukas Maximilian , Brühmann Boris Alexander , Watter Manuel , Binder Harald , Knaus Jochen
Published: November 2022

Purpose

One of the currently debated changes in scientific practice is the implementation of data sharing requirements for peer-reviewed publication to increase transparency and intersubjective verifiability of results. However, it seems that data sharing is a not fully adopted behavior among researchers. The theory of planned behavior was repeatedly applied to explain drivers of data sharing from the perspective of data donors (researchers). However, data sharing can be viewed from another perspective as well: survey participants. The research questions (RQs) for this study were as follows: 1 Does data sharing increase participant's nonresponse? 2 Does data sharing influence participant's response behavior? The purpose of this paper is to address these issues.

Design/methodology/approach

To answer the RQs, a mixed methods approach was applied, consisting of a qualitative prestudy and a quantitative survey including an experimental component. The latter was a two-group setup with an intervention group (A) and a control group (B). A list-based recruiting of members of the Medical Faculty of the University of Freiburg was applied for 15 days. For exploratory data analysis of dropouts and nonresponse, we used Fisher's exact tests and binary logistic regressions.

Findings

In sum, we recorded 197 cases for Group A and 198 cases for Group B. We found no systematic group differences regarding response bias or dropout. Furthermore, we gained insights into the experiences our sample made with data sharing: half of our sample already requested data of other researchers or shared data on request of other researchers. Data repositories, however, were used less frequently: 28% of our respondents used data from repositories and 19% stored data in a repository.

Originality/value

To the authors’ knowledge, their study is the first study that includes researchers as survey subjects investigating the effect of data sharing on their response patterns.
The footprints of Russia–Ukraine war on the intraday (in)efficiency of energy markets: a multifractal analysis
Authors: Aslam Faheem , Slim Skander , Osman Mohamed , Tabche Ibrahim
Published: November 2022

Purpose

This paper examines the impact of Russian invasion of Ukraine on the intraday efficiency of four major energy markets, namely, diesel oil, Brent oil, light oil and natural gas.

Design/methodology/approach

This study applies the multifractal detrended fluctuation analysis (MFDFA) to high-frequency returns (30-min intervals) for the period from October 21, 2021, to May 20, 2022. The data sample of 5,141 observations is divided into two sub-samples, before and after the invasion of 24th February 2022. Additionally, the magnitude of long memory index is employed to investigate the presence of herding behavior around the invasion period.

Findings

Results confirm the presence of multifractality in energy markets and reveal significant changes of multifractal strength due to the invasion, indicating a decline of intraday efficiency for oil markets. Surprisingly, the natural gas market, being the least efficient before the invasion, turns out to be more efficient after the invasion. The findings also suggest that investors in these energy markets are likely to show herding, more prominently after the invasion.

Practical implications

The multifractal patterns, in particular the long memory property of energy markets, can help investors develop profitable investment strategies. Furthermore, the improved efficiency observed in the natural gas market, after the invasion, highlights its unique traits and underlying complexity.

Originality/value

This study is the first attempt to assess the impact of the Russia–Ukraine war on the efficiency of global commodity markets. This is quite important because the adverse effects of the war on financial markets may potentially cause destabilizing outcomes and negative effects on social welfare on a global scale.
Breaking down the components of the competition‐colonization trade‐off: New insights into its role in diverse systems
Authors: Ferzoco Ilia Maria C. , McCauley Shannon J.
Published: November 2022

Performance trade‐offs between competition and colonization can be an important mechanism facilitating regional coexistence of competitors. However, empirical evidence for this trade‐off is mixed, raising questions about the extent to which it shapes diverse ecological communities. Here, we outline a framework that can be used to improve empirical tests of the competition‐colonization trade‐off.

We argue that tests of the competition‐colonization trade‐off have been diverted into unproductive paths when dispersal mode and/or competition type have been inadequately defined. To generate comparative predictions of associations between dispersal and competitive performance, we develop a conceptual trait‐based framework that clarifies how dispersal mode and type of competitor shape this trade‐off at the stage of dispersal and establishment in a variety of systems. Our framework suggests that competition‐colonization trade‐offs may be less common for passively dispersing organisms when competitive dominants are those best able to withstand resource depletion (competitive response), and for active dispersers when traits for dispersal performance are positively associated with resource pre‐emption (competitive effect).

The framework presented here is designed to provide common ground for researchers working in different systems in order to prompt more effective assessment of this performance trade‐off and its role in shaping community structure. By delineating key system properties that mediate the trade‐off between competitive and colonization performance and their relationship to individual‐level traits, researchers in disparate systems can structure their predictions about this trade‐off more effectively and compare across systems more clearly.
Density‐dependent plasticity in territoriality revealed using social network analysis
Authors: Webber Quinn M. R. , Dantzer Ben , Lane Jeffrey E. , Boutin Stan , McAdam Andrew G.
Published: November 2022

Territories are typically defined as spatially exclusive areas that are defended against conspecifics. Given the spatial nature of territoriality, it is inherently density dependent, but the economics of territoriality also depend on the distribution and abundance of defended resources. Our objectives were to assess the effects of changing population density and food availability on individually based territorial phenotypes.

We developed a novel analytical framework that bridges spatially explicit territories with social network analysis to model density‐dependent territorial phenotypes. Using the outputs from our data pipeline, we modelled plasticity in territory size and territory intrusion rates in a long‐term study population of North American red squirrels Tamiasciurus hudsonicus. Red squirrels defend year‐round territories around a central hoard (midden) of white spruce Picea glauca cones. Importantly, white spruce is a masting species that produces large cone crops every 4–7 years (i.e. mast years) in our study area interspersed with non‐mast years when few cones are produced. In the spring following mast years, populations are approximately double in size, but are lower in the spring of non‐mast years.

We predicted that territory size and intrusion rates would decrease as resource abundance, and consequently population density, increased. By contrast, as resource abundance decreased via depletion, and therefore density decreased, territories should increase in size and intrusions should also increase.

As we expected, individual territory size and territorial intrusions were negatively density dependent, such that increased density after mast years resulted in smaller territories and fewer intrusions. When considering between‐individual variation in plasticity across a density gradient, individuals responded differently to changes in population density within their lifetime.

Our results show that territory size and intrusion rates display negative density dependence. When food becomes available in the autumn of a mast year and density in spring of the following year increases, territories shrink in size to effectively a small area around the midden. While our findings for red squirrels are unique compared to other systems, they serve as a reminder that the direction and strength of fundamental ecological relationships can depend on the nature of the system.
Arbuscular mycorrhizal fungi communities shaped by host‐plant affect the outcome of plant–soil feedback in dryland restoration
Authors: Medeiros Adler Santana , Scaloppi Julie Christine , Damasceno Edjane Silva , Goto Bruno Tomio , Vieira Daniela Cristine Mascia , Socolowski Fábio , Rodrigues Renato Garcia , Yano‐Melo Adriana Mayumi
Published: November 2022

Plant inoculation with arbuscular mycorrhizal fungi (AMF) can be a useful tool to overcome challenges in dry forest restoration. However, advances are still needed to guide choices regarding soil origin and inoculum production methods, since outcomes can vary due to plant–soil feedbacks (PSF). We evaluate how soil origin and host plant used for inoculum production affect AMF community and therefore the plant biomass accumulation and functional traits.

In the conditioning phase, we investigated whether soils originating from a recovered area (Quarry) and a vegetation fragment (Caatinga) would have their AMF communities modified due to the growth of Sorghum bicolor (used for inoculum production) and Senna uniflora (used in Brazilian semiarid restoration). In the feedback phase, we compared the performance of four plants species growing on a degraded soil and inoculated or not by a mixture of AMF isolates in comparison to soil inoculum prepared from the conditioning phase.

The inoculum from Caatinga presented seven times more AMF species compared to that from the Quarry, which presented ruderal and stress tolerant species. The soil inoculum conditioned by S. uniflora, regardless of origin, presented greater evenness compared to the soil inoculum produced with S. bicolor and promoted 33% more plant biomass compared to the control without inoculation. Root colonization by AMF increased PSF and decreased plant investment in functional traits such as specific root length (SRL) and specific leaf area (SLA).

Our results demonstrate the importance of adopting strategies that preserve local adaptation of inoculants produced. The use of native plant for propagation of native AMF in the conditioning phase provided more positive responses for Mesosphaerum suaveolens and Rhaphiodon echinus than inoculated with introduced AMF isolates. This is probably due to the interaction of inoculated plants with responsive AMF present in the soil.

Synthesis and applications. Our study shows that conditioning field‐collected soil with Senna uniflora and using it for inoculation can be a simple technique to promote biomass accumulation for other native herbaceous species. This preserves the compatibility between the soil inoculum produced with native AMF and native plants, representing an important tool for restoration programs.
Prairie strips reduce fecal indicator bacteria concentrations in simulated runoff
Authors: Craig Andrew J. , Rehmann Chris R. , Alt Laura M. , Schulte Lisa A. , Soupir Michelle L.
Published: November 2022

Vegetative filter strips (VFS) have shown promising results in reducing the downstream transport of many agroecosystem contaminants. A recently developed type of VFS, prairie strips, has been shown to significantly reduce the impact of corn and soybean production systems on water quality in terms of sediment, nitrogen, and phosphorus losses. This study assessed potential additional benefits of prairie strips to include the reduction of pathogens. To assess the impact of prairie strips on manure‐laden agricultural runoff, we utilized a physical model of prairie strips in a laboratory flume to conduct highly controlled overland flow experiments. Escherichia coli and Enterococcus concentration reductions of up to 45% and 65% were observed for runoff and infiltration flows, respectively, while mass load reductions of up to 65% were observed for surficial runoff flows. The degree of concentration or mass load reductions was dependent on the residence time of the flow within the strip and the partitioning of overland flow running onto the strip to infiltration and runoff flows. Based on our results and a review of the literature, we developed a design method to provide guidance on the width of prairie strip buffer needed to achieve a user‐defined reduction of fecal bacteria concentration.
Oral oxycodone self‐administration leads to features of opioid misuse in male and female mice
Authors: Slivicki Richard A. , Earnest Tom , Chang Yu‐Hsuan , Pareta Rajesh , Casey Eric , Li Jun‐Nan , Tooley Jessica , Abiraman Kavitha , Vachez Yvan M. , Wolf Drew K. , Sackey Jason T. , Kumar Pitchai Dhinesh , Moore Terrill , Gereau Robert W. , Copits Bryan A. , Kravitz Alexxai V. , Creed Meaghan C.
Published: November 2022

Use of prescription opioids, particularly oxycodone, is an initiating factor driving the current opioid epidemic. There are several challenges with modelling oxycodone abuse. First, prescription opioids including oxycodone are orally self‐administered and have different pharmacokinetics and dynamics than morphine or fentanyl, which have been more commonly used in rodent research. This oral route of administration determines the pharmacokinetic profile, which then influences the establishment of drug‐reinforcement associations in animals. Moreover, the pattern of intake and the environment in which addictive drugs are self‐administered are critical determinants of the levels of drug intake, of behavioural sensitization and of propensity to relapse behaviour. These are all important considerations when modelling prescription opioid use, which is characterized by continuous drug access in familiar environments. Thus, to model features of prescription opioid use and the transition to abuse, we designed an oral, homecage‐based oxycodone self‐administration paradigm. Mice voluntarily self‐administer oxycodone in this paradigm without any taste modification such as sweeteners, and the majority exhibit preference for oxycodone, escalation of intake, physical signs of dependence and reinstatement of seeking after withdrawal. In addition, a subset of animals demonstrate drug taking that is resistant to aversive consequences. This model is therefore translationally relevant and useful for studying the neurobiological substrates of prescription opioid abuse.