bluuebunny/crossref_metadata_2025 huggingface dataset:
YAP/TAZ enhance P-body formation to promote tumorigenesis
Authors: Shen Xia , Peng Xiang , Guo Yuegui , Dai Zhujiang , Cui Long , Yu Wei , Liu Yun , Liu Chen-Ying
Published: June 2023

The role of Processing bodies (P-bodies) in tumorigenesis and tumor progression is not well understood. Here, we showed that the oncogenes YAP/TAZ promote P-body formation in a series of cancer cell lines. Mechanistically, both transcriptional activation of the P- body-related genes SAMD4A, AJUBA, and WTIP and transcriptional suppression of the tumor suppressor gene PNRC1 are involved in enhancing the effects of YAP/TAZ on P- body formation in CRC cells. By reexpression of PNRC1 or knockdown of P-body core genes (DDX6, DCP1A, and LSM14A), we determined that disruption of P-bodies attenuates cell proliferation, cell migration and tumor growth induced by overexpression of YAP5SAin CRC. Analysis of a pancancer CRISPR screen database (DepMap) revealed codependencies between YAP/TEAD and the P-body core genes and correlations between the mRNA levels of SAMD4A, AJUBA, WTIP, PNRC1 and YAP target genes. Our study suggests that the P-body is a new downstream effector of YAP/TAZ, which implies that reexpression of PNRC1 or disruption of P-bodies is a potential therapeutic strategy for tumors with active YAP.
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Authors: Aßmann Eva , Agrawal Shelesh , Orschler Laura , Böttcher Sindy , Lackner Susanne , Hölzer Martin
Published: June 2023

Background

Sequencing of SARS-CoV-2 RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances of SARS-CoV-2 variants in a community. By analyzing the viral genetic material present in wastewater, public health officials can gain early insights into the spread of the virus and inform timely intervention measures. The construction of reference datasets from known SARS-CoV-2 lineages and their mutation profies has become state-of-the-art for assigning viral lineages and their relative abundances from wastewater sequencing data. However, the selection of reference sequences or mutations directly affects the predictive power.

Results

Here, we show the impact of amutation-andsequence-basedreference reconstruction for SARS-CoV-2 abundance estimation. We benchmark three data sets: 1) synthetic “spike-in” mixtures, 2) German samples from early 2021, mainly comprising Alpha, and 3) samples obtained from wastewater at an international airport in Germany from the end of 2021, including 1rst signals of Omicron. The two approaches differ in sub-lineage detection, with the marker-mutation-basedmethod, in particular, being challenged by the increasing number of mutations and lineages. However, the estimations of both approaches depend on selecting representative references and optimized parameter settings. By performing parameter escalation experiments, we demonstrate the effects of reference size and alternative allele frequency cutoffs for abundance estimation. We show how different parameter settings can lead to different results for our test data sets, and illustrate the effects of virus lineage composition of wastewater samples and references.

Conclusions

Here, we compare amutation-andsequence-basedreference construction and assignment for SARS-CoV-2 abundance estimation from wastewater samples. Our study highlights current computational challenges, focusing on the general reference design, which significantly and directly impacts abundance allocations. We illustrate advantages and disadvantages that may be relevant for further developments in the wastewater community and in the context of higher standardization.
The ORP9-ORP11 dimer promotes sphingomyelin synthesis
Authors: Cabukusta Birol , Pauwels Shalom Borst , Akkermans Jimmy J.L.L. , Blomberg Niek , Mulder Aat A. , Koning Roman I. , Giera Martin , Neefjes Jacques
Published: June 2023

Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-transGolgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.
Genetic diversity, determinants, and dissemination ofBurkholderia pseudomalleilineages implicated in melioidosis in northeast Thailand
Authors: Seng Rathanin , Chomkatekaew Chalita , Tandhavanant Sarunporn , Saiprom Natnaree , Phunpang Rungnapa , Thaipadungpanit Janjira , Batty Elizabeth M , Day Nicholas PJ , Chantratita Wasun , West T. Eoin , Thomson Nicholas R , Parkhill Julian , Chewapreecha Claire , Chantratita Narisara
Published: June 2023

Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacteriumBurkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conducted a comprehensive genomic analysis of 1,391B. pseudomalleiisolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identified three dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific adaptation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage revealed heightened expression of lineage-specific genes in environmental versus infection conditions, notably under nutrient depletion, highlighting environmental persistence as a key factor in the success of dominant lineages. The study also revealed the role of environmental factors – slope of terrain, altitude, direction of rivers, and the northeast monsoons – in shapingB. pseudomalleigeographical dispersal. Collectively, our findings highlight persistence in the environment as a pivotal element facilitatingB. pseudomalleispread, and as a prelude to exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
Elucidating the mechanism of microbial thermogenesis
Authors: Dhatt Puneet Singh , Moon Tae Seok
Published: June 2023

Organisms necessarily release heat energy in their pursuit of survival. This process is known as cellular thermogenesis and is implicated in many processes from cancer metabolism to spontaneous farm fires1,2. However, the molecular basis for this fundamental phenomenon is yet to be elucidated. Here, we show that the major players involved in cellular thermogenesis are the protein kinases ArcB, GlnL, and YccC inEscherichia coli. We also reveal the substrate-level control of ATP-driven autophosphorylation that governs cellular thermogenesis. Through live-cell microcalorimetric experimentation, we find that only three of the 231 regulatory proteins, when knocked out in a modelEscherichia colistrain, dysregulate cellular thermogenesis. This dysregulation can be seen in an average 25% or greater increase in heat output by these cells. We also discover that both heat output and intracellular ATP levels are maximal during the late log phase of growth. Our results demonstrate a correlation between ATP concentrations in the cell and a cell’s ability to generate excess heat. We expect this work to be the foundation for engineering a new generation of thermogenically-tuned organisms for a variety of applications.
Morphological brain networks of white matter: mapping, evaluation, characterization and application
Authors: Li Junle , Li Zhen , Yang Yuping , Luo Zhenzhen , Liu Yaou , Wang Jinhui
Published: June 2023

Neuroimaging-based connectomics studies have long focused on the wiring patterns between gray matter regions. In recent years, increasing evidence emerges that neural activity in specific sets of white matter (WM) tracts dynamically fluctuates in a coordinated manner. However, the structural basis underlying the coordination is poorly understood largely due to the lack of approaches for estimating structural relations between WM regions. Here, we developed an approach to construct morphological WM networks based on structural magnetic resonance imaging. We found that the morphological WM networks exhibited nontrivial organizational principles, presented good to excellent short- and long-term reliability, accounted for phenotypic interindividual differences (Motor and Cognition), and were under genetic control. Interestingly, highly heritable edges contributed largely to interindividual differences in phenotype. Through integration with other multimodal and multiscale data, we further showed that the morphological WM networks were able to predict regional profiles of hamodynamic coherence, metabolic synchronization, gene co-expression and chemoarchitectonic covariance. Moreover, the prediction followed functional connectomic hierarchy of WM for hamodynamic coherence, was driven by genes enriched in the forebrain neuron development and differentiation for gene co-expression, and was attributed to serotonergic system-related receptors and transporters for chemoarchitectonic covariance. Finally, applying our approach to multiple sclerosis and neuromyelitis optica spectrum disorders, we found that both diseases were associated with morphological WM dysconnectivity, which was correlated with clinical variables and able to diagnose and differentiate the diseases. Altogether, our findings indicate that morphological WM networks provide a reliable and meaningful means to explore WM architecture in health and disease.
Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages and bacterial genes
Authors: Hugerth Luisa W. , Krog Maria Christine , Vomstein Kilian , Du Juan , Bashir Zahra , Kaldhusdal Vilde , Fransson Emma , Engstrand Lars , Nielsen Henriette Svarre , Schuppe-Koistinen Ina
Published: June 2023

Background

The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene and phage levels.

Results

Based on the daily shifts in community state types (CSTs) during a menstrual cycle the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated byL. iners. TheirGardnerella spp.strains were also more likely to harbour bacteriocin-coding genes.

Conclusions

The VCDs present a novel time series classification which highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage levels and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCD’s to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two-three mid-cyclical samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women’s health and reproduction.
Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis
Authors: Wang Fangyan , Liu Xiujie , Huang Furong , Zhou Yan , Wang Xinyu , Song Zhengyang , Wang Sisi , Wang Xiaoting , Shi Dibang , Ruan Gaoyi , Ji Xiawei , Zhang Eryao , Tan Zenglin , Ye Yuqing , Wang Chuang , Zhu Jesse , Wang Wantie
Published: June 2023

Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation (FMT) treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase (GAD) and putrescine aminotransferase (PAT), in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.
Extracting thermodynamic properties from van ’t Hoff plots with emphasis on temperature-sensing ion channels
Authors: Bullerjahn Jakob Tómas , Hanson Sonya M.
Published: June 2023

Transient receptor potential (TRP) ion channels are among the most well-studied classes of temperature-sensing molecules. Yet, the molecular mechanism and thermodynamic basis for the temperature sensitivity of TRP channels remains to this day poorly understood. One hypothesis is that the temperature-sensing mechanism can simply be described by a difference in heat capacity between the closed and open channel states. While such a two-state model may be simplistic it nonetheless has descriptive value, in the sense that it can be used to to compare overall temperature sensitivity between different channels and mutants. Here, we introduce a mathematical framework based on the two-state model to reliably extract temperature-dependent thermodynamic potentials and heat capacities from measurements of equilibrium constants at different temperatures. Our framework is implemented in an open-source data analysis package that provides a straightforward way to fit both linear and nonlinear van ‘t Hoff plots, thus avoiding some of the previous, potentially erroneous, assumptions when extracting thermodynamic variables from TRP channel electrophysiology data.
Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting
Authors: Wu Yangyu , Yan Yangyang , Yang Youshan , Bian Shumin , Rivetta Alberto , Allen Ken , Sigworth Fred J.
Published: June 2023

We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 Å, and 2.9Å. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin α-Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na+solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na+solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs
Authors: Özden Furkan , Minary Peter
Published: June 2023

CRISPR-based genome editing technologies have revolutionised the field of molecular biology, offering unprecedented opportunities for precise genetic manipulation. However, off-target effects remain a significant challenge, potentially leading to unintended consequences and limiting the applicability of CRISPR-based genome editing technologies in clinical settings. Current literature predominantly focuses on point predictions for off-target activity, which may not fully capture the range of possible outcomes and associated risks. Here, we present crispAI, a neural network architecture-based approach for predicting uncertainty estimates for off-target cleavage activity, providing a more comprehensive risk assessment and facilitating improved decision-making in single guide RNA (sgRNA) design. Our approach makes use of the count noise model Zero Inflated Negative Binomial (ZINB) to model the uncertainty in the off-target cleavage activity data. In addition, we present the first-of-its-kind genome-wide sgRNA efficiency score, crispAI-aggregate, enabling prioritization among sgRNAs with similar point aggregate predictions by providing richer information compared to existing aggregate scores. We show that uncertainty estimates of our approach are calibrated and its predictive performance is superior to state-of-the-artin silicooff-target cleavage activity prediction methods.
Utilizing Large Language Models to Simplify Radiology Reports: a comparative analysis of ChatGPT3.5, ChatGPT4.0, Google Bard, and Microsoft Bing
Authors: Doshi Rushabh , Amin Kanhai , Khosla Pavan , Bajaj Simar , Chheang Sophie , Forman Howard P.
Published: June 2023

This paper investigates the application of Large Language Models (LLMs), specifically OpenAI’s ChatGPT3.5, ChatGPT4.0, Google Bard, and Microsoft Bing, in simplifying radiology reports, thus potentially enhancing patient understanding. We examined 254 anonymized radiology reports from diverse examination types and used three different prompts to guide the LLMs’ simplification processes. The resulting simplified reports were evaluated using four established readability indices. All LLMs significantly simplified the reports, but performance varied based on the prompt used and the specific model. The ChatGPT models performed best when additional context was provided (i.e., specifying user as a patient or requesting simplification at the 7th grade level). Our findings suggest that LLMs can effectively simplify radiology reports, although improvements are needed to ensure accurate clinical representation and optimal readability. These models have the potential to improve patient health literacy, patient-provider communication, and ultimately, health outcomes.
Mental health issues among medical students: Exploring predictors of mental health in Dhaka during COVID-19 pandemic
Authors: Lama Subigya Man , Ahad Md. Toufiq Elahi
Published: June 2023

Background

Mental health has always been under the shadow of everyone’s belief about their health. Concerns about mental health have already risen in the whole world. The COVID-19 pandemic has caused havoc worldwide, notably in the educational system. It has been difficult to quantify the influence of COVID-19 on the mental health of medical students in Bangladesh.

Aims

This study was conducted to assess medical students’ mental health status in Dhaka during COVID-19 pandemic.

Methods

This study was undertaken at Dhaka Medical College, Dhaka, Bangladesh and 359 medical students were the primary respondents for this study.

Results

Depression, anxiety and stress were found in around half of the study participants. Overall, three-fourth of the medical students had poor mental health status. The research study showed that depression, anxiety and stress were dependent on various socio-demographic and behavioral characteristics of medical students.

Conclusion

Poor mental health is still highly prevalent in the medical students. Different factors like age, gender, academic year, and physical exercise behavior have affected medical students’ mental health. This calls for attention towards the needs of the more vulnerable demographics and creating a welcoming environment for medical students.
Prevalence and Recurrence of Pica Behaviors in Early Childhood: Findings from the ALSPAC Birth Cohort
Authors: Papini Natalie M. , Bulik Cynthia M. , Chawner Samuel JRA , Micali Nadia
Published: June 2023

Objective

Pica has been largely understudied in general population samples. Pica occurs most often in childhood and appears more prevalent in individuals with autism and developmental delays (DD). Pica occurrence in the general population is poorly understood due to few epidemiological studies.

Method

Data on 10,109 caregivers from the Avon Longitudinal Study of Parents and Children (ALSPAC) study who reported pica behavior at 36, 54, 66, 77, and 115 months on their child were included. Autism was obtained through clinical and education records, while DD was derived from the Denver Developmental Screening Test.

Results

A total of 312 parents reported pica behaviors in their child. Of these, 19.55% reported pica at least at two waves (n=61). Pica was most common at 36 months (N=226; 2.29%) and decreased as children aged. A significant association was found between pica and autism at all five waves (p < .001). There was a significant relationship between pica and DD, with individuals with DD more likely to experience pica than those without DD at 36 (p = .01), and 54 (p < .001), 65 (p=.04), 77 (p <.001), and 115 months (p=.006). Exploratory analyses examined pica behaviors with broader eating difficulties and child body mass index.

Discussion

Pica is an uncommon behavior in childhood; however, children with DD or autism may benefit from pica screening and diagnosis between ages 36-115 months. Children who exhibit undereating, overeating, and food fussiness may also engage in pica behaviors.
Residual Radiation Risk Disparities Across Sex and Race or Ethnic Groups for Lifetime Never-Smokers on Lunar Missions
Authors: Cucinotta Francis A. , Saganti Premkumar B.
Published: June 2023

In the current decade missions to the Earth’s moon are of scientific and societal interest, however pose the problem of risks of late effects for returning crew persons, most importantly cancer and circulatory diseases. In this paper, we discuss NSCR-2022 model risk estimates for lunar missions for US racial and ethnic groups comparing never-smokers to US averages for each group and sex. We show that differences within groups between men and women are largely reduced for NS compared to the average population. Race and ethnic group dependent cancer and circulatory disease risks are reduced by 10% to 40% for NS with the largest decrease for Whites. Circulatory disease risks are changed by less than 10% for NS and in several cases modestly increased due to increased lifespan for NS. Asian-Pacific Islander (API) and Hispanics NS are at lower risk compared to Whites and Blacks. Differences between groups is narrowed for NS compared to predictions for average populations, however disparities remain especially for Blacks and to a lesser extent Whites compared to API or Hispanic NS groups.
Reduced SARS-CoV-2 infection and altered antiviral transcriptional response in IBD intestinal organoids
Authors: Jelusic Barbara , Boerno Stefan , Wurm Philipp , Przysiecki Nicole , Watschinger Christina , Wolfgruber Stella , Anthofer Margit , Ehman Sandra , Klages Sven , Zatloukal Kurt , Timmermann Bernd , Moschen Alexander , Gorkiewicz Gregor
Published: June 2023

IBD is characterized by altered immune reactions and infections are thought to trigger the chronic inflammatory response in IBD. The gut represents a productive reservoir for SARS-CoV-2 and the aforementioned factors together with immunosuppression used to treat IBD are likely influencing the outcomes of IBD patients in COVID-19. We used large and small intestinal organoids from IBD patients and controls to comparatively assess the transcriptional response of the gut epithelium during SARS- CoV-2 infection. Our analysis showed that IBD epithelia exhibit reduced viral loads compared to controls associated with a reduced expression of SARS-CoV-2 entry factors including the host receptor ACE2. Moreover, several genes implicated in the epithelial response to viral infection are intrinsically altered in IBD likely counteracting viral propagation. Notably, differences between IBD phenotypes exist wherein ulcerative colitis represents with induced cell death pathways and an induction of IL-1β despite overall lower viral loads suggestive of increased epithelial stress in this IBD phenotype. Altogether our analysis shows that IBD epithelia are not more prone to SARS-CoV-2 infection but epithelia from ulcerative colitis and Crohn’s disease exhibit specific differences which might explain the differing COVID-19 outcomes between IBD phenotypes.
Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
Authors: Hari Sundar G Vivek , Swetha Chenna , Basu Debjani , Pachamuthu Kannan , Raju Steffi , Chakraborty Tania , Mosher Rebecca A. , Shivaprasad P.V.
Published: June 2023

Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared withArabidopsis. Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.
Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10
Authors: Kolenko Petr , Mikulecký Pavel , Pham Phuong Ngoc , Malý Martin , Schneider Bohdan
Published: June 2023

Binder H33 is a small protein binder engineered by ribosome display to bind human interleukin 10. Crystals of binder H33 display severe diffraction anisotropy. A set of data files with correction for diffraction anisotropy based on different local signal-to-noise ratios was prepared. Paired refinement was used to find the optimal anisotropic high-resolution diffraction limit of the data: 3.13–2.47 Å. The structure of binder H33 belongs to the 2% of crystal structures with the highest solvent content in the Protein Data Bank.
Putting the customer at the center: does store managers' ethical leadership make a difference in authentic customer orientation?
Authors: Ruiz-Palomino Pablo , Linuesa-Langreo Jorge , Rincón-Ornelas Rosa María , Martinez-Ruiz M. Pilar
Published: June 2023

Purpose

The purpose of this article is to explore the mediating role of both ethical climate and frontline employees' ethical intent on the relationship between store managers' ethical leadership and frontline employees’ customer orientation (FECO).

Design/methodology/approach

Original data on small and medium-sized enterprises in the Mexican retail industry were used. A survey provided a sample of 332 frontline employees. To test the hypotheses, the authors conducted a partial least squares (PLS) analysis.

Findings

The results show the positive effect of ethical leadership is mainly direct. This can primarily be explained through the mechanisms of social exchange theory. Additionally, the results show that ethical climate and ethical intent act as essential partial mediators.

Originality/value

Although managers' ethical leadership typically exercises a direct and positive influence on employees' work performance, the path linking the ethical leadership of the upper echelons to this outcome has not been frequently studied, especially in terms of its impact on meeting customers' needs (i.e. frontline employees' customer orientation, or FECO). This study expands on existing knowledge by considering that a true FECO is necessarily linked to being “oriented to others”, which is fostered by the perception that moral values (i.e. honesty) are embedded in an organization's culture.
Understanding drivers of intrafirm coopetition: perspective of corporate groups
Authors: Mierzejewska Wioletta , Górska Rumiana , Aluchna Maria , Krejner-Nowecka Anna , Dziurski Patryk
Published: June 2023

Purpose

Coopetition is ubiquitous in the economy, but managing effectively this type of relationship between firms remains a challenge for many organizations. This paper investigates the coopetition within corporate groups and focus on factors that determine the simultaneous competition and cooperation between subsidiaries therein.

Design/methodology/approach

Drawing on a dataset of 121 corporate groups listed on the Warsaw Stock Exchange (WSE), this paper theoretically advances and empirically validates the impact of 18 factors which determine the coopetition relationship.

Findings

This study's findings confirm the importance of an organizational design among external and internal drivers of intrafirm coopetition. However, the role of an environmental uncertainty as a driver of intrafirm coopetition is not proven. Furthermore, the paper finds that internal determinants explain the phenomenon of coopetition between subsidiaries within a corporate group more than determinants related to the environment.

Originality/value

The paper contributes to the coopetition theory by empirical identification of drivers of intrafirm coopetition and advances the corporate groups studies by exploring internal relationships (cooperation and competition) and the determinants therein.
The status quo of Indian data repositories indexed in re3data registry
Authors: S.N. Archana , P.K. Padmakumar
Published: June 2023

Purpose

The purpose of this study was to understand the landscape of Indian research data repositories (RDRs) indexed in the re3data.org. The study analysed the metadata elements of Indian RDRs to identify their disciplinary orientations, typology, standards adopted, foreign collaborations, etc. The study ascertained the current status of the Indian RDRs by visiting their respective websites and tried to identify and map the exact disciplinary orientation of each RDR.

Design/methodology/approach

The study used “content analysis” of the metadata elements extracted from re3data.org along with the information analysis of the respective websites of the registered RDRs.

Findings

The study identified that only 80% of the Indian RDRs listed by the re3data.org is currently active. Most of the Indian RDRs are hosted by the central and state governments and are almost equally distributed among Life Sciences, Natural Sciences and Social Sciences domains. The data provided by the re3data.org for the Indian RDRs are not complete and up-to-date.

Practical implications

The findings indicate the presence of a good number of inactive RDRs in the re3data.org. The study suggests using a revised version of the DFG subject classification scheme or considering a standard classification scheme for subject indexing.

Originality/value

To the best of the authors’ knowledge, this study is the first of its kind that critically analysed the metadata values extracted and moved further to identify the current status of Indian RDRs.
Segmented research and parameter optimization of double-layer vibrating screen
Authors: Li Zhanfu , Liang Jianbin , Jia Peiyu , Zheng Shaoqi , Zhou Hongzhi , Tong Xin
Published: June 2023

Purpose

The purpose of this paper is to study the screen surface parameters of the double deck vibrating screen, in sections, to determine the influence of each part of the screen surface on the screening efficiency of the vibrating screen. Finally, the best screening parameters were calculated to obtain the best screening performance.

Design/methodology/approach

In this paper, the discrete element method is used to simulate the process of two-layer subsection screening. Response surface test was used to analyze the influence of various factors and their interactions on screening results. Finally, based on the binomial regression model of screening efficiency, the optimal combination of vibration parameters is calculated.

Findings

In the screening process of vibrating screen, due to the different screening environments in each area of the screen surface, the single-layer linear vibrating screen with equal screen surface parameters cannot obtain the best screening performance. Among the single factors, the effect of vibration frequency is the most significant.

Originality/value

To address the issue of single layer linear vibrating screens with equal screen surface parameters being unable to maintain optimal screening performance when handling large amounts of materials. This article proposes a double layer vibrating screen with different screen surface grids and screen surface angles to address the problem of low screening performance of traditional single layer linear vibrating screens.
Returnee firms, R&D input and innovation performance: critical roles of political and economic stakeholders
Authors: Dong Caiting , Liu Xielin , Zhang Si
Published: June 2023

Purpose

Although the role of returnees is critical to firm innovation, the literature offers inconsistent findings regarding returnees' effect on firms' innovation performance. To reconcile this issue, the authors argue that taking the types of innovation into account – i.e. technical innovation and commercial innovation – is necessary. Thus, the purpose of this study is to examine how firms led by returnees affect the relationship between research and development (R&D) input and above two types of innovation output, as well as the contingent role of political connections (PCs) and venture capital funding (VC funding).

Design/methodology/approach

This study empirically tested the hypotheses using a dataset of 54,617 firm-year observations for 18,475 Chinese firms in Zhongguancun Science Park (ZSP) from 2009 to 2014.

Findings

The results show that the positive effect of R&D input on technical innovation performance (TIP) is reinforced when firms are led by returnees, while the positive effect of R&D input on commercial innovation performance (CIP) is weakened when firms are led by returnees compared with those firms led by the local counterparts. The findings further show that returnee firms' positive effect on the relationship between R&D input and technical innovation performance is more salient for firms with more PCs but weakened for those with more VC funding.

Originality/value

This study enriches the research on returnee firms' advantages and disadvantages in transforming R&D input into innovation performance, and the findings highlight that firms led by returnees can increase R&D efficiency of technical innovation, but reduce R&D efficiency of commercial innovation. Moreover, this study offers a contingent view of political and economic stakeholders' roles in returnee firms' innovation, by revealing PCs help returnee firms to enhance R&D efficiency in technological innovation, while venture capital can hamper such R&D efficiency.
The interplay between firms’ capabilities and ownership in explaining environmental performance
Authors: Forés Beatriz , Camisón-Zornoza César , Fernández-Yáñez José María
Published: June 2023

Purpose

This study empirically assesses the effects of two key types of organizational and managerial capabilities—dynamic capabilities, and coordination and cohesion capabilities—on environmental performance, considering the moderating effect of family ownership. By applying the tenets of the natural resource-based view and the dynamic capabilities theory, this paper offers new insights into the topic.

Design/methodology/approach

The article presents empirical evidence from a survey of 1,019 firms operating in the Spanish tourism sector analyzed using multiple linear regression.

Findings

Overall, our results show that both dynamic capabilities and coordination and cohesion capabilities have direct and synergetic positive effects on environmental performance. In addition, the results confirm recent studies that report conflicting evidence on how family ownership affects environmental performance: family ownership is found to exert a distinct direct effect on environmental performance and on the development and application of the capabilities required to improve such performance.

Originality/value

This article sheds light on the conceptual frontiers between the different types of capabilities, as well as provides practical ways of measuring them. The article also brings evidence to bear on the debate concerning the direct and moderating effect that family ownership exerts on the relationship between both types of capabilities over environmental performance. The results of this analysis confirm the complexity of the family ownership effect on this aspect, and provide important insights for both business practitioners and academics.
A historical review of sustainable construction in Nigeria: a decade of development and progression
Authors: Isang Inimbom Walter
Published: June 2023

Purpose

Research studies related to sustainability and green building have made monumental contributions to the concept of sustainable construction (SC) in Nigeria. This paper therefore aims to present a historical review of the development of SC in Nigeria over a 10 year period. The review also provides constructive perspective on the benefits of SC and the present state of enforcement of green building in Nigeria.

Design/methodology/approach

A historical review strategy was applied to the study. Using secondary data sources, 47 influential journals from emerald, scopus and science direct database focusing on “SC”, “sustainability” and “green building” in Nigeria between 2012 and 2022 were used for the analysis.

Findings

The analysis deduced that the development of SC in Nigeria have undergone a triple period of development: the inception period (2012–2016), the transition period (2016–2020) and the advancement period (2020–present). The review juxtaposes the three timeline to show rapid growth in the awareness of SC, but revealed moderate levels of implementation in some major cities in Nigeria. Therefore, the author finds and argues that the advancement of SC in Nigeria can be achieved through the synergy, commitment and active roles of researchers, academics, practitioners, policy makers and the government in enforcing existing green policies.

Originality/value

The study is the first academic paper to undertake a decade long historical review of SC in Nigeria. This review provides an up-to-date understanding of the developments, changing dynamics and future progressions in the field of SC in Nigeria.
Strategic factors conferring organizational resilience in SMEs during economic crises: a measurement scale
Authors: Verreynne Martie-Louise , Ford Jerad , Steen John
Published: June 2023

Purpose

The paper aims to develop a strategic conceptualization and measurement scale of organizational resilience to support researchers examining how small firms prepare and respond deliberately to general disruptions in the operating environment over more extended time frames.

Design/methodology/approach

The paper uses a four-step process to develop, present and test (for predictive validity) a scale of strategic organizational resilience for frequent events or those needing long-term responses.

Findings

The resulting seven-factor measurement scale of organizational resilience consists of readiness, slack, problem-solving, flexibility, connectedness, adaptiveness and proactiveness.

Originality/value

The literature on organizational resilience explains how organizations recover from rare but catastrophic events by focusing on adaptation principles and short-term survival. The broader conceptualization presented here enables the study of organizational resilience in small-medium size enterprises (SMEs) across more frequent and pervasive events, such as financial crises, industry downturns and other forms of structural change and technological disruption. This is operationalized in a measure that includes new strategic factors associated with forward-planning and more traditional operationally focused elements.
How family firms can avoid the trap of strong social ties and still achieve innovation: critical roles of market orientation and transgenerational intent
Authors: Dayan Mumin , Ng Poh Yen , De Clercq Dirk
Published: June 2023

Purpose

To extend family business research, this article proposes and tests a curvilinear relationship between social ties and family firm innovation, with the firm's market orientation and transgenerational intent as moderators.

Design/methodology/approach

Representatives from a sample of 150 family firms in the United Arab Emirates completed self-administered questionnaires. Regression analyses on the collected data test the conceptual model and proposed hypotheses.

Findings

The empirical study reveals an inverted U-shaped relationship, such that a high market orientation mitigates the diminishing returns of social ties on enhancing family firm innovation. Similarly, at high levels of transgenerational intent, family firm innovation increases due to social ties, instead of exhibiting diminishing returns.

Originality/value

These results help explain contradictory outcomes previously attributed to social ties and offer clear guidelines for how family firms can leverage these ties more effectively to enhance their own innovation.
Festival hiatus, resilience and innovation during COVID-19: learnings from the Edinburgh festivals
Authors: Ali-Knight Jane , Kerr Gary , Stewart Hannah , Holmes Kirsten
Published: June 2023

Purpose

In this paper, the authors explore how Edinburgh's key Festivals have adapted to the COVID-19 pandemic. Their response presents the emergence of more innovative festival delivery models and a different imagining of the festival space.

Design/methodology/approach

The authors use a qualitative mixed methods research design involving 13 in-depth semi-structured interviews with Edinburgh's Festival Directors and other cultural and policy stakeholders as part of a University-funded stand-alone research project. The interviews were supplemented with participant observation at festivals virtually and in-person to experience new and emerging formats of festival content delivery, adherence to Scottish Government guidelines on COVID-19 safety, and to experience attending festivals during a pandemic.

Findings

The authors present findings on how Edinburgh's Festivals have responded to Covid-19 and how they have adapted – and in some cases reimagined – their business models to survive.

Originality/value

The authors propose a new theoretical framework that establishes a model for how festivals can approach risk management within their business model, focused on the ‘3R's’ – respond, resilience and reimagine –with communication and support being central to this framework.
Organizational mission and digital platform evolution: an investigation of entrepreneurial organizations in nascent markets
Authors: Roberts Nicholas , Kim Inchan
Published: June 2023

Purpose

Although digital platforms have become important to organizations and society, little is known about how platforms evolve over time. This is particularly true for early-stage platforms provided by entrepreneurial firms competing in nascent markets. This study aims to investigate the relationship between a platform provider's mission and the evolution of its digital platform.

Design/methodology/approach

This study conducted an exploratory, multi-case study of startups in the emerging health/fitness wearables market over the period 2007 to 2016.

Findings

This study emerged two organizational mission constructs – consistency and specificity – and two evolutionary dynamics of digital platforms – unity and evolution rate. It also considered unity and evolution rate in terms of features created by the platform provider and features connected by external parties. This study found relationships between aspects of mission consistency and platform unity and identified relationships between aspects of mission specificity and platform evolution rates.

Originality/value

This study formalized findings into a set of theoretical propositions, thereby enriching the understanding of the relationship between organizational mission and digital platform evolution in nascent markets. This study provides new constructs and relationships that can be tested and refined in future research.