bluuebunny/crossref_metadata_2025 huggingface dataset:
Muricauda spongiicola sp. nov., isolated from the sponge Callyspongia elongata
Authors: Shin Ji-Yoon , Park Jin-Sook
Published: February 2023

A novel Gram-stain-negative, thin-rod-shaped, aerobic, non-motile and yellow-pigmented marine bacterium (designated strain 2012CJ35-5T) was isolated from a marine sponge Callyspongia elongata sampled in Jeju-do, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2012CJ35-5T belonged to the family

Flavobacteriaceae

, and was most closely related to

Muricauda olearia

KCCM 90075T (96.3 %),

Muricauda alvinocaridis

JCM 33425T (95.7 %),

Muricauda flava

KCTC 22665T (95.6 %),

Muricauda koreensis

KCTC 52351T (95.6 %) and

Muricauda eckloniae

KCTC 22266T (94.9 %). Average nucleotide identity, amino acid identities and digital DNA–DNA hybridization between strain 2012CJ35-5T and the closest related strain were 72.6, 73.6 and 17.3 % respectively, indicating that strain 2012CJ35-5T represents a novel species of the genus

Muricauda

. The genome size of strain 2012CJ35-5T is 3.8 Mbp and the G+C content is 43.9 mol%. Strain 2012CJ35-5T contained menaquinone 6 as the major respiratory quinone and phosphatidylethanolamine, four unidentified aminophospholipids and five unidentified lipids as major polar lipids. The fatty acids were mainly (>15 %) defined as C15 : 0 iso (31.7 %), C15 : 1 iso G (29.2 %) and C17 : 0 iso 3OH (18.0 %). Strain 2012CJ35-5T could be distinguished from the other members of the genus

Muricauda

by a number of chemotaxonomic and phenotypic characteristics. Based on the results of polyphasic taxonomic analysis, strain 2012CJ35-5T (=KACC 22643T=LMG 32584T) represents a novel species within the genus

Muricauda

, for which the name Muricauda spongiicola sp. nov. is proposed.
Antitumor activity of intraperitoneal paclitaxel in orthotopic patient-derived xenograft models of mucinous appendiceal adenocarcinoma
Authors: Ito Ichiaki , Yousef Abdelrahman MG , Dickson Princess N , Naini Zahra A , White Michael G , Fleten Karianne G , Flatmark Kjersti , Fournier Keith F , Fowlkes Natalie W , Shen John Paul
Published: February 2023

Appendiceal adenocarcinomas (AAs) are a rare and heterogeneous mix of tumors for which few preclinical models exist. The rarity of AA has made performing prospective clinical trials difficult, and in part because of this AA remains an orphan disease with no chemotherapeutic agents approved by the FDA for its treatment. AA has a unique biology in which it frequently forms diffuse peritoneal metastases, but almost never spreads via a hematogenous route and rarely spreads to lymphatics. Given its localization to the peritoneal space we hypothesized that intraperitoneal (IP) delivery of chemotherapy could be an effective treatment strategy. Here we tested the efficacy paclitaxel given by IP administration using three orthotopic PDX models of AA established in NSG mice. Weekly treatment of 25.0 mg/kg of IP paclitaxel dramatically reduced AA tumor growth in TM00351 (81.9% reduction vs. control), PMP-2 (98.3% reduction vs. control), and PMCA-3 (71.4% reduction vs. control) PDX models. Comparing the safety and efficacy of intravenous (IV) to IP administration in PMCA-3, neither 6.25 nor 12.5 mg/kg of IV paclitaxel significantly reduced tumor growth. These results suggest that IP administration of paclitaxel is favorable to IV administration. Given the established safety record of IP paclitaxel in gastric and ovarian cancers, and lack of effective chemotherapeutics for AA, these data showing the activity of IP paclitaxel in orthotopic PDX models of mucinous AA support the evaluation of IP paclitaxel in a prospective clinical trial.
Safety, Virology, Pharmacokinetics, and Clinical Experience of High-dose Intravenous Sotrovimab for the Treatment of Mild to Moderate COVID-19: An Open-label Clinical Trial
Authors: Moya Jaynier , Temech Marisol , Parra Sergio , Juarez Erick , Hernandez-Loy Reinaldo , Moises Gutierrez Juan C. , Diaz Jorge , Hussain Rubaba , Segal Scott , Xu Claire , Skingsley Andrew , Schnell Gretja , El-Zailik Asma , Sager Jennifer E. , Aldinger Melissa , Alexander Elizabeth L. , Acloque Gerard
Published: February 2023

Background

500 mg intravenous (IV) sotrovimab has been shown to be well tolerated and efficacious against pre-Omicron strains in treating patients with mild to moderate coronavirus disease 2019 (COVID-19) at high risk for disease progression.

Methods

This was an open-label, single-arm substudy of phase 3 COMET-TAIL (NCT04913675) assessing the safety and tolerability of a 2000 mg IV dose of sotrovimab. Symptomatic patients (aged ≥18 years) with COVID-19 at high risk for progression were enrolled from June 30 through July 11, 2022, when Omicron BA.5, BA.2.12.1, and BA.4 were the predominant circulating variants in the United States. The primary endpoint was occurrence of adverse events (AEs), serious AEs (SAEs), AEs of special interest, and COVID-19 disease-related events (DREs) through Day 8. Safety, pharmacokinetics, viral load, and hospitalization >24 hours for acute management of illness or death through Day 29 were assessed.

Results

All participants (n=81) were Hispanic, 58% were female, and 51% were aged ≥55 years. Through Day 8, no AEs, including infusion-related reactions or hypersensitivity, were reported; 2 participants reported DREs (mild cough, n=2). One SAE (acute myocardial infarction), which was considered unrelated to sotrovimab or COVID-19 by the investigator, occurred on Day 27 and was the only hospitalization reported. Maximum serum concentration (geometric mean) was 745.9 µg/mL. Viral load decreased from baseline through Day 29; only 2 participants (3%) had persistently high viral load (≥4.1 log10copies/mL) at Day 8.

Conclusions

2000 mg IV sotrovimab was well tolerated, with no new unanticipated safety signals observed.

Key points summary

In participants with mild to moderate coronavirus disease 2019 at risk for progression to severe disease, a 2000 mg intravenous dose of sotrovimab had a low frequency of adverse events, with no hypersensitivity, infusion-related reactions, or deaths observed.
Impacts of age on the gut microbiota in captive giant pandas
Authors: Li Huixin , Lu Kangning , Li Guo , Li Ti , Zhang Le , Li Chao , Xie Qingyang , Liu Huaiting , Zhang Xinxing , Gong Minghao , Liu Gang , Zhang Guiquan
Published: February 2023

The gut microbiota is the most complex and most abundant symbiotic microbial ecosystem in animals. Aging is one of the main factors that cause gut microbiota structure changes, and the relationship between age and the gut microbiota in the giant panda has been a key focus of attention. The giant panda has a specialized diet of bamboo, and it relies on the microbiota that colonizes its gut to complete digestion. However, there is no in-depth understanding of the changes in the gut microbiota across the lifespan of giant pandas. Here, we identified the differences in the gut microbiota between four age groups (cubs, juveniles, adults, and geriatrics) using 16S rRNA gene high-throughput sequencing on an Illumina MiSeq platform. The results revealed that Firmicutes (mean±SD: 65.45±30.21%; range: 0.91–99.62%) and Proteobacteria (mean±SD: 31.49±27.99%; range: 0.26–85.35%) were the dominant phyla. The relative abundance ofEscherichia-Shigellawas high in both the cubs and juveniles. It is interesting to note that the adults had the highest richness and lowest diversity, while the cubs had the opposite. In summary, our study indicates that the gut microbial community composition, abundance, and functional pathways differ across four age groups of giant pandas. Exploring the influence of age, an endogenous influencing factor, on gut microbes provides basic scientific data for monitoring gut microbial dynamics and formulating gut microbial health management approaches, thereby improving the protection of giant pandas.
Glycaemic control and associated factors among patients living with type 2 diabetes in Kinshasa, Democratic Republic of the Congo: a Cross-sectional study
Authors: Lubaki Jean-Pierre Fina , Omole Olufemi Babatunde , Francis Joel Msafiri
Published: February 2023

Objectives

To assess the prevalence and factors associated with glycaemic control to inform potential interventions to improve glycaemic control in Kinshasa, Democratic Republic of the Congo.

Design

This was a cross-sectional study conducted between November 2011–September 2022. We conducted the selection of the participants through a two-stage sampling process. Participants were asked to complete a structured questionnaire and to provide two millilitres of blood for Hb1AC assay. We performed univariate and multivariable logistic regressions to identify factors associated with poor glycaemic control.

Setting

A total of 20 randomly selected primary care facilities in Kinshasa, Democratic Republic of the Congo.

Participants

The sample included 620 patients living with type 2 diabetes with a median age of 60 (IQR=53.5-69) years.

Results

Most of the study participants were female (66.1%), unemployed (67.8%), having income below the poverty line (76.4%), and without health insurance (92.1%). Two-thirds of the participants (420; 67.6%) had poor glycaemic control. Those participants having taken only insulin (AOR=1.64, 95%CI 1.10 to 2.45) and those on a treatment duration ≥7 years (AOR=1.45, 95%CI 1.01 to 2.08) were associated with increased odds of poor glycaemic control, while being overweight (AOR= 0.47, 95%CI 0.26 to 0.85) and those with uncontrolled blood pressure (AOR=0.65, 95% CI 0.48 to 0.90) were protective for poor glycaemic control.

Conclusions

This study confirms that poor glycaemic control is common among patients living with type 2 diabetes in Kinshasa, DRC. There is a need for targeted interventions to improve glycaemic control, including metabolic and clinical comorbidity control, lifestyle modifications, and health system factors.

SIGNIFICANCE OF THE STUDY

What is already known on this topic

Glycaemic control is poor in most of the SSA settings, with glycaemic control ranging from 10–60%.

Factors associated with glycaemic control are context specific; in the Democratic Republic of the Congo, few studies have investigated poor glycaemic control.

What this study adds

The extent of poor glycaemic control among patients living with type 2 diabetes is determined in Kinshasa, Democratic Republic of the Congo.

Identification of factors associated with poor glycaemic control in Kinshasa: taking only insulin and having a treatment duration ≥7 years increased the likelihood of poor glycaemic control, while being overweight and having uncontrolled blood pressure were protective.

How this study might affect research, practice or policy

The study findings will inform potential interventions to improve glycaemic control in Kinshasa, DRC or similar settings elsewhere.
Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016)
Authors: Martínez José RW , Planet Paul J. , Maria Spencer-Sandino , Lina Rivas , Lorena Díaz , Ana Quesille-Villalobos , Roberto Riquelme-Neira , Manuel Alcalde-Rico , Blake Hanson , Carvajal Lina P , Sandra Rincón , Jinnethe Reyes , Marusella Lam , Rafael Araos , Patricia García , Arias César A. , Munita José M.
Published: February 2023

The global dissemination of methicillin-resistantStaphylococcus aureus(MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in the last years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary healthcare center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000-2016 in a tertiary healthcare center in Chile. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r=0.8748, p<0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016. The temporal trend analysis revealed that in the period 2000-2003 most of the isolates (94.2%; n=98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013-2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage in Chile. However, this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America.

Importance

Methicillin-resistantStaphylococcus aureus(MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or classical typing techniques with several limitations to depict an accurate description of their genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000-2016 in Chile to provide the largest and most detailed study of clonal dynamics of MRSA carried out in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing their frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
At least 10 genes on chromosome 5 ofCandida albicansare downregulated in concert to control cell wall and to confer adaptation to caspofungin
Authors: Sah Sudisht K. , Yadav Anshuman , Rustchenko Elena
Published: February 2023

Candida albicansis part of normal microbiota, however, can cause superficial and life threatening infection in immune-compromised individuals. Drugs from echinocandin (ECN) class that disrupt cell wall synthesis, are being used as a major treatment strategy against candidiasis. As the use of ECNs for the treatment of candidiasis is increasing, resistance against ECNs is also emerging. Previously, we reported involvement of 5 chromosome 2 (Ch2) genes in adaptation to ECN drugs. Here, we explored 22 candidate-genes on Ch5 that are consistently downregulated in independent mutants adapted to caspofungin (CAS), for their role in ECN adaptation. We also compared cell wall remodelling in CAS-adapted mutants and in 10 knockouts (KOs) from Ch5. Independent KO experiments as combined with broth microdilution assay, demonstrated that, as expected, 10 out of 22 Ch5 genes decrease ECN susceptibility by controlling the levels of three major components of the cell wall, glucan, mannan, and chitin. Some KOs decreased glucan or increased chitin or both. Similar cell wall remodelling, decreased glucan and increased chitin, was found in CAS-adapted mutants with no ploidy change. Some other KOs had no glucan change, but increased the level of either mannan or chitin. Our results identify the function of two uncharacterized genes, orf19.970 and orf19.4149.1, and expand the functions ofDUS4, RPS25B, UAP1, URA7, RPO26, HAS1, andCKS1. The function ofCHT2, as negative regulator of ECN susceptibility, has been previously established. Importantly, half of the above genes are essential indicating that essential processes are involved in cell wall remodelling for adaptation to ECNs. Also important, orf19.970 and orf19.4149.1 have no human orthologues. Finally, our work shows that multiple mechanisms are used byC. albicanscells to remodel cell wall in order to adapt to CAS. This work continues to identify common pathways that are involved in drug adaptation, as well as new genes controlling ECN susceptibility and reveals new targets for development of novel antifungal drugs.
Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship
Authors: Hantz Eric R. , Tikunova Svetlana B. , Belevych Natalya , Davis Jonathan P. , Reiser Peter J. , Lindert Steffen
Published: February 2023

Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering systolic calcium concentration, thereby strengthening cardiac function. Here, we examined the effect of our previously identified calcium sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This led to the identification of three novel low affinity binders, which had similar binding affinities to known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117 ± 17μM.
Plasmacytoid dendritic cells mediate CpG-ODN induced increase in survival in a mouse model of lymphangioleiomyomatosis
Authors: Amosu Mayowa M , Jankowski Ashleigh M , McCright Jacob C , Yang Bennett E , Fernandez Juan Grano de Oro , Moore Kaitlyn A , Gadde Havish S , Donthi Mehul , Kaluzienski Michele L , Sriram Vedanth , Maisel Katharina
Published: February 2023

Lymphangioleiomyomatosis (LAM) is a devastating disease primarily found in women of reproductive age that leads to cystic destruction of the lungs. Recent work has shown that LAM causes immunosuppression and that checkpoint inhibitors can be used as LAM treatment. Toll-like receptor (TLR) agonists can also re-activate immunity and the TLR9 agonist, CpG-ODN, has been effective in treating lung cancer in animal models. Here we investigate the use of TLR9 agonist CpG-ODN as LAM immunotherapy in combination with checkpoint inhibitor, anti-PD1, standard of care rapamycin and determine the immune mechanisms underlying therapeutic efficacy. We used survival studies, flow cytometry, ELISA, and histology to assess immune response and survival after intranasal treatment with CpG-ODN in combination with rapamycin or anti-PD1 therapy in a mouse model of metastatic LAM. We found that local administration of CpG-ODN enhances survival in a mouse model of LAM. We found that a lower dose led to longer survival likely due to fewer local side effects but increased LAM nodule count and size compared to the higher dose. CpG-ODN treatment also reduced regulatory T cells and increased the number of Th17 helper T cells as well as cytotoxic T cells. These effects appear to be mediated in part by plasmacytoid dendritic cells (pDCs), as depletion of pDCs reduces survival and abrogates Th17 T cell response. Finally, we found that CpG-ODN treatment is effective in early stage and progressive disease and is additive with anti-PD1 therapy and rapamycin. In summary, we have found that TLR9 agonist CpG-ODN can be used as LAM immunotherapy and effectively synergizes with rapamycin and anti-PD1 therapy in LAM.
Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells
Authors: Leitão Dos Santos Otávio Augusto , Carneiro Rodolfo L. , Requião Rodrigo D. , Ribeiro-Alves Marcelo , Domitrovic Tatiana , Palhano Fernando L.
Published: February 2023

During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Though RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed a widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in protein content. We experimentally demonstrated that this disparity arises from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influences RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under non-stress conditions.
Radioprotective drug screening in a salivary gland tissue chip
Authors: Piraino L. , Chen C.Y. , Mereness J. , Dunman P. M. , Ovitt C. E. , Benoit D. S. W. , DeLouise L. A.
Published: February 2023

Ionizing radiation damage to the salivary glands during head and neck cancer treatment often causes a permanent loss of secretory function. Due to the resulting decrease in saliva production, patients experience difficulty with eating, speaking, and swallowing and are predisposed to oral infections and tooth decay. While the radioprotective drug amifostine is approved to prevent radiation-induced hyposalivation, it has intolerable side effects that limit its use and motivate research into discovering alternatives. To address this issue, we have developed a salivary gland mimetic (SGm) tissue chip platform for use in high-content drug discovery. Here, we report on the development and validation of in-chip assays to quantify reduced glutathione and cellular senescence (β-galactosidase) as measures of radiation damage and protection using WR-1065, the active form of amifostine. Following validation, we next tested our assays using other reported radioprotective drugs including Edaravone, Tempol, N-acetylcysteine, Rapamycin, Ex-Rad, and Palifermin. The validated assays were then used to screen a library of FDA-approved compounds for radioprotection. We screened 438 compounds, obtained 25 hits that were further tested for EC50values and downselected using information from the PubChem database. Lead compounds were identified that are being tested in preclinical models.
Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching
Authors: Song Hyun-Seob , Ahamed Firnaaz , Lee Joon-Yong , Henry Christopher C. , Edirisinghe Janaka N. , Nelson William C. , Chen Xingyuan , Moulton J. David , Scheibe Timothy D.
Published: February 2023

Integration of genome-scale metabolic networks with reactive transport models (RTMs) is an advanced simulation technique that enables predicting the changes of microbial growth and metabolism in space and time. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated implementation of linear programming (LP) to get flux balance analysis (FBA) solutions in every time step and every spatial grid. To address this challenge, we propose a new simulation method where we train/validate artificial neural networks (ANNs) using FBA solutions randomly sampled and incorporate the resulting reduced-order FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study ofShewanella oneidensisMR-1 strain. During the aerobic growth on lactate,S. oneidensisproduces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred ones are depleted. Simulating such intricate dynamics posed a considerable challenge, which we overcame by adopting the cybernetic approach that describes metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based reduced-order models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Importantly, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.
IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods
Authors: Yan Aimin , Baricordi Cristina , Nguyen Quoc , Barbarossa Luigi , Loperfido Mariana , Biasco Luca
Published: February 2023

Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed standardized bioinformatics pipelines to process IS sequencing data, to generate reports, and/or to perform comparative studies across different GT trials. Keeping up with the technological advances in the field of IS analysis, different computational pipelines have been published over the past decade. These pipelines focus on identifying integration sites (IS) from single-read sequencing or paired-end sequencing data either using read-based or using sonication fragment-based methods, but there is a lack of a bioinformatics tool that automatically includes unique molecular identifiers (UMI) for IS abundance estimations and allows comparing multiple quantification methods in one integrated pipeline. Here we present IS-seq a bioinformatics pipeline that can process data from paired-end sequencing of both old restriction sites-based IS collection methods and new sonication-based IS retrieval systems while allowing the selection of different abundance estimation methods, including read-based, Fragment-based and UMI-based systems. We validated the performance of IS-Seq testing it against the most widely used analytical workflow available in the literature (INSPIIRED) and using different scenarios. Lastly, by performing a comprehensive wet-lab assessment of our IS-Seq pipeline we could show that in clinically relevant scenarios, UMI quantification provides better accuracy than the currently most widely used sonication fragment counts as a method for IS abundance estimation.
ABI5-FLZ13 Module Transcriptionally Represses Growth-related Genes to Delay Seed Germination in Response to ABA
Authors: Yang Chao , Li Xibao , Chen Shunquan , Liu Chuanliang , Yang Lianming , Li Kailin , Liao Jun , Zheng Xuanang , Li Hongbo , Li Yongqing , Zeng Shaohua , Zhuang Xiaohong , Rodriguez Pedro L. , Luo Ming , Wang Ying , Gao Caiji
Published: February 2023

The bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) is a master regulator determining seed germination and postgerminative growth in response to abscisic acid (ABA), but the detailed molecular mechanism underlying the repression function of ABI5 in plant growth remains to be characterized. In this study, we used proximity labeling (PL) to map the neighboring proteome of ABI5 and identified FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13) as an up-to-now unknown ABI5-interacting partner. Phenotypic analysis offlz13mutants andFLZ13-overexpressing lines demonstrated that FLZ13 acts as a positive regulator of ABA signaling. Interestingly, transcriptomic analysis showed that ABI5 and FLZ13 co-downregulate the expression of ABA-repressed and growth-related genes involved in chlorophyll biosynthesis, photosynthesis and cell wall organization, thereby repressing seed germination and seedling establishment in response to ABA. Further genetic analysis proved that FLZ13 works synergistically with ABI5 to regulate seed germination. Collectively, our study reveals a previously uncharacterized transcriptional regulatory mechanism regarding ABA-inhibited seed germination and seedling establishment.
The hierarchical structure of canine cognition: two domains and a general cognitive factor
Authors: Bognár Zsófia , Turcsán Borbála , Faragó Tamás , Szabó Dóra , Iotchev Ivaylo Borislavov , Kubinyi Enikő
Published: February 2023

The complex human environment results in a hard-to-bridge gap between human and animal studies on general cognitive abilities (g; colloquially often referred to as “intelligence”). Pet dogs are adapted to our environment, but a convincing demonstration ofgis missing. Exploratory and confirmatory factor analyses on seven tasks revealed a hierarchical structure with two cognitive domains (problem solving, learning) and an overarchingcanine g. Age did not affect the structure.Canine gwas negatively linked to age, height, and the owner’s emotional attitude but positively to training level, activity/excitability trait, experienced trauma and normal body condition. The longitudinal analyses over three years differentiated three main trajectory clusters: declining, stable, improving. The diversity of ageing phenotypes supports dogs’ translational value ingfactor and ageing research.

One-Sentence Summary

Thecanine gfactor is linked to age, height, training level, personality, body condition, and owner’s attitude.
ADP-ribose-acceptor hydrolase 2(Arh2) deficiency results in cardiac dysfunction, tumorigenesis, inflammation, and decreased survival
Authors: Kato Jiro , Yamashita Sachiko , Ishiwata-Endo Hiroko , Oka Shunya , Yu Zu-Xi , Liu Chengyu , Springer Danielle A. , Noguchi Audrey , Peiravi Morteza , Hoffmann Victoria , Lizak Martin J. , Medearis Matthew , Kim In-Kwon , Moss Joel
Published: February 2023

ADP-ribosylation is a reversible reaction with ADP-ribosyltransferases catalyzing the forward reaction and ADP-ribose-acceptor hydrolases (ARHs) hydrolyzing the ADP-ribose acceptor bond. ARH2 is a member of the 39-kDa ARH family (ARH1-3), which is expressed in heart and skeletal muscle. ARH2 failed to exhibit any in vitro enzymatic activity. To determine its possible in vivo activities,Arh2-knockout (KO) and - heterozygous (Het) mice were generated using CRISPR-Cas9.Arh2-KO mice exhibited decreased cardiac contractility by MRI, echocardiography and dobutamine stress with cardiomegaly and abnormal motor function.Arh2-Het mice showed results similar to those seen inArh2-KO mice except for cardiomegaly.Arh2-KO and -Het mice and mouse embryonic fibroblasts (MEFs) developed spontaneous tumors and subcutaneous tumors in nude mice. We identified 13 mutations inArh2-Het MEFs and heterozygous tumors, corresponding to humanARH2mutations in cancers obtained from COSMIC. Of interest, the L116R mutation inArh2gene plays a critical role in aggressive tumorigenesis in nude mice, corresponding to humanARH2mutations in stomach adenocarcinoma. Both genders ofArh2-KO and -Het mice showed increased unexpectedly deaths and decreased survival rate during a 24-month observation, caused by tumor, inflammation, non-inflammation (e.g., cardiomegaly, dental dysplasia), and congenital diseases. Thus,Arh2plays a pivotal role in cardiac function, tumorigenesis, inflammation, and overall survival.
Application of G-N high-order boundary condition on time harmonic analysis of concrete gravity dam-reservoir systems
Authors: Dehghanmarvasty Solmaz , Lotfi Vahid
Published: February 2023

Purpose

The response of an idealized triangular concrete gravity dam is studied due to horizontal and vertical ground motions for both fully reflective and absorptive reservoir bottom conditions. For each combination, in this paper different orders of Givoli-Neta (G-N) high-order truncation condition are aimed to be evaluated from accuracy point of view by comparing the results against corresponding exact solutions which relies on utilizing a two-dimensional fluid hyper-element.

Design/methodology/approach

In present study, the dynamic analysis of concrete gravity dam-reservoir systems is formulated by Finite Element (FE)-(FE-TE) approach. In this technique, dam and reservoir are discretized by plane solid and fluid finite elements. Moreover, the G-N high-order condition imposed at the reservoir truncation boundary. This task is formulated by employing a truncation element at that boundary. It is emphasized that reservoir far-field is excluded from the discretized model.

Findings

It was observed that trend in gaining accuracy with increase in the order of G-N condition were basically the same for both horizontal and vertical ground motions under full reflective reservoir bottom condition. Moreover, convergence rate increases for absorptive reservoir bottom condition cases in comparison with fully reflective cases. It is also noticed that in certain cases, the responses are hardly distinguishable from corresponding exact responses. This reveals that proposed FE-(FE-TE) analysis technique based on G-N condition is quite successful, and one may fully rely on that for accurate and efficient analysis of concrete gravity dam-reservoir systems.

Originality/value

Dynamic analysis of concrete gravity dam-reservoir systems are formulated by a new method. The salient aspect of the technique is that it utilizes G-N high-order condition at the truncation boundary. This is achieved by developing a special truncation element which its generalized matrices are derived for Finite Element Method (FEM) programmers. The method is discussed for all types of excitation and reservoir bottom conditions. It must be emphasized that although time harmonic analysis is considered in the present study, the main part of formulation is explained in the context of time domain. Therefore, the approach can easily be extended for transient type of analysis.
Knowledge graph embedding for experimental uncertainty estimation
Authors: Ramalli Edoardo , Pernici Barbara
Published: February 2023

Purpose

Experiments are the backbone of the development process of data-driven predictive models for scientific applications. The quality of the experiments directly impacts the model performance. Uncertainty inherently affects experiment measurements and is often missing in the available data sets due to its estimation cost. For similar reasons, experiments are very few compared to other data sources. Discarding experiments based on the missing uncertainty values would preclude the development of predictive models. Data profiling techniques are fundamental to assess data quality, but some data quality dimensions are challenging to evaluate without knowing the uncertainty. In this context, this paper aims to predict the missing uncertainty of the experiments.

Design/methodology/approach

This work presents a methodology to forecast the experiments’ missing uncertainty, given a data set and its ontological description. The approach is based on knowledge graph embeddings and leverages the task of link prediction over a knowledge graph representation of the experiments database. The validity of the methodology is first tested in multiple conditions using synthetic data and then applied to a large data set of experiments in the chemical kinetic domain as a case study.

Findings

The analysis results of different test case scenarios suggest that knowledge graph embedding can be used to predict the missing uncertainty of the experiments when there is a hidden relationship between the experiment metadata and the uncertainty values. The link prediction task is also resilient to random noise in the relationship. The knowledge graph embedding outperforms the baseline results if the uncertainty depends upon multiple metadata.

Originality/value

The employment of knowledge graph embedding to predict the missing experimental uncertainty is a novel alternative to the current and more costly techniques in the literature. Such contribution permits a better data quality profiling of scientific repositories and improves the development process of data-driven models based on scientific experiments.
Resilient SMEs and entrepreneurs: evidence from the UK craft brewing sector
Authors: Waehning Nadine , Bosworth Gary , Cabras Ignazio , Shakina Ekatarina , Sohns Franziska
Published: February 2023

Purpose

The paper examines the sudden changes and challenges experienced by British craft breweries because of COVID-19. The purpose is twofold; firstly, to evaluate the overall growth trajectory of the craft brewing sector prior to the pandemic crisis and, secondly, to identify features of resilience and adaptability that aided business survival.

Design/methodology/approach

The authors conducted 24 interviews with a sample of craft brewers during 2020, supplemented with a focus group later in 2021, to understand the impacts of COVID-19 on their businesses. Inductive thematic analysis followed a flexible six-stage approach to generating codes. Qualitative findings were set in the context of the pre-COVID-19 industry trends which were analysed using panel data from the Society of Independent Brewers' (SIBA) Annual Surveys between 2015 and 2018.

Findings

Findings from the analysis reveal a range of factors influencing growth in the UK craft beer sector before the pandemic crisis, such as levels of investment and local network ties, and identify a range of strategies implemented by brewers in response to the crisis, including new packaging and supply channels, more intensive marketing and greater online engagement with customers. Analysis of the intersection between aspects of individual and organisational resilience also revealed that dynamic responses to an external crisis depend on individual resilience characteristics before organisational strategies can be developed.

Originality/value

The study provides fresh empirical evidence to practitioners and policymakers to help forecast and future-proof the UK craft beer sector, as well as elucidating aspects of resilience that apply to SMEs in the global industry who face similar challenges. Moving towards a post-COVID-19 economy, the paper offers important theoretical insights into how the resilience of breweries, and other SMEs, is shaped by complex interdependencies and networks and how their adaptive responses might strengthen future business models.
Students between science and society: why students’ learning experiences in transformative spaces are vital to higher education institutions
Authors: Trechsel Lilian Julia , Diebold Clara Léonie , Zimmermann Anne Barbara , Fischer Manuel
Published: February 2023

Purpose

This study aims to explore how the boundary between science and society can be addressed to support the transformation of higher education towards sustainable development (HESD) in the sense of the whole institution approach. It analyses students’ learning experiences in self-led sustainability projects conducted outside formal curricula to highlight their potential contribution to HESD. The students’ projects are conceived as learning spaces in “sustainability-oriented ecologies of learning” (Wals, 2020) in which five learning dimensions can be examined.

Design/methodology/approach

Using an iterative, grounded-theory-inspired qualitative approach and sensitising concepts, 13 in-depth semi-structured interviews were conducted exploring students’ learning experiences. Interviews were categorised in MAXQDA and analysed against a literature review.

Findings

Results revealed that students’ experiences of non-formal learning in self-led projects triggered deep learning and change agency. Trust, social cohesion, empowerment and self-efficacy were both results and conditions of learning. Students’ learnings are classified according to higher education institutions’ (HEIs) sustainability agendas, providing systematised insights for HEIs regarding their accommodative, reformative or transformative (Sterling, 2021) path to sustainable development.

Originality/value

The education for sustainable development (ESD) debate focuses mainly on ESD competences in formal settings. Few studies explore students’ learnings where formal and non-formal learning meet. This article investigates a space where students interact with different actors from society while remaining rooted in their HEIs. When acting as “change agents” in this hybrid context, students can also become “boundary agents” helping their HEIs move the sustainability agenda forward towards a whole institution approach. Learning from students’ learnings is thus proposed as a lever for transformation.
To automate or not to automate? A contingency approach to service automation
Authors: Hottat Eline , Leroi-Werelds Sara , Streukens Sandra
Published: February 2023

Purpose

Following a contingency approach, this paper aims to understand when service automation can enhance or destroy value for customers in the frontline by (1) providing a comprehensive overview of factors that influence the value co-creation/co-destruction potential of service automation and (2) zooming in on the combination of service contexts and service tasks to develop research propositions.

Design/methodology/approach

This paper uses a grounded theory approach based on qualitative data from multiple methods (i.e. a diary study with follow-up interviews, a consultation of academic experts and a storyboard study) as well as a systematic literature review to develop (1) a Framework of Automated Service Interactions (FASI) and (2) a contingency model for service tasks/contexts.

Findings

This paper presents a framework which gives an overview of factors influencing the value co-creation/co-destruction potential of service automation. The framework discerns between three types of factors: service design (i.e. controllable and manageable by the organization), static contingency (i.e. uncontrollable and fixed) and dynamic contingency (i.e. uncontrollable and flexible). Furthermore, the paper presents a contingency model based on the combination of service contexts and service tasks which results in seven research propositions.

Originality/value

This paper brings structure in the fragmented field of service automation. It integrates and summarizes insights regarding service automation and sheds more light on when service automation has the potential to create or destroy value in the organizational frontline.
The interrelationship of family identities, personalities, and expressions on family winery websites
Authors: Berndt Adele , Meintjes Corné
Published: February 2023

Purpose

Family businesses feature prominently in economies, including the South African wine industry, using websites to convey their family identity. This research paper aims to explore the family identity elements that family wineries use on their websites, their alignment and how these are communicated online.

Design/methodology/approach

Based on Gioia’s methodology, a two-pronged approach was used to analyze 113 wineries’ websites’ text using Atlas. ti from an interpretivist perspective.

Findings

South African wineries use corporate identity, corporate personality and corporate expression to illustrate their familiness on their websites. It is portrayed through their family name and heritage, supported by their direction, purpose and aspirations, which emerge from the family identity and personality. These are dynamic and expressed through verbal and visual elements. Wineries described their behaviour, relevant competencies and passion as personality traits. Sustainability was considered an integral part of their brand promise, closely related to their family identity and personality, reflecting their family-oriented philosophy. These findings highlight the integration that exists among these components.

Practical implications

Theoretically, this study proposes a family business brand identity framework emphasising the centrality of familiness to its identity, personality and expression. Using websites to illustrate this familiness is emphasised with the recommendation that family businesses leverage this unique attribute in their identity to communicate their authenticity.

Originality/value

This study contributes to understanding what family wineries communicate on their websites, specifically by examining the elements necessary to create a family business brand based on the interrelationship between family identity, personality and expression with familiness at its core, resulting in a proposed family business brand identity framework.
Executive functioning during verbal fluency tasks in bilinguals: A systematic review
Authors: Giovannoli Jasmine , Martella Diana , Casagrande Maria
Published: February 2023

Background

Bilingualism is widespread and being bilingual is more common than being monolingual. The lifelong practice bilinguals receive from managing two languages seems to lead to a cognitive benefit. Conversely, bilingualism seems to affect language ability negatively due to less use of each known language.

Aims

This systematic review aims to summarize the results of the studies on the effect of bilingualism on executive functioning assessed by verbal fluency tasks. The verbal fluency task is a neuropsychological measure of lexical retrieval efficiency and executive functioning.

Methods

The review was conducted according to the PRISMA statement through searches in the scientific databases PsycINFO, PsycARTICLES, MEDLINE, PubMed, Web of Science and SCOPUS. Studies included in this review had at least one bilingual and monolingual group, participants over 18 years and one verbal fluency task. Studies that considered bimodal bilingual, second language learners, trilingual or multilingual people, and clinical populations were excluded. A total of 38 studies were included in the systematic review.

Main Contribution

Quantitative analysis of performance did not show significant differences between monolinguals and bilinguals. Qualitative results are mixed, and no definitive conclusions can be drawn about a bilingual advantage or disadvantage in the verbal fluency tasks.

Conclusions

Normative data based on the monolingual population are not appropriate to test a bilingual population. It is necessary to take precautions in using this task, especially in clinical practice.

WHAT THIS PAPER ADDS

What is already known on the subject

Bilingualism seems to lead to a cognitive benefit due to constantly monitoring the known languages to select the most suitable one for each interactional context and to affect language ability negatively due to less use of each known language but also to language ability negatively.

What this paper adds to the existing knowledge

This systematic review summarizes the results of the studies on the effect of bilingualism on executive functioning assessed by verbal fluency tasks, a neuropsychological measure of lexical retrieval efficiency and executive functioning.

What are the potential or actual clinical implications of this work?

Normative data based on the monolingual population are not appropriate to test a bilingual population. It is necessary to take precautions in using this task, especially in clinical practice.