bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides
Authors: Saad Hamada , Majer Thomas , Bhattarai Keshab , Lampe Sarah , Nguyen Dinh T. , Kramer Markus , Straetener Jan , Brötz-Oesterhelt Heike , Mitchell Douglas A. , Gross Harald 
Published: March 2023

AbstractLasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.
Antibacterial Effect of Oral Care Gel-Containing Hinokitiol and 4-isopropyl-3-methylphenol Against Intraoral Pathogenic Microorganisms
Authors: Ohara Hiroshi , Odanaka Keita , Shiine Miku , Hayasaka Masataka 
Published: March 2023

AbstractObjectiveDeterioration of oral hygiene is closely related to increase severity and mortality of corona virus disease-19 (COVID-19), and also contribute to the development of various diseases such as aspiration pneumonia or Alzheimer’s. Oral care is attracting high interest in Japan, which has entered a super-aging society. In this study, we aimed to investigate whether commercially available Hinora®(HO) that oral care gels-containing hinokitiol and 4-isopropyl-3-methylphenol (IPMP) have biofilm formation inhibitory and antibacterial activities against various intraoral pathogen microorganisms.MethodCandidaspp.,Aggregatibacter actinomycetemcomitans, Staphylococcus aureus, andPseudomonas aeruginosawere selected during the study period, all which were analyzed using antimicrobial disc, microorganism turbidity, and crystal violet assays. In addition, the germ tube test usingC. albicanswas performed with a modification of Mackenzie’s method. Images for morphological observation of the germ tubes were acquired with an inverted microscope. For comparison between products, we used Refrecare®(RC), which contains only hinokitiol (not containing IPMP).ResultsAll the intraoral pathogenic microorganisms showed drug susceptibility against undiluted form HO and/or RC. In particular, HO was more effective at lower concentrations than RC. In the HO-added group, inhibition circles were observed in all bacteria exceptP. aeruginosawhen added at a concentration of 0.5 g/mL or more. The optical density values at 590 nm (crystal violet) and/or 600 nm (microorganism turbidity) of all the fungi and bacteria were significantly lower when cultured in medium with HO. Inhibition of growth or biofilm formation was observed when HO was added at a concentration of 0.05 g/mL or higher. To investigate the action mechanism of HO, germ tube tests were performed inC. albicans. The results show that culturingC. albicansin soyabean-casein digest broth with HO (0.05 g/mL) significantly suppressed germ tube formation.ConclusionsThese data suggest that oral care gel-containing hinokitiol and IPMP has strong biofilm formation inhibitory, antifungal and antibacterial effects againstCandidafungi and multiple intraoral pathogenic microorganisms. Therefore, it may be a promising treatment option for oral infections.
Embracing firefly flash pattern variability with data-driven species classification
Authors: Martin Owen , Nguyen Chantal , Sarfati Raphael , Chowdhury Murad , Iuzzolino Michael L. , Nguyen Dieu My T. , Layer Ryan M. , Peleg Orit 
Published: March 2023

AbstractMany nocturnally active fireflies use precisely timed bioluminescent patterns to identify mates, making them especially vulnerable to light pollution. As urbanization continues to brighten the night sky, firefly populations are under constant stress, and close to half of the species are now threatened. Ensuring the survival of firefly biodiversity depends on a large-scale conservation effort to monitor and protect thousands of populations. While species can be identified by their flash patterns, current methods require expert measurement and manual classification and are infeasible given the number and geographic distribution of fireflies. Here we present the application of a recurrent neural network (RNN) for accurate automated firefly flash pattern classification. Using recordings from commodity cameras, we can extract flash trajectories of individuals within a swarm and classify their species with a precision and recall of approximately seventy percent. In addition to scaling population monitoring, automated classification provides the means to study firefly behavior at the population level. We employ the classifier to measure and characterize the variability within and between swarms, unlocking a new dimension of their behavior. Our method is open source, and deployment in community science applications could revolutionize our ability to monitor and understand firefly populations.
Comprehensive analysis of autophagic functions of WIPI family proteins and their implications for the pathogenesis of β-propeller associated neurodegeneration
Authors: Shimizu Takahiro , Tamura Norito , Nishimura Taki , Saito Chieko , Yamamoto Hayashi , Mizushima Noboru 
Published: March 2023

Abstractβ-propellers that bind polyphosphoinositides (PROPPINs) are an autophagy-related protein family conserved throughout eukaryotes. The PROPPIN family includes Atg18, Atg21, and Hsv2 in yeast and WD-repeat protein interacting with phosphoinositides (WIPI)1–4 in mammals. Mutations in theWIPIgenes are associated with human neuronal diseases, including β-propeller associated neurodegeneration (BPAN) caused by mutations inWDR45(encoding WIPI4). In contrast to yeast PROPPINs, the functions of mammalian WIPI1–WIPI4 have not been systematically investigated. Although the involvement of WIPI2 in autophagy has been clearly shown, the functions of WIPI1, WIPI3, and WIPI4 in autophagy remain poorly understood. In this study, we comprehensively analyzed the roles of WIPI proteins by usingWIPI-knockout (single, double, and quadruple knockout) HEK293T cells and recently developed HaloTag-based reporters, which enable us to monitor autophagic flux sensitively and quantitatively. We found that WIPI2 was nearly essential for autophagy and partially redundant with WIPI1. Autophagic flux was unaffected or only slightly reduced by single deletion of WIPI3 (encoded byWDR45B) or WIPI4 but was profoundly reduced by double deletion of WIPI3 and WIPI4. Furthermore, we revealed variable effects of BPAN-related missense mutations on the autophagic activity of WIPI4. BPAN is characterized by neurodevelopmental and neurodegenerative abnormalities, and we found a possible association between the magnitude of the defect of the autophagic activity of WIPI4 mutants and the severity of neurodevelopmental symptoms. However, some of the BPAN-related missense mutations, which produce neurodegenerative signs, showed almost normal autophagic activity, suggesting that non-autophagic functions of WIPI4 may be related to neurodegeneration in BPAN.
KCNN4 links PIEZO-dependent mechanotransduction to NLRP3 inflammasome activation
Authors: Ran Li , Ye Tao , Erbs Eric , Ehl Stephan , Spassky Nathalie , Sumara Izabela , Zhang Zhirong , Ricci Romeo 
Published: March 2023

AbstractImmune cells sense the microenvironment to fine-tune their inflammatory responses. Patients with cryopyrin associated periodic syndrome (CAPS), caused by mutations in theNLRP3gene, develop auto-inflammation triggered by non-antigenic, e.g. environmental cues. However, the underlying mechanisms are poorly understood. Here, we uncover that KCNN4, a calcium-activated potassium channel, links PIEZO-mediated mechanotransduction to NLRP3 inflammasome activation. Yoda1, a PIEZO1 agonist, lowers the threshold for NLRP3 inflammasome activation. PIEZO-mediated sensing of stiffness and shear stress increases NLRP3-dependent inflammation. Myeloid-specific deletion ofPIEZO1/2protects mice from gouty arthritis. Activation of PIEZO1 triggers calcium influx, which activates KCNN4 to evoke potassium efflux promoting NLRP3 inflammasome activation. Activation of PIEZO signaling is sufficient to activate the inflammasome in cells expressing CAPS-causing NLRP3 mutants via KCNN4. Finally, pharmacologic inhibition of KCNN4 alleviates auto-inflammation in CAPS patient cells and in CAPS-mimicking mice. Thus, PIEZO-dependent mechanical inputs augment inflammation in NLRP3-dependent diseases including CAPS.One Sentence SummaryPIEZO-mediated mechanotransduction stimulates KCNN4-dependent potassium efflux to potentiate NLRP3 inflammasome activation.
The ABI3-ERF1 module mediates ABA-auxin crosstalk to regulate lateral root emergence
Authors: Zhang Jing , Zhao Pingxia , Chen Siyan , Sun Liangqi , Mao Jieli , Tan Shutang , Xiang Chengbin 
Published: March 2023

SummaryLateral root (LR) development is regulated by hormones and environmental signals. Abscisic acid (ABA) is involved in LR development, but it is not well understood how ABA signaling interacts with auxin to regulate LR formation. Here, we report thatArabidopsis ERF1is responsive to ABA during LR development and mediates the crosstalk between ABA and auxin signaling to regulate LR emergence. ABA attenuates ERF1-mediated excessive auxin accumulation with altered distribution known to inhibit LR emergence. ABI3 acts as a negative factor in LR emergence and transcriptionally activatesERF1by binding to the RY motif in its promoter, and reciprocally, ERF1 activatesABI3, which forms a positive regulatory loop that enables rapid signal amplification. Notably, ABI3 physically interacts with ERF1, consequently reducing theciselement-binding activities of both ERF1 and ABI3 and thus attenuating ERF1-regulated transcription ofPIN1,AUX1, andARF7involved in the modulation of LR emergence and ABI3-regulatedABI5in ABA signaling, which may provide a molecular rheostat to avoid overamplification of auxin and ABA signaling. Taken together, our findings unveil the pivotal ABI3-ERF1 module that mediates the crosstalk between ABA and auxin signaling in LR emergence.
CEP76 is a critical regulator of male germ cell transition zone function and tail composition
Authors: Houston Brendan J. , Jo Merriner D. , Gemma Stathatos G. , O’Connor Anne E. , Lopes Alexandra M. , Conrad Donald F. , Baker Mark , Dunleavy Jessica E.M. , O’Bryan Moira K. 
Published: March 2023

AbstractThe transition zone is a specialised gate at the base of cilia/flagella, which segregates the ciliary compartment from the cytoplasm and strictly regulates protein entry. In this study, we have identified CEP76 as an essential germ cell transition zone protein, involved in the selective entry and incorporation of key proteins required for sperm function and fertility into the ciliary compartment and ultimately the sperm tail. In its absence sperm tails are shorter and immotile as a consequence of deficits in essential sperm motility proteins including DNAH2 and AKAP4, which accumulate at the sperm neck in the mutant. We demonstrate CEP76 is required for sperm tail fibrous sheath formation, outer dense fibre loading and axoneme stability in the principal piece and ultimately sperm motility. Finally, we identify that CEP76 dictates annulus positioning and composition, adding further evidence that the spermatid transition zone and annulus are part of the same functional structure.
Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease
Authors: Boeynaems Steven , Ma X. Rosa , Yeong Vivian , Ginell Garrett M. , Chen Jian-Hua , Blum Jacob A. , Nakayama Lisa , Sanyal Anushka , Briner Adam , Van Haver Delphi , Pauwels Jarne , Ekman Axel , Schmidt H. Broder , Sundararajan Kousik , Porta Lucas , Lasker Keren , Larabell Carolyn , Hayashi Mirian A. F. , Kundaje Anshul , Impens Francis , Obermeyer Allie , Holehouse Alex S. , Gitler Aaron D. 
Published: March 2023

ABSTRACTPositively charged repeat peptides are emerging as key players in neurodegenerative diseases. These peptides can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic peptides and found that they all share similar sequence features that drive their aberrant condensation with these positively charged peptides. We trained a machine learning algorithm to detect such sequence features and unexpectedly discovered that this mode of toxicity is not limited to human repeat expansion disorders but has evolved countless times across the tree of life in the form of cationic antimicrobial and venom peptides. We demonstrate that an excess in positive charge is necessary and sufficient for this killer activity, which we name ‘polycation poisoning’. These findings reveal an ancient and conserved mechanism and inform ways to leverage its design rules for new generations of bioactive peptides.
Learning to teach: an investigation into pre-service biology teachers' perceptions toward lesson study
Authors: Jayanti Ummi Nur Afinni Dwi , Adlini Miza Nina 
Published: March 2023

PurposeDespite numerous kinds of research regarding the potential of lesson study (LS) in internship and microteaching in teacher education curricula, studies examining the adaptation of LS in the lesson planning (LP) course have not been established. To fill this gap, this study aims to explore the perceptions of pre-service biology teachers of an adapted LS in the LP course toward their instructional design skills and teaching competency.Design/methodology/approachThis study opted for basic qualitative studies. The participants were eleven pre-service biology teachers in their third year who had already taken a LP course. Data were collected through semi-structured interviews. Collected data were then transcribed and thematically analyzed using grounded theory and focused on participants' perceptions about the development of their teaching competency in lesson planning through LS.FindingsThe findings revealed that participants appreciated the planning and consultation phases, teaching practice, peer observation as well as observer feedback from the reflection phase in supporting the development of their basic teaching skills. There was also a change in their perceptions related to the concept of teaching.Originality/valueThe findings of this study offer insight regarding the benefits and challenges of involving pre-service biology teacher students in the LS for biology teacher education programs with a focus on the method or LP course.
IPO valuation in an emerging market – a study in Iran
Authors: Hekmat Hanieh , Rahmani Ali , Yazdifar Hassan 
Published: March 2023

Purpose
This study aims to highlight the accuracy, performance and selection of the IPO valuation methods in the Islamic Republic of Iran’s emerging market.

Design/methodology/approach
The authors performed accurate ex ante evaluations based on a pre-IPO data set obtained from valuation institutions. This study considered valuation methods through correlations, Mann–Whitney U tests and regression analysis, using a sample of 83 IPOs from January 2017 to March 2021.

Findings
The authors found that the dividend discount model (DDM) was the most popular in Iran. Even after controlling firm characteristics and market circumstances, the IPO price was highly correlated to pre-IPO reports’ estimates. The results showed that firms’ age, size and profitability affected the selection of valuation methods. The valuers did not apply forward P/E in a volatile market. Firm size affected the weights assigned to free cash flow to the firm, and the valuers considered the asset-in-place intensity to determine the weights of DDM, P/E and net asset value, and they mainly used the P/E to value old firms. Finally, this study estimated the accuracy of the pre-IPO report at 61% and found the highest accuracy to be associated with DDM.

Originality/value
IPO pricing in emerging markets constitutes a more significant dilemma than in developed markets. This paper provides empirical evidence of IPO pricing focusing on valuation methods used in the context of an emerging market – the Islamic Republic of Iran.
The building as a palimpsest: heritage, memory and adaptive reuse beyond intervention
Authors: Lanz Francesca 
Published: March 2023

PurposeThis paper contributes to this special issue on the ethics and aesthetics of adaptive reuse with a reflection on the specific case of the reuse of those sites and buildings that can be regarded as “difficult”, “uncomfortable”, or “neglected” heritage (MacDonald, 2009; Logan and Keir, 2009; Pendlebury et al., 2018; Lanz, 2021). By doing so it is the author's intention to add to the most recent research-driven and theory-oriented strand of the contemporary architectural debate on adaptive reuse (Lanz and Pendlebury, 2022). They also intend to encourage increased research engagement within such a debate, both across disciplines and with methods and approaches that may be able to bring in greater critical consideration of the more-than-architectural aspects involved in adaptive reuse practices.Design/methodology/approachBuilding equally on a comprehensive literature review on the subject and extensive field work, the paper works through one paradigmatic example – the San Girolamo mental asylum in Volterra, Italy – and combines on-site observation, field notes, qualitative interviews and archival research with theory-driven reflections to discuss the ramifications of adaptive reuse processes in place-based memory and heritage practices.FindingsThe case of the former mental asylum San Girolamo in Volterra, today abandoned and decaying on the landscape, is discussed via the metaphor of the building as palimpsest to explore the significance of this built heritage in both its materiality and meanings. The San Girolamo asylum demonstrates the value, complexity and potential of this heritage site, and other alike, to act as a powerful place which connects the past and present that might serve as a platform to promote productive discourses about contemporary sensible topics, ethics of care and human rights. Drawing on these observations, the paper concludes by expanding on how the case of the San Girolamo former asylum both showcases and advocates the need for developing more creative, explorative, trans-disciplinary and collaborative approaches and methodologies to the study and implementation of adaptive reuse projects for these site “beyond intervention”.Originality/valueThis paper draws on and contributes to the more recent research-driven and theory-oriented corpus of studies focussing on adaptive reuse.
Resilience, complexity and digital transformation: three case studies in the valves industry
Authors: Codara Lino , Sgobbi Francesca 
Published: March 2023

PurposeThis paper shows how the interplay between organisational resilience and environmental complexity justifies the existence of differentiated yet successful approaches to digital transformation.Design/methodology/approachA multi-case method is applied to test our research hypotheses by contrasting the digital transformation of three Italian companies in the valves industry.FindingsDifferent combinations of technological and organisational tools, hence diversified digital transformations, can be successful, provided that they are supported by a coherent set of resilience factors and allow for the implementation of strategic approaches aligned with the resilience capacity of the firm.Practical implicationsAwareness that resilience capacity shapes digital transformation and the strategies available to engage with external complexity should focus managers to invest in the alignment and the reinforcement of the factors underlying organisational resilience.Originality/valueMost literature so far focused on the antecedents to digital transformation. In contrast, this paper focuses on the transformation process and highlights how the resilience capacity of the firm affects the unfolding of digital transformation and the emergence of diversified yet successful paths. In addition, in contrast with a dichotomous approach to external complexity this paper shows that digital transformation involves a mix of complexity reduction and complexity absorption strategies.
Packaging plastic waste management in the cosmetic industry
Authors: De Sanjeet Kumar , Kawdia Priyanshi , Gupta Dipti , Pragya Namita 
Published: March 2023

PurposeThis paper aims to explore the relationship between the various variables present in the packaging plastic waste management system in the cosmetics industry.Design/methodology/approachIn this paper, the authors deal with plastic packaging waste in the cosmetic industry with the help of system dynamics. The model broadly divides the system into six sections – Cosmetic Packaging, Waste Generation, Waste Collected, Waste Sorted, Waste Treated and Waste Dumped. Businesses have been investing in each section depending on their progress and targets. The authors are looking at case studies of two leading cosmetic brands, L'Oréal and L'Occitane en Provence, to validate the industry practices against our model.FindingsFrom a business perspective, using the case study methodology for L'Oréal and L'Occitane, the authors inferred that out of the various investment vehicles available, companies are targeting technological advancement and third-party collaborations as they have the potential to offer the greatest visible change. However, most of these investments are going toward the treatment subsection. Still, there is a scope for improvement in the collection and sorting subsystems, increasing the efficiency of the whole chain.Originality/valueThere has been a lot of research on packaging plastic waste management in the past, but only a few of them focused on the cosmetic industry. This study aims to connect all the possible variables involved in the cosmetic industry’s packaging plastic waste management system and provide a clear output variable for various businesses looking to manage their packaging waste because of their products efficiently.