bluuebunny/crossref_metadata_2025_split huggingface dataset:
CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics
Authors: Kalogeropoulos Konstantinos , Haack Aleksander Moldt , Madzharova Elizabeta , Lorenzo Antea Di , Hanna Rawad , Schoof Erwin M. , auf dem Keller Ulrich 
Published: December 2023

AbstractPositional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, such progress has not been observed to the same extent in data analysis and post-processing steps, which arguably constitute the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms, and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available athttps://github.com/UadKLab/CLIPPER-2.0.
HPClas: A data-driven approach for identifying halophilic proteins based on catBoost
Authors: Hu Shantong , Wang Xiaoyu , Wang Zhikang , Chang Yongfei , Tian Yun , Li Zhuoqian , Jiang Menghan , Wang Shihui , Wang Wenya , Song Jiangning , Zhang Guimin 
Published: December 2023

AbstractHalophilic proteins possess unique structural properties and exhibit high stability under extreme conditions. Such distinct characteristic makes them invaluable for applications in various aspects such as bioenergy, pharmaceuticals, environmental clean-up and energy production. Generally, halophilic proteins are discovered and characterized through labor-intensive and time-consuming wetlab experiments. Here, we introduced HPClas, a machine learning-based classifier developed using the catBoost ensemble learning technique to identify halophilic proteins. Extensivein silicocalculations were conducted on a large public data set of 12574 samples and an independent test set of 200 sample pairs, on which HPClas achieved an AUROC of 0.877 and 0.845, respectively. The source code and curated data set of HPClas are publicly available athttps://github.com/Showmake2/HPClas. In conclusion, HPClas can be explored as a promising tool to aid in the identification of halophilic proteins and accelerate their applications in different fields.Impact StatementIn this study, we used a method based on prediction of proteins secreted by extreme halophilic bacteria to successfully extract a large number of halophilic proteins. Using this data, we have trained an accurate halophilic protein classifier that could determine whether an input protein is halophilic with a high accuracy of 84.5%. This research could not only promote the exploration and mining of halophilic proteins in nature, but also provide guidance for the generation of mutant halophilic enzymes.
CO2Reduction by the Iron Nitrogenase Competes with N2Fixation Under Physiological Conditions
Authors: Oehlmann Niels N. , Schmidt Frederik V. , Herzog Marcello , Goldman Annelise L. , Rebelein Johannes G. 
Published: December 2023

AbstractNitrogenases are the only known enzymes that reduce molecular nitrogen (N2) to ammonia. Recent findings have demonstrated that nitrogenases also reduce the greenhouse gas carbon dioxide (CO2), suggesting CO2to be a competitor of N2. Intriguingly, nitrogenase isoforms (i.e., molybdenum (Mo), vanadium and iron (Fe) nitrogenase) differ significantly in their ability to reduce CO2,but the mechanisms underlying these differences remain elusive. Here, we study the competing reduction of CO2and N2by the two nitrogenases ofRhodobacter capsulatus, the Mo and Fe nitrogenase. Analyzing their full CO2reduction product spectrumin vitro, we find the Fe nitrogenase almost three-fold more efficient in CO2reduction than the Mo isoform. Furthermore, thein vitrocompetition experiments reveal the Fe nitrogenase to be profoundly less selective for the reduction of N2than the Mo nitrogenase. We observe the same effectsin vivo, where adding CO2drastically increases the doubling times of diazotrophically grownR. capsulatusstrains that rely on the Fe nitrogenase. The Fe nitrogenase-dependentR. capsulatusstrains reduce CO2to methane under physiological conditions, highlighting the potential of the Fe nitrogenase for the biotechnological conversion of CO2into value-added compounds. Furthermore, both products are secreted into the surrounding, potentially influencing the composition of microbial communities in Mo-deficient environments.
Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation
Authors: Sun Yulin , Lorenzen Eline D. , Westbury Michael V. 
Published: December 2023

AbstractThe polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many characteristics adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered genomic regions containing an array of key genes highly differentiated between polar and brown bears, many of which were linked to the novel Arctic environment. Further research suggested fixed alleles in these genes arose from selection on both standing variation andde novomutations in the evolution of polar bears. Here, we reevaluate these findings by incorporating more genomic data from previously unavailable polar and brown bear populations, and assess the timing of allele fixation by utilising the genomes of two Late Pleistocene polar bears (aged 130-100,000 years old and 100-70,000 years old). Contrary to previous results, we found no evidence for alleles fixed in all polar bears within these key genes arising fromde novomutation. Most alleles fixed in modern polar bears were also fixed in the Late Pleistocene bears, suggesting selection occurred prior to 70,000 years ago. However, some sites fixed in modern polar bears were not fixed in the Late Pleistocene bears, including at sites within APOB, LYST, and TTN. The functions of these three genes are associated with the cardiovascular functions, metabolism, and pigmentation, suggesting that selection may have acted on different loci at different times.
Alternative Polyadenylation Determines the Functional Landscape of Inverted Alu Repeats
Authors: Ku Jayoung , Kim Sujin , Lee Keonyong , Ku Doyeong , Kim Namwook , Do Hyunsu , Lee Hyeonjung , Han Jinju , Lee Young-suk , Kim Yoosik 
Published: December 2023

SummaryInverted Alu repeats (IRAlus) are abundantly found in the transcriptome, especially in introns and 3′ UTRs. Yet, the biological significance of 3′ UTR IRAlus remains largely unknown. Here, we find that IRAlus induce the silencing of genes involved in essential signaling pathways. We utilize J2 antibody to directly capture and map the double-stranded RNA structure of 3′ UTR IRAlus in the transcriptome. Bioinformatic analysis reveals alternative polyadenylation as a major axis of IRAlus-mediated gene regulation. Notably, the expression of mouse double minute 2 (MDM2), an inhibitor of p53, is upregulated by the exclusion of IRAlus during UTR shortening, which is exploited to silence p53 during tumorigenesis. Moreover, the transcriptome-wide UTR lengthening in neural progenitor cells results in the global downregulation of genes associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis, via IRAlus inclusion. Our study establishes the functional landscape of 3′ UTR IRAlus and its role in human pathophysiology.
Warm temperature and mild water stress cooperatively promote root elongation
Authors: Hayes Scott , Leong Cheuk Ka , Zhang Wenyan , Lamain Marthe , Lamers Jasper , de Zeeuw Thijs , Verstappen Francel , Hiltbrunner Andreas , Testerink Christa 
Published: December 2023

SummaryWarm temperatures have a dramatic effect on plant development. In shoots, stems elongate, and leaves are raised in a developmental programme called thermomorphogenesis. This results in enhanced leaf cooling capacity1. Thermomorphogenesis is tightly intertwined with light signalling pathways. The level of integration is so high that it has been proposed that shoot temperature sensing may have evolved from the co-option of an existing light signalling pathway during the colonisation of land by plants2. Roots also undergo thermomorphogenesis, but the mechanism by which this occurs is less well understood. Main root elongation is enhanced at warm temperatures, and this response is independent of many of the light and temperature signalling components of the shoot3. Roots develop in darkness and so it is a reasonable assumption that root temperature signalling is not through modulation of light signalling. It was recently speculated that due to the close correlation between warm temperature and soil moisture content, root temperature signalling could feasibly be related to water availability signals2. In this study we tested the interaction between temperature and water availability signalling in plant roots. We found that these environmental factors co-operatively enhance main root elongation. This interaction effect was dependent on SUCROSE NON-FERMENTING RELATED KINASE 2.2 (SnRK2.2) and SnRK2.3 and the E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). We found that SnRK2.2 / 2.3 and COP1 have opposite effects on the stability of the transcription factor ELONGATED HYPOCOTYL 5 (HY5) in elongation zone hair cells. The stability of HY5 in these cell types generally corresponded to the degree of root elongation seen in each mutant background. Our study reveals several molecular components of root thermomorphogenesis and highlights the importance of an integrative approach to plant environmental signalling. Our results may have direct implications for agricultural land management, especially as global climates become more unpredictable.
Engrailed transcription factors direct excitatory cerebellar neuron diversity and survival
Authors: Krishnamurthy Anjana , Lee Andrew S. , Bayin N. Sumru , Stephen Daniel N. , Nasef Olivia , Lao Zhimin , Joyner Alexandra L. 
Published: December 2023

ABSTRACTThe excitatory neurons of the three cerebellar nuclei (eCN) form the primary output for the cerebellar circuit. The medial eCN (eCNm) were recently divided into molecularly defined subdomains in the adult, however how they are established during development is not known. We define molecular subdomains of the eCNm using scRNA-seq and spatial expression analysis and show they evolve during embryogenesis to resemble the adult. Furthermore, the eCNm is transcriptionally divergent from the rest of the eCN by E14.5. We previously showed that loss of the homeobox genesEn1andEn2leads to death of a subset of embryonic eCNm. We demonstrate that mutation ofEn1/2in embryonic eCNm results in cell death of specific posterior eCNm molecular subdomains and loss of TBR2 (EOMES) expression in an anterior subdomain, as well as reduced synaptic gene expression. We further reveal a similar function for EN1/2 in mediating TBR2 expression, neuron differentiation and survival in the two other cerebellar excitatory neuron types. Thus, our work defines embryonic eCNm molecular diversity and reveals conserved roles for EN1/2 in the cerebellar excitatory neuron lineage.
The Right Atrium Affects in silico Arrhythmia Vulnerability in Both Atria
Authors: Martínez Díaz Patricia , Sánchez Jorge , Fitzen Nikola André , Ravens Ursula , Dössel Olaf , Loewe Axel 
Published: December 2023

AbstractIntroductionThe role of the right atrium (RA) in atrial fibrillation (AF) has long been overlooked. Computer models of the atria can aid in assessing how the RA influences arrhythmia vulnerability and in studying the role of RA drivers in the induction of AF, both aspects challenging to assess in living patients. It remains unclear if incorporating the RA influences the reentry inducibility of the model. As personalized ablation strategies rely on non-inducibility criteria, the adequacy of left atrium (LA)-only models for developing such ablation tools is uncertain.AimTo evaluate the effect of incorporating the RA in 3D patient-specific computer models on arrhythmia vulnerability.MethodsImaging data from 8 subjects were obtained to generate patient-specific computer models. We created 2 models for each subject: a monoatrial with only the LA and a biatrial with both the RA and LA. We considered 3 different states of substrate remodeling: healthy (H), mild (M), and severe (S). The Courte-manche et al. cellular model was modified from control conditions to a setup representing AF-induced remodeling with 0 %, 50 %, and 100 % changes for H, M, and S, respectively. Conduction velocity was set to 1.2, 1.0, and 0.8 m/s for each remodeling state. Fibrosis extent corresponded to Utah 2 (5-20 %) and Utah 4 (>35 %) stages for M and S, while the H state was modeled without fibrosis. Arrhythmia vulnerability was assessed by virtual S1S2 pacing from different points separated by 2cm using openCARP. A point was classified as inducing arrhythmia if reentry was maintained for at least 1 s. The vulnerability ratio was defined as the number of inducing points divided by the number of stimulation points. The mean tachycardia cycle length (TCL) was assessed at the stimulation site. We compared LA vulnerability ratios in monoatrial and biatrial models.ResultsIncorporating the RA increased the mean LA vulnerability ratio by 115.8 % (0.19±0.13 to 0.41±0.22,p= 0.033) in state M and 29.0 % in state S (0.31±0.14 to 0.40±0.15,p= 0.219). No arrhythmia was induced in the H models. RA inclusion increased the TCL of LA reentries by 5.5 % (186.9±13.3 ms to 197.2±18.3 ms,p= 0.006) in scenario M and decreased it by 7.2 % (224.3±27.6 ms to 208.2±34.8ms,p= 0.010) in scenario S. RA inclusion increased LA inducibility revealing 5.5±3.0 new points per patient in the LA for the biatrial model, which did not induce reentry in the monoatrial model.ConclusionsLA reentry vulnerability in a biatrial model is higher than in a monoatrial model. Incorporating the RA in patient-specific computational models unmasked potential inducing points in the LA. The RA had a substrate-dependent effect on reentry dynamics, altering the TCL of LA-induced reentries. Our results provide evidence for an important role of the RA in the maintenance and induction of arrhythmia in patient-specific computational models, thus suggesting the use of biatrial models.
The pathogenic coronatine toxin hijacks host redox signalling to suppress plant immunity
Authors: Frungillo Lucas , Oka Nodoka , Lee Sang-Uk , Nomoto Mika , Yun Byung-Wook , Tada Yasuomi , Spoel Steven H. 
Published: December 2023

ABSTRACTReciprocal antagonism between the hormones salicylic acid (SA) and jasmonic acid (JA) is particularly important during infection by the bacterial pathogenPseudomonas syringae.P. syringaesecretion of the virulence-promoting toxin, coronatine, is thought to suppress SA-induced immune responses by manipulating host JA signalling. Here, we report an unexpected JA-independent role of coronatine in promoting pathogen virulence. While JA induced resistance toP. syringae, coronatine promoted pathogen virulence by suppressing cellular accumulation of glutathione, a vital antioxidant required for immunity. Coronatine-mediated suppression of glutathione levels prevented activation of NPR1, a redox-sensitive master regulator of SA-responsive immune genes. Moreover, the accrual of nitric oxide (NO) restored virulence of coronatine-deficientP. syringae, but was counteracted by expression of the hostS-nitrosothiol reductase, Thioredoxinh5. Thus, our findings indicateP. syringaeutilises coronatine to suppresses host immunity by precisely manipulating glutathione- and NO-mediated redox signalling networks.
Exploring the differential effects of consumer brand attitude persuasion for printed advertisements in luxury and nonluxury brands
Authors: Jayawardena Nirma Sadamali , Quach Sara , Bandyopadhyay Chinmoy , Thaichon Park 
Published: December 2023

PurposeThis study examined the differential effects of printed advertisements with luxury and nonluxury brands on consumer brand attitude persuasion using a qualitative experimental approach.Design/methodology/approachThe authors adopted a qualitative experimental approach and the authors conducted two experiments over six months. In the first experiment, participants were asked to view five print advertisements related to five different luxury brands. In the second experiment, the same participants were asked to view another five print advertisements on non-luxury brands. The qualitative thematic differences for each brand were analyzed using NVivo software, employing the theoretical assumptions of Petty and Cacioppo's (1981) elaboration likelihood model (ELM).FindingsIn experiments 1 and 2, it was identified that brand experience, personalized brand experience, product quality, product quantity, personal image-conscious, nonpersonal image-conscious, affordability and unaffordability as the main thematic findings leading to consumer attitude persuasion.Practical implicationsThe two main contributions are as follows: theoretically, applying a social psychology theory to the advertising industry offers an understanding of the social cognition stages of a human mindset. As a practical implication, this study's findings guide advertising agencies, marketers and salespeople regarding how to design effective print advertisements in a way that persuades consumer attitudes.Originality/valueThrough the theoretical assumptions of Petty and Cacioppo's (1981) ELM, this paper can be considered one of the first studies to combine social psychology and advertising to investigate the differential effects on consumer brand attitude persuasion for luxury and nonluxury brands.
Addressing global overconsumption: positioning the anti-consumption through communication appeals
Authors: Lučić Andrea , Uzelac Marija 
Published: December 2023

PurposeThe study aims to analyse the possibilities of positioning the anti-consumption through different communication appeals. It analyses commercial and social marketing campaigns in the global context, with the aim to recommend communication guidelines to empower anti-consumption among different industries.Design/methodology/approachThe study conducted a qualitative content analysis of marketing communication focused on anti-consumption promotion.FindingsThe results bring a comprehensive overview of possible communication appeals of anti-consumption and prove feasibility of their implementation. The analysis of used appeals leads to recommendations for developing effective marketing communication for promoting anti-consumption.Practical implicationsThe recommendations can serve both for-profit and non-profit organization as a showcase to discover the idea of anti-consumption as communication appeals. By empowering anti-consumption, consumers could reach personal welfare and participate in social equilibrium. Also, the study brings recommendations for further research considering the evaluation of the implemented strategies.Originality/valueThe study covers a gap in published literature focusing on comprehensive analysis of existing anti-consumption marketing communication strategies and appeals and brings an overview of potential strategies for empowering anti-consumption among modern consumers.
The relationship between labour-only procurement and health and safety performance of construction projects
Authors: Umeokafor Nnedinma , Windapo Abimbola , Olatunji Oluwole Alfred 
Published: December 2023

PurposeThe purpose of this study is to investigate the influences of the characteristics of procurement strategies, in this instance labour-only, on project performance concerning health and safety (H&S), a project performance indicator.Design/methodology/approachUsing non-probability purposeful and snowballing sampling methods, questionnaires were used to collect data from construction professionals in Nigeria. This was then analysed using descriptive (frequency and mean scores) and inferential statistics (Mann–Whitney-U and Kendall's Tau_b tests).FindingsThe findings indicate a statistically significant negative correlation between ‘the level of client involvement and ‘fatalities' and a positive one with ‘conducting of health and safety risk assessment' and ‘conducting employee surveys on health and safety attitude’. Poor hygiene is found to be the worst lagging indicator, while conducting of inspection is the most adopted leading indicator of project health and safety performance. It also emerged that there is no significant difference in the health and safety performance of projects procured through the procurement strategy in urban and rural areas.Practical implicationsThe study provides valuable insight into the complexities in H&S management due to the high level of client involvement in labour-only procurement system (LoPS) projects and the level of diversity in their responsibilities therein. It creates a fundamental direction for developing a detailed framework or guidance notes for client involvement in the integration of H&S into LoPS projects.Originality/valueThis is the first study that examines the influence of the characteristics of procurement strategy on project health and safety performance. Evidence in the literature shows that project delivery outcomes significantly improve if procurement is strategically used, including when it is considered early in projects. However, integrating H&S into procurement strategies has received little attention.
Essential building blocks for future blended learning with the right amount of blend
Authors: Savara Vandana , Assaf Yousef , Hariri Mustafa , Alastal Haya Bassam , Asad Rania 
Published: December 2023

PurposeThis paper aims to shed light on how the composition of future blended learning (BL) courses can be changed to provide students with quality academic learning experiences. The model suggested in this study will guide instructors on how to design their course learning outcomes to ensure effective delivery.Design/methodology/approachThe new model has been developed by combining Bloom's taxonomy and Carman's model. Later, a new framework entitled “PATHCO” based on an extensive literature review is applied to enhance the quality of all five components of Carman's model.FindingsThe PATHCO conceptual framework has been developed to ensure quality in the five main teaching and learning factors. This framework covers criteria like pedagogical, assessments, technical, health care and organizational. Further research is required to broaden the main elements of the suggested framework and to validate this research through a case study.Originality/valueThe COVID-19 pandemic has transformed the landscape of the education sector by encouraging an extensive acceptance of technology-enhanced learning and teaching. Blended learning (BL) has become the most appropriate medium to deliver online learning (OL). However, educators and students have reported dissatisfaction with the BL mode of delivery. To address this dissatisfaction, this study outlines, using the PATHCO model, all the essential building blocks which are required to find the right blend of both face-to-face and online components.