bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSAURON: a tool for assessing protein annotation across a broad range of species
Authors: Sommer Markus J. , Zimin Aleksey V. , Salzberg Steven L. 
Published: May 2024

AbstractEvaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there is no broadly applicable solution. In this manuscript we introduce PSAURON (Protein Sequence Assessment Using a Reference ORF Network), a novel software tool developed to assess the quality of protein-coding gene annotations. Utilizing a machine learning model trained on a diverse dataset from over 1000 plant and animal genomes, PSAURON assigns a score to coding DNA or protein sequence that reflects the likelihood that the sequence is a genuine protein coding region. PSAURON scores can be used for genome-wide protein annotation assessment as well as the rapid identification of potentially spurious annotated proteins. Validation against established benchmarks demonstrates PSAURON’s effectiveness and correlation with recognized measures of protein quality, highlighting its potential use as a general-purpose method to evaluate gene annotation. PSAURON is open source and freely available athttps://github.com/salzberg-lab/PSAURON.One-Sentence SummaryPSAURON is a machine learning-based tool for rapid assessment of protein coding gene annotation.
MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data
Authors: Sakamoto Nami , Oka Takaki , Matsuzawa Yuki , Nishida Kozo , Hori Aya , Arita Makoto , Tsugawa Hiroshi 
Published: May 2024

AbstractUntargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence is still guaranteed by manual curation by analytical chemists, although various software tools have been developed for automatic spectral processing based on rule-based fragment annotations. In this study, we provide a novel machine learning model, MS2Lipid, for the prediction of lipid subclasses from MS/MS queries to provide an orthogonal decision of lipidomics software programs to determine the lipid subclass of ion features, in which a new descriptor, MCH (mode of carbon and hydrogen), was designed to increase the specificity of lipid subclasses in nominal mass resolution MS data. The model trained with 5,224 and 5,408 manually curated MS/MS spectra for the positive- and negative-ion modes mapped the query into one or several categories of 97 lipid subclasses, with an accuracy of 95.5% queries in the test set. Our program outperformed the CANOPUS ontology prediction program, providing correct annotations for 38.7% of the same test set. The program was further validated using various datasets from different machines and curators, and the average accuracy exceeded 87.4 %. Furthermore, the function of MS2Lipid was showcased by the annotation of novel esterified bile acids, whose abundance was significantly increased in obese patients in a human cohort study, suggesting that the machine learning model provides an independent criterion for lipid subclass classification, in addition to an environment for annotating lipid metabolites that have been previously unknown.
Kinetic properties of optogenetic DNA editing by LiCre-loxP
Authors: Dufour Alice , Duplus-Bottin Hélène , Boukéké-Lesplulier Thomas , Casassa Eliane , Triqueneaux Gérard , Darthenay-Kiennemann Camille , Dumont Agnès , Moali Catherine , Vittoz Franck , Jost Daniel , Yvert Gaël 
Published: May 2024

ABSTRACTPreviously, we developed an optogenetic tool made of a single chimeric protein called LiCre that enables the edition of specific changes in the genome of live cells with blue light via DNA recombination betweenloxPsites (Duplus-Bottin et al., 2021). Here, we usedin vitroandin vivoexperiments combined with kinetic modeling to provide a deeper characterization of the photo-activated LiCre-loxPrecombination reaction. We find that LiCre binds DNA with high affinity in absence of light stimulus, that this binding is cooperative although not as much as for the Cre recombinase from which LiCre was derived and that increasing temperature from 20°C to 37°C gradually increased LiCre efficiency. The recombination kinetics in live cells can be explained by a model where photo-activation of two or more DNA-bound LiCre units (happening in seconds) can produce (in several minutes) a functional recombination synapse. Our conclusions provide helpful guidelines to induce specific genetic changes in live cells using light.
RUNX2 Isoform II Protects Cancer Cells from Ferroptosis and Apoptosis by Promoting PRDX2 Expression in Oral Squamous Cell Carcinoma
Authors: Huang Junjun , Jia Rong , Guo Jihua 
Published: May 2024

AbstractFerroptosis is a distinct iron-dependent programmed cell death and plays important roles in tumor suppression. However, the regulatory mechanisms of ferroptosis need further exploration. RUNT-related transcription factor 2 (RUNX2), a transcription factor, is essential for osteogenesis. RUNX2 has two types of transcripts produced by two alternative promoters. In the present study, we surprisingly find that RUNX2 isoform II is a novel ferroptosis and apoptosis suppressor. RUNX2 isoform II can bind to the promoter of peroxiredoxin-2 (PRDX2), a ferroptosis inhibitor, and activate its expression. Knockdown of RUNX2 isoform II suppresses cell proliferationin vitroand tumorigenesisin vivoin oral squamous cell carcinoma (OSCC). Interestingly, homeobox A10 (HOXA10), an upstream positive regulator of RUNX2 isoform II, is required for the inhibition of ferroptosis and apoptosis through the RUNX2 isoform II/PRDX2 pathway. Consistently, RUNX2 isoform II is overexpressed in OSCC, and associated with OSCC progression and poor prognosis. Collectively, OSCC cancer cells can up-regulate RUNX2 isoform II to inhibit ferroptosis and apoptosis, and facilitate tumorigenesis through the novel HOXA10/RUNX2 isoform II/PRDX2 pathway.Research organismHuman, Mouse, Oral Squamous Cell Carcinoma
Voltage Sensor Conformations Induced by LQTS-associated Mutations in hERG Potassium Channels
Authors: Chan Aaron N. , Handlin Lucas J. , Lessie Erin N. , Tajkhorshid Emad , Dai Gucan 
Published: May 2024

ABSTRACTVoltage sensors are essential for electromechanical coupling in hERG K+channels, critical to cardiac rhythm. These sensors detect changes in membrane voltage and move in response to the transmembrane electric field. Mutations in voltage-sensing arginines of hERG, associated with Long QT syndrome, alter channel gating, though mechanisms in these mutants remain unclear. Using fluorescence lifetime imaging microscopy (FLIM), transition metal FRET (tmFRET), dual stop-codon mediated noncanonical amino acid incorporation, and molecular dynamics (MD) simulations, we identified distinct intermediate voltage-sensor conformations caused by these mutations. Phasor plot analysis of the FLIM-tmFRET donor revealed multiple FRET states in mutant hERG channels, in contrast to the single high-FRET state observed in unmutated controls. These intermediate FRET states correspond to specific mutation sites and align with distinct intermediate voltage-sensor conformations identified in MD simulations. This study provides novel insights into cardiac channelopathies, highlighting structural underpinnings underlying voltage sensing in cardiac arrhythmias.
BMP4 regulates asymmetric Pkd2 distribution in mouse nodal immotile cilia and ciliary mechanosensing required for left–right determination
Authors: Katoh Takanobu A. , Lange Tim , Nakajima Yoshiro , Yashiro Kenta , Okada Yasushi , Hamada Hiroshi 
Published: May 2024

AbstractBackgroundMouse nodal immotile cilia mechanically sense the bending direction for left–right (L–R) determination and activate the left-side-specific signaling cascade, leading to increasedNodalactivity. Asymmetric distribution of Pkd2, a crucial channel for L-R determination, on immotile cilia has been reported recently. However, the causal relationship between the asymmetric Pkd2 distribution and direction-dependent flow sensing is not well understood. Furthermore, the underlying molecular mechanism directing this asymmetric Pkd2 distribution remains unclear.ResultsThe effects of several recombinant proteins and inhibitors on the Pkd2 distribution were analyzed using super-resolution microscopy. Notably, bone morphogenetic protein 4 (BMP4) affected the Pkd2 distribution. Additionally, three-dimensional manipulation of nodal immotile cilia using optical tweezers revealed that excess BMP4 caused defects in the mechanosensing ability of the cilia.ConclusionsExperimental data together with model calculations suggest that BMP4 regulates the asymmetric distribution of Pkd2 in nodal immotile cilia, thereby affecting the ability of these cilia to sense the bending direction for L–R determination. This study, for the first time, provides insight into the relationship between the asymmetric protein distribution in cilia and their function.
Metabolic Responses to an Acute Glucose Challenge: The Differential Effects of Eight Weeks of Almond vs. Cracker Consumption in Young Adults
Authors: Dhillon Jaapna , Pandey Saurabh , Newman John W. , Fiehn Oliver , Ortiz Rudy M. 
Published: May 2024

ABSTRACTThis study investigated the dynamic responses to an acute glucose challenge following chronic almond versus cracker consumption for 8 weeks (clinicaltrials.gov ID:NCT03084003). Seventy-three young adults (age: 18-19 years, BMI: 18-41 kg/m2) participated in an 8-week randomized, controlled, parallel-arm intervention and were randomly assigned to consume either almonds (2 oz/d, n=38) or an isocaloric control snack of graham crackers (325 kcal/d, n=35) daily for 8 weeks. Twenty participants from each group underwent a 2-hour oral glucose tolerance test (oGTT) at the end of the 8-week intervention. Metabolite abundances in the oGTT serum samples were quantified using untargeted metabolomics, and targeted analyses for free PUFAs, total fatty acids, oxylipins, and endocannabinoids. Multivariate, univariate, and chemical enrichment analyses were conducted to identify significant metabolic shifts. Findings exhibit a biphasic lipid response distinguished by higher levels of unsaturated triglycerides in the earlier periods of the oGTT followed by lower levels in the latter period in the almond versus cracker group (p-value<0.05, chemical enrichment analyses). Almond (vs. cracker) consumption was also associated with higher AUC120 minof aminomalonate, and oxylipins (p-value<0.05), but lower AUC120 minof L-cystine, N-acetylmannosamine, and isoheptadecanoic acid (p-value<0.05). Additionally, the Matsuda Index in the almond group correlated with AUC120 minof CE 22:6 (r=- 0.46; p-value<0.05) and 12,13 DiHOME (r=0.45; p-value<0.05). Almond consumption for 8 weeks leads to dynamic, differential shifts in response to an acute glucose challenge, marked by alterations in lipid and amino acid mediators involved in metabolic and physiological pathways.
Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion
Authors: Miguel Trabajo Tania , Guex Isaline , Dubey Manupriyam , Sarton-Lohéac Elvire , Todorov Helena , Richard Xavier , Mazza Christian , van der Meer Jan Roelof 
Published: May 2024

AbstractInteractions between species are thought to be crucial for modulating their growth and behaviour within communities, and determinant for the emergence of community functions. Several different interaction concepts exist, but there is no consensus on how interactions should be quantified and integrated in community growth theory. Here we expand on existing concepts of real-time measurements of pure culture microcolony growth to develop and benchmark coculture microcolony experiments, and show how these can both parametrize growth kinetic and interspecific interaction effects. We follow surface growth by time-lapse microscopy of fluorescently taggedPseudomonas putidaandPseudomonas veroniiunder substrate competition with succinate, or under substrate indifference with D-mannitol and putrescine. Monoculture-grown microcolonies showed substrate concentration dependent expansion rates as expected from Monod relations, whereas individual microcolony yields were strongly dependent on densities and spatial positioning of founder cells. Maximum specific growth rates in cocultures under substrate competition were diminished by ca. 15%, which was seeding-density independent. The collectiveP. putidapopulation dominated growth over that ofP. veronii, but with 27% yield loss under competition compared to monoculture growth; and 90% for that ofP. veronii. Incidental local reversal of competition was observed whereP. veroniimicrocolonies profited at the detriment ofP. putida, and between 9 and 43% ofP. veroniimicrocolonies grew bigger than expected from bulk competition, depending on seeding density. Simulations with a cell-agent Monod surface growth model suggested that colony expansion rate decrease in competitive coculture is caused by metabolite cross-feeding, which was supported by exometabolite analysis during and after growth of the strains on their individual or swapped supernatant. Coculture microcolony growth experiments thus provide a flexible platform for analysis of kinetic and interspecific interactions, expanding from individual microcolony phenotypic effects to averaged behaviour across all microcolony pairs. The system in theory is scalable to follow real-time growth of multiple species simultaneously into communities.
Diagnostic Performance of ChatGPT to Perform Emergency Department Triage: A Systematic Review and Meta-analysis
Authors: Kaboudi Navid , Firouzbakht Saeedeh , Eftekhar Mohammad Shahir , Fayazbakhsh Fatemeh , Joharivarnoosfaderani Niloufar , Ghaderi Salar , Dehdashti Mohammadreza , Kia Yasmin Mohtasham , Afshari Maryam , Vasaghi-Gharamaleki Maryam , Haghani Leila , Moradzadeh Zahra , Khalaj Fattaneh , Mohammadi Zahra , Hasanabadi Zahra , Shahidi Ramin 
Published: May 2024

AbstractBackgroundArtificial intelligence (AI), particularly ChatGPT developed by OpenAI, has shown potential in improving diagnostic accuracy and efficiency in emergency department (ED) triage. This study aims to evaluate the diagnostic performance and safety of ChatGPT in prioritizing patients based on urgency in ED settings.MethodsA systematic review and meta-analysis were conducted following PRISMA guidelines. Comprehensive literature searches were performed in Scopus, Web of Science, PubMed, and Embase. Studies evaluating ChatGPT’s diagnostic performance in ED triage were included. Quality assessment was conducted using the QUADAS-2 tool. Pooled accuracy estimates were calculated using a random-effects model, and heterogeneity was assessed with the I² statistic.ResultsFourteen studies with a total of 1,412 patients or scenarios were included. ChatGPT 4.0 demonstrated a pooled accuracy of 0.86 (95% CI: 0.64-0.98) with substantial heterogeneity (I² = 93%). ChatGPT 3.5 showed a pooled accuracy of 0.63 (95% CI: 0.43-0.81) with significant heterogeneity (I² = 84%). Funnel plots indicated potential publication bias, particularly for ChatGPT 3.5. Quality assessments revealed varying levels of risk of bias and applicability concerns.ConclusionChatGPT, especially version 4.0, shows promise in improving ED triage accuracy. However, significant variability and potential biases highlight the need for further evaluation and enhancement.
Examining the effectiveness of knowledge governance mechanisms in mobile messaging groups within construction project teams
Authors: Jia Jianyao , Wu Ming 
Published: May 2024

PurposeMobile messaging groups (MMGs) have been widely adopted in construction practice, yet, little is known about how to foster knowledge sharing (KS) in MMGs, characterized by communication visibility. This study is thus motivated to investigate mechanisms for KS in this context.Design/methodology/approachThe paper employs knowledge governance theory to construct a theoretical model and develop hypotheses. Specifically, psychological safety is identified as a mediator between knowledge governance mechanism (KGM) and KS, and promotion regulatory focus is identified as a moderator between KGM and psychological safety. Data from 208 Chinese construction project team members are collected to test the proposed theoretical model.FindingsThe results suggest that both formal and informal KGM positively affect psychological safety, which in turn improves KS (quantity and quality). Moreover, the mediating role of psychological safety is confirmed, and the moderating role of promotion regulatory focus is validated.Originality/valueThis study explores how to foster KS in MMGs, which are pervasive in today’s digital age. The findings in this study enhance the understanding of KS in digital environments and afford important insights into knowledge management within construction project teams.
The predictive power of prior attitudes: understanding employee workspace satisfaction in activity-based work environments
Authors: Halldorsson Freyr , Valgeirsson Halldór , Kristinsson Kari 
Published: May 2024

Purpose
This study aims to examine if and how an activity-based work environment affects employee workspace satisfaction – an attitude linked to important employee outcomes. By comparing perceptions before and after implementation, the research draws attention to factors that may help explain the impact of an activity-based work environment. Specifically, prior attitudes toward activity-based work environments and gender are tested.

Design/methodology/approach
The present study uses a longitudinal design to explore how implementing an activity-based work environment impacts employees’ workspace satisfaction (e.g. privacy, air quality, lighting, temperature, etc.). A sample of 100 employees in a government organization implementing an activity-based working environment was investigated using a longitudinal design, with employees being surveyed thrice – once before and twice after implementation.

Findings
The results indicate that when workspace satisfaction is impacted by implementing an activity-based work environment, this effect seems primarily based on employees’ prior attitude toward such work environments. In addition, employee gender emerges as a potentially important factor in workspace satisfaction, though not exclusive to the activity-based work environment.

Originality/value
Using a longitudinal approach – which allows for observing potential changes over time – and robust statistical methods, this study supports the importance of employees’ initial attitude toward an activity-based work environment concerning workspace satisfaction. This finding has practical implications for organizations and advances the understanding of why an activity-based work environment may positively affect workspace satisfaction for some employees while negatively affecting others.
Assessing the determinants of human development in OECD economies: evidence from labor productivity and investment decisions
Authors: Akinyele Olawale Daniel 
Published: May 2024

PurposeDevelopment has been a long-age phenomenon from the millennium to sustainability. This is because the new millennium ushered in the episode of development in the global economy from the role of inputs to the role of productivity and knowledge. Thus, understanding the forefront of initiatives to develop better policies for better lives and to find fact-based answers to social, economic, and environmental problems becomes unavoidable.Design/methodology/approachThe study therefore assesses the impact of labor productivity and investment decisions on human development. A modified production theory was adopted for OECD economies. To address the problem of endogeneity and cross-sectional dependence, a two-step system generalized method of moments, Driscoll–Kraay estimator, and Panel Corrected Standard Error were used.FindingsThe findings reveal that the impact of labor productivity on human development differs significantly from the impact of investment decisions. The result shows that investment decisions will have a positive impact on human development when there is an insignificant capital fixed formation to boost the productivity of OECD economies. Further, the result shows that the organization governments through the provision of social security and essential services have a positive impact on the OECD human development.Originality/valueThis study has contributed significantly to assessing the drivers of human development within the purview of labor productivity, investment decisions and government expenditure in OECD countries.
Does education promote risk-taking? Evidence from Vietnam
Authors: Tran Dai Binh , Tran Hanh Thi My 
Published: May 2024

PurposeThis study examines the impact of schooling on risk perceptions and the moderation role of a non-cognitive skill, locus of control.Design/methodology/approachUsing information from the Thailand Vietnam Socio Economic Panel data set, the study employs Generalised Method of Moments (GMM) to address the potential endogeneity problem of the schooling variable.FindingsThe findings indicate that a higher level of willingness to take risks is correlated with additional schooling years. In other words, those with higher levels of education are more prone to take more risks. The result demonstrates that the association between education and risk attitudes is moderated by locus of control.Originality/valueThis study contributes to the growing literature on education in emerging countries by addressing the endogeneity problem of schooling variables using the GMM method. Moreover, this study examines the mediating role of personal non-cognitive skills, namely locus of control, in the relationship between education and risk attitudes.
Enhancing AAA capabilities in humanitarian supply chains through 4PL adoption
Authors: Tickle Matthew , Schiffling Sarah , Verma Gaurav 
Published: May 2024

Purpose
This paper aims to explore the impact of fourth-party logistics (4PL) adoption on the agility, adaptability and alignment (AAA) capabilities within humanitarian supply chains (HSCs).

Design/methodology/approach
Semi-structured interviews with individuals from a large non-government organisation were combined with secondary data to assess the influence of 4PL adoption on AAA capabilities in HSCs.

Findings
The results indicate that HSCs exhibit some of the AAA antecedents but not all are fully realised. While 4PL positively affects the AAA capabilities of HSCs, its adoption faces challenges such as the funding environment, data security/confidentiality and alignment with humanitarian principles. The study suggests an AAA antecedent realignment, positioning alignment as a precursor to agility and adaptability. It also identifies three core antecedents in HSCs: flexibility, speed and environmental uncertainty.

Practical implications
The study shows the positive impact 4PL adoption can have on the AAA capabilities of HSCs. The findings have practical relevance for those wishing to optimise HSC performance through 4PL adoption, by identifying the inhibiting factors to its adoption as well as strategies to address them.

Originality/value
This research empirically explores 4PL’s impact on AAA capabilities in HSCs, highlighting the facilitating and hindering factors of 4PL adoption in this environment as well as endorsing a realignment of AAA antecedents. It also contributes to the growing research on SC operations in volatile settings.