bluuebunny/crossref_metadata_2025_split huggingface dataset:
Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher
Authors: Jones Robert E. , Tice Alexander K. , Eliáš Marek , Eme Laura , Kolísko Martin , Nenarokov Serafim , Pánek Tomáš , Rokas Antonis , Salomaki Eric , Strassert Jürgen F. H. , Shen Xing‐Xing , Žihala David , Brown Matthew W. 
Published: January 2024

AbstractPhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein‐coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user‐created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast‐evolving sites, removal of fast‐evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Constructing a phylogenomic datasetBasic Protocol 2: Performing phylogenomic analysesSupport Protocol 1: Installing PhyloFisherSupport Protocol 2: Creating a custom phylogenomic database
Enterprise risk management and firm performance: The mediating role of corporate social responsibility in the European Union region
Authors: Resende Sérgio , Monje‐Amor Ariadna , Calvo Nuria 
Published: January 2024

AbstractThis study's aim is to examine the impact of enterprise risk management (ERM) on firm performance when aligned with firm strategy, with a particular emphasis on the mediating role of corporate social responsibility (CSR) in this relationship. Previous studies established a connection between ERM and firm performance, as well as between CSR and firm performance. However, the ERM effect on firm performance via CSR remains unexplored. Structural equation modeling (SEM) was used to assess how the ERM affects the firm's performance, both directly and indirectly, through the influence of CSR strategy. The ERM is represented through risk indicators collected from 222 companies in the European Union. The data were gathered from 2015 to 2019 and applied to a structural equations‐based model to analyze how CSR acts as a mediator between ERM and firm performance. The findings suggest that ERM has a significant impact on firm performance, both directly and indirectly, through the effect of the CSR strategy.
Multi‐omics integration reveals a nonlinear signature that precedes progression of lung fibrosis
Authors: Pattaroni Céline , Begka Christina , Cardwell Bailey , Jaffar Jade , Macowan Matthew , Harris Nicola L , Westall Glen P , Marsland Benjamin J 
Published: January 2024

AbstractObjectivesIdiopathic pulmonary fibrosis (IPF) is a devastating progressive interstitial lung disease with poor outcomes. While decades of research have shed light on pathophysiological mechanisms associated with the disease, our understanding of the early molecular events driving IPF and its progression is limited. With this study, we aimed to model the leading edge of fibrosis using a data‐driven approach.MethodsMultiple omics modalities (transcriptomics, metabolomics and lipidomics) of healthy and IPF lung explants representing different stages of fibrosis were combined using an unbiased approach. Multi‐Omics Factor Analysis of datasets revealed latent factors specifically linked with established fibrotic disease (Factor1) and disease progression (Factor2).ResultsFeatures characterising Factor1 comprised well‐established hallmarks of fibrotic disease such as defects in surfactant, epithelial–mesenchymal transition, extracellular matrix deposition, mitochondrial dysfunction and purine metabolism. Comparatively, Factor2 identified a signature revealing a nonlinear trajectory towards disease progression. Molecular features characterising Factor2 included genes related to transcriptional regulation of cell differentiation, ciliogenesis and a subset of lipids from the endocannabinoid class. Machine learning models, trained upon the top transcriptomics features of each factor, accurately predicted disease status and progression when tested on two independent datasets.ConclusionThis multi‐omics integrative approach has revealed a unique signature which may represent the inflection point in disease progression, representing a promising avenue for the identification of therapeutic targets aimed at addressing the progressive nature of the disease.
Seize the engine: Emerging cell cycle targets in breast cancer
Authors: Fuentes‐Antrás Jesús , Bedard Philippe L. , Cescon David W. 
Published: January 2024

AbstractBreast cancer arises from a series of molecular alterations that disrupt cell cycle checkpoints, leading to aberrant cell proliferation and genomic instability. Targeted pharmacological inhibition of cell cycle regulators has long been considered a promising anti‐cancer strategy. Initial attempts to drug critical cell cycle drivers were hampered by poor selectivity, modest efficacy and haematological toxicity. Advances in our understanding of the molecular basis of cell cycle disruption and the mechanisms of resistance to CDK4/6 inhibitors have reignited interest in blocking specific components of the cell cycle machinery, such as CDK2, CDK4, CDK7, PLK4, WEE1, PKMYT1, AURKA and TTK. These targets play critical roles in regulating quiescence, DNA replication and chromosome segregation. Extensive preclinical data support their potential to overcome CDK4/6 inhibitor resistance, induce synthetic lethality or sensitise tumours to immune checkpoint inhibitors. This review provides a biological and drug development perspective on emerging cell cycle targets and novel inhibitors, many of which exhibit favourable safety profiles and promising activity in clinical trials.
Assessment of six surrogate insulin resistance indexes for predicting cardiometabolic multimorbidity incidence in Chinese middle‐aged and older populations: Insights from the China health and retirement longitudinal study
Authors: Xiao Danrui , Sun Honglin , Chen Long , Li Xiang , Huo Huanhuan , Zhou Guo , Zhang Min , He Ben 
Published: January 2024

AbstractAimsInsulin resistance (IR) is associated with cardiometabolic multimorbidity (CMM). We aimed to explore the predictive value of six surrogate IR indexes—Chinese visceral adiposity index (CVAI), lipid accumulation product (LAP), triglyceride‐glucose (TyG), atherogenic index of plasma (AIP), TyG‐body mass index (TyGBMI), and TyG‐waist circumference (TyGwaist)—to establish the CMM incidence in Chinese middle‐aged and older populations.Material and MethodsTo estimate the odds ratio (OR) with a 95% confidence interval (95% CI) for incident CMM using six surrogates, we analysed data from the China Health and Retirement Longitudinal Study using multivariate logistic regression models. The nonlinear dose‐response correlation was evaluated using restricted cubic spline analysis; predictive performance was assessed using receiver operator characteristic curves.ResultsAmong 6451 eligible participants, 268 (4.2%) developed CMM during the 4‐year follow‐up period. The ORs (95% CI) for incident CMM increased with increasing CVAI quartiles (Q) [Q2: 1.71, 1.03–2.90; Q3: 2.72, 1.70–4.52; Q4: 5.16, 3.29–8.45; all p < 0.05] after full adjustment, with Q1 as the reference. Other indexes yielded similar results. These associations remained significant in individuals with a normal body mass index. Notably, CVAI, AIP, and TyG exhibited a linear dose‐response relationship with CMM (Pnonlinear ≥0.05), whereas LAP, TyGBMI, and TyGwaist displayed significant nonlinear correlations (Pnonlinear <0.05). The area under the curve for the CVAI (0.691) was significantly superior to that of other indexes (all p < 0.05).ConclusionsThe six IR surrogates were independently associated with CMM incidence. CVAI may be the most appropriate indicator for predicting CMM in middle‐aged and older Chinese populations.
Analysis of drugs seized from amnesty bins at two major United Kingdom summer music festivals using two portable gas chromatography‐mass spectrometry (GC–MS) instruments
Authors: Frinculescu Anca , Shine Trevor , Ramsey John , Couchman Lewis , Frascione Nunzianda , Abbate Vincenzo 
Published: January 2024

AbstractGlobally, the number of drug users and the proportion of the drug using population has increased from 210 million in 2009 to 269 million in 2019. Several studies suggest that music festival attendees are more likely to abuse illicit substances and have a high‐risk profile. Consequently, it is crucial to develop robust field drug analysis methods that facilitate harm reduction and drug monitoring. The work presented in this report aimed at developing and validating qualitative analytical methods for 3,4‐methylenedioxymethamphetamine, 4‐bromo‐2,5‐dimethoxyphenethylamine (2C‐B), ketamine and N‐ethylpentylone on two portable gas chromatography–mass spectrometry (GC–MS) systems: Griffin G510 (Teledyne FLIR, West Lafayette, IN) and Torion T‐9 (PerkinElmer, Shelton, CT). The diagnostic ability of the mobile GC–MS units was assessed on 200 samples in total, seized at two large summer music festivals in the United Kingdom. The method validation process included selectivity/specificity, limit of identification, carry‐over, ruggedness/robustness, and inter‐ and intra‐day precision (repeatability and reproducibility). The Griffin G510 demonstrated a limit of identification from 1 mg/mL for 2C‐B to 0.063 mg/mL for ketamine and good ruggedness and precision results. The precision for 2C‐B using the Torion T‐9 was poorer than for the Griffin G510, but equivalent for the other compounds tested. Correct identifications (versus benchtop GC–MS) for the two festivals were 85%–86% and 74%–83% for the Griffin G510 and the Torion T‐9, respectively. The two portable instruments were able to adequately cover current on‐site drug‐testing analytical gaps and proved to be a powerful addition to the on‐site drug analysis techniques.
Identification of thermolabile positional isomers of N‐(2‐hydroxybenzyl)‐2‐(dimethoxyphenyl)ethanamines (NBOH series) using chromatography and mass spectrometry methods
Authors: Kupriyanova Olga V. , Shevyrin Vadim A. , Sadykova Raziya G. , Shafran Yuri M. 
Published: January 2024

AbstractAmong N‐((2‐substituted)benzyl)phenylethanamines, N‐(2‐hydroxybenzyl)phenylethanamines are a special type of compounds which are thermolabile and degrade in the course of analysis by means of gas chromatography–mass spectrometry (GC–MS). This can lead to substantial errors, in the identification of legally controlled compounds of this series containing methoxy groups at positions 2 and 5 of the benzene ring of the phenylethyl fragment by GC–MS, which is commonly used in forensic and toxicological laboratories. Exemplified by the five isomeric 2‐(dimethoxyphenyl)‐N‐(2‐hydroxybenzyl)ethanamines, it was shown that their derivatization with trifluoroacetic anhydride (same as in the case of the N‐(2‐methoxybenzyl)‐, N‐(2‐fluorobenzyl)‐, N‐(2‐chlorobenzyl)‐, and N‐(2‐bromobenzyl)substitutes phenylethanamines [NBOMe, NBF, NBCl, and NBBr, respectively] series described earlier) results in only one product, N‐monosubstituted derivative, for each positional isomer within a series, which makes it possible to reliably identify each compound by the GC–MS method. In addition, chromatographic conditions for sufficient separation of trifluoroacetyl derivatives of these positional isomers of the NBOH series in 25 min are proposed, which is an important aspect for analysis in forensic laboratories engaged in the determination of narcotic drugs and new psychoactive substances. As an alternative approach, a method for identifying positional isomers of the NBOH series by the high‐performance liquid chromatography–high‐resolution mass spectrometry (HPLC‐HRMS) method without derivatization is proposed.
19th International Xenopus Conference Meeting Report: Latest developments and future perspectives
Authors: Zhou Coral , Kulkarni Saurabh 
Published: January 2024

AbstractThe African clawed frog, Xenopus laevis, and the Western clawed frog, Xenopus tropicalis, have been foundational model organisms for establishing key principles of embryonic development. Today, the utility of Xenopus has been greatly expanded for studying a wide range of biological processes both in health and disease. Here, we describe the latest advancements from the Xenopus community, which span the molecular, cellular, tissue, and organismal scales.
Association between red blood cell distribution width‐to‐albumin ratio and prognosis in non‐ischaemic heart failure
Authors: Zhou Ping , Tian Peng‐Chao , Zhai Mei , Huang Yan , Zhou Qiong , Zhuang Xiao‐Feng , Liu Hui‐Hui , Wang Jin‐Xi , Zhang Yu‐Hui , Zhang Jian 
Published: January 2024

AbstractAimsRed blood cell distribution width‐to‐albumin ratio (RAR), an innovate biomarker of inflammation, can independently predict adverse cardiovascular outcomes. However, the association between RAR and prognosis in patients with non‐ischaemic heart failure (NIHF) remains unclear.Methods and resultsA total of 2077 NIHF patients admitted to the Heart Failure Care Unit, Fuwai Hospital, were consecutively enrolled from December 2006 to October 2017 in this retrospective study. The primary endpoint was a composite outcome of all‐cause mortality and heart transplantation. The correlation between RAR and the composite outcome was assessed by the Kaplan–Meier survival analysis and the Cox regression analysis. Incremental predictive values and the clinical performance of RAR for all‐cause mortality or heart transplantation were also assessed based on a 12‐variable traditional risk model. The median follow‐up time in this study was 1433 (1341, 1525) days. As the gender no longer satisfied the Cox proportional risk assumption after 1150 days, we set 1095 days as the follow‐up time for analysis. A total of 500 patients reached the composite outcome. Multivariable Cox regression showed that per log2 increase of RAR was significantly associated with a 132.9% [hazard ratio 2.329, 95% confidence interval (CI) 1.677–3.237, P < 0.001] increased risk of all‐cause mortality or heart transplantation. Better model discrimination [concordance index: 0.766 (95% CI 0.754–0.778) vs. 0.758 (95% CI 0.746–0.770), P < 0.001], calibration (Akaike information criterion: 1487.3 vs. 1495.74; Bayesian information criterion: 1566.25 vs. 1569.43; Brier score: 1569.43 vs. 1569.43; likelihood ratio test P < 0.001), and reclassification (integrated discrimination improvement: 1.35%, 95% CI 0.63–2.07%, P < 0.001; net reclassification improvement: 13.73%, 95% CI 2.05–27.18%, P = 0.034) were improved after adding RAR to the traditional model (P < 0.001 for all). A higher overall net benefit was also obtained in the threshold risk probability of 20–55%.ConclusionsHigh level of RAR was an independent risk factor of poor outcome in NIHF.
Slow relaxation of magnetization in the Co(II)‐phosphotungstate Keggin polyoxometalate
Authors: Martinez Lara , Alborés Pablo 
Published: January 2024

AbstractWe are reporting the single crystal structure of the tetrabutylammonium (TBA) salt of the old Co(II) Keggin phosphotungstate anion (Co(II)POM) and a study of the magnetic behaviour of this well‐known POM. This Co(II)POM crystallizes in a cubic cell and this high symmetry obscure a precise characterization of Co(II) coordination sphere metrics due to positional disordered. We employed DFT and SA‐SOC‐CASSCF as auxiliary tools to complement DC and AC magnetic data collected. The studied complex behaves as a field‐induced single ion magnet (SIM) showing slow relaxing magnetization below 5 K under small DC applied magnetic fields. Raman relaxation mechanisms dominates with different relaxation times observed when switching from the TBA salt to the K salt of the Co(II)POM.
Multivalent Aminoseptanose Mimetics by Copper‐Catalyzed (3+2) Cycloadditions of Azidomethyl‐Substituted Bicyclic 1,2‐Oxazines
Authors: Bouché Léa , Zimmer Reinhold , Reissig Hans‐Ulrich 
Published: January 2024

AbstractStarting from readily available enantiopure azidomethyl‐substituted bicyclic 1,2‐oxazine derivatives and mono‐, di‐ or trialkynes, their copper‐catalyzed (3+2) cycloadditions furnished a series of 1,2,3‐triazolyl‐linked compounds in good yields. These click reactions proceeded smoothly at room temperature when copper iodide as catalyst was used in the presence of triethylamine and tris[(1‐gbenzyl‐1H‐1,2,3‐triazol‐4‐yl)methyl]amine as ligand. Generally, the unprotected bicyclic 1,2‐oxazine derivatives seemed to show slightly higher reactivity and provided better yields compared with their silyl‐protected counterparts. Exhaustive hydrogenolysis with cleavage of the 1,2‐oxazine N−O bonds in the presence of palladium on charcoal as promotor is feasible but was found to be capricious. Reasonable results were obtained when acetic acid was employed as cosolvent. By applying these conditions, several of the bicyclic 1,2‐oxazine derivatives were successfully converted into the expected mono‐ or divalent aminooxepine derivatives which can be regarded as aminoseptanose mimetics.
Robust control of wind turbines to reduce wind power fluctuation
Authors: Tang Minan , Wang Wenjuan , Zhen Xiaofei , An Bo , Zhang Yaqi , Yan Yaguang 
Published: January 2024

AbstractThe wind power generation system of a 5 MW horizontal axis wind turbine has a high wind energy conversion efficiency. The proportion of installed capacity in practical production applications is increasing year on year, so that the stability of its operation becomes a central factor in determining the productivity of the wind farm in question. This paper takes a 5 MW wind turbine as the research object and proposes a parameter‐adaptive robust model predictive control method to achieve self‐optimization of controller parameters through a Bayesian optimization approach. A robust model predictive control strategy, aiming to reduce the power fluctuation while maximizing the power output, is developed in this paper to enhance the dynamic economic performance under uncertain wind speed variation. A Bayesian algorithm is used in this paper to optimize the parameters of the controller. Moreover, wind speeds are simulated using TurbSim for different turbulence intensities of 5%, 10%, and 15% turbulence. Finally, the robust model predictive control toolbox in MATLAB is designed and simulated. The results show that the operational instability of the wind energy system is overcome. Meanwhile, the robustness of the wind energy system operation is improved compared to the traditional model predictive control approach.
Short‐term biogeomorphology of a gravel‐bed river: Integrating remote sensing with hydraulic modelling and field analysis
Authors: Latella Melissa , Notti Davide , Baldo Marco , Giordan Daniele , Camporeale Carlo 
Published: January 2024

AbstractIn recent decades, fluvial geomorphology and ecohydraulic research have extensively used field observations, remote sensing or hydrodynamic modelling to understand river systems. This study presents an innovative approach that combines field surveys, Light Detection and Ranging (LiDAR)‐based topographical and biomass analyses and model‐derived hydro‐morphodynamic geostatistics to examine short‐term biogeomorphological changes in the wandering gravel‐bed Orco River in Italy. Our primary hypothesis is that hydro‐morphological variables can be robust descriptors for riparian vegetation distribution. From a geomorphological perspective, our study confirms the prevalent wandering behaviour of the Orco River. Moreover, we identified a widening trend in braiding and anabranching sections, particularly downstream. This is evident because of hotspots of flood‐induced morphological reactivation and the redistribution of sediments from the riverbed to lateral bars, resulting in a multi‐thread pattern. Our analysis reveals a net increase in biomass during the observation period despite frequent flood disturbances. We attributed it to two opposing biogeomorphological dynamics: the reduced flow disturbance in some regions due to flood‐induced geomorphological changes and the self‐healing of lateral connectivity through river wandering. Such a net increase indicates that transitional rivers store carbon in the form of vegetation biomass due to their short‐term morphological instability and the different timescales between vegetation and morphological adjustments. Finally, we supported our initial hypothesis with three key findings: (i) a signature of vegetation not just on topography but also on hydro‐morphological conditions, summarised by inundation probability; (ii) the lower variance in vertical topographical changes in vegetated areas compared with bare ones; and (iii) the introduction of a new parameter, named inundation viscosity, derived from the product of mean bed shear stress and average inundation duration, as a discriminating factor for colonisation conditions. These results underscore the value of our comprehensive approach.
Spatial relationship of landform surface features and biocrusts, and their effect on soil microbial biomass on an alluvial fan
Authors: Hassanzadeh Bashtian Mahvan , Karimi Alireza , Sepehr Adel , Lakzian Amir , Caballero Emilio Rodriguez 
Published: January 2024

AbstractThe spatial cover of biocrusts represents a suitable habitat for the activity of soil microorganisms in semi‐arid and arid regions. Microorganisms are one of the essential components of soil quality. Therefore, it is necessary to understand the processes of biocrust habitat formation in landforms and their mutual relationship with soil properties. We studied the spatial distribution of biocrusts and their effect on soil microbial biomass and carbon activity in a semi‐arid alluvial fan in NE Iran. A total of 72 soil samples (using plots 0.25 m2) from the topsoil layers (0–5 cm) were collected along the alluvial fan in September 2020. Soil surface properties and microbial biomass in two categories of biocrust and non‐biocrust were investigated in three classes of biocrusts coverage obtained by geostatistics. Our results revealed that biocrusts had a negative correlation with gravel coverage and elevation; in contrast, the suitable spaces for biocrusts growth were created by cobble clasts. The biocrusts have provided favourable conditions for soil microorganisms by altering the properties of the soil (such as increasing organic carbon, nitrogen and available phosphorus and decreasing pH), and thus they increased basal soil respiration and microbial biomass. Different microbial activities were led by the predominant type of biocrusts, as the chlorolichen crusts had the most significant effect on increasing the microbial biomass phosphorus while cyanolichen crusts increased the microbial biomass carbon. Moss and cyanolichen crusts increased microbial activity and respiration more than cyanobacteria crusts. Therefore, the soil quality has improved by biocrusts in semi‐arid ecosystems.