bluuebunny/crossref_metadata_2025 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

PhyloFisher 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 dataset

Basic Protocol 2: Performing phylogenomic analyses

Support Protocol 1: Installing PhyloFisher

Support 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

This 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

Objectives

Idiopathic 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.

Methods

Multiple 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).

Results

Features 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.

Conclusion

This 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

Breast 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

Aims

Insulin 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 Methods

To 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.

Results

Among 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).

Conclusions

The 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

Globally, 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

Among 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

The 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

Aims

Red 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 results

A 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%.

Conclusions

High 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

We 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

Starting 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.
Large‐Scale H2 Storage and Transport with Liquid Organic Hydrogen Carrier Technology: Insights into Current Project Developments and the Future Outlook
Authors: Distel Max M. , Margutti Joao M. , Obermeier Jonas , Nuß Andreas , Baumeister Ina , Hritsyshyna Maryna , Weiß Alexander , Neubert Michael
Published: January 2024

The green hydrogen economy is evolving rapidly, accompanied by the need to establish trading routes on a global scale. Currently, several technologies are competing for a leadership role in future hydrogen value chains. Within this context, liquid organic hydrogen carrier (LOHC) technology represents an excellent solution for large‐scale storage and safe transportation of hydrogen. This article presents LOHC technology, recent progress, as well as further potential of this technology with focus on benzyltoluene as the carrier material. Furthermore, this contribution offers an insight into previous and ongoing project development activities led by Hydrogenious LOHC Technologies together with an evaluation of the economic viability and an overview of the regulatory aspects of LOHC technology.
Nickel‐Foam‐ and Carbon‐Nanotubes‐Fiber‐Supported Bismuth Oxide/Nickel Oxide Composite; Highly Active and Stable Bifunctional Electrocatalysts for Water Splitting in Neutral and Alkaline Media
Authors: Tariq Irsa , Ali Abid , Haider Ali , Iqbal Waheed , Asghar Muhammad Adeel , Badshah Amin , Mansoor Muhammad Adil , Nisar Talha , Wagner Veit , Abbas Syed Mustansar , Talat Rabia
Published: January 2024

To increase the effectiveness of both the cathodic hydrogen evolution reaction (HER) and the anodic oxygen evolution reaction (OER), significant efforts are made to produce bifunctional water‐splitting electrocatalysts. In this study, bismuth oxide/nickel oxide (Bi2O3/NiO)‐based composite is supported over the nickel foam (Bi2O3/NiO‐NF) and carbon nanotube fiber (Bi2O3/NiO‐CNTF) to develop two different electrode systems for water‐splitting studies. For OER, Bi2O3/NiO‐NF and Bi2O3/NiO‐CNTF require overpotential of 401 and 369 mV, respectively, to achieve the current density of 50 mA cm−2 in alkaline media, while the current density of 50 mA cm−2 is achieved at overpotential of 398 and 304 mV, respectively, in neutral media. For HER, Bi2O3/NiO‐NF and Bi2O3/NiO‐CNTF achieve the current density of 50 mA cm−2 at overpotential of 301 and 268 mV, respectively, in neutral media. For overall water splitting in neutral media, Bi2O3/NiO‐CNTF achieves the current density of 50 mA cm−2 at cell voltage of 1.654 V. The promising performance of synthesized electrocatalysts reveals that the mixed metal oxides (p‐block and d‐block elements)‐based electrocatalysts can be potential candidates for practical water splitting in basic (1 M KOH) as well as neutral media (1 M phosphate‐buffered saline).
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

The 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

In 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

The 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.
Metagenomics reveals microbial communities and functional differences during chili pepper (Capsicum frutescens L.) natural fermentation: Effects of brines and containers
Authors: Zhang Shiyao , Bao Xi , Xiao Yue , Wang Tao , Chu Chuanqi , Hu Xiaosong , Yi Junjie
Published: January 2024

The study aimed to investigate the effect of fermentation brines and containers on the composition and functional dissimilarity of microbiota in fermented chili peppers: pool with fresh brine (PFB), pool with aged brine (PAB), jar with FB, and jar with AB. The results showed that brines had a greater impact on microbial diversity and fungal community structure than containers, whereas containers had a greater impact on bacterial community structure than brines. At the end of chili pepper fermentation, the dominant bacteria were unclassified_g__Pseudomonas, Lactobacillus_alimentarius, and Halococcus_thailandensis, whereas the dominant fungi were Pichia_membranifaciens and Wallemia_ichthyophaga. Based on the metagenomics functional analysis, the dominant bacteria and fungi were highly related to amino acid metabolism, glycerophospholipid metabolism, and most enzymes that promote carbohydrate substrate modulation. The fermented brines had a larger impact than containers on microbial function. Specifically, the use of FB was found to be beneficial for the biosynthesis of tetracycline, carotenoid, and isoflavonoid. On the other hand, AB was found to be beneficial for the biosynthesis of unsaturated fatty acids, amino acids, and various types of N‐glycan.
Updating Angling Records to Advance Sport Fish Conservation: A Case Study of IGFA's Black Bass World Records
Authors: Taylor Andrew T , Bellapigna Zachary L , Pohlot Bruce G
Published: January 2024

As taxonomic studies revise our understanding of biodiversity, both fisheries managers and the angling public must adapt to best conserve fisheries. Unfortunately, communication gaps between scientists and anglers may result in lags and inaccuracies in the taxonomic information available to anglers. We updated the International Game Fish Association (IGFA)'s black bass Micropterus spp. world records to current taxonomic consensus. Seven new species were acknowledged for all-tackle world record availability, and four of seven existing species records were revised. Florida Bass M. salmoides (formerly M. floridanus), Neosho Bass M. velox, and four members of the Redeye Bass species complex (M. cahabae, M. chattahoochae, M. tallapoosae, and M. warriorensis) are now recognized. Additionally, Alabama Bass M. henshalli—an emerging invasive species—is now distinguished from the smaller, broadly distributed Spotted Bass M. punctulatus. A misidentified specimen resulted in vacant all-tackle records for Shoal Bass M. cataractae and Redeye Bass M. coosae. Genetic verification is warranted in the future, but implementation may create accessibility barriers to record submissions. We hope these efforts will encourage anglers to learn more about black bass diversity, to pursue their own world record catches, and to gain awareness of the conservation challenges threatening this iconic group.
Development of water management strategies in southern Mesopotamia during the fourth and third millennium B.C.E.
Authors: Mantellini Simone , Picotti Vincenzo , Al‐Hussainy Abbas , Marchetti Nicolò , Zaina Federico
Published: January 2024

The last two decades witnessed increasing scholarly interest in the history of water management in southern Mesopotamia. Thanks to many geoarchaeological research projects conducted throughout the central and southern Iraqi floodplains, a general understanding of the macrophases of anthropogenic manipulation of this vast hydraulic landscape has been achieved. However, current narratives mostly rely on studies at a regional scale and are based on excessively long chronological phases (often spanning a whole millennium). A finer‐tuned analysis at a submillennial scale is needed to better appreciate the dynamics that led to the development of artificial canals and irrigation systems and the creation of harbours in cities and other navigation‐related facilities. The Iraqi‐Italian QADIS project is addressing this issue through a systematic geoarchaeological investigation in the south‐eastern area of the Qadisiyah province. We aim to update the current narrative by analysing case studies involving specific periods of occupation. We performed 17 boreholes to propose a date on the functioning period of the hydraulic works in five selected archaeological sites of this region. This approach allowed us to understand changes in water management strategies in both the short and the medium term (i.e., on a scale of centuries). In this paper, we present the results for the fourth and third millennia B.C.E. This period witnessed a crucial passage from the basic exploitation of natural watercourses for irrigation and occasional navigation to the emergence of the first system of artificial canals and intraurban harbours.
simmrd: An open‐source tool to perform simulations in Mendelian randomization
Authors: Lorincz‐Comi Noah , Yang Yihe , Zhu Xiaofeng
Published: January 2024

Mendelian randomization (MR) has become a popular tool for inferring causality of risk factors on disease. There are currently over 45 different methods available to perform MR, reflecting this extremely active research area. It would be desirable to have a standard simulation environment to objectively evaluate the existing and future methods. We present simmrd, an open‐source software for performing simulations to evaluate the performance of MR methods in a range of scenarios encountered in practice. Researchers can directly modify the simmrd source code so that the research community may arrive at a widely accepted framework for researchers to evaluate the performance of different MR methods.
Squeezing unsteady nanofluid flow among two parallel plates with first‐order chemical reaction and velocity slip
Authors: Maiti Hiranmoy , Mukhopadhyay Swati
Published: January 2024

The squeezing flow bears a major importance in everyday phenomena and has vast industrial and biomedical applications. The current study looks at the nanofluid flow among two infinite “parallel plates” that are squeezed. The velocity slip and first‐order compound response have been considered in this problem for a clear understanding of their consequences in the flow of nanofluid and heat transport mechanism. This fluid replica thinks about “Brownian motion” and the influences of “thermophoresis” of nanofluid. The novelty of this work lies in exploring the combined effects of first‐order chemical reaction and the velocity slip on unsteady squeezing flow of nanofluid between two parallel plates as one has not yet reported such effects. The prevailing equations are altered into simplified forms by deploying suitable similarity transformations. Then “numerical solutions” of these equations are obtained by applying the fourth‐order “Runge–Kutta method” with the help of the shooting technique. The accuracy is verified by using two different methods and also comparing our data with the available existing literature. The main goal is to study heat and mass transfer through unsteady squeezing plates by the influence of velocity slip and chemical reaction. The consequences of diverse pertinent parameters on fluid flow, thermal, and concentration fields have been explored in this study. With the rise in “velocity slip parameter” from 0 to 1, 81.37% decrease in skin friction coefficient, 15.81% increase in Nusselt number, and 29.13% increase in Sherwood number are observed. Rising values of the chemical reaction parameter from 0.3 to 0.5, the mass transfer coefficient increases by 66.94%.
Effective and simple interventions to improve outcomes for preterm infants worldwide: The FIGO PremPrep‐5 initiative
Authors: Hall Megan , Valencia Catalina M. , Soma‐Pillay Priya , Luyt Karen , Jacobsson Bo , Shennan Andrew ,   the FIGO Preterm Birth Committee
Published: January 2024

Preterm birth remains the leading cause of mortality among under‐5's and is a major contributor to the reduction in quality‐of‐life adjusted years and reduction in human capital. Globally, there are many interventions and care bundles that aim to reduce the impact of preterm birth once preterm labor has ensued and into the neonatal period; not all of these are applicable in all settings. Here, we introduce the FIGO PremPrep‐5 initiative, which aims to disseminate key information on the most simple and effective interventions with the aim of increasing implementation globally. Before delivery, we recommend a course of antenatal corticosteroids, and intrapartum magnesium sulfate. At delivery, we recommend delayed cord clamping. Postnatally, we recommend early feeding with breast milk and immediate kangaroo care. While there are many other interventions that may improve outcomes at the time of labor and after preterm birth, these are clinically effective and relatively inexpensive options that can be practiced in most settings and supplemented with more advanced care. We include examples of a training video and infographics that will be used for dissemination.
Rapid and non‐invasive detection of cystic echinococcosis in sheep based on serum fluorescence spectrum combined with machine learning algorithms
Authors: Xu Shengke , Dawuti Wubulitalifu , Maimaitiaili Maierhaba , Dou Jingrui , Aizezi Malike , Aimulajiang Kalibixiati , Lü Xiaoyi , Lü Guodong
Published: January 2024

Cystic echinococcosis (CE) is a grievous zoonotic parasitic disease. Currently, the traditional technology of screening CE is laborious and expensive, developing an innovative technology is urgent. In this study, we combined serum fluorescence spectroscopy with machine learning algorithms to develop an innovative screening technique to diagnose CE in sheep. Serum fluorescence spectra of Echinococcus granulosus sensu stricto‐infected group (n = 63) and uninfected E. granulosus s.s. group (n = 60) under excitation at 405 nm were recorded. The linear support vector machine (Linear SVM), Quadratic SVM, medium radial basis function (RBF) SVM, K‐nearest neighbor (KNN), and principal component analysis‐linear discriminant analysis (PCA‐LDA) were used to analyze the spectra data. The results showed that Quadratic SVM had the great classification capacity, its sensitivity, specificity, and accuracy were 85.0%, 93.8%, and 88.9%, respectively. In short, serum fluorescence spectroscopy combined with Quadratic SVM algorithm has great potential in the innovative diagnosis of CE in sheep.
Community perceptions of contributors and solutions related to neighborhood violent crime: A qualitative interview study
Authors: Stager Catanya G. , Whitfield Samantha , Osborne Tiffany , Adedoyin Christson , Okoro Grace , Carley Erin , Schoenberger Yu‐Mei , Crawford Dwayne A. , Thompson Melissa , Stafford Sharela , Bateman Lori B.
Published: January 2024

The current study is part of a community engaged planning phase and aimed to identify perceptions related to the prevalence of violent crime, crime contributors, the relationship between the community and law enforcement, and potential interventions and solutions. In March 2021, semistructured interviews were conducted with individuals from five groups who resided or worked in Bessemer, Alabama: (1) Law Enforcement, (2) Residents, (3) Civic Leaders, (4) Community Leaders, and (5) Victims of Crime. Interviews lasted approximately 60 min and were audio recorded, transcribed, and analyzed according to the guidelines of thematic analysis using NVivo 12. Emerging themes were examined in accordance with the CDC Social‐Ecological Model: A Framework for Prevention. Participants (N = 18) were 50.0% female and 77.8% African American with an age range of 25–59 (mean = 43.4 years). Themes that emerged related to crime were: (1) impact, (2) contributors, and (3) solutions. Results indicate that impacts of violent crime at the individual level focused on fear, which led to widespread mental health issues. Relationship level impacts included a lack of trust of law enforcement and neighbors, and community level impacts were decreased neighborhood social cohesion as well as decreased safety. At the societal level, the poor reputation of the city was consistently highlighted. For contributors of crime, being a youth under age 30, drugs, and money were discussed as factors at the individual level. At the relationship level, participants mentioned poor parenting and gangs as crime contributing factors to violent crime. Furthermore, contributing issues related to underresourced schools as well as a poor relationship with law enforcement were brought up at the community level. Similarly, poverty was the overarching contributing issue at the societal level. Solutions that emerged included: education and training in life skills, focusing on young people, family/parenting, conflict resolution programs, programs within schools, improved relationships with law enforcement, and inclusive economic opportunities. Intervention plans are discussed that can merge these stakeholder findings with other data sources.
Potential for managing pool levels in a flood‐control reservoir to increase nitrate‐nitrogen load reductions
Authors: Schilling Keith E. , Streeter Matthew T. , Anderson Elliot , Merryman Jennifer , Isenhart Thomas , Arenas‐Amado Antonio , Theiling Chuck
Published: January 2024

Few strategies are available to reduce nitrate‐nitrogen (NO3‐N) loads at larger landscape scales, but flood control reservoirs are known to reduce riverine loads. In this study, we evaluated the potential to increase nitrogen (N) loss at Lake Red Rock, a large reservoir located in central Iowa, by evaluating the inundation of sediments deposited at the reservoir inflow. Sediment samples were collected at 51 locations in the lower delta region and analyzed for particle size and nutrient content. Nitrogen loss rates in delta sediments were determined from laboratory assays, and satellite imagery was used to develop a rating curve to quantify land area inundated within the delta. The daily mass of NO3‐N reduced with delta inundation was estimated by applying the mean N 24‐h loss rate (0.66 g N m2 day−1) by the area of inundation (m2). Results indicated that raising pool elevations to inundate more of the delta would result in greater N losses, ranging from 2 to 377 Mg per year. Potential N loss of 102 Mg achieved by increasing pool stage by 0.5 m would be equivalent to installing nearly 650 edge‐of‐field practices in the watershed. Although more work is needed to integrate with an existing environmental pool management plan, study results indicate that reservoir management could achieve N reductions at a novel landscape scale.
Proton pump inhibitors in esophageal atresia: A systematic review and meta‐analysis
Authors: Dimitrov Georges , Aumar Madeleine , Duhamel Alain , Wanneveich Mathilde , Gottrand Frédéric
Published: January 2024

Gastroesophageal reflux disease (GERD) is frequent and prolonged in esophageal atresia (EA) pediatric patients requiring routine use of proton pump inhibitors (PPIs). However, there are still controversies on the prophylactic use of PPIs and the efficacy of PPIs on GERD and EA complications in this special condition. The aim of the study is to assess the prophylactic use of PPIs in pediatric patients with EA and its complications. We, therefore, performed a systematic review including all reports on the subject from 1980 to 2022. We conducted meta‐analysis of the pooled proportion of PPI—and no PPI groups using random effect model, meta‐regression, and estimate heterogeneity by heterogeneity index I2. Thirty‐eight reports on the topic met the criteria selection, representing a cumulative 6044 patients with EA. Prophylactic PPI prescription during the first year of life does not appear to prevent GERD persistence at follow‐up and is not associated with a significantly reduced rate of antireflux surgical procedures (ARP). PPIs improve peptic esophagitis and induce remission of eosinophilic esophagitis at a rate of 50%. Their effect on other GERD outcomes is uncertain. Evidence suggests that PPIs do not prevent anastomotic stricture, Barrett's esophagus, or respiratory complications. PPI use in EA can improve peptic and eosinophilic esophagitis but is ineffective on the other EA complications. Side effects of PPIs in EA are almost unknown.
Sciadonic acid ameliorates cyclophosphamide‐induced immunosuppression by modulating the immune response and altering the gut microbiota
Authors: Chen Lin , Jiang Qihong , Yao Shiwei , Jiang Chenkai , Lu Hongling , Hu Wenjun , Yu Shaofang , Li Mingqian , Feng Yongcai , Tan Chin Ping , Xiang Xingwei , Shen Guoxin
Published: January 2024

BACKGROUND

Cyclophosphamide (Cy) is a frequently used chemotherapeutic drug, but long‐term Cy treatment can cause immunosuppression and intestinal mucosal damage. The intestinal mucosal barrier and gut flora play important roles in regulating host metabolism, maintaining physiological functions and protecting immune homeostasis. Dysbiosis of the intestinal flora affects the development of the intestinal microenvironment, as well as the development of various external systemic diseases and metabolic syndrome.

RESULTS

The present study investigated the influence of sciadonic acid (SA) on Cy‐induced immunosuppression in mice. The results showed that SA gavage significantly alleviated Cy‐induced immune damage by improving the immune system organ index, immune response and oxidative stress. Moreover, SA restored intestinal morphology, improved villus integrity and activated the nuclear factor κB signaling pathway, stimulated cytokine production, and reduced serum lipopolysaccharide (LPS) levels. Furthermore, gut microbiota analysis indicated that SA increased t beneficial bacteria (Alistipes, Lachnospiraceae_NK4A136_group, Rikenella and Odoribacter) and decreased pathogenic bacteria (norank‐f‐Oscillospiraceae, Ruminococcus and Desulfovibrio) to maintain intestinal homeostasis.

CONCLUSION

The present study provided new insights into the SA regulation of intestinal flora to enhance immune responses. © 2024 Society of Chemical Industry.
Clinical outcomes in patients with adamantinoma: Report from the bone and soft tissue tumor registry in Japan
Authors: Shimizu Junya , Emori Makoto , Murahashi Yasutaka , Kawai Akira , Teramoto Atsushi
Published: January 2024

Background

Adamantinomas are rare malignant bone tumors. Due to their low incidence, there are few reports on the clinical results of adamantinoma.

Objectives

This study aims to clarify outcomes in patients with adamantinoma using data from the National Bone and Soft Tissue Tumor Registry.

Methods

From 2006 to 2019, 38 cases of tibial origin were included. Twenty‐four were male and 14 were female, with a mean age of 37 (6–87) years and a mean follow‐up of 35 (1–128) months.

Results

Surgery was performed in 33 cases (87%) (curettage: 4 cases, wide resection: 27 cases, amputation: 2 cases). Reconstruction was performed in 27 patients who underwent wide resection. A total of 12 additional surgeries were performed in 11 patients. The main reason for the additional surgeries was nonunion of grafting bone in 6 cases. Oncologic outcomes were DOC (death from other causes) in one case and NED (no evidence of disease) in 37 cases.

Conclusions

The results of treatment of adamantinomas in Japan have been extremely favorable. This may be due in part to the large number of cases with wide resection.
The effect of Covid‐19 depression on spirituality and psychological well‐being through the perceived environmental restorativeness of a pilgrimage route: Focusing on pilgrims on Seoul Catholic Pilgrimage Route
Authors: Kim Jinok Susanna , Lee Dong Cheol , Cho Hangun , Jo Hyeyoung
Published: January 2024

During the COVID‐19 pandemic, policies adopted by various countries to prevent the spread of the disease exacerbated social isolation among people, and their prolonged implementation has had a negative effect on people's mental health, leading to increased anxiety, stress, and depression. Group religious activities were prohibited, so believers continued their faith practices through individual pilgrimages. Therefore, the purpose of this study is to clarify the relationship between depression caused by COVID‐19 and its impact on spirituality and psychological well‐being, through the perceived restorative environment of the Seoul Catholic Pilgrimage Route. The results confirmed that COVID‐19 depression had a negative effect on perceived environmental restorativeness and psychological well‐being but perceived environmental restorativeness had a positive effect on Spirituality, and Spirituality had a positive effect on psychological well‐being. These results imply that pilgrims who have experienced depression due to the pandemic can improve their spirituality and psychological well‐being through nature‐based pilgrimages.