bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using qPCR of environmental DNA (eDNA) to estimate the biomass of juvenile Pacific salmon (Oncorhynchus spp.)
Authors: Benoit Natalie P. , Robinson Kristin Meagher , Kellogg Colleen T. E. , Lemay Matthew A. , Hunt Brian P. V. 
Published: May 2023

AbstractDuring the outmigration of Pacific Salmon, the early marine phase is a critical period when high mortality can occur. Traditional sampling and monitoring of juvenile salmon migration can be limited by logistically intensive gear requirements, accessibility, and cost. Improved understanding of the early marine phase, for example, migration duration and habitat use, requires innovative techniques that can improve the spatial and temporal coverage of monitoring. Environmental DNA (eDNA) is genetic fragments present in the environment that can be used as a proxy for organism presence and can be effectively and efficiently collected through water samples. Estimating fish abundance or biomass from eDNA concentration data would provide a valuable fisheries tool but remains challenging to calibrate. To quantify the relationship between eDNA abundance and fish biomass, we used a controlled mesocosm experiment, in which eDNA samples were collected from 15 aquaria (340 L) with varying densities of juvenile Chinook salmon per tank (0, 5, 10, 20, and 30). The concentration of eDNA was obtained by qPCR scaled with fish biomass (ANOVA, p < 0.05). However, we also observed that variability of eDNA concentrations among replicates of the same treatment positively scaled biomass (ANOVA, p < 0.05). Therefore, higher biomasses of fish can yield more challenging data to interpret. This study lays important groundwork for the application of eDNA for monitoring juvenile salmonids yet highlights caveats for the applicability of eDNA as a stand‐alone method to assess biomass in a field setting.
Knowledge, Information, and Data Readiness Levels (KaRLs) for Risk Assessment, Communication, and Governance of Nano‐, New, and Other Advanced Materials
Authors: Drobne Damjana , Ciornii Dmitri , Hodoroaba Vasile‐Dan , Bohmer Nils , Novak Sara , Kranjc Eva , Kononenko Veno , Reuther Rudolf 
Published: May 2023

AbstractThe obvious benefits derived from the increasing use of engineered nano‐, new, and advanced materials and associated products have to be weighed out by a governance process against their possible risks. Differences in risk perception (beliefs about potential harm) among stakeholders, in particular nonscientists, and low transparency of the underlying decision processes can lead to a lack of support and acceptance of nano‐, new, and other advanced material enabled products. To integrate scientific outcomes with stakeholders needs, this work develops a new approach comprising a nine‐level, stepwise categorization and guidance system entitled “Knowledge, Information, and Data Readiness Levels” (KaRLs), analogous to the NASA Technology Readiness Levels. The KaRL system assesses the type, extent, and usability of the available data, information, and knowledge and integrates the participation of relevant and interested stakeholders in a cocreation/codesign process to improve current risk assessment, communication, and governance. The novelty of the new system is to communicate and share all available and relevant elements on material related risks in a user/stakeholder‐friendly, transparent, flexible, and holistic way and so stimulate reflection, awareness, communication, and a deeper understanding that ultimately enables the discursive process that is needed for the sustainable risk governance of new materials.
Is it all in the baseline? Trajectories of chair stand performance over 4 years and their association with grey matter structure in older adults
Authors: Demnitz Naiara , Gates Anne T. , Mortensen Erik L. , Garde Ellen , Wimmelmann Cathrine L. , Siebner Hartwig R. , Kjaer Michael , Boraxbekk Carl‐Johan 
Published: May 2023

AbstractUnderstanding individual variability in response to physical activity is key to developing more effective and personalised interventions for healthy ageing. Here, we aimed to unpack individual differences by using longitudinal data from a randomised‐controlled trial of a 12‐month muscle strengthening intervention in older adults. Physical function of the lower extremities was collected from 247 participants (66.3 ± 2.5 years) at four time‐points. At baseline and at year 4, participants underwent 3 T MRI brain scans. K‐means longitudinal clustering was used to identify patterns of change in chair stand performance over 4 years, and voxel‐based morphometry was applied to map structural grey matter volume at baseline and year 4. Results identified three groups showing trajectories of poor (33.6%), mid (40.1%), and high (26.3%) performance. Baseline physical function, sex, and depressive symptoms significantly differed between trajectory groups. High performers showed greater grey matter volume in the motor cerebellum compared to the poor performers. After accounting for baseline chair stand performance, participants were re‐assigned to one of four trajectory‐based groups: moderate improvers (38.9%), maintainers (38.5%), improvers (13%), and decliners (9.7%). Clusters of significant grey matter differences were observed between improvers and decliners in the right supplementary motor area. Trajectory‐based group assignments were unrelated to the intervention arms of the study. In conclusion, patterns of change in chair stand performance were associated with greater grey matter volumes in cerebellar and cortical motor regions. Our findings emphasise that how you start matters, as baseline chair stand performance was associated with cerebellar volume 4 years later.
Differences in infant negative affectivity during the COVID‐19 pandemic
Authors: Morris Alyssa R. , Saxbe Darby E. 
Published: May 2023

AbstractThis longitudinal study compared infant temperament rated at 3 months postpartum by 263 United‐States‐based women who gave birth during the COVID‐19 pandemic and 72 who gave birth prior to the pandemic. All women completed questionnaires assessing perinatal mental health, social contact, and infant temperament. Mothers whose infants were born during the pandemic reported higher levels of infant negative affectivity as compared with mothers whose infants were born earlier (F(1, 324) = 18.28, p < .001), but did not differ in their ratings of surgency or effortful control. Maternal prenatal depressive symptoms, prenatal stress, and postpartum stress mediated differences in infant negative affectivity between pandemic and pre‐pandemic groups. Within the pandemic group, decreased postpartum social contact was associated with higher ratings of infant negative affectivity. These findings suggest that the pandemic has affected maternal perceptions of infant temperament, perinatal mental health, and social contact.
In silico exploration of antioxidants as oxidation protectant for PITRM1 peptidase activity, an Alzheimer disease target
Authors: Wilson Alphonse Carlton Ranjith , Kannan Rajaretinam Rajesh 
Published: May 2023

AbstractTo find efficient antioxidants to protect oxidation prone cysteine residues of the peptidase PITRM1 using molecular docking and simulation techniques. A total of 50 antioxidants were docked with PITRM1 at the oxidation prone region Cys89 and Cys96 using Autodock Vina software. The lowest socred compounds were predicted for its Blood brain barrier permeability using LightBBB. Molecular dynamic simulations of the PITRM1 and Ascorbic acid/Silymarin complex were performed using the GROMACS 2020.1 package and the free energy calculations were performed using gmx_MMPBSA. The RMSD, RMSF, Rg, Minimum distance and Hydrogen bonds were also evaluated. Silymarin, Ascorbic acid, Naringenin, Gallic acid, Chlorogenic acid, Rosmarinic acid, (‐)‐Epicatechin, Genistein showed a docking score of above –5.3 kcal/mol. Silymarin and Ascorbic acid were predicted to cross the Blood Brain Barrier. Molecular dynamic simulation and mmPBSA analysis revealed that Silymarin showed a positive free energy implying no affinity to PITRM1 and ascorbic acid has low ΔG with –13.13 kJ/mol. The stability of the ascorbic acid complex was high (RMSD: 0.160 ± 0.018 nm, Minimum Distance: 0.163 ± 0.001 nm and four hydrogen bonds) and fluctuation induced due to ascorbic acid was low. Ascorbic acid was found to effectively interact with the cysteine oxidation prone region and can have a potential role in reducing the oxidised cysteine in PITRM1 to modulate its peptidase activity.
Five‐year follow‐up study on quantitative muscle magnetic resonance imaging in facioscapulohumeral muscular dystrophy: The link to clinical outcome
Authors: Vincenten Sanne C.C. , Mul Karlien , van As Daniël , Jansen Julia J. , Heskamp Linda , Heerschap Arend , van Engelen Baziel G.M. , Voermans Nicol C. 
Published: May 2023

AbstractBackgroundIt is unclear how changes in quantitative muscle magnetic resonance imaging (MRI) relate to changes in clinical outcome in facioscapulohumeral muscular dystrophy (FSHD), although this information is crucial for optimal use of MRI as imaging biomarker in trials. We therefore assessed muscle MRI and clinical outcome measures in a large longitudinal prospective cohort study.MethodsAll patients were assessed by MRI at baseline and at 5‐year follow‐up, employing 2pt‐Dixon and turbo inversion recovery magnitude (TIRM) sequences, after which fat fraction and TIRM positivity of 19 leg muscles were determined bilaterally. The MRI compound score (CoS) was defined as the mean fat fraction of all muscles weighted for cross‐sectional area. Clinical outcome measures included the Ricci‐score, FSHD clinical score (FSHD‐CS), MRC sumscore (MRC‐SS), and motor‐function‐measure (MFM).ResultsWe included 105 FSHD patients [mean age 54 ± 14 years, median Ricci‐score 7 (range 0–10)]. The median change over 5 years' time in the MRI‐CoS was 2.0% (range −4.6 to +12.1; P < 0.001). The median change over 5 years' time in clinical outcome measures was small in all measures, with z‐scores ranging from 5.0 to 7.2 (P < 0.001). The change in MRI‐CoS correlated with change in FSHD‐CS and Ricci‐score (ρ = 0.25, respectively; ρ = 0.23, P < 0.05). The largest median increase in MRI‐CoS was seen in baseline subgroups with an MRI‐CoS 20–40% (6.1%), with ≥2 TIRM positive muscles (3.5%) or with an FSHD‐CS 5–10 (3.1%).ConclusionsThis 5‐year study showed significant changes in MRI and clinical outcome measures and a significant correlation between changes in MRI‐CoS and changes in clinical outcome measures. In addition, we identified subgroups of patients that are most prone to radiological disease progression. This knowledge further establishes quantitative MRI parameters as prognostic biomarkers in FSHD and as efficacy biomarkers in upcoming clinical trials.
Establishment and validation of a clinical severity scoring system for succinic semialdehyde dehydrogenase deficiency
Authors: Tokatly Latzer Itay , Roullet Jean‐Baptiste , Gibson K. Michael , Pearl Phillip L. 
Published: May 2023

AbstractSuccinic semialdehyde dehydrogenase deficiency (SSADHD) is an inherited metabolic disorder with a variable phenotype and rate of progression. We aimed to develop and validate a clinical severity scoring (CSS) system applicable to the clinical setting and composed of five domains reflecting the principal manifestations of this disorder: cognitive, communication, motor, epilepsy, and psychiatry. A prospectively characterized cohort of 27 SSADHD subjects (55% females, median [IQR] age 9.2 [4.6–16.2] years) who enrolled in the SSADHD Natural History Study were included. The CSS was validated by comparison to an objective severity scoring (OSS) system based on comprehensive neuropsychologic and neurophysiologic assessments, which mirror and complement the domains of the CSS. The total CSS was sex and age‐independent, and 80% of its domains lacked interdependence. With increasing age, there was a significant improvement in communication abilities (p = 0.05) and a worsening of epilepsy and psychiatric manifestations (p = 0.004 and p = 0.02, respectively). There was a significant correlation between all the CSS and OSS domain scores, as well as between the total CSS and OSS (R = 0.855, p < 0.001). Additionally, there were no significant demographic or clinical differences in the ratio of individuals in the upper quartile to the lower three quartiles of the CSS and OSS. The SSADHD CSS is validated using objective measures and offers a reliable condition‐specific instrument universally applicable in clinical settings. This severity score may be utilized for family and patient counseling, genotype–phenotype correlations, biomarker development, clinical trials, and objective descriptions of the natural history of SSADHD.
A substrate for a cell free in vitro assay system to screen drugs targeting trypsin like protease‐based cleavage of SARS‐CoV‐2 spike glycoprotein and viral entry
Authors: Begum Feroza , Srivastava Amit K. , Tripathi Prem Prakash , Ray Upasana 
Published: May 2023

AbstractHost proteases trypsin and trypsin‐like proteases have been reported to facilitate the entry of coronavirus SARS‐CoV‐2 in its host cells. These protease enzymes cleave the viral surface glycoprotein, spike, leading to successful cell surface receptor attachment, fusion and entry of the virus in its host cell. The spike protein has protease cleavage sites between the two domains S1 and S2. Since the cleavage site is recognized by the host proteases, it can be a potential antiviral therapeutic target. Trypsin‐like proteases play an important role in virus infectivity and the property of spike protein cleavage by trypsin and trypsin‐like proteases can be used to design assays for screening of antiviral candidates against spike protein cleavage. Here, we have documented the development of a proof‐of‐concept assay system for screening drugs against trypsin/trypsin‐like proteases that cleave spike protein between its S1 and S2 domains. The assay system developed uses a fusion substrate protein containing a NanoLuc luciferase reporter protein, the protease cleavage site between S1 and S2 domains of SARS‐CoV‐2 spike protein and a cellulose binding domain. The substrate protein can be immobilized on cellulose via the cellulose binding domain of the substrate. When trypsin and trypsin‐like proteases cleave the substrate, the cellulose binding domain remain bound to the cellulose and the reporter protein is dislodged. Reporter assay using the released reporter protein is the read out of the protease activity. We have demonstrated the proof‐of‐concept using multiple proteases like trypsin, TMPRSS2, furin, cathepsin B, human airway trypsin and cathepsin L. A significant increment in fold change was observed with increasing enzyme concentration and incubation time. Introduction of increasing amounts of enzyme inhibitors in the reaction reduced the luminescent signal, thus validating the assay. Furthermore, we used SDS‐PAGE and immunoblot analyses to study the cleavage band pattern and re‐confirm the cleavage for enzymes tested in the assay. Taken together, we have tested an in‐vitro assay system using the proposed substrate for screening drugs against trypsin like protease‐based cleavage of SARS‐CoV‐2 spike glycoprotein. The assay system can also be potentially used for antiviral drug screening against any other enzyme that might cleave the used cleavage site.
The effects of disturbance on the microbial mediation of sediment stability
Authors: Zhang Naiyu , Thompson Charlotte E. L. , Townend Ian H. 
Published: May 2023

AbstractIn coastal areas, biofilms are often subject to disturbance by hydrodynamic forcing, bioturbation and human activities. These factors affect the influences biofilms have on the sediment. To reveal these effects, we studied laboratory‐incubated and field‐collected biotic sediments reworked by disturbances, and examined their stabilities and three‐dimensional microstructures using laboratory annular flume tests and a wet‐staining X‐ray microcomputed tomography method. We find that, when subject to disturbance, biofilms do not always establish mat‐like matrices that firmly armor the seabed and bio‐stabilize sediments, but instead, have a range of effects on sediment stability, including both bio‐stabilization and destabilization. Disturbance considerably alters microbial influences on sediment stability, but is not the only control. Given equal disturbance, whether or not sediments are bio‐stabilized largely depends on the state of bio‐sediment formation. At a relatively well‐developed state, an organic‐rich, adhesive polymer network tightly interconnects large amounts of sediment particles into aggregates, forms complex internal structures, and enhances sediment stability. By contrast, some bio‐sediment formations only ever reach a less well‐developed state, where scattered organic patches bind relatively few particles into aggregates and reduce sediment stability. Microbial growth likely has two opposing effects on sediment stability, by enhancing either weight/friction or lift/drag on aggregated particles. The former has the positive effect of enhancing sediment stability, whereas the latter can result in greater flow resistance and so have the opposite effect. A conceptual framework is put forward to characterize the different states of bio‐sediment formation and their distinct effects on sediment stability.
Toughening of Bio‐Based PA 6.19 by Copolymerization with PA 6.6 – Synthesis and Production of Melt‐Spun Monofilaments and Knitted Fabrics
Authors: Rist Maximilian , Löcken Henning , Ortega Mathias , Greiner Andreas 
Published: May 2023

AbstractThis work reports on the synthesis of statistical copolymers of bio‐based PA 6.19 and PA 6.6 together with the production of melt‐spun monofilaments for the production of sustainable textile fibers. The plant oil‐based 1.19‐nonadecanedioic acid is synthesized from bio‐derived oleic acid via isomerizing methoxycarbonylation. The homopolymer PA 6.19 with a carbon‐based bio‐content of 72% shows a good elongation at break of 166%, but lower tensile strength than commercial PA 6 (43 MPa versus 82 MPa). Addition of adipic acid to form statistical PA 6.6/6.19 copolymers improves toughness while maintaining the high elongation at break. Two PA 6.6/6.19 copolymers with a carbon‐based bio‐content of 26% and 33% are successfully synthesized and exhibited comparable toughness (94 ± 6 MPa and 92 ± 2 MPa) to the commercial PA 6 (92 ± 15 MPa). The bio‐based copolymers also exhibit a much lower water uptake than PA 6 and PA 6.6, resulting in a higher dimensional stability. Melt spinning of the oleic acid‐based polyamides is successfully carried out to produce monofilaments with sufficient properties for further processing in a knitting process, demonstrating the capabilities of the bio‐based PA 6.6/6.19 copolymers for use in the textile industry.
Evaluation of crack locations in beam using artificial neural network‐based modified curvature damage index
Authors: Gupta S. K. , Das S. 
Published: May 2023

AbstractAlthough the frequency response‐curvature methodology is commonly used to detect irregularities in mechanical and civil structures, the artificial neural network‐based frequency response‐curvature damage index method may have good efficacy in the detection and localization of structural damages. By utilizing experimental data sets, a novel method is proposed to pinpoint a saw‐cut damage location and the degree of damage in beam models. Using a dynamic data logger, the frequency response function of a beam model is obtained for altering damage levels at different positions. As frequency response data contains environmental and operational noise, the accuracy of obtained results may get reduced. To improve the accuracy by reducing the noise effect, the experimentally obtained frequency response data is trained through an artificial neural network. Using central difference approximation, the sets of trained modal data are utilized to determine the improved mode shape curvature. The curvature damage index is then obtained by using the improved mode shape curvature for different damaged scenarios to ultimately identify structural damages.
The epigenetic regulatory mechanisms of ferroptosis and its implications for biological processes and diseases
Authors: Yang Molin , Luo Hanshen , Yi Xin , Wei Xiang , Jiang Ding‐Sheng 
Published: May 2023

AbstractFerroptosis is a form of regulated cell death triggered by the iron‐dependent peroxidation of phospholipids. Interactions of iron and lipid metabolism factors jointly promote ferroptosis. Ferroptosis has been demonstrated to be involved in the development of various diseases, such as tumors and degenerative diseases (e.g., aortic dissection), and targeting ferroptosis is expected to be an effective strategy for the treatment of these diseases. Recent studies have shown that the regulation of ferroptosis is affected by multiple mechanisms, including genetics, epigenetics, posttranscriptional modifications, and protein posttranslational modifications. Epigenetic changes have garnered considerable attention due to their importance in regulating biological processes and potential druggability. There have been many studies on the epigenetic regulation of ferroptosis, including histone modifications (e.g., histone acetylation and methylation), DNA methylation, and noncoding RNAs (e.g., miRNAs, circRNAs, and lncRNAs). In this review, we summarize recent advances in research on the epigenetic mechanisms involved in ferroptosis, with a description of RNA N6‐methyladenosine (m6A) methylation included, and the importance of epigenetic regulation in biological processes and ferroptosis‐related diseases, which provides reference for the clinical application of epigenetic regulators in the treatment of related diseases by targeting ferroptosis.
Three optimal families of three‐sub‐step dissipative implicit integration algorithms with either second, third, or fourth‐order accuracy for second‐order nonlinear dynamics
Authors: Li Jinze , Yu Kaiping , Zhao Rui , Fang Yong 
Published: May 2023

SummaryThis paper reviews the published composite three‐sub‐step implicit algorithms all of which adopt the trapezoidal rule in the first sub‐step. Three optimal families of three‐sub‐step implicit algorithms are developed to achieve second, third, and fourth‐order accuracy. The present second‐ and third‐order methods achieve identical effective stiffness matrices, thus embedding optimal spectral characteristics. Besides, both of them impose two dissipative parameters ( and ) to control numerical dissipation imposed in the second and third sub‐steps. The parameter adjusts overall numerical dissipation in the whole integration schemes, while the firstly used parameter can change numerical dissipation in the second sub‐step. The numerical example has shown the superiority of controlling middle sub‐step dissipation via . The present fourth‐order method is moderately dissipative due to achieving higher‐order accuracy, but it presents a more reasonable sub‐step division than the published fourth‐order three‐sub‐step trapezoidal rule. Linear and nonlinear examples are simulated to show the numerical performance and superiority of the three novel methods. This paper recommends using the proposed second‐ and third‐order three‐sub‐step methods to solve various dynamic problems.