bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stock identification and age prediction of Red Mullet Mullus barbatus in the western Black Sea (Türkiye) as inferred from otolith shape descriptors
Authors: Yildiz Taner , Cömert Nurdan , Kahraman Abdullah E. , Karakulak F. Saadet 
Published: December 2024

Abstract

Objective
In this study, we applied shape analysis to differentiate two Red Mullet Mullus barbatus stocks in the western Black Sea and assessed the generalized linear model (GLM) for age prediction based on otolith dimensions and weight.

Methods
Sagittal otoliths from 259 fish were collected by commercial bottom trawl vessels in İğneada and Şile, Türkiye, between October 2017 and April 2018. Otolith shape was described using wavelet transformation (contour shape) along with four morphometric characteristics (otolith length, area, width, and perimeter) and six shape indices (circularity, rectangularity, form factor, roundness, ellipticity, and aspect ratio) to reveal differences between the two regions. Shape indices were explored using multivariate statistical methods, including multivariate analysis of variance (MANOVA) and canonical discriminant analysis (CDA). Canonical analysis of principal coordinates (CAP) provided an overview of the differentiation in the otolith outline shape between the two stocks by using the wavelet coefficients. The GLMs predicted age using otolith size parameters, shape indices, and otolith weight.

Result
The MANOVA showed no significant differences between sexes but notable differences between right and left otoliths. The CDA achieved a discrimination rate of 65.7% for age 1 and 64.8% for age 3, indicating distinct local populations. The otolith contours varied between Red Mullet sampled in the two regions, with CAP achieving an overall accuracy of 67.1% for both regions, 68.12% accuracy for İğneada, and 66.20% accuracy for Şile. The GLMs identified otolith length, weight, width, and perimeter and fish sex as key factors, with otolith length being the most significant predictor for age estimation.

Conclusion
The close alignment of observed and estimated ages highlights the potential for using otolith length in age estimation.
Protein engineering in the deep learning era
Authors: Zhou Bingxin , Tan Yang , Hu Yutong , Zheng Lirong , Zhong Bozitao , Hong Liang 
Published: December 2024

AbstractAdvances in deep learning have significantly aided protein engineering in addressing challenges in industrial production, healthcare, and environmental sustainability. This review frames frequently researched problems in protein understanding and engineering from the perspective of deep learning. It provides a thorough discussion of representation methods for protein sequences and structures, along with general encoding pipelines that support both pre‐training and supervised learning tasks. We summarize state‐of‐the‐art protein language models, geometric deep learning techniques, and the combination of distinct approaches to learning from multi‐modal biological data. Additionally, we outline common downstream tasks and relevant benchmark datasets for training and evaluating deep learning models, focusing on satisfying the particular needs of protein engineering applications, such as identifying mutation sites and predicting properties for candidates' virtual screening. This review offers biologists the latest tools for assisting their engineering projects while providing a clear and comprehensive guide for computer scientists to develop more powerful solutions by standardizing problem formulation and consolidating data resources. Future research can foresee a deeper integration of the communities of biology and computer science, unleashing the full potential of deep learning in protein engineering and driving new scientific breakthroughs.
Analysis and Optimisation of Obstacle‐Crossing Performance of Electric Shovel Based on DEM‐MBD Coupling Method
Authors: Chen Zeren , Guan Wei , Li Ruibin , Li Guang , Xue Duomei , Liu Zhengbin , Wang Guoqiang 
Published: December 2024

ABSTRACTTo study and enhance the obstacle‐crossing performance of the electric shovel, an obstacle‐crossing model that employs a coupling methodology integrating the discrete element method (DEM) and multi‐body dynamics (MBD) is constructed. Secondly, the influence of grouser height (GH), track velocity (TV), slope inclination (SI) and slope height (SH) on obstacle‐crossing performance is investigated through DEM‐MBD simulation, with the objective of obtaining an obstacle‐crossing surrogate model through the Kriging method and Box‐Behnken experimental design. On this basis, two optimisation solutions for the obstacle‐crossing performance of the electric shovel are proposed based on a genetic algorithm (GA), and the corresponding obstacle‐crossing performances are analysed. The results demonstrate that the coupling effect between SI and SH exerts a considerable influence on the ground pressure coefficient (GPC), power and disturbance potential energy (DPE). When the optimal TV and GH are set at 0.1 m/s and 9.38 mm, the GPC, power and disturbance kinetic energy (DKE) are observed to diminish to varying degrees, thereby indicating that the obstacle‐crossing performance of the electric shovel has been enhanced.
Early Childhood in Precolonial South America: Breastfeeding, Infant Mortality, and Stable Isotopes Analysis in Southeastern Shell Mound Builders During the Middle Holocene (7th–5th Millennium BP)
Authors: Di Giusto Marina , Herrscher Estelle , Jaouen Klervia , Bastos Murilo , Mion Leïa , Wesolowski Veronica 
Published: December 2024

ABSTRACTThis article presents and discusses isotopic data on breastfeeding, weaning, and complementary diet during early childhood in Middle Holocene southeastern Brazil. The study focuses on human individuals from two contemporaneous shell mounds, Piaçaguera (7151–5668 yBP) and Moraes (6791–5590 yBP), which show distinct patterns of infant mortality. We conducted δ15N and δ13C analyses on collagen extracted from subadult bones (Piaçaguera: n = 13; Moraes: n = 13) and sequential dentine slices from permanent (Piaçaguera: n = 7; Moraes: n = 11) and deciduous teeth (Moraes: n = 5). Our findings indicate that weaning ended between 2 and 4 years old in Piaçaguera, with complementary foods similar to the adults. At Moraes, weaning ended between 2 and 5 years old, with a higher consumption of freshwater fish during early childhood and by pregnant women. The weaning ages at Piaçaguera and Moraes align with those documented in other precolonial South American groups. However, our study suggests different dietary preferences and strategies within each group, possibly linked to distinct patterns of infant mortality, particularly evident in the Moraes group.
Clinician Perspectives on the Management of Hearing Loss in Patients With Limited English Proficiency
Authors: Govindan Aparna , Singer Adina , Zekavat Lily , Jia Tianyi , Wong Kevin , Kuang Jianjing , Cosetti Maura K. , Hwa Tiffany P. 
Published: December 2024

AbstractObjectiveClinicians face challenges in managing the growing population of patients with limited English proficiency (LEP) and hearing loss (HL) in the United States. This study seeks to investigate provider perspectives on evaluating, counseling, and treating HL in LEP patients.Study DesignProspective descriptive study.SettingTertiary care center.MethodsResearchers employed a mixed methods design: (1) structured clinician interviews, (2) cross‐sectional, national electronic survey, both regarding perspectives on managing hearing loss in LEP patients. Structured interviews were analyzed using modified grounded theory.ResultsTwenty‐nine providers participated in interviews (16 otologists, 13 audiologists). The most reported non‐English language was Spanish, followed by Chinese languages. Four thematic domains were derived: barriers to care, cochlear implant (CI) candidacy evaluation, counseling, and ideal resources. Major barriers were patient desire (97%; n = 28), and lack of validated tests (72%; n = 21). Methods of CI evaluation included improvising on validated speech perception testing (59%; n = 17) and use of non‐speech evaluation (52%; n = 15). One‐quarter forgoes speech testing in non‐Spanish‐speaking patients (24%; n = 7). Suggestions to improve management include in‐person interpreters (62%; n = 18) and testing battery in all languages (31%; n = 9). National survey results (n = 87 providers) demonstrated that respondents were significantly less confident in the methods of speech perception testing and in counseling on surgical hearing rehabilitation in LEP.ConclusionClinicians encounter challenges in managing LEP patients with HL, including limitations in audiometric and CI candidacy assessment, communication barriers, information accessibility, and cultural competency. Opportunities for improving care include developing language‐specific test batteries, linguistically and culturally appropriate education materials, and cultural competency training.
Comparison of the Thrombolytic Effects of Urokinase Delivered by Normothermic Machine Perfusion or Hypothermic Machine Perfusion in a Pair of Human Kidneys With Microthrombus
Authors: Yu Shuangjin , Wu Guobin , Huang Yang , Chen Haiwei , Chen Tong , Ruan Hehuan , He Xiaoshun , Chen Guodong , Qiu Jiang 
Published: December 2024

ABSTRACTExtensive glomerular thrombosis can be a reason for the non‐use of donor kidneys, which exacerbates donor shortage. Pre‐transplantation intervention with thrombolytic drugs delivered via hypothermic machine perfusion (HMP) can dissolve thrombi in kidneys with thrombosis. However, this method requires a long intervention time to fully eliminate all thrombi. This increases the period of ischemia and limits the improvement of the kidney. We compared the effect of short‐term thrombolysis by urokinase combined with normothermic machine perfusion (NMP) versus HMP in a pair of clinically discarded and pathologically confirmed thrombotic human donor kidneys. During perfusion with urokinase for 1 h, improvement of kidney appearance, perfusion flow, urine production, thrombus break‐down, and plasminogen consumption were all greater with NMP than with HMP. The renal glomerular thrombosis rate in the NMP‐treated kidney decreased from 13.3% (2 in 15) to 8.3% (1 in 12) after 30 min of urokinase administration, accompanied by decreased levels of plasminogen in the renal tubular cells (the positive area decreased from 13.1% to 7.5%). In contrast, both the renal glomerular thrombosis rate and plasminogen level were unchanged during HMP. Furthermore, D‐dimer in the NMP perfusate increased rapidly from 1.55 to 7.33 µg/mL, compared with from 0.33 µg/mL to 0.86 µg/mL in HMP perfusate. Our findings indicate that the effect of urokinase to facilitate rapid thrombolysis before transplantation is greater when administered by NMP than by HMP. NMP can, therefore, improve donor kidney quality more efficiently than HMP.
Pan‐Cancer Analysis of Ezrin: A Comprehensive Examination of Its Prognostic Value and Immunological Implications
Authors: Chen Ruiqi , Xu Hongbiao , Jurat Elfira , Huang Hewang , Yang Shangwu , Han Liang , Wang Fengyun 
Published: December 2024

ABSTRACTBackgroundEzrin, a member of the ERM protein family, has emerged as a pivotal player in the progression of diverse tumor types and exhibits substantial immunomodulatory capabilities in inflammatory disorders and tumor‐associated immune reactions. Studies have validated the antitumor efficacy of ezrin inhibitors. However, a comprehensive pan‐cancer analysis to fully elucidate the functional implications of ezrin has not been performed.MethodsHerein, we performed a multifaceted database investigation to evaluate ezrin expression patterns in relation to clinical outcomes, immune checkpoint modulators, prognostic indicators, genomic profiles, and immunological features.ResultsOur analysis revealed distinct ezrin expression patterns across various cancers, with a pronounced association between ezrin expression and immune cell infiltration. Furthermore, drug sensitivity assessments using the GDSC and CTRP databases underscored a robust correlation between ezrin expression and responsiveness to anticancer agents, highlighting its potential as a therapeutic target. Notably, ezrin expression also correlated with patient survival outcomes in the context of anti‐PD1 therapy treatment, suggesting its potential role as a predictive biomarker for immune checkpoint blockade therapies.ConclusionOur results indicate ezrin as a promising immunomodulatory target and a valuable diagnostic and prognostic marker for select cancer types. However, the intricate mechanisms underlying ezrin involvement in tumor immune responses necessitate further in‐depth investigation to fully harness its therapeutic and prognostic potential.
Problem Behavior and Depression in Chinese Adolescents: A Moderated Multiple Mediation Model
Authors: Zhang Ling , Zhou Jingwen , Wei Ruigang 
Published: December 2024

ABSTRACTThis study explores the complex relationships among emotional and behavioral problems, self‐esteem, subjective well‐being, school satisfaction, and depression in adolescents. We conducted a comprehensive survey of 958 students aged 9–15 using self‐report questionnaires covering emotional and behavioral problems, self‐esteem, subjective well‐being, school satisfaction, and a depression symptom self‐assessment scale. The results reveal significant positive correlations between self‐esteem, subjective well‐being, and school satisfaction, and significant negative correlations between these factors and both emotional and behavioral problems and depression. Further analysis identified self‐esteem as both a parallel and sequential mediator between emotional and behavioral problems and depression, with the multiple mediation effect accounting for 28.23% of the total impact. Additionally, school satisfaction moderates the mediation process by influencing the relationship between self‐esteem and subjective well‐being, thereby mitigating the effect of subjective well‐being on depression. These findings highlight the importance of enhancing self‐esteem, fostering a positive school atmosphere, and improving adolescents' subjective well‐being to reduce the risk of depression.
Registration of ‘Avalon’ winter malt barley
Authors: Brooks Wynse , Griffey Carl , Sabadin Felipe , Vaughn Mark , Liu Limei , Seago John , Thomason Wade , Light Jon , Rucker Elizabeth , Browning Phillip , McMaster Niki , Schmale David , Saville Brooks , Hardiman Thomas , Custis J. Tommy , Jones Karl , Jones Ned , Lillard Gregory , Marshall David , Fountain Myron , Tuong Tan , Lee Michelle , Oakes Joseph , Mott Joshua , Martens Christopher , Walling Jason , Bettenhausen Harmonie , Macleod Aaron , Santantonio Nicholas 
Published: December 2024

Abstract‘Avalon’ (Reg. no. CV‐383, PI 700308) is the first two‐row, winter malt barley (Hordeum vulgare L.) cultivar developed by the Virginia Agricultural Experimental Station. Avalon was released in May 2020. Prior to being named, Avalon was tested under the experimental designation VA16M‐81. Avalon was evaluated from 2018 to 2023 in the Eastern Malt Barley Trials (EMBT) at one to three locations in three states and in the Winter Malt Barley Trial (WMBT) from 2020 to 2023 in six to 15 states. In the EMBT in Virginia, mean grain yield (5604 kg ha−1) of Avalon was higher to cultivar ‘Violetta’, but lower than those of ‘Flavia’, ‘Calypso’, and ‘Thoroughbred’. Average grain volume weight of Avalon (64.9 kg hL−1) was significantly (P ≤ 0.05) higher than the check cultivars, except Violetta. Head emergence of Avalon was 3 days earlier than Flavia and Calypso and 1 to 2 days later than Violetta and Thoroughbred, respectively. Avalon was developed primarily as a malt barley cultivar. On the basis of malting evaluations, Avalon has acceptable quality profiles with specific quality traits including high extract, low protein content, and low beta‐glucan for the years tested. Avalon provides malt barley producers and end users in the eastern United States with excellent malt quality and a unique and distinct flavor profile having good to moderate resistance to all diseases prevalent in the eastern United States. It is moderately susceptible to Fusarium head blight but has moderately low deoxynivalenol accumulation in the grain.
Solvent‐Assisted Prototopic Switching of Norharmane Along Hydrogen‐Bonded Network: Assessing the Precise Length of Network
Authors: Paul Suvendu , Dey Nilanjan 
Published: December 2024

ABSTRACTIn this article, the proton transfer dynamics along a stable norharmane•(H2O)n (n = 2–4) hydrogen‐bonded cluster on conversion from the neutral to cationic form of norharmane (NHM) in water medium was demonstrated experimentally and theoretically. The distinct absorption and emission bands of different prototropic forms of NHM are well‐known in the literature. Initially, the conversion from neutral to cationic form of NHM on moving from a polar aprotic (acetonitrile) to a polar protic (water) solvent was ensured by steady‐state absorption and fluorescence studies. The analysis of IR spectra and steady‐state anisotropy data of NHM confirmed the possibility of the formation of a hydrogen‐bonded network in the presence of water. The length of the network was explored and assumed by extensive Density Functional Theory (DFT) calculations. Then, by time‐dependent density functional theory (TD‐DFT), the excited state proton transfer (ESPT) pathway was established interrogating the NHM‐water cluster with different numbers of water molecules. The theoretical analysis assured that the NHM•(H2O)2 cluster was incapable of maintaining the stable hydrogen bonding wire in the course of the ESPT mechanism. Rather, NHM•(H2O)3 and NHM•(H2O)4 clusters were simultaneously involved in operating the ESPT mechanism. The NHM•(H2O)4 cluster was more feasible to carry out the proton transfer than the NHM•(H2O)3 cluster. To the best of our knowledge, this was possibly the first theoretical evidence behind the conversion from neutral to cationic form of NHM via the formation of a hydrogen‐bonded network.
Restoring adapter protein complex 4 function with small molecules: an in silico approach to spastic paraplegia 50
Authors: Francisco Serena , Lamacchia Lorenzo , Turco Attilio , Ermondi Giuseppe , Caron Giulia , Rossi Sebastiano Matteo 
Published: December 2024

AbstractThis study focuses on spastic paraplegia type 50 (SPG50), an adapter protein complex 4 deficiency syndrome caused by mutations in the adapter protein complex 4 subunit mu‐1 (AP4M1) gene, and on the downstream alterations of the AP4M1 protein. We applied a battery of heterogeneous computational resources, encompassing two in‐house tools described here for the first time, to (a) assess the druggability potential of AP4M1, (b) characterize SPG50‐associated mutations and their 3D scenario, (c) identify mutation‐tailored drug candidates for SPG50, and (d) elucidate their mechanisms of action by means of structural considerations on homology models of the adapter protein complex 4 core. Altogether, the collected results indicate R367Q as the mutation with the most promising potential of being corrected by small‐molecule drugs, and the flavonoid rutin as best candidate for this purpose. Rutin shows promise in rescuing the interaction between the AP4M1 and adapter protein complex subunit beta‐1 (AP4B1) subunits by means of a glue‐like mode of action. Overall, this approach offers a framework that could be systematically applied to the investigation of mutation‐wise molecular mechanisms in different hereditary spastic paraplegias, too.
Environmental Sustainability, Food Quality and Convertibility of Bio‐Based Barrier Coatings for Fibre‐Based Food Packaging: A Semisystematic Review
Authors: Vinitskaia Natalia , Lindstad Agnete Jordhøy , Lev Roman , Kvikant Minette , Xu Chunlin , Leminen Ville , Li Kloce Dongfang , Pettersen Marit Kvalvåg , Grönman Kaisa 
Published: December 2024

ABSTRACTThe ongoing legislative drive to reduce plastic consumption and promote the circularity of materials in Europe is reshaping food packaging market dynamics and making sustainability a key competitive factor in the sector. Legislation accelerates research and innovation in bio‐based, biodegradable and recyclable alternatives and motivates the industry to adopt sustainable designs while enhancing compliance with environmental standards. Renewable and natural resource‐based materials, such as polysaccharides, nanocellulose, lignin, lipids, phenolic compounds and proteins, have been extensively investigated in the last decade. Their use in dispersion coatings and biopolymer compounds for paper and paperboard barriers is often referred to as a sustainable packaging solution. This semisystematic review compiled available quantitative and qualitative data on the environmental sustainability, food quality and convertibility of novel bio‐based barrier coatings for food packaging. The results highlight a research gap in assessing environmental performance and the overuse of the term ‘sustainable’ and ‘biodegradable’. However, convertibility and film formability issues remain major obstacles that must be overcome before the scaling up of production of such coatings. Although bio‐based coatings demonstrate potential to extend the shelf life of certain fruits and mushrooms compared with uncoated paper or paperboard, numerous studies lack direct comparisons with conventional packaging methods. Further exploration of these aspects will facilitate science‐ and data‐driven innovation and decision‐making in industry, policy and academia in the development of sustainable bio‐based packaging.
Computing the Matching Polynomials and Independence Polynomials of Phenylene Chains
Authors: Chen Hanlin , Gao Xiang 
Published: December 2024

ABSTRACTPhenylene, a significant structural motif in organic chemistry, exhibits remarkable electron delocalization and stability. In this paper, we first present reduction formulas for computing the matching polynomial and the independence polynomial of any phenylene chain using the transfer matrix technique. We then derive computational formulas for the Hosoya index and the Merrifield–Simmons index of phenylene chains. Additionally, we obtain the expected values of the Hosoya index and the Merrifield–Simmons index for a random phenylene chain.
A nanofilm‐based fluorescent sensor for determination and identification of gas‐phase alkylamine
Authors: Hu Jiahui , Liu Xiangquan , Wei Hexi , Huang Rongrong , Zhai Binbin , Luo Yan , Yan Junbao , Peng Lingya , Liu Mei , Fang Yu 
Published: December 2024

AbstractOn‐site and real‐time detection and identification of alkylamines are important, but remain as a challenge. In this work, we report a unique nanofilm and the nanofilm‐based high‐performance fluorescent alkylamine sensor. The nanofilm was prepared at the air/dimethyl sulfoxide interface with 4,4′,4″‐nitrilo‐tribenzohydrazide (TPATH) and 4,7‐diphenylaldehyde‐benzothiadiazole (BT‐2CHO) as the building blocks, and depicted self‐standing, defect‐free, fluorescence active, and superior adhesive properties, enabling fabrication of a robust fluorescence film sensor. The response time of the sensor to the tested alkylamines is within 0.2 s, and the detection limits for butylamine, dimethylamine and triethylamine are 4, 8 and 70 ppm, respectively. Moreover, the profiles of the fluorescence emission spectra of the nanofilm recorded after exposure to alkylamines of primary, secondary, and tertiary structures are different from one to another, enabling discrimination of them. The diversified response behavior and the related identification property of the sensor to the different alkylamines was ascribed to the formation of different complexes between the analytes and the nanofilm. The high performance of the BT‐TPATH nanofilm‐based alkylamine sensor may guarantee its application in disease diagnosis, food spoilage monitoring, environmental monitoring, etc.