bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors and management strategies of inadvertent facial nerve stimulation in cochlear implant recipients: A systematic review
Authors: Alahmadi Asma , Abdelsamad Yassin , Yousef Medhat , Alhabib Salman F , Alshalan Afrah , Hamed Nezar , Alzhrani Farid 
Published: September 2023

AbstractObjectivesTo systematically review the prevalence and risk factors of inadvertent facial nerve stimulation (FNS) after cochlear implant (CI) surgery. And to report the different management strategies used for reducing and resolving FNS.Data SourceWeb of Science, Scopus, PubMed, Cochrane Library, and Virtual Health Library (VHL) of the World Health Organization (WHO).Review MethodsA systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) on studies that reported FNS as a complication after CI. A comprehensive electronic search strategy was used to identify the relevant articles. We extracted the data on the prevalence of FNS after CI activation, the reported grades, and the management strategies. The number of associated electrodes; cause of deafness; co‐anomalies; and duration of hearing loss and their relationships with FNS were also studied.ResultsTwenty‐one relevant articles were included in this review. The prevalence of FNS among the CI populations was 5.29% (175/3306 patients). Among those whose ages were reported, 58.3% (95/163) were adults, and 41.7% (68/163) were pediatrics. Modifying the different fitting parameters was the most used strategy, as it successfully resolved FNS in 85.5% of the patients (142/166). The second commonly used management strategy was surgical intervention (reimplantation or explantation), which was reported in seven studies for 23 patients.ConclusionFNS after CI activation could be controlled and resolved with many advances that range from readjusting the fitting parameters to surgical intervention. However, further studies are required to validate the efficacy of each management strategy and its impact on patients' performance. Our findings demonstrate that CI recipients with FNS could still benefit from the CI devices and their FNS could be controlled.
Use of tree‐based machine learning methods to screen affinitive peptides based on docking data
Authors: Feng Hua , Wang Fangyu , Li Ning , Xu Qian , Zheng Guanming , Sun Xuefeng , Hu Man , Li Xuewu , Xing Guangxu , Zhang Gaiping 
Published: September 2023

AbstractScreening peptides with good affinity is an important step in peptide‐drug discovery. Recent advancement in computer and data science have made machine learning a useful tool in accurately affinitive‐peptide screening. In current study, four different tree‐based algorithms, including Classification and regression trees (CART), C5.0 decision tree (C50), Bagged CART (BAG) and Random Forest (RF), were employed to explore the relationship between experimental peptide affinities and virtual docking data, and the performance of each model was also compared in parallel. All four algorithms showed better performances on dataset pre‐scaled, ‐centered and ‐PCA than other pre‐processed dataset. After model re‐built and hyperparameter optimization, the optimal C50 model (C50O) showed the best performances in terms of Accuracy, Kappa, Sensitivity, Specificity, F1, MCC and AUC when validated on test data and an unknown PEDV datasets evaluation (Accuracy=80.4 %). BAG and RFO (the optimal RF), as two best models during training process, did not performed as expecting during in testing and unknown dataset validations. Furthermore, the high correlation of the predictions of RFO and BAG to C50O implied the high stability and robustness of their prediction. Whereas although the good performance on unknown dataset, the poor performance in test data validation and correlation analysis indicated CARTO could not be used for future data prediction. To accurately evaluate the peptide affinity, the current study firstly gave a tree‐model competition on affinitive peptide prediction by using virtual docking data, which would expand the application of machine learning algorithms in studying PepPIs and benefit the development of peptide therapeutics.
Assessing mechanisms for microbial taxa and community dynamics using process models
Authors: Wu Linwei , Yang Yunfeng , Ning Daliang , Gao Qun , Yin Huaqun , Xiao Naija , Zhou Benjamin Y. , Chen Si , He Qiang , Zhou Jizhong 
Published: September 2023

AbstractDisentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time‐series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.
A novel application of recovered stresses in stress intensity factors extraction methods for the generalized/extended finite element method
Authors: Lins Rafael M. , Fonseca Gabriela M. , Barros Felício B. 
Published: September 2023

SummaryAn efficient improvement to compute Stress Intensity Factors (SIFs) in two‐dimensional fracture mechanics problems solved by Generalized/eXtended Finite Element Method and Stable Generalized Finite Element Method is proposed. A stress field obtained by a recovery procedure based on a locally weighted projection of the approximate stresses, is used in the formulation of two energy‐based SIFs extraction methods: the Contour Integral Method (CIM) and the Interaction Integral strategy. The accuracy and the path independence feature of the proposed approach are investigated in three numerical examples, considering crack opening modes I and II, different crack orientations and the presence of holes. The results demonstrate that the recovered stresses significantly improve the accuracy of the CIM and ensure a notable decrease in SIFs variation for different integration paths. On the other hand, an equivalent impact is not observed for the Interaction Integral strategy.
Towards a benchmark framework for model order reduction in the Mathematical Research Data Initiative (MaRDI)
Authors: Benner Peter , Lund Kathryn , Saak Jens 
Published: September 2023

AbstractThe race for the most efficient, accurate, and universal algorithm in scientific computing drives innovation. At the same time, this healthy competition is only beneficial if the research output is actually comparable to prior results. Fairly comparing algorithms can be a complex endeavor, as the implementation, configuration, compute environment, and test problems need to be well‐defined. Due to the increase in computer‐based experiments, new infrastructure for facilitating the exchange and comparison of new algorithms is also needed. To this end, we propose a benchmark framework as a set of generic specifications for comparing implementations of algorithms using test cases native to a community. Its value lies in its ability to fairly compare and validate existing methods for new applications, as well as compare newly developed methods with existing ones. As a prototype for a more general framework, we have begun building a benchmark tool for the model order reduction (MOR) community. The data basis of the tool is the collection of the Model Order Reduction Wiki (MORWiki). The wiki features three main categories: benchmarks, methods, and software. An editorial board curates submissions and patrols edited entries. Data sets for linear and parametric‐linear models are already well represented in the existing collection. Data sets for non‐linear or procedural models, for which only evaluation data, or codes/algorithmic descriptions, rather than equations, are available, are being added and extended. Properties and interesting characteristics used for benchmark selection and later assessments are recorded in the model metadata. Our tool, the Model Order Reduction Benchmarker (MORB), is under active development for linear time‐invariant systems and solvers. An ontology (MORBO) and knowledge graph are being developed in parallel. They catalog benchmark problem sets and their metadata and will also be integrated into the Mathematical Research Data Initiative (MaRDI) Portal to help improve the findability of such data sets. MORB faces a number of technical and field‐specific challenges, and we hope to recruit community input and feedback while presenting some initial results.
Friction and wear characteristics of Furcraea foetida fiber‐reinforced epoxy composites
Authors: Hussain Haja Syed , Mohd Jamir Mohd Ridzuan , Abdul Majid Mohd Shukry , Sapuan S. M. , Yudhanto Ferriawan , Nugroho Aris Widyo , Rani Muhammad Faiz Hilmi 
Published: September 2023

AbstractIn the current study, the friction and wear properties of Furcraea foetida fiber‐reinforced epoxy composites were investigated. This study evaluated the effect of Furcraea foetida fiber content on the tribological behavior of composites. A water‐retting method was employed to extract the fibers, and resin transfer molding was used to fabricate the composites. The frictional force, coefficient of friction (COF), and wear rate were measured under dry test conditions and various applied loads (80, 100, 120, and 140 N). Microstructural analysis was conducted using scanning electron microscopy to investigate the surface morphology and wear mechanisms of the composites. The results revealed that the composite with 50 vol% of fibers exhibits the lowest frictional force and COF in both normal and parallel orientations with overall average COF of 0.43 in normal orientation and 0.42 in parallel orientation. Moreover, the composite with 60 vol% demonstrates the best wear resistance with an overall average specific wear rate of 2.1982 ×  in normal orientation and 4.3478 × () in parallel orientation. Overall, this study provides valuable insights into the tribological behavior of Furcraea foetida fiber‐reinforced epoxy composites and identifies the optimal volume fractions for improved friction and wear performance.Highlights
Higher vol% yields denser composites with minimized voids.
Normal fiber orientation shows maximum SWR of 10.0614 × () .
Optimal frictional force and COF in 50 vol% composite.
Enhanced wear resistance observed in 60 vol% composite.
Higher vol% increases interfacial bonding and wear resistance in composites.
Enhancement of thermal and mechanical properties of polymer composite using a novel milled bamboo filler
Authors: Dutta Hrishikesh , Gurusamy P. , Halder Sudipta 
Published: September 2023

AbstractThis work presents the thermal and mechanical characterization of epoxy composites reinforced with different fillers developed by modifying thermo‐mechanically extracted bamboo micron fibers. The modification of bamboo fibers was done by adding carbon nanoparticles to their surface and also by making powdered fillers using the process of ball milling. A decrease in water absorption in case of surface coated bamboo fibers was observed. The glass transition behavior was enhanced for composites filled with milled bamboo fillers as compared to neat epoxy. Better mechanical properties were observed for composites reinforced with milled bamboo fillers compared to that of composites filled with bamboo fibers. The highest tensile strength (90.258 MPa) was observed for composites reinforced with 5 wt% of milled bamboo fillers depicting an increase of 93.01% compared to that of neat epoxy (46.762 MPa).Highlights
Bamboo fibers were modified with a sizing agent and carbon nanoparticles.
A novel “milled bamboo filler” was produced and incorporated in composites.
Thermal properties of epoxy composite were enhanced by the novel filler.
Tensile strength of the composite was significantly enhanced.
The novel filler has the future scope of application in various composite products.
Quantitative determination of specialised metabolites in different parts of Juglans regia Linn. and Carya illinoinensis (Wangenh.) K. Koch by using UHPLC‐DAD‐QTOF‐MS/MS
Authors: Devidas Shinde Bhagatsing , Bhandari Pamita 
Published: September 2023

AbstractIntroductionJuglans regia Linn. and Carya illinoinensis (Wangenh.) K. Koch are nut‐producing plant species of the Juglandaceae family. Bioactive compounds like naphthoquinones, tetralones, and diarylheptanoids are dominant in these species.ObjectiveThe study aimed to develop and validate a fast and sensitive analytical method by ultrahigh‐performance liquid chromatography diode array detection mass spectrometry (UHPLC‐DAD‐MS) for quantification and identification of bioactive compounds in fruit pericarps and leaves of J. regia and C. illinoinensis collected from two different states of north India.MethodologyThe dried pericarps of J. regia and C. illinoinensis (500 mg) were extracted with ethyl acetate–methanol (50:50 v/v, 20 mL, 50°C, 30 min) by ultrasonication and analysed by ultrahigh‐performance liquid chromatography diode array detection quadrupole time‐of‐flight tandem mass spectrometry (UHPLC‐DAD‐QTOF‐MS/MS) for qualitative and quantitative examination of phytoconstituents. The method was validated according to International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human use (ICH) guidelines for linearity, precision, accuracy, limit of detection (LOD), and limit of quantification (LOQ).ResultsHere, we report the quantification of dihydrophaseic acid (1), 4,5‐dihydroxytetralone (2), 4,8‐dihydroxytetralone (3), 5,8‐dihydroxy‐3‐methoxytetralone (4), and juglanin A (5) in the pericarps and leaves of J. regia and C. illinoinensis. Furthermore, using the hyphenated analytical method, a total of 62 compounds were tentatively characterised in different samples. The principal component analysis (PCA) showed diversity between the analysed sample's composition. Also, the study evaluated the variation of bioactive compounds among different parts of J. regia and C. illinoinensis collected from different regions of northern India by UHPLC‐DAD‐QTOF‐MS/MS.ConclusionThe developed method is simple, rapid, and selective for the identification and characterisation of bioactive molecules.
Crucial differential diagnosis of rapidly progressive dementia: A case of leptomeningeal metastasis
Authors: Mimura Yu , Oi Hiroki , Takata Taketo , Mimura Masaru , Funayama Michitaka 
Published: September 2023

AbstractBackgroundDementia that advances subacutely without accompanying neurological symptoms can often be misdiagnosed as a psychiatric condition. Leptomeningeal metastasis (LM), caused by the spread of malignant cells to the leptomeninges and the subarachnoid space, is a relatively unfamiliar condition to psychiatrists in this context. The diagnosis of LM remains challenging due to the scarcity of diagnostic tools possessing high sensitivity and specificity.Case PresentationWe present the clinical presentation of a male in his seventies with LM secondary to gastric ring cell carcinoma. The patient exhibited an acute confusional state, visual hallucinations, irritability, and cognitive impairments over a 3‐week period. Initially, the patient was misdiagnosed with several conditions, including alcohol withdrawal syndrome, psychosis, and delirium associated with dementia, as there were no noteworthy findings on neurological examination or the head magnetic resonance imaging (MRI). Given the rapidly progressive cognitive decline, we maintained vigilance for potential neurological conditions, and a repeat investigation using head MRI and cerebrospinal fluid analysis led to the diagnosis of LM.ConclusionThis critical case report underscores the rarity of psychiatric‐onset LM originating from gastric cancer and highlights the importance of comprehensive neurological evaluations.
Delayed neuropsychiatric sequelae with improvement of decreased cerebral bold flow by single‐photon emission computed tomography during hyperbaric oxygen therapy: A case report with a 10‐year follow‐up
Authors: Hagiwara Kosuke , Matsubara Toshio , Nakagawa Shin 
Published: September 2023

AbstractBackgroundDelayed neuropsychiatric sequelae (DNS) occurs in 10%–30% of acute carbon monoxide poisoning cases. Patients with this condition present higher brain dysfunction. Hyperbaric oxygen (HBO) therapy was reportedly an effective treatment for DNS in the acute phase. Favorable predictive factors affecting the prognosis of patients with DNS after HBO therapy include younger age and longer interictal periods. However, the relationship between these factors and neuroimaging findings remains unclear.Case PresentationThe patient was a 59‐year‐old man with DNS, who developed major depressive disorder and attempted suicide with charcoal briquettes. He was diagnosed with carbon monoxide poisoning and underwent acute HBO therapy. After a 1‐month lucid period, the patient developed intermittent carbon monoxide poisoning with cognitive dysfunction, following which HBO therapy was re‐initiated. Following treatment, the patient returned to work for 10 years. Frontal lobe hypoperfusion, measured by single‐photon emission computed tomography and cognitive impairment, improved with HBO therapy. However, magnetic resonance imaging revealed brain volume atrophy over time.ConclusionThis study reported a case of DNS that completely resolved within a 10‐year follow‐up period. Cerebral blood flow reduction, mainly in the frontal lobe, improved along with cognitive recovery during HBO therapy. Despite gradually progressive brain atrophy over the past decade, no noted deficits in cerebral blood flow were observed in the frontal lobes. These findings suggest that improvement in cerebral blood flow during HBO therapy and its retention may be factors associated with a favorable prognosis in patients with DNS.
Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server
Authors: Kotelnikov Sergei , Ashizawa Ryota , Popov Konstantin I. , Khan Omeir , Ignatov Mikhail , Li Stan Xiaogang , Hassan Mosavverul , Coutsias Evangelos A. , Poda Gennady , Padhorny Dzmitry , Tropsha Alexander , Vajda Sandor , Kozakov Dima 
Published: September 2023

AbstractIn the ligand prediction category of CASP15, the challenge was to predict the positions and conformations of small molecules binding to proteins that were provided as amino acid sequences or as models generated by the AlphaFold2 program. For most targets, we used our template‐based ligand docking program ClusPro ligTBM, also implemented as a public server available at https://ligtbm.cluspro.org/. Since many targets had multiple chains and a number of ligands, several templates, and some manual interventions were required. In a few cases, no templates were found, and we had to use direct docking using the Glide program. Nevertheless, ligTBM was shown to be a very useful tool, and by any ranking criteria, our group was ranked among the top five best‐performing teams. In fact, all the best groups used template‐based docking methods. Thus, it appears that the AlphaFold2‐generated models, despite the high accuracy of the predicted backbone, have local differences from the x‐ray structure that make the use of direct docking methods more challenging. The results of CASP15 confirm that this limitation can be frequently overcome by homology‐based docking.
Cyclin B3 plays pleiotropic roles in female reproductive organogenesis and early embryogenesis in the silkworm, Bombyx mori
Authors: Hu Hai , Tan Duan , Luo Tianfu , Tong Xiaoling , Han Minjin , Shen Jianghong , Dai Fangyin 
Published: September 2023

AbstractBACKGROUNDThe reproductive system plays a crucial role in insect survival, reproduction and species specificity. Understanding the molecular mechanisms underlying reproductive organogenesis contributes to improving the efficiency of sterile insect technique marked by an eco‐friendly pest management strategy. Lepidoptera is one of the largest orders of insects, most of which are major pests in agriculture and forestry. Our study aimed to screen the genes responsible for reproductive organogenesis and unravel the mechanism underlying female reproductive organ defects.RESULTSMorphological investigation of female reproductive organs showed a defective connection between oviductus geminus and oviductus communis on the second day of pupa (P2) in Speckled mutant silkworm. RNA_Seq identified a total of 18 049 transcripts that were expressed in the P2 female internal reproductive organs without ovary in Spc/+ compared to +Spc/+Spc. Differential expression analysis identified 312 up‐regulated genes and 221 down‐regulated genes in Spc/+. KEGG analysis identified 44 significantly enriched pathways. The results of qRT‐PCR performed on 33 genes significantly matched the outcomes of the RNA_Seq. Dysfunction of Cyclin B3 resulted in a defective connection of the oviductus communis with the ovariole, dysfunction of oogenesis, and a petite body. Moreover, homozygous recessive lethality of Cyclin B3/Cyclin B3 occurred during early embryogenesis.CONCLUSIONOur results suggest that Cyclin B3 is a pleiotropic functional gene that regulates early embryogenesis, oogenesis, development, and female reproductive organogenesis. These results showed that Cyclin B3 has significant effects on lepidopteran mortality, growth, and reproductive physiology, which might be considered a novel and potentially eco‐friendly target for lepidopteran pest management. © 2023 Society of Chemical Industry.