bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentially Missed Diagnoses in Prenatal Versus Postnatal Exome Sequencing in the Lack of Informative Phenotype: Lessons Learned From a Postnatal Cohort
Authors: Brabbing‐Goldstein Dana , Bazak Lily , Ruhrman‐Shahar Noa , Lidzbarsky Gabriel Arie , Orenstein Naama , Lifshiz‐Kalis Marina , Asia‐Batzir Nurit , Goldberg Yael , Basel‐Salmon Lina 
Published: September 2024

ABSTRACTObjectiveTo investigate how many novel pathogenic (P) and likely pathogenic (LP) nonprotein‐truncating or noncanonical splicing variants would be classified as variants of unknown significance (VUS) if they were detected in fetuses without abnormalities.MethodsThe study included 156 patients with neurodevelopmental disorders diagnosed through postnatal exome sequencing. Causative P/LP nonprotein‐truncating and noncanonical splicing variants were retrospectively reclassified in cases without specific prenatal manifestations, disregarding postnatal symptoms.ResultsOf the 156 patients, 72 had a nontruncating or noncanonical splicing variant. Six patients were excluded for having more than one possible causative variant. Twelve patients had prenatal malformations known to be associated with the diagnosed disorder; therefore, variant interpretation remained unchanged. In 33 of the 54 remaining cases, the variant had been previously reported as P/LP. Reclassification of the other 21 LP/P variants revealed that 16 would have been classified as VUS if detected prenatally.ConclusionIn our cohort, ∼24% (16/66) of causative nonprotein‐truncating/noncanonical splicing variants would have been classified as VUS if sequencing had been conducted during pregnancy. The potential for false‐negative results, stemming from limitations in the phenotypic information available prenatally, should be discussed with prospective parents. The criteria for classifying and reporting variants in the prenatal setting may require adjustment.
Cobalt Ferrite–Silica–Gold Nanocomposite: Synthesis, Structural Characterization, and Magneto‐Plasmonic Properties
Authors: Alves Thiago. E. P. , Almeida Thatielly F. , Franco Adolfo , Burda Clemens 
Published: September 2024

AbstractCobalt ferrite–silica–gold nanocomposite (CoFe2O4@SiO2@Au) is synthesized using a new method involving: i) the polyol method for cobalt ferrite nanoparticles (CoFe2O4), ii) the Stober method for silica coating, iii) surface functionalization with 3‐aminopropyl triethoxysilane (APTES), and iv) decoration with gold nanoparticles via tetrakis hydroxy‐methyl‐phosphonium (THPC) reduction. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) confirm the morphology of the nanoparticles and coatings for the nanocomposites. Ultraviolet–visible (UV–Vis) absorption spectra exhibit plasmon resonance peaks with tuned shifts, discuss in terms of the difference in dielectric permittivity in the core where gold nanoparticles are anchored. Magnetic hysteresis analysis reveals superparamagnetic behavior with reduced saturation magnetization for the nanocomposites. These findings are useful, as superparamagnetic behavior combined with control of plasmonic emission is highly relevant for several magneto‐plasmonic applications.
Montmorillonite Clay as an Adsorbent for the Remediation of Cd (II) Ions in Aqueous Solutions: A Comparison With Pb (II) Ions
Authors: Tako Edlira , Baraj Edlira , Mele Altin , Hoxha Vjosana 
Published: September 2024

ABSTRACTHeavy metal ions are hazardous to both human health and the environment. Montmorillonite (MMT) clay has recently piqued interest for its adsorption capacity of heavy metals and its use in controlling contaminants, in particular in surface and waste waters. This research sheds light on the possibility of the application of natural Albanian MMT clay from the Prrenjas Region of Albania as an adsorbent of Cd (II) ions in aqueous solutions, making a comparison with the capacity of such clay for the adsorption of Pb (II) ions. The set of variables studied included concentrations of metal ions, amount of clay pH, time, and temperature of interaction and adsorption process (all of them following batch technique), and optimal conditions have been determined. The adsorption capacity of natural clay for Cd (II) ions was 6.735 mg/g, as compared to 17.9 mg/g for Pb (II) ions. Langmuir and Freundlich isotherms were applied to evaluate the mode of adsorption with results showing that all isotherms are linear and the Langmuir model fitted better with the experimental data. It is determined that the adsorption of Cd (II), similar to that of Pb (II), is well‐fitted by the second‐order reaction kinetic following the Lagergen model. The results demonstrate good potentiality for Prrenjas MMT as a low‐cost adsorbent to remove Cd (II) from aqueous systems, in particular, for wastewater treatment.
A Joint Temporal Model for Hospitalizations and ICU Admissions Due to COVID‐19 in Quebec
Authors: Carmona‐Baez Mariana , Schmidt Alexandra M. , Golchi Shirin , Buckeridge David 
Published: September 2024

ABSTRACTInfectious respiratory diseases have been of interest in recent years for the great burden they place on health systems, for instance, the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) that caused the global COVID‐19 pandemic. As many of these diseases might require hospitalization and even intensive care unit (ICU) admission, understanding the joint dynamics of hospitalizations and ICU admissions across time and different groups of the population remains of great importance. We aim to understand the joint evolution of hospital and ICU admissions given COVID‐19 test‐positive cases in the province of Quebec, Canada. We obtain the daily counts, by age group, on the number of confirmed COVID‐19 cases, the number of hospitalizations and the number of ICU admissions due to COVID‐19, from March 2020 through October 2021 in Quebec. We propose a joint Bayesian generalized dynamic linear model for the number of hospitalizations and ICU admissions to study their temporal trends and possible associations with sex and age group. Additionally, we use transfer functions to investigate if there is a memory effect of the number of cases on hospitalizations across the different age groups. The results suggest that there is a clear distinction in the patterns of hospitalizations and ICU admissions across age groups and that the number of cases has a persistent effect on the rate of hospitalization.
Strut‐and‐tie model for column‐to‐drilled shaft connections in reinforced concrete bridge columns subjected to lateral loads
Authors: Zhang Penghui , Zhou Lianxu , Guo Junjun , Wang Zhiqiang 
Published: September 2024

AbstractDrilled shafts with a larger diameter than columns are frequently adopted as the foundation of highway bridge columns due to their superior economic efficiency and lower impact on existing facilities in the urban built‐up area. Different section dimensions lead to a socket connection between the column and the oversized shaft and a noncontact lap splice of their longitudinal bars. The force‐transfer mechanism and failure process of column‐to‐drilled shaft connections were deeply revealed in this study. Detailed FE models were developed at the Diana platform and validated against previous experimental results. Subsequently, a parametric study investigated the effect of the shear span‐to‐depth ratio, diameter ratio of shaft‐to‐column, column embedment depth, and shaft stirrup ratio. Finally, a modified strut‐and‐tie model (STM) was proposed to design stirrups of the transition region efficiently considering the experimental failure mechanism. Results indicate that the numerical models built in the Diana platform can precisely simulate the mechanical behavior of column‐to‐drilled shaft connections. The failure mechanism of column‐to‐drilled shaft connections is shaft stirrups yield at the compressive side induced by extrusion between the embedded column and shaft. The lateral loading capacity of column‐to‐drilled shaft connections increases with the increase of shear span‐to‐depth ratio, diameter ratio of shaft‐to‐column, column embedment depth, and shaft stirrup ratio. The modified STM is able to reveal the variation tendency of shaft transverse reinforcement demand with the various design parameters and give an average stirrup stress ratio of 1.20 and a coefficient of variation of only 8.31%.
Exploring the frontiers of generative AI in assessment: Is there potential for a human‐AI partnership?
Authors: DiSabito David , Hansen Lisa , Mennella Thomas , Rodriguez Josephine 
Published: September 2024

AbstractThis chapter investigates the integration of generative AI (GenAI), specifically ChatGPT, into institutional and course‐level assessment at Western New England University. It explores the potential of GenAI to streamline the assessment process, making it more efficient, equitable, and objective. Through the development of a proprietary GenAI tool, the study examines GenAI's assessment of student evidence, including written assignments and computer coding tasks, against human assessment. It addresses challenges such as data collection, coordination, and the need for well‐defined and precise rubrics. We found notable differences in GenAI and human scoring in some cases, indicating GenAI's potential in certain assessment contexts while also acknowledging its limitations in others. Our research suggests that GenAI could enhance educational assessment processes, but its integration requires addressing biases in training data and securing buy‐in from various stakeholders. Using GenAI to handle particular routine tasks can potentially free up faculty to engage in richer discussions and educational improvements.
Thermomechanical interaction in a living tissue due to variable thermal loading with memory
Authors: Abbas Ibrahim A. , Sur Abhik 
Published: September 2024

AbstractIn order to address various clinical applications within living tissue, the aim of this work is to analytically study the thermomechanical interaction for a living tissue which is subjected to variable thermal loadings. Human tissues undergoing regional hyperthermia treatment for cancer therapy is based on graded changes of the cells, and as a consequences, the constitutive equations have been formulated using the nonlocal elasticity theory. The heat transport equation for the present problem is formulated in the context of Moore‐Gibson‐Thompson theory of generalized thermoelasticity assimilating the memory‐dependent derivative within a slipping interval. Both the boundaries of the tissue is maintaining the condition of zero traction. The lower boundary of the tissue is subjected to prescribed thermal loading while, the upper boundary is kept at zero temperature. Utilizing the Laplace transform mechanism, the governing equations have been solved and the general solutions have been obtained in the transformed domain. In order to arrive at the solutions in the real space‐time domain, suitable inversion of the Laplace transform has been carried out numerically using the method of Zakian. Numerical findings suggest that thermomechanical waves propagate through skin tissue over finite distances, which helps mitigate the unrealistic predictions made by the Pennes' model. Significant effect due to different effective parameter such as nonlocal parameter and the time‐delay parameter is reported. Also, how a nonlinear kernel function can be more effective in bio‐heat transfer, is outlined in the study also.
A Deep Dive Into Effects of Structural Bias on CMA-ES Performance Along Affine Trajectories
Authors: van Stein Niki , Thomson Sarah L. , Kononova Anna V. 
Published: September 2024

AbstractTo guide the design of better iterative optimisation heuristics, it is imperative to understand how inherent structural biases within algorithm components affect the performance on a wide variety of search landscapes. This study explores the impact of structural bias in the modular Covariance Matrix Adaptation Evolution Strategy (modCMA), focusing on the roles of various modulars within the algorithm. Through an extensive investigation involving $$435\,456$$

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configurations of modCMA, we identified key modules that significantly influence structural bias of various classes. Our analysis utilized the Deep-BIAS toolbox for structural bias detection and classification, complemented by SHAP analysis for quantifying module contributions. The performance of these configurations was tested on a sequence of affine-recombined functions, maintaining fixed optimum locations while gradually varying the landscape features. Our results demonstrate an interplay between module-induced structural bias and algorithm performance across different landscape characteristics.
Nambu-Goto equation from three-dimensional gravity
Authors: Banerjee Avik , Mukhopadhyay Ayan , Policastro Giuseppe 
Published: September 2024

Abstract
We demonstrate that the solutions of three-dimensional gravity obtained by gluing two copies of a spacetime across a junction constituted of a tensile string are in one-to-one correspondence with the solutions of the Nambu-Goto equation in the same spacetime up to a finite number of rigid deformations related to worldsheet and spacetime isometries. The non-linear Nambu-Goto equation satisfied by the average of the embedding coordinates of the junction emerges directly from the junction conditions along with the rigid deformations and corrections due to the tension. Therefore, the equivalence principle generalizes non-trivially to the string. Our results are valid both in three-dimensional flat and AdS spacetimes. In the context of AdS3/CFT2 correspondence, our setup could be used to describe a class of interfaces in the conformal field theory featuring relative time reparametrization at the interface which encodes the solution of the Nambu-Goto equation corresponding to the bulk junction.
PNN Enhanced Seismic Inversion for Porosity Modeling and Delineating the Potential Heterogeneous Gas Sands via Comparative Inversion Analysis in the Lower Indus Basin
Authors: Shakir Urooj , Ali Aamir , Hussain Muyyassar , Radwan Ahmed E. , Aal Ahmed Abd El 
Published: September 2024

AbstractSeismic inversion has been in use for the last two decades to measure inverted impedances using an integrated data set approach. This research focuses on the application of multi-attribute seismic inversion and the geostatistical probabilistic neural network (PNN) approach for determining rock properties and litho-fluid classification in the Mehar-Mazarani Field of the Lower Indus Basin (LIB), Pakistan. The study compares five different inversion techniques, including model-based inversion (MBI), colored inversion (CI), linear sparse spike inversion (LSSI), band-limited inversion (BLI), and maximum likelihood sparse spike inversion (MLSSI). The inverted outputs, such as acoustic P-impedance (Zp), density (ρ), porosity (φ), and shale volume (Vsh), were analyzed in Paleocene and Cretaceous geological complex reservoirs to identify gas-bearing zones. The results indicated the existence of gas between 1630 and 1700 ms (ms) and corresponding depth ranges from approximately 3200 m up to 4200 m with varying thickness. Amongst the inversion techniques, MBI demonstrated greater accuracy, with inverted density volumes showing a strong correlation coefficient of 0.98 and the lowest root mean square error (RMSE) and relative error of 0.10 m/s * g/cc. A geostatistical PNN approach was employed to estimate variations in Vsh and φ within the sand reservoir. MBI again yielded more reliable results, with a strong correlation between the measured and inverted attributes. High φ and low Vsh were observed in predetermined low-impedance zones. Overall, MBI is proven to be the most accurate and reliable technique, providing clear identification of the gas occurrence. This research highlights the effectiveness of seismic inversion, particularly the application of MBI, in determining rock properties and identifying gas-bearing zones within the Mehar-Mazarani gas field.
Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C
Authors: Wachowski Nicholas A. , Pippin James A. , Boehm Keith , Lu Sumei , Leonard Michelle E. , Manduchi Elisabetta , Parlin Ursula W. , Wabitsch Martin , Chesi Alessandra , Wells Andrew D. , Grant Struan F. A. , Pahl Matthew C. 
Published: September 2024

Abstract
Aims/hypothesis
Genome-wide association studies (GWAS) have identified hundreds of type 2 diabetes loci, with the vast majority of signals located in non-coding regions; as a consequence, it remains largely unclear which ‘effector’ genes these variants influence. Determining these effector genes has been hampered by the relatively challenging cellular settings in which they are hypothesised to confer their effects.

Methods
To implicate such effector genes, we elected to generate and integrate high-resolution promoter-focused Capture-C, assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq datasets to characterise chromatin and expression profiles in multiple cell lines relevant to type 2 diabetes for subsequent functional follow-up analyses: EndoC-BH1 (pancreatic beta cell), HepG2 (hepatocyte) and Simpson–Golabi–Behmel syndrome (SGBS; adipocyte).

Results
The subsequent variant-to-gene analysis implicated 810 candidate effector genes at 370 type 2 diabetes risk loci. Using partitioned linkage disequilibrium score regression, we observed enrichment for type 2 diabetes and fasting glucose GWAS loci in promoter-connected putative cis-regulatory elements in EndoC-BH1 cells as well as fasting insulin GWAS loci in SGBS cells. Moreover, as a proof of principle, when we knocked down expression of the SMCO4 gene in EndoC-BH1 cells, we observed a statistically significant increase in insulin secretion.

Conclusions/interpretation
These results provide a resource for comparing tissue-specific data in tractable cellular models as opposed to relatively challenging primary cell settings.

Data availability
Raw and processed next-generation sequencing data for EndoC-BH1, HepG2, SGBS_undiff and SGBS_diff cells are deposited in GEO under the Superseries accession GSE262484. Promoter-focused Capture-C data are deposited under accession GSE262496. Hi-C data are deposited under accession GSE262481. Bulk ATAC-seq data are deposited under accession GSE262479. Bulk RNA-seq data are deposited under accession GSE262480.

Graphical Abstract
Reappraisal of the mechanism of cardiovascular responses to sympathomimetic amines in anaesthetised rats: dual α1-adrenoceptor and trace amine receptor mechanisms
Authors: Broadley Kenneth J. 
Published: September 2024

AbstractEstablished dogma is that sympathomimetic amines, including β-phenylethylamine (PEA), increase blood pressure by releasing noradrenaline from sympathetic neurons. Recent evidence allowing longer contact with isolated immersed tissues indicates other mechanisms. The present study re-evaluates the mechanism of pressor responses to PEA in anaesthetised rats with longer exposure to infusions. Blood pressure and heart rate were monitored by cannulating a common carotid artery of anaesthetised male Sprague–Dawley rats. Drugs were administered by bolus doses or by 20-min infusions via a cannulated jugular vein. Increases in blood pressure by bolus doses of the α-adrenoceptor agonist, phenylephrine, were converted to depressor responses by prazosin and therefore α-adrenoceptor-mediated. Pressor responses to bolus doses of PEA were reduced. PEA infusions yielded four-phase responses: An initial increase in pressure (phase 1) blocked by prazosin was due to α-adrenoceptor vasoconstriction and a secondary fall in pressure (phase 2) due to vasodilatation by nitric oxide release. A later pressure increase (phase 3), further elevated after infusion stopped (phase 4), was not attenuated by prazosin and therefore non-adrenergic. This study showed for the first time that the sympathomimetic amine, β-phenylethylamine, increases blood pressure by two mechanisms. The established indirect sympathomimetic mechanism applies to bolus dose administration. However, with prolonged exposure to infusions, an additional slow-onset sustained non-adrenergic blood pressure increase occurs, most likely mediated via trace amine-associated receptors (TAAR-1). This response will dominate with prolonged exposures in clinical practice. These results prompt a re-evaluation of established dogma on the indirect sympathomimetic mechanisms of these amines.
Voriconazole therapeutic drug monitoring including analysis of CYP2C19 phenotype in immunocompromised pediatric patients with invasive fungal infections
Authors: Resztak Matylda , Zalewska Paulina , Wachowiak Jacek , Sobkowiak-Sobierajska Agnieszka , Główka Franciszek K. 
Published: September 2024

Abstract
Purpose
Therapeutic drug monitoring (TDM) of voriconazole (VCZ) should be mandatory for all pediatric patients with invasive fungal infections (IFIs). The narrow therapeutic index, inter-individual variability in VCZ pharmacokinetics, and genetic polymorphisms cause achieving therapeutic concentration during therapy to be challenging in this population.

Methods
The study included 44 children suffering from IFIs treated with VCZ. Trough concentrations (Ctrough) of VCZ ware determined by the HPLC-FLD method. Identification of the CYP2C19*2 and CYP2C19*17 genetic polymorphisms was performed by PCR–RFLP. The correlation between polymorphisms and VCZ Ctrough was analyzed. Moreover, the effect of factors such as dose, age, sex, route of administration, and drug interactions was investigated.

Results
VCZ was administered orally and intravenously at a median maintenance dosage of 14.7 mg/kg/day for a median of 10 days. The VCZ Ctrough was highly variable and ranged from 0.1 to 6.8 mg/L. Only 45% of children reached the therapeutic range. There was no significant association between Ctrough and dosage, age, sex, route of administration, and concomitant medications. The frequencies of variant phenotype normal (NM), intermediate (IM), rapid (RM) and ultrarapid metabolizers (UM) were 41%, 18%, 28%, and 13%, respectively. Ctrough of VCZ were significantly higher in NM and IM groups compared with RM, and UM groups.

Conclusion
The Ctrough of VCZ is characterized by inter-individual variability and a low rate of patients reaching the therapeutic range. The significant association exists in children between VCZ Ctrough and CYPC19 phenotype. The combination of repeated TDM and genotyping is necessary to ensure effective treatment.