bluuebunny/crossref_metadata_2025_split huggingface dataset:
The completed mitochondrial genomes of Globodera vulgaris reveals new insights into the genus Globodera phylogeny
Authors: Yang Sihua , Zhu Huiying , Yang Zaifu , Li Xingyue , Pan Yonglang , Xu Chunling , Xie Hui 
Published: March 2024

AbstractDue to the highly conserved structure, animal mitochondrial genome (mtDNA) is widely used in classification, evolution, phylogeny, population genetic structure and other fields. We reported on the five circle multipartite mtDNAs of a newly described species of Globodera, Globodera vulgaris (Gv) from potatoes in China. The results showed that the mtDNA of Gv was obtained through second- and third-generation sequencing, with a total length of 42,995 bp. It contained 12 protein-coding genes, two rRNA genes and 17 tRNA genes, which were distributed in different subgenomic circles. Comparison of the differences in mtDNA among Gv, G. rostochiensis, G. pallida and G. ellingtonae showed that the size and arrangement of the genes in the mtDNA of the genus Globodera were variable and not conserved. The codon usage bias of the mitochondrial protein-coding gene of Gv showed that Gv might have originated from locally and more primitive group of existing Globodera. Based on the cytochrome c oxidase subunits I genes (COX1) and the nicotinamide adenine dinucleotide dehydrogenase subunits I genes (ND1), and the results showed that Gv was clustered with Globodera spp. according to the COX1 and ND1 in scmtDNA-V, while Gv was clustered with Meloidogyne spp. according to ND1 in scmtDNA-III. The results of this study provided a new basis for understanding the multipartite structure of mtDNA as a phylogenetic and taxonomic feature of the genus Globodera. The number of subgenomic circles is a diagnostic feature of species and the arrangement order and size of mitochondrial protein-coding genes also have important application value in species identification within the genus.
Association of anti-diabetic drugs and COVID-19 outcomes in patients with diabetes mellitus type 2 and cardiomyopathy
Authors: Dimnjaković Jelena , Buble Tamara , Ivanko Pero , Pristaš Ivan , Brborović Ognjen , Brborović Hana 
Published: March 2024

AbstractThere is a scarcity of information on the population with diabetes mellitus type 2 and cardiomyopathy (PDMC) in COVID-19, especially on the association between anti-diabetic medications and COVID-19 outcomes. Study is designed as a retrospective cohort analysis covering 2020 and 2021. Data from National Diabetes Registry (CroDiab) were linked to hospital data, primary healthcare data, the SARS-CoV-2 vaccination database, and the SARS-CoV-2 test results database. Study outcomes were cumulative incidence of SARS-CoV-2 positivity, COVID-19 hospitalizations, and COVID-19 deaths. For outcome predictors, logistic regression models were developed. Of 231 796 patients with diabetes mellitus type 2 in the database, 14 485 patients had cardiomyopathy. The two2-year cumulative incidence of all three studies' COVID-19 outcomes was higher in PDMC than in the general diabetes population (positivity 15.3% vs. 14.6%, p = 0.01; hospitalization 7.8% vs. 4.4%, p < 0.001; death 2.6% vs. 1.2%, p < 0.001). Sodium-Glucose Transporter 2 (SGLT-2) inhibitors therapy was found to be protective of SARS-CoV-2 infections [OR 0.722 (95% CI 0.610–0.856)] and COVID-19 hospitalizations [OR 0.555 (95% CI 0.418–0.737)], sulfonylureas to be risk factors for hospitalization [OR 1.184 (95% CI 1.029–1.362)] and insulin to be a risk factor for hospitalization [OR 1.261 (95% CI 1.046–1.520)] and death [OR 1.431 (95% CI 1.080–1.897)]. PDMC are at greater risk of acquiring SARS-CoV-2 infection and having worse outcomes than the general diabetic population. SGLT-2 inhibitors therapy was a protective factor against SARS-CoV-2 infection and against COVID-19 hospitalization, sulfonylurea was the COVID-19 hospitalization risk factor, while insulin was a risk factor for all outcomes. Further research is needed in this diabetes sub-population.
Automated analysis of knee joint alignment using detailed angular values in long leg radiographs based on deep learning
Authors: Lee Hong Seon , Hwang Sangchul , Kim Sung-Hwan , Joon Nam Bum , Kim Hyeongmin , Hong Yeong Sang , Kim Sungjun 
Published: March 2024

AbstractMalalignment in the lower limb structure occurs due to various causes. Accurately evaluating limb alignment in situations where malalignment needs correction is necessary. To create an automated support system to evaluate lower limb alignment by quantifying mechanical tibiofemoral angle (mTFA), mechanical lateral distal femoral angle (mLDFA), medial proximal tibial angle (MPTA), and joint line convergence angle (JLCA) on full-length weight-bearing radiographs of both lower extremities. In this retrospective study, we analysed 404 radiographs from one hospital for algorithm development and testing and 30 radiographs from another hospital for external validation. The performance of segmentation algorithm was compared to that of manual segmentation using the dice similarity coefficient (DSC). The agreement of alignment parameters was assessed using the intraclass correlation coefficient (ICC) for internal and external validation. The time taken to load the data and measure the four alignment parameters was recorded. The segmentation algorithm demonstrated excellent agreement with human-annotated segmentation for all anatomical regions (average similarity: 89–97%). Internal validation yielded good to very good agreement for all the alignment parameters (ICC ranges: 0.7213–0.9865). Interobserver correlations between manual and automatic measurements in external validation were good to very good (ICC scores: 0.7126–0.9695). The computer-aided measurement was 3.44 times faster than was the manual measurement. Our deep learning-based automated measurement algorithm accurately quantified lower limb alignment from radiographs and was faster than manual measurement.
Complex and variable regulation of ΔNp63 and TAp63 by TGFβ has implications for the dynamics of squamous cell epithelial to mesenchymal transition
Authors: Pokorná Zuzana , Tylichová Zuzana , Vojtesek Borivoj , Coates Philip J. 
Published: March 2024

AbstractTGFβ has roles in inflammation, wound healing, epithelial to mesenchymal transition (EMT), and cancer stem cell states, and acts as a tumor suppressor gene for squamous cell carcinoma (SCC). SCCs are also characterized by high levels of ΔNp63, which induces epithelial cell phenotypes and maintains squamous stem cells. Previous studies indicate a complex interplay between ΔNp63 and TGFβ signaling, with contradictory effects reported. We investigated the effects of TGFβ on p63 isoform proteins and mRNAs in non-malignant squamous and SCC cells, and the role of either canonical or non-canonical TGFβ signaling pathways. TGFβ selectively increased ΔNp63 protein levels in non-malignant keratinocytes in association with SMAD3 activation and was prevented by TGFβ receptor inhibition, indicating activation of canonical TGFβ pathway signaling. TP63 isoform mRNAs showed discordance from protein levels, with an initial increase in both TAP63 and ΔNP63 mRNAs followed by a decrease at later times. These data demonstrate complex and heterogeneous effects of TGFβ in squamous cells that depend on the extent of canonical TGFβ pathway aberrations. The interplay between TGFβ and p63 is likely to influence the magnitude of EMT states in SCC, with clinical implications for tumor progression and response to therapy.
Miniaturized equal/unequal Wilkinson power dividers capable of harmonic suppression utilizing microstrip π-shaped resonators modified by lumped elements
Authors: Abdipour Ashkan , Makki Seyed Vahab Al-Din 
Published: March 2024

AbstractIn this paper, modified π-shaped resonator composed of both microstrip transmission lines and lumped elements are employed to design a Wilkinson power divider. Utilizing these resonators leads to designing a compact divider featuring a selectable operating frequency with optional power division ratio and very wide-range harmonic suppression. To vary the operating frequency and the power division ratio, the values of just the utilized lumped elements are changed without manipulating the dimensions of microstrip lines. As a design sample, a miniaturized divider capable of operating at four frequencies i.e., 0.5, 1.0, 1.5 and 2 GHz with optional equal or unequal power division and harmonic suppression ability at each of these frequencies is designed and simulated. Finally, as a feasible sample, another Wilkinson power divider which can optionally operate at 700 MHz with equal power division or 1.2 GHz with unequal power division is designed and implemented. Based on the measurement results, the spurious harmonics from 2nd to 25th in the 700 MHz-divider and 2nd to 15th in the 1.2 GHz-divider are suppressed. Moreover, almost 96% and 93% size reduction at 700 MHz and 1.2 GHz, respectively, are achieved. The S21 and S31of the unequal divider are − 8.8 and − 3.73 dB, which indicate an unequal 3.2:1 power division.
Predicting reduced left atrial appendage velocity from echocardiographic left atrial function parameters in patients with atrial fibrillation undergoing catheter ablation
Authors: Uziębło-Życzkowska Beata , Kiliszek Marek , Maciorowska Małgorzata , Potapowicz-Krysztofiak Magdalena , Krzyżanowski Krystian , Jurek Agnieszka , Krzesiński Paweł 
Published: March 2024

AbstractDecreased left atrial appendage velocity (LAAV) is considered a significant risk factor thrombus formation in the left atrial appendage (LAA). The aim of this study was to assess the role of echocardiographic left atrial (LA) function parameters in predicting LAAV in patients with persistent atrial fibrillation (AF) undergoing catheter ablation. We prospectively enrolled consecutive patients with persistent AF undergoing transesophageal echocardiography (TEE) directly before the first AF ablation in 2019–2022. Of the 150 patients enrolled in the study, 29.3% (n = 44) had reduced LAAV values defined as < 25 cm/s. Patients with decreased LAAV values exhibited significantly reduced left atrial reservoir and conduit strain (LASr and LAScd), LA emptying fraction, and average e′ values. This group also presented with a high LA stiffness index (LASI), high LA and right atrial area, and high LA volume index (LAVI) and E/e′ ratio. In multivariable logistic regression analysis, LASI and LAVI remained significant predictors of the reduced LAAV. The threshold values were 1.6 for LASI and 44.47 ml/m2 for LAVI, with area under the curve values of 0.809 and 0.755, respectively. Among all noninvasive echocardiographic parameters, LASI and LAVI were found to be the best predictors of reduced LAAV, with good sensitivity and specificity. Moreover, LASI was found to be the only significant predictor of reduced LAAV defined as < 20 cm/s as well as < 25 cm/s.
Atomistic description of conductive bridge formation in two-dimensional material based memristor
Authors: Mitra Sanchali , Mahapatra Santanu 
Published: March 2024

AbstractIn-memory computing technology built on 2D material-based nonvolatile resistive switches (aka memristors) has made great progress in recent years. It has however been debated whether such remarkable resistive switching is an inherent property of the 2D materials or if the metal electrode plays any role? Can the metal atoms penetrate through the crystalline 2D materials to form conductive filaments as observed in amorphous oxide-based memristors? To find answers, here we investigate MoS2and h-BN-based devices with electrochemically passive and active (metal) electrodes using reactive molecular dynamics with a charge equilibration approach. We find that the SET and RESET processes in active electrode-based multilayer devices involve the formation and disruption of metal filaments linking the two electrodes exclusively through the grain boundaries, the configuration of which affects the volatility of the resistive switching. Whereas the switching mechanisms in passive electrode-based devices require the formation of interlayer B-N bonds and popping of the S atom to the Mo plane at the point defects. We also show that metal atom adsorption at the point defects causes resistive switching in monolayer MoS2. Our atomic-level understanding provides explanations to the apparently contradictory experimental findings and enables defect-engineering guidelines in 2D materials for such disruptive technology.
Inhibition of complement C3 prevents osteoarthritis progression in guinea pigs by blocking STAT1 activation
Authors: Xu Jen X. , Xu Frank Z. , Furbish Amelia , Braxton Alicia M. , Brumfield Brook , Helke Kristi L. , Peterson Yuri K. 
Published: March 2024

AbstractOsteoarthritis (OA) is one of the leading causes of disability, affecting over 500 million adults worldwide. Previous studies have found that various inflammatory factors can contribute to the pathogenesis of OA, including complement factors in the synovial fluid of OA patients. However, the pathogenesis of this disease is still not known, and the only therapy of severe OA is total joint replacements. Total joint replacements are invasive, expensive, and affect quality of life. Here we show that when human articular chondrocytes are stimulated with pro-inflammatory mediator interleukin-1β (IL-1β) there is an increase in inflammatory factors including complement component 3 (C3). We also found the transcription factor, signal transducer and activator of transcription 1 (STAT1), is responsible for increased C3 expression after IL-1β stimulation in human articular chondrocytes. A specific STAT1 inhibitor, fludarabine, attenuates the hyper-expression of C3 and delays/prevents spontaneous OA in Dunkin-Hartley guinea pigs. Since fludarabine is already clinically used for chemotherapy, this study has great translational potential as a unique disease-modifying osteoarthritis drug (DMOAD) in treating primary OA.
Computational mechanistic investigation of the kinetic resolution of α-methyl-phenylacetaldehyde by norcoclaurine synthase
Authors: Zhang Shiqing , Zhang Chenghua , Guo Aijing , Liu Baoyan , Su Hao , Sheng Xiang 
Published: March 2024

AbstractNorcoclaurine synthase from Thalictrum flavum (TfNCS) demonstrated high stereospecificity and yield in catalyzing the Pictet-Spengler reaction of dopamine with chiral aldehydes, achieving kinetic resolution of aldehydes. However, the mechanism and the factors contributing to the stereoselectivity remain unclear. Herein, by using quantum chemical calculations, the mechanisms of TfNCS-catalyzed reactions of dopamine with both enantiomers of α-methyl-phenylacetaldehyde are studied. The calculations reveal a mechanism mirroring the reaction of natural substrates, for which the deprotonation of the C5−H of the cyclized intermediate is rate-limiting. The calculated overall barriers are 20.1 kcal mol-1 and 21.6 kcal mol-1 for the reactions of (R)- and (S)-α-methyl-phenylacetaldehyde, respectively. The M97 and L72 residues are proposed to be the key residues contributing to the stereospecificity. The obtained detailed information is helpful for designing new variants of TfNCS with extended substrate scope, and also advancing our understanding of TfNCS reactions for potential applications.
Anti-repeating earthquakes and how to explain them
Authors: Cesca Simone , Niemz Peter , Dahm Torsten , Ide Satoshi 
Published: March 2024

AbstractRepeating earthquakes, or repeaters, affecting overlapping rupture patches with a similar focal mechanism, have important implications to track fault slip rates, aseismic deformation, slow earthquakes and earthquake nucleation processes. They are often detected based on highly similar waveforms. Here, we discuss earthquakes with highly anti-correlated waveforms, denoting a reversed seismogenic process at the same or a neighbouring location, which we refer to as true and quasi anti-repeaters. We first report a range such observations in different environments, including volcano seismicity, intermediate depth seismicity and injection-induced microseismicity. Then, we review conceptual models proposed to explain them. True and quasi anti-repeaters can be robustly identified via a three-component single station or distributed network data. They are key indicators for stress perturbation transients or local stress heterogeneities. Since most of these observations were explained as the response to fluid migration processes, they may help to identify and track fluid movements in the subsurface.
The online metacognitive control of decisions
Authors: Bénon Juliette , Lee Douglas , Hopper William , Verdeil Morgan , Pessiglione Mathias , Vinckier Fabien , Bouret Sebastien , Rouault Marion , Lebouc Raphael , Pezzulo Giovanni , Schreiweis Christiane , Burguière Eric , Daunizeau Jean 
Published: March 2024

AbstractDifficult decisions typically involve mental effort, which scales with the deployment of cognitive (e.g., mnesic, attentional) resources engaged in processing decision-relevant information. But how does the brain regulate mental effort? A possibility is that the brain optimizes a resource allocation problem, whereby the amount of invested resources balances its expected cost (i.e. effort) and benefit. Our working assumption is that subjective decision confidence serves as the benefit term of the resource allocation problem, hence the “metacognitive” nature of decision control. Here, we present a computational model for the online metacognitive control of decisions or oMCD. Formally, oMCD is a Markov Decision Process that optimally solves the ensuing resource allocation problem under agnostic assumptions about the inner workings of the underlying decision system. We demonstrate how this makes oMCD a quasi-optimal control policy for a broad class of decision processes, including -but not limited to- progressive attribute integration. We disclose oMCD’s main properties (in terms of choice, confidence and response time), and show that they reproduce most established empirical results in the field of value-based decision making. Finally, we discuss the possible connections between oMCD and most prominent neurocognitive theories about decision control and mental effort regulation.
Fully polarized Compton scattering in plane waves and its polarization transfer
Authors: Tang Suo , Xin Yu , Wen Meng , Bake Mamat Ali , Xie Baisong 
Published: March 2024

Fully polarized Compton scattering from a beam of spin-polarized electrons is investigated in plane-wave backgrounds in a broad intensity region from the perturbative to the nonperturbative regimes. In the perturbative regime, polarized linear Compton scattering is considered for investigating polarization transfer from a single laser photon to a scattered photon, and in the high-intensity region, the polarized locally monochromatic approximation and locally constant field approximation are established and are employed to study polarization transfer from an incoming electron to a scattered photon. The numerical results suggest an appreciable improvement of about 10% in the scattering probability in the intermediate-intensity region if the electron’s longitudinal spin is parallel to the laser rotation. The longitudinal spin of the incoming electron can be transferred to the scattered photon with an efficiency that increases with laser intensity and collisional energy. For collision between an optical laser with frequency ∼1 eV and a 10 GeV electron, this polarization transfer efficiency can increase from about 20% in the perturbative regime to about 50% in the nonperturbative regime for scattered photons with relatively high energy.
Unleashing potential: Boosting physical activity in children with developmental disabilities via a family-dog-assisted intervention
Authors: Darling S. , Wanser S.H. , Jiang D. , Schuna J.M. , Udell M.A.R. , MacDonald M. 
Published: March 2024

Abstract

In the context of a global crisis, where over 80% of children fail to meet minimum standards of physical activity, children with developmental disabilities may face an even greater health disparity. Despite being disproportionately less physically active than the broader population, those with developmental disabilities are often excluded from mainstream interventions. This study evaluated a novel animal-assisted intervention (AAI) that incorporated the family pet dog, with the goal of increasing physical activity in children with developmental disabilities. The intervention involved teaching child participants to engage in “Do as I Do” (DAID) reciprocal-imitation training with their dog over ten 60-min sessions. After enrollment, 45 child-dog pairs of children and their family dogs were randomly assigned to either the experimental intervention (DAID) group, the active control group (dog walking control [DWC]), or the passive control group (waitlist control [WC]). Physical activity was measured using a 7-day ActiGraph accelerometer monitoring process, and data were analyzed for children who wore the accelerometer for a minimum of 4 days at both assessment time points (N = 14). Participation in the intervention (DAID) group was found to significantly increase moderate-to-vigorous physical activity (MVPA) by 1.2 min/h (
p
= 0.0087; Cohen’s
d
= 1.7) and significantly reduce sedentary behavior by 4.03 min/h (
p
= 0.027;
d
= 1.3), outperforming the waitlist control group. Our findings demonstrate the potential of this novel dog-assisted intervention to improve physical activity in this population, thereby contributing to a reduction in health disparities.
A unified photo-excited GaAs model from ab initio simulation in terahertz regime
Authors: Huang Ning Qian , Shi Yan , Meng Zan Kui , Ban Zhen Guo 
Published: March 2024

Abstract
In this paper, we present a unified model for gallium arsenide (GaAs) based on ab initio simulations which characterizes its terahertz (THz) properties when excited by optical pump. We use density functional perturbation theory to calculate the dielectric properties of GaAs, and investigate the relaxation time of photo-excited GaAs through electron–phonon interactions. In light of the complexities arising from the mixed absorption mechanisms and the sensitivity of GaAs to laser parameters, we have developed a method that leverages time-dependent density functional theory and Boltzmann transport theory. This approach enables us to establish an accurate relationship between the pump laser intensity and the carrier concentration by introducing the percentage of excited electrons, facilitating the quantitative characterization of GaAs’s response under different optical pump intensities. Using the microscopic material parameters solved by first principles, we develop a unified Drude model to describe the macroscopic electromagnetic responses of photo-excited GaAs. We simulate several reported numerical examples of photo-excited GaAs, including a GaAs wafer and GaAs-based THz metamaterial modulators, to validate the proposed unified model as a reliable approach for predicting the THz properties of GaAs. The good agreement between the simulation and measurement results demonstrates that our model successfully captures the dynamic responses of photo-generated carriers and provides guidance for the design of optoelectronic devices based on GaAs. Furthermore, our modeling approach based on ab initio simulations is free from empirical parameters, providing a solid THz modeling method for other photo-excited semiconductor materials.